WO2013027217A1 - Zymoxins and methods of using the same - Google Patents

Zymoxins and methods of using the same Download PDF

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Publication number
WO2013027217A1
WO2013027217A1 PCT/IL2012/050320 IL2012050320W WO2013027217A1 WO 2013027217 A1 WO2013027217 A1 WO 2013027217A1 IL 2012050320 W IL2012050320 W IL 2012050320W WO 2013027217 A1 WO2013027217 A1 WO 2013027217A1
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toxin
seq
polypeptide
another embodiment
attached
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PCT/IL2012/050320
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French (fr)
Inventor
Itai Benhar
Assaf Shapira
Meital Gal-Tanamy
Romy Zemel
Ran Tur-Kaspa
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Ramot At Tel-Aviv University Ltd.
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Publication of WO2013027217A1 publication Critical patent/WO2013027217A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/24—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Enterobacteriaceae (F), e.g. Citrobacter, Serratia, Proteus, Providencia, Morganella, Yersinia
    • C07K14/245—Escherichia (G)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/50—Fusion polypeptide containing protease site
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/55—Fusion polypeptide containing a fusion with a toxin, e.g. diphteria toxin
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/60—Fusion polypeptide containing spectroscopic/fluorescent detection, e.g. green fluorescent protein [GFP]
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • a polypeptide and polynucleotides encoding same comprising a toxin, a protease cleavage site, an anti-toxin and a subcellular localization domain designated herein as zymoxins are provided.
  • Pharmaceutical compositions comprising the polypeptide and polynucleotides of the invention and methods of using same are also disclosed.
  • Zymogens are inactive enzyme precursors that are converted to their active form following a biochemical modification, such as proteolytic processing.
  • a biochemical modification such as proteolytic processing.
  • enzymes that are proteolytically activated are secreted digestive enzymes like pepsin and trypsin, the cysteine aspartic acid proteases (caspases) which play an essential role at various stages of the apoptotic process; and blood coagulating factors.
  • the MazEF system which is an exemplary member of the toxin-antitoxin (TA) system, includes two active protein components: the long lived MazF toxin and the labile MazE antitoxin.
  • MazF induced toxicity is executed by blocking de-novo protein synthesis through its endoribonuclease activity that catalyze the cleavage of single-stranded mRNAs at ACA sequences.
  • the MazE antitoxin forms a complex with the toxin and a catalytically inactive heterohexamer is formed in which a MazE dimer is sandwiched between two MazF dimers (MazF2-MazE2-MazF2).
  • HCV is a small, enveloped RNA virus belonging to the Hepacivirus genus of the Flaviviridae family, which has been recognized as a major cause of chronic liver disease and affects approximately 200 million people worldwide. Persistent infection is associated with the development of chronic hepatitis, hepatic steatosis, cirrhosis, and hepatocellular carcinoma.
  • a prophylactic or protective vaccine for HCV is not yet available, and even the most recent combination of pegylated a-interferon and ribavirin is often poorly tolerated and effective in only approximately 50% of genotype 1 - infected patients.
  • the HCV genome encodes one large open reading frame that is translated as a polyprotein and proteolytically processed to yield the viral structural and nonstructural (NS) proteins .
  • the non-structural proteins include the NS2-3 protease, the NS3 serine protease/R A helicase and its co-factor NS4A, the NS4B and NS5A proteins and the NS5B RNA- dependent RNA polymerase (RdRp).
  • Two virally encoded proteases participate in polyprotein processing, the NS2-3 autoprotease (which cleaves in cis at the NS2-3 junction) and the NS3-4A serine protease (which cleaves at four downstream NS protein junctions).
  • NS3 is an extensively studied HCV protein that possesses multiple enzymatic activities that are essential for HCV replication.
  • the remaining 2/3 of the protein has a helicase and NTPase activities, both of which are essential for HCV replication.
  • WO2012/038950 to some of the inventors discloses activatable toxin complexes which include a cleavable inhibitory peptide, and use thereof for treating infections and malignant diseases.
  • the present invention provides chimeric polypeptides having a toxin and an inhibitory peptide anti-toxin separated from one another by a sequence comprising a protease cleavage site, where the anti-toxin is further attached to a subcellular anchoring domain. Upon cleavage the toxin is released from the chimeric polypeptide complex and the inhibitory peptide is segregated therefrom, rendering the toxin active.
  • the present invention provides a chimeric polypeptide comprising a toxin, a protease cleavage site, an endogenous anti-toxin and a subcellular localization anchoring domain.
  • the protease cleavage site is attached to the carboxy terminus of the toxin
  • the endogenous anti-toxin is attached to the carboxy terminus of the protease cleavage site
  • the subcellular anchoring domain is attached to the carboxy terminus of the anti-toxin.
  • the endogenous antitoxin is attached to the carboxy terminus of the subcellular anchoring domain
  • the protease cleavage site attached to the carboxy terminus of the anti-toxin
  • the toxin is attached to the carboxy terminus of the protease cleavage site.
  • linker or spacer peptides may be present between functional elements or domains of the chimeric polypeptides.
  • the present invention provides a polynucleotide comprising a coding portion encoding a polypeptide, wherein the polypeptide comprises a toxin, a protease cleavage site, an endogenous anti-toxin and a subcellular localization anchoring domain.
  • the present invention provides a chimeric polypeptide comprising a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of the anti-toxin.
  • the subcellular localization domain is an endoplasmic reticulum (ER) anchoring domain.
  • the present invention further provides a polynucleotide comprising a coding portion encoding a polypeptide, wherein the polypeptide comprises a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin (or segment thereof which still has full antitoxin activity) attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of the anti-toxin.
  • the subcellular localization domain is an endoplasmic reticulum (ER) anchoring domain.
  • the present invention further provides a method for eliminating a cell, comprising the step of contacting the cell with: (1) a polypeptide comprising a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of the anti-toxin; or (2) a vector comprising a polynucleotide, wherein the polynucleotide comprises a coding portion encoding a polypeptide, said polypeptide comprises a toxin, a hepatitis C virus protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of the anti-toxin; or (2) a vector
  • a protease directed against the protease cleavage site is a protease that specifically cleaves the protease cleavage site.
  • the present invention further provides a method for treating a subject infected with a protease bearing virus, comprising the step of administering to the subject: (1) a polypeptide comprising a toxin, a viral protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of the anti-toxin; or (2) a vector comprising a polynucleotide, the polynucleotide comprises a coding portion encoding a polypeptide, wherein the polypeptide comprises a toxin, a virus protease cleavage site attached to the carboxy terminus of the tox
  • the present invention further provides a method for treating a subject afflicted with Hepatitis C, comprising the step of administering to the subject: (1) a polypeptide comprising a toxin, a Hepatitis C virus protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of the anti-toxin; or (2) a vector comprising a polynucleotide, wherein the polynucleotide comprises a coding portion encoding a polypeptide, the polypeptide comprises a toxin, a hepatitis C virus protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular
  • FIG 1 is a schematic representation of the construct "mCherry-NS3-activated MazF” and the hypothetical mechanism of its activation by NS3 protease.
  • the NS3-activated MazF zymoxin was constructed by fusing 5 elements in the following order (from the N terminus): monomeric red fluorescence protein mCherry, E.
  • the NS3 cleavage site that is located between the ribonuclease and the inhibitory peptide in the "mCherry-NS3- activated MazF" construct (which is active as a dimer but for convenience is illustrated here in its monomeric form) is cleaved by the HCV- NS3 protease which is also localized to the cytoplasmic side of the ER membrane.
  • the toxic ribonuclease no longer covalently tethered to its ER-anchored inhibitor, is now free to diffuse to the cytoplasm (which lacks the antidote) and exert its destructive activity.
  • FIG. 2 is a photograph showing a colony formation assay for the assessment of "mCherry-NS3-activated MazF" cytotoxicity toward naive cells.
  • a day before transfection 7.5 x lO 5 293 T-Rex cells where seeded per well in 6 wells plate and subsequently transfected with 2 ⁇ g of plasmids encoding either mCherry-NS3-activated MazF , mCherry (only the fluorescence protein) or EGFP- MazF (where MazF is not fused to its inhibitory peptide). 48 hours later, transfection efficiency was assessed by fluorescence microscopy and was determined to be equal between the three plasmids.
  • Transfected cells were than trypsinized, counted and seeded in 3 fold dilutions (starting from 150,000 cells/well) in 6 well plates and were incubated for 10 days in the presence of lmg/ml of G418 (to which all three plasmids confer resistance). Survived colonies were fixed and stained with Giemsa.
  • FIGs. 3A-D depict micrographs of an in vivo assay for co localization of NS3 protease and the ER-targeted MazF based construct.
  • l x lO 5 Tet-inducible full NS3-4A/constitutive uncleavable MazF expressing 293 T-Rex cells were seeded on poly-L-lysine coated cover- slips in a 24 well-plate. 12 hours later, the cells were supplemented with ⁇ g/ml of tetracycline for another 24 hours and then were fixed. Following nuclear staining by Hoechst 33258 (Blue) (Fig. 3B), Slides were examined by confocal fluorescence microscopy.
  • FIG. 4 is a bar graph illustrating the inhibition of de-novo protein synthesis by NS3- activated MazF based zymoxin in NS3-expressing cells.
  • l x lO 5 Tet-inducible full NS3- 4A/constitutive NS3-activated MazF or Tet-inducible full NS3-4A/constitutive uncleavable MazF expressing cells were seeded per well in 24-wells plate. 24 or 48 hours later, cells were supplemented with tetracycline to a final concentration of lOOOng/ml, or left untreated (48h tet, 24h tet and no tet, respectively).
  • Tet-inducible full NS3-4A No MazF
  • Tet-inducible full NS3-4A/constitutive NS3-activated MazF NS3- activated MazF
  • Tet-inducible full NS3 -4 A/constitutive uncleavable MazF uncleavable MazF expressing 293 T-Rex cells were seeded in 96 well plates (2> ⁇ 10 4 cells per well). After 24 hours, cells were supplemented with 3 fold dilutions of tetracycline, starting with concentration of lOOOng/ml, or left untreated.
  • Fig. 5B 30ng of total protein from lysates of Tet-inducible full NS3-4A/constitutive uncleavable MazF expressing cells that were supplemented with 3 fold dilutions of tetracycline for 48 hours were analyzed by immunob lotting with mouse anti-EGFP (for the detection of EGFP-NS3) and mouse anti- actin antibodies (loading control) followed by HRP-conjugated secondary antibodies and ECL development.
  • FIGs. 6A-D depict micrographs showing expression of mCherry-NS3 activated MazF results in growth inhibition and morphological changes in NS3 expressing cells.
  • l x lO 5 Tet- inducible full NS3-4A/constitutive NS3 activated MazF or Tet-inducible full NS3- 4A/constitutive uncleavable MazF expressing 293 T-Rex cells were seeded on poly-L-lysine coated cover-slips in a 24 well-plate. 12 hours later, cells were supplemented with lOng/ml or lOOOng/ml of tetracycline, or left untreated. 36 hours later, cells were fixed.
  • Fig. 6A Tet-inducible full NS3-4A/constitutive uncleavable MazF with Tetracycline (lOOOng/ml);
  • Fig. 6B Tet-inducible full NS3-4A/constitutive NS3-activated MazF without Tetracycline;
  • Fig. 6C Tet-inducible full NS3-4A/constitutive NS3-activated MazF with Tetracycline (lOng/ml);
  • Fig. 6D Tet-inducible full NS3-4A/constitutive NS3-activated MazF with Tetracycline (lOOOng/ml).
  • FIGs. 7A-D depict micrographs showing fluorescence microscopy analysis of adenovirus producing foci.
  • 3x 10 5 HEK 293 cells were seeded per well in 6 wells plate. When they reached 90% confluence, cells were infected with 10 fold dilutions of recombinant adenoviruses encoding for mCherry-NS3 activated MazF (Figs 7A and 7C) or mCherry- uncleavable-MazF (Figs. 7B and 7D), starting from 2.5 ⁇ 10 6 PFU per well. After 36 hours, cells were fixed and examined under a fluorescence microscope.
  • FIGs. 8A-B show a bar graph (Fig. 8A) and micrographs (Fig. 8B) showing the eradication of NS3-expressing Huh7.5 cells by recombinant adenovirus-mediated delivery of mCherry-NS3 activated MazF encoding cassette.
  • l x lO 4 w.t or EGFP-full NS3-4A expressing Huh7.5 cells were seeded per well in 96 plates.
  • Fig. 8A MTT viability assay: 4 days post infection, the relative fraction of viable cells (relatively to uninfected controls) was determined using an enzymatic MTT assay. A representative graph of three independent experiments is shown. Each bar represents the mean ⁇ SD of a set of data determined in triplicates. Fig.
  • FIG. 9 is a bar graph illustrating the result of treating HCV-infected/uninfected mixed culture of hepatocytes with recombinant adenovirus delivering MazF based zymoxin.
  • Uninfected (HCV-negative) Huh7.5 cells and a mixed culture of HCV infected and uninfected cells at 1 : 1 ratio were seeded in 96-well plates (l x lO 4 cells/well). After 24 hours, cells were treated with recombinant adenoviruses (MOI of ⁇ 3) encoding for the mCherry fused NS3 activated MazF or uncleavable-MazF zymoxins. Control cells remained untreated. 72 hours post treatment, the relative fraction of viable cells (relatively to untreated controls) was determined using an enzymatic MTT assay. The graph represents three independent experiments. Each bar represents the mean ⁇ SD of a set of data determined in triplicates.
  • FIGs 10A-F Depict micrographs of microscopic examination according to the setting described for FIG 9: 3 days post zymoxins treatment, the zymoxins treated uninfected (HCV- negative) Huh7.5 cells (Figs. 10E and 10F), the zymoxins treated mixed culture of HCV infected and uninfected cells (Figs. 10B and IOC) and the control untreated cells (Figs. 10A and 10D) were fixed and subjected to microscopic examination.
  • FIGs 11A-C Depict micrographs of microscopic examination showing eradication of HCV-infected hepatocytes by recombinant adenovirus delivering the MazF based zymoxin.
  • 3x l0 4 cells from the mixed HCV infected and uninfected culture (as described in Fig. 9) were seeded per well into 8-well chamber slides. 24 hours later, cells were treated with recombinant adenoviruses (MOI of ⁇ 3) encoding for the mCherry fused NS3 activated MazF (Fig. 11C) or uncleavable-MazF zymoxins (Fig. 11B). Control cells remained untreated (Fig. 11 A).
  • FIG. 12 is a bar graph illustrating the results obtained in accordance to the experimental procedure described in FIG 11 : the fraction (given in percentage) of the HCV- infected cells from the general cell population was evaluated, for each treatment, by dividing the number of the green, HCV-core positive cells by the general number of cells (DAPI stained). Each bar represents the mean ⁇ SD of a set of data collected from five representative microscopic fields. Numbers in brackets represent the percentage of the HCV -infected cells in each treatment relatively to their percentage in the untreated culture.
  • FIG. 13 Depicts the amino acid sequences of: (A) NS3 activated MazF zymoxin; and (B) the control construct of uncleavable MazF zymoxin.
  • the different segments of the polypeptides of 13A and 13B are also provided. Indicated numbers refer to the amino acid sequence to their right.
  • FIG. 14 is a bar graph illustrating the results of an MTT viability assay obtained in Tet-inducible full NS3-4A expressing cells that co-express an NS3 activated MazF zymoxin polypeptide missing the C-terminal ER membrane anchor of tyrosine phosphatase PTP1B.
  • the high viability rates suggest that a polypeptide of the invention lacking the tyrosine phosphatase PTP1B segment is substantially ineffective in killing of full NS3-4A expressing cells.
  • the present invention provides a chimeric polypeptide comprising a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of the anti-toxin.
  • the present invention provides a polypeptide having the following domains from amino to carboxy terminus: N-terminal: toxin-protease cleavage site-endogenous anti-toxin-subcellular anchoring domain: C-terminal.
  • the present invention provides a polypeptide having the following domains from amino to carboxy terminus: N-terminal: subcellular anchoring domain -antitoxin-protease cleavage site-toxin: C-terminal.
  • the present invention provides that the polypeptide further includes at least one peptide linker linking at least two domains.
  • the polypeptides of the invention comprising a toxin-antitoxin (antidote) system are termed zymoxins.
  • the subcellular localization domain is an endoplasmic reticulum (ER) anchoring domain.
  • endogenous anti-toxin As used herein, the terms “endogenous anti-toxin”, “anti-toxin”, “endogenous antitoxin”, “antitoxin” may interchangeably be used. In some embodiments, the terms “toxin” and “endogenous toxin” may interchangeably be used. As used herein, the term “endogenous” with respect to a toxin-antitoxin system is directed to include the natural (cognate) anti-toxin of the specified toxin.
  • the present invention provides a polypeptide comprising a toxin-antitoxin system.
  • the present invention provides a polypeptide comprising a toxin-antitoxin type II system.
  • the present invention provides a polypeptide comprising a toxin-antitoxin system, wherein the toxin-antitoxin system comprises at least a fragment of the toxin and/or at least a fragment of the antitoxin.
  • the present invention provides a polypeptide comprising a toxin- antitoxin system and a subcellular anchoring domain, such as, an ER anchoring domain.
  • the present invention provides a toxin-antitoxin system found on a bacterial chromosome. In another embodiment, the present invention provides that a toxin- antitoxin system is found on an Escherichia coli chromosome. In another embodiment, the present invention provides a polypeptide comprising a mazEF toxin-antitoxin system, wherein the mazF is the toxin and MazE is the antitoxin. In another embodiment, the present invention provides a polypeptide comprising a chpBIK toxin-antitoxin system, wherein the toxin is chpBK and the antitoxin is chpBl.
  • the present invention provides a polypeptide comprising a relBE toxin-antitoxin system, wherein the toxin is relE and the antitoxin is relB.
  • the present invention provides a polypeptide comprising a yefM-yoeB toxin-antitoxin system, wherein the toxin is yoeB and the antitoxin is yefM.
  • the present invention provides a polypeptide comprising a dinJ-yafQ toxin-antitoxin system, wherein the toxin is yafQ and the antitoxin is dinJ.
  • the present invention provides a polypeptide comprising a hicAhicB toxin-antitoxin system, wherein the toxin is HicA and the antitoxin is HicB.
  • the present invention provides a polypeptide comprising a prlFyhaV toxin-antitoxin system, wherein the toxin is YhaV and the antitoxin is prlF.
  • the present invention provides a polypeptide comprising a mqsRmqsA toxin- antitoxin system, wherein the toxin is MqsR and the antitoxin is MqsA.
  • the present invention provides a polypeptide comprising a rnlArnlB toxin- antitoxin system, wherein the toxin is RnlA and the antitoxin is RnlB.
  • the present invention provides a polypeptide comprising a yaf yafO toxin- antitoxin system, wherein the toxin is YafO and the antitoxin is YafN.
  • the present invention provides a polypeptide comprising a higBhigA toxin- antitoxin system, wherein the toxin is HigB and the antitoxin is HigA.
  • the present invention provides a polypeptide comprising a ratAyfjF toxin- antitoxin system, wherein the toxin is Rat A and the antitoxin is YfjF.
  • the present invention provides a polypeptide comprising a yeeUcbtA toxin- antitoxin system, wherein the toxin is YeeU and the antitoxin is CbtA.
  • the present invention provides a polypeptide comprising a yafWykfl toxin- antitoxin system, wherein the toxin is Ykfl and the antitoxin is YafW.
  • the present invention provides a polypeptide comprising a yfjZypjF toxin- antitoxin system, wherein the toxin is YpjF and the antitoxin is YfjZ.
  • the present invention provides a polypeptide comprising a gnsAymcE toxin- antitoxin system, wherein the toxin is GnsA and the antitoxin is YmcE.
  • the present invention provides a polypeptide comprising a hipBhipA toxin- antitoxin system, wherein the toxin is Hip A and the antitoxin is HipB.
  • the present invention provides a polypeptide comprising a yjhXyjhQ toxin- antitoxin system, wherein the toxin is YjhX and the antitoxin is YjhQ.
  • the present invention provides a polypeptide comprising a ydaSydaT toxin- antitoxin system, wherein the toxin is YdaS and the antitoxin is YdaT.
  • the present invention provides a toxin-antitoxin system encoded by a bacterial chromosome.
  • the present invention provides a toxin-antitoxin system encoded by a bacterial plasmid.
  • the present invention provides a toxin-antitoxin system found in genomes of prokaryotes other than bacteria.
  • the present invention provides that a toxin-antitoxin system encoded by genomes of prokaryotes other than bacteria.
  • the toxin-antitoxin system is found on genomes of prokaryotes other than bacteria, such as disclosed by Makarova, et.al., the content of which is incorporated herein in its entirety.
  • the present invention provides that the toxin-antitoxin system within the polypeptide of the invention is regulatable and responsible for cell death. In another embodiment, the present invention provides that the toxin-antitoxin system within the polypeptide of the invention is regulatable and responsible for programmed cell death. In another embodiment, the present invention provides that the toxin is MazF which inhibits translation by cleaving mR A at a specific site(s). In another embodiment, the present invention provides that the antitoxin is MazE. In another embodiment, MazE counteracts the action of MazF.
  • the present invention provides that the use of an endogenous toxin-antitoxin system is safer than the use of a system utilizing a toxin and an antitoxin each derived from a different source.
  • the present invention provides that the specificity of an endogenous toxin-antitoxin system renders it safe.
  • the present invention provides that the toxin within the polypeptide of the invention is inactive as long as the antitoxin is bound to the toxin directly, via a protease cleavage site, or via a linker/linkers.
  • the present invention provides that the toxin within the polypeptide becomes active only upon cleavage of the protease cleavage site.
  • the present invention provides that cleavage within the protease cleavage site of the polypeptide results in two separate polypeptides: the first comprises the active toxin and a first fragment of the protease cleavage site and the second polypeptide comprises a second fragment of the protease cleavage site, the antitoxin and the subcellular anchoring domain (such as an ER anchoring domain).
  • the present invention provides that cleavage within the protease cleavage site of the polypeptide results in two separate polypeptides: the first comprises the active toxin, possibly a linker and a first fragment of the protease cleavage site and the second polypeptide comprises a second fragment of the protease cleavage site, possibly a linker, the antitoxin, possibly a linker, and the subcellular anchoring domain (such as an ER anchoring domain).
  • endogenous toxin-antitoxin is a toxin and its antidote.
  • endogenous toxin-antitoxin is a toxin and its polypeptidic antidote.
  • an endogenous toxin-antitoxin is derived from a single organism (or encoded by a single genetic element).
  • an endogenous toxin-antitoxin is utilized endogenically in a single organism.
  • the present invention is based on a single polypeptide that upon intracellular cleavage separates into two moieties, thus activating a toxin.
  • the toxin becomes active upon separation from the antitoxin which remains bound to the subcellular anchoring domain (such as an ER anchoring domain) and to a segment of the protease cleavage site.
  • the mere separation of the toxin-antitoxin system due to cleavage is not sufficient for the induction of cell death within a target cell.
  • the present invention is based on the unexpected discovery that the antitoxin must be removed from the vicinity of the toxin.
  • the present invention is based on the unexpected discovery that there must be an intracellular/subcellular compartmental separation or segregation between the antitoxin and the toxin in order to render the toxin active and thus induce cell death.
  • the present invention is based on the unexpected need to immobilize the antitoxin at a site discrete from the toxin in order to induce cell death.
  • the present invention is based on the unexpected discovery that immobilizing the antitoxin to a subcellular compartment (location), such as, the ER, renders the toxin active following the proteolytic cleavage that separates it from the antitoxin.
  • the toxin is MazF.
  • MazF comprises SEQ ID NO: 1.
  • SEQ ID NO: 1 comprises the following amino acid (AA) sequence:
  • the antitoxin is MazE C-terminal 35 amino-acids (which encompass the 23 amino-acids inhibitory peptide (MazEp). In another embodiment, the antitoxin comprises MazE C-terminal 35 amino-acids (which encompass the 23 amino-acids inhibitory peptide (MazEp). In another embodiment, the antitoxin comprises the full MazE peptide. In another embodiment, the antitoxin comprises a fragment of MazE peptide having MazP antitoxin activity. In another embodiment, MazE comprises SEQ ID NO: 2. In another embodiment, SEQ ID NO: 2 comprises the following amino acid (AA) sequence: RKEPVFTLAELVNDITPENLHENIDWGEPKDKEVW.
  • the toxin comprises or selected from: HicA, YhaV, MqsR, RnlA, YafO, HigB, RatA, YeeU, Ykfl, YpjF, GnsA, HipA, YjhX, YdaS, MazF, or any fragment thereof.
  • HicA YhaV
  • MqsR RnlA
  • YafO HigB
  • RatA YeeU
  • Ykfl YpjF
  • GnsA GnsA
  • HipA YjhX
  • YdaS YdaS
  • MazF or any fragment thereof.
  • the anti-toxin comprises or selected from: HicB, prlF, MqsA, RnlB, YafN, HigA, YfjF, CbtA, YafW, YfjZ, YmcE, HipB, YjhQ, YdaT, MazE, or any fragment thereof.
  • subcellular anchoring domain is a domain that can target, sort, localize or anchor a desired peptide or protein to a specific subcellular localization.
  • the subcellular localization may be selected from, but not limited to: endoplasmic reticulum (ER) membranes, plasma membrane(s), nuclear membranes, mitochondrial membranes, cytoplasm, nucleus, mitochondria, ER, and the like. Each possibility is a separate embodiment.
  • the subcellular localization domain is a signal peptide, a localization signal, and the like.
  • the subcellular localization domain is an ER anchoring domain.
  • the ER anchoring domain comprises the amino acid sequence of SEQ ID NO: 3 (PTPIB ER anchor).
  • SEQ ID NO: 3 comprises the following amino acid (AA) sequence: SGLRSFLVNMCVATVLTAGAYLCYRFLFNSNT.
  • the ER anchoring domain comprises an amino acid sequence of SEQ ID NO: 25 (synaptobrevin 1; H. sapiens). In another embodiment, the ER anchoring domain comprises an amino acid sequence of SEQ ID NO: 26 (Synaptobrevin 2; H. sapiens). In another embodiment, the ER anchoring domain comprises an amino acid sequence of SEQ ID NO: 27 (Synaptobrevin 8; Mus musculus). In another embodiment, the ER anchoring domain comprises an amino acid sequence of SEQ ID NO: 28 (cytochrome b5 ; H. sapiens).
  • the ER anchoring domain comprises an amino acid sequence of SEQ ID NO: 29 (microsomal aldehyde dehydrogenase; Rattus norvegicus). In another embodiment, the ER anchoring domain comprises an amino acid sequence of SEQ ID NO: 30 (myotonic dystrophy protein kinase (Mus musculus)). In another embodiment, the ER anchoring domain comprises an amino acid sequence of SEQ ID NO: 31 (Heme Oxygenase- 1, H. sapiens).
  • the ER anchoring domain comprises an amino acid sequence selected from, but not limited to: SEQ ID NO:3, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28; SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, or combinations thereof. Each possibility is a separate embodiment.
  • the protease cleavage site is a viral protease cleavage site. In another embodiment, the protease cleavage site is NS3 cleavage site. In another embodiment, the protease cleavage site comprises the amino acid sequence of SEQ ID NO: 4. In another embodiment, SEQ ID NO: 4 comprises the following amino acid (AA) sequence: SEEDDTTVCCSMSYSWTGAL.
  • the polypeptide of the invention comprising a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain (such as an endoplasmic reticulum (ER) anchoring domain) attached to the carboxy terminus of the anti-toxin comprises SEQ ID NO: 5.
  • SEQ ID NO: 5 comprises the following amino acid (AA) sequence:
  • the present invention provides that the polypeptide of the invention comprises SEQ ID NO: 6.
  • SEQ ID NO: 6 comprises the following amino acid (AA) sequence:
  • the polypeptide of the invention further includes a fluorescent peptide or protein attached to the amino terminus of the toxin.
  • the polypeptide of the invention further includes a fluorescent peptide or protein attached to the carboxy terminus of the toxin.
  • the polypeptide of the invention further comprising a fluorescent protein attached to the amino terminus of the toxin comprises SEQ ID NO: 7.
  • SEQ ID NO: 7 comprises the following amino acid (AA) sequence:
  • the fluorescent peptide or protein may be selected from, but not limited to: mPlum, tdTomato, mStrawberry, J-Red, DsRed-monomer, mOrange, m O, mCitrine, Venus, YPet, EYFP, Emerald, EGFP, CyPet, mCFPm, Cerulean, T-Sapphire, SEQ ID NO: 7, or any combination thereof.
  • a fluorescent moiety can be attached to the polypeptide of the invention.
  • the fluorescent moiety may be any molecule having fluorescent properties.
  • the linker comprises SEQ ID NO: 8.
  • SEQ ID NO: 8 comprises the following amino acid (AA) sequence: SGRTQISS.
  • the linker comprises the amino acid (AA) sequence: GGS.
  • the linker comprises SEQ ID NO: 9.
  • SEQ ID NO: 9 comprises the following amino acid (AA) sequence: GGGGS.
  • the linker comprises SEQ ID NO: 10.
  • SEQ ID NO: 10 comprises the following amino acid (AA) sequence: SSGGSGGGSGSGG.
  • the toxin, the antitoxin, the protease cleavage site, and possibly the fluorescent protein are segments of the polypeptide.
  • the segments are directly linked/attached by a peptide bond.
  • the terms "linked” and “attached” are used interchangeably.
  • at least two segments are linked/attached by linker.
  • SEQ ID NO: 6 provides an amino acid sequence of the polypeptide wherein the segments are linked/attached via peptide linkers.
  • the cleavage site is attached to the carboxy terminus of the toxin via a linker
  • the endogenous anti-toxin is attached to the carboxy terminus of the cleavage site via a linker
  • the ER anchoring domain is attached to the carboxy terminus of the anti-toxin via a linker, or any combination thereof.
  • the antitoxin is flanked by linkers.
  • the protease cleavage site is flanked by linkers.
  • the toxin is flanked by linkers.
  • the linker is a single amino acid.
  • the linker is a peptide linker comprising amino acids or mimetics thereof.
  • the linker is glycosylated. In another embodiment, a peptide linker is 2-50 amino acids long. In another embodiment, a peptide linker is 2-25 amino acids long. In another embodiment, a peptide linker is 5-20 amino acids long. In another embodiment, a peptide linker is 5-15 amino acids long.
  • the polypeptide further comprises a signal peptide (signal sequence) such as but not limited to KDEL (SEQ ID NO: 24).
  • signal peptide such as but not limited to KDEL (SEQ ID NO: 24).
  • the signal peptide is a motif composed of four amino acids at the end of the polypeptide sequence.
  • the signal peptide is a sub-endoplasmic reticulum localization signal.
  • the toxin is a variant of SEQ ID NO: 1 comprising apoptotic inducing activity or any cell-killing activity.
  • the antitoxin is a variant of SEQ ID NO: 2 comprising MazF inhibitory activity.
  • the ER anchoring domain is a variant of SEQ ID NO: 3 comprising ER anchoring activity.
  • the cleavage site is a variant of SEQ ID NO: 4 recognizable/cleavable by a protease.
  • the cleavage site is specifically designed to be cleaved only by a specific protease.
  • a specific protease is present only in a diseased cell.
  • a specific protease is a viral protease present only in a cell infected by a virus.
  • the virus is the disease causing agent.
  • a variant as described herein differs from the native segment of SEQ ID NOs: 1-4 by 1 conservative amino acid substitution. In another embodiment, a variant as described herein differs from the native segment of SEQ ID NOs: 1-4 by 2 conservative amino acid substitution. In another embodiment, a variant as described herein differs from the native segment of SEQ ID NOs: 1-4 by 3 conservative amino acid substitution. In another embodiment, a variant as described herein differs from the native segment of SEQ ID NOs: 1-4 by 4 conservative amino acid substitution. In another embodiment, a variant as described herein differs from the native segment of SEQ ID NOs: 1-4 by 5 conservative amino acid substitution.
  • a variant as described herein is at least 70% homologous to the native segments of SEQ ID NOs: 1-4. In another embodiment, a variant as described herein is at least 80% homologous to the native segments of SEQ ID NOs: 1-4. In another embodiment, a variant as described herein is at least 90% homologous to the native segments of SEQ ID NOs: 1-4. In another embodiment, a variant as described herein is at least 95% homologous to the native segments of SEQ ID NOs: 1-4.
  • polypeptides of the invention include homologues of the polypeptides described herein.
  • the present invention further provides a polynucleotide encoding a segment of the polypeptides described herein.
  • the present invention provides a polynucleotide comprising a coding portion encoding a polypeptide of the invention, wherein the polypeptide comprises a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain (such as an endoplasmic reticulum (ER) anchoring domain) attached to the carboxy terminus of the anti-toxin.
  • ER endoplasmic reticulum
  • the present invention further provides a polynucleotide encoding a variant of a segment of the polypeptides described herein. In another embodiment, the present invention further provides a polynucleotide encoding polypeptides comprising at least one linker, linking at least two segments. In another embodiment, the present invention further provides a polynucleotide encoding the polypeptide of SEQ ID NO: 5. In another embodiment, the present invention further provides a polynucleotide encoding the polypeptide of SEQ ID NO: 6. In another embodiment, the present invention further provides a polynucleotide encoding the polypeptide of SEQ ID NO: 7.
  • a polynucleotide is composed of DNA bases.
  • a polynucleotide is composed of RNA bases.
  • a polynucleotide of the invention is a homologue of a polynucleotide encoding a polypeptide or a segment of a polypeptide as described herein.
  • a method for eliminating a cell comprising the step of contacting the cell with a polypeptide comprising a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain (such as an endoplasmic reticulum (ER) anchoring domain) attached to the carboxy terminus of the antitoxin, wherein the cell comprises a protease directed against the protease cleavage site.
  • eliminating a cell is inducing cell death in a cell.
  • eliminating a cell is inducing apoptosis in a cell.
  • eliminating a cell is inducing necrosis in a cell.
  • a method for eliminating a cell comprising the step of contacting the cell with a polynucleotide encoding a polypeptide comprising a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain (such as an endoplasmic reticulum (ER) anchoring domain) attached to the carboxy terminus of the anti-toxin, wherein the cell comprises a protease directed against the protease cleavage site.
  • eliminating a cell is inducing cell death in a cell.
  • eliminating a cell is inducing apoptosis in a cell.
  • contacting a cell with a polynucleotide is contacting a cell with a vector comprising the polynucleotide.
  • contacting a cell with a polynucleotide is contacting a cell with a vector comprising the polynucleotide.
  • contacting a cell with a polynucleotide is contacting a cell with a viral vector comprising the polynucleotide.
  • contacting a cell with a polynucleotide is contacting a cell with an adenoviral vector comprising the polynucleotide.
  • the cell is a eukaryotic cell. In another embodiment, the cell is a diseased cell. In another embodiment, the cell is a diseased cell characterized by having a protease that is present only in the disease state. In another embodiment, a diseased cell comprising a unique protease present only in the disease state if differentially eliminated by the polypeptide of the invention. In another embodiment, a diseased cell comprising a unique protease present only in the disease state if differentially eliminated by the polypeptide of the invention. In another embodiment, a protease cleavage site is engineered according to the unique protease expressed in the diseased cell.
  • a diseased cell is a cancerous cell and the protease is present in a cancerous but not in a non-cancerous cell.
  • a diseased cell is a cell infected by an intracellular parasite comprising a protease or having a nucleic acid encoding a protease.
  • a diseased cell is a cell infected by a virus comprising a protease or encoding a protease.
  • the present invention is based inter alia on the presence of a unique protease in the diseased cell and the absence of the unique protease in a healthy cell.
  • the present invention is based inter alia on a difference between levels of protease activity which are high in a diseased cell and low in a healthy cell. While the former is relevant to infections be protease-encoding pathogens, the latter is the case in disease such as cancer.
  • a cell infected by a virus expresses a viral protease that is not expressed endogenically by the cell.
  • a cell expressing a viral protease is differentially eliminated while cells that do not express the viral protease are spared.
  • the polypeptide of the invention becomes active only after cleavage by an exogenic protease (exogenic to the cell such as a viral protease).
  • an exogenic protease is a protease that was initially encoded by a foreign nucleic acid.
  • an exogenic protease is a protease that was initially encoded by a viral nucleic acid.
  • one of skill in the art can readily identify exogenic and endogenic proteases.
  • the cell is a hepatocyte. In another embodiment, the cell is infected by the hepatitis C virus (HCV). In another embodiment, the cell is located within a tissue at risk of being infected by HCV. In another embodiment, the cell is a liver cell of a subject having a risk of being infected by HCV. In another embodiment, a subject having a risk of being infected by HCV is a drug addict (needle sharing). In another embodiment, a subject having a risk of being infected by HCV is a subject in need of blood transfusion, blood products, or organ transplantation. In another embodiment, a subject having a risk of being infected by HCV is a medical professional. In another embodiment, the present invention eliminates non-liver cells infected with HCV. In another embodiment, the present invention eliminates extra-hepatic reservoirs of HCV.
  • HCV hepatitis C virus
  • contacting a cell with a polypeptide of the invention comprises administering the polypeptide to the extracellular environment.
  • contacting a cell with a polypeptide of the invention comprises administering the polypeptide via a vehicle which enables the penetration of the active polypeptide into the cell.
  • methods for stabilizing a polypeptide on a vehicle that transports the polypeptide into the cell are known to one of skill in the art.
  • a cell comprising a protease directed against the protease cleavage site is a cell comprising a protease that cleaves the cleavage site thus triggering apoptosis via separation of the toxin from the antitoxin.
  • a cell comprising a protease directed against the protease cleavage site is a cell comprising a viral protease.
  • a cell comprising a protease directed against the protease cleavage site is a cell comprising a viral protease.
  • a cell comprising a protease directed against the protease cleavage site is a cell comprising a protease that is not endogenically expressed by the cell.
  • a cell comprising a protease is a cell comprising a protease that is encoded by a parasite.
  • a cell comprising a protease is a cell comprising a protease that is encoded by a virus.
  • a cell comprising a protease is a cell comprising a unique protease that is encoded by a parasite or a virus.
  • a cell comprising a protease is a cell comprising an exogenous protease.
  • the protease cleavage site is not recognizable or cleavable by an endogenic protease.
  • the protease cleavage site is only recognizable or cleavable by a viral protease.
  • the protease cleavage site is only recognizable or cleavable by an intracellular parasitic protease.
  • contacting a cell with a polynucleotide of the invention comprises administering a vector or a transgene comprising the polynucleotide to the extracellular environment.
  • contacting a cell with a polynucleotide of the invention comprises administering the polynucleotide via a vehicle which enables the penetration of the polynucleotide into the cell.
  • methods for delivering and/or stabilizing polynucleotides including the use of various vectors that enable the expression of the polynucleotide within a cell are known to one of skill in the art.
  • a method for treating a subject afflicted with Hepatitis C comprising the step of administering to the subject a vector such as but not limited to an adenoviral vector comprising a polynucleotide, wherein the polynucleotide comprises a coding portion encoding a polypeptide, the polypeptide comprises a toxin, a hepatitis C virus protease cleavage site (such as NS3) attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain (such as an endoplasmic reticulum (ER) anchoring domain) attached to the carboxy terminus of the anti-toxin.
  • a vector carrying the polynucleotide of the invention is administered within a pharmaceutical composition.
  • a method for treating a subject infected with a protease bearing virus comprising the step of administering to the subject: (1) a polypeptide comprising a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain (such as an endoplasmic reticulum (ER) anchoring domain) attached to the carboxy terminus of the anti-toxin; or (2) a vector comprising a polynucleotide, the polynucleotide comprises a coding portion encoding a polypeptide, the polypeptide comprises a toxin, a hepatitis C virus protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease
  • the protease bearing virus causes a known disease.
  • a protease bearing virus is a virus bearing the protease.
  • a protease bearing virus is a virus bearing the nucleic acid molecule which encodes a protease.
  • the subject comprises cells infected by a virus.
  • cells infected by a virus according to the present invention comprise a viral protease directed against the protease cleavage site.
  • the protease is a unique protease that is encoded by a virus and not by the cell.
  • the protease is an exogenous protease.
  • the protease cleavage site is not recognizable or cleavable by a cell's endogenic protease.
  • the protease cleavage site is only recognizable or cleavable by the viral protease.
  • viruses that comprise/encode a unique protease that is not expressed endogenically by the subject's cells and cause a disease including but not limited to: hepatitis C virus (HCV), West Nile virus (WNV), dengue fever virus (DFV), yellow fever virus (YFV), Human immunodeficiency virus- 1 (HIV-1), coxsackievirus, poliovirus hepatitis A virus, coronaviruses (CoV), severe acute respiratory syndrome (SARS) causative SARS- CoV, varicella-zoster virus (VZV), or Epstein-Bar virus (EBV).
  • HCV hepatitis C virus
  • WNV West Nile virus
  • DDV dengue fever virus
  • YFV yellow fever virus
  • HIV-1 Human immunodeficiency virus- 1
  • coxsackievirus poliovirus hepatitis A virus, coronaviruses (CoV), severe acute respiratory syndrome (SARS) causative SARS- CoV, varicella
  • a subject infected with a protease bearing virus is a subject suffering from a disease caused by the protease bearing virus.
  • a method for treating a subject afflicted with Hepatitis C comprising the step of administering to the subject: (1) a polypeptide comprising a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain (such as an endoplasmic reticulum (ER) anchoring domain) attached to the carboxy terminus of the anti-toxin; or (2) a vector (such as an adenoviral vector) comprising a polynucleotide, the polynucleotide comprises a coding portion encoding a polypeptide, the polypeptide comprises a toxin, a hepatit
  • the toxin is MazF.
  • the protease cleavage site is NS3 cleavage sequence derived from 2A genotype NS5A/B (strain JFHl).
  • the endogenous anti-toxin is MazE or MazE derived polypeptide.
  • a MazE derived polypeptide is a fragment of MazE having MazE antitoxin activity.
  • the endoplasmic reticulum (ER) anchoring domain is the tyrosine phosphatase PTP1B.
  • a subject afflicted with Hepatitis C is a subject infected with Hepatitis C virus.
  • a subject afflicted with Hepatitis C suffers from a liver disease.
  • a subject afflicted with Hepatitis C is an asymptomatic patient infected with Hepatitis C virus.
  • treating is ameliorating the disease condition.
  • treating is inhibiting the progression of a liver disease.
  • treating is reducing the risk of infectivity.
  • treating is reducing the risk of developing a chronic infection in an asymptomatic patient.
  • treating is reversing a chronic infection.
  • treating is reducing the symptoms associated with a chronic infection.
  • treating is inhibiting the progression of chronic infection.
  • treating is inhibiting or reducing the risk of fibrosis.
  • treating is inhibiting or reducing the risk of cirrhosis.
  • treating is reducing the risk of liver failure or other complications of cirrhosis, including liver cancer or life threatening esophageal varices and gastric varices.
  • treating is reducing the risk of hepatitis C virus propagation and spread.
  • treating is inhibiting, ameliorating, or reducing the symptoms of persistent infection.
  • polypeptide as used herein encompasses native polypeptides (either degradation products, synthetically synthesized polypeptides or recombinant polypeptides) and peptidomimetics (typically, synthetically synthesized polypeptides), as well as peptoids and semipeptoids which are polypeptide analogs, which have, in some embodiments, modifications rendering the polypeptides even more stable while in a body or more capable of penetrating into cells.
  • Methods for preparing peptidomimetic compounds are well known in the art and are specified, for example, in Quantitative Drug Design, C.A. Ramsden Gd., Chapter 17.2, F. Choplin Pergamon Press (1992), which is incorporated by reference as if fully set forth herein. Further details in this respect are provided hereinunder.
  • peptide bonds (-CO-NH-) within the polypeptide are substituted.
  • the polypeptide bonds are substituted by N-methylated bonds (-N(CH3)-CO-).
  • the polypeptide bonds are substituted by ester bonds (-C(R)H-C-0-0-C(Pv)-N-).
  • the polypeptide bonds are substituted by ketomethylen bonds (-CO-CH2-).
  • the polypeptide bonds are substituted by a-aza bonds (-NH-N(R)-CO-), wherein R is any alkyl, e.g., methyl, carba bonds (-CH2-NH-).
  • natural aromatic amino acids of the polypeptide such as Trp, Tyr and Phe
  • synthetic non-natural acid such as Phenylglycine, TIC, naphthylelanine (Nol), ring-methylated derivatives of Phe, halogenated derivatives of Phe or o-methyl-Tyr.
  • the polypeptides of the present invention include one or more modified amino acid or one or more non-amino acid monomers (e.g. fatty acid, complex carbohydrates etc).
  • amino acid or “amino acid” is understood to include the 20 naturally occurring amino acid; those amino acid often modified post-translationally in vivo, including, for example, hydroxyproline, phosphoserine and phosphothreonine; and other unusual amino acid including, but not limited to, 2-aminoadipic acid, hydroxy lysine, isodesmosine, nor-valine, nor-leucine and ornithine.
  • amino acid includes both D- and L-amino acid.
  • the polypeptides of the present invention are utilized in therapeutics which requires the polypeptides to be in a soluble form.
  • the polypeptides of the present invention include one or more non-natural or natural polar amino acid, including but not limited to serine and threonine which are capable of increasing polypeptide solubility due to their hydroxyl-containing side chain.
  • polypeptides of the present invention are utilized in a linear form, although it will be appreciated by one skilled in the art that in cases where cyclicization does not severely interfere with polypeptides characteristics, cyclic forms of the polypeptides can also be utilized.
  • the polypeptides of present invention are biochemically synthesized such as by using standard solid phase techniques.
  • these biochemical methods include exclusive solid phase synthesis, partial solid phase synthesis, fragment condensation, or classical solution synthesis.
  • solid phase polypeptides synthesis procedures are well known to one skilled in the art and further described by John Morrow Stewart and Janis Dillaha Young, Solid Phase Polypeptide Syntheses (2nd Ed., Pierce Chemical Company, 1984).
  • synthetic polypeptides are purified by preparative high performance liquid chromatography [Creighton T. (1983) Proteins, structures and molecular principles. WH Freeman and Co. N.Y.] and the composition of which can be confirmed via amino acid sequencing by methods known to one skilled in the art.
  • recombinant protein techniques are used to generate the polypeptides of the present invention.
  • recombinant protein techniques are used for generation of relatively long polypeptides (e.g., longer than 18-25 amino acids). In some embodiments, recombinant protein techniques are used for the generation of large amounts of the polypeptides of the present invention. In some embodiments, recombinant techniques are described by Bitter et al, (1987) Methods in Enzymol. 153:516-544, Studier et al. (1990) Methods in Enzymol. 185:60-89, Brisson et al. (1984) Nature 310:511-514, Takamatsu et al. (1987) EMBO J. 3:17-311, Coruzzi et al. (1984) EMBO J.
  • polypeptides of the present invention are synthesized using a polynucleotide such as described herein encoding a polypeptide of the present invention.
  • polynucleotides of the invention are inserted into transfection/infection vectors.
  • transfection/infection vectors are used for expressing the polypeptides of the present invention in target cells.
  • a target cell is a cell comprising a unique protease which cleaves the protease cleavage site.
  • a target cell is a cell utilized for the manufacture/expression of the polypeptides of the invention (the polypeptides of the invention are refractory within this target cell that does not carry a unique protease which cleaves the protease cleavage site).
  • the polynucleotide encoding polypeptides of the present invention is ligated into an expression vector such as but not limited to an adenoviral vector, comprising a transcriptional control of a cis-regulatory sequence (e.g., promoter sequence).
  • the cis-regulatory sequence is suitable for directing constitutive expression of the polypeptides of the present invention.
  • the cis-regulatory sequence is suitable for directing tissue specific expression of the polypeptides of the present invention. In some embodiments, the cis-regulatory sequence is suitable for directing inducible expression of the polypeptides of the present invention.
  • tissue-specific promoters suitable for use with the present invention include sequences which are functional in specific cell population, example include, but are not limited to promoters such as albumin that is liver specific [Pinkert et al., (1987) Genes Dev. 1 :268-277], lymphoid specific promoters [Calame et al, (1988) Adv. Immunol. 43:235-275]; in particular promoters of T-cell receptors [Winoto et al, (1989) EMBO J. 8:729-733] and immunoglobulins; [Banerji et al.
  • neuron-specific promoters such as the neurofilament promoter [Byrne et al. (1989) Proc. Natl. Acad. Sci. USA 86:5473-5477], pancreas-specific promoters [Edlunch et al. (1985) Science 230:912- 916] or mammary gland-specific promoters such as the milk whey promoter (U.S. Pat. No. 4,873,316 and European Application Publication No. 264,166).
  • Inducible promoters suitable for use with the present invention include for example the tetracycline-inducible promoter (Srour, M.A., et al, 2003. Thromb. Haemost. 90: 398-405).
  • a polynucleotide refers to a DNA molecule.
  • a polynucleotide refers to a single or double stranded nucleic acid sequence which be isolated and provided in the form of an RNA sequence, a complementary polynucleotide sequence (cDNA), a genomic polynucleotide sequence and/or a composite polynucleotide sequences (e.g., a combination of the above).
  • complementary polynucleotide sequence refers to a sequence, which results from reverse transcription of messenger RNA using a reverse transcriptase or any other RNA dependent DNA polymerase.
  • the sequence can be subsequently amplified in vivo or in vitro using a DNA polymerase.
  • genomic polynucleotide sequence refers to a sequence derived (isolated) from a chromosome and thus it represents a contiguous portion of a chromosome.
  • composite polynucleotide sequence refers to a sequence, which is at least partially complementary and at least partially genomic.
  • a composite sequence can include some exonal sequences required to encode the polypeptide of the present invention, as well as some intronic sequences interposing there between.
  • the intronic sequences can be of any source, including of other genes, and typically will include conserved splicing signal sequences.
  • intronic sequences include cis acting expression regulatory elements.
  • the polynucleotides of the present invention further comprise a signal sequence encoding a signal peptide for the secretion of the polypeptide of the present invention.
  • the signal peptides are cleaved from the precursor polypeptide resulting in the mature polypeptide.
  • polynucleotides of the present invention are prepared using PCR techniques, or any other method or procedure known to one skilled in the art.
  • the procedure involves the ligation of two different DNA sequences (See, for example, "Current Protocols in Molecular Biology", eds. Ausubel et al, John Wiley & Sons, 1992).
  • the expression vector is an adenoviral vector.
  • polynucleotides of the present invention are inserted into expression vectors (i.e., a nucleic acid construct) to enable expression of the recombinant polypeptide.
  • the expression vector of the present invention includes additional sequences which render this vector suitable for replication and integration in prokaryotes.
  • the expression vector of the present invention includes additional sequences which render this vector suitable for replication and integration in eukaryotes.
  • the expression vector of the present invention includes a shuttle vector which renders this vector suitable for replication and integration in both prokaryotes and eukaryotes.
  • cloning vectors comprise transcription and translation initiation sequences (e.g., promoters, enhances) and transcription and translation terminators (e.g., polyadenylation signals).
  • prokaryotic or eukaryotic cells can be used as host- expression systems to express the polypeptides of the present invention.
  • these include, but are not limited to, microorganisms, such as bacteria transformed with a recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vector containing the polypeptide coding sequence; yeast transformed with recombinant yeast expression vectors containing the polypeptide coding sequence; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors, such as Ti plasmid, containing the polypeptide coding sequence.
  • microorganisms such as bacteria transformed with a recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vector containing the polypeptide coding sequence
  • yeast transformed with recombinant yeast expression vectors containing the polypeptide coding sequence e.
  • non-bacterial expression systems are used (e.g. mammalian expression systems such as CHO cells) to express the polypeptides of the present invention.
  • the expression vector used to express polynucleotides of the present invention in mammalian cells is pCI-DHFR vector comprising a CMV promoter and a neomycin resistance gene. Construction of the pCI-dhfr vector is described, according to one embodiment, in Example 1.
  • a number of expression vectors can be advantageously selected depending upon the use intended for the polypeptide expressed.
  • large quantities of polypeptide are desired.
  • vectors that direct the expression of high levels of the protein product, possibly as a fusion with a hydrophobic signal sequence, which directs the expressed product into the periplasm of the bacteria or the culture medium where the protein product is readily purified are desired.
  • vectors adaptable to such manipulation include, but are not limited to, the pET series of E. coli expression vectors [Studier et al, Methods in Enzymol. 185:60-89 (1990)].
  • yeast expression systems are used.
  • a number of vectors containing constitutive or inducible promoters can be used in yeast as disclosed in U.S. Pat. Application. No: 5,932,447.
  • vectors which promote integration of foreign DNA sequences into the yeast chromosome are used.
  • the expression vector of the present invention can further include additional polynucleotide sequences that allow, for example, the translation of several proteins from a single mRNA such as an internal ribosome entry site (IRES) and sequences for genomic integration of the promoter-chimeric polypeptide.
  • IRS internal ribosome entry site
  • mammalian expression vectors include, but are not limited to, pcDNA3, pcDNA3.1 (+/-), pGL3, pZeoSV2(+/-), pSecTag2, pDisplay, pEF/myc/cyto, pCMV/myc/cyto, pCR3.1, pSinRep5, DH26S, DHBB, pNMTl, pNMT41, pNMT81, which are available from Invitrogen, pCI which is available from Promega, pMbac, pPbac, pBK- RSV and pBK-CMV which are available from Strategene, pTRES which is available from Clontech, and their derivatives.
  • expression vectors containing regulatory elements from eukaryotic viruses such as retroviruses are used by the present invention.
  • SV40 vectors include pSVT7 and pMT2.
  • vectors derived from bovine papilloma virus include pBV-lMTHA, and vectors derived from Epstein Bar virus include pHEBO, and p205.
  • exemplary vectors include pMSG, pAV009/A + , pMTO10/A + , pMAMneo-5, baculovirus pDSVE, and any other vector allowing expression of proteins under the direction of the SV-40 early promoter, SV-40 later promoter, metallothionein promoter, murine mammary tumor virus promoter, Rous sarcoma virus promoter, polyhedrin promoter, or other promoters shown effective for expression in eukaryotic cells.
  • recombinant viral vectors are useful for in vivo expression of the polypeptides of the present invention since they offer advantages such as lateral infection and targeting specificity.
  • the viral vector is an adenovirus.
  • lateral infection is inherent in the life cycle of, for example, retrovirus and is the process by which a single infected cell produces many progeny virions that bud off and infect neighboring cells.
  • the result is that a large area becomes rapidly infected, most of which was not initially infected by the original viral particles.
  • viral vectors are produced that are unable to spread laterally. In one embodiment, this characteristic can be useful if the desired purpose is to introduce a specified gene into only a localized number of targeted cells.
  • various methods can be used to introduce the expression vector of the present invention into cells. Such methods are generally described in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Springs Harbor Laboratory, New York (1989, 1992), in Ausubel et al, Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1989, 1992), Chang et al, Somatic Gene Therapy, CRC Press, Ann Arbor, Mich. (1995), Vega et al, Gene Targeting, CRC Press, Ann Arbor Mich. (1995), Vectors: A Survey of Molecular Cloning Vectors and Their Uses, Butterworths, Boston Mass. (1988) and Gilboa et at.
  • introduction of nucleic acid by viral infection offers several advantages over other methods such as lipofection and electroporation, since higher transfection efficiency can be obtained due to the infectious nature of viruses.
  • the polypeptides of the present invention can also be expressed from a nucleic acid construct administered to the individual employing any suitable mode of administration, described hereinabove (i.e., in-vivo gene therapy).
  • the nucleic acid construct is introduced into a suitable cell via an appropriate gene delivery vehicle/method (transfection, infection, transduction, homologous recombination, etc.) and an expression system as needed and then the modified cells are expanded in culture and returned to the individual (i.e., ex- vivo gene therapy).
  • in vivo gene therapy using a polypeptide has been attempted in animal models such as rodents [Bohl et al, Blood. 2000; 95:2793-2798], primates [Gao et al, Blood, 2004, Volume 103, Number 9] and has proven successful in human clinical trials for patients with chronic renal failure [Lippin et al Blood 2005, 106, Number 7].
  • plant expression vectors are used.
  • the expression of a polypeptide coding sequence is driven by a number of promoters.
  • viral promoters such as the 35S RNA and 19S RNA promoters of CaMV [Brisson et al., Nature 310:511-514 (1984)], or the coat protein promoter to TMV [Takamatsu et al., EMBO J. 3:17-311 (1987)] are used.
  • plant promoters are used such as, for example, the small subunit of RUBISCO [Coruzzi et al., EMBO J.
  • constructs are introduced into plant cells using Ti plasmid, Ri plasmid, plant viral vectors, direct DNA transformation, microinjection, electroporation and other techniques well known to the skilled artisan. See, for example, Weissbach & Weissbach [Methods for Plant Molecular Biology, Academic Press, NY, Section VIII, pp 421-463 (1988)].
  • Other expression systems such as insects and mammalian host cell systems, which are well known in the art, can also be used by the present invention.
  • the expression construct of the present invention can also include sequences engineered to optimize stability, production, purification, yield or activity of the expressed polypeptide.
  • Various methods can be used to introduce the expression vector of the present invention into the host cell system.
  • such methods are generally described in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Springs Harbor Laboratory, New York (1989, 1992), in Ausubel et al, Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1989, 1992), Chang et al, Somatic Gene Therapy, CRC Press, Ann Arbor, Mich. (1995), Vega et al, Gene Targeting, CRC Press, Ann Arbor Mich. (1995), Vectors: A Survey of Molecular Cloning Vectors and Their Uses, Butterworths, Boston Mass. (1988) and Gilboa et at.
  • transformed cells are cultured under effective conditions, which allow for the expression of high amounts of recombinant polypeptide.
  • effective culture conditions include, but are not limited to, effective media, bioreactor, temperature, pH and oxygen conditions that permit protein production.
  • an effective medium refers to any medium in which a cell is cultured to produce the recombinant polypeptide of the present invention.
  • a medium typically includes an aqueous solution having assimilable carbon, nitrogen and phosphate sources, and appropriate salts, minerals, metals and other nutrients, such as vitamins.
  • cells of the present invention can be cultured in conventional fermentation bioreactors, shake flasks, test tubes, microtiter dishes and petri plates.
  • culturing is carried out at a temperature, pH and oxygen content appropriate for a recombinant cell.
  • culturing conditions are within the expertise of one of ordinary skill in the art.
  • resultant polypeptides of the present invention either remain within the recombinant cell, secreted into the fermentation medium, secreted into a space between two cellular membranes, such as the periplasmic space in E. coli; or retained on the outer surface of a cell or viral membrane.
  • the phrase "recovering the recombinant polypeptide" used herein refers to collecting the whole fermentation medium containing the polypeptide and need not imply additional steps of separation or purification.
  • polypeptides of the present invention are purified using a variety of standard protein purification techniques, such as, but not limited to, affinity chromatography, ion exchange chromatography, filtration, electrophoresis, hydrophobic interaction chromatography, gel filtration chromatography, reverse phase chromatography, concanavalin A chromatography, chromatofocusing and differential solubilization.
  • standard protein purification techniques such as, but not limited to, affinity chromatography, ion exchange chromatography, filtration, electrophoresis, hydrophobic interaction chromatography, gel filtration chromatography, reverse phase chromatography, concanavalin A chromatography, chromatofocusing and differential solubilization.
  • the expressed coding sequence can be engineered to encode the polypeptide of the present invention and fused cleavable moiety.
  • a fusion protein can be designed so that the polypeptide can be readily isolated by affinity chromatography; e.g., by immobilization on a column specific for the cleavable moiety.
  • a cleavage site is engineered between the polypeptide and the cleavable moiety and the polypeptide can be released from the chromatographic column by treatment with an appropriate enzyme or agent that specifically cleaves the fusion protein at this site [e.g., see Booth et al., Immunol. Lett. 19:65-70 (1988); and Gardella et al., J. Biol. Chem. 265: 15854-15859 (1990)].
  • polypeptide of the present invention is retrieved in "substantially pure” form.
  • the phrase "substantially pure” refers to a purity that allows for the effective use of the protein in the applications described herein.
  • the polypeptide of the present invention can also be synthesized using in vitro expression systems.
  • in vitro synthesis methods are well known in the art and the components of the system are commercially available.
  • the polypeptides of the invention further comprise a target-cell binding and internalization component/s.
  • the polypeptides of the invention are packaged onto a carrier such as but not limited to: liposome or other particles capable of carrying the polypeptides to target cells.
  • the recombinant polypeptides are synthesized and purified; their therapeutic efficacy can be assayed either in vivo or in vitro. In one embodiment, the binding activities of the recombinant polypeptides are ascertained.
  • in vitro binding activity is ascertained by measuring the ability of the polypeptides, as described herein as well as pharmaceutical compositions comprising the same to treat diseases such as HCV, liver cancers, liver diseases or other types of cancers such as hairy cell leukemia, malignant melanoma, Kaposi's sarcoma, bladder cancer, chronic myelocytic leukemia, kidney cancer, carcinoid tumors, non-Hodgkin's lymphoma, ovarian cancer, and skin cancers (for interferons).
  • diseases such as HCV, liver cancers, liver diseases or other types of cancers such as hairy cell leukemia, malignant melanoma, Kaposi's sarcoma, bladder cancer, chronic myelocytic leukemia, kidney cancer, carcinoid tumors, non-Hodgkin's lymphoma, ovarian cancer, and skin cancers (for interferons).
  • in vivo activity is deduced by known measures of the disease that is being treated.
  • polypeptides of the present are administered in a dose of 1-90 micrograms in 0.1-5 ml solution. In another embodiment, polypeptides of the present invention are administered in a dose of 1-50 micrograms in 0.1-5 ml solution. In another embodiment, polypeptides of the present invention are administered in a dose of 1-25 micrograms in 0.1-5 ml solution. In another embodiment, polypeptides of the present invention are administered in a dose of 50-90 micrograms in 0.1-5 ml solution. In another embodiment, polypeptides of the present invention are administered in a dose of 10-50 micrograms in 0.1-5 ml solution.
  • polypeptides are administered in a dose of 1-90 micrograms in 0.1-5 ml solution by intramuscular (IM) injection, subcutaneous (SC) injection, or intravenous (IV) injection once a week.
  • polypeptides of the present invention are administered in a dose of 1-90 micrograms in 0.1-5 ml solution by intramuscular (IM) injection, subcutaneous (SC) injection, or intravenous (IV) injection twice a week.
  • polypeptides of the present invention are administered in a dose of 1-90 micrograms in 0.1-5 ml solution by intramuscular (IM) injection, subcutaneous (SC) injection, or intravenous (IV) injection three times a week.
  • polypeptides of the present invention are administered in a dose of 1-90 micrograms in 0.1-5 ml solution by intramuscular (IM) injection, subcutaneous (SC) injection, or intravenous (IV) injection once every two weeks.
  • polypeptides of the present invention are administered in a dose of 1-90 micrograms in 0.1-5 ml solution by intramuscular (IM) injection, subcutaneous (SC) injection, or intravenous (IV) injection once every 17 days.
  • polypeptides of the present invention are administered in a dose of 1-90 micrograms in 0.1-5 ml solution by intramuscular (IM) injection, subcutaneous (SC) injection, or intravenous (IV) injection once every 19 days weeks.
  • polypeptides of the present invention can be provided to the individual per se.
  • polypeptides of the present invention can be provided to the individual as part of a pharmaceutical composition where it is mixed with a carrier such as a pharmaceutically acceptable carrier.
  • a "pharmaceutical composition” refers to a preparation of one or more of the active ingredients described herein with other chemical components such as physiologically suitable carriers and excipients.
  • the purpose of a pharmaceutical composition is to facilitate administration of the polypeptides to an organism.
  • active ingredient refers to the polypeptide, which is accountable for the biological effect.
  • the present invention provides combined preparations.
  • a combined preparation defines especially a "kit of parts" in the sense that the combination partners as defined above can be dosed independently or by use of different fixed combinations with distinguished amounts of the combination partners i.e., simultaneously, concurrently, separately or sequentially.
  • the parts of the kit of parts can then, e.g., be administered simultaneously or chronologically staggered, that is at different time points and with equal or different time intervals for any part of the kit of parts.
  • the ratio of the total amounts of the combination partners in some embodiments, can be administered in the combined preparation.
  • the combined preparation can be varied, e.g., in order to cope with the needs of a patient subpopulation to be treated or the needs of the single patient which different needs can be due to a particular disease, severity of a disease, age, sex, or body weight as can be readily made by a person skilled in the art.
  • physiologically acceptable carrier and “pharmaceutically acceptable carrier” which be interchangeably used refer to a carrier or a diluent that does not cause significant irritation to an organism and does not abrogate the biological activity and properties of the administered compound.
  • An adjuvant is included under these phrases.
  • one of the ingredients included in the pharmaceutically acceptable carrier can be for example polyethylene glycol (PEG), a biocompatible polymer with a wide range of solubility in both organic and aqueous media (Mutter et al. (1979).
  • excipient refers to an inert substance added to a pharmaceutical composition to further facilitate administration of an active ingredient.
  • excipients include calcium carbonate, calcium phosphate, various sugars and types of starch, cellulose derivatives, gelatin, vegetable oils and polyethylene glycols.
  • suitable routes of administration include oral, rectal, transmucosal, transnasal, intestinal or parenteral delivery, including intramuscular, subcutaneous and intramedullary injections as well as intrathecal, direct intraventricular, intravenous, intraperitoneal, intranasal, or intraocular injections.
  • the preparation is administered in a local rather than systemic manner, for example, via injection of the preparation directly into a specific region of a patient's body.
  • the dosage of the polypeptides of the present invention in one embodiment, is in the range of 0.005- 100 mg/day. In another embodiment, the dosage is in the range of 0.005-5 mg/day. In another embodiment, the dosage is in the range of 0.01-50 mg/day. In another embodiment, the dosage is in the range of 0.1-20 mg/day. In another embodiment, the dosage is in the range of 0.1-10 mg/day. In another embodiment, the dosage is in the range of 0.01-5 mg/day. In another embodiment, the dosage is in the range of 0.001-0.01 mg/day. In another embodiment, the dosage is in the range of 0.001-0.1 mg/day.
  • the dosage is in the range of 0.1-5 mg/day. In another embodiment, the dosage is in the range of 0.5-50 mg/day. In another embodiment, the dosage is in the range of 0.2-15mg/day. In another embodiment, the dosage is in the range of 0.8-65 mg/day. In another embodiment, the dosage is in the range of 1-50 mg/day. In another embodiment, the dosage is in the range of 5-10 mg/day. In another embodiment, the dosage is in the range of 8-15 mg/day. In another embodiment, the dosage is in a range of 10- 20mg/day. In another embodiment, the dosage is in the range of 20-40 mg/day. In another embodiment, the dosage is in a range of 60-120 mg/day.
  • the dosage is in the range of 12-40 mg/day. In another embodiment, the dosage is in the range of 40-60 mg/day. In another embodiment, the dosage is in a range of 50-100mg/day. In another embodiment, the dosage is in a range of 1-60 mg/day. In another embodiment, the dosage is in the range of 15-25 mg/day. In another embodiment, the dosage is in the range of 5-10 mg/day. In another embodiment, the dosage is in the range of 55-65 mg/day.
  • a polypeptide is formulated in an intranasal dosage form. In another embodiment, a polypeptide is formulated in an injectable dosage form. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 0.0001 mg to 0.6 mg. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 0.001 mg to 0.005 mg. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 0.005 mg to 0.01 mg. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 0.01 mg to 0.3 mg. In another embodiment, a polypeptide is administered to a subject in a dose in a dose ranging from 0.2 mg to 0.6 mg.
  • a polypeptide is administered to a subject in a dose ranging from 1-100 micrograms. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 10-80 micrograms. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 20-60 micrograms. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 10-50 micrograms. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 40-80 micrograms. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 10-30 micrograms.
  • a polypeptide is administered to a subject in a dose ranging from 30-60 micrograms. [0136] In another embodiment, a polypeptide is administered to a subject in a dose ranging from 0.2 mg to 2 mg. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 2 mg to 6 mg. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 4 mg to 10 mg. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 5 mg and 15 mg.
  • a polypeptide is injected into the muscle (intramuscular injection). In another embodiment, a polypeptide is injected below the skin (subcutaneous injection). In another embodiment, a polypeptide is injected into the muscle. In another embodiment, a polypeptide is injected below the skin.
  • a polypeptide is administered to a subject once a day. In another embodiment, a polypeptide is administered to a subject once every two days. In another embodiment, a polypeptide is administered to a subject once every three days. In another embodiment, a polypeptide is administered to a subject once every four days. In another embodiment, a polypeptide is administered to a subject once every five days. In another embodiment, a polypeptide is administered to a subject once every six days. In another embodiment, a polypeptide is administered to a subject once every week. In another embodiment, a polypeptide is administered to a subject once every 7-14 days. In another embodiment, a polypeptide is administered to a subject once every 10-20 days. In another embodiment, a polypeptide is administered to a subject once every 5-15 days. In another embodiment, a polypeptide is administered to a subject once every 15-30 days.
  • the dosage is in a range of 50-500 mg/day. In another embodiment, the dosage is in a range of 50-150 mg/day. In another embodiment, the dosage is in a range of 100-200 mg/day. In another embodiment, the dosage is in a range of 150-250 mg/day. In another embodiment, the dosage is in a range of 200-300 mg/day. In another embodiment, the dosage is in a range of 250-400 mg/day. In another embodiment, the dosage is in a range of 300- 500 mg/day. In another embodiment, the dosage is in a range of 350-500 mg/day.
  • the dosage is 20 mg/day. In one embodiment, the dosage is 30 mg/day. In one embodiment, the dosage is 40 mg/day. In one embodiment, the dosage is 50 mg/day. In one embodiment, the dosage is 0.01 mg/day. In another embodiment, the dosage is 0.1 mg/day. In another embodiment, the dosage is 1 mg/day. In another embodiment, the dosage is 0.530 mg/day. In another embodiment, the dosage is 0.05 mg/day. In another embodiment, the dosage is 50 mg/day. In another embodiment, the dosage is 10 mg/day. In another embodiment, the dosage is 20-70 mg/day. In another embodiment, the dosage is 5 mg/day.
  • the dosage is 1-90 mg/day. In another embodiment, the dosage is 1-90 mg/2 days. In another embodiment, the dosage is 1-90 mg/3 days. In another embodiment, the dosage is 1-90 mg/4 days. In another embodiment, the dosage is 1-90 mg/5 days. In another embodiment, the dosage is 1-90 mg/6 days. In another embodiment, the dosage is 1-90 mg/week. In another embodiment, the dosage is 1-90 mg/9 days. In another embodiment, the dosage is 1-90 mg/11 days. In another embodiment, the dosage is 1-90 mg/14 days.
  • the polypeptide dosage is 10-50 mg/day. In another embodiment, the dosage is 10-50 mg/2 days. In another embodiment, the dosage is 10-50 mg/3 days. In another embodiment, the dosage is 10-50 mg/4 days. In another embodiment, the dosage is 10-50 micrograms mg/5 days. In another embodiment, the dosage is 10-50 mg/6 days. In another embodiment, the dosage is 10-50 mg/week. In another embodiment, the dosage is 10-50 mg/9 days. In another embodiment, the dosage is 10-50 mg/11 days. In another embodiment, the dosage is 10-50 mg/14 days.
  • Oral administration in one embodiment, comprises a unit dosage form comprising tablets, capsules, lozenges, chewable tablets, suspensions, emulsions and the like.
  • unit dosage forms comprise a safe and effective amount of the polypeptide of the invention, each of which is in one embodiment, from about 0.7 or 3.5 mg to about 280 mg/70 kg, or in another embodiment, about 0.5 or 10 mg to about 210 mg/70 kg.
  • the pharmaceutically-acceptable carriers suitable for the preparation of unit dosage forms for peroral administration are well- known in the art.
  • tablets typically comprise conventional pharmaceutically-compatible adjuvants as inert diluents, such as calcium carbonate, sodium carbonate, mannitol, lactose and cellulose; binders such as starch, gelatin and sucrose; disintegrants such as starch, alginic acid and croscarmelose; lubricants such as magnesium stearate, stearic acid and talc.
  • glidants such as silicon dioxide can be used to improve flow characteristics of the powder-mixture.
  • coloring agents such as the FD&C dyes, can be added for appearance.
  • Sweeteners and flavoring agents such as aspartame, saccharin, menthol, peppermint, and fruit flavors, are useful adjuvants for chewable tablets.
  • Capsules typically comprise one or more solid diluents disclosed above.
  • the selection of carrier components depends on secondary considerations like taste, cost, and shelf stability, which are not critical for the purposes of this invention, and can be readily made by a person skilled in the art.
  • the oral dosage form comprises predefined release profile.
  • the oral dosage form of the present invention comprises an extended release tablets, capsules, lozenges or chewable tablets.
  • the oral dosage form of the present invention comprises a slow release tablets, capsules, lozenges or chewable tablets.
  • the oral dosage form of the present invention comprises an immediate release tablets, capsules, lozenges or chewable tablets.
  • the oral dosage form is formulated according to the desired release profile of the pharmaceutical active ingredient as known to one skilled in the art.
  • Peroral compositions in some embodiments, comprise liquid solutions, emulsions, suspensions, and the like.
  • pharmaceutically-acceptable carriers suitable for preparation of such compositions are well known in the art.
  • liquid oral compositions comprise from about 0.001% to about 0.933% of the desired compound or compounds, or in another embodiment, from about 0.01% to about 10 %.
  • compositions for use in the methods of this invention comprise solutions or emulsions, which in some embodiments are aqueous solutions or emulsions comprising a safe and effective amount of the compounds of the present invention and optionally, other compounds, intended for topical intranasal administration.
  • h compositions comprise from about 0.001% to about 10.0% w/v of a subject compound, more preferably from about 00.1% to about 2.0, which is used for systemic delivery of the compounds by the intranasal route.
  • the pharmaceutical compositions are administered by intravenous, intra-arterial, or intramuscular injection of a liquid preparation.
  • liquid formulations include solutions, suspensions, dispersions, emulsions, oils and the like.
  • the pharmaceutical compositions are administered intravenously, and are thus formulated in a form suitable for intravenous administration.
  • the pharmaceutical compositions are administered intra-arterially, and are thus formulated in a form suitable for intra-arterial administration.
  • the pharmaceutical compositions are administered intramuscularly, and are thus formulated in a form suitable for intramuscular administration.
  • compositions of the present invention are manufactured by processes well known in the art, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or lyophilizing processes.
  • compositions for use in accordance with the present invention is formulated in conventional manner using one or more physiologically acceptable carriers comprising excipients and auxiliaries, which facilitate processing of the active ingredients into preparations which, can be used pharmaceutically.
  • formulation is dependent upon the route of administration chosen.
  • injectables, of the invention are formulated in aqueous solutions.
  • injectables, of the invention are formulated in physiologically compatible buffers such as Hank's solution, Ringer's solution, or physiological salt buffer.
  • physiologically compatible buffers such as Hank's solution, Ringer's solution, or physiological salt buffer.
  • penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.
  • the preparations described herein are formulated for parenteral administration, e.g., by bolus injection or continuous infusion.
  • formulations for injection are presented in unit dosage form, e.g., in ampoules or in multidose containers with optionally, an added preservative.
  • compositions are suspensions, solutions or emulsions in oily or aqueous vehicles, and contain formulatory agents such as suspending, stabilizing and/or dispersing agents.
  • compositions also comprise, in some embodiments, preservatives, such as benzalkonium chloride and thimerosal and the like; chelating agents, such as edetate sodium and others; buffers such as phosphate, citrate and acetate; tonicity agents such as sodium chloride, potassium chloride, glycerin, mannitol and others; antioxidants such as ascorbic acid, acetylcystine, sodium metabisulfote and others; aromatic agents; viscosity adjusters, such as polymers, including cellulose and derivatives thereof; and polyvinyl alcohol and acid and bases to adjust the pH of these aqueous compositions as needed.
  • the compositions also comprise, in some embodiments, local anesthetics or other actives.
  • the compositions can be used as sprays, mists, drops, and the like.
  • compositions for parenteral administration include aqueous solutions of the active preparation in water-soluble form.
  • suspensions of the active ingredients are prepared as appropriate oily or water based injection suspensions.
  • Suitable lipophilic solvents or vehicles include, in some embodiments, fatty oils such as sesame oil, or synthetic fatty acid esters such as ethyl oleate, triglycerides or liposomes.
  • Aqueous injection suspensions contain, in some embodiments, substances, which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol or dextran.
  • the suspension also contain suitable stabilizers or agents which increase the solubility of the active ingredients to allow for the preparation of highly concentrated solutions.
  • the polypeptide is delivered in a vesicle, in particular a liposome (see Langer, Science 249: 1527-1533 (1990); Treat et al, in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez- Berestein and Fidler (eds.), Liss, New York, pp. 353- 365 (1989); Lopez-Berestein, ibid., pp. 317-327; see generally ibid).
  • a liposome see Langer, Science 249: 1527-1533 (1990); Treat et al, in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez- Berestein and Fidler (eds.), Liss, New York, pp. 353- 365 (1989); Lopez-Berestein, ibid., pp. 317-327; see generally ibid).
  • the pharmaceutical composition delivered in a controlled release system is formulated for intravenous infusion, implantable osmotic pump, transdermal patch, liposomes, or other modes of administration.
  • a pump is used (see Langer, supra; Sefton, CRC Crit. Ref. Biomed. Eng. 14:201 (1987); Buchwald et al, Surgery 88:507 (1980); Saudek et al, N. Engl. J. Med. 321 :574 (1989).
  • polymeric materials can be used.
  • a controlled release system can be placed in proximity to the therapeutic target, i.e., the brain, thus requiring only a fraction of the systemic dose (see, e.g., Goodson, in Medical Applications of Controlled Release, supra, vol. 2, pp. 115-138 (1984). Other controlled release systems are discussed in the review by Langer ⁇ Science 249: 1527-1533 (1990).
  • the active ingredient is in powder form for constitution with a suitable vehicle, e.g., sterile, pyrogen-free water based solution, before use.
  • a suitable vehicle e.g., sterile, pyrogen-free water based solution
  • Compositions are formulated, in some embodiments, for atomization and inhalation administration. In another embodiment, compositions are contained in a container with attached atomizing means.
  • compositions suitable for use in context of the present invention include compositions wherein the polypeptides are contained in an amount effective to achieve the intended purpose.
  • a therapeutically effective amount means an amount of the polypeptide effective to prevent, alleviate or ameliorate symptoms of disease or prolong the survival of the subject being treated.
  • the disease is a liver disease caused by HCV.
  • determination of a therapeutically effective amount is well within the capability of those skilled in the art.
  • substances which can serve as carriers or components thereof are sugars, such as lactose, glucose and sucrose; starches, such as corn starch and potato starch; cellulose and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose, and methyl cellulose; powdered tragacanth; malt; gelatin; talc; solid lubricants, such as stearic acid and magnesium stearate; calcium sulfate; vegetable oils, such as peanut oil, cottonseed oil, sesame oil, olive oil, corn oil and oil of theobroma; polyols such as propylene glycol, glycerine, sorbitol, mannitol, and polyethylene glycol; alginic acid; emulsifiers, such as the TweenTM brand emulsifiers; wetting agents, such sodium lauryl sulfate; coloring agents; flavoring agents; tableting agents, stabilizers; antioxidants; preservatives;
  • a pharmaceutically-acceptable carrier to be used in conjunction with the compound is basically determined by the way the compound is to be administered. If the subject compound is to be injected, in one embodiment, the pharmaceutically-acceptable carrier is sterile, physiological saline, with a blood-compatible suspending agent, the pH of which has been adjusted to about 7.4.
  • compositions further comprise binders (e.g. acacia, cornstarch, gelatin, carbomer, ethyl cellulose, guar gum, hydroxypropyl cellulose, hydroxypropyl methyl cellulose, povidone), disintegrating agents (e.g.
  • binders e.g. acacia, cornstarch, gelatin, carbomer, ethyl cellulose, guar gum, hydroxypropyl cellulose, hydroxypropyl methyl cellulose, povidone
  • disintegrating agents e.g.
  • cornstarch potato starch, alginic acid, silicon dioxide, croscarmelose sodium, crospovidone, guar gum, sodium starch glycolate), buffers (e.g., Tris- HCL, acetate, phosphate) of various pH and ionic strength, additives such as albumin or gelatin to prevent absorption to surfaces, detergents (e.g., Tween 20, Tween 80, Pluronic F68, bile acid salts), protease inhibitors, surfactants (e.g.
  • sodium lauryl sulfate sodium lauryl sulfate
  • permeation enhancers solubilizing agents (e.g., glycerol, polyethylene glycerol), anti-oxidants (e.g., ascorbic acid, sodium metabisulfite, butylated hydroxyanisole), stabilizers (e.g. hydroxypropyl cellulose, hyroxypropylmethyl cellulose), viscosity increasing agents(e.g. carbomer, colloidal silicon dioxide, ethyl cellulose, guar gum), sweeteners (e.g. aspartame, citric acid), preservatives (e.g., Thimerosal, benzyl alcohol, parabens), lubricants (e.g.
  • stearic acid magnesium stearate, polyethylene glycol, sodium lauryl sulfate), flow-aids (e.g. colloidal silicon dioxide), plasticizers (e.g. diethyl phthalate, triethyl citrate), emulsifiers (e.g. carbomer, hydroxypropyl cellulose, sodium lauryl sulfate), polymer coatings (e.g., poloxamers or poloxamines), coating and film forming agents (e.g. ethyl cellulose, acrylates, polymethacrylates) and/or adjuvants.
  • plasticizers e.g. diethyl phthalate, triethyl citrate
  • emulsifiers e.g. carbomer, hydroxypropyl cellulose, sodium lauryl sulfate
  • polymer coatings e.g., poloxamers or poloxamines
  • coating and film forming agents e.g. ethyl cellulose
  • Typical components of carriers for syrups, elixirs, emulsions and suspensions include ethanol, glycerol, propylene glycol, polyethylene glycol, liquid sucrose, sorbitol and water.
  • typical suspending agents include methyl cellulose, sodium carboxymethyl cellulose, cellulose (e.g. AvicelTM, RC-591), tragacanth and sodium alginate;
  • typical wetting agents include lecithin and polyethylene oxide sorbitan (e.g. polysorbate 80).
  • Typical preservatives include methyl paraben and sodium benzoate.
  • peroral liquid compositions also contain one or more components such as sweeteners, flavoring agents and colorants disclosed above.
  • compositions also include incorporation of the polypeptide into or onto particulate preparations of polymeric compounds such as polylactic acid, polglycolic acid, hydrogels, etc, or onto liposomes, microemulsions, micelles, unilamellar or multilamellar vesicles, erythrocyte ghosts, or spheroplasts.)
  • polymeric compounds such as polylactic acid, polglycolic acid, hydrogels, etc, or onto liposomes, microemulsions, micelles, unilamellar or multilamellar vesicles, erythrocyte ghosts, or spheroplasts.
  • particulate compositions coated with polymers e.g. poloxamers or poloxamines
  • polymers e.g. poloxamers or poloxamines
  • polypeptides modified by the covalent attachment of water- soluble polymers such as polyethylene glycol, copolymers of polyethylene glycol and polypropylene glycol, carboxymethyl cellulose, dextran, polyvinyl alcohol, polyvinylpyrrolidone or polyproline.
  • the modified compounds exhibit substantially longer half-lives in blood following intravenous injection than do the corresponding unmodified compounds.
  • modifications also increase the polypeptide's solubility in aqueous solution, eliminate aggregation, enhance the physical and chemical stability of the compound, and greatly reduce the immunogenicity and reactivity of the compound.
  • the desired in vivo biological activity is achieved by the administration of such polymer-compound abducts less frequently or in lower doses than with the unmodified compound.
  • preparation of effective amount or dose can be estimated initially from in vitro assays.
  • a dose can be formulated in animal models and such information can be used to more accurately determine useful doses in humans.
  • toxicity and therapeutic efficacy of the polypeptide described herein can be determined by standard pharmaceutical procedures in vitro, in cell cultures or experimental animals.
  • the data obtained from these in vitro and cell culture assays and animal studies can be used in formulating a range of dosage for use in human.
  • the dosages vary depending upon the dosage form employed and the route of administration utilized.
  • the exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. [See e.g., Fingl, et al, (1975) "The Pharmacological Basis of Therapeutics", Ch. 1 p. l].
  • dosing can be of a single or a plurality of administrations, with course of treatment lasting from several days to several weeks or until cure is effected or diminution of the disease state is achieved.
  • the amount of a composition to be administered will, of course, be dependent on the subject being treated, the severity of the affliction, the manner of administration, the judgment of the prescribing physician, etc.
  • compositions including the preparation of the present invention formulated in a compatible pharmaceutical carrier are also be prepared, placed in an appropriate container, and labeled for treatment of an indicated condition.
  • a polypeptide as described herein is administered via systemic administration.
  • a polypeptide as described herein is administered by intravenous, intramuscular or subcutaneous injection.
  • a polypeptides as described herein is lyophilized (i.e., freeze-dried) preparation in combination with complex organic excipients and stabilizers such as nonionic surface active agents (i.e., surfactants), various sugars, organic polyols and/or human serum albumin.
  • a pharmaceutical composition comprises a lyophilized polypeptide as described in sterile water for injection.
  • a pharmaceutical composition comprises a lyophilized polypeptide as described in sterile PBS for injection.
  • a pharmaceutical composition comprises a lyophilized polypeptide as described in sterile 0.9% NaCl for injection.
  • the pharmaceutical composition comprises a polypeptide as described herein and complex carriers such as human serum albumin, polyols, sugars, and anionic surface active stabilizing agents. See, for example, WO 89/10756 (Hara et al.- containing polyol and p-hydroxybenzoate).
  • the pharmaceutical composition comprises a polypeptide as described herein and lactobionic acid and an acetate/glycine buffer.
  • the pharmaceutical composition comprises a polypeptide as described herein and amino acids, such as arginine or glutamate that increase the solubility of interferon compositions in water.
  • the pharmaceutical composition comprises a lyophilized polypeptide as described herein and glycine or human serum albumin (HSA), a buffer (e g. acetate) and an isotonic agent (e.g NaCl).
  • HSA human serum albumin
  • a buffer e g. acetate
  • an isotonic agent e.g NaCl
  • the pharmaceutical composition comprises a lyophilized polypeptide as described herein and phosphate buffer, glycine and HSA.
  • the pharmaceutical composition comprising a polypeptide as described herein is stabilized when placed in buffered solutions having a pH between about 4 and 7.2.
  • the pharmaceutical composition comprising a polypeptide as described herein is stabilized with an amino acid as a stabilizing agent and in some cases a salt (if the amino acid does not contain a charged side chain).
  • the pharmaceutical composition comprising a polypeptide as described herein is a liquid composition comprising a stabilizing agent at between about 0.3% and 5% by weight which is an amino acid.
  • the pharmaceutical composition comprising a polypeptide as described herein provides a liquid formulation permitting storage for a long period of time in a liquid state facilitating storage and shipping prior to administration.
  • the pharmaceutical composition comprising a polypeptide as described herein comprises solid lipids as matrix material.
  • the injectable pharmaceutical composition comprising a polypeptide as described herein comprises solid lipids as matrix material.
  • the production of lipid microparticles by spray congealing was described by Lucasr (Speiser and al, Pharm. Res. 8 (1991) 47-54) followed by lipid nanopellets for peroral administration (Speiser EP 0167825 (1990)).
  • lipids, which are used are well tolerated by the body (e. g. glycerides composed of fatty acids which are present in the emulsions for parenteral nutrition).
  • the pharmaceutical composition comprising a polypeptide as described herein is in the form of liposomes (J. E. Diederichs and al., Pharm./nd. 56 (1994) 267- 275).
  • the pharmaceutical composition comprising a polypeptide as described herein comprises polymeric microparticles. In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein comprises polymeric nanoparticles. In another embodiment, the injectable pharmaceutical composition comprising a polypeptide as described herein comprises polymeric microparticles. In another embodiment, the injectable pharmaceutical composition comprising a polypeptide as described herein comprises polymeric nanoparticles. In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein comprises nanoparticles. In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein comprises liposomes.
  • the pharmaceutical composition comprising a polypeptide as described herein comprises lipid emulsion In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein comprises microspheres. In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein comprises lipid nanoparticles. In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein comprises lipid nanoparticles comprising amphiphilic lipids. In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein comprises lipid nanoparticles comprising a drug, a lipid matrix and a surfactant. In another embodiment, the lipid matrix has a monoglyceride content which is at least 50% w/w.
  • compositions of the present invention are presented in a pack or dispenser device, such as an FDA approved kit, which contain one or more unit dosage forms containing the active ingredient.
  • the pack for example, comprise metal or plastic foil, such as a blister pack.
  • the pack or dispenser device is accompanied by instructions for administration.
  • the pack or dispenser is accommodated by a notice associated with the container in a form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals, which notice is reflective of approval by the agency of the form of the compositions or human or veterinary administration.
  • a notice associated with the container in a form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals, which notice is reflective of approval by the agency of the form of the compositions or human or veterinary administration.
  • Such notice is labeling approved by the U.S. Food and Drug Administration for prescription drugs or of an approved product insert.
  • polypeptides of the present invention can be provided to the individual with additional active agents to achieve an improved therapeutic effect as compared to treatment with each agent by itself.
  • measures e.g., dosing and selection of the complementary agent
  • E. coli Escherichia coli
  • XL-1 Blue and DH5a (Stratagene, USA) for plasmid propagation
  • BJ5183 (Stratagene, USA) for the generation of recombinant adenovirus plasmid DNA.
  • AdEasy plasmid system (pShuttle and pAdEasy-1) (He et al, 1998), that was used for generation of recombinant human type 5 adenoviral vectors for gene delivery of the zymoxins expression cassettes, was a generous gift from Dr. Bert Vogelstein, Johns Hopkins Oncology Center, Baltimore, MD. All plasmid and DNA fragment purifications were carried out with High-Speed Plasmid Mini Kit and Gel/PCR DNA fragments Extraction Kit (Geneaid Biotech Ltd., Taiwan) unless mentioned otherwise. T4 DNA ligase and restriction enzymes were purchased from New England Biolabs (USA). DNA ligations were carried out at 16°C overnight. Molecular cloning Oligonucleotides
  • a PCR was carried out using a single colony of E. coli strain XL-1 as template, the forward primer: 40- clvmazf and the reverse primers: 41-clvmazf, 42-clvmazf, 43-clvmazf, 44-clvmazf, 45-clvmazf, 46-clvmazf and 47-clvmazf.
  • the PCR product encoding for a fusion polypeptide composed of (from the N terminus) MazF, HCV P10-P10' NS3 cleavage sequence derived from genotype 2a (strain JFH1) NS5A/B junction, a short flexible linker, a short inhibitory peptide corresponding to MazE C-terminal 35 amino-acids (which encompass the 23 amino-acids inhibitory peptide (MazEp) that has been described by Li et al.
  • a PCR was carried out using DNA of plasmid "pmCherry (in EGFP C2 backbone) - MazF-full JFH NS5AB-linker-inhibitor peptide-ER" as template, the forward primer: 40- clvmazf and the reverse primers: 50-unclmazf and 51-unclmazf.
  • the PCR product was digested with EcoRV and Nrul, and the digestion product of 233bp was cloned between the corresponding sites of the same plasmid that has been used as the template, generating the plasmid: "pmCherry (in EGFP C2 backbone) - MazF- mutated NS5AB-linker-inhibitor peptide-ER".
  • This plasmid encodes for an uncleavable construct in which the NS3 cleavage sequence was replaced by a mutated 14 amino acids cleavage sequence (P10-P4') from HCV genotype la NS5A/B junction in which P3 valine was substituted by alanine, P2 cysteine by glycine, PI cysteine by glycine and P4' tyrosine by alanine.
  • the amino acid sequence of the zymoxin described herein is shown in Fig. 13B.
  • the sequence of the red fluorescent protein mCherry was amplified by PCR from an expression cassette (see construction of the vector encoding for "mCherry-NS3-activated MazF") using the forward primer: 48- clvmazf and the reverse primer: 49- clvmazf.
  • the PCR product was digested with Nhel and BgUl and was cloned between the corresponding sites of the plasmid pEGFP C2, generating the plasmid "pmCherry (in EGFP C2 backbone)".
  • the resulting vectors were digested with Pmel, purified, and 400ng of the digested vectors where mixed with lOOng of the plasmid pAdEasy-1.
  • DNA mixture was electroporated (in 2.0 mm cuvettes at 2,500V, 25 ⁇ ) into E. coli strain BJ5183 electro-competent cells (Stratagene, USA). After phenotypic expression of 1 hour, bacteria were seeded on LB agar plates containing 50 ⁇ g/ml of kanamycin and were grown at 37°C over-night.
  • the plasmids which were denoted "pAdEasy-mCherry-NS3 activated MazF” and "pAdEasy- mCherry-uncleavable MazF” were isolated from chosen "positive" clones and were digested with Pad. Digested DNA was purified using ZymocleanTM Gel DNA Recovery Kit (ZYMO RESEARCH, USA) according to the manufacturer instructions. 1.5 ⁇ g of the purified, digested plasmids were used to transfect HEK293 cells at 50-70% confluence in 60mm culture dish using the calcium-phosphate method.
  • CPE cytopathic effect
  • virus particle When a third to half of the cells is detached (usually after 3-5 days), virus particle were released by freeze/thaw cycles as described, and a second amplification cycle was performed, as described, by infecting HEK293 cells at 70%> confluence in two 100mm dishes. The supernatant containing viruses was kept at -80°C.
  • Viral titers were determined by an end- point dilution assay: HEK293 cells were grown to about 70%> confluence in 96-wells plates. The recombinant adenovirus stock solution was 10 fold serially diluted to a concentrations range of 10 "3 -10 "10 into growth medium. 1 Ox 100 of each dilution were added to 10 wells in the 96-well plate.
  • the calcium-phosphate transfection method was applied for introducing 2 ⁇ g of the plasmid "pmCherry (in pEGFP C2 backbone)- MazF-full JFH NS5AB-linker-inhibitor peptide-ER" or the plasmid "pmCherry (in EGFP C2 backbone)- MazF- mutated NS5AB- linker-inhibitor peptide-ER" into T-Rex 293 cells inducibly expressing EGFP-Full NS3-4A seeded 1.5 x lO 6 cells per 60mm plate 24 hours before transfection.
  • Stable transfectants inducibly expressing EGFP-Full NS3-4A and constitutively expressing mCherry-NS3 activated MazF (denoted "Tet-inducible full NS3-4A/constitutive NS3 activated MazF expressing cells") or mCherry-uncleavable MazF (denoted "Tet-inducible full NS3-4A / constitutive uncleavable MazF expressing cells”) were selected in a medium containing lmg/ml of G418 (A.G. Scientific, USA). Cell clones that express high level of the cleavable construct or the uncleavable control were identified by fluorescence microscopy and isolated.
  • protein samples were separated on a 12% SDS/polyacrylamide gel, transferred to nitrocellulose and detected using rabbit polyclonal anti-GFP antibody (Santa- Cruz, USA) or mouse monoclonal anti-actin antibody (Abeam, USA), followed by horseradish peroxidase (HRP)-conjugated goat anti-rabbit or anti-mouse antibodies (Jackson ImmunoResearch Laboratories, USA) and enhanced chemiluminescence (ECL) detection using SuperSignal West Pico Chemiluminescent Substrate (Thermo SCIENTIFIC/Pierce, USA).
  • HRP horseradish peroxidase
  • ECL enhanced chemiluminescence
  • HCV Viral infection
  • Virus infection assays were carried out with an inter-genotypic chimeric hepatitis C virus (HCV) produced by replacing the core-NS2 segment of the JFH-1 virus genome with the comparable segment of the genotype la H77 virus.
  • HCV inter-genotypic chimeric hepatitis C virus
  • This chimeric virus, HJ3-5 (Kindly provided by Prof. Stanley Lemon, University of Texas at Galveston), contains two compensatory mutations that promote its growth in cell culture as described previously (Yi et al, 2007).
  • HCV RNAs were transcribed in vitro and electroporated into cells essentially as described previously (Yi and Lemon, 2004; Yi et al, 2006).
  • HCV RNA in vitro- synthesized HCV RNA was mixed with 5x 10 6 Huh7.5 cells in a 2-mm cuvette and pulsed twice at 1.4 kV and 25 ⁇ . Cells were seeded into 12-well plates or 25-cm 2 flasks, and passaged at 3 -to 4-day intervals post-transfection by trypsinization and reseeding with a 1 :3 to 1 :4 split into fresh culture vessels.
  • T-REx 293 cells inducibly expressing EGFP-fuU NS3-4A (supplemented with different tetracycline concentrations) and constitutively expressing mCherry-NS3 activated MazF or mCherry-uncleavable MazF
  • l lO 5 Tet-inducible full NS3-4A/constitutive NS3 activated MazF or Tet-inducible full NS3-4A/constitutive uncleavable MazF expressing cells were seeded on poly-L-lysine coated cover-slips in a 24 well-plate. 12 hours later, cells were supplemented with lOng/ml or lOOOng/ml of tetracycline, or left untreated. 36 hours later, cells were fixed with 4% formaldehyde in PBS.
  • Huh7.5 cells infected with HCV HJ3-5 chimeric virus were seeded into 8-well chamber slides (Nalge Nunc, USA). After 24 hours, cells were fixed and permeabilized with 1 :1 acetone/methanol mixture and stained with 1 :300 diluted mouse monoclonal antibody C7- 50 (Affinity BioReagents, USA) specific for the HCV core protein followed by staining with 1 :100 diluted Cy2-conjugated goat anti-mouse IgG (Jackson ImmunoResearch Laboratories, USA). Nuclei were then stained with DAPI (Sigma, Israel) and slides were washed with PBS, mounted (SouthernBiotech, USA) and examined using a fluorescence microscope.
  • 7.5x 10 s 293 T-Rex cells were seeded per well in 6 wells plate. 24 hours later, cells were transfected with 2 ⁇ gr of the plasmids "pmCherry (in EGFP C2 backbone)- MazF-full JFH NS5AB-linker-inhibitor peptide-ER", "pmCherry (in EGFP C2 backbone)” or "pEGFP- MazF” encoding for mCherry-NS3-activated MazF, mCherry (just the fluorescence protein) or EGFP- MazF (where MazF is not fused to its inhibitor peptide), respectively.
  • Transfection was carried out using FuGENE 6 reagent (Roche, Germany) according to the manufacturer instructions. After 48 hours, transfection efficiency was assessed by fluorescence microscopy and was determined as equal between the three plasmids. Transfected cells were then trypsinized and seeded in 3 fold dilutions (starting from 150,000 cells/well) in 6 well plates and were incubated for 10 days in the presence of lmg/ml of G418 (to which all the three plasmids confer resistance). Surviving colonies were fixed with 4% formaldehyde in PBS and stained with Giemsa (sigma, USA). Cell- viability assay
  • Tet-inducible full NS3-4A, Tet-inducible full NS3-4A/constitutive NS3-activated MazF or Tet-inducible full NS3 -4 A/constitutive uncleavable MazF expressing cells were seeded in 96 well plates (2> ⁇ 10 4 cells per well). After 24 hours, cells were supplemented with serial 3 fold dilutions of tetracycline, starting with concentration on lOOOng/ml.
  • MTT Thiazolyl Blue Tetrazoliam Bromide (Sigma, Israel) dissolved in PBS) reagent and the cells were incubated for further 30 minutes. MTT-formazan crystals were dissolved by the addition of extraction solution (20% SDS, 50% N, N-Dimethyl Formamide (DMF), pH 4.7) (100 ⁇ per well) and incubation for 16 hours at 37°C. Absorbance at 570 nm was recorded on an automated microtiter plate reader. The results were expressed as percentage of living cells relatively to the untreated controls.
  • l x lO 4 w.t or EGFP-full NS3-4A expressing Huh7.5 cells were seeded per well in 96 plates. After 24 hours, growth media were replaced by fresh media containing recombinant adenoviruses encoding for mCherry-NS3 activated MazF or mCherry-uncleavable-MazF at Multiplicity of infection (MOI) of ⁇ 3. Four days post infection, the media were replaced by fresh media (100 ⁇ per well) containing 1 mg/ml MTT (except in representative wells in which cells were fixed and microscopically examined) and the cells were incubated for further 60 minutes. The next steps were identical to theses described above.
  • Uninfected Huh7.5 cells and mixed population of HCV infected and uninfected cells at 1 : 1 ratio (50%> infected culture) were seeded in 96-well plates (l x lO 4 cells/well). After 24 hours, cells were treated with recombinant adenoviruses (MOI of ⁇ 3) encoding for mCherry- NS3 activated MazF or mCherry-uncleavable-MazF zymoxins. Control cells remained untreated.
  • MOI recombinant adenoviruses
  • HCV-infection immunofluorescence analysis 3x 10 4 cells from the mixed HCV infected and uninfected culture were seeded per well into 8-well chamber slides (Nalge Nunc, USA). 24 hours later, cells were treated with recombinant adenoviruses (MOI of ⁇ 3) encoding for the mCherry-NS3 activated MazF or mCherry-uncleavable-MazF zymoxins. Control cells were left untreated.
  • MOI recombinant adenoviruses
  • the pellet was then dissolved in 300 ⁇ 1 of 0.1M NaOH, transferred to a scintillation tube and neutralized with 0.2ml 1M HC1. 4ml of scintillation liquid was added and radioactivity was counted by a beta-counter device.
  • the MazF coding sequence was amplified from genomic DNA of E. coli strain XL-1 and was fused through its C terminus to the HCV P10-P10' NS3 cleavage sequence derived from the genotype 2a (strain JFH1) NS5A/B junction.
  • a short inhibitory peptide corresponding to MazE C-terminal 35 amino-acids (which encompass the 23 amino-acids inhibitory peptide (MazEp) that has been described by Li et al.
  • mCherry-NS3 -activated MazF The rationale behind the design of this construct, which was denoted "mCherry-NS3 -activated MazF", was that the coupling between the ribonuclease and its antidote may enable high level of expression of the non-toxic fusion on the ER membrane of uninfected mammalian cells without causing any deleterious effect.
  • the fusion protein In HCV infected cells, the fusion protein is expected to colocalize with the ER-bound viral NS3 protease (in infected cells, NS3 is localized to the cytosolic side of ER membranes and membranes of ER-like modified compartments) that cleaves the linker between the toxin and its inhibitory peptide.
  • the toxic ribonuclease no longer covalently tethered to its ER-anchored inhibitor, is now free to diffuse to the cytoplasm (which lacks the antidote) and exert its destructive activity. Finally, fusion to the fluorescence protein mCherry makes the whole construct trackable and facilitates the determination of its expression level and intracellular localization by fluorescence microscopy examination.
  • an uncleavable construct (denoted "mCherry-uncleavable MazF", SEQ ID NO: 23) was constructed in which the NS3 cleavage sequence was replaced (underlined sequence within SEQ ID NO: 23) by a mutated 14 amino acids cleavage sequence (P10-P4') from HCV genotype la NS5A/B junction in which the P3 valine was substituted by alanine, the P2 cysteine by glycine, the PI cysteine by glycine and the P4' tyrosine by alanine (MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKG GPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVT QDSSLQDGEFIYKVKLRGTNFPSDGPVMQK TMGWEASSERMYPEDGALKGEIKQR
  • FIG. 1 A schematic representation of the NS3-activated MazF-based zymoxin ("mCherry-NS3-activated MazF") and the hypothetical mechanism of its cleavage by NS3 protease on the cytoplasmic side of the ER membrane are shown in Fig. 1.
  • NS3 activated MazF is not toxic when expressed in naive cells
  • mCherry-NS3-activated MazF is not toxic to cells that do not express the NS3 protease (cells free of HCV)
  • a colony formation assay was performed in which HEK 293 T-Rex cells where transfected with 2 ⁇ g of plasmids encoding either mCherry-NS3-activated MazF , mCherry (just the fluorescent protein) or EGFP- MazF (where MazF is not fused to its inhibitor peptide). 48 hours later, transfected cells were seeded in 3 fold dilutions and were treated with G418 (to which all three plasmids confer resistance). After 10 days of selection, surviving colonies were stained.
  • the ER-targeted zymoxin colocalizes with NS3 protease in vivo
  • HEK293 cell line which inducibly express (by addition of tetracycline) a fusion between EGFP and the coding sequence of the full length NS3 (including the helicase domain) followed by NS4A from la HCV genotype (Shapira et al, 2011) was used.
  • the above cells denoted “Tet-inducible full NS3-4A expressing cells”, were stably transfected with plasmids encoding the NS3-activated zymoxin "mCherry-NS3- activated MazF" or its uncleavable control ("mCherry-uncleavable MazF").
  • Tet-inducible full NS3 -4 A/constitutive uncleavable MazF expressing cells were induced for EGFP-full NS3-4A expression by supplementation with tetracycline (Fig. 3A). 24 hours later, nuclei were stained (Fig. 3B) and cells were visualized by confocal fluorescence microscopy. A clear colocalization of the two fluorescent fusion proteins was observed (Fig. 3D), confirming that indeed both the protease and the modified ribonuclease are targeted to the ER membrane, as discussed earlier (shown in Fig. 1).
  • Tet-inducible full NS3-4A/constitutive NS3-activated MazF and Tet-inducible full NS3 -4 A/constitutive uncleavable MazF expressing cells were supplemented with tetracycline for 24 or 48 hours to induced NS3 expression, or left untreated. Levels of de-novo protein synthesis were than determined by 3 H-leucine incorporation assay. As shown in Fig. 4, a complete shutoff in protein synthesis was observed as soon as 24 hours post NS3 induction in cells that express the cleavable construct, indicating proteolytic activation of the zymoxin. As expected, Protein synthesis was not impaired following NS3 induction in cells that express the uncleavable construct.
  • NS3-activated MazF eradicates cells that express the NS3 protease
  • the expression level of NS3 can be roughly tuned by modulation of the final tetracycline concentration in the growth media, with around 10 ng/ml as an intermediate concentration for induction of low NS3 expression level. Indeed, strong cytotoxicity was clearly evident when Tet-inducible full NS3-4A/constitutive NS3 -activated MazF expressing cells where treated with tetracycline concentrations as low as 4 ng/ml.
  • Tet-inducible full NS3 -4 A/constitutive NS3-activated MazF and Tet-inducible full NS3-4A/constitutive uncleavable MazF expressing cells were supplemented with tetracycline at a final concentration of lOng/ml or 1000 ng/ml (for low and high induction levels of NS3 expression, respectively), or left untreated. 36 hours later, nuclei were stained and cells were examined under a fluorescent microscope. The results, shown in Figs. 6A-D (Fig.
  • Figs. 7A-B Red- fluorescent comet-like adeno virus-producing foci were apparent upon infection of packaging cells with both recombinant viruses (encoding cleavable or uncleavable constructs) (Figs. 7A-B, respectively).
  • the production yields for both viruses were ⁇ 3> ⁇ 10 8 plaque forming units (PFU)/ml, after two "cycles" of virus amplification (see “materials and methods").
  • Figs. 7C-D shows the phase contrast images of Figs. 7A-B, respectively).
  • Adenovirus-mediated delivery of NS3 activated MazF encoding cassette specifically eradicates HCV infected hepatocytes
  • Huh7.5 hepatoma cells were infected with the HCV la/2a chimeric virus HJ3-5 (encoding the structural proteins of genotype la strain H77S within the background of genotype 2a strain JFH1) (Yi et al., 2007).
  • HCV la/2a chimeric virus HJ3-5 encoding the structural proteins of genotype la strain H77S within the background of genotype 2a strain JFH1
  • infection reached -50% about 50% of the cultured cells showed expression of the HCV-core protein, as detected by immunostaining and fluorescence microscopy analysis; see "Materials and Methods”
  • the mixed culture and a control of uninfected cells
  • An essential step in the replication cycle of many viruses is the processing of a polyprotein precursor by a viral-encoded protease.
  • a partial list of human diseases associated viruses encoding protease(s) in their genome include flaviviruses such as hepatitis C virus (HCV), West Nile virus (WNV), dengue fever virus (DFV) and yellow fever virus (YFV); retroviruses such as HIV-1, picornaviruses such as coxsackievirus, poliovirus and hepatitis A virus, nidoviruses such as coronaviruses (CoV), including the severe acute respiratory syndrome (SARS) causative SARS-CoV and herpesviruses such as varicella-zoster virus (VZV) and Epstein-Bar virus (EBV).
  • flaviviruses such as hepatitis C virus (HCV), West Nile virus (WNV), dengue fever virus (DFV) and yellow fever virus (YFV)
  • an ER membrane "anchoring peptide" that was fused to the C terminus of the construct, subsequently to the MazE derived inhibitory peptide improved the responsiveness of the zymoxin to the presence of low levels of cellular-expressed viral protease. This also enabled a co-localization between the ER-bound NS3 protease and its zymoxin substrate thus maximizing cleavage efficiency. Indeed, such a colocalization could be observed, as shown above. Moreover, activation of the zymoxin was evident also upon expression of very low cellular levels of the viral protease.
  • the applicability and the described zymoxin can be extended to eradication of cells that are infected with protease expressing viruses other than HCV (a partial list of protease expressing viruses is given herein). This can be done by replacing the cleavage sequence that separates between the toxic moiety and the inhibitory peptide to one that is sensitive to a predetermined viral protease. In addition, one may replace the C terminal ER anchoring peptide with sequence that tethers the construct to a destined intracellular location in which the viral protease resides. That way, co-localization between the zymoxin and the predetermined viral protease may be achieved.
  • the presented anti-viral agent was designed under the previously described "zymoxins" concept in which a constitutively active toxin is converted into a “zymogenized”, viral-protease activated from.
  • ThemazF-based zymoxin that is delivered into target cells by means of adenovirus mediated gene delivery, shows very low toxicity to naive cells and enhanced responsiveness to low viral-protease expression level, when compared to our previously presented constructs.
  • the DTA based zymoxins had a therapeutic index of >40 in Tet-induced NS3 expressing cells and 17.5 in HCV infected Huh7.5 cells
  • RTA based zymoxins had a therapeutic index of 38 in Tet-induced NS3 expressing cells and 8 in HCV infected Huh7.5 cells
  • the MazF-based zymoxin has a much better safety profile since it is essentially non toxic to naive cells that do not express the NS3 protease.
  • the MazF based zymoxin eradicates NS3-expressing model cells and HCV infected cells with remarkable efficiency and specificity, providing further proof to the concept of zymoxins and a potential new means of fighting viral diseases.
  • the C-terminal ER membrane anchor of the tyrosine phosphatase PTP1B is essential for the polypeptide's activity
  • the present polypeptide utilizing a zymoxin of an endogenous toxin-antitoxin system requires the ER anchoring peptide in order to colocalize the zymoxin with the protease (thus enhancing cleavage efficiency) and physically separate (compartmental separation), following cleavage, the toxin from the antitoxin thus enabling the toxin's activity.

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Abstract

A chimeric polypeptide denoted herein by the term zymoxin including a toxin/antitoxin system, a unique protease cleavage site and a subcellular anchoring moiety and polynucleotides encoding same are provided. The zymoxin, composed of a toxin/antidote system, a unique protease cleavage site and a subcellular anchoring moiety, releases the active toxin upon cleavage by a suitable protease. Pharmaceutical compositions comprising the polypeptides and polynucleotides of the invention and methods of using same are also disclosed.

Description

ZYMOXINS AND METHODS OF USING THE SAME
FIELD OF INVENTION
[001] A polypeptide and polynucleotides encoding same comprising a toxin, a protease cleavage site, an anti-toxin and a subcellular localization domain designated herein as zymoxins are provided. Pharmaceutical compositions comprising the polypeptide and polynucleotides of the invention and methods of using same are also disclosed.
BACKGROUND OF THE INVENTION [002] Zymogens are inactive enzyme precursors that are converted to their active form following a biochemical modification, such as proteolytic processing. Among the known and important groups of enzymes that are proteolytically activated are secreted digestive enzymes like pepsin and trypsin, the cysteine aspartic acid proteases (caspases) which play an essential role at various stages of the apoptotic process; and blood coagulating factors. [003] The MazEF system, which is an exemplary member of the toxin-antitoxin (TA) system, includes two active protein components: the long lived MazF toxin and the labile MazE antitoxin. MazF induced toxicity is executed by blocking de-novo protein synthesis through its endoribonuclease activity that catalyze the cleavage of single-stranded mRNAs at ACA sequences. When co-expressed with MazF, the MazE antitoxin forms a complex with the toxin and a catalytically inactive heterohexamer is formed in which a MazE dimer is sandwiched between two MazF dimers (MazF2-MazE2-MazF2).
[004] HCV is a small, enveloped RNA virus belonging to the Hepacivirus genus of the Flaviviridae family, which has been recognized as a major cause of chronic liver disease and affects approximately 200 million people worldwide. Persistent infection is associated with the development of chronic hepatitis, hepatic steatosis, cirrhosis, and hepatocellular carcinoma. A prophylactic or protective vaccine for HCV is not yet available, and even the most recent combination of pegylated a-interferon and ribavirin is often poorly tolerated and effective in only approximately 50% of genotype 1 - infected patients. The HCV genome encodes one large open reading frame that is translated as a polyprotein and proteolytically processed to yield the viral structural and nonstructural (NS) proteins . [005] The non-structural proteins include the NS2-3 protease, the NS3 serine protease/R A helicase and its co-factor NS4A, the NS4B and NS5A proteins and the NS5B RNA- dependent RNA polymerase (RdRp). Two virally encoded proteases participate in polyprotein processing, the NS2-3 autoprotease (which cleaves in cis at the NS2-3 junction) and the NS3-4A serine protease (which cleaves at four downstream NS protein junctions). NS3 is an extensively studied HCV protein that possesses multiple enzymatic activities that are essential for HCV replication. The N-terminus, in complex with its ER-anchored co-factor NS4A, primarily functions as a serine protease, which cleaves the viral polyprotein precursor downstream to NS3. The remaining 2/3 of the protein has a helicase and NTPase activities, both of which are essential for HCV replication.
[006] WO2012/038950 to some of the inventors discloses activatable toxin complexes which include a cleavable inhibitory peptide, and use thereof for treating infections and malignant diseases.
[007] Nowhere in the background art is it disclosed that a subcellular localization or anchoring domain may be necessary to segregate one of the components of a toxin anti-toxin complex to a specific compartment within the cell.
SUMMARY OF THE INVENTION
[008] The present invention provides chimeric polypeptides having a toxin and an inhibitory peptide anti-toxin separated from one another by a sequence comprising a protease cleavage site, where the anti-toxin is further attached to a subcellular anchoring domain. Upon cleavage the toxin is released from the chimeric polypeptide complex and the inhibitory peptide is segregated therefrom, rendering the toxin active.
[009] In some embodiments, the present invention provides a chimeric polypeptide comprising a toxin, a protease cleavage site, an endogenous anti-toxin and a subcellular localization anchoring domain. In some embodiments, the protease cleavage site is attached to the carboxy terminus of the toxin, the endogenous anti-toxin is attached to the carboxy terminus of the protease cleavage site and the subcellular anchoring domain is attached to the carboxy terminus of the anti-toxin. In some embodiments, the endogenous antitoxin is attached to the carboxy terminus of the subcellular anchoring domain, the protease cleavage site attached to the carboxy terminus of the anti-toxin and the toxin is attached to the carboxy terminus of the protease cleavage site. In some embodiments, linker or spacer peptides may be present between functional elements or domains of the chimeric polypeptides.
[010] In further embodiments, the present invention provides a polynucleotide comprising a coding portion encoding a polypeptide, wherein the polypeptide comprises a toxin, a protease cleavage site, an endogenous anti-toxin and a subcellular localization anchoring domain.
[Oi l] In one embodiment, the present invention provides a chimeric polypeptide comprising a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of the anti-toxin. In some embodiments, the subcellular localization domain is an endoplasmic reticulum (ER) anchoring domain.
[012] In another embodiment, the present invention further provides a polynucleotide comprising a coding portion encoding a polypeptide, wherein the polypeptide comprises a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin (or segment thereof which still has full antitoxin activity) attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of the anti-toxin. In some embodiments, the subcellular localization domain is an endoplasmic reticulum (ER) anchoring domain.
[013] In another embodiment, the present invention further provides a method for eliminating a cell, comprising the step of contacting the cell with: (1) a polypeptide comprising a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of the anti-toxin; or (2) a vector comprising a polynucleotide, wherein the polynucleotide comprises a coding portion encoding a polypeptide, said polypeptide comprises a toxin, a hepatitis C virus protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of the anti-toxin, wherein the cell comprises a protease directed against the protease cleavage site. In some embodiments the subcellular localization domain is an endoplasmic reticulum (ER) anchoring domain.
[014] A protease directed against the protease cleavage site is a protease that specifically cleaves the protease cleavage site. [015] In another embodiment, the present invention further provides a method for treating a subject infected with a protease bearing virus, comprising the step of administering to the subject: (1) a polypeptide comprising a toxin, a viral protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of the anti-toxin; or (2) a vector comprising a polynucleotide, the polynucleotide comprises a coding portion encoding a polypeptide, wherein the polypeptide comprises a toxin, a virus protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring attached to the carboxy terminus of the anti-toxin. In some embodiments the subcellular localization domain is an endoplasmic reticulum (ER) anchoring domain.
[016] In another embodiment, the present invention further provides a method for treating a subject afflicted with Hepatitis C, comprising the step of administering to the subject: (1) a polypeptide comprising a toxin, a Hepatitis C virus protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of the anti-toxin; or (2) a vector comprising a polynucleotide, wherein the polynucleotide comprises a coding portion encoding a polypeptide, the polypeptide comprises a toxin, a hepatitis C virus protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of the anti-toxin. In some embodiments the subcellular localization domain is an endoplasmic reticulum (ER) anchoring domain.
BRIEF DESCRIPTION OF THE DRAWINGS
[017] FIG 1 is a schematic representation of the construct "mCherry-NS3-activated MazF" and the hypothetical mechanism of its activation by NS3 protease. The NS3-activated MazF zymoxin was constructed by fusing 5 elements in the following order (from the N terminus): monomeric red fluorescence protein mCherry, E. coli MazF ribonuclease, HCV P10-P10' NS3 cleavage sequence derived from genotype 2a (strain JFHl) NS5A/B junction, a short inhibitory peptide corresponding to MazE C-terminal 35 amino-acids (which encompass the 23 amino-acids inhibitory peptide (MazEp)) and the C-terminal ER membrane anchor of the tyrosine phosphatase PTP1B. After being anchored to the ER membrane, the NS3 cleavage site that is located between the ribonuclease and the inhibitory peptide in the "mCherry-NS3- activated MazF" construct (which is active as a dimer but for convenience is illustrated here in its monomeric form) is cleaved by the HCV- NS3 protease which is also localized to the cytoplasmic side of the ER membrane. The toxic ribonuclease, no longer covalently tethered to its ER-anchored inhibitor, is now free to diffuse to the cytoplasm (which lacks the antidote) and exert its destructive activity.
[018] FIG. 2 is a photograph showing a colony formation assay for the assessment of "mCherry-NS3-activated MazF" cytotoxicity toward naive cells. A day before transfection, 7.5 x lO5 293 T-Rex cells where seeded per well in 6 wells plate and subsequently transfected with 2μg of plasmids encoding either mCherry-NS3-activated MazF , mCherry (only the fluorescence protein) or EGFP- MazF (where MazF is not fused to its inhibitory peptide). 48 hours later, transfection efficiency was assessed by fluorescence microscopy and was determined to be equal between the three plasmids. Transfected cells were than trypsinized, counted and seeded in 3 fold dilutions (starting from 150,000 cells/well) in 6 well plates and were incubated for 10 days in the presence of lmg/ml of G418 (to which all three plasmids confer resistance). Survived colonies were fixed and stained with Giemsa.
[019] FIGs. 3A-D depict micrographs of an in vivo assay for co localization of NS3 protease and the ER-targeted MazF based construct. l x lO5 Tet-inducible full NS3-4A/constitutive uncleavable MazF expressing 293 T-Rex cells were seeded on poly-L-lysine coated cover- slips in a 24 well-plate. 12 hours later, the cells were supplemented with ^g/ml of tetracycline for another 24 hours and then were fixed. Following nuclear staining by Hoechst 33258 (Blue) (Fig. 3B), Slides were examined by confocal fluorescence microscopy.
[020] FIG. 4 is a bar graph illustrating the inhibition of de-novo protein synthesis by NS3- activated MazF based zymoxin in NS3-expressing cells. l x lO5 Tet-inducible full NS3- 4A/constitutive NS3-activated MazF or Tet-inducible full NS3-4A/constitutive uncleavable MazF expressing cells were seeded per well in 24-wells plate. 24 or 48 hours later, cells were supplemented with tetracycline to a final concentration of lOOOng/ml, or left untreated (48h tet, 24h tet and no tet, respectively). 72 hours after seeding, levels of de-novo protein synthesis were determined by [3H] -leucine incorporation assay, as described under "materials and methods". Results are expressed as percent of the value obtained for cells which were not induced to express the NS3 protease (No tet). Each bar represents the mean ±SD of a set of data determined in triplicates. [021] FIGs. 5A-B include a bar graph (Fig. 5 A) and a gel micrograph (Fig. 5B) showing the eradication of NS3 expressing cells by mCherry-NS3 activated MazF. Fig. 5 A: Tet-inducible full NS3-4A (No MazF), Tet-inducible full NS3-4A/constitutive NS3-activated MazF (NS3- activated MazF) or Tet-inducible full NS3 -4 A/constitutive uncleavable MazF (uncleavable MazF) expressing 293 T-Rex cells were seeded in 96 well plates (2>< 104 cells per well). After 24 hours, cells were supplemented with 3 fold dilutions of tetracycline, starting with concentration of lOOOng/ml, or left untreated. 72 hours later, the fraction of viable cells (relatively to the untreated controls) was determined using an enzymatic MTT assay. Each bar represents the mean ±SD of a set of data from six wells. Fig. 5B: 30ng of total protein from lysates of Tet-inducible full NS3-4A/constitutive uncleavable MazF expressing cells that were supplemented with 3 fold dilutions of tetracycline for 48 hours were analyzed by immunob lotting with mouse anti-EGFP (for the detection of EGFP-NS3) and mouse anti- actin antibodies (loading control) followed by HRP-conjugated secondary antibodies and ECL development.
[022] FIGs. 6A-D depict micrographs showing expression of mCherry-NS3 activated MazF results in growth inhibition and morphological changes in NS3 expressing cells. l x lO5 Tet- inducible full NS3-4A/constitutive NS3 activated MazF or Tet-inducible full NS3- 4A/constitutive uncleavable MazF expressing 293 T-Rex cells were seeded on poly-L-lysine coated cover-slips in a 24 well-plate. 12 hours later, cells were supplemented with lOng/ml or lOOOng/ml of tetracycline, or left untreated. 36 hours later, cells were fixed. Following nuclear staining by Hoechst 33258 (Blue), slides were examined by fluorescence microscopy. Fig. 6A- Tet-inducible full NS3-4A/constitutive uncleavable MazF with Tetracycline (lOOOng/ml); Fig. 6B- Tet-inducible full NS3-4A/constitutive NS3-activated MazF without Tetracycline; Fig. 6C- Tet-inducible full NS3-4A/constitutive NS3-activated MazF with Tetracycline (lOng/ml); Fig. 6D- Tet-inducible full NS3-4A/constitutive NS3-activated MazF with Tetracycline (lOOOng/ml).
[023] FIGs. 7A-D depict micrographs showing fluorescence microscopy analysis of adenovirus producing foci. 3x 105 HEK 293 cells were seeded per well in 6 wells plate. When they reached 90% confluence, cells were infected with 10 fold dilutions of recombinant adenoviruses encoding for mCherry-NS3 activated MazF (Figs 7A and 7C) or mCherry- uncleavable-MazF (Figs. 7B and 7D), starting from 2.5 χ 106 PFU per well. After 36 hours, cells were fixed and examined under a fluorescence microscope. Red fluorescent adeno virus- producing foci from wells infected with 2.5 χ 103 PFU are shown (Fig. 7A-B). [024] FIGs. 8A-B show a bar graph (Fig. 8A) and micrographs (Fig. 8B) showing the eradication of NS3-expressing Huh7.5 cells by recombinant adenovirus-mediated delivery of mCherry-NS3 activated MazF encoding cassette. l x lO4 w.t or EGFP-full NS3-4A expressing Huh7.5 cells were seeded per well in 96 plates. After 24 hours, recombinant adenoviruses encoding for NS3 activated MazF or uncleavable-MazF zymoxins were added at MOI of ~3. Fig. 8A: MTT viability assay: 4 days post infection, the relative fraction of viable cells (relatively to uninfected controls) was determined using an enzymatic MTT assay. A representative graph of three independent experiments is shown. Each bar represents the mean ±SD of a set of data determined in triplicates. Fig. 8B: Microscopic examination: 4 days post infection, w.t (Panels C-D) or EGFP-full NS3-4A expressing Huh7.5 cells (panels A-B), uninfected (Panels A and C) or infected with recombinant adenoviruses encoding for mCherry fused NS3-activated MazF zymoxin (MOI of ~ 3) (Panels B and D), were fixed and subjected to microscopic examination.
[025] FIG. 9 is a bar graph illustrating the result of treating HCV-infected/uninfected mixed culture of hepatocytes with recombinant adenovirus delivering MazF based zymoxin. Uninfected (HCV-negative) Huh7.5 cells and a mixed culture of HCV infected and uninfected cells at 1 : 1 ratio were seeded in 96-well plates (l x lO4 cells/well). After 24 hours, cells were treated with recombinant adenoviruses (MOI of ~3) encoding for the mCherry fused NS3 activated MazF or uncleavable-MazF zymoxins. Control cells remained untreated. 72 hours post treatment, the relative fraction of viable cells (relatively to untreated controls) was determined using an enzymatic MTT assay. The graph represents three independent experiments. Each bar represents the mean ±SD of a set of data determined in triplicates.
[026] FIGs 10A-F Depict micrographs of microscopic examination according to the setting described for FIG 9: 3 days post zymoxins treatment, the zymoxins treated uninfected (HCV- negative) Huh7.5 cells (Figs. 10E and 10F), the zymoxins treated mixed culture of HCV infected and uninfected cells (Figs. 10B and IOC) and the control untreated cells (Figs. 10A and 10D) were fixed and subjected to microscopic examination.
[027] FIGs 11A-C Depict micrographs of microscopic examination showing eradication of HCV-infected hepatocytes by recombinant adenovirus delivering the MazF based zymoxin. 3x l04 cells from the mixed HCV infected and uninfected culture (as described in Fig. 9) were seeded per well into 8-well chamber slides. 24 hours later, cells were treated with recombinant adenoviruses (MOI of ~3) encoding for the mCherry fused NS3 activated MazF (Fig. 11C) or uncleavable-MazF zymoxins (Fig. 11B). Control cells remained untreated (Fig. 11 A). 72 hours post treatment, cells were fixed, permeabilized and immunostained with mouse anti-HCV core and FITC-conjugated goat anti mouse antibodies (Panels A2, B2 and C2) for visualization of HCV infected cells (originally green). Cell nuclei were then stained with DAPI (Panels A3, B3 and C3 (originally cyan)) and slides were visualized by fluorescence microscopy. Panels A4, B4 and C4 depict merge of mCherry (recombinant adenovirus infected cells; panels Al, Bl and CI; originally red) with both FITC and DAPI staining. The bar represents ΙΟΟμιη.
[028] FIG. 12 is a bar graph illustrating the results obtained in accordance to the experimental procedure described in FIG 11 : the fraction (given in percentage) of the HCV- infected cells from the general cell population was evaluated, for each treatment, by dividing the number of the green, HCV-core positive cells by the general number of cells (DAPI stained). Each bar represents the mean ±SD of a set of data collected from five representative microscopic fields. Numbers in brackets represent the percentage of the HCV -infected cells in each treatment relatively to their percentage in the untreated culture.
[029] FIG. 13 Depicts the amino acid sequences of: (A) NS3 activated MazF zymoxin; and (B) the control construct of uncleavable MazF zymoxin. The different segments of the polypeptides of 13A and 13B are also provided. Indicated numbers refer to the amino acid sequence to their right.
[030] FIG. 14 is a bar graph illustrating the results of an MTT viability assay obtained in Tet-inducible full NS3-4A expressing cells that co-express an NS3 activated MazF zymoxin polypeptide missing the C-terminal ER membrane anchor of tyrosine phosphatase PTP1B. The high viability rates suggest that a polypeptide of the invention lacking the tyrosine phosphatase PTP1B segment is substantially ineffective in killing of full NS3-4A expressing cells.
DETAILED DESCRIPTION OF THE INVENTION
[031] In one embodiment, the present invention provides a chimeric polypeptide comprising a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of the anti-toxin. In another embodiment, the present invention provides a polypeptide having the following domains from amino to carboxy terminus: N-terminal: toxin-protease cleavage site-endogenous anti-toxin-subcellular anchoring domain: C-terminal. In another embodiment, the present invention provides a polypeptide having the following domains from amino to carboxy terminus: N-terminal: subcellular anchoring domain -antitoxin-protease cleavage site-toxin: C-terminal. In another embodiment, the present invention provides that the polypeptide further includes at least one peptide linker linking at least two domains. In another embodiment, the polypeptides of the invention comprising a toxin-antitoxin (antidote) system are termed zymoxins. In some embodiments the subcellular localization domain is an endoplasmic reticulum (ER) anchoring domain.
[032] As used herein, the terms "endogenous anti-toxin", "anti-toxin", "endogenous antitoxin", "antitoxin" may interchangeably be used. In some embodiments, the terms "toxin" and "endogenous toxin" may interchangeably be used. As used herein, the term "endogenous" with respect to a toxin-antitoxin system is directed to include the natural (cognate) anti-toxin of the specified toxin.
[033] In another embodiment, the present invention provides a polypeptide comprising a toxin-antitoxin system. In another embodiment, the present invention provides a polypeptide comprising a toxin-antitoxin type II system. In another embodiment, the present invention provides a polypeptide comprising a toxin-antitoxin system, wherein the toxin-antitoxin system comprises at least a fragment of the toxin and/or at least a fragment of the antitoxin. In another embodiment, the present invention provides a polypeptide comprising a toxin- antitoxin system and a subcellular anchoring domain, such as, an ER anchoring domain. In another embodiment, the present invention provides a toxin-antitoxin system found on a bacterial chromosome. In another embodiment, the present invention provides that a toxin- antitoxin system is found on an Escherichia coli chromosome. In another embodiment, the present invention provides a polypeptide comprising a mazEF toxin-antitoxin system, wherein the mazF is the toxin and MazE is the antitoxin. In another embodiment, the present invention provides a polypeptide comprising a chpBIK toxin-antitoxin system, wherein the toxin is chpBK and the antitoxin is chpBl. In another embodiment, the present invention provides a polypeptide comprising a relBE toxin-antitoxin system, wherein the toxin is relE and the antitoxin is relB. In another embodiment, the present invention provides a polypeptide comprising a yefM-yoeB toxin-antitoxin system, wherein the toxin is yoeB and the antitoxin is yefM. In another embodiment, the present invention provides a polypeptide comprising a dinJ-yafQ toxin-antitoxin system, wherein the toxin is yafQ and the antitoxin is dinJ. In another embodiment, the present invention provides a polypeptide comprising a hicAhicB toxin-antitoxin system, wherein the toxin is HicA and the antitoxin is HicB. In another embodiment, the present invention provides a polypeptide comprising a prlFyhaV toxin-antitoxin system, wherein the toxin is YhaV and the antitoxin is prlF. In another embodiment, the present invention provides a polypeptide comprising a mqsRmqsA toxin- antitoxin system, wherein the toxin is MqsR and the antitoxin is MqsA. In another embodiment, the present invention provides a polypeptide comprising a rnlArnlB toxin- antitoxin system, wherein the toxin is RnlA and the antitoxin is RnlB. In another embodiment, the present invention provides a polypeptide comprising a yaf yafO toxin- antitoxin system, wherein the toxin is YafO and the antitoxin is YafN. In another embodiment, the present invention provides a polypeptide comprising a higBhigA toxin- antitoxin system, wherein the toxin is HigB and the antitoxin is HigA. In another embodiment, the present invention provides a polypeptide comprising a ratAyfjF toxin- antitoxin system, wherein the toxin is Rat A and the antitoxin is YfjF. In another embodiment, the present invention provides a polypeptide comprising a yeeUcbtA toxin- antitoxin system, wherein the toxin is YeeU and the antitoxin is CbtA. In another embodiment, the present invention provides a polypeptide comprising a yafWykfl toxin- antitoxin system, wherein the toxin is Ykfl and the antitoxin is YafW. In another embodiment, the present invention provides a polypeptide comprising a yfjZypjF toxin- antitoxin system, wherein the toxin is YpjF and the antitoxin is YfjZ. In another embodiment, the present invention provides a polypeptide comprising a gnsAymcE toxin- antitoxin system, wherein the toxin is GnsA and the antitoxin is YmcE. In another embodiment, the present invention provides a polypeptide comprising a hipBhipA toxin- antitoxin system, wherein the toxin is Hip A and the antitoxin is HipB. In another embodiment, the present invention provides a polypeptide comprising a yjhXyjhQ toxin- antitoxin system, wherein the toxin is YjhX and the antitoxin is YjhQ. In another embodiment, the present invention provides a polypeptide comprising a ydaSydaT toxin- antitoxin system, wherein the toxin is YdaS and the antitoxin is YdaT. In another embodiment, the present invention provides a toxin-antitoxin system encoded by a bacterial chromosome. In another embodiment, the present invention provides a toxin-antitoxin system encoded by a bacterial plasmid. Sequences and other information related to members of the toxin-anti-toxin system can be found in the Protein Data Bank (https://www.rcsb.org/pdb/home/home.do). [034] In another embodiment, the present invention provides a toxin-antitoxin system found in genomes of prokaryotes other than bacteria. In another embodiment, the present invention provides that a toxin-antitoxin system encoded by genomes of prokaryotes other than bacteria. In some embodiments, the toxin-antitoxin system is found on genomes of prokaryotes other than bacteria, such as disclosed by Makarova, et.al., the content of which is incorporated herein in its entirety.
[035] In another embodiment, the present invention provides that the toxin-antitoxin system within the polypeptide of the invention is regulatable and responsible for cell death. In another embodiment, the present invention provides that the toxin-antitoxin system within the polypeptide of the invention is regulatable and responsible for programmed cell death. In another embodiment, the present invention provides that the toxin is MazF which inhibits translation by cleaving mR A at a specific site(s). In another embodiment, the present invention provides that the antitoxin is MazE. In another embodiment, MazE counteracts the action of MazF. In another embodiment, the present invention provides that the use of an endogenous toxin-antitoxin system is safer than the use of a system utilizing a toxin and an antitoxin each derived from a different source. In another embodiment, the present invention provides that the specificity of an endogenous toxin-antitoxin system renders it safe. In another embodiment, the present invention provides that the toxin within the polypeptide of the invention is inactive as long as the antitoxin is bound to the toxin directly, via a protease cleavage site, or via a linker/linkers. In another embodiment, the present invention provides that the toxin within the polypeptide becomes active only upon cleavage of the protease cleavage site. In another embodiment, the present invention provides that cleavage within the protease cleavage site of the polypeptide results in two separate polypeptides: the first comprises the active toxin and a first fragment of the protease cleavage site and the second polypeptide comprises a second fragment of the protease cleavage site, the antitoxin and the subcellular anchoring domain (such as an ER anchoring domain). In another embodiment, the present invention provides that cleavage within the protease cleavage site of the polypeptide results in two separate polypeptides: the first comprises the active toxin, possibly a linker and a first fragment of the protease cleavage site and the second polypeptide comprises a second fragment of the protease cleavage site, possibly a linker, the antitoxin, possibly a linker, and the subcellular anchoring domain (such as an ER anchoring domain).
[036] In another embodiment, endogenous toxin-antitoxin is a toxin and its antidote. In another embodiment, endogenous toxin-antitoxin is a toxin and its polypeptidic antidote. In another embodiment, an endogenous toxin-antitoxin is derived from a single organism (or encoded by a single genetic element). In another embodiment, an endogenous toxin-antitoxin is utilized endogenically in a single organism.
[037] The present invention is based on a single polypeptide that upon intracellular cleavage separates into two moieties, thus activating a toxin. In another embodiment, the toxin becomes active upon separation from the antitoxin which remains bound to the subcellular anchoring domain (such as an ER anchoring domain) and to a segment of the protease cleavage site. In another embodiment, it was surprisingly found that the mere separation of the toxin-antitoxin system due to cleavage is not sufficient for the induction of cell death within a target cell. In another embodiment, the present invention is based on the unexpected discovery that the antitoxin must be removed from the vicinity of the toxin. In another embodiment, the present invention is based on the unexpected discovery that there must be an intracellular/subcellular compartmental separation or segregation between the antitoxin and the toxin in order to render the toxin active and thus induce cell death. In another embodiment, the present invention is based on the unexpected need to immobilize the antitoxin at a site discrete from the toxin in order to induce cell death. In another embodiment, the present invention is based on the unexpected discovery that immobilizing the antitoxin to a subcellular compartment (location), such as, the ER, renders the toxin active following the proteolytic cleavage that separates it from the antitoxin.
[038] In another embodiment, the toxin is MazF. In another embodiment, MazF comprises SEQ ID NO: 1. In another embodiment, SEQ ID NO: 1 comprises the following amino acid (AA) sequence:
MVSRYVPDMGDLIWVDFDPTKGSEQAGHRPAVVLSPFMYNNKTGMCLCVPCTTQS KGYPFEVVLSGQERDGVALADQVKSIAWRARGATK GTVAPEELQLIKAKINVLI.
[039] In another embodiment, the antitoxin is MazE C-terminal 35 amino-acids (which encompass the 23 amino-acids inhibitory peptide (MazEp). In another embodiment, the antitoxin comprises MazE C-terminal 35 amino-acids (which encompass the 23 amino-acids inhibitory peptide (MazEp). In another embodiment, the antitoxin comprises the full MazE peptide. In another embodiment, the antitoxin comprises a fragment of MazE peptide having MazP antitoxin activity. In another embodiment, MazE comprises SEQ ID NO: 2. In another embodiment, SEQ ID NO: 2 comprises the following amino acid (AA) sequence: RKEPVFTLAELVNDITPENLHENIDWGEPKDKEVW.
[040] In other embodiments, the toxin comprises or selected from: HicA, YhaV, MqsR, RnlA, YafO, HigB, RatA, YeeU, Ykfl, YpjF, GnsA, HipA, YjhX, YdaS, MazF, or any fragment thereof. Each possibility is a separate embodiment.
[041] In other embodiments, the anti-toxin comprises or selected from: HicB, prlF, MqsA, RnlB, YafN, HigA, YfjF, CbtA, YafW, YfjZ, YmcE, HipB, YjhQ, YdaT, MazE, or any fragment thereof. Each possibility is a separate embodiment.
[042] In some embodiments, the terms "subcellular anchoring domain", "subcellular sorting domain", and "subcellular localization domain" may interchangeably be used. A subcellular anchoring domain (moiety) is a domain that can target, sort, localize or anchor a desired peptide or protein to a specific subcellular localization. The subcellular localization may be selected from, but not limited to: endoplasmic reticulum (ER) membranes, plasma membrane(s), nuclear membranes, mitochondrial membranes, cytoplasm, nucleus, mitochondria, ER, and the like. Each possibility is a separate embodiment. In some embodiments, the subcellular localization domain is a signal peptide, a localization signal, and the like.
[043] In some embodiments, the subcellular localization domain is an ER anchoring domain. In one embodiment, the ER anchoring domain comprises the amino acid sequence of SEQ ID NO: 3 (PTPIB ER anchor). In another embodiment, SEQ ID NO: 3 comprises the following amino acid (AA) sequence: SGLRSFLVNMCVATVLTAGAYLCYRFLFNSNT.
[044] In another embodiment, the ER anchoring domain comprises an amino acid sequence of SEQ ID NO: 25 (synaptobrevin 1; H. sapiens). In another embodiment, the ER anchoring domain comprises an amino acid sequence of SEQ ID NO: 26 (Synaptobrevin 2; H. sapiens). In another embodiment, the ER anchoring domain comprises an amino acid sequence of SEQ ID NO: 27 (Synaptobrevin 8; Mus musculus). In another embodiment, the ER anchoring domain comprises an amino acid sequence of SEQ ID NO: 28 (cytochrome b5 ; H. sapiens). In another embodiment, the ER anchoring domain comprises an amino acid sequence of SEQ ID NO: 29 (microsomal aldehyde dehydrogenase; Rattus norvegicus). In another embodiment, the ER anchoring domain comprises an amino acid sequence of SEQ ID NO: 30 (myotonic dystrophy protein kinase (Mus musculus)). In another embodiment, the ER anchoring domain comprises an amino acid sequence of SEQ ID NO: 31 (Heme Oxygenase- 1, H. sapiens).
[045] In some embodiments, the ER anchoring domain comprises an amino acid sequence selected from, but not limited to: SEQ ID NO:3, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28; SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, or combinations thereof. Each possibility is a separate embodiment.
[046] In another embodiment, the protease cleavage site is a viral protease cleavage site. In another embodiment, the protease cleavage site is NS3 cleavage site. In another embodiment, the protease cleavage site comprises the amino acid sequence of SEQ ID NO: 4. In another embodiment, SEQ ID NO: 4 comprises the following amino acid (AA) sequence: SEEDDTTVCCSMSYSWTGAL.
[047] In one embodiment, the polypeptide of the invention comprising a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain (such as an endoplasmic reticulum (ER) anchoring domain) attached to the carboxy terminus of the anti-toxin comprises SEQ ID NO: 5. In another embodiment, SEQ ID NO: 5 comprises the following amino acid (AA) sequence:
MVSRYVPDMGDLIWVDFDPTKGSEQAGHRPAVVLSPFMYNNKTGMCLCVPCTTQS KGYPFEVVLSGQERDGVALADQVKSIAWRARGATK GTVAPEELQLIKAKINVLISE EDDTTVCCSMSYSWTGALRKEPVFTLAELVNDITPENLHENIDWGEPKDKEVWSGL RSFLVNMCVATVLTAGAYLCYRFLFNSNT.
[048] In one embodiment, the present invention provides that the polypeptide of the invention comprises SEQ ID NO: 6. In another embodiment, SEQ ID NO: 6 comprises the following amino acid (AA) sequence:
SGRTQISSMVSRYVPDMGDLIWVDFDPTKGSEQAGHRPAVVLSPFMYNNKTGMCLC VPCTTQSKGYPFEVVLSGQERDGVALADQVKSIAWRARGATKKGTVAPEELQLIKA KINVLIGGSSEEDDTTVCCSMSYSWTGALGGGGSRKEPVFTLAELVNDITPENLHENI DWGEPKDKEVWSSGGSGGGSGSGGSGLRSFLVNMCVATVLTAGAYLCYRFLFNSN
T.
[049] In another embodiment, the polypeptide of the invention further includes a fluorescent peptide or protein attached to the amino terminus of the toxin. In another embodiment, the polypeptide of the invention further includes a fluorescent peptide or protein attached to the carboxy terminus of the toxin. In another embodiment, the polypeptide of the invention further comprising a fluorescent protein attached to the amino terminus of the toxin comprises SEQ ID NO: 7. In another embodiment, SEQ ID NO: 7 comprises the following amino acid (AA) sequence:
MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKG
GPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTV
TQDSSLQDGEFIYKVKLRGTNFPSDGPVMQK TMGWEASSERMYPEDGALKGEIKQ
RLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAEG
RHSTGGMDELYKMVSRYVPDMGDLIWVDFDPTKGSEQAGHRPAVVLSPFMYNNKT
GMCLCVPCTTQSKGYPFEVVLSGQERDGVALADQVKSIAWRARGATK GTVAPEEL
QLIKAKINVLISEEDDTTVCCSMSYSWTGALRKEPVFTLAELVNDITPENLHENIDWG
EPKDKEVWSGLRSFLVNMCVATVLTAGAYLCYRFLFNSNT.
[050] In another embodiment, the fluorescent peptide or protein may be selected from, but not limited to: mPlum, tdTomato, mStrawberry, J-Red, DsRed-monomer, mOrange, m O, mCitrine, Venus, YPet, EYFP, Emerald, EGFP, CyPet, mCFPm, Cerulean, T-Sapphire, SEQ ID NO: 7, or any combination thereof. Each possibility is a separate embodiment.
[051] In some embodiments, a fluorescent moiety can be attached to the polypeptide of the invention. The fluorescent moiety may be any molecule having fluorescent properties.
[052] In another embodiment, the linker comprises SEQ ID NO: 8. In another embodiment, SEQ ID NO: 8 comprises the following amino acid (AA) sequence: SGRTQISS. In another embodiment, the linker comprises the amino acid (AA) sequence: GGS. In another embodiment, the linker comprises SEQ ID NO: 9. In another embodiment, SEQ ID NO: 9 comprises the following amino acid (AA) sequence: GGGGS. In another embodiment, the linker comprises SEQ ID NO: 10. In another embodiment, SEQ ID NO: 10 comprises the following amino acid (AA) sequence: SSGGSGGGSGSGG.
[053] In another embodiment, the toxin, the antitoxin, the protease cleavage site, and possibly the fluorescent protein are segments of the polypeptide. In another embodiment, the segments are directly linked/attached by a peptide bond. In another embodiment, the terms "linked" and "attached" are used interchangeably. In another embodiment, at least two segments are linked/attached by linker. In another embodiment SEQ ID NO: 6 provides an amino acid sequence of the polypeptide wherein the segments are linked/attached via peptide linkers. In another embodiment, the cleavage site is attached to the carboxy terminus of the toxin via a linker, the endogenous anti-toxin is attached to the carboxy terminus of the cleavage site via a linker, the ER anchoring domain is attached to the carboxy terminus of the anti-toxin via a linker, or any combination thereof. In another embodiment, the antitoxin is flanked by linkers. In another embodiment, the protease cleavage site is flanked by linkers. In another embodiment, the toxin is flanked by linkers. In another embodiment, the linker is a single amino acid. In another embodiment, the linker is a peptide linker comprising amino acids or mimetics thereof. In another embodiment, the linker is glycosylated. In another embodiment, a peptide linker is 2-50 amino acids long. In another embodiment, a peptide linker is 2-25 amino acids long. In another embodiment, a peptide linker is 5-20 amino acids long. In another embodiment, a peptide linker is 5-15 amino acids long.
[054] In another embodiment, the polypeptide further comprises a signal peptide (signal sequence) such as but not limited to KDEL (SEQ ID NO: 24). In another embodiment, the signal peptide is a motif composed of four amino acids at the end of the polypeptide sequence. In another embodiment, the signal peptide is a sub-endoplasmic reticulum localization signal.
[055] In another embodiment, the toxin is a variant of SEQ ID NO: 1 comprising apoptotic inducing activity or any cell-killing activity. In another embodiment, the antitoxin is a variant of SEQ ID NO: 2 comprising MazF inhibitory activity. In another embodiment, the ER anchoring domain is a variant of SEQ ID NO: 3 comprising ER anchoring activity. In another embodiment, the cleavage site is a variant of SEQ ID NO: 4 recognizable/cleavable by a protease. In another embodiment, the cleavage site is specifically designed to be cleaved only by a specific protease. In another embodiment, a specific protease is present only in a diseased cell. In another embodiment, a specific protease is a viral protease present only in a cell infected by a virus. In another embodiment, the virus is the disease causing agent.
[056] In another embodiment, a variant as described herein differs from the native segment of SEQ ID NOs: 1-4 by 1 conservative amino acid substitution. In another embodiment, a variant as described herein differs from the native segment of SEQ ID NOs: 1-4 by 2 conservative amino acid substitution. In another embodiment, a variant as described herein differs from the native segment of SEQ ID NOs: 1-4 by 3 conservative amino acid substitution. In another embodiment, a variant as described herein differs from the native segment of SEQ ID NOs: 1-4 by 4 conservative amino acid substitution. In another embodiment, a variant as described herein differs from the native segment of SEQ ID NOs: 1-4 by 5 conservative amino acid substitution. In another embodiment, a variant as described herein is at least 70% homologous to the native segments of SEQ ID NOs: 1-4. In another embodiment, a variant as described herein is at least 80% homologous to the native segments of SEQ ID NOs: 1-4. In another embodiment, a variant as described herein is at least 90% homologous to the native segments of SEQ ID NOs: 1-4. In another embodiment, a variant as described herein is at least 95% homologous to the native segments of SEQ ID NOs: 1-4.
[057] In another embodiment, polypeptides of the invention include homologues of the polypeptides described herein.
[058] In another embodiment, the present invention further provides a polynucleotide encoding a segment of the polypeptides described herein. In another embodiment, the present invention provides a polynucleotide comprising a coding portion encoding a polypeptide of the invention, wherein the polypeptide comprises a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain (such as an endoplasmic reticulum (ER) anchoring domain) attached to the carboxy terminus of the anti-toxin. In another embodiment, the present invention further provides a polynucleotide encoding a variant of a segment of the polypeptides described herein. In another embodiment, the present invention further provides a polynucleotide encoding polypeptides comprising at least one linker, linking at least two segments. In another embodiment, the present invention further provides a polynucleotide encoding the polypeptide of SEQ ID NO: 5. In another embodiment, the present invention further provides a polynucleotide encoding the polypeptide of SEQ ID NO: 6. In another embodiment, the present invention further provides a polynucleotide encoding the polypeptide of SEQ ID NO: 7.
[059] In another embodiment, a polynucleotide is composed of DNA bases. In another embodiment, a polynucleotide is composed of RNA bases. In another embodiment, a polynucleotide of the invention is a homologue of a polynucleotide encoding a polypeptide or a segment of a polypeptide as described herein. Methods
[060] In another embodiment, provided a method for eliminating a cell, comprising the step of contacting the cell with a polypeptide comprising a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain (such as an endoplasmic reticulum (ER) anchoring domain) attached to the carboxy terminus of the antitoxin, wherein the cell comprises a protease directed against the protease cleavage site. In another embodiment, eliminating a cell is inducing cell death in a cell. In another embodiment, eliminating a cell is inducing apoptosis in a cell. In another embodiment, eliminating a cell is inducing necrosis in a cell.
[061] In another embodiment, provided a method for eliminating a cell, comprising the step of contacting the cell with a polynucleotide encoding a polypeptide comprising a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain (such as an endoplasmic reticulum (ER) anchoring domain) attached to the carboxy terminus of the anti-toxin, wherein the cell comprises a protease directed against the protease cleavage site. In another embodiment, eliminating a cell is inducing cell death in a cell. In another embodiment, eliminating a cell is inducing apoptosis in a cell. In another embodiment, contacting a cell with a polynucleotide is contacting a cell with a vector comprising the polynucleotide. In another embodiment, contacting a cell with a polynucleotide is contacting a cell with a vector comprising the polynucleotide. In another embodiment, contacting a cell with a polynucleotide is contacting a cell with a viral vector comprising the polynucleotide. In another embodiment, contacting a cell with a polynucleotide is contacting a cell with an adenoviral vector comprising the polynucleotide.
[062] In another embodiment, the cell is a eukaryotic cell. In another embodiment, the cell is a diseased cell. In another embodiment, the cell is a diseased cell characterized by having a protease that is present only in the disease state. In another embodiment, a diseased cell comprising a unique protease present only in the disease state if differentially eliminated by the polypeptide of the invention. In another embodiment, a diseased cell comprising a unique protease present only in the disease state if differentially eliminated by the polypeptide of the invention. In another embodiment, a protease cleavage site is engineered according to the unique protease expressed in the diseased cell. In another embodiment, a diseased cell is a cancerous cell and the protease is present in a cancerous but not in a non-cancerous cell. In another embodiment, a diseased cell is a cell infected by an intracellular parasite comprising a protease or having a nucleic acid encoding a protease. In another embodiment, a diseased cell is a cell infected by a virus comprising a protease or encoding a protease. In another embodiment, the present invention is based inter alia on the presence of a unique protease in the diseased cell and the absence of the unique protease in a healthy cell. In another embodiment, the present invention is based inter alia on a difference between levels of protease activity which are high in a diseased cell and low in a healthy cell. While the former is relevant to infections be protease-encoding pathogens, the latter is the case in disease such as cancer.
[063] In another embodiment, a cell infected by a virus expresses a viral protease that is not expressed endogenically by the cell. In another embodiment, a cell expressing a viral protease is differentially eliminated while cells that do not express the viral protease are spared. In another embodiment, the polypeptide of the invention becomes active only after cleavage by an exogenic protease (exogenic to the cell such as a viral protease). In another embodiment, an exogenic protease is a protease that was initially encoded by a foreign nucleic acid. In another embodiment, an exogenic protease is a protease that was initially encoded by a viral nucleic acid. In another embodiment, one of skill in the art can readily identify exogenic and endogenic proteases.
[064] In another embodiment, the cell is a hepatocyte. In another embodiment, the cell is infected by the hepatitis C virus (HCV). In another embodiment, the cell is located within a tissue at risk of being infected by HCV. In another embodiment, the cell is a liver cell of a subject having a risk of being infected by HCV. In another embodiment, a subject having a risk of being infected by HCV is a drug addict (needle sharing). In another embodiment, a subject having a risk of being infected by HCV is a subject in need of blood transfusion, blood products, or organ transplantation. In another embodiment, a subject having a risk of being infected by HCV is a medical professional. In another embodiment, the present invention eliminates non-liver cells infected with HCV. In another embodiment, the present invention eliminates extra-hepatic reservoirs of HCV.
[065] In another embodiment, contacting a cell with a polypeptide of the invention comprises administering the polypeptide to the extracellular environment. In another embodiment, contacting a cell with a polypeptide of the invention comprises administering the polypeptide via a vehicle which enables the penetration of the active polypeptide into the cell. In another embodiment, methods for stabilizing a polypeptide on a vehicle that transports the polypeptide into the cell are known to one of skill in the art.
[066] In another embodiment, a cell comprising a protease directed against the protease cleavage site is a cell comprising a protease that cleaves the cleavage site thus triggering apoptosis via separation of the toxin from the antitoxin. In another embodiment, a cell comprising a protease directed against the protease cleavage site is a cell comprising a viral protease. In another embodiment, a cell comprising a protease directed against the protease cleavage site is a cell comprising a viral protease. In another embodiment, a cell comprising a protease directed against the protease cleavage site is a cell comprising a protease that is not endogenically expressed by the cell. In another embodiment, a cell comprising a protease is a cell comprising a protease that is encoded by a parasite. In another embodiment, a cell comprising a protease is a cell comprising a protease that is encoded by a virus. In another embodiment, a cell comprising a protease is a cell comprising a unique protease that is encoded by a parasite or a virus. In another embodiment, a cell comprising a protease is a cell comprising an exogenous protease. In another embodiment, the protease cleavage site is not recognizable or cleavable by an endogenic protease. In another embodiment, the protease cleavage site is only recognizable or cleavable by a viral protease. In another embodiment, the protease cleavage site is only recognizable or cleavable by an intracellular parasitic protease.
[067] In another embodiment, contacting a cell with a polynucleotide of the invention comprises administering a vector or a transgene comprising the polynucleotide to the extracellular environment. In another embodiment, contacting a cell with a polynucleotide of the invention comprises administering the polynucleotide via a vehicle which enables the penetration of the polynucleotide into the cell. In another embodiment, methods for delivering and/or stabilizing polynucleotides including the use of various vectors that enable the expression of the polynucleotide within a cell are known to one of skill in the art.
[068] In another embodiment, provided herein a method for treating a subject afflicted with Hepatitis C, comprising the step of administering to the subject a vector such as but not limited to an adenoviral vector comprising a polynucleotide, wherein the polynucleotide comprises a coding portion encoding a polypeptide, the polypeptide comprises a toxin, a hepatitis C virus protease cleavage site (such as NS3) attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain (such as an endoplasmic reticulum (ER) anchoring domain) attached to the carboxy terminus of the anti-toxin. In another embodiment, a vector carrying the polynucleotide of the invention is administered within a pharmaceutical composition.
[069] In another embodiment, provided herein a method for treating a subject infected with a protease bearing virus, comprising the step of administering to the subject: (1) a polypeptide comprising a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain (such as an endoplasmic reticulum (ER) anchoring domain) attached to the carboxy terminus of the anti-toxin; or (2) a vector comprising a polynucleotide, the polynucleotide comprises a coding portion encoding a polypeptide, the polypeptide comprises a toxin, a hepatitis C virus protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain (such as an endoplasmic reticulum (ER) anchoring domain) attached to the carboxy terminus of the anti-toxin.
[070] In another embodiment, the protease bearing virus causes a known disease. In another embodiment, a protease bearing virus is a virus bearing the protease. In another embodiment, a protease bearing virus is a virus bearing the nucleic acid molecule which encodes a protease.
[071] In another embodiment, the subject comprises cells infected by a virus. In another embodiment, cells infected by a virus according to the present invention comprise a viral protease directed against the protease cleavage site. In another embodiment, the protease is a unique protease that is encoded by a virus and not by the cell. In another embodiment, the protease is an exogenous protease. In another embodiment, the protease cleavage site is not recognizable or cleavable by a cell's endogenic protease. In another embodiment, the protease cleavage site is only recognizable or cleavable by the viral protease.
[072] In another embodiment, viruses that comprise/encode a unique protease that is not expressed endogenically by the subject's cells and cause a disease including but not limited to: hepatitis C virus (HCV), West Nile virus (WNV), dengue fever virus (DFV), yellow fever virus (YFV), Human immunodeficiency virus- 1 (HIV-1), coxsackievirus, poliovirus hepatitis A virus, coronaviruses (CoV), severe acute respiratory syndrome (SARS) causative SARS- CoV, varicella-zoster virus (VZV), or Epstein-Bar virus (EBV).
[073] In another embodiment, a subject infected with a protease bearing virus is a subject suffering from a disease caused by the protease bearing virus. In another embodiment, provided herein a method for treating a subject afflicted with Hepatitis C, comprising the step of administering to the subject: (1) a polypeptide comprising a toxin, a protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain (such as an endoplasmic reticulum (ER) anchoring domain) attached to the carboxy terminus of the anti-toxin; or (2) a vector (such as an adenoviral vector) comprising a polynucleotide, the polynucleotide comprises a coding portion encoding a polypeptide, the polypeptide comprises a toxin, a hepatitis C virus protease cleavage site attached to the carboxy terminus of the toxin, an endogenous anti-toxin attached to the carboxy terminus of the protease cleavage site, and a subcellular anchoring domain (such as an endoplasmic reticulum (ER) anchoring domain) attached to the carboxy terminus of the anti-toxin. In another embodiment, a polypeptide, a polynucleotide, or a vector of the invention is administered within a pharmaceutical composition.
[074] In another embodiment, the toxin is MazF. In another embodiment, the protease cleavage site is NS3 cleavage sequence derived from 2A genotype NS5A/B (strain JFHl). In another embodiment, the endogenous anti-toxin is MazE or MazE derived polypeptide. In another embodiment, a MazE derived polypeptide is a fragment of MazE having MazE antitoxin activity. In another embodiment, the endoplasmic reticulum (ER) anchoring domain is the tyrosine phosphatase PTP1B.
[075] In another embodiment, a subject afflicted with Hepatitis C is a subject infected with Hepatitis C virus. In another embodiment, a subject afflicted with Hepatitis C suffers from a liver disease. In another embodiment, a subject afflicted with Hepatitis C is an asymptomatic patient infected with Hepatitis C virus.
[076] In another embodiment, treating is ameliorating the disease condition. In another embodiment, treating is inhibiting the progression of a liver disease. In another embodiment, treating is reducing the risk of infectivity. In another embodiment, treating is reducing the risk of developing a chronic infection in an asymptomatic patient. In another embodiment, treating is reversing a chronic infection. In another embodiment, treating is reducing the symptoms associated with a chronic infection. In another embodiment, treating is inhibiting the progression of chronic infection. In another embodiment, treating is inhibiting or reducing the risk of fibrosis. In another embodiment, treating is inhibiting or reducing the risk of cirrhosis. In another embodiment, treating is reducing the risk of liver failure or other complications of cirrhosis, including liver cancer or life threatening esophageal varices and gastric varices. In another embodiment, treating is reducing the risk of hepatitis C virus propagation and spread. In another embodiment, treating is inhibiting, ameliorating, or reducing the symptoms of persistent infection.
[077] In some embodiments, "polypeptide" as used herein encompasses native polypeptides (either degradation products, synthetically synthesized polypeptides or recombinant polypeptides) and peptidomimetics (typically, synthetically synthesized polypeptides), as well as peptoids and semipeptoids which are polypeptide analogs, which have, in some embodiments, modifications rendering the polypeptides even more stable while in a body or more capable of penetrating into cells.
[078] In some embodiments, modifications include, but are not limited to N terminus modification, C terminus modification, polypeptide bond modification, including, but not limited to, CH2-NH, CH2-S, CH2-S=0, 0=C-NH, CH2-0, CH2-CH2, S=C-NH, CH=CH or CF=CH, backbone modifications, and residue modification. Methods for preparing peptidomimetic compounds are well known in the art and are specified, for example, in Quantitative Drug Design, C.A. Ramsden Gd., Chapter 17.2, F. Choplin Pergamon Press (1992), which is incorporated by reference as if fully set forth herein. Further details in this respect are provided hereinunder.
[079] In some embodiments, peptide bonds (-CO-NH-) within the polypeptide are substituted. In some embodiments, the polypeptide bonds are substituted by N-methylated bonds (-N(CH3)-CO-). In some embodiments, the polypeptide bonds are substituted by ester bonds (-C(R)H-C-0-0-C(Pv)-N-). In some embodiments, the polypeptide bonds are substituted by ketomethylen bonds (-CO-CH2-). In some embodiments, the polypeptide bonds are substituted by a-aza bonds (-NH-N(R)-CO-), wherein R is any alkyl, e.g., methyl, carba bonds (-CH2-NH-). In some embodiments, the polypeptide bonds are substituted by hydroxyethylene bonds (-CH(OH)-CH2-). In some embodiments, the polypeptide bonds are substituted by thioamide bonds (-CS-NH-). In some embodiments, the polypeptide bonds are substituted by olefmic double bonds (-CH=CH-). In some embodiments, the polypeptide bonds are substituted by retro amide bonds (-NH-CO-). In some embodiments, the polypeptide bonds are substituted by polypeptide derivatives (-N(R)-CH2-CO-), wherein R is the "normal" side chain, naturally presented on the carbon atom. In some embodiments, these modifications occur at any of the bonds along the polypeptide chain and even at several (2-3 bonds) at the same time. [080] In some embodiments, natural aromatic amino acids of the polypeptide such as Trp, Tyr and Phe, are substituted for synthetic non-natural acid such as Phenylglycine, TIC, naphthylelanine (Nol), ring-methylated derivatives of Phe, halogenated derivatives of Phe or o-methyl-Tyr. In some embodiments, the polypeptides of the present invention include one or more modified amino acid or one or more non-amino acid monomers (e.g. fatty acid, complex carbohydrates etc).
[081] In one embodiment, "amino acid" or "amino acid" is understood to include the 20 naturally occurring amino acid; those amino acid often modified post-translationally in vivo, including, for example, hydroxyproline, phosphoserine and phosphothreonine; and other unusual amino acid including, but not limited to, 2-aminoadipic acid, hydroxy lysine, isodesmosine, nor-valine, nor-leucine and ornithine. In one embodiment, "amino acid" includes both D- and L-amino acid.
[082] In some embodiments, the polypeptides of the present invention are utilized in therapeutics which requires the polypeptides to be in a soluble form. In some embodiments, the polypeptides of the present invention include one or more non-natural or natural polar amino acid, including but not limited to serine and threonine which are capable of increasing polypeptide solubility due to their hydroxyl-containing side chain.
[083] In some embodiments, the polypeptides of the present invention are utilized in a linear form, although it will be appreciated by one skilled in the art that in cases where cyclicization does not severely interfere with polypeptides characteristics, cyclic forms of the polypeptides can also be utilized.
[084] In some embodiments, the polypeptides of present invention are biochemically synthesized such as by using standard solid phase techniques. In some embodiments, these biochemical methods include exclusive solid phase synthesis, partial solid phase synthesis, fragment condensation, or classical solution synthesis.
[085] In some embodiments, solid phase polypeptides synthesis procedures are well known to one skilled in the art and further described by John Morrow Stewart and Janis Dillaha Young, Solid Phase Polypeptide Syntheses (2nd Ed., Pierce Chemical Company, 1984). In some embodiments, synthetic polypeptides are purified by preparative high performance liquid chromatography [Creighton T. (1983) Proteins, structures and molecular principles. WH Freeman and Co. N.Y.] and the composition of which can be confirmed via amino acid sequencing by methods known to one skilled in the art. [086] In some embodiments, recombinant protein techniques are used to generate the polypeptides of the present invention. In some embodiments, recombinant protein techniques are used for generation of relatively long polypeptides (e.g., longer than 18-25 amino acids). In some embodiments, recombinant protein techniques are used for the generation of large amounts of the polypeptides of the present invention. In some embodiments, recombinant techniques are described by Bitter et al, (1987) Methods in Enzymol. 153:516-544, Studier et al. (1990) Methods in Enzymol. 185:60-89, Brisson et al. (1984) Nature 310:511-514, Takamatsu et al. (1987) EMBO J. 6:307-311, Coruzzi et al. (1984) EMBO J. 3:1671-1680 and Brogli et al, (1984) Science 224:838-843, Gurley et al. (1986) Mol. Cell. Biol. 6:559-565 and Weissbach & Weissbach, 1988, Methods for Plant Molecular Biology, Academic Press, NY, Section VIII, pp 421-463.
[087] In another embodiment, polypeptides of the present invention are synthesized using a polynucleotide such as described herein encoding a polypeptide of the present invention. In another embodiment, polynucleotides of the invention are inserted into transfection/infection vectors. In another embodiment, transfection/infection vectors are used for expressing the polypeptides of the present invention in target cells. In another embodiment, a target cell is a cell comprising a unique protease which cleaves the protease cleavage site. In another embodiment, a target cell is a cell utilized for the manufacture/expression of the polypeptides of the invention (the polypeptides of the invention are refractory within this target cell that does not carry a unique protease which cleaves the protease cleavage site). In some embodiments, the polynucleotide encoding polypeptides of the present invention is ligated into an expression vector such as but not limited to an adenoviral vector, comprising a transcriptional control of a cis-regulatory sequence (e.g., promoter sequence). In some embodiments, the cis-regulatory sequence is suitable for directing constitutive expression of the polypeptides of the present invention. In some embodiments, the cis-regulatory sequence is suitable for directing tissue specific expression of the polypeptides of the present invention. In some embodiments, the cis-regulatory sequence is suitable for directing inducible expression of the polypeptides of the present invention.
[088] In some embodiments, tissue-specific promoters suitable for use with the present invention include sequences which are functional in specific cell population, example include, but are not limited to promoters such as albumin that is liver specific [Pinkert et al., (1987) Genes Dev. 1 :268-277], lymphoid specific promoters [Calame et al, (1988) Adv. Immunol. 43:235-275]; in particular promoters of T-cell receptors [Winoto et al, (1989) EMBO J. 8:729-733] and immunoglobulins; [Banerji et al. (1983) Cell 33729-740], neuron-specific promoters such as the neurofilament promoter [Byrne et al. (1989) Proc. Natl. Acad. Sci. USA 86:5473-5477], pancreas-specific promoters [Edlunch et al. (1985) Science 230:912- 916] or mammary gland-specific promoters such as the milk whey promoter (U.S. Pat. No. 4,873,316 and European Application Publication No. 264,166). Inducible promoters suitable for use with the present invention include for example the tetracycline-inducible promoter (Srour, M.A., et al, 2003. Thromb. Haemost. 90: 398-405).
[089] In one embodiment, the phrase "a polynucleotide" refers to a DNA molecule. In another embodiment, the phrase "a polynucleotide" refers to a single or double stranded nucleic acid sequence which be isolated and provided in the form of an RNA sequence, a complementary polynucleotide sequence (cDNA), a genomic polynucleotide sequence and/or a composite polynucleotide sequences (e.g., a combination of the above).
[090] In one embodiment, "complementary polynucleotide sequence" refers to a sequence, which results from reverse transcription of messenger RNA using a reverse transcriptase or any other RNA dependent DNA polymerase. In one embodiment, the sequence can be subsequently amplified in vivo or in vitro using a DNA polymerase.
[091] In one embodiment, "genomic polynucleotide sequence" refers to a sequence derived (isolated) from a chromosome and thus it represents a contiguous portion of a chromosome.
[092] In one embodiment, "composite polynucleotide sequence" refers to a sequence, which is at least partially complementary and at least partially genomic. In one embodiment, a composite sequence can include some exonal sequences required to encode the polypeptide of the present invention, as well as some intronic sequences interposing there between. In one embodiment, the intronic sequences can be of any source, including of other genes, and typically will include conserved splicing signal sequences. In one embodiment, intronic sequences include cis acting expression regulatory elements.
[093] In one embodiment, the polynucleotides of the present invention further comprise a signal sequence encoding a signal peptide for the secretion of the polypeptide of the present invention. In one embodiment, following expression and secretion, the signal peptides are cleaved from the precursor polypeptide resulting in the mature polypeptide.
[094] In some embodiments, polynucleotides of the present invention are prepared using PCR techniques, or any other method or procedure known to one skilled in the art. In some embodiments, the procedure involves the ligation of two different DNA sequences (See, for example, "Current Protocols in Molecular Biology", eds. Ausubel et al, John Wiley & Sons, 1992).
[095] In one embodiment, the expression vector is an adenoviral vector. In one embodiment, polynucleotides of the present invention are inserted into expression vectors (i.e., a nucleic acid construct) to enable expression of the recombinant polypeptide. In one embodiment, the expression vector of the present invention includes additional sequences which render this vector suitable for replication and integration in prokaryotes. In one embodiment, the expression vector of the present invention includes additional sequences which render this vector suitable for replication and integration in eukaryotes. In one embodiment, the expression vector of the present invention includes a shuttle vector which renders this vector suitable for replication and integration in both prokaryotes and eukaryotes. In some embodiments, cloning vectors comprise transcription and translation initiation sequences (e.g., promoters, enhances) and transcription and translation terminators (e.g., polyadenylation signals).
[096] In one embodiment, a variety of prokaryotic or eukaryotic cells can be used as host- expression systems to express the polypeptides of the present invention. In some embodiments, these include, but are not limited to, microorganisms, such as bacteria transformed with a recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vector containing the polypeptide coding sequence; yeast transformed with recombinant yeast expression vectors containing the polypeptide coding sequence; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors, such as Ti plasmid, containing the polypeptide coding sequence.
[097] In some embodiments, non-bacterial expression systems are used (e.g. mammalian expression systems such as CHO cells) to express the polypeptides of the present invention. In one embodiment, the expression vector used to express polynucleotides of the present invention in mammalian cells is pCI-DHFR vector comprising a CMV promoter and a neomycin resistance gene. Construction of the pCI-dhfr vector is described, according to one embodiment, in Example 1.
[098] In some embodiments, in bacterial systems of the present invention, a number of expression vectors can be advantageously selected depending upon the use intended for the polypeptide expressed. In one embodiment, large quantities of polypeptide are desired. In one embodiment, vectors that direct the expression of high levels of the protein product, possibly as a fusion with a hydrophobic signal sequence, which directs the expressed product into the periplasm of the bacteria or the culture medium where the protein product is readily purified are desired. In one embodiment, certain fusion protein engineered with a specific cleavage site to aid in recovery of the polypeptide. In one embodiment, vectors adaptable to such manipulation include, but are not limited to, the pET series of E. coli expression vectors [Studier et al, Methods in Enzymol. 185:60-89 (1990)].
[099] In one embodiment, yeast expression systems are used. In one embodiment, a number of vectors containing constitutive or inducible promoters can be used in yeast as disclosed in U.S. Pat. Application. No: 5,932,447. In another embodiment, vectors which promote integration of foreign DNA sequences into the yeast chromosome are used.
[0100] In one embodiment, the expression vector of the present invention can further include additional polynucleotide sequences that allow, for example, the translation of several proteins from a single mRNA such as an internal ribosome entry site (IRES) and sequences for genomic integration of the promoter-chimeric polypeptide.
[0101] In some embodiments, mammalian expression vectors include, but are not limited to, pcDNA3, pcDNA3.1 (+/-), pGL3, pZeoSV2(+/-), pSecTag2, pDisplay, pEF/myc/cyto, pCMV/myc/cyto, pCR3.1, pSinRep5, DH26S, DHBB, pNMTl, pNMT41, pNMT81, which are available from Invitrogen, pCI which is available from Promega, pMbac, pPbac, pBK- RSV and pBK-CMV which are available from Strategene, pTRES which is available from Clontech, and their derivatives.
[0102] In some embodiments, expression vectors containing regulatory elements from eukaryotic viruses such as retroviruses are used by the present invention. SV40 vectors include pSVT7 and pMT2. In some embodiments, vectors derived from bovine papilloma virus include pBV-lMTHA, and vectors derived from Epstein Bar virus include pHEBO, and p205. Other exemplary vectors include pMSG, pAV009/A+, pMTO10/A+, pMAMneo-5, baculovirus pDSVE, and any other vector allowing expression of proteins under the direction of the SV-40 early promoter, SV-40 later promoter, metallothionein promoter, murine mammary tumor virus promoter, Rous sarcoma virus promoter, polyhedrin promoter, or other promoters shown effective for expression in eukaryotic cells.
[0103] In some embodiments, recombinant viral vectors are useful for in vivo expression of the polypeptides of the present invention since they offer advantages such as lateral infection and targeting specificity. In one embodiment, the viral vector is an adenovirus. In one embodiment, lateral infection is inherent in the life cycle of, for example, retrovirus and is the process by which a single infected cell produces many progeny virions that bud off and infect neighboring cells. In one embodiment, the result is that a large area becomes rapidly infected, most of which was not initially infected by the original viral particles. In one embodiment, viral vectors are produced that are unable to spread laterally. In one embodiment, this characteristic can be useful if the desired purpose is to introduce a specified gene into only a localized number of targeted cells.
[0104] In one embodiment, various methods can be used to introduce the expression vector of the present invention into cells. Such methods are generally described in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Springs Harbor Laboratory, New York (1989, 1992), in Ausubel et al, Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1989, 1992), Chang et al, Somatic Gene Therapy, CRC Press, Ann Arbor, Mich. (1995), Vega et al, Gene Targeting, CRC Press, Ann Arbor Mich. (1995), Vectors: A Survey of Molecular Cloning Vectors and Their Uses, Butterworths, Boston Mass. (1988) and Gilboa et at. [Biotechniques 4 (6): 504-512, 1986] and include, for example, stable or transient transfection, lipofection, electroporation and infection with recombinant viral vectors. In addition, see U.S. Pat. Nos. 5,464,764 and 5,487,992 for positive-negative selection methods.
[0105] In some embodiments, introduction of nucleic acid by viral infection offers several advantages over other methods such as lipofection and electroporation, since higher transfection efficiency can be obtained due to the infectious nature of viruses.
[0106] In one embodiment, it will be appreciated that the polypeptides of the present invention can also be expressed from a nucleic acid construct administered to the individual employing any suitable mode of administration, described hereinabove (i.e., in-vivo gene therapy). In one embodiment, the nucleic acid construct is introduced into a suitable cell via an appropriate gene delivery vehicle/method (transfection, infection, transduction, homologous recombination, etc.) and an expression system as needed and then the modified cells are expanded in culture and returned to the individual (i.e., ex- vivo gene therapy).
[0107] In one embodiment, in vivo gene therapy using a polypeptide has been attempted in animal models such as rodents [Bohl et al, Blood. 2000; 95:2793-2798], primates [Gao et al, Blood, 2004, Volume 103, Number 9] and has proven successful in human clinical trials for patients with chronic renal failure [Lippin et al Blood 2005, 106, Number 7]. [0108] In one embodiment, plant expression vectors are used. In one embodiment, the expression of a polypeptide coding sequence is driven by a number of promoters. In some embodiments, viral promoters such as the 35S RNA and 19S RNA promoters of CaMV [Brisson et al., Nature 310:511-514 (1984)], or the coat protein promoter to TMV [Takamatsu et al., EMBO J. 6:307-311 (1987)] are used. In another embodiment,, plant promoters are used such as, for example, the small subunit of RUBISCO [Coruzzi et al., EMBO J. 3: 1671- 1680 (1984); and Brogli et al, Science 224:838-843 (1984)] or heat shock promoters, e.g., soybean hspl7.5-E or hspl7.3-B [Gurley et al, Mol. Cell. Biol. 6:559-565 (1986)]. In one embodiment, constructs are introduced into plant cells using Ti plasmid, Ri plasmid, plant viral vectors, direct DNA transformation, microinjection, electroporation and other techniques well known to the skilled artisan. See, for example, Weissbach & Weissbach [Methods for Plant Molecular Biology, Academic Press, NY, Section VIII, pp 421-463 (1988)]. Other expression systems such as insects and mammalian host cell systems, which are well known in the art, can also be used by the present invention.
[0109] It will be appreciated that other than containing the necessary elements for the transcription and translation of the inserted coding sequence (encoding the polypeptide), the expression construct of the present invention can also include sequences engineered to optimize stability, production, purification, yield or activity of the expressed polypeptide.
[0110] Various methods, in some embodiments, can be used to introduce the expression vector of the present invention into the host cell system. In some embodiments, such methods are generally described in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Springs Harbor Laboratory, New York (1989, 1992), in Ausubel et al, Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1989, 1992), Chang et al, Somatic Gene Therapy, CRC Press, Ann Arbor, Mich. (1995), Vega et al, Gene Targeting, CRC Press, Ann Arbor Mich. (1995), Vectors: A Survey of Molecular Cloning Vectors and Their Uses, Butterworths, Boston Mass. (1988) and Gilboa et at. [Biotechniques 4 (6): 504-512, 1986] and include, for example, stable or transient transfection, lipofection, electroporation and infection with recombinant viral vectors. In addition, see U.S. Pat. Nos. 5,464,764 and 5,487,992 for positive-negative selection methods.
[0111] In some embodiments, transformed cells are cultured under effective conditions, which allow for the expression of high amounts of recombinant polypeptide. In some embodiments, effective culture conditions include, but are not limited to, effective media, bioreactor, temperature, pH and oxygen conditions that permit protein production. In one embodiment, an effective medium refers to any medium in which a cell is cultured to produce the recombinant polypeptide of the present invention. In some embodiments, a medium typically includes an aqueous solution having assimilable carbon, nitrogen and phosphate sources, and appropriate salts, minerals, metals and other nutrients, such as vitamins. In some embodiments, cells of the present invention can be cultured in conventional fermentation bioreactors, shake flasks, test tubes, microtiter dishes and petri plates. In some embodiments, culturing is carried out at a temperature, pH and oxygen content appropriate for a recombinant cell. In some embodiments, culturing conditions are within the expertise of one of ordinary skill in the art.
[0112] In some embodiments, depending on the vector and host system used for production, resultant polypeptides of the present invention either remain within the recombinant cell, secreted into the fermentation medium, secreted into a space between two cellular membranes, such as the periplasmic space in E. coli; or retained on the outer surface of a cell or viral membrane.
[0113] In one embodiment, following a predetermined time in culture, recovery of the recombinant polypeptide is effected.
[0114] In one embodiment, the phrase "recovering the recombinant polypeptide" used herein refers to collecting the whole fermentation medium containing the polypeptide and need not imply additional steps of separation or purification.
[0115] In one embodiment, polypeptides of the present invention are purified using a variety of standard protein purification techniques, such as, but not limited to, affinity chromatography, ion exchange chromatography, filtration, electrophoresis, hydrophobic interaction chromatography, gel filtration chromatography, reverse phase chromatography, concanavalin A chromatography, chromatofocusing and differential solubilization.
[0116] In one embodiment, to facilitate recovery, the expressed coding sequence can be engineered to encode the polypeptide of the present invention and fused cleavable moiety. In one embodiment, a fusion protein can be designed so that the polypeptide can be readily isolated by affinity chromatography; e.g., by immobilization on a column specific for the cleavable moiety. In one embodiment, a cleavage site is engineered between the polypeptide and the cleavable moiety and the polypeptide can be released from the chromatographic column by treatment with an appropriate enzyme or agent that specifically cleaves the fusion protein at this site [e.g., see Booth et al., Immunol. Lett. 19:65-70 (1988); and Gardella et al., J. Biol. Chem. 265: 15854-15859 (1990)].
[0117] In one embodiment, the polypeptide of the present invention is retrieved in "substantially pure" form.
[0118] In one embodiment, the phrase "substantially pure" refers to a purity that allows for the effective use of the protein in the applications described herein.
[0119] In one embodiment, the polypeptide of the present invention can also be synthesized using in vitro expression systems. In one embodiment, in vitro synthesis methods are well known in the art and the components of the system are commercially available. In another embodiment, the polypeptides of the invention further comprise a target-cell binding and internalization component/s. In another embodiment, the polypeptides of the invention are packaged onto a carrier such as but not limited to: liposome or other particles capable of carrying the polypeptides to target cells.
[0120] In some embodiments, the recombinant polypeptides are synthesized and purified; their therapeutic efficacy can be assayed either in vivo or in vitro. In one embodiment, the binding activities of the recombinant polypeptides are ascertained.
[0121] In another embodiment, in vitro binding activity is ascertained by measuring the ability of the polypeptides, as described herein as well as pharmaceutical compositions comprising the same to treat diseases such as HCV, liver cancers, liver diseases or other types of cancers such as hairy cell leukemia, malignant melanoma, Kaposi's sarcoma, bladder cancer, chronic myelocytic leukemia, kidney cancer, carcinoid tumors, non-Hodgkin's lymphoma, ovarian cancer, and skin cancers (for interferons). In another embodiment, in vivo activity is deduced by known measures of the disease that is being treated.
[0122] In another embodiment, polypeptides of the present are administered in a dose of 1-90 micrograms in 0.1-5 ml solution. In another embodiment, polypeptides of the present invention are administered in a dose of 1-50 micrograms in 0.1-5 ml solution. In another embodiment, polypeptides of the present invention are administered in a dose of 1-25 micrograms in 0.1-5 ml solution. In another embodiment, polypeptides of the present invention are administered in a dose of 50-90 micrograms in 0.1-5 ml solution. In another embodiment, polypeptides of the present invention are administered in a dose of 10-50 micrograms in 0.1-5 ml solution. [0123] In another embodiment, the polypeptides are administered in a dose of 1-90 micrograms in 0.1-5 ml solution by intramuscular (IM) injection, subcutaneous (SC) injection, or intravenous (IV) injection once a week. In another embodiment, polypeptides of the present invention are administered in a dose of 1-90 micrograms in 0.1-5 ml solution by intramuscular (IM) injection, subcutaneous (SC) injection, or intravenous (IV) injection twice a week. In another embodiment, polypeptides of the present invention are administered in a dose of 1-90 micrograms in 0.1-5 ml solution by intramuscular (IM) injection, subcutaneous (SC) injection, or intravenous (IV) injection three times a week. In another embodiment, polypeptides of the present invention are administered in a dose of 1-90 micrograms in 0.1-5 ml solution by intramuscular (IM) injection, subcutaneous (SC) injection, or intravenous (IV) injection once every two weeks. In another embodiment, polypeptides of the present invention are administered in a dose of 1-90 micrograms in 0.1-5 ml solution by intramuscular (IM) injection, subcutaneous (SC) injection, or intravenous (IV) injection once every 17 days. In another embodiment, polypeptides of the present invention are administered in a dose of 1-90 micrograms in 0.1-5 ml solution by intramuscular (IM) injection, subcutaneous (SC) injection, or intravenous (IV) injection once every 19 days weeks.
[0124] In another embodiment, the polypeptides of the present invention can be provided to the individual per se. In one embodiment, the polypeptides of the present invention can be provided to the individual as part of a pharmaceutical composition where it is mixed with a carrier such as a pharmaceutically acceptable carrier.
[0125] In another embodiment, a "pharmaceutical composition" refers to a preparation of one or more of the active ingredients described herein with other chemical components such as physiologically suitable carriers and excipients. The purpose of a pharmaceutical composition is to facilitate administration of the polypeptides to an organism.
[0126] In another embodiment, "active ingredient" refers to the polypeptide, which is accountable for the biological effect.
[0127] In one embodiment, the present invention provides combined preparations. In one embodiment, "a combined preparation" defines especially a "kit of parts" in the sense that the combination partners as defined above can be dosed independently or by use of different fixed combinations with distinguished amounts of the combination partners i.e., simultaneously, concurrently, separately or sequentially. In some embodiments, the parts of the kit of parts can then, e.g., be administered simultaneously or chronologically staggered, that is at different time points and with equal or different time intervals for any part of the kit of parts. The ratio of the total amounts of the combination partners, in some embodiments, can be administered in the combined preparation. In one embodiment, the combined preparation can be varied, e.g., in order to cope with the needs of a patient subpopulation to be treated or the needs of the single patient which different needs can be due to a particular disease, severity of a disease, age, sex, or body weight as can be readily made by a person skilled in the art.
[0128] In another embodiment, the phrases "physiologically acceptable carrier" and "pharmaceutically acceptable carrier" which be interchangeably used refer to a carrier or a diluent that does not cause significant irritation to an organism and does not abrogate the biological activity and properties of the administered compound. An adjuvant is included under these phrases. In one embodiment, one of the ingredients included in the pharmaceutically acceptable carrier can be for example polyethylene glycol (PEG), a biocompatible polymer with a wide range of solubility in both organic and aqueous media (Mutter et al. (1979).
[0129] In another embodiment, "excipient" refers to an inert substance added to a pharmaceutical composition to further facilitate administration of an active ingredient. In one embodiment, excipients include calcium carbonate, calcium phosphate, various sugars and types of starch, cellulose derivatives, gelatin, vegetable oils and polyethylene glycols.
[0130] Techniques for formulation and administration of drugs are found in "Remington's Pharmaceutical Sciences," Mack Publishing Co., Easton, PA, latest edition, which is incorporated herein by reference.
[0131] In another embodiment, suitable routes of administration, for example, include oral, rectal, transmucosal, transnasal, intestinal or parenteral delivery, including intramuscular, subcutaneous and intramedullary injections as well as intrathecal, direct intraventricular, intravenous, intraperitoneal, intranasal, or intraocular injections.
[0132] In another embodiment, the preparation is administered in a local rather than systemic manner, for example, via injection of the preparation directly into a specific region of a patient's body.
[0133] Various embodiments of dosage ranges are contemplated by this invention. The dosage of the polypeptides of the present invention, in one embodiment, is in the range of 0.005- 100 mg/day. In another embodiment, the dosage is in the range of 0.005-5 mg/day. In another embodiment, the dosage is in the range of 0.01-50 mg/day. In another embodiment, the dosage is in the range of 0.1-20 mg/day. In another embodiment, the dosage is in the range of 0.1-10 mg/day. In another embodiment, the dosage is in the range of 0.01-5 mg/day. In another embodiment, the dosage is in the range of 0.001-0.01 mg/day. In another embodiment, the dosage is in the range of 0.001-0.1 mg/day. In another embodiment, the dosage is in the range of 0.1-5 mg/day. In another embodiment, the dosage is in the range of 0.5-50 mg/day. In another embodiment, the dosage is in the range of 0.2-15mg/day. In another embodiment, the dosage is in the range of 0.8-65 mg/day. In another embodiment, the dosage is in the range of 1-50 mg/day. In another embodiment, the dosage is in the range of 5-10 mg/day. In another embodiment, the dosage is in the range of 8-15 mg/day. In another embodiment, the dosage is in a range of 10- 20mg/day. In another embodiment, the dosage is in the range of 20-40 mg/day. In another embodiment, the dosage is in a range of 60-120 mg/day. In another embodiment, the dosage is in the range of 12-40 mg/day. In another embodiment, the dosage is in the range of 40-60 mg/day. In another embodiment, the dosage is in a range of 50-100mg/day. In another embodiment, the dosage is in a range of 1-60 mg/day. In another embodiment, the dosage is in the range of 15-25 mg/day. In another embodiment, the dosage is in the range of 5-10 mg/day. In another embodiment, the dosage is in the range of 55-65 mg/day.
[0134] In another embodiment, a polypeptide is formulated in an intranasal dosage form. In another embodiment, a polypeptide is formulated in an injectable dosage form. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 0.0001 mg to 0.6 mg. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 0.001 mg to 0.005 mg. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 0.005 mg to 0.01 mg. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 0.01 mg to 0.3 mg. In another embodiment, a polypeptide is administered to a subject in a dose in a dose ranging from 0.2 mg to 0.6 mg.
[0135] In another embodiment, a polypeptide is administered to a subject in a dose ranging from 1-100 micrograms. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 10-80 micrograms. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 20-60 micrograms. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 10-50 micrograms. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 40-80 micrograms. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 10-30 micrograms. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 30-60 micrograms. [0136] In another embodiment, a polypeptide is administered to a subject in a dose ranging from 0.2 mg to 2 mg. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 2 mg to 6 mg. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 4 mg to 10 mg. In another embodiment, a polypeptide is administered to a subject in a dose ranging from 5 mg and 15 mg.
[0137] In another embodiment, a polypeptide is injected into the muscle (intramuscular injection). In another embodiment, a polypeptide is injected below the skin (subcutaneous injection). In another embodiment, a polypeptide is injected into the muscle. In another embodiment, a polypeptide is injected below the skin.
[0138] In another embodiment, a polypeptide is administered to a subject once a day. In another embodiment, a polypeptide is administered to a subject once every two days. In another embodiment, a polypeptide is administered to a subject once every three days. In another embodiment, a polypeptide is administered to a subject once every four days. In another embodiment, a polypeptide is administered to a subject once every five days. In another embodiment, a polypeptide is administered to a subject once every six days. In another embodiment, a polypeptide is administered to a subject once every week. In another embodiment, a polypeptide is administered to a subject once every 7-14 days. In another embodiment, a polypeptide is administered to a subject once every 10-20 days. In another embodiment, a polypeptide is administered to a subject once every 5-15 days. In another embodiment, a polypeptide is administered to a subject once every 15-30 days.
[0139] In another embodiment, the dosage is in a range of 50-500 mg/day. In another embodiment, the dosage is in a range of 50-150 mg/day. In another embodiment, the dosage is in a range of 100-200 mg/day. In another embodiment, the dosage is in a range of 150-250 mg/day. In another embodiment, the dosage is in a range of 200-300 mg/day. In another embodiment, the dosage is in a range of 250-400 mg/day. In another embodiment, the dosage is in a range of 300- 500 mg/day. In another embodiment, the dosage is in a range of 350-500 mg/day.
[0140] In one embodiment, the dosage is 20 mg/day. In one embodiment, the dosage is 30 mg/day. In one embodiment, the dosage is 40 mg/day. In one embodiment, the dosage is 50 mg/day. In one embodiment, the dosage is 0.01 mg/day. In another embodiment, the dosage is 0.1 mg/day. In another embodiment, the dosage is 1 mg/day. In another embodiment, the dosage is 0.530 mg/day. In another embodiment, the dosage is 0.05 mg/day. In another embodiment, the dosage is 50 mg/day. In another embodiment, the dosage is 10 mg/day. In another embodiment, the dosage is 20-70 mg/day. In another embodiment, the dosage is 5 mg/day.
[0141] In another embodiment, the dosage is 1-90 mg/day. In another embodiment, the dosage is 1-90 mg/2 days. In another embodiment, the dosage is 1-90 mg/3 days. In another embodiment, the dosage is 1-90 mg/4 days. In another embodiment, the dosage is 1-90 mg/5 days. In another embodiment, the dosage is 1-90 mg/6 days. In another embodiment, the dosage is 1-90 mg/week. In another embodiment, the dosage is 1-90 mg/9 days. In another embodiment, the dosage is 1-90 mg/11 days. In another embodiment, the dosage is 1-90 mg/14 days.
[0142] In another embodiment, the polypeptide dosage is 10-50 mg/day. In another embodiment, the dosage is 10-50 mg/2 days. In another embodiment, the dosage is 10-50 mg/3 days. In another embodiment, the dosage is 10-50 mg/4 days. In another embodiment, the dosage is 10-50 micrograms mg/5 days. In another embodiment, the dosage is 10-50 mg/6 days. In another embodiment, the dosage is 10-50 mg/week. In another embodiment, the dosage is 10-50 mg/9 days. In another embodiment, the dosage is 10-50 mg/11 days. In another embodiment, the dosage is 10-50 mg/14 days.
[0143] Oral administration, in one embodiment, comprises a unit dosage form comprising tablets, capsules, lozenges, chewable tablets, suspensions, emulsions and the like. Such unit dosage forms comprise a safe and effective amount of the polypeptide of the invention, each of which is in one embodiment, from about 0.7 or 3.5 mg to about 280 mg/70 kg, or in another embodiment, about 0.5 or 10 mg to about 210 mg/70 kg. The pharmaceutically-acceptable carriers suitable for the preparation of unit dosage forms for peroral administration are well- known in the art. In some embodiments, tablets typically comprise conventional pharmaceutically-compatible adjuvants as inert diluents, such as calcium carbonate, sodium carbonate, mannitol, lactose and cellulose; binders such as starch, gelatin and sucrose; disintegrants such as starch, alginic acid and croscarmelose; lubricants such as magnesium stearate, stearic acid and talc. In one embodiment, glidants such as silicon dioxide can be used to improve flow characteristics of the powder-mixture. In one embodiment, coloring agents, such as the FD&C dyes, can be added for appearance. Sweeteners and flavoring agents, such as aspartame, saccharin, menthol, peppermint, and fruit flavors, are useful adjuvants for chewable tablets. Capsules typically comprise one or more solid diluents disclosed above. In some embodiments, the selection of carrier components depends on secondary considerations like taste, cost, and shelf stability, which are not critical for the purposes of this invention, and can be readily made by a person skilled in the art.
[0144] In one embodiment, the oral dosage form comprises predefined release profile. In one embodiment, the oral dosage form of the present invention comprises an extended release tablets, capsules, lozenges or chewable tablets. In one embodiment, the oral dosage form of the present invention comprises a slow release tablets, capsules, lozenges or chewable tablets. In one embodiment, the oral dosage form of the present invention comprises an immediate release tablets, capsules, lozenges or chewable tablets. In one embodiment, the oral dosage form is formulated according to the desired release profile of the pharmaceutical active ingredient as known to one skilled in the art.
[0145] Peroral compositions, in some embodiments, comprise liquid solutions, emulsions, suspensions, and the like. In some embodiments, pharmaceutically-acceptable carriers suitable for preparation of such compositions are well known in the art. In some embodiments, liquid oral compositions comprise from about 0.001% to about 0.933% of the desired compound or compounds, or in another embodiment, from about 0.01% to about 10 %.
[0146] In some embodiments, compositions for use in the methods of this invention comprise solutions or emulsions, which in some embodiments are aqueous solutions or emulsions comprising a safe and effective amount of the compounds of the present invention and optionally, other compounds, intended for topical intranasal administration. In some embodiments, h compositions comprise from about 0.001% to about 10.0% w/v of a subject compound, more preferably from about 00.1% to about 2.0, which is used for systemic delivery of the compounds by the intranasal route.
[0147] In another embodiment, the pharmaceutical compositions are administered by intravenous, intra-arterial, or intramuscular injection of a liquid preparation. In some embodiments, liquid formulations include solutions, suspensions, dispersions, emulsions, oils and the like. In one embodiment, the pharmaceutical compositions are administered intravenously, and are thus formulated in a form suitable for intravenous administration. In another embodiment, the pharmaceutical compositions are administered intra-arterially, and are thus formulated in a form suitable for intra-arterial administration. In another embodiment, the pharmaceutical compositions are administered intramuscularly, and are thus formulated in a form suitable for intramuscular administration. [0148] In one embodiment, pharmaceutical compositions of the present invention are manufactured by processes well known in the art, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or lyophilizing processes.
[0149] In one embodiment, pharmaceutical compositions for use in accordance with the present invention is formulated in conventional manner using one or more physiologically acceptable carriers comprising excipients and auxiliaries, which facilitate processing of the active ingredients into preparations which, can be used pharmaceutically. In one embodiment, formulation is dependent upon the route of administration chosen.
[0150] In one embodiment, injectables, of the invention are formulated in aqueous solutions. In one embodiment, injectables, of the invention are formulated in physiologically compatible buffers such as Hank's solution, Ringer's solution, or physiological salt buffer. In some embodiments, for transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.
[0151] In one embodiment, the preparations described herein are formulated for parenteral administration, e.g., by bolus injection or continuous infusion. In some embodiments, formulations for injection are presented in unit dosage form, e.g., in ampoules or in multidose containers with optionally, an added preservative. In some embodiments, compositions are suspensions, solutions or emulsions in oily or aqueous vehicles, and contain formulatory agents such as suspending, stabilizing and/or dispersing agents.
[0152] The compositions also comprise, in some embodiments, preservatives, such as benzalkonium chloride and thimerosal and the like; chelating agents, such as edetate sodium and others; buffers such as phosphate, citrate and acetate; tonicity agents such as sodium chloride, potassium chloride, glycerin, mannitol and others; antioxidants such as ascorbic acid, acetylcystine, sodium metabisulfote and others; aromatic agents; viscosity adjusters, such as polymers, including cellulose and derivatives thereof; and polyvinyl alcohol and acid and bases to adjust the pH of these aqueous compositions as needed. The compositions also comprise, in some embodiments, local anesthetics or other actives. The compositions can be used as sprays, mists, drops, and the like.
[0153] In some embodiments, pharmaceutical compositions for parenteral administration include aqueous solutions of the active preparation in water-soluble form. Additionally, suspensions of the active ingredients, in some embodiments, are prepared as appropriate oily or water based injection suspensions. Suitable lipophilic solvents or vehicles include, in some embodiments, fatty oils such as sesame oil, or synthetic fatty acid esters such as ethyl oleate, triglycerides or liposomes. Aqueous injection suspensions contain, in some embodiments, substances, which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol or dextran. In another embodiment,, the suspension also contain suitable stabilizers or agents which increase the solubility of the active ingredients to allow for the preparation of highly concentrated solutions.
[0154] In another embodiment, the polypeptide is delivered in a vesicle, in particular a liposome (see Langer, Science 249: 1527-1533 (1990); Treat et al, in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez- Berestein and Fidler (eds.), Liss, New York, pp. 353- 365 (1989); Lopez-Berestein, ibid., pp. 317-327; see generally ibid).
[0155] In another embodiment, the pharmaceutical composition delivered in a controlled release system is formulated for intravenous infusion, implantable osmotic pump, transdermal patch, liposomes, or other modes of administration. In one embodiment, a pump is used (see Langer, supra; Sefton, CRC Crit. Ref. Biomed. Eng. 14:201 (1987); Buchwald et al, Surgery 88:507 (1980); Saudek et al, N. Engl. J. Med. 321 :574 (1989). In another embodiment, polymeric materials can be used. In yet another embodiment, a controlled release system can be placed in proximity to the therapeutic target, i.e., the brain, thus requiring only a fraction of the systemic dose (see, e.g., Goodson, in Medical Applications of Controlled Release, supra, vol. 2, pp. 115-138 (1984). Other controlled release systems are discussed in the review by Langer {Science 249: 1527-1533 (1990).
[0156] In some embodiments, the active ingredient is in powder form for constitution with a suitable vehicle, e.g., sterile, pyrogen-free water based solution, before use. Compositions are formulated, in some embodiments, for atomization and inhalation administration. In another embodiment, compositions are contained in a container with attached atomizing means.
[0157] In some embodiments, pharmaceutical compositions suitable for use in context of the present invention include compositions wherein the polypeptides are contained in an amount effective to achieve the intended purpose. In some embodiments, a therapeutically effective amount means an amount of the polypeptide effective to prevent, alleviate or ameliorate symptoms of disease or prolong the survival of the subject being treated. In one preferred embodiment, the disease is a liver disease caused by HCV. [0158] In one embodiment, determination of a therapeutically effective amount is well within the capability of those skilled in the art.
[0159] Some examples of substances which can serve as carriers or components thereof are sugars, such as lactose, glucose and sucrose; starches, such as corn starch and potato starch; cellulose and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose, and methyl cellulose; powdered tragacanth; malt; gelatin; talc; solid lubricants, such as stearic acid and magnesium stearate; calcium sulfate; vegetable oils, such as peanut oil, cottonseed oil, sesame oil, olive oil, corn oil and oil of theobroma; polyols such as propylene glycol, glycerine, sorbitol, mannitol, and polyethylene glycol; alginic acid; emulsifiers, such as the Tween™ brand emulsifiers; wetting agents, such sodium lauryl sulfate; coloring agents; flavoring agents; tableting agents, stabilizers; antioxidants; preservatives; pyrogen-free water; isotonic saline; and phosphate buffer solutions. The choice of a pharmaceutically-acceptable carrier to be used in conjunction with the compound is basically determined by the way the compound is to be administered. If the subject compound is to be injected, in one embodiment, the pharmaceutically-acceptable carrier is sterile, physiological saline, with a blood-compatible suspending agent, the pH of which has been adjusted to about 7.4.
[0160] In addition, the compositions further comprise binders (e.g. acacia, cornstarch, gelatin, carbomer, ethyl cellulose, guar gum, hydroxypropyl cellulose, hydroxypropyl methyl cellulose, povidone), disintegrating agents (e.g. cornstarch, potato starch, alginic acid, silicon dioxide, croscarmelose sodium, crospovidone, guar gum, sodium starch glycolate), buffers (e.g., Tris- HCL, acetate, phosphate) of various pH and ionic strength, additives such as albumin or gelatin to prevent absorption to surfaces, detergents (e.g., Tween 20, Tween 80, Pluronic F68, bile acid salts), protease inhibitors, surfactants (e.g. sodium lauryl sulfate), permeation enhancers, solubilizing agents (e.g., glycerol, polyethylene glycerol), anti-oxidants (e.g., ascorbic acid, sodium metabisulfite, butylated hydroxyanisole), stabilizers (e.g. hydroxypropyl cellulose, hyroxypropylmethyl cellulose), viscosity increasing agents(e.g. carbomer, colloidal silicon dioxide, ethyl cellulose, guar gum), sweeteners (e.g. aspartame, citric acid), preservatives (e.g., Thimerosal, benzyl alcohol, parabens), lubricants (e.g. stearic acid, magnesium stearate, polyethylene glycol, sodium lauryl sulfate), flow-aids (e.g. colloidal silicon dioxide), plasticizers (e.g. diethyl phthalate, triethyl citrate), emulsifiers (e.g. carbomer, hydroxypropyl cellulose, sodium lauryl sulfate), polymer coatings (e.g., poloxamers or poloxamines), coating and film forming agents (e.g. ethyl cellulose, acrylates, polymethacrylates) and/or adjuvants. [0161] Typical components of carriers for syrups, elixirs, emulsions and suspensions include ethanol, glycerol, propylene glycol, polyethylene glycol, liquid sucrose, sorbitol and water. For a suspension, typical suspending agents include methyl cellulose, sodium carboxymethyl cellulose, cellulose (e.g. Avicel™, RC-591), tragacanth and sodium alginate; typical wetting agents include lecithin and polyethylene oxide sorbitan (e.g. polysorbate 80). Typical preservatives include methyl paraben and sodium benzoate. In another embodiment, peroral liquid compositions also contain one or more components such as sweeteners, flavoring agents and colorants disclosed above.
[0162] The compositions also include incorporation of the polypeptide into or onto particulate preparations of polymeric compounds such as polylactic acid, polglycolic acid, hydrogels, etc, or onto liposomes, microemulsions, micelles, unilamellar or multilamellar vesicles, erythrocyte ghosts, or spheroplasts.) Such compositions will influence the physical state, solubility, stability, rate of in vivo release, and rate of in vivo clearance.
[0163] Also comprehended by the invention are particulate compositions coated with polymers (e.g. poloxamers or poloxamines) and the polypeptide coupled to antibodies directed against tissue-specific receptors, ligands or antigens or coupled to ligands of tissue-specific receptors.
[0164] In some embodiments, polypeptides modified by the covalent attachment of water- soluble polymers such as polyethylene glycol, copolymers of polyethylene glycol and polypropylene glycol, carboxymethyl cellulose, dextran, polyvinyl alcohol, polyvinylpyrrolidone or polyproline. In another embodiment, the modified compounds exhibit substantially longer half-lives in blood following intravenous injection than do the corresponding unmodified compounds. In one embodiment, modifications also increase the polypeptide's solubility in aqueous solution, eliminate aggregation, enhance the physical and chemical stability of the compound, and greatly reduce the immunogenicity and reactivity of the compound. In another embodiment, the desired in vivo biological activity is achieved by the administration of such polymer-compound abducts less frequently or in lower doses than with the unmodified compound.
[0165] In some embodiments, preparation of effective amount or dose can be estimated initially from in vitro assays. In one embodiment, a dose can be formulated in animal models and such information can be used to more accurately determine useful doses in humans. [0166] In one embodiment, toxicity and therapeutic efficacy of the polypeptide described herein can be determined by standard pharmaceutical procedures in vitro, in cell cultures or experimental animals. In one embodiment, the data obtained from these in vitro and cell culture assays and animal studies can be used in formulating a range of dosage for use in human. In one embodiment, the dosages vary depending upon the dosage form employed and the route of administration utilized. In one embodiment, the exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. [See e.g., Fingl, et al, (1975) "The Pharmacological Basis of Therapeutics", Ch. 1 p. l].
[0167] In one embodiment, depending on the severity and responsiveness of the condition to be treated, dosing can be of a single or a plurality of administrations, with course of treatment lasting from several days to several weeks or until cure is effected or diminution of the disease state is achieved.
[0168] In one embodiment, the amount of a composition to be administered will, of course, be dependent on the subject being treated, the severity of the affliction, the manner of administration, the judgment of the prescribing physician, etc.
[0169] In one embodiment, compositions including the preparation of the present invention formulated in a compatible pharmaceutical carrier are also be prepared, placed in an appropriate container, and labeled for treatment of an indicated condition.
[0170] In another embodiment, a polypeptide as described herein is administered via systemic administration. In another embodiment, a polypeptide as described herein is administered by intravenous, intramuscular or subcutaneous injection. In another embodiment, a polypeptides as described herein is lyophilized (i.e., freeze-dried) preparation in combination with complex organic excipients and stabilizers such as nonionic surface active agents (i.e., surfactants), various sugars, organic polyols and/or human serum albumin. In another embodiment, a pharmaceutical composition comprises a lyophilized polypeptide as described in sterile water for injection. In another embodiment, a pharmaceutical composition comprises a lyophilized polypeptide as described in sterile PBS for injection. In another embodiment, a pharmaceutical composition comprises a lyophilized polypeptide as described in sterile 0.9% NaCl for injection.
[0171] In another embodiment, the pharmaceutical composition comprises a polypeptide as described herein and complex carriers such as human serum albumin, polyols, sugars, and anionic surface active stabilizing agents. See, for example, WO 89/10756 (Hara et al.- containing polyol and p-hydroxybenzoate). In another embodiment, the pharmaceutical composition comprises a polypeptide as described herein and lactobionic acid and an acetate/glycine buffer. In another embodiment, the pharmaceutical composition comprises a polypeptide as described herein and amino acids, such as arginine or glutamate that increase the solubility of interferon compositions in water. In another embodiment, the pharmaceutical composition comprises a lyophilized polypeptide as described herein and glycine or human serum albumin (HSA), a buffer (e g. acetate) and an isotonic agent (e.g NaCl). In another embodiment, the pharmaceutical composition comprises a lyophilized polypeptide as described herein and phosphate buffer, glycine and HSA.
[0172] In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein is stabilized when placed in buffered solutions having a pH between about 4 and 7.2. In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein is stabilized with an amino acid as a stabilizing agent and in some cases a salt (if the amino acid does not contain a charged side chain).
[0173] In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein is a liquid composition comprising a stabilizing agent at between about 0.3% and 5% by weight which is an amino acid.
[0174] In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein provides a liquid formulation permitting storage for a long period of time in a liquid state facilitating storage and shipping prior to administration.
[0175] In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein comprises solid lipids as matrix material. In another embodiment, the injectable pharmaceutical composition comprising a polypeptide as described herein comprises solid lipids as matrix material. In another embodiment, the production of lipid microparticles by spray congealing was described by Speiser (Speiser and al, Pharm. Res. 8 (1991) 47-54) followed by lipid nanopellets for peroral administration (Speiser EP 0167825 (1990)). In another embodiment, lipids, which are used, are well tolerated by the body (e. g. glycerides composed of fatty acids which are present in the emulsions for parenteral nutrition). [0176] In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein is in the form of liposomes (J. E. Diederichs and al., Pharm./nd. 56 (1994) 267- 275).
[0177] In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein comprises polymeric microparticles. In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein comprises polymeric nanoparticles. In another embodiment, the injectable pharmaceutical composition comprising a polypeptide as described herein comprises polymeric microparticles. In another embodiment, the injectable pharmaceutical composition comprising a polypeptide as described herein comprises polymeric nanoparticles. In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein comprises nanoparticles. In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein comprises liposomes. In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein comprises lipid emulsion In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein comprises microspheres. In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein comprises lipid nanoparticles. In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein comprises lipid nanoparticles comprising amphiphilic lipids. In another embodiment, the pharmaceutical composition comprising a polypeptide as described herein comprises lipid nanoparticles comprising a drug, a lipid matrix and a surfactant. In another embodiment, the lipid matrix has a monoglyceride content which is at least 50% w/w.
[0178] In one embodiment, compositions of the present invention are presented in a pack or dispenser device, such as an FDA approved kit, which contain one or more unit dosage forms containing the active ingredient. In one embodiment, the pack , for example, comprise metal or plastic foil, such as a blister pack. In one embodiment, the pack or dispenser device is accompanied by instructions for administration. In one embodiment, the pack or dispenser is accommodated by a notice associated with the container in a form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals, which notice is reflective of approval by the agency of the form of the compositions or human or veterinary administration. Such notice, in one embodiment, is labeling approved by the U.S. Food and Drug Administration for prescription drugs or of an approved product insert. [0179] In one embodiment, it will be appreciated that the polypeptides of the present invention can be provided to the individual with additional active agents to achieve an improved therapeutic effect as compared to treatment with each agent by itself. In another embodiment, measures (e.g., dosing and selection of the complementary agent) are taken to adverse side effects which are associated with combination therapies.
[0180] Additional objects, advantages, and novel features of the present invention will become apparent to one ordinarily skilled in the art upon examination of the following examples, which are not intended to be limiting. Additionally, each of the various embodiments and aspects of the present invention as delineated hereinabove and as claimed in the claims section below finds experimental support in the following examples.
EXAMPLES
[0181] Generally, the nomenclature used herein and the laboratory procedures utilized in the present invention include molecular, biochemical, microbiological and recombinant DNA techniques. Such techniques are thoroughly explained in the literature. See, for example, "Molecular Cloning: A laboratory Manual" Sambrook et al., (1989); "Current Protocols in Molecular Biology" Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al, "Current Protocols in Molecular Biology", John Wiley and Sons, Baltimore, Maryland (1989); Perbal, "A Practical Guide to Molecular Cloning", John Wiley & Sons, New York (1988); Watson et al., "Recombinant DNA", Scientific American Books, New York; Birren et al. (eds) "Genome Analysis: A Laboratory Manual Series", Vols. 1-4, Cold Spring Harbor Laboratory Press, New York (1998); methodologies as set forth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and 5,272,057; "Cell Biology: A Laboratory Handbook", Volumes I-III Cellis, J. E., ed. (1994); "Culture of Animal Cells - A Manual of Basic Technique" by Freshney, Wiley-Liss, N. Y. (1994), Third Edition; "Current Protocols in Immunology" Volumes I-III Coligan J. E., ed. (1994); Stites et al. (eds), "Basic and Clinical Immunology" (8th Edition), Appleton & Lange, Norwalk, CT (1994); Mishell and Shiigi (eds), "Selected Methods in Cellular Immunology", W. H. Freeman and Co., New York (1980); available immunoassays are extensively described in the patent and scientific literature, see, for example, U.S. Pat. Nos. 3,791,932; 3,839,153; 3,850,752; 3,850,578; 3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281,521; "Oligonucleotide Synthesis" Gait, M. J., ed. (1984); "Nucleic Acid Hybridization" Hames, B. D., and Higgins S. J., eds. (1985); "Transcription and Translation" Hames, B. D., and Higgins S. J., eds. (1984); "Animal Cell Culture" Freshney, R. I., ed. (1986); "Immobilized Cells and Enzymes" IRL Press, (1986); "A Practical Guide to Molecular Cloning" Perbal, B., (1984) and "Methods in Enzymology" Vol. 1-317, Academic Press; "PCR Protocols: A Guide To Methods And Applications", Academic Press, San Diego, CA (1990); Marshak et al., "Strategies for Protein Purification and Characterization - A Laboratory Course Manual" CSHL Press (1996); all of which are incorporated by reference. Other general references are provided throughout this document.
MATERIALS AND METHODS:
Bacterial strains
[0182] The following Escherichia coli (E. coli) strains were used: XL-1 Blue and DH5a (Stratagene, USA) for plasmid propagation and BJ5183 (Stratagene, USA) for the generation of recombinant adenovirus plasmid DNA.
Recombinant DNA techniques and vectors
[0183] Recombinant DNA techniques were carried out according to standard protocols or as recommended by suppliers. Nucleotide sequences were determined using the PRISM 3100 Genetic Analyzer (Applied Biosystems, USA) according to the supplier's recommendations. The eukaryotic CMV promoter-based GFP-fusion expression vector pEGFP C2, which was used for expression of mCherry, MazF and MazF based zymoxins, was from Clontech (USA). The AdEasy plasmid system (pShuttle and pAdEasy-1) (He et al, 1998), that was used for generation of recombinant human type 5 adenoviral vectors for gene delivery of the zymoxins expression cassettes, was a generous gift from Dr. Bert Vogelstein, Johns Hopkins Oncology Center, Baltimore, MD. All plasmid and DNA fragment purifications were carried out with High-Speed Plasmid Mini Kit and Gel/PCR DNA fragments Extraction Kit (Geneaid Biotech Ltd., Taiwan) unless mentioned otherwise. T4 DNA ligase and restriction enzymes were purchased from New England Biolabs (USA). DNA ligations were carried out at 16°C overnight. Molecular cloning Oligonucleotides
[0184] All the oligonucleotides that were used in this study were purchased from Hylabs, Israel (Table 1).
Table 1
Figure imgf000049_0001
Figure imgf000050_0001
Construction of mCherry-NS3 activated MazF zvmoxin expressing vector
[0185] A PCR was carried out using a single colony of E. coli strain XL-1 as template, the forward primer: 40- clvmazf and the reverse primers: 41-clvmazf, 42-clvmazf, 43-clvmazf, 44-clvmazf, 45-clvmazf, 46-clvmazf and 47-clvmazf. The PCR product, encoding for a fusion polypeptide composed of (from the N terminus) MazF, HCV P10-P10' NS3 cleavage sequence derived from genotype 2a (strain JFH1) NS5A/B junction, a short flexible linker, a short inhibitory peptide corresponding to MazE C-terminal 35 amino-acids (which encompass the 23 amino-acids inhibitory peptide (MazEp) that has been described by Li et al. (Li et al., 2006)), a flexible linker and the C-terminal ER membrane anchor of the tyrosine phosphatase PTP1B (Anderie et al, 2007) was digested with Xhol and EcoRI and was cloned between the corresponding sites in the plasmid pEGFP-C2, generating plasmid "pEGFP C2- MazF-full 2a JFH NS5AB-linker-inhibitor peptide-ER". Next, the sequence of the red fluorescent protein mCherry (Shaner et al., 2004) was amplified by PCR from an expression cassette (kindly provided by Prof. Adi Avni, Department of Molecular Biology and Ecology of Plants, Tel- Aviv university, Israel) using the forward primer: 48- clvmazf and the reverse primer: 49- clvmazf. The PCR product was digested with Nhel and Xhol and was cloned between the corresponding sites of the plasmid "pEGFP C2- MazF-full 2a JFH NS5AB-linker-inhibitor peptide-ER" (replacing the EGFP coding sequence), generating plasmid: "pmCherry (in pEGFP C2 backbone)- MazF-full JFH NS5AB-linker-inhibitor peptide-ER". The amino acid sequence of the zymoxin described herein is shown in Fig. 13 A.
Construction of the vector encoding for "mCherry-uncleavable MazF"
[0186] A PCR was carried out using DNA of plasmid "pmCherry (in EGFP C2 backbone) - MazF-full JFH NS5AB-linker-inhibitor peptide-ER" as template, the forward primer: 40- clvmazf and the reverse primers: 50-unclmazf and 51-unclmazf. The PCR product was digested with EcoRV and Nrul, and the digestion product of 233bp was cloned between the corresponding sites of the same plasmid that has been used as the template, generating the plasmid: "pmCherry (in EGFP C2 backbone) - MazF- mutated NS5AB-linker-inhibitor peptide-ER". This plasmid encodes for an uncleavable construct in which the NS3 cleavage sequence was replaced by a mutated 14 amino acids cleavage sequence (P10-P4') from HCV genotype la NS5A/B junction in which P3 valine was substituted by alanine, P2 cysteine by glycine, PI cysteine by glycine and P4' tyrosine by alanine. The amino acid sequence of the zymoxin described herein is shown in Fig. 13B.
Construction of the vector encoding for "EGFP-MazF"
[0187] The mutated variant of an "intermediate" vector used in the construction process of the "mCherry-NS3-activated MazF" encoding vector (see above). In this variant, a nonsense mutation was inserted instead of the tyrosine in the SMSY sequence of the NS3 recognition site, generating the plasmid "pEGFP-MazF" that encodes for a truncated EGFP-MazF fusion protein that lacks the MazE derived inhibitor peptide and the ER anchor.
Construction of the vector encoding for mCherry
[0188] The sequence of the red fluorescent protein mCherry (Shaner et al, 2004) was amplified by PCR from an expression cassette (see construction of the vector encoding for "mCherry-NS3-activated MazF") using the forward primer: 48- clvmazf and the reverse primer: 49- clvmazf. The PCR product was digested with Nhel and BgUl and was cloned between the corresponding sites of the plasmid pEGFP C2, generating the plasmid "pmCherry (in EGFP C2 backbone)".
Construction and propagation of recombinant adenovirus vectors
[0189] Construction and propagation of recombinant human type 5 adenoviral vectors for gene delivery of the mCherry-NS3 activated MazF and mCherry-uncleavable MazF expression cassettes were carried out using the AdEasy system (a generous gift from Dr. Bert Vogelstein, Johns Hopkins Oncology Center, Baltimore, MD) essentially as described in (He et al, 1998; Luo et al, 2007). Briefly, the DNA sequence of the mCherry-NS3 activated MazF and mCherry-uncleavable MazF expression cassettes was cloned into "pShuttle" vectors by standard methods. The resulting vectors were digested with Pmel, purified, and 400ng of the digested vectors where mixed with lOOng of the plasmid pAdEasy-1. DNA mixture was electroporated (in 2.0 mm cuvettes at 2,500V, 25 μΡ) into E. coli strain BJ5183 electro-competent cells (Stratagene, USA). After phenotypic expression of 1 hour, bacteria were seeded on LB agar plates containing 50 μg/ml of kanamycin and were grown at 37°C over-night. 15 smallest colonies were picked, grown for 12 hours in LB containing 25 μg/ml of kanamycin and plasmids form 5ml of each culture were purified by standard miniprep procedure. Pad digested plasmids were analyzed by 0.8% TAE agarose gel electrophoresis. "Candidate" plasmids that yield a large fragment (near 30 kb), plus a smaller fragment of 3.0kb or 4.5kb, were transfomed into E. coli DH5a competent cells. Plasmids were isolated by standard miniprep procedure and were sequenced to confirm their predicted composition. For production of virus particles, the plasmids, which were denoted "pAdEasy-mCherry-NS3 activated MazF" and "pAdEasy- mCherry-uncleavable MazF" were isolated from chosen "positive" clones and were digested with Pad. Digested DNA was purified using Zymoclean™ Gel DNA Recovery Kit (ZYMO RESEARCH, USA) according to the manufacturer instructions. 1.5 μg of the purified, digested plasmids were used to transfect HEK293 cells at 50-70% confluence in 60mm culture dish using the calcium-phosphate method. 7 to 10 days post-transfection, when cytopathic effect (CPE) was clearly observed, cells were collected by scraping them off the dish and collecting them along with any floating cells in the culture by centrifugation. The cell pellet was washed once with PBS, suspended in 0.5ml PBS and was subjected to 4 cycles of freeze/thaw for lysis. Cell debris were precipitated by brief centrifugation and 300μ1 of the supernatant that contains virus particles were used to infect 70% confluent HEK293 cells in two 60mm dishes (first amplification "cycle"). When a third to half of the cells is detached (usually after 3-5 days), virus particle were released by freeze/thaw cycles as described, and a second amplification cycle was performed, as described, by infecting HEK293 cells at 70%> confluence in two 100mm dishes. The supernatant containing viruses was kept at -80°C. Viral titers were determined by an end- point dilution assay: HEK293 cells were grown to about 70%> confluence in 96-wells plates. The recombinant adenovirus stock solution was 10 fold serially diluted to a concentrations range of 10"3-10"10 into growth medium. 1 Ox 100
Figure imgf000052_0001
of each dilution were added to 10 wells in the 96-well plate. After cultured for 10 days, plaque forming units (PFU) in one ml of the concentrated sample was calculated according to the formula of titer (pfu/mL) = lO^ + °'8 when X represents the sum of the fractions of CPE positive wells for each dilution (10 of 10 wells with CPE is calculated as "1") . Cell culture, transfection, protein extraction and immunoblotting
[0190] Human embryonic kidney cells HEK293, stably expressing the tetracycline repressor protein (T-REx 293 Cell Line, Invitrogen, USA), and human hepatoma cells Huh7.5 (Blight et al., 2002) were used throughout this study. Cell lines were maintained in DMEM supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin (Biological Industries, Israel) in a humidified 5% C02 incubator at 37°C.
[0191] The calcium-phosphate transfection method was applied for introducing 2μg of the plasmid "pmCherry (in pEGFP C2 backbone)- MazF-full JFH NS5AB-linker-inhibitor peptide-ER" or the plasmid "pmCherry (in EGFP C2 backbone)- MazF- mutated NS5AB- linker-inhibitor peptide-ER" into T-Rex 293 cells inducibly expressing EGFP-Full NS3-4A seeded 1.5 x lO6 cells per 60mm plate 24 hours before transfection. Stable transfectants, inducibly expressing EGFP-Full NS3-4A and constitutively expressing mCherry-NS3 activated MazF (denoted "Tet-inducible full NS3-4A/constitutive NS3 activated MazF expressing cells") or mCherry-uncleavable MazF (denoted "Tet-inducible full NS3-4A / constitutive uncleavable MazF expressing cells") were selected in a medium containing lmg/ml of G418 (A.G. Scientific, USA). Cell clones that express high level of the cleavable construct or the uncleavable control were identified by fluorescence microscopy and isolated.
[0192] For protein extraction, 48 hours post-transfection the cells were washed with PBS, scraped and lysed in a buffer containing 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 10 mM Tris(HCl) pH 7.5, and protease inhibitors cocktail (Sigma, Israel). Following 30 minutes of incubation on ice, lysates were cleared by centrifugation at 20,000 g for 10 minutes, at 4°C. For immunoblotting, protein samples were separated on a 12% SDS/polyacrylamide gel, transferred to nitrocellulose and detected using rabbit polyclonal anti-GFP antibody (Santa- Cruz, USA) or mouse monoclonal anti-actin antibody (Abeam, USA), followed by horseradish peroxidase (HRP)-conjugated goat anti-rabbit or anti-mouse antibodies (Jackson ImmunoResearch Laboratories, USA) and enhanced chemiluminescence (ECL) detection using SuperSignal West Pico Chemiluminescent Substrate (Thermo SCIENTIFIC/Pierce, USA).
Viral infection (HCV)
[0193] Virus infection assays were carried out with an inter-genotypic chimeric hepatitis C virus (HCV) produced by replacing the core-NS2 segment of the JFH-1 virus genome with the comparable segment of the genotype la H77 virus. This chimeric virus, HJ3-5 (Kindly provided by Prof. Stanley Lemon, University of Texas at Galveston), contains two compensatory mutations that promote its growth in cell culture as described previously (Yi et al, 2007). HCV RNAs were transcribed in vitro and electroporated into cells essentially as described previously (Yi and Lemon, 2004; Yi et al, 2006). In brief, 10 μg of in vitro- synthesized HCV RNA was mixed with 5x 106 Huh7.5 cells in a 2-mm cuvette and pulsed twice at 1.4 kV and 25 μΡ. Cells were seeded into 12-well plates or 25-cm2 flasks, and passaged at 3 -to 4-day intervals post-transfection by trypsinization and reseeding with a 1 :3 to 1 :4 split into fresh culture vessels. When infectivity reached -50%, as was monitored by immunofiuorescent staining with anti HCV core protein mouse monoclonal antibody (Affinity BioReagents, USA) and Cy2-conjugated goat anti-mouse IgG (Jackson ImmunoResearch Laboratories, USA) (infectivity assay- see below), the mixed culture (of uninfected and HCV infected cells in 1 :1 ratio) was taken for cytotoxicity assays.
Fluorescence/Immunofluorescence Microscopy
Visualizing T-REx 293 cells inducibly expressing EGFP-fuU NS3-4A and constitutively expressing mCherry- uncleavable MazF
[0194] l x lO5 Tet-inducible full NS3-4A/constitutive uncleavable MazF expressing cells were seeded on poly-L-lysine coated cover-slips in a 24 well-plate. 12 hours later, the cells were supplemented with 1 μg/ml of tetracycline for another 24 hours and then were fixed with 4% formaldehyde in PBS. Following nuclear staining by Hoechst 33258 for 1 hour at room temperature, Slides were washed with PBS, mounted in ImmuGlo Mounting Medium flMMCO Diagnostics, USA) and examined using a Zeiss LSM 510 META laser scanning confocal microscope.
Visualizing T-REx 293 cells inducibly expressing EGFP-fuU NS3-4A (supplemented with different tetracycline concentrations) and constitutively expressing mCherry-NS3 activated MazF or mCherry-uncleavable MazF
[0195] l lO5 Tet-inducible full NS3-4A/constitutive NS3 activated MazF or Tet-inducible full NS3-4A/constitutive uncleavable MazF expressing cells were seeded on poly-L-lysine coated cover-slips in a 24 well-plate. 12 hours later, cells were supplemented with lOng/ml or lOOOng/ml of tetracycline, or left untreated. 36 hours later, cells were fixed with 4% formaldehyde in PBS. Following nuclear staining by Hoechst 33258 for 1 hour at room temperature, Slides were washed with PBS, mounted in ImmuGlo Mounting Medium and examined using a fluorescence microscope. Visualizing HEK293 cells infected with recombinant adenovirus encoding for mCherry-NS3 activated MazF or mCherry-uncleavable-MazF
[0196] 3 l05 HEK293 cells were seeded per well in 6 wells plate. When 90% confluence was reached, the growth medium was replaced by fresh medium containing 10 fold dilutions of recombinant adenoviruses encoding for mCherry-NS3 activated MazF or mCherry- uncleavable-MazF, starting from 2.5 χ 106 PFU per well. After 36 hours, cells were fixed with 4% formaldehyde in PBS and examined using a fluorescence microscope.
Visualizing HCV infected cells (infectivity assay)
[0197] Huh7.5 cells infected with HCV HJ3-5 chimeric virus were seeded into 8-well chamber slides (Nalge Nunc, USA). After 24 hours, cells were fixed and permeabilized with 1 :1 acetone/methanol mixture and stained with 1 :300 diluted mouse monoclonal antibody C7- 50 (Affinity BioReagents, USA) specific for the HCV core protein followed by staining with 1 :100 diluted Cy2-conjugated goat anti-mouse IgG (Jackson ImmunoResearch Laboratories, USA). Nuclei were then stained with DAPI (Sigma, Israel) and slides were washed with PBS, mounted (SouthernBiotech, USA) and examined using a fluorescence microscope.
Visualizing zymoxin-treated mixed population of uninfected and HCV infected cells :
[0198] See "Cell- viability assay "subsection.
Colony formation assay
[0199] 7.5x 10s 293 T-Rex cells were seeded per well in 6 wells plate. 24 hours later, cells were transfected with 2μgr of the plasmids "pmCherry (in EGFP C2 backbone)- MazF-full JFH NS5AB-linker-inhibitor peptide-ER", "pmCherry (in EGFP C2 backbone)" or "pEGFP- MazF" encoding for mCherry-NS3-activated MazF, mCherry (just the fluorescence protein) or EGFP- MazF (where MazF is not fused to its inhibitor peptide), respectively. Transfection was carried out using FuGENE 6 reagent (Roche, Germany) according to the manufacturer instructions. After 48 hours, transfection efficiency was assessed by fluorescence microscopy and was determined as equal between the three plasmids. Transfected cells were then trypsinized and seeded in 3 fold dilutions (starting from 150,000 cells/well) in 6 well plates and were incubated for 10 days in the presence of lmg/ml of G418 (to which all the three plasmids confer resistance). Surviving colonies were fixed with 4% formaldehyde in PBS and stained with Giemsa (sigma, USA). Cell- viability assay
[0200] The Cell-killing activities of NS3 activated MazF and uncleavable MazF zymoxins were measured by a Thiazolyl Blue Tetrazoliam Bromide (MTT) assay.
Cytotoxicity assay of intracellularly expressed mCherry-NS3 activated MazF or mCherry- uncleavable MazF in T-Rex 293 cells inducibly expressing EGFP-Full NS3-4A
[0201] Tet-inducible full NS3-4A, Tet-inducible full NS3-4A/constitutive NS3-activated MazF or Tet-inducible full NS3 -4 A/constitutive uncleavable MazF expressing cells were seeded in 96 well plates (2>< 104 cells per well). After 24 hours, cells were supplemented with serial 3 fold dilutions of tetracycline, starting with concentration on lOOOng/ml. 72 hours later, the media was replaced by fresh media (100 μΐ per well) containing 1 mg/ml MTT (Thiazolyl Blue Tetrazoliam Bromide (Sigma, Israel) dissolved in PBS) reagent and the cells were incubated for further 30 minutes. MTT-formazan crystals were dissolved by the addition of extraction solution (20% SDS, 50% N, N-Dimethyl Formamide (DMF), pH 4.7) (100 μΐ per well) and incubation for 16 hours at 37°C. Absorbance at 570 nm was recorded on an automated microtiter plate reader. The results were expressed as percentage of living cells relatively to the untreated controls.
Cytotoxicity assay of recombinant adenoviruses encoding for mCherry-NS3 activated MazF or mCherry-uncleavable-MazF on full NS3-4A expressing Huh7.5 cells
[0202] l x lO4 w.t or EGFP-full NS3-4A expressing Huh7.5 cells (Shapira et al, 2011) were seeded per well in 96 plates. After 24 hours, growth media were replaced by fresh media containing recombinant adenoviruses encoding for mCherry-NS3 activated MazF or mCherry-uncleavable-MazF at Multiplicity of infection (MOI) of ~3. Four days post infection, the media were replaced by fresh media (100 μΐ per well) containing 1 mg/ml MTT (except in representative wells in which cells were fixed and microscopically examined) and the cells were incubated for further 60 minutes. The next steps were identical to theses described above.
Cytotoxicity assay of recombinant adenoviruses encoding for mCherry-NS3 activated MazF or mCherry-uncleavable-MazF on a mixed culture of uninfected and HCV-infected Huh7.5 cells
[0203] Uninfected Huh7.5 cells and mixed population of HCV infected and uninfected cells at 1 : 1 ratio (50%> infected culture) were seeded in 96-well plates (l x lO4 cells/well). After 24 hours, cells were treated with recombinant adenoviruses (MOI of ~3) encoding for mCherry- NS3 activated MazF or mCherry-uncleavable-MazF zymoxins. Control cells remained untreated. 72 hours later, the media was replaced by fresh media (100 μΐ per well) containing 1 mg/ml MTT (except in representative wells in which cells were fixed and microscopically examined) and the cells were incubated for further 60 minutes. The next steps were identical to theses described above.
[0204] For HCV-infection immunofluorescence analysis, 3x 104 cells from the mixed HCV infected and uninfected culture were seeded per well into 8-well chamber slides (Nalge Nunc, USA). 24 hours later, cells were treated with recombinant adenoviruses (MOI of ~3) encoding for the mCherry-NS3 activated MazF or mCherry-uncleavable-MazF zymoxins. Control cells were left untreated. 72 hours post treatment, cells were fixed and permeabilized with 1 : 1 (v/v) acetone/methanol mixture and stained with 1 :300 diluted mouse monoclonal antibody C7-50 (Affinity BioReagents, USA) specific for the HCV core protein followed by staining with 1 :100 diluted FITC-conjugated goat anti-mouse IgG (Jackson ImmunoResearch Laboratories, USA). Nuclei were then stained with DAPI and slides were mounted (SouthernBiotech, USA) and examined using a fluorescence microscope. For each treatment, evaluation of the fraction of the HCV -infected cells from the general cell population was performed by dividing the number of the green, HCV-core positive cells, by the general number of cells (DAPI stained) from five representative microscopic fields.
[3H1 -leucine incorporation assay
[0205] l x lO5 Tet-inducible full NS3-4A/constitutive NS3-activated MazF or Tet-inducible full NS3 -4 A/constitutive uncleavable MazF expressing cells were seeded per well in a 24- wells plate. 24 or 48 hours later, cells were supplemented with tetracycline to a final concentration of 1 OOOng/ml, or left untreated. 72 hours after seeding, cells were supplemented with [3H]-leucine (Perkin Elmar, USA) to a final concentration of ^Ci/ml and returned to incubation. After 6 hours, cells were scraped, washed with PBS and lysed by four freeze/thaw cycles. 7μg total protein form the lysate of each treatment were then added to a solution containing PBS and a final concentration of 150μg bovine serum albumin (BSA) in a total volume of 75 μΐ. The solution was then precipitated by mixing with an identical volume of ice-cold 10% trichloro acetic acid (TCA). Mixtures were then incubated on ice for 30 minutes and centrifuged for 10 minutes at 20,000g, 4°C, after which the pellet was washed with ice- cold 5% TCA, followed by washing with ice-cold 80% ethanol. The pellet was then dissolved in 300μ1 of 0.1M NaOH, transferred to a scintillation tube and neutralized with 0.2ml 1M HC1. 4ml of scintillation liquid was added and radioactivity was counted by a beta-counter device.
EXAMPLE 1
The construction of MazF-based zytnoxin
[0206] For the construction of NS3-activated MazF based zymoxin, the MazF coding sequence was amplified from genomic DNA of E. coli strain XL-1 and was fused through its C terminus to the HCV P10-P10' NS3 cleavage sequence derived from the genotype 2a (strain JFH1) NS5A/B junction. A short inhibitory peptide corresponding to MazE C-terminal 35 amino-acids (which encompass the 23 amino-acids inhibitory peptide (MazEp) that has been described by Li et al. (Li et al, 2006)) was then fused, preceded by a short flexible linker, to the C terminus of the MazF-NS3 cleavage site sequence. A flexible linker, followed by the C- terminal ER membrane anchor of the tyrosine phosphatase PTP1B (Anderie et al., 2007) was than fused to the C terminus of the inhibitory peptide. Next, the whole construct was fused to the C terminus of the monomeric red fluorescence protein mCherry (see Fig. l). The rationale behind the design of this construct, which was denoted "mCherry-NS3 -activated MazF", was that the coupling between the ribonuclease and its antidote may enable high level of expression of the non-toxic fusion on the ER membrane of uninfected mammalian cells without causing any deleterious effect. In HCV infected cells, the fusion protein is expected to colocalize with the ER-bound viral NS3 protease (in infected cells, NS3 is localized to the cytosolic side of ER membranes and membranes of ER-like modified compartments) that cleaves the linker between the toxin and its inhibitory peptide. The toxic ribonuclease, no longer covalently tethered to its ER-anchored inhibitor, is now free to diffuse to the cytoplasm (which lacks the antidote) and exert its destructive activity. Finally, fusion to the fluorescence protein mCherry makes the whole construct trackable and facilitates the determination of its expression level and intracellular localization by fluorescence microscopy examination. As a control, an uncleavable construct (denoted "mCherry-uncleavable MazF", SEQ ID NO: 23) was constructed in which the NS3 cleavage sequence was replaced (underlined sequence within SEQ ID NO: 23) by a mutated 14 amino acids cleavage sequence (P10-P4') from HCV genotype la NS5A/B junction in which the P3 valine was substituted by alanine, the P2 cysteine by glycine, the PI cysteine by glycine and the P4' tyrosine by alanine (MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKG GPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVT QDSSLQDGEFIYKVKLRGTNFPSDGPVMQK TMGWEASSERMYPEDGALKGEIKQR LKLKDGGHYDAEVKTTYKAK PVQLPGAYNVNIKLDITSHNEDYTIVEQYERAEGRH STGGMDELY SGRTOISSMVSRYVPDMGDLIWVDFDPT GSEOAGHRPAVVLSPFM YNNKTGMCLCVPCTTQSKGYPFEVVLSGQERDGVALADQVKSIAWRARGATKKGT VAPEELOLIKAKINVLIGGSGADTEDVAGGSMSATWTGGGGSRKEPVFTLAELVNDIT PENLHENIDWGEPKDKEVWSSGGSGGGSGSGGSGLRSFLVNMCVATVLTAGAYLCY RFLFNSNT (SEQ ID NO: 23) (linkers are the double underlined segments). A schematic representation of the NS3-activated MazF-based zymoxin ("mCherry-NS3-activated MazF") and the hypothetical mechanism of its cleavage by NS3 protease on the cytoplasmic side of the ER membrane are shown in Fig. 1.
EXAMPLE 2
NS3 activated MazF is not toxic when expressed in naive cells
[0207] In order to verify that "mCherry-NS3-activated MazF" is not toxic to cells that do not express the NS3 protease (cells free of HCV), a colony formation assay was performed in which HEK 293 T-Rex cells where transfected with 2 μg of plasmids encoding either mCherry-NS3-activated MazF , mCherry (just the fluorescent protein) or EGFP- MazF (where MazF is not fused to its inhibitor peptide). 48 hours later, transfected cells were seeded in 3 fold dilutions and were treated with G418 (to which all three plasmids confer resistance). After 10 days of selection, surviving colonies were stained. As shown in Fig. 2, approximately the same number of surviving colonies was observed when the cells were transfected with the plasmids encoding mCherry-NS3-activated MazF or the red fluorescent protein alone, suggesting that expression of NS3 -activated ribonuclease in naive HEK 293 T-Rex cells (that do not express NS3) causes minimal toxicity, if any. As expected, growth was severely inhibited when cells were transfected with the EGFP-fused active toxin (EGFP-MazF).
EXAMPLE 3
The ER-targeted zymoxin colocalizes with NS3 protease in vivo
[0208] For the next cell-transfection experiments, HEK293 cell line which inducibly express (by addition of tetracycline) a fusion between EGFP and the coding sequence of the full length NS3 (including the helicase domain) followed by NS4A from la HCV genotype (Shapira et al, 2011) was used. The above cells, denoted "Tet-inducible full NS3-4A expressing cells", were stably transfected with plasmids encoding the NS3-activated zymoxin "mCherry-NS3- activated MazF" or its uncleavable control ("mCherry-uncleavable MazF"). Following selection, clones that constitutively express high level of the cleavable construct (denoted "Tet-inducible full NS3-4A/constitutive NS3-activated MazF expressing cells") or the uncleavable control (denoted "Tet-inducible full NS3-4A/constitutive uncleavable MazF expressing cells") were isolated. For determination of the intracellular localization of the mCherry labeled ribonuclease relatively to the EGFP-labeled full NS3-4A, Tet-inducible full NS3 -4 A/constitutive uncleavable MazF expressing cells were induced for EGFP-full NS3-4A expression by supplementation with tetracycline (Fig. 3A). 24 hours later, nuclei were stained (Fig. 3B) and cells were visualized by confocal fluorescence microscopy. A clear colocalization of the two fluorescent fusion proteins was observed (Fig. 3D), confirming that indeed both the protease and the modified ribonuclease are targeted to the ER membrane, as discussed earlier (shown in Fig. 1).
EXAMPLE 4
NS3-mediated proteolytic activation MazF based zymoxin inhibits de-novo cellular protein synthesis
[0209] Tet-inducible full NS3-4A/constitutive NS3-activated MazF and Tet-inducible full NS3 -4 A/constitutive uncleavable MazF expressing cells were supplemented with tetracycline for 24 or 48 hours to induced NS3 expression, or left untreated. Levels of de-novo protein synthesis were than determined by 3H-leucine incorporation assay. As shown in Fig. 4, a complete shutoff in protein synthesis was observed as soon as 24 hours post NS3 induction in cells that express the cleavable construct, indicating proteolytic activation of the zymoxin. As expected, Protein synthesis was not impaired following NS3 induction in cells that express the uncleavable construct.
EXAMPLE 5
NS3-activated MazF eradicates cells that express the NS3 protease
[0210] In order to evaluate the potential of the NS3-cleavable MazF based zymoxin in eradication of NS3 expressing cells, three 96 plates were seeded with Tet-inducible full NS3- 4A, Tet-inducible full NS3-4A/constitutive NS3-activated MazF or Tet-inducible full NS3- 4A/constitutive uncleavable MazF expressing cells and were supplemented with 3 fold dilutions of tetracycline. After 72 hours, the relative fraction of viable cells was determined using an enzymatic MTT assay. As shown in Fig. 5B, the expression level of NS3 can be roughly tuned by modulation of the final tetracycline concentration in the growth media, with around 10 ng/ml as an intermediate concentration for induction of low NS3 expression level. Indeed, strong cytotoxicity was clearly evident when Tet-inducible full NS3-4A/constitutive NS3 -activated MazF expressing cells where treated with tetracycline concentrations as low as 4 ng/ml. No cytotoxic effect was detected when the controls Tet-inducible full NS3- 4A/constitutive uncleavable MazF (uncleavable construct in the presence of protease) or Tet- inducible full NS3-4A (protease only) expressing cells were similarly treated (Fig. 5A). These findings demonstrate the deleterious effect of the MazF based zymoxin specifically toward NS3 protease expressing cells, as well as its competence to be activated by very low cellular levels of protease. In order to obtain a visual insight at the cell level, Tet-inducible full NS3 -4 A/constitutive NS3-activated MazF and Tet-inducible full NS3-4A/constitutive uncleavable MazF expressing cells were supplemented with tetracycline at a final concentration of lOng/ml or 1000 ng/ml (for low and high induction levels of NS3 expression, respectively), or left untreated. 36 hours later, nuclei were stained and cells were examined under a fluorescent microscope. The results, shown in Figs. 6A-D (Fig. 6A- Tet-inducible full NS3 -4 A/constitutive uncleavable MazF with Tetracycline (lOOOng/ml); Fig. 6B- Tet- inducible full NS3-4A/constitutive NS3-activated MazF without Tetracycline; Fig. 6C- Tet- inducible full NS3-4A/constitutive NS3-activated MazF with Tetracycline (lOng/ml); Fig. 6D- Tet-inducible full NS3-4A/constitutive NS3-activated MazF with Tetracycline (1000ng/ml)) indicated that both lower and higher induction levels of NS3 protease caused growth inhibition and morphological changes such as rounding and nuclear shrinkage in cells that constitutively expresses the cleavable MazF. Furthermore, both green and red fluorescence were faint in these cells, probably due to the destructive ribonuclease activity of the cleaved toxin toward the NS3 protease and its own mRNA. As expected, none of the above observations was evident when these cells were not supplemented with tetracycline or when NS3 expression was induced to high level in cells that constitutively express the uncleavable toxin. EXAMPLE 6
Adenovirus-mediated delivery of mCherry-NS3 activated MazF encoding cassette specifically eradicates NS3 expressing hepatocytes
[0211] In order to achieve efficient DNA delivery into mammalian cells, the expression cassette encoding of mCherry-NS3 activated MazF was cloned into a "first generation" ΔΕ1/ΔΕ3 human type 5 adenoviral vector plasmid DNA by homologous recombination in bacteria (Siegall et al, 1997). Virus particles were propagated in HEK293 packaging cells as described in the "Materials and Methods" section. In addition, a control adenoviral vector was constructed for the delivery of a similar cassette that encodes for the uncleavable version of the construct (mCherry-uncleavable MazF). Red- fluorescent comet-like adeno virus-producing foci were apparent upon infection of packaging cells with both recombinant viruses (encoding cleavable or uncleavable constructs) (Figs. 7A-B, respectively). The production yields for both viruses were ~3>< 108 plaque forming units (PFU)/ml, after two "cycles" of virus amplification (see "materials and methods"). Figs. 7C-D shows the phase contrast images of Figs. 7A-B, respectively).
[0212] In order to evaluate the ability of adenovirus- mediated delivery of NS3 activated MazF encoding cassette to eradicate NS3 expressing hepatocytes, w.t Huh7.5 hepatoma cells and our previously described EGFP-full NS3-4A expressing Huh7.5 cells (Shapira et al, 2011) were infected with the NS3-activated or uncleavable MazF encoding viruses at MOI of ~3. As shown in Figs. 8A-B, infection with the NS3-activated zymoxin resulted in a considerable cytotoxic effect, decreasing viability of the protease expressing cells to less than 40% relatively to uninfected control. In contrast, infection of w.t Huh7.5 cells with the same MOI did not cause a significant cytotoxic effect. As expected, no enhanced cytotoxicity against NS3 expressing Huh7.5 cells (relatively to w.t Huh7.5 cells) was observed upon infection with the uncleavable MazF encoding viruses.
EXAMPLE 7
Adenovirus-mediated delivery of NS3 activated MazF encoding cassette specifically eradicates HCV infected hepatocytes
[0213] In order to test the competence of the MazF based zymoxin to specifically eradicate HCV infected hepatocytes, the currently used models to study hepatitis C virus in which recombinant infectious HCV particles are produced in cell culture (HCVcc) based on Huh7 (or Huh7.5) hepatoma cell line (for review, see (Bartenschlager and Sparacio, 2007; Tellinghuisen et al, 2007) was used. As the main purpose of zymoxins based treatment is the specific eradication of HCV infected cells from a background of healthy tissue, "mixed culture" experiments were conducted. In these experiments, Huh7.5 hepatoma cells were infected with the HCV la/2a chimeric virus HJ3-5 (encoding the structural proteins of genotype la strain H77S within the background of genotype 2a strain JFH1) (Yi et al., 2007). When infection reached -50% (about 50% of the cultured cells showed expression of the HCV-core protein, as detected by immunostaining and fluorescence microscopy analysis; see "Materials and Methods"), the mixed culture (and a control of uninfected cells) were treated with NS3 activated MazF and uncleavable-MazF encoding adenoviruses at MOI of ~3. 72 hours post adenoviral infection; viability assay and microscopic examination that included immunostaining for HCV-core protein were performed. As shown, treating the mixed culture with NS3-activated MazF encoding adenovirus reduced the viable cells population to about 65% relatively to the untreated control; while viability of the uninfected cells ("HCV negative") was barely affected by this treatment (Fig. 9). Microscopic examination of the treated mixed culture (Figs. 10A-F) revealed two cell populations that differ in their appearance. While one population is characterized by "typical" Huh7.5 cell morphology (hollow arrows, Fig. IOC), the other is composed of partially detached cells with round, condensed or distorted shape (filled arrows, Fig. IOC) that are hypothesized to be zymoxin- intoxicated HCV infected cells. In order to validate this, the fraction of HCV infected cells from the general population was evaluated by immunofluorescence analysis using anti-HCV core protein specific antibodies (Fig. 1 1). Indeed, treatment with the NS3-activated zymoxin (Fig. 11C) showed a "curing effect" upon the partially infected culture, considerably reducing the fraction of the HCV infected cells from the general population. No significant effect upon the HCV infected cell population was observed following treatment with the uncleavable zymoxin (Fig. 11B) which appear similar to the untreated cells shown in Fig. 11 A. The results are further presented in Fig. 12, which show a bar graph illustrating the results obtained in accordance to the experimental procedure described in FIG 11, whereby the fraction (given in percentage) of the HCV-infected cells from the general cell population was evaluated, for each treatment, by dividing the number of the green, HCV-core positive cells by the general number of cells (DAPI stained).
[0214] An essential step in the replication cycle of many viruses is the processing of a polyprotein precursor by a viral-encoded protease. A partial list of human diseases associated viruses encoding protease(s) in their genome include flaviviruses such as hepatitis C virus (HCV), West Nile virus (WNV), dengue fever virus (DFV) and yellow fever virus (YFV); retroviruses such as HIV-1, picornaviruses such as coxsackievirus, poliovirus and hepatitis A virus, nidoviruses such as coronaviruses (CoV), including the severe acute respiratory syndrome (SARS) causative SARS-CoV and herpesviruses such as varicella-zoster virus (VZV) and Epstein-Bar virus (EBV).
[0215] In the current study, MazF, an endoribonuclease was chosen together with its polypeptidic antidote, MazE. In order to convert MazF into a zymoxin, a fusion polypeptide was constructed in which an inhibitory peptide derived from the MazE antitoxin was fused to the C terminus of the MazF toxin via an NS3-cleavable linker. Regarding the issue of incomplete inhibition of zymoxin' s activity in uncleaved form, it should be mentioned that in contrast to previous constructs, in which a "rationally designed" peptide is appended to provide the inhibition of the toxin's activity; in the MazF based-zymoxin, a "natural" inhibitory polypeptide was chosen for that purpose. Antidote polypeptides in toxin-antitoxin systems strongly inhibit the destructive activity of their toxic counterparts. Thus, a very efficient inhibition was achieved when using them as inhibitor peptides in the construction of zymoxins. Indeed, the current results show that the fused MazE-derived inhibitory peptide diminishes the toxin's activity to such an extent that enables its non-lethal overexpression in na'ive cells.
[0216] In further improvement, an ER membrane "anchoring peptide" that was fused to the C terminus of the construct, subsequently to the MazE derived inhibitory peptide improved the responsiveness of the zymoxin to the presence of low levels of cellular-expressed viral protease. This also enabled a co-localization between the ER-bound NS3 protease and its zymoxin substrate thus maximizing cleavage efficiency. Indeed, such a colocalization could be observed, as shown above. Moreover, activation of the zymoxin was evident also upon expression of very low cellular levels of the viral protease.
[0217] Using a recombinant adenoviral vector gene-delivery system, a specific eradication of full NS3-4A expressing Huh7.5 cells, sparing "na'ive" cells which do not express the protease, was demonstrated. Furthermore, specific eradication of HCV infected cells was also achieved using the described adenoviral gene delivery system, demonstrating a prominent "curing effect" when tested on a mixed cultures of healthy and HCV infected hepatocytes. Delivery of a transgene encoding for a foreign protein which has no endogenous counterpart in target cells, such as MazF, may reduce that risk. Furthermore, it should be remembered that MazF possess a ribonuclease activity that is also capable of processing multiple potential cleavage sites in the HCV genome. Although not evaluated in this study, a direct attack on the parasite's genetic material may represent an additional mode of anti-viral activity that works in parallel with host-cell protein synthesis shutoff
[0218] Of note, the applicability and the described zymoxin can be extended to eradication of cells that are infected with protease expressing viruses other than HCV (a partial list of protease expressing viruses is given herein). This can be done by replacing the cleavage sequence that separates between the toxic moiety and the inhibitory peptide to one that is sensitive to a predetermined viral protease. In addition, one may replace the C terminal ER anchoring peptide with sequence that tethers the construct to a destined intracellular location in which the viral protease resides. That way, co-localization between the zymoxin and the predetermined viral protease may be achieved.
[0219] In conclusion, the presented anti-viral agent was designed under the previously described "zymoxins" concept in which a constitutively active toxin is converted into a "zymogenized", viral-protease activated from. The MazF-based zymoxin, that is delivered into target cells by means of adenovirus mediated gene delivery, shows very low toxicity to naive cells and enhanced responsiveness to low viral-protease expression level, when compared to our previously presented constructs. In fact, while the DTA based zymoxins had a therapeutic index of >40 in Tet-induced NS3 expressing cells and 17.5 in HCV infected Huh7.5 cells, and while RTA based zymoxins had a therapeutic index of 38 in Tet-induced NS3 expressing cells and 8 in HCV infected Huh7.5 cells, the MazF-based zymoxin has a much better safety profile since it is essentially non toxic to naive cells that do not express the NS3 protease. As evident from the results presented herein, the MazF based zymoxin eradicates NS3-expressing model cells and HCV infected cells with remarkable efficiency and specificity, providing further proof to the concept of zymoxins and a potential new means of fighting viral diseases.
EXAMPLE 8
The C-terminal ER membrane anchor of the tyrosine phosphatase PTP1B is essential for the polypeptide's activity
[0220] In this experiment, the significance of the ER anchoring peptide (which in this study was derived from the tyrosine phosphatase PTP1B) to the activity of the polypeptide was evaluated. As shown in Fig. 14, a polypeptide missing the ER anchoring peptide is substantially ineffective in induction of cell death in the concentrations range tested. These results demonstrate that the ER anchoring peptide is absolutely essential for the polypeptide's activity in eradication of full NS3-4A protease expressing cells. Thus, the present polypeptide utilizing a zymoxin of an endogenous toxin-antitoxin system requires the ER anchoring peptide in order to colocalize the zymoxin with the protease (thus enhancing cleavage efficiency) and physically separate (compartmental separation), following cleavage, the toxin from the antitoxin thus enabling the toxin's activity.
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Claims

1. A chimeric polypeptide comprising a toxin, a protease cleavage site attached to the carboxy terminus of said toxin, an endogenous anti-toxin attached to the carboxy terminus of said protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of said anti-toxin.
2. The polypeptide of claim 1, wherein said toxin comprises a toxin selected from: MazF, HicA, YhaV, MqsR, RnlA, YafO, HigB, RatA, YeeU, Ykfl, YpjF, GnsA, HipA, YjhX, YdaS, and fragments thereof.
3. The polypeptide of claim 1, wherein said toxin comprises the amino acid sequence of SEQ ID NO: 1.
4. The polypeptide of claim 1, wherein said anti-toxin comprises an anti-toxin selected from MazE, HicB, prlF, MqsA, RnlB, YafN, HigA, YfjF, CbtA, YafW, YfjZ, YmcE, HipB, YjhQ, YdaT, and fragments thereof.
5. The polypeptide of claim 1, wherein said anti-toxin comprises the amino acid sequence of SEQ ID NO: 2.
6. The polypeptide of claim 1, wherein said subcellular anchoring domain comprises an ER anchoring domain.
7. The polypeptide of claim 6, wherein said ER anchoring domain comprises an amino acid sequence as set forth by SEQ ID NO:3, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, or SEQ ID NO: 31.
8. The polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO: 4.
9. The polypeptide of claim 1, further comprising a fluorescent protein attached to the amino terminus of said toxin.
10. The polypeptide of claim 1, wherein at least one of said cleavage site is attached to the carboxy terminus of said toxin via a linker, said endogenous anti-toxin is attached to the carboxy terminus of said cleavage site via a linker, said subcellular anchoring domain is attached to the carboxy terminus of said anti-toxin via a linker, or any combination thereof.
11. The polypeptide of claim 10, wherein said linker is an amino acid or a peptide comprising 2-25 amino acids.
12. The polypeptide of claim 1, further comprising a signal peptide.
13. A composition comprising the polypeptide of claim 1 and a carrier.
14. A polynucleotide comprising a coding portion encoding a polypeptide, said polypeptide comprises a toxin, a protease cleavage site attached to the carboxy terminus of said toxin, an endogenous anti-toxin attached to the carboxy terminus of said protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of said anti-toxin.
15. The polynucleotide of claim 14, wherein at least one of said cleavage site is attached to the carboxy terminus of said toxin via a linker, said endogenous anti-toxin is attached to the carboxy terminus of said cleavage site via a linker, said ER anchoring domain is attached to the carboxy terminus of said anti-toxin via a linker, or any combination thereof, wherein said linker is an amino acid or a peptide comprising 2-25 amino acids.
16. The polynucleotide of claim 14, wherein said toxin comprises a toxin selected from:
MazF, HicA, YhaV, MqsR, RnlA, YafO, HigB, RatA, YeeU, Ykfl, YpjF, GnsA, HipA, YjhX, YdaS, and fragments thereof.
17. The polynucleotide of claim 14, wherein said toxin comprises the amino acid sequence of SEQ ID NO: 1.
18. The polynucleotide of claim 14, wherein said anti-toxin comprises an anti-toxin selected from MazE, HicB, prlF, MqsA, RnlB, YafN, HigA, YfjF, CbtA, YafW, YfjZ, YmcE, HipB, YjhQ, YdaT, and fragments thereof.
19. The polynucleotide of claim 14, wherein said anti-toxin comprises the amino acid sequence of SEQ ID NO: 2.
20. The polynucleotide of claim 14, wherein said subcellular anchoring domain comrises an ER anchoring domain.
21. The polynucleotide of claim 20, wherein said ER anchoring domain comprises the amino acid sequence as set forth by SEQ ID NO:3, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, or SEQ ID NO: 31.
22. The polynucleotide of claim 14, wherein said polypeptide comprises the amino acid sequence of SEQ ID NO: 4.
23. The polynucleotide of claim 14, wherein said polypeptide further comprises a fluorescent protein attached to the amino terminus of said toxin.
24. An expression vector comprising the polynucleotide of claim 14.
25. A cell comprising the expression vector of claim 24.
26. A composition comprising the expression vector of claim 25.
27. A method for eliminating a cell, comprising the step of contacting said cell with: (1) a polypeptide comprising a toxin, a protease cleavage site attached to the carboxy terminus of said toxin, an endogenous anti-toxin attached to the carboxy terminus of said protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of said anti-toxin; or (2) a vector comprising a polynucleotide, said polynucleotide comprises a coding portion encoding a polypeptide, said polypeptide comprises a toxin, a hepatitis C virus protease cleavage site attached to the carboxy terminus of said toxin, an endogenous anti-toxin attached to the carboxy terminus of said protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of said anti-toxin, wherein said cell comprises a protease directed against said protease cleavage site, thereby eliminating a cell.
28. The method of claim 27, wherein said toxin comprises a toxin selected from: MazF, HicA, YhaV, MqsR, RnlA, YafO, HigB, RatA, YeeU, Ykfl, YpjF, GnsA, HipA, YjhX, YdaS, and fragments thereof.
29. The method of claim 27, wherein said toxin comprises the amino acid sequence of SEQ ID NO: 1.
30. The method of claim 27, wherein said anti-toxin comprises an anti-toxin selected from MazE, HicB, prlF, MqsA, RnlB, YafN, HigA, YfjF, CbtA, YafW, YfjZ, YmcE, HipB, YjhQ, YdaT, and fragments thereof.
31. The method of claim 27, wherein said anti-toxin comprises the amino acid sequence of SEQ ID NO: 2.
32. The method of claim 27, wherein said subcellular anchoring domain comrises an ER anchoring domain..
33. The method of claim 32, wherein said ER anchoring domain comprises the amino acid sequence as set forth by SEQ ID NO:3, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, or SEQ ID NO: 31.
34. The method of claim 27, wherein said polypeptide comprises the amino acid sequence of SEQ ID NO: 4.
35. The method of claim 27, wherein said vector is an adenovirus vector.
36. A method for treating a subject infected with a protease bearing virus, comprising the step of administering to said subject: (1) a polypeptide comprising a toxin, a protease cleavage site attached to the carboxy terminus of said toxin, an endogenous anti-toxin attached to the carboxy terminus of said protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of said anti-toxin; or (2) a vector comprising a polynucleotide, said polynucleotide comprises a coding portion encoding a polypeptide, said polypeptide comprises a toxin, a hepatitis C virus protease cleavage site attached to the carboxy terminus of said toxin, an endogenous anti-toxin attached to the carboxy terminus of said protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of said anti-toxin, thereby treating a subject infected with a protease bearing virus.
37. The method of claim 36, wherein said virus is hepatitis C virus (HCV), West Nile virus (WNV), dengue fever virus (DFV), yellow fever virus (YFV), HIV-1, coxsackievirus, poliovirus hepatitis A virus, coronaviruses (CoV), including the severe acute respiratory syndrome (SARS) causative SARS-CoV, varicella-zoster virus (VZV), or Epstein-Bar virus (EBV).
38. The method of claim 36, wherein said toxin comprises a toxin selected from: MazF, HicA, YhaV, MqsR, RnlA, YafO, HigB, RatA, YeeU, Ykfl, YpjF, GnsA, HipA, YjhX, YdaS, and fragments thereof.
39. The method of claim 36, wherein said toxin comprises the amino acid sequence of SEQ ID NO: 1.
40. The method of claim 36, wherein said anti-toxin comprises an anti-toxin selected from MazE, HicB, prlF, MqsA, RnlB, YafN, HigA, YfjF, CbtA, YafW, YfjZ, YmcE, HipB, YjhQ, YdaT and fragments thereof.
41. The method of claim 36, wherein said anti-toxin comprises the amino acid sequence of SEQ ID NO: 2.
42. The method of claim 36, wherein said subcellular anchoring domain comrises an ER anchoring domain.
43. The method of claim 42, wherein said ER anchoring domain comprises the amino acid sequence as set forth by SEQ ID NO:3, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, or SEQ ID NO: 31.
44. The method of claim 36, wherein said polypeptide comprises the amino acid sequence of SEQ ID NO: 4.
45. The method of claim 36, wherein said vector is an adenovirus vector.
46. A method for treating a subject afflicted with Hepatitis C, comprising the step of administering to said subject: (1) a polypeptide comprising a toxin, a protease cleavage site attached to the carboxy terminus of said toxin, an endogenous anti-toxin attached to the carboxy terminus of said protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of said anti-toxin; or (2) a vector comprising a polynucleotide, said polynucleotide comprises a coding portion encoding a polypeptide, said polypeptide comprises a toxin, a hepatitis C virus protease cleavage site attached to the carboxy terminus of said toxin, an endogenous anti-toxin attached to the carboxy terminus of said protease cleavage site, and a subcellular anchoring domain attached to the carboxy terminus of said anti-toxin, thereby treating a subject afflicted with Hepatitis C.
47. The method of claim 46, wherein said toxin comprises a toxin selected from: MazF, HicA, YhaV, MqsR, RnlA, YafO, HigB, RatA, YeeU, Ykfl, YpjF, GnsA, HipA, YjhX, YdaS, and fragments thereof.
48. The method of claim 46, wherein said toxin comprises the amino acid sequence of SEQ ID NO: 1.
49. The method of claim 46, wherein said anti-toxin comprises an anti-toxin selected from MazE, HicB, prlF, MqsA, RnlB, YafN, HigA, YfjF, CbtA, YafW, YfjZ, YmcE, HipB, YjhQ, YdaT, and fragments thereof.
50. The method of claim 46, wherein said anti-toxin comprises the amino acid sequence of SEQ ID NO: 2.
51. The method of claim 46, wherein said subcellular anchoring domain comrises an ER anchoring domain.
52. The method of claim 46, wherein said ER anchoring domain comprises the amino acid sequence as set forth by SEQ ID NO:3, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, or SEQ ID NO: 31.
53. The method of claim 46, wherein said polypeptide comprises the amino acid sequence of SEQ ID NO: 4.
54. The method of claim 46, wherein said vector is an adenovirus vector.
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