RU2788628C2 - Activin receptor-like kinase inhibitors - Google Patents

Abstract

FIELD: activin receptor-like kinase-2 inhibitors.

SUBSTANCE: invention relates to inhibitors of activin receptor-like kinase-2 (ALK2). A compound of formula (I) or a pharmaceutically acceptable salt thereof is provided, wherein ring A is selected from phenyl, a 5-6-membered monocyclic heteroaryl containing 1-3 ring heteroatoms selected from O, N and S, quinolinyl and an 8-10-membered bicyclic a heterocyclyl containing 1-3 ring heteroatoms selected from O, N and S, where only one ring of said bicyclic heterocyclyl is aromatic; R² is a bond or -O-; R³ is selected from C₁-C₆ alkyl, -(C₀-C₃ alkylene)-(C₃-C₆ carbocyclyl) and -(C₀-C₁ alkylene)-(4-6 membered monocyclic O-containing or 4-membered S-containing heterocyclyl) ; R⁴ is selected from hydrogen, C₁-C₂ alkyl, C₃ alkynyl, -C(O)-(C₂ alkyl), halogen and cyano; n is 0, 1, 2 or 3; and p is 1 or 2. Specific compounds and uses of the compounds for the treatment of specific diseases are also provided.

EFFECT: obtaining inhibitors of activin receptor-like kinase-2 (ALK2).

26 cl, 3 tbl, 11 ex

Description

[0001] The present disclosure relates to activin receptor-like kinase-2 (ALK2) inhibitors.

[0002] The present application claims priority under pending US Patent Application Serial No. 62/574,200, filed October 18, 2017; which is incorporated herein in its entirety.

[0003] Activin receptor-like kinase-2 (ALK2) is encoded by the activin A receptor type I (ACVR1) gene. ALK2 is a serine/threonine kinase in the bone morphogenetic protein (BMP) pathway (Shore et al., Nature Genetics 2006, 38:525-27). It binds to complexes containing bone morphogenetic proteins (BMPs) and is responsible for BMP transduction signals. Several mutations in ALK2 cause constitutive kinase activity and are associated with various diseases. Fibrodysplasia ossificans progressive (FOP) is a rare, severe, debilitating hereditary disease characterized by progressive heterotopic ossification in areas outside the skeleton. In individuals with this disease, mobility is significantly reduced and life expectancy is shortened. Modern therapy is limited to reducing edema (exacerbations) that are characteristic of this disease.

[0004] All FOP patients carry heterozygous activating mutations in the ACVR1 gene. In addition, the vast majority of FOP patients have the same R206H mutation in ALK2. Transgenic mice that express ALK2 R206H mimic key features of human disease, including malformation of the hind limb thumb, inflammatory infiltration, and muscle cell apoptosis followed by heterotopic bone formation via the endochondral pathway (Chakkalakal et al., J Bone Miner Res. 2012, 27 (8): 1746-1756). A second genetically engineered mouse strain was developed that expresses an activated ALK2-Q207D variant in muscle and phenocopies of key human FOP features. Treatment of these mice with a BMP type 1 receptor kinase inhibitor resulted in inhibition of SMAD signaling and reduction in ectopic ossification and associated functional impairment (Fukuda et al., Genesis 2006, 44, 159-167). Other mutations in ALK2 that are associated with FOP include, but are not limited to, L196P, PF197-8L, R202I, R258S, R258G, G328A, G328W, G328E, G328R, G356D, and R375P (Kaplan et al., Hum Mutat. 2009, 30 (3): 379 - 390; Gregson et al., Bone 2011, 48:654-658; Kaplan et al., Am J Med Genet 2015, 167: 2265-2271; Petrie et al., PLoS One 2009, 4( 3): e5005; Bocciardi et al., Eur J Hum Genetics 2009, 17:311-318; Pacifici and Shore, Cytokine & Growth Factor Reviews 2016, 27:93-104).

[0005] In some cases, heterotopic ossification (HO) can also be induced in humans with wild-type ALK2. These cases may include osteochondromas, major surgery, trauma (such as head trauma or blast injury), prolonged immobilization, or severe burns. Debilitating HO can occur in diseases such as hereditary multiple exostoses. An ALK2 inhibitor has the potential to be an effective therapy for the treatment of FOP and other conditions caused by HO.

[0006] Diffuse brainstem glioma (DIPG) is a rare, aggressive, and correctly fatal pediatric malignant brainstem tumor with no effective treatment options. Due to its anatomical location and diffuse nature, DIPG cannot be surgically treated. DIPG occurs exclusively in young children, and the two-year survival rate is approximately less than 10%. Due to their location in the brainstem, DIPGs put pressure on the cranial nerves resulting in double vision, difficulty in controlling eye movement, difficulty in chewing and/or swallowing, and weakness in the arms and or legs leading to loss of ability to movement and difficulty speaking. As the tumor progresses, pressure builds up inside the skull, causing severe headaches, nausea/vomiting, and fatigue. Unlike many other types of malignant tumors in children, little progress has been made in the past few decades in improving the treatment of DIPG. Historically, a lack of understanding regarding the driving factors of DIPG has hindered the identification of potential new treatment options. Consequently, the medical need for therapies for DIPG is extremely high. Recent genomic characterization has demonstrated that approximately 25% of DIPG tumors have somatic, heterozygous ALK2 activating mutations. Mutations in ALK2 associated with DIPG include, but are not limited to, R206H, G328V, G328W, G328E, and G356D (Jones and Baker, Nature Rev Cancer 2014, 14:651-661).

[0007] Notably, ALK2 mutations found in DIPG overlap with mutations found in FOP, indicating potential synergy between inhibitor development efforts for the two diseases (e.g., through overlapping screening funnel plot and chemical efforts). The finding that a significant proportion of DIPG contains activating ALK2 mutations suggests that ALK2 inhibitors may be clinically useful in patients with DIPG.

[0008] Anemia in chronic disease, inflammation, or cancer may develop in the setting of a chronic inflammatory, infectious, or neoplastic disease. In this form of anemia, inflammatory cytokines induce hepatic expression of hepcidin, which suppresses iron bioavailability by inactivating ferroportin. Hepcidin is transcriptionally regulated by bone morphogenetic protein (BMP) signaling. Inhibition of BMP phosphorylation via ALK2 inhibition can modulate BMP-mediated signaling, thereby reducing hepcidin expression. Decreasing hepcidin expression may be an effective strategy for the treatment of anemia in chronic disease, inflammation, or cancer.

[0009] The present disclosure relates to ALK2 inhibitors and ALK2 mutants, eg, ALK2 mutants, as defined herein, eg, inhibitors of formula (I) and their pharmaceutically acceptable salts and compositions. The present disclosure further relates to methods of using the compounds of the present disclosure and their pharmaceutically acceptable salts and compositions to inhibit ALK2 activity or ALK2 mutants in a cell or patient. The present disclosure further relates to methods of using the compounds of the present disclosure and their pharmaceutically acceptable salts and compositions for the treatment of a subject or patient suffering from a condition mediated by aberrant ALK2 activity, such as at least one of fibrodysplasia ossificans progressive (FOP) , or heterotopic ossification, or diffuse brainstem glioma (DIPG), or anemia in chronic disease, or anemia in inflammation, or anemia in malignancy.

[0010] According to one aspect, the present disclosure relates to a compound of formula (I) or at least one pharmaceutically acceptable salt thereof:

where each ring A, R ¹ , R ² , R ³ , R ⁴ and n are defined in the present invention.

[0011] According to another aspect, the present disclosure relates to pharmaceutical compositions containing a compound of formula (I), or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.

[0012] According to another aspect, the present disclosure relates to a method for treating or alleviating progressive fibrodysplasia ossificans in a subject. In some embodiments, said method comprises administering to said subject a therapeutically effective amount of a compound of formula (I), or a pharmaceutically acceptable salt or composition thereof. In some embodiments, the subject has a mutation in the ALK2 gene that results in the expression of an ALK2 enzyme having at least one amino acid modification selected from L196P, PF197-8L, R202I, R206H, Q207E, R258S, R258G, G328A, G328W, G328E, G328R, G356D and R375P.

[0013] According to another aspect, the present disclosure relates to a method for treating or alleviating diffuse brainstem glioma in a subject. In some embodiments, said method comprises administering to said subject a therapeutically effective amount of a compound of formula (I), or a pharmaceutically acceptable salt or composition thereof. In some embodiments, the subject has a mutation in the ALK2 gene that results in the expression of an ALK2 enzyme having at least one amino acid modification selected from R206H, G328V, G328W, G328E, and G356D.

[0014] According to another aspect, the present disclosure relates to a method for inhibiting aberrant ALK2 activity in a subject. In some embodiments, said method comprises administering to said subject a therapeutically effective amount of a compound of formula (I), or a pharmaceutically acceptable salt or composition thereof. In some embodiments, the subject has a mutation in the ALK2 gene that results in the expression of an ALK2 enzyme having at least one amino acid modification selected from L196P, PF197-8L, R202I, R206H, Q207E, R258S, R258G, G328A, G328V, G328W, G328E, G328R, G356D and R375P.

[0015] The methods described herein may further include various evaluation steps before, during, and/or after treatment with a compound of the present disclosure. In some embodiments, before, during, and/or after treatment with a compound of the present disclosure, the method further comprises the step of evaluating, eg, imaging, heterotopic ossification in a subject. This can be achieved by spectroscopic analysis, eg magnetic resonance analysis, eg MRI, positron emission tomography (PET), microcomputed tomography (μCT), or by histology.

[0016] In some embodiments, the methods include assessing the pre-treatment or baseline level of heterotopic ossification in a subject, e.g., using spectroscopic analysis, e.g., magnetic resonance-based analysis, e.g., MRI, positron emission tomography (PET), microcomputed tomography (μCT), or by histology. In some embodiments, the methods further comprise administering to the subject a compound according to the present disclosure; assessing the level after treatment of heterotopic ossification, for example, using spectroscopic analysis, for example, analysis based on magnetic resonance, for example, MRI, positron emission tomography (PET), microcomputed tomography (μCT), or using histology; comparing the subject's post-treatment level of heterotopic ossification with the pre-treatment or baseline level of heterotopic ossification and determining whether treatment should continue, e.g. using spectroscopic analysis, e.g. magnetic resonance analysis, e.g. MRI, positron emission tomography (PET), microcomputed tomography (μCT), or by histology.

[0017] In some embodiments, heterotopic ossification is preceded by edema, such as prolonged edema.

[0018] As used herein, the terms “patient,” “subject,” “individual,” and “recipient” refer to either a human or non-human animal suffering or suspected of suffering from a disease or disorder associated with aberrant ALK2 activity (i.e., i.e. aberrant ALK2 activity due to a mutation in the ALK2 gene that results in the expression of an ALK2 enzyme having an amino acid modification) or aberrant ALK2 biological activity.

[0019] As used herein, the terms "treat", "treatment", and "process of treating" such a disease or disorder refer to alleviating at least one symptom of the disease or disorder described herein. These terms, when used in conjunction with a condition such as fibrodysplasia ossificans progressive, refer to one or more of the control of heterotrophic bone growth rate; reducing pain and inflammation associated with new bone development; prolongation of the expected survival time of the patient; reducing the size or number of heterotopic bone growth lesions; maintaining or improving mobility; prevention or treatment of new exacerbations; inhibiting the development of new lesions of heterotopic bone; enabling surgical intervention to remove existing heterotopic ossifications to restore limb function and/or mobility; increased survival; increased survival without progression of the disease; increasing time to progression; inhibition of edema caused by FOP-related damage and/or improvement in quality of life. When used in conjunction with a condition such as diffuse brainstem glioma, these terms refer to one or more of preventing glioma growth, causing reduction in glioma mass or volume, prolonging patient survival time, inhibiting growth of glial tissue, reducing glial tumor mass, reducing the size or number of metastatic lesions, inhibiting the development of new metastatic lesions, prolonging survival, prolonging progression-free survival, prolonging time to progression, and/or improving quality of life.

[0020] As used herein, the term "therapeutic effect" refers to a beneficial local or systemic effect in animals, in particular mammals, and more specifically humans, caused by the administration of a compound or composition according to the present disclosure. The phrases "therapeutically effective amount" and "pharmaceutically effective amount" are used interchangeably and mean that amount of a compound or composition according to the present disclosure that is effective in treating a disease or condition associated with aberrant ALK2 activity, with a reasonable balance of benefit and risk. A therapeutically effective amount of such a substance will vary, for example, depending on the subject and the disease state being treated, the subject's weight and age, the severity of the disease state, the route of administration, etc., as can be readily determined by one of ordinary skill in the art.

[0021] As used herein, "aliphatic group" refers to a straight chain, branched chain, or cyclic hydrocarbon group, and includes saturated and unsaturated groups such as an alkyl group, an alkenyl group, or an alkynyl group.

[0022] As used herein, "alkenyl" refers to an aliphatic group containing at least one double bond.

[0023] "Alkylene" refers to a divalent radical of an alkyl group, such as -CH ₂ -, -CH ₂ CH ₂ - and -CH ₂ CH ₂ CH ₂ -.

[0024] As used herein, "alkynyl" refers to a straight or branched hydrocarbon chain containing two to twelve carbon atoms, and is characterized in that it contains one or more triple bonds. Examples of alkynyl groups include, without limitation, ethynyl, propargyl, and 3-hexynyl. One of the carbons of the triple bond may optionally be the point of attachment of the alkynyl substituent.

[0025] "Alkyl" or "alkyl group" refers to a monovalent radical of a saturated straight or branched hydrocarbon, such as a straight or branched group of 1-12, 1-10, or 1-6 carbon atoms, referred to herein as C ₁ -C ₁₂ alkyl, C ₁ -C ₁₀ alkyl and C ₁ -C ₆ alkyl, respectively. Example alkyl groups include, without limitation, methyl, ethyl, propyl, isopropyl, 2-methyl-1-propyl, 2-methyl-2-propyl, 2-methyl-1-butyl, 3-methyl-1-butyl, 2- methyl-3-butyl, 2,2-dimethyl-1-propyl, 2-methyl-1-pentyl, 3-methyl-1-pentyl, 4-methyl-1-pentyl, 2-methyl-2-pentyl, 3- methyl-2-pentyl, 4-methyl-2-pentyl, 2,2-dimethyl-1-butyl, 3,3-dimethyl-1-butyl, 2-ethyl-1-butyl, butyl, isobutyl, tert-butyl, pentyl, isopentyl, neopentyl, hexyl, heptyl and octyl.

[0026] "Aromatic" when referring to a ring refers to a fully conjugated, unsaturated ring that contains (4n + 2π) electrons and is often characterized by structural formulas that show alternating double and single bonds. Aromatic rings include both aryl rings (eg, benzene) and heteroaryl rings (eg, rings containing one or more heteroatoms selected from N, O, and S).

[0027] "Aryl" refers to a monocyclic, bicyclic or polycyclic hydrocarbon ring system, where at least one ring is aromatic.

[0028] "Halogen" refers to any halogen radical, such as -F, -Cl, -Br, or -I.

[0029] "Carbocyclic ring system" refers to a monocyclic, bicyclic, or polycyclic hydrocarbon ring system where each ring is either fully saturated or contains one or more unsaturation units, but where neither ring is aromatic.

[0030] "Carbocyclyl" refers to a monovalent radical of a carbocyclic ring system. Illustrative carbocyclyl groups include cycloalkyl groups (eg, cyclopentyl, cyclobutyl, cyclopentyl, cyclohexyl, and the like) and cycloalkenyl groups (eg, cyclopentenyl, cyclohexenyl, cyclopentadienyl, and the like). As used herein, carbocyclyls are monovalent radicals of partially saturated monocyclic, bicyclic, or polycyclic hydrocarbon ring systems containing an sp2 point of attachment to the remainder of the molecule.

[0031] "Cycloalkyl" refers to cyclic, bicyclic, tricyclic or polycyclic non-aromatic hydrocarbon groups containing from 3 to 12 carbon atoms. Any substituted ring atom may be substituted (eg, with one or more substituents). Cycloalkyl groups may contain fused or spiro rings. Fused rings are rings that share at least two common (carbon) atoms. Examples of cycloalkyl moieties include, without limitation, cyclopropyl, cyclohexyl, methylcyclohexyl, adamantyl, and norbornyl.

[0032] "Heteroalkyl" refers to a monovalent, straight or branched alkyl chain, where one methylene unit, excluding the methylene unit associated with the remainder of the molecule, is replaced by -O-, -S- or -N(R ^d ), where R ^d defined below. For complete clarity, the -CH ₂ -NH-CH ₃ moiety will be heteroalkyl, but -NH-CH ₂ -CH ₃ will not, since the NH group is linked to the remainder of the molecule.

[0033] "Heteroalkylene" refers to a divalent radical of a heteroalkyl group.

"Heteroaromatic ring system" refers to a monocyclic, bicyclic, or polycyclic ring system wherein at least one ring is aromatic, and contains at least one heteroatom (eg, N, O, or S); and where no other rings are heterocyclyl (as defined below). In some cases, a ring that is aromatic and contains a heteroatom contains 1, 2, 3 or 4 ring heteroatoms in such a ring.

[0034] "Heteroaryl" refers to a monovalent radical of a heteroaromatic ring system. Illustrative heteroaryl groups include ring systems where (i) each ring contains a heteroatom and is aromatic, e.g. , naphthyridinyl and pteridinyl; (ii) each ring is aromatic or carbocyclyl, at least one aromatic ring contains a heteroatom, and at least one other ring is a hydrocarbon ring or, for example, indolyl, isoindolyl, benzothienyl, benzofuranyl, dibenzofuranyl, indazolyl, benzimidazolyl, benzthiazolyl, quinolyl , isoquinolyl, cinnolinyl, phthalazinyl, quinazolinyl, hinocalinil, carbazolyl, acridinyl, phenazinyl, phenothiazinyl, phenoxazinyl, pyrido[2,3-b]-1,4-oxazin-3-(4H)-one, 5,6,7, 8-tetrahydroquinolyl and 5,6,7,8-tetrahydroisoquinolyl; and (iii) each ring is aromatic or carbocyclyl and at least one aromatic ring shares a heteroatom at the beginning of the bridge with another aromatic ring, eg 4H-quinolizinyl.

[0035] "Heterocyclic ring system" refers to a monocyclic, bicyclic and polycyclic ring system where at least one ring is saturated or partially unsaturated (but not aromatic) and that the ring contains at least one heteroatom. A heterocyclic ring system may be attached to its pendant group at any heteroatom or carbon atom resulting in a stable structure, and any of the ring atoms may be optionally substituted. Heterocyclic ring systems may be fused rings or spiro rings.

[0036] "Heterocyclyl" refers to a monovalent radical of a heterocyclic ring system. Exemplary heterocyclyls include ring systems in which (i) each ring is non-aromatic and at least one ring contains a heteroatom, e.g. , dioxolanil, diazepinil, oxazepinil, thiazepinil, morpholinyl and quinuclidinil; (ii) at least one ring is non-aromatic and contains a heteroatom and at least one other ring is an aromatic carbon ring, eg 1,2,3,4-tetrahydroquinolinyl, 1,2,3,4-tetrahydroisoquinolinyl; and (iii) at least one ring is non-aromatic and contains a heteroatom and at least one other ring is aromatic and contains a heteroatom, e.g., 3,4-dihydro-1H-pyrano[4,3-c]pyridine and 1, 2,3,4-tetrahydro-2,6-naphthyridine.

[0037] "Cyano" refers to the -CN radical.

[0038] "Hydroxy" or "hydroxyl" refers to -OH.

[0039] Certain compounds of the present disclosure may exist in particular geometric or stereoisomeric forms. This disclosure contemplates all such compounds, including cis- and trans-isomers, R- and S-enantiomers, diastereomers, (D)-isomers, (L)-isomers, racemic mixtures thereof, and other mixtures thereof, which fall within the scope of this disclosure. . Additional asymmetric carbon atoms may be present on a substituent such as an alkyl group. All such isomers, as well as mixtures thereof, are intended to be included in the present disclosure. Thus, if a disclosed compound is named or depicted by a structure without defining stereochemistry and contains one or more chiral centers, it is understood that it represents all possible stereoisomers of the compound as well as enantiomeric mixtures thereof. If a disclosed compound is named or depicted by a structure with stereochemistry defined at each chiral center, it is understood that it only represents a compound with designated stereochemistry at such chiral centers. However, if a disclosed compound defines stereochemistry at some but not all chiral centers, it is understood that it represents all possible stereoisomers at undefined chiral centers of the compound, as well as enantiomeric mixtures thereof.

[0040] If, for example, a particular enantiomer of a compound of the present disclosure is desired, it can be obtained by asymmetric synthesis or derivation with a chiral auxiliary, where the resulting diastereomeric mixture is separated and the auxiliary group is cleaved off to give the pure desired enantiomers. Alternatively, if the molecule contains a basic functional group such as amino or an acidic functional group such as carboxyl, diastereomeric salts are formed with the appropriate optically active acid or base, followed by cleavage of the diastereomers thus formed by fractional crystallization or chromatographic methods well known from field of technology, and subsequent recovery of pure enantiomers.

[0041] The "enantiomeric excess" or "% enantiomeric excess" of a composition can be calculated using the equation shown below. In the example shown below, the composition contains 90% of one enantiomer, eg the S enantiomer, and 10% of the other enantiomer, ie, the R enantiomer.

e. and. = (90-10)/100 = 80%.

[0042] Thus, a composition containing 90% of one enantiomer and 10% of the other enantiomer is said to have an enantiomeric excess of 80%.

[0043] the Compounds or compositions described in the present invention may contain an enantiomeric excess of at least 50%, 75%, 90%, 95% or 99% of one form of the compound, for example, S-enantiomer. In other words, such compounds or compositions contain an enantiomeric excess of the S enantiomer over the R enantiomer.

[0044] The compounds described herein may also contain unnatural proportions of atomic isotopes at one or more of the atoms that make up such compounds. For example, the compounds may be radiolabeled radioactive isotopes such as, for example, deuterium ( ² H), tritium ( ³ H), carbon-13 ( ¹³ C) or carbon-14 ( ¹⁴ C). It is envisaged that all isotopic variations of the compounds disclosed in the present invention, radioactive or not, are covered within the scope of this disclosure. In addition, it is contemplated that all tautomeric forms of the compounds described herein are within the scope of the claimed disclosure.

[0045] The compound may be applicable as a free base or as a salt. Illustrative salts include hydrobromide, hydrochloride, sulfate, bisulfate, phosphate, nitrate, acetate, valerate, oleate, palmitate, stearate, laurate, benzoate, lactate, phosphate, tosylate, citrate, maleate, fumarate, succinate, tartrate, naphtholate, mesylate , glucoheptanoate, lactobionate and lauryl sulfonate salts, etc. (See, for example, Berge et al. (1977) "Pharmaceutical Salts", J. Pharm. Sci. 66:1-19.)

[0046] Described in the present invention, the compounds of the present disclosure may contain "optionally substituted" fragments. In general, the term "substituted", whether preceded by the term "optionally" or not, means that one or more hydrogen atoms of the specified moiety are replaced by a suitable substituent. Unless otherwise noted, an "optionally substituted" group may contain a suitable substituent at each substitutable position of the group, and if more than one position in any given structure may be substituted with more than one substituent selected from a particular group, the substituent may be either the same, or different in each position. The combinations of substituents provided in the present disclosure are preferably such that they lead to the formation of stable or chemically feasible compounds. As used herein, the term "stable" refers to compounds that are substantially unchanged when subjected to conditions that allow their preparation, definability, and, in certain embodiments, their recovery, purification, and use for one or more of the purposes disclosed herein. .

[0047] Suitable substituents for an optionally substituted alkyl, alkylene, carbocyclyl, heterocyclyl, aryl, or heteroaryl group include halo, ═O, -CN, -OR ^c , -NR ^d R ^e , -S(O) _k R ^c , -NR ^c S(O) ₂ R ^c , -S(O) ₂ NR ^d R ^e , -C(=O)OR ^c , -OC(=O)OR ^c , -OC(=O)R ^c , -OC(=S)OR ^c , -C(=S)OR ^c , -O(C=S)R ^c , -C(=O)NR ^d R ^e , -NR ^c C(=O)R ^c , -C(=S)NR ^d R ^e , -NR ^c C(=S)R ^c , -NR ^c (C=O)OR ^c , -O(C=O)NR ^d R ^e , -NR ^c (C =S)OR ^c , -O(C=S)NR ^d R ^e , -NR ^c (C=O)NR ^d R ^e , -NR ^c (C=S)NR ^d R ^e , -C(=S) R ^c , -C(=O)R ^c , C ₁ -C ₆ alkyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl, carbocyclyl, (C ₁ -C ₆ alkylene) carbocyclyl, (C ₁ - C ₆ heteroalkylene) -carbocyclyl, heterocyclyl, (C ₁ -C ₆ alkylene) -heterocyclyl, (C ₁ -C ₆ heteroalkylene) -heterocyclyl, aryl, (C ₁ -C ₆ alkylene) -aryl, (C ₁ -C ₆ heteroalkylene)-aryl, heteroaryl, (C ₁ -C ₆ alkylene)-heteroaryl or (C ₁ -C ₆ heteroalkylene)-heteroaryl, where each specified alkyl, alkylene, heteroalkyl, heteroalkylene, carboc iclyl, heterocyclyl, aryl and heteroaryl are optionally substituted with one or more of halo, OR ^c , -NO ₂ , -CN, -NR ^c C(=O)R ^c , -NR ^d R ^e , -S(O) _k R ^c , -C(=O)OR ^c , -C(=O)NR ^d R ^e , -C(=O)R ^c , C ₁ -C ₆ alkyl, C ₁ -C ₆ haloalkyl or C ₁ -C ₆ heteroalkyl , and where R ^c represents hydrogen, hydroxy, C ₁ -C ₆ alkyl, C ₁ -C ₆ heteroalkyl, carbocyclyl, (C ₁ -C ₆ alkylene)-carbocyclyl, (C ₁ -C ₆ heteroalkylene) -carbocyclyl, heterocyclyl , (C ₁ -C ₆ alkylene) -heterocyclyl, (C ₁ -C ₆ heteroalkylene) -heterocyclyl, aryl, (C ₁ -C ₆ alkylene) -aryl, (C ₁ -C ₆ heteroalkylene) -aryl, heteroaryl, ( C ₁ -C ₆ alkylene)-heteroaryl or (C ₁ -C ₆ heteroalkylene)-heteroaryl, each of which is optionally substituted with one or more of halogen, hydroxy, C ₁ -C ₆ alkyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl, carbocyclyl, heterocyclyl, aryl or heteroaryl; R ^d and R ^e are each independently selected from hydrogen, C ₁ -C ₆ alkyl, and C ₁ -C ₆ heteroalkyl; and k is 0, 1, or 2. The claimed disclosure is not intended to be limited in any way by the list of substituents of the above example.

[0048] According to one aspect, the present disclosure relates to a compound of formula (I):

or its pharmaceutically acceptable salt, where:

ring A is selected from monocyclic aryl, monocyclic heteroaryl, quinolinyl and bicyclic heterocyclyl, where only one ring of said bicyclic heterocyclyl is aromatic;

each R ¹ is independently selected from halo, cyano, oxo, C ₁ -C ₄ alkyl, -O-(C ₁ -C ₄ alkyl), -C(O)-(C ₁ -C ₄ alkyl), -C(O )-O-(C ₁ -C ₄ alkyl), -C(O)-N(R ⁸ )-(C ₁ -C ₄ alkyl), -N(R ⁸ ) ₂ , -N(R ⁸ )-C (O)-(C ₁ -C ₄ alkyl), -S(O) _p -(C ₁ -C ₄ alkyl), -O-(C ₁ -C ₄ alkylene) -C(O) -O-(C ₁ -C ₄ alkyl), -O-(C ₁ -C ₄ alkylene) -N(R ⁸ ) ₂ , -O-(C ₁ -C ₄ alkylene) -C(O) -N(R ⁸ ) ₂ , -Si(R ⁹ )(C ₁ -C ₄ alkyl) ₂ , C ₃ -C ₈ carbocyclyl, -C(O)-(C ₃ -C ₈ carbocyclyl), -O-(C ₀ -C ₄ alkylene)- (C ₃ -C ₈ carbocyclyl), -O-(C ₀ -C ₄ alkylene) -C (O) - (C ₃ -C ₈ carbocyclyl), -(C ₀ -C ₄ alkylene) -aryl, -O- (C ₀ -C ₄ alkylene)-aryl, heterocyclyl, -C(O)-heterocyclyl, -O-(C ₀ -C ₄ alkylene)-heterocyclyl and -O-(C ₀ -C ₄ alkylene) -C(O )-heterocyclyl, where:

any specified alkyl or specified alkylene part of R ¹ is optionally substituted with one to five substituents independently selected from halogen, cyano, hydroxyl and -O-(C ₁ -C ₄ alkyl); and

any said carbocyclyl, said aryl, or said heterocyclyl moiety of R ¹ is optionally substituted with one to five substituents independently selected from halogen, C ₁ -C ₄ alkyl, C ₁ -C ₄ haloalkyl, cyano, hydroxyl, -O-(C ₁ -C ₄ alkyl), heterocyclyl, -N(R ⁸ ) ₂ and -N(R ⁸ )-C(O)-O-(C ₁ -C ₄ alkyl);

R ² is a bond or -O-;

R ³ is selected from C ₁ -C ₆ alkyl, -(C ₀ -C ₆ alkylene)-(C ₃ -C ₈ carbocyclyl) and -(C ₀ -C ₆ alkylene)-(monocyclic O- or S-containing heterocyclyl) , where:

the carbon atom of said monocyclic heterocyclyl is the point of attachment of said monocyclic heterocyclyl;

any specified alkyl or specified alkylene portion of R ³ is optionally substituted with one to five substituents independently selected from halogen, cyano, hydroxyl, C ₁ -C ₄ alkyl, -O-(C ₁ -C ₄ alkyl), -O-(C ₃ -C ₈ cycloalkyl) and -S(O) _p -(C ₁ -C ₄ alkyl); and

any said carbocyclyl or said heterocyclyl portion of R ³ is optionally substituted with one to five substituents independently selected from halogen, cyano, oxo, hydroxyl, C ₁ -C ₄ alkyl, C ₁ -C ₄ haloalkyl, -O-(C ₁ -C ₄ alkyl), -O-(C ₁ -C ₄ haloalkyl), -C(O)-(C ₁ -C ₄ alkyl), -C(O)-O-(C ₁ -C ₄ alkyl), -S( O) _p -(C ₁ -C ₄ alkyl), -O-phenyl, -(C ₁ -C ₄ alkyl)-phenyl and morpholin-4-yl;

R ⁴ is selected from hydrogen, C ₁ -C ₄ alkyl, C ₂ -C ₄ alkenyl, C ₂ -C ₄ alkynyl, C ₃ -C ₆ cycloalkyl, -C(O)-(C ₁ -C ₄ alkyl), halogen and cyano, where:

any specified alkyl part of R ⁴ is optionally substituted by hydroxyl;

each R ⁸ is independently selected from hydrogen and C ₁ -C ₄ alkyl, or two R ⁸ together with the nitrogen atom to which they are connected form a heterocyclyl;

each R ⁹ is independently selected from hydrogen, C ₁ -C ₄ alkyl and hydroxyl;

n is 0, 1, 2, 3, 4, 5 or 6; and

p is 0, 1 or 2.

[0049] In some embodiments, p is 0. In some embodiments, p is 1. In some embodiments, p is 2. In some embodiments, p is 1 or 2.

[0050] In some embodiments, n is 0. In some embodiments, n is 1. In some embodiments, n is 2. In some embodiments, n is 3. In some embodiments, n is 4. In some embodiments, n is 4. In some embodiments, n is 4. in some embodiments, n is 5. In some embodiments, n is 6. In some embodiments, n is 1, 2, or 3.

[0051] In some embodiments, R ⁴ is cyano, methyl, chlorine, bromine, fluorine, but-2-ynyl, or butan-2-onyl.

[0052] In some embodiments, Ring A is selected from 6-membered monocyclic aryl, 5-membered heteroaryl, 6-membered monocyclic heteroaryl, 9-membered bicyclic heterocyclyl, and 10-membered bicyclic heterocyclyl.

и

[0053] For example, in some embodiments, ring A is selected from phenyl, pyrrolyl, pyrazolyl, imidazolyl, thiazolyl, isothiazolyl, oxazolyl, isoxazolyl, thiophenyl, 1,2,4-thiadiazolyl, 1,3,4-thiadiazolyl, 1,2 ,3-triazolyl, pyridinyl, pyrimidinyl, pyrazinyl,

and

[0054] For example, according to some embodiments, ring A is selected from:

where:

X is selected from O, N and S(O) _p ;

Y is CH or N;

W is selected from CH, N, S and O;

Z is selected from CH, NH, S and O; and

p is 0, 1 or 2.

[0055] In some embodiments, ring A is selected from

и

, где:

and

, where:

R ^1B is selected from hydrogen, halogen, cyano, C ₁ -C ₄ alkyl, -O-(C ₁ -C ₄ alkyl), -C(O)-(C ₁ -C ₄ alkyl), -C(O)- (C ₃ -C ₆ cycloalkyl), -C(O)-O-(C ₁ -C ₄ alkyl), -N(R ⁸ )-C(O)-(C ₁ -C ₄ alkyl), -S( O) _p -(C ₁ -C ₄ alkyl), C ₃ -C ₆ cycloalkyl and 3-6 membered heterocyclyl, where:

any specified alkyl portion of R ^1B is optionally substituted with one to five substituents independently selected from halo and cyano;

any specified cycloalkyl or specified heterocyclyl part of R ^1B is optionally substituted with one to five substituents independently selected from halogen, -N(R ⁸ ) ₂ , C ₁ -C ₄ alkyl, heterocyclyl and C ₁ -C ₄ haloalkyl;

p is 0, 1 or 2; and

if R ^1B is hydrogen then n1 is 0, 1, 2, 3, 4, 5 or 6 and if R ^1B is not hydrogen then n1 is 0, 1, 2, 3, 4 or 5.

[0056] In some embodiments, Ring A is selected from:

где:

where:

R ^1B is selected from C ₁ -C ₄ alkyl, C ₃ -C ₆ cycloalkyl, -(C ₀ -C ₄ alkylene)-aryl, heterocyclyl and -S(O) _p -(C ₁ -C ₄ alkyl), where:

any specified alkyl portion of R ^1B is optionally substituted with one to five substituents independently selected from halo and cyano;

p is 0, 1 or 2;

each R ¹ is independently selected from C ₁ -C ₄ alkyl, C ₃ -C ₆ cycloalkyl, halogen, cyano and -N(R ⁸ ) ₂ where:

any specified alkyl portion of R ^1B is optionally substituted with one to five substituents independently selected from halo and cyano;

each R ⁸ is independently selected from C ₁ -C ₄ alkyl; and

if R ^1B is hydrogen then n1 is 0, 1, 2, 3, 4, 5 or 6 and if R ^1B is not hydrogen then n1 is 0, 1, 2, 3, 4 or 5.

[0057] In some embodiments, ring A is selected from:

Согласно некоторым неограничивающим вариантам осуществления каждый R¹ независимо выбран из C₁-C₄ алкила, C₃-C₆ циклоалкила, -O-(C₁-C₄ алкил), -C(O)-гетероциклила и циано, где любая указанная алкильная часть R¹ необязательно замещена одним-пятью заместителями, независимо выбранными из галогена, гидроксила и циано.

In some non-limiting embodiments, each R ¹ is independently selected from C ₁ -C ₄ alkyl, C ₃ -C ₆ cycloalkyl, -O-(C ₁ -C ₄ alkyl), -C(O)-heterocyclyl, and cyano, where any specified the alkyl portion of R ¹ is optionally substituted with one to five substituents independently selected from halogen, hydroxyl and cyano.

[0058] In some embodiments, ring A is selected from:

Согласно некоторым неограничивающим вариантам осуществления каждый R¹ независимо выбран из C₁-C₄ алкила, необязательно замещенного одним-пятью заместителями, независимо выбранными из галогена, гидроксила и циано.

In some non-limiting embodiments, each R ¹ is independently selected from C ₁ -C ₄ alkyl optionally substituted with one to five substituents independently selected from halogen, hydroxyl, and cyano.

[0059] In some embodiments, ring A is selected from

Согласно некоторым неограничивающим вариантам осуществления каждый R¹ независимо выбран из C₁-C₄ алкила и циано, где любая указанная алкильная часть R¹ необязательно замещена одним-пятью заместителями, независимо выбранными из галогена, гидроксила и циано.

In some non-limiting embodiments, each R ¹ is independently selected from C ₁ -C ₄ alkyl and cyano, wherein any specified alkyl portion of R ¹ is optionally substituted with one to five substituents independently selected from halogen, hydroxyl, and cyano.

[0060] In some embodiments, each R ¹ is independently selected from tetrahydropyranyl, tetrahydrofuranyl, 3,6-dihydro-2H--pyranyl, piperidinyl, piperazinyl, oxetanyl, cyano, C ₁ -C ₄ alkyl, -S(O)-( C ₁ -C ₄ alkyl), -S(O) ₂ -(C ₁ -C ₄ alkyl), -C (O) - (C ₁ -C ₄ alkyl), -C (O) -heterocyclyl, -O- (C ₁ -C ₄ alkyl), halogen, C ₃ -C ₆ cycloalkyl, -O-(C ₃ -C ₆ cycloalkyl), -N(CH ₃ ) ₂ , Si(CH ₃ ) ₂ OH, -NH-C (O)-CH ₃ , -O-(C ₀ -C ₄ alkylene)-aryl and morpholinyl, where:

said piperidinyl is optionally substituted with one substituent selected from morpholinyl, -O-(C ₁ -C ₄ alkyl), C ₁ -C ₄ alkyl and C ₁ -C ₄ haloalkyl, or one or two substituents independently selected from halogen;

said tetrahydropyranyl or tetrahydrofuranyl is optionally substituted with one substituent selected from hydroxyl and -O-(C ₁ -C ₄ alkyl);

said oxetanyl is optionally substituted with one substituent selected from C ₁ -C ₄ alkyl;

said piperazinyl is optionally substituted with one substituent selected from C ₁ -C ₄ alkyl and halo;

any specified cycloalkyl part of R ¹ is optionally substituted with one substituent selected from cyano and hydroxyl;

any specified alkyl portion of R ¹ is optionally substituted with one to five substituents independently selected from halogen, cyano, hydroxyl and -O-(C ₁ -C ₄ alkyl).

[0061] In some embodiments, R ³ is selected from C ₁ -C ₆ alkyl, -(C ₀ -C ₃ alkylene) -(C ₃ -C ₆ carbocyclyl) and -(C ₀ -C ₃ alkylene) -(monocyclic O - or S-containing heterocyclyl), where:

any specified alkyl or specified alkylene part of R ³ is optionally substituted with one to five substituents independently selected from halogen, cyano and hydroxyl; and

any said carbocyclyl or said heterocyclyl portion of R ³ is optionally substituted with one to four substituents independently selected from halogen, cyano, hydroxyl, C ₁ -C ₄ alkyl, C ₁ -C ₄ haloalkyl, -O-(C ₁ -C ₄ alkyl) , -O-(C ₁ -C ₄ haloalkyl), -C(O)-(C ₁ -C ₄ alkyl), -C(O)-O-(C ₁ -C ₄ alkyl), -S(O) _p -(C ₁ -C ₄ alkyl), -O-phenyl, -(C ₁ -C ₄ alkyl)-phenyl and morpholin-4-yl.

[0062] For example, in some embodiments, R ³ is selected from cyclobutyl, cyclopropyl, cyclohexanyl, oxetanyl, thietanyl, tetrahydrofuranyl, and tetrahydropyranyl. In some embodiments, R ³ is selected from -(C ₁ alkylene)-tetrahydropyranyl, -(C ₁ alkylene)-tetrahydrofuranyl, -(C ₁ or C ₂ alkylene)-oxetanyl, -(C ₁ or C ₂ alkylene)-cyclopropyl, -(C ₁ or C ₂ alkylene)-cyclobutyl; and -(C ₁ or C ₂ alkylene)-cyclooxanyl. In some embodiments, said cyclopropyl, said cyclobutyl, or said cyclohexanyl group is independently substituted with one to four substituents independently selected from halo, hydroxyl, and cyano.

[0063] In some embodiments, R ³ is selected from cyclobutyl, cyclopropyl, and cyclohexanyl, wherein said cyclobutyl, said cyclopropyl, or said cyclohexanyl is independently substituted with one to four halogen groups. In some embodiments, R ³ is selected from cyclobutyl, cyclopropyl, and cyclohexanyl, wherein said cyclobutyl, said cyclopropyl, or said cyclohexanyl is substituted with one cyano or hydroxyl group. In some embodiments, R ³ is selected from oxetanyl and -(C ₁ alkylene)-oxetanyl, wherein said oxetanyl moiety of R ³ is substituted with C ₁ -C ₄ alkyl.

[0064] In some embodiments, R ³ is C ₁ -C ₆ alkyl. In some embodiments, R ³ is C ₁ -C ₆ alkyl independently substituted with one to four halo groups.

[0065] In some embodiments, the compound is a compound of formula (I) selected from the compounds of Table 1.

[0066] In another aspect, the present disclosure provides a pharmaceutical composition comprising a compound of formula (I) (eg, a compound of Table 1) or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.

[0067] Table 1 below shows the structures of the compounds described in the present invention.

[0068] According to another aspect, the present disclosure relates to a method of treating or alleviating progressive fibrodysplasia ossificans in a subject, comprising administering to the subject a pharmaceutically effective amount of a compound described herein (for example, a compound in Table 1), or a pharmaceutically acceptable salt thereof, or a pharmaceutical formulation thereof. compositions.

[0069] In another aspect, the present disclosure relates to a method of treating or alleviating diffuse brainstem glioma in a subject, comprising administering to the subject a pharmaceutically effective amount of a compound described herein (e.g., a compound in Table 1), or a pharmaceutically acceptable salt thereof, or its pharmaceutical composition.

[0070] According to another aspect, the present disclosure provides a method for inhibiting aberrant ALK2 activity in a subject, comprising administering to the subject a therapeutically effective amount of a compound described herein (e.g., a compound in Table 1), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition thereof.

[0071] Pharmaceutically acceptable salts of such compounds are also considered for the uses described in the present invention.

[0072] A "pharmaceutically acceptable salt" refers to any salt of a compound of the present disclosure that retains its biological properties and that is not toxic or otherwise undesirable for pharmaceutical use. Pharmaceutically acceptable salts can be derived from various organic and inorganic counterions. Such salts include one or more of: (1) acid addition salts formed with organic or inorganic acids such as hydrochloric, hydrobromic, sulfuric, nitric, phosphoric, sulfamic, acetic, trifluoroacetic, trichloroacetic, propionic, hexanoic, cyclopentylpropionic , glycolic, glutaric, pyruvic, lactic, malonic, succinic, sorbic, ascorbic, malic, maleic, fumaric, tartaric, citric, benzoic, 3-(4-hydroxybenzoyl)benzoic, picric, cinnamon, almond, phthalic, lauric, methanesulfonic, ethanesulfonic, 1,2-ethanedisulfonic, 2-hydroxyethanesulfonic, benzenesulfonic, 4-chlorobenzenesulfonic, 2-naphthalenesulfonic, 4-toluenesulfonic, camphoric, camphorsulfonic, 4-methylbicyclo[2.2.2]-oct-2-en-1-carboxylic, glucoheptonic , 3-phenylpropionic, trimethylacetic, tert-butylacetic, lauryl sulfuric, gluconic, benzoic, glutamic, hydroxynaphthoic, salicylic, stearic, cyclohexylsulfamic, quinic, muconic acid and the like; or (2) salts formed if an acidic proton present in the parent compound is or (a) replaced by a metal ion, such as an alkali metal ion, an alkaline earth metal ion, or an aluminum ion, or alkali metal or alkaline earth metal hydroxides such as sodium hydroxide , potassium, calcium, magnesium, aluminium, lithium, zinc and barium, ammonium, or (b) matched with an organic base such as aliphatic, alicyclic or aromatic organic amines such as ammonia, methylamine, dimethylamine, diethylamine, picoline, ethanolamine, diethanolamine, triethanolamine, ethylenediamine, lysine, arginine, ornithine, choline, N,N'-dibenzylethylenediamine, chlorprocaine, diethanolamine, procaine, N-benzylphenethylamine, N-methylglucaminepiperazine, tris(hydroxymethyl)-aminomethane, tetramethylammonium hydroxide, etc. Pharmaceutical acceptable salts further include, by way of example only, sodium, potassium, calcium, magnesium, ammonium, tetraalkylammonium, and the like, and if the compound contains a basic functional group, salts of non-toxic organic or inorganic acids such as hydrochloride, hydrobromide, tartrate, mesylate, besylate, acetate, maleate, oxalate, and the like. A pharmaceutically acceptable salt according to the disclosure includes at least one salt and may also be mixtures of more than one salt.

[0073] Pharmaceutical compositions of the present disclosure include one or more compounds of the present disclosure and one or more pharmaceutically acceptable carrier(s). The term “pharmaceutically acceptable carrier” refers to a pharmaceutically acceptable substance, composition, or carrier vehicle, such as a liquid or solid excipient, diluent, excipient, solvent, or coating agent, included in the transfer or transport of any contemplated composition or component thereof. Each carrier may be "acceptable" in the sense that it is compatible with the composition in question and its components and is not harmful to the patient. Some examples of substances that can serve as pharmaceutically acceptable carriers include: (1) sugars such as lactose, glucose and sucrose; (2) starches such as corn starch and potato starch; (3) cellulose and its derivatives such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; (4) powdered gum tragacanth; (5) malt; (6) gelatin; (7) talc; (8) fillers such as cocoa butter and wax candles; (9) oils such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols such as propylene glycol; (11) polyols such as glycerol, sorbitol, mannitol and polyethylene glycol; (12) esters such as ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents such as magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16) pyrogen-free water; (17) isotonic saline solution; (18) Ringer's solution; (19) ethyl alcohol; (20) phosphate buffer solutions; and (21) other non-toxic compatible substances used in pharmaceutical formulations.

[0074] Compositions of the present disclosure may be administered orally, parenterally, by inhalation spray, topically, rectally, nasally, buccally, vaginally, or by an implanted reservoir. As used herein, the term "parenteral" includes subcutaneous, intravenous, intramuscular, intraarticular, intrasynovial, intrasternal, intrathecal, intrahepatic, intralesional, and intracranial injection or infusion techniques. In some embodiments, the compositions of the present disclosure are administered orally, intraperitoneally, or intravenously. Sterile injectable forms of the compositions of the present disclosure may be an aqueous or oily suspension. Such suspensions may be formulated according to techniques known in the art using suitable dispersing or wetting agents and suspending agents. The sterile injectable may also be a sterile injectable solution or suspension in a non-toxic, parenterally acceptable diluent or vehicle, such as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that may be used are water, Ringer's solution and isotonic sodium chloride solution. In addition, sterile, fatty oils are traditionally used as solvents or suspending media.

[0075] For this purpose, any light fixed oil can be used, including synthetic mono - or diglycerides. Fatty acids such as butyric acid and its glyceride derivatives are useful in the preparation of injectables, as are natural pharmaceutically acceptable oils such as olive oil or castor oil, especially in their polyethoxylated versions. Such oily solutions or suspensions may also contain a long chain alcohol diluent or dispersant such as carboxymethyl cellulose or similar dispersants commonly used in pharmaceutically acceptable dosage forms, including emulsions and suspensions. Other commonly used surfactants such as Tween, Spans and other emulsifiers or bioactive enhancers that are commonly used in the manufacture of pharmaceutically acceptable solid, liquid or other dosage forms can also be used for formulation purposes.

[0076] The pharmaceutically acceptable compositions of the present disclosure may be orally administered in any orally acceptable dosage form, including, without limitation, capsules, tablets, aqueous suspensions, or solutions. In the case of tablets for oral use, carrier vehicles commonly used include lactose and cornstarch. Lubricants such as magnesium stearate are typically added. For oral administration in capsule form, useful diluents include lactose and dry corn starch. If aqueous suspensions are required for oral administration, the active ingredient is combined with emulsifying and suspending agents. Sweetening, flavoring or coloring agents may also be added, if desired.

[0077] Alternatively, pharmaceutically acceptable compositions of the present disclosure may be administered in the form of suppositories for rectal administration. They can be prepared by mixing the agent with a suitable non-irritating excipient which is solid at room temperature but liquid at rectal temperature and thus will melt in the rectum to release the drug. Such substances include cocoa butter, beeswax and polyethylene glycols.

[0078] The pharmaceutically acceptable compositions of the present disclosure may also be administered topically, especially if the target of treatment includes areas or organs readily accessible by topical administration, including diseases of the eye, skin, or lower digestive tract. Suitable local formulations are readily available for each of these areas or bodies. Topical administration to the lower digestive tract can be done as a rectal suppository formulation (see above) or in a suitable enema formulation. Topical transdermal patches may also be used.

[0079] For topical applications, pharmaceutically acceptable compositions may be formulated as a suitable ointment containing the active ingredient suspended or dissolved in one or more carrier vehicles. Vehicles for topical administration of the compounds of the present disclosure include, but are not limited to, mineral oil, liquid petrolatum, white petrolatum, propylene glycol, polyoxyethylene, prolyoxypropylene compound, emulsifying wax, and water. Alternatively, pharmaceutically acceptable compositions may be formulated as a suitable lotion or cream containing the active ingredients suspended or dissolved in one or more pharmaceutically acceptable carrier vehicles. Suitable carrier vehicles include, without limitation, mineral oil, sorbitan monostearate, polysorbate 60, cetyl ester wax, cetearyl alcohol, 2-octyldodecanol, benzyl alcohol, and water.

[0080] Pharmaceutically acceptable compositions of the present disclosure may also be administered by nasal spray or inhalation. Such compositions are prepared according to techniques well known in the art of pharmaceutical formulation and may be prepared as solutions in saline using benzyl alcohol or other suitable preservatives, absorption accelerators to enhance bioavailability, fluorocarbons, and/or other conventional solubilizing or dispersing agents.

[0081] The amount of compounds of the present disclosure that may be combined with a carrier to form a composition in a single dosage form will vary depending on the host treated, the particular route of administration, and other factors determined by the individual who administered the single dosage form.

[0082] The toxicity and therapeutic efficacy of the compounds of the present disclosure, including pharmaceutically acceptable salts and deuterated variants, can be determined by standard pharmaceutical procedures in cell cultures or experimental animals. LD ₅₀ is the lethal dose for 50% of the population. The ED ₅₀ is the dose that is therapeutically effective in 50% of the population. The ratio of doses with toxic and therapeutic effects (LD ₅₀ /ED ₅₀ ) is a therapeutic index. Compounds that exhibit large therapeutic indices are preferred. Although compounds that exhibit toxic side effects may be used, care should be taken to develop a delivery system that targets such compounds to the site of diseased tissue in order to minimize potential damage to non-infected cells and thus reduce side effects.

[0083] Data obtained from cell culture assays and animal studies can be used in formulating a dosage range for use in humans. The dosage of such compounds may be in the range of circulating concentrations that include the ED ₅₀ with little or no toxicity. The dosage may vary within this range depending on the dosage form used and the route of administration used. For any compound, a therapeutically effective dose can be estimated initially from cell culture assays. The dose may be formulated in animal models to achieve a range of circulating plasma concentrations that includes the IC ₅₀ (i.e., the concentration of test compound that achieves half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine applicable doses for humans. Plasma levels can be measured, for example, using high performance liquid chromatography.

[0084] It should also be appreciated that the specific dosage and treatment regimen for any particular patient will depend on a number of factors, including, without limitation, the potency of the particular compound used, age, body weight, general health, sex, diet, time administration, rate of elimination, combination of drugs, the opinion of the attending physician, and the severity of the particular disease to be treated. The amount of a compound of the present disclosure in a composition will also depend on the particular compound in the composition.

[0085] Mutations in ALK2 cause inappropriate kinase activity and are associated with various diseases. The present disclosure relates to compounds that inhibit a mutant ALK2 gene, such as a mutant ALK2 gene, which results in the expression of an ALK2 enzyme having an amino acid modification. In another aspect, the present disclosure relates to compounds that inhibit both the wild-type (WT) ALK2 protein and mutant forms of the ALK2 protein. For the purposes of this disclosure, sequence information for ALK2 is located on the National Center for Biological Information (NCBI) web page (https://www.ncbi.nlm.nih.gov/) under the name ACVR1 type Activin A 1 receptor [Homo sapiens (human )]; Gene ID in the Entrez (NCBI) database: 90. Also known as FOP; ALK2; SKR1; TSRI; ACTRI; ACVR1A; ACVRLK2, with said sequence information incorporated herein by reference.

[0086] In some embodiments, the present disclosure relates to a method for inhibiting aberrant ALK2 activity in a subject, comprising the step of administering to a subject in need thereof a pharmaceutically effective amount of at least one compound or pharmaceutical composition described herein. In some embodiments, aberrant ALK2 activity is caused by a mutation in the ALK2 gene that results in the expression of an ALK2 enzyme having an amino acid modification selected from one or more of L196P, PF197-8L, R202I, R206H, Q207E, R258S, R258G, G328A, G328V, G328W, G328E, G328R, G356D and R375P. In some embodiments, the ALK2 enzyme has the amino acid modification R206H.

[0087] Due to their activity against ALK2, the compounds described herein can be used to treat a patient with a condition associated with aberrant ALK2 activity. In some embodiments, the condition associated with aberrant ALK2 activity is progressive fibrodysplasia ossificans. The diagnosis of FOP is based on the presence of congenital malformations of the big toes (hallux valgus) and the formation of fibrous nodules in the soft tissues. The nodules may or may not transform into heterotopic bone. Such soft tissue lesions are often first noted in the head, on the back of the head. Approximately 97% of FOP patients have the same c.617G>A, R206H mutation in the ACVR1 (Alk2) gene. There is a genetic test available through the University of Pennsylvania (Kaplan et al., Pediatrics 2008, 121(5): e1295-e1300).

[0088] Other common congenital anomalies include thumb malformations, short broad femoral necks, tibial osteochondromas, and fused facet joints of the cervical spine. The fused facet joints in the neck often cause babies to slide on their buttocks instead of crawling. FOP is commonly misdiagnosed (approximately 80%; malignancy or fibromatosis) and patients are often subjected to inappropriate diagnostic procedures, such as biopsies, which exacerbate the disease and cause permanent disability.

[0089] In some embodiments, the present disclosure relates to a method for treating or alleviating progressive fibrodysplasia ossificans in a subject, said method comprising administering to said subject in need thereof a pharmaceutically effective amount of a compound or pharmaceutical composition described herein.

[0090] In some embodiments, the condition associated with aberrant ALK2 activity is fibrodysplasia ossificans progressive (FOP) and the subject has a mutation in the ALK2 gene that results in the expression of an ALK2 enzyme having an amino acid modification selected from one or more of L196P , PF197-8L, R202I, R206H, Q207E, R258S, R258G, G328A, G328W, G328E, G328R, G356D and R375P. In some embodiments, the ALK2 enzyme has the amino acid modification R206H.

[0091] The present disclosure includes methods for identifying and/or diagnosing patients for treatment with one or more of the compounds or pharmaceutical compositions described herein. In some embodiments, the present disclosure relates to a method for detecting a condition associated with aberrant ALK2 activity, e.g., FOB, in a subject, the method comprising (a) obtaining a sample, e.g., plasma, from the subject, e.g., a sick human; and (b) detecting the presence in the sample of one or more mutations in the ALK2 gene described herein. According to another embodiment, the present disclosure relates to a method for diagnosing a condition associated with aberrant ALK2 activity in a subject, the method comprising (a) obtaining a sample from the subject; (b) detecting the presence in a sample of one or more mutations in the ALK2 gene described herein using the detection method described herein; and (c) diagnosing the condition in the subject by detecting the presence of one or more mutations. Mutation detection methods include, without limitation, hybridization-based methods, amplification-based methods, microarray analysis, flow cytometry analysis, DNA sequencing, next generation sequencing (NGS), primer extension, PCR, in situ hybridization, dot blotting, and southern blotting. In some embodiments, the present disclosure relates to a method for diagnosing and treating a condition associated with aberrant ALK2 activity in a subject, the method comprising (a) obtaining a sample from the subject; (b) detecting the presence in a sample of one or more mutations in the ALK2 gene described herein using the detection method described herein; (c) diagnosing a condition in a subject by detecting the presence of one or more mutations; and (d) administering an effective amount of one or more of the compounds or pharmaceutical compositions described herein to the patient with the diagnosis. In some embodiments, the present disclosure relates to a method of treating a condition associated with aberrant ALK2 activity in a subject, said method comprising (a) determining, establishing, or obtaining information that said subject has one or more mutations in the ALK2 gene, described in this document; (b) identifying the subject as responding to one or more of the compounds or pharmaceutical composition described herein; and (c) administering an effective amount of one or more compounds or pharmaceutical compositions to a subject.

[0092] In some embodiments, the condition associated with aberrant ALK2 activity is a brain tumor, such as a glial tumor. In some embodiments, the glioma is a diffuse brainstem glioma (DIPG). In some embodiments, the present disclosure relates to a method of treating or alleviating diffuse brainstem glioma in a subject in need thereof, said method comprising administering to said subject a pharmaceutically effective amount of a compound or pharmaceutical composition described herein.

[0093] In some embodiments, the condition associated with aberrant ALK2 activity is diffuse brainstem glioma, and the subject has a mutation in the ALK2 gene that results in the expression of an ALK2 enzyme having at least one amino acid modification selected from R206H, G328V, G328W, G328E and G356D. In some embodiments, the ALK2 enzyme has the amino acid modification R206H.

[0094] In some embodiments, the condition associated with aberrant ALK2 activity is anemia associated with inflammation, cancer, or chronic disease.

[0095] In some embodiments, the condition associated with aberrant ALK2 activity is trauma- or surgical-induced heterotopic ossification.

[0096] In some embodiments, a compound of the present disclosure is co-administered (either as part of a combination dosage form or as a separate dosage form administered before, concurrently, or after administration) with a second therapeutic agent useful in the treatment of the disease being treated, e.g. FOP. In some embodiments, a compound of the present disclosure is co-administered with a steroid (eg, prednisone) or other antiallergic agents such as omalizumab.

[0097] In some embodiments, a compound of the present disclosure is co-administered with a RAR-γ agonist or anti-Activin-A antibody to treat the disease being treated, eg, FOP. In some embodiments, the RAR-γ agonist to be co-administered is palovarotene. In some embodiments, the anti-Activin-A antibody to be co-administered is REGN2477.

[0098] In some embodiments, a compound of the present disclosure is co-administered with mast cell-targeting therapeutics useful in the treatment of FOP. In some embodiments, a compound of the present disclosure is co-administered with a mast cell inhibitor, including but not limited to a KIT inhibitor. In some embodiments, the mast cell inhibitor to be co-administered is selected from cromolyn sodium (or sodium cromoglycate), brentuximab (ADCETRIS®), ibrutinib (IMBRUVICA®), omalizumab (XOLAIR®), anti-leukotriene agents (e.g., montelukast (SINGULAIR®) or zileitone (ZYFLO® or ZYFLO CR®)) and KIT inhibitors (eg, imatinib (GLEEVEC®), midostaurin (PKC412A), masitinib (MASIVET® or KINAVET®), BLU-285, DCC-2618, PLX9486).

[0099] the Compounds of the present disclosure, including their salts and N-oxides, can be obtained using known methods of organic synthesis and can be synthesized according to any of the many possible synthetic routes presented in the schemes below. The reactions to prepare the compounds of the present invention can be carried out in suitable solvents, which can be quickly selected by a person skilled in the art of organic synthesis. Suitable solvents may be substantially non-reactive with the starting materials (reagents), intermediates, or products at the temperatures at which the reactions are carried out, for example, temperatures that may range from the freezing point of the solvent to the boiling point of the solvent. The reaction shown can be carried out in a single solvent or in a mixture of more than one solvent. Depending on the particular reaction step, suitable solvents for the particular reaction step may be selected by one skilled in the art.

[00100] Preparation of the compounds of the present invention may include the introduction and deprotection of various chemical groups. The need for protection and deprotection and selection of appropriate protecting groups can be quickly ascertained by a person skilled in the art. The chemistry of protecting groups can be found in, for example, Wuts and Greene, Protective Groups in Organic Synthesis, 4th ed., John Wiley & Sons: New Jersey, (2006), which is incorporated herein by reference in its entirety.

[00101] The reactions could be observed using any suitable method known in the art. For example, product formation could be observed using spectroscopic techniques such as nuclear magnetic resonance (NMR) spectroscopy (e.g. ¹ H or ¹³ C), infrared (IR) spectroscopy, spectrophotometry (e.g. UV visible), mass spectrometry (MS) or chromatographic methods such as high performance liquid chromatography (HPLC) or thin layer chromatography (TLC).

[00102] LC-MS/HPLC : Unless otherwise noted, all liquid chromatography-mass spectrometry (LC-MS) data (sample analyzed for purity and specificity) was obtained using one of the following instruments and mobile phases:

[00103] An Agilent Model-1260 LC system (or Model 1200) using an Agilent Model 6120 (or 1956) mass spectrometer using ES-API ionization, equipped with an Agilent Poroshel 120 reverse phase column (EC-C18, particle size 2, 7 µm, dimensions 3.0×50 mm) at 22.4 degrees Celsius. The mobile phase consisted of a solvent mixture of 0.1% formic acid in water and 0.1% formic acid in acetonitrile. Used constant ingredient from 95% aqueous/5% organic to 5% aqueous/95% organic mobile phase over 4 minutes. The flow rate was constant at approximately 1 ml/min.

[00104] LC-MS: main mobile phase: A: water (10 mM NH ₄ HCO ₃ ) B: ACN; gradient: 5% B increase to 95% B in 1.2 min, 95% B in 1.3 min, again to 5% B in 0.01 min; flow rate: 2 ml/min; column: XBridge, 3.5 µm, 50×4.6 mm; thermostat temperature setting: 50°C. Acidic mobile phase: A: water (0.01% TFA) B: CAN (0.01% TFA); gradient: 5% B increase to 95% B in 1.2 min, 95% B in 1.3 min, again to 5% B in 0.01 min; flow rate: 2 ml/min; column: Sunfire, 3.5 µm, 50×4.6 mm; thermostat temperature setting: 50°C.

[00105] HPLC: main mobile phase: A: water (10 mM NH ₄ HCO ₃ ) B: ACN; gradient: 5% B increase to 95% B in 1.2 min, 95% B in 1.3 min, again to 5% B in 0.01 min; flow rate: 2 ml/min; column: XBridge, 3.5 µm, 50×4.6 mm; thermostat temperature setting: 50°C. Acidic mobile phase: A: water (0.01% TFA) B: ACN (0.01% TFA); gradient: 0 min 5% B, 3 min 5% B, 10 min 95% B, 15 min 95% B; flow rate: 1.2 ml/min; column: Eclipse XDB-C18, 4.6×150 mm, 5 µm; thermostat temperature setting: 40°C.

[00106] Prep-LC-MS Method 1 : Preparative HPLC was performed on a Shimadzu Discovery VP® preparative system equipped with a Luna 5u C18(2) 100A reverse phase column packed with AXIA, 250 x 21.2 mm at 22.4 degrees Celcius. The mobile phase consisted of a solvent mixture of 0.1% formic acid in water and 0.1% formic acid in acetonitrile. Used constant ingredient from 95% aqueous/5% organic to 5% aqueous/95% organic mobile phase in 25 minutes. The flow rate was constant at approximately 20 ml/min. Reactions carried out under microwave irradiation were carried out in this manner in a Biotage Initiator microwave unit.

[00107] Rev. LC-MS, method 2:

[00108] MS method: capillary (kv): 3.5; cone (v): 20; extractor (v): 3; RF lenses (v): 0.5; pace. source (°C): 100°; pace. empty (°C): 400.

[00109] Injection method: solvent: CH ₃ OH, H ₂ O, 0.001 TFA/5-95 NH3/CAN/5-95 TFA/CAN; gradient: 10-70; recording time: 3.5 min; flow rate: 60 ml/min.

[00110] Fractional method: fraction trigger: wt.; divide/gather delay (sec): 10.5; maximum tube filling (%) 85; positive ion detection--min. intensity threshold (mit): 2000000; column id: X-bridge, C18, 20 mm×50 mm, 10 µm.

[00111] Chiral HPLC : Preparative HPLC for the resolution of chiral mixtures was performed on the following instruments using one of the columns and group of general conditions set forth below.

[00112] SFC details:

[00113] Instrument: SFC-80 (Thar, Waters) or SFC-200 (Thar, Waters)

Column: AD-H 20×250 mm, 5 µm (Daicel)

Column temperature: 35°C

Mobile phase: CO ₂ /methanol (0.1% NH ₄ OH) = 40/60-90/10

Flow rate: 80-180g/min

Overpressure: 100 bar

Detector Wavelength: 214-360nm

[00114] HPLC details:

[00115] Device: Gilson-281

Column: AD-H 20×250, 10 µm (Daicel)

Mobile phase: hexane (0.1% DEA): EtOH (0.1% DEA)=0/100-100/0

[00116] Column temperature: 40°C

Injection volume: 1 ml

Detector Wavelength: 214-360nm

[00117] Column:

AD-H DAICEL 10 µm Φ2.5cm*2 Φ5.0cm*2 OD-H Φ2.5cm*2 Φ5.0cm*1 OJ-H Φ2.5cm*2 Φ5.0cm*1 AS-H Φ2.5cm*1 Φ5.0cm*1 OZ-H Φ2.5cm*1 Φ5.0cm*1 AY-H Φ2.5cm*2 Φ5.0cm*1 IC Φ2.5cm*1 IA Φ2.5cm*1 RegisCell Φ2.5cm*1 (R,R)-Whelk-O1 Φ2.5cm*1 Φ5.0cm*1 Cellulose-SC Φ2.5cm*1 Amylose-C Φ2.5cm*1

[00118] Silica gel chromatography: Silica gel chromatography was performed on either a Teledyne Isco CombiFlash® Rf block or a Biotage® Isolera Four block.

[00119] Proton NMR : Unless otherwise noted, all ¹ H NMR spectra were obtained on a Varian 400 MHz Unity Inova 400 MHz NMR instrument (detection time = 3.5 seconds with 1 second delay; 16 - 64 scans)., Bruker, AVANCE III 500MHz UltraShield-Plus digital NMR spectrometer or Bruker, AVANCE III 400MHz UltraShield-Plus digital NMR spectrometer. If performance is shown, all protons are reported in DMSO-d ₆ solvent as parts per million (ppm) relative to residual DMSO (2.50 ppm).

Examples

[00120] The following examples are intended to be illustrative and are not meant to be limiting in any way.

[00121] The diagrams below are intended to provide basic guidance with respect to the preparation of the compounds of the present invention. A person skilled in the art will appreciate that the preparations shown in the diagrams may be modified or optimized using general knowledge of organic chemistry to obtain various compounds of the present invention.

Synthesis Protocol A

[00122] Pyrrolopyridine A can be protected with a sulfonyl group to give intermediate B. Intermediate B can be functionalized with piperazine C in a substitution reaction to give intermediate D. Intermediate D may be protected with a group such as Boc (intermediate E ) and then specifically halogenated to give intermediate F. Intermediate F may undergo a halogen-metal exchange reaction to give intermediate G as a boronate or tin intermediate. Intermediate F can also be coupled to a boronate, boronate ester, trialkylol or alkylzinc reagent by a palladium-mediated coupling reaction, such as Suzuki, Stille or Negishi coupling, to give intermediate H. Such transformations are also possible for Intermediate G to be exposed to Intermediate H. Deprotection (de-Boc) of compound H followed by a capping reaction such as amide bond formation or carbamate formation gave intermediate I. Final compounds J can be obtained by deprotection (sulfonyl group) from intermediate I. As shown below, compounds 20, 262, and 410 of Tables 1, 2, and 3 were prepared using Synthesis Protocol A.

Example 1 Synthesis of tert-butyl 4-(2-iodo-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-4-yl)piperazine-1-carboxylate

[00123] Step 1. Synthesis of 4-chloro-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridine

Compound A (50 g, 0.3276 mol, 1 equiv.), 500 ml dichloromethane (DCM), triethylamine (TEA) (50 g, 0.4941 mol, 1.5 equiv.) and dimethylaminopyridine (DMAP) (4 g , 0.0327 mol, 0.1 equiv.) were combined in a 1 L round bottom flask (RBF) at 20°C. The mixture was then cooled to 10°C and then BsCl (70 g, 0.3963 mol, 1.2 equiv.) was added dropwise at 10-20°C. After stirring at 20°C for 18 hours using LC-MS observed the ratio of A /BsCl/ B =0/8/84. The reaction mixture was diluted in 250 ml of water. The organic phase was separated and washed with 250 ml sat. Na ₂ CO ₃ , 250 ml water and 250 ml brine. The organic layer was dried over Na ₂ SO ₄ , concentrated and slurried with petroleum ether to give 83 g of the title product (99% pure, 86% yield).

[00124] Step 2 and 3. Synthesis of tert-butyl 4-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-4-yl)piperazine-1-carboxylate

[00125] Compound B (27 g, 0.0631 mol, 1.0 equiv.), Compound C (24 g, 0.2786 mol, 3.0 equiv.) and 190 ml of N-methylpyrrolidone (NMP) were added to 500 ml RBF at 15°C. The mixture was heated to 140°C and stirred for 3 hours. By LC-MS, a B/D ratio of 0/83 was observed. The mixture was cooled to 15°C and stirred for an additional 18 hours. The insoluble solid was then filtered off and Boc ₂ O (85 g, 0.3895 mol, 4.2 equiv) was added dropwise at 10-25°C. The mixture was stirred for 18 hours at 15°C; using LS-MS observed the ratio of D/E 0/81. 540 ml of ethyl acetate was then added to the mixture and then filtered. The filtrate was washed three times with 200 ml of water and the resulting organic phase was washed with aq. NaHSO ₄ (12.5 g in 150 ml water) and water (200 ml). The organic layer was dried over Na ₂ SO ₄ and concentrated to give the crude product. The crude product was dissolved in 150 ml of DCM, followed by the dropwise addition of 750 ml of petroleum ether at 15° C. over 30 minutes. The solution was then stirred for 30 minutes at 15°C with the formation of a precipitate. 21 g of the title product as a white solid was obtained followed by filtration (99% pure, 51% yield (two steps)).

[00126] Step 4. Synthesis of tert-butyl 4-(2-iodo-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-4-yl)piperazine-1-carboxylate

[00127] Lithium diisopropylamide (LDA) (2 M, 62 ml, 124 mmol) was added dropwise to a mixture of tert-butyl-4-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridine-4- yl)piperazine-1-carboxylate (50 g, 113 mmol) in THF (600 ml) at -78°C. The mixture was stirred at -78°C for 1 h. I ₂ (31 g, 122 mmol) in THF (100 ml) was added at -78°C and the mixture was stirred at -78°C for 1 h. °C and stirred for 0.5 h. The reaction was quenched with aq. Na ₂ S ₂ O ₃ and aq. NH ₄ Cl, extracted with ethyl acetate. Concentrate and purify by silica gel chromatography (petroleum ether:ethyl acetate = 1:1) to give the title product (45 g, 70%) as a light yellow solid. MS (ES+) C ₂₂ H ₂₅ IN ₄ O ₄ S required: 568, obtained: 569 [M+H] ⁺ .

Example 2 Synthesis of oxetan-3-yl-4-(2-(4-(trifluoromethyl)thiazol-2-yl)-1 H -pyrrolo[2,3-b]pyridin-4-yl)piperazine-1-carboxylate

[00128] Step 1. Synthesis of oxetan-3-yl-4-(1-(phenylsulfonyl)-2-(tributylstannyl)-1H-pyrrolo[2,3-b]pyridin-4-yl)piperazin-1-carboxylate

[00129] n-BuLi (21.2 mmol, 2.5 M) was added to a solution of oxetan-3-yl-4-(2-iodo-1-(phenylsulfonyl)-1H- pyrrolo [2,3-b] pyridin-4-yl)piperazine-1-carboxylate (10 g, 17.6 mmol) in THF (150 ml) at -78°C. After stirring at -78° C. for 1 h, Bu ₃ SnCl (6.9 g, 21.2 mmol) was added. The reaction mixture was stirred at -78°C for another 1 h, and then stirred at room temperature overnight. The reaction mixture was extracted with ethyl acetate (200 ml), washed with brine, dried over Na ₂ SO ₄ , filtered and concentrated. The residue was purified by silica gel chromatography (petroleum ether:ethyl acetate = 10:3) to give the title product (5 g, 92%), yield: 39%. MS (ES+) C ₃₃ H ₄₈ N ₄ O ₅ SSn required: 731, obtained 732 [M+H] ⁺ .

[00130] Step 2. Synthesis of oxetan-3-yl-4-(1-(phenylsulfonyl)-2-(4-(trifluoromethyl)thiazol-2-yl)-1H-pyrrolo[2,3-b]pyridin-4 -yl)piperazine-1-carboxylate

[00131] Oxetan-3-yl-4-(1-(phenylsulfonyl)-2-(tributylstannyl)-1 H -pyrrolo[2,3-b]pyridin-4-yl)piperazin-1-carboxylate mixture (250 mg , 342 µmol), 2-bromo-4-(trifluoromethyl)thiazole (120 mg, 513 µmol), CuI (65 mg, 342 mmol) and Pd(PPh ₃ ) ₄ (197 mg, 171 µmol) in toluene (10 ml ) was degassed with N ₂ and then stirred at 100° C. for 16 h under N ₂ atmosphere. The mixture was cooled to room temperature and concentrated. The residue was immediately purified by silica gel chromatography (ethyl acetate:petroleum ether = 3:10) to give the title product (70 mg, 35% yield) as a light yellow solid. MS (ES+) C ₂₅ H ₂₂ F ₃ N ₅ O ₅ S ₂ necessary: 593, obtained: 594 [M+H] ⁺ .

[00132] Step 3. Synthesis of oxetan-3-yl-4-(2-(4-(trifluoromethyl)thiazol-2-yl)-1H-pyrrolo[2,3-b]pyridin-4-yl)piperazin-1 -carboxylate

[00133] Tetrabutylammonium fluoride hydrate (TBAF) (2 ml, 1 M, 2.0 mmol) was added to a solution of oxetan-3-yl-4-(1-(phenylsulfonyl)-2-(4-(trifluoromethyl)thiazol-2 -yl)-1 H -pyrrolo[2,3-b]pyridin-4-yl)piperazin-1-carboxylate (70 mg, 118 μmol) in THF (5 ml). The reaction mixture was stirred at 60° C. for 6 hours. Completion of the reaction was observed by LC-MS. The mixture was diluted with DCM, washed with water and brine, then concentrated. The residue was immediately purified on a silica gel column (MeOH:DCM=1:15) and prep-HPLC to give the title product (13.9 mg, 26% yield) as a white solid. MS (ES+) C ₁₉ H ₁₈ F ₃ N ₅ O ₃ S needed: 453, obtained: 454 [M+H] ⁺ .

Example 3 Synthesis of 2,2-difluorocyclobutyl-4-(2-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-4-yl)piperazin-1-carboxylate

[00134] Step 1. Synthesis of 2-(benzyloxy)cyclobutanone

[00135] 1,2-Bis((trimethylsilyl)oxy)cyclobut-1-ene (1 g, 4.33 mmol) was added to a solution of phenylmethanol (561 mg, 5.19 mmol) in 4 M HCl/dioxane (2 mL ) at room temperature. The reaction mixture was heated to 80° C. for 4 hours. After concentration, the residue was purified by silica gel chromatography (petroleum ether:ethyl acetate=10:1) to give the title product (0.3 g, 39%) as a colorless oil.

[00136] Step 2: Synthesis of ((2,2-difluorocyclobutoxy)methyl)benzene

[00137] A mixture of 2-(benzyloxy)cyclobutanone (0.3 g, 1.70 mmol) in DCM was cooled to 0° C. and diethylaminosulfur trifluoride (DAST) (548 mg, 3.40 mmol) was added. After stirring at room temperature for 4 hours, the reaction mixture was diluted with DCM and washed with aq. NaHCO ₃ and saline. The organic extracts were dried, filtered and concentrated. The residue was purified by silica gel chromatography (petroleum ether:ethyl acetate = 20:1) to give the title product (60 mg, 18%) as a colorless oil.

[00138] Step 3. Synthesis of 2,2-difluorocyclobutanol

[00139] A suspension mixture of ((2,2-difluorocyclobutoxy)methyl)benzene (60 mg, 0.3027 mmol) and 10% Pd/C (100 mg) in diethyl ether was stirred under H ₂ atmosphere for 15 h. After filtration the residue was used in the next step as a solution of ether.

[00140] Step 4. Synthesis of 2,2-difluorocyclobutyl-1H-imidazole-1-carboxylate

[00141] A mixture of 2,2-difluorocyclobutanol (the above ether solution, 0.3027 mmol is acceptable) and CDI (50 mg, 0.305 mmol) in DCM was stirred at room temperature for 4 hours. The resulting solution was used in the next step without further purification. MS (ES+) C ₈ H ₈ F ₂ N ₂ O ₂ required: 202, obtained 203 [M+H] ⁺ .

[00142] Step 5. Synthesis of 2,2-difluorocyclobutyl-4-(2-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-4-yl)piperazin- 1-carboxylate

[00143] Triethylamine (60.0 mg, 0.5934 mmol) was added to a mixture of 2-(1-methyl- 1H -pyrazol-4-yl)-4-(piperazin-1-yl)-1H- pyrrolo [ 2,3-b]pyridine hydrochloride (94.5 mg, 0.2967 mmol) in DCM and stirred for 10 min at room temperature, then a solution of 2,2-difluorocyclobutyl- 1H -imidazole-1-carboxylate ( 60 mg, 0.2967 mmol) in DCM. After stirring at room temperature for 15 hours, the reaction mixture was diluted with DCM and washed with water. The organic layer was dried, filtered and concentrated. The residue was purified by silica gel chromatography (DCM:MeOH=10:1) and then purified by prep-HPLC to give the title product (14.4 mg, 12%) as a white solid. MS (ES+) C ₂₀ H ₂₂ F ₂ N ₆ O ₂ required: 416, obtained 417 [M+H] ⁺ .

Example 4 Synthesis of cyclobutyl (4-(2-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-4-yl)piperazin-1-yl)methanone

[00144] Step 1. Synthesis of 2-(1-methyl-1H-pyrazol-4-yl)-1-(phenylsulfonyl)-4-(piperazin-1-yl)-1H-pyrrolo[2,3-b]pyridine

[00145] MeOH/HCl (5 ml) was added to compound 1 (200 mg, 0.45 mmol). The mixture was stirred at 30°C for 5 hours. The mixture was concentrated in vacuo to give the desired compound.

[00146] Step 2. Synthesis of cyclobutyl(4-(2-(1-methyl-1H-pyrazol-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-4-yl) piperazin-1-yl) methanone

[00147] Cyclobutanecarboxylic acid (14 mg, 0.14 mmol), N-methylmorpholine (NMM) (61 mg, 0.60 mmol) and HBTU (49 mg, 0.13 mmol) were added to a mixture of compound 2 (50 mg, 0.12 mmol) in DMF (1.5 ml). The mixture was stirred at 25°C for 5 hours. The mixture was used immediately in the next step.

[00148] Step 3. Synthesis of cyclobutyl(4-(2-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-4-yl)piperazin-1-yl) methanone

[00149] KOH (10 eq.) was added to compound 3 (1.0 eq.) in 2 ml MeOH. The mixture was stirred at room temperature for 3 hours. Acetic acid was added to the mixture to adjust the pH to 7, and the mixture was purified by prep-HPLC to give the desired compound.

Synthesis Protocol B

[00150] Intermediate H was prepared using the methods described in Synthesis Protocol A. Intermediate H can be further functionalized by halogenation, after halogenation, a palladium-mediated coupling reaction is performed (e.g., Suzuki, Stille, Sonogashira, or Negishi coupling), or by metalation, after which was reacted with an electrophile to give intermediate K. Deprotection of (de-Boc) K followed by a capping reaction such as amide bond formation or carbamate formation gave intermediate L. Final compounds M can be obtained by deprotection (sulfonyl group) from the intermediate compound L . As shown below, compounds 132, 258 and 267 of Tables 1, 2 and 3 were prepared using Synthesis Protocol B.

Example 5 Synthesis of (1r,3r)-3-fluorocyclobutyl-4-(3-fluoro-2-(1-methyl-1 H -pyrazol-4-yl)-1 H -pyrrolo[2,3-b]pyridin-4-yl)piperazine-1-carboxylate

[00151] Step 1: Synthesis of (tert-butyl-4-(3-fluoro-2-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-4-yl )piperazine-1-carboxylate

[00152] N-Fluoro-N-(phenylsulfonyl)benzenesulfonamide (82.4 mg, 0.2614 mmol) was added to a solution of t-butyl-4-(2-(1-methyl- 1H -pyrazol-4-yl) -1 H -pyrrolo[2,3-b]pyridin-4-yl)piperazine-1-carboxylate (100 mg, 0.2614 mmol) in DCM. After stirring at room temperature for 15 hours, the reaction mixture was diluted with DCM and washed with aq. _NaHC03 . The organic layer was dried, filtered and concentrated. The residue was purified by silica gel chromatography (DCM:MeOH=20:1) to give the title product (30 mg, 40% pure, 12%) as a yellow solid. MS (ES+) C ₂₀ H ₂₅ FN ₆ O ₂ needed: 400, obtained 401 [M+H] ⁺ .

[00153] Step 2. Synthesis of 3-fluoro-2-(1-methyl-1H-pyrazol-4-yl)-4-(piperazin-1-yl)-1H-pyrrolo[2,3-b]pyridine

[00154] 4 M HCl/dioxane was added to a solution of tert-butyl-4-(3-fluoro-2-(1-methyl- 1H -pyrazol-4-yl)-1H- pyrrolo [2,3-b] pyridin-4-yl)piperazine-1-carboxylate (60 mg, 0.1498 mmol) in DCM. After stirring at room temperature for 3 hours, the reaction mixture was concentrated to give the title product (crude HCl salt, 45 mg, quantitatively) as a yellow solid. MS (ES+) C ₁₅ H ₁₇ FN ₆ required: 300, obtained 301 [M+H] ⁺ .

[00155] Step 3. Synthesis of (1r,3r)-3-fluorocyclobutyl-4-(3-fluoro-2-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b] pyridin-4-yl)piperazine-1-carboxylate

[00156] CDI (72.8 mg, 0.4494 mmol) was added to a solution of (1r,3r)-3-fluorocyclobutanol (40.4 mg, 0.4494 mmol) in DCM (3 mL). After stirring for 6 hours at room temperature, the resulting solution was added to a mixture of 3-fluoro-2-(1-methyl- 1H -pyrazol-4-yl)-4-(piperazin-1-yl)-1H- pyrrolo [ 2,3-b]pyridine (45 mg, 0.1498 mmol) and TEA (30 mg, 0.30 mmol) in DCM. After stirring at room temperature for another 15 hours, the reaction mixture was diluted with DCM and washed with water. The organic layer was dried, filtered and concentrated. The resulting precipitate was washed with MeOH to give the title product (34.8 mg, 56%) as a yellow solid. MS (ES+) C ₂₀ H ₂₂ F ₂ N ₆ O ₂ required: 416, obtained 417 [M+H] ⁺ .

Example 6 Synthesis of ethyl 4-(3-cyano-2-(1-(difluoromethyl)-1 H -pyrazol-4-yl)-1 H -pyrrolo[2,3-b]pyridin-4-yl)piperazine-1-carboxylate

[00157] Step 1. Synthesis of tert-butyl-4-(2-(1-(difluoromethyl)-1H-pyrazol-4-yl)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[ 2,3-b]pyridin-4-yl)piperazine-1-carboxylate

[00158] A mixture of 1-(difluoromethyl)-4-iodo- 1H -pyrazole (200 mg, 819 µmol) and (4-(4-(tert-butoxycarbonyl)piperazin-1-yl)-1-((2- (trimethylsilyl)ethoxy)methyl)-1 H -pyrrolo[2,3-b]pyridin-2-yl)boronic acid (390 mg, 819 µmol), Na ₂ CO ₃ (259 mg, 2.45 mmol) and Pd (dppf)Cl ₂ (60 mg, 82 μmol) in THF (20 ml)/H ₂ O (2 ml) was stirred at 75° C. under N ₂ for another 1 hour. Completion of the reaction was observed by LC-MS. The reaction mixture was cooled, concentrated and immediately purified on a silica gel column (ethyl acetate/petroleum ether=1/5-5/1) to give the title compound (312 mg, 69% yield) as a colorless oil. MS (ES+) C ₂₆ H ₃₈ F ₂ N ₆ O ₃ Si required: 548, 549 obtained [M+H] ⁺ .

[00159] Step 2. Synthesis of tert-butyl-4-(3-bromo-2-(1-(difluoromethyl)-1H-pyrazol-4-yl)-1-((2-(trimethylsilyl)ethoxy)methyl)- 1H-pyrrolo[2,3-b]pyridin-4-yl)piperazine-1-carboxylate

[00160] N-Bromosuccinimide (NBS) (101 mg, 568 µmol) was added to a solution of tert-butyl-4-(2-(1-(difluoromethyl)-1H- pyrazol -4-yl)-1-((2 -(trimethylsilyl)ethoxy)methyl)-1H- pyrrolo [2,3-b]pyridin-4-yl)piperazin-1-carboxylate (312 mg, 568 µmol) in DCM (20 ml) at room temperature and then stirred at RT for 1 hour. Completion of the reaction was observed by LC-MS. The reaction mixture was concentrated, and the residue was immediately purified on a silica gel column (ethyl acetate/petroleum ether=1/5-5/1) to give the title compound (281 mg, 79% yield) as a colorless oil. MS (ES+) C ₂₆ H ₃₇ BrF ₂ N ₆ O ₃ Si required: 626, 628, obtained 627, 629 [M+H] ⁺ .

[00161] Step 3. Synthesis of tert-butyl-4-(3-cyano-2-(1-(difluoromethyl)-1H-pyrazol-4-yl)-1-((2-(trimethylsilyl)ethoxy)methyl)- 1H-pyrrolo[2,3-b]pyridin-4-yl)piperazine-1-carboxylate

[00162] A mixture of tert-butyl-4-(3-bromo-2-(1-(difluoromethyl)-1 H -pyrazol-4-yl)-1-((2-(trimethylsilyl)ethoxy)methyl)-1 H -pyrrolo[2,3-b]pyridin-4-yl)piperazin-1-carboxylate (281 mg, 447 µmol), dicyanozinc (104 mg, 894 µmol) and Pd(PPh ₃ ) ₄ (51.6 mg, 44 .7 μmol) in DMA (2 ml) was stirred at 120° C. for 1 h. Completion of the reaction was observed by LC-MS. The reaction mixture was cooled and concentrated. The residue was purified on a silica gel column (ethyl acetate/petroleum ether=3/10-3:1) to give the title compound (223 mg, 86% yield) as a white solid. MS (ES+) C ₂₇ H ₃₇ F ₂ N ₇ O ₃ Si required: 573, obtained 574 [M+H] ⁺ .

[00163] Step 4. Synthesis of 2-(1-(difluoromethyl)-1H-pyrazol-4-yl)-4-(piperazin-1-yl)-1H-pyrrolo[2,3-b]pyridine-3-carbonitrile

[00164] TFA (1 ml) was added to a solution of tert-butyl-4-(3-cyano-2-(1-(difluoromethyl)-1H- pyrazol -4-yl)-1-((2-(trimethylsilyl) ethoxy)methyl)-1 H -pyrrolo[2,3-b]pyridin-4-yl)piperazine-1-carboxylate (225 mg, 392 µmol) in DCM (2 ml) at room temperature, then stirred for 16 hours Using LC-MS observed the completion of the reaction. The reaction mixture was concentrated to give the crude product (130 mg) as a yellow oil. MS (ES+) C ₁₆ H ₁₅ F ₂ N ₇ required: 343, obtained 344 [M+H] ⁺ .

[00165] Step 5. Synthesis of ethyl 4-(3-cyano-2-(1-(difluoromethyl)-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-4-yl) piperazine-1-carboxylate

[00166] Ethyl chloroformate (38 mg, 348 µmol) was added to a solution of 2-(1-(difluoromethyl)-1H- pyrazol -4-yl)-4-(piperazin-1-yl)-1H- pyrrolo [2, 3-b]pyridine-3-carbonitrile (60 mg, 174 µmol) and triethylamine (522 mg, 522 µmol) in DMF (2 ml) and then stirred at room temperature for 1 h. Completion was observed by LC-MS reactions. The reaction mixture was concentrated and purified by prep-HPLC to give the title compound (33.1 mg, 45%) as a white solid. MS (ES+) C ₁₉ H ₁₉ F ₂ N ₇ O ₂ required: 415, obtained 416 [M+H] ⁺ .

Example 7 Synthesis of ethyl 4-(2-(1-methyl-1H-pyrazol-4-yl)-3-(prop-1-yn-1-yl)-1 H -pyrrolo[2,3-b]pyridin-4-yl)piperazine-1-carboxylate

[00167] Step 1. Synthesis of tert-butyl-4-(2-(1-methyl-1H-pyrazol-4-yl)-1-(phenylsulfonyl)-3-(prop-1-yn-1-yl)- 1H-pyrrolo[2,3-b]pyridin-4-yl)piperazine-1-carboxylate

[ 00168 ] tert-Butyl-4-(3-bromo-2-(1-methyl- 1H -pyrazol-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridine mixture -4-yl)piperazin-1-carboxylate (600mg, 1.0mmol), trimethyl(prop-1-yn-1-yl)silane (560mg, 5.0mmol), Pd(t-Bu ₃ P ) ₂ (100 mg, 0.20 mmol), CuI (38 mg, 0.20 mmol), triethylamine (500 mg, 5.0 mmol) and K ₂ CO ₃ (408 mg, 3.0 mmol) in DMF ( 10 ml) was degassed with nitrogen and then stirred at 100°C for 3 hours. The reaction mixture was evaporated to dryness. The residue was purified by flash column chromatography (petroleum ether:ethyl acetate=10:1-1:5) to give the title compound (200 mg, 35% yield) as a yellow solid. MS (ES+) C ₂₉ H ₃₂ N ₆ O ₄ S required: 560, 561 obtained [M+H] ⁺ .

[00169] Step 2. Synthesis of 2-(1-methyl-1H-pyrazol-4-yl)-1-(phenylsulfonyl)-4-(piperazin-1-yl)-3-(prop-1-yn-1- yl)-1H-pyrrolo[2,3-b]pyridine

[00170] TFA (1 ml) was added to a solution of tert-butyl-4-(2-(1-methyl- 1H -pyrazol-4-yl)-1-(phenylsulfonyl)-3-(prop-1-yn- 1-yl)-1 H -pyrrolo[2,3-b]pyridin-4-yl)piperazin-1-carboxylate (200 mg, 0.35 mmol) in DCM (3 ml) and then stirred at room temperature in within 4 hours. Using LC-MS, complete consumption of the starting material was observed. The reaction mixture was evaporated to dryness to give the crude product without further purification. MS (ES+) C ₂₄ H ₂₄ N ₆ O ₂ S required: 460, obtained 461 [M+H] ⁺ .

[00171] Step 3. Synthesis of ethyl 4-(2-(1-methyl-1H-pyrazol-4-yl)-1-(phenylsulfonyl)-3-(prop-1-yn-1-yl)-1H- pyrrolo[2,3-b]pyridin-4-yl)piperazine-1-carboxylate

[00172] Ethyl chloroformate (57 mg, 0.53 mmol) was added to a solution of 2-(1-methyl- 1H -pyrazol-4-yl)-1-(phenylsulfonyl)-4-(piperazin-1-yl)-3 -(prop-1-yn-1-yl)-1 H -pyrrolo[2,3-b]pyridine (crude, 0.35 mmol) and triethylamine (350 mg, 3.5 mmol) in DCM (3 ml) and then stirred at room temperature for 2 hours. The reaction mixture was diluted with DCM and washed with water and brine. The organic layer was evaporated to dryness to give the crude product without further purification. MS (ES+) C ₂₇ H ₂₈ N ₆ O ₄ S needed: 532, obtained 533 [M+H] ⁺ .

[00173] Step 4. Synthesis of ethyl 4-(2-(1-methyl-1H-pyrazol-4-yl)-3-(prop-1-yn-1-yl)-1H-pyrrolo[2,3- b]pyridin-4-yl)piperazine-1-carboxylate

[00174] TBAF (1.0 M in THF, 1.0 ml, 1.0 mmol) was added to a solution of ethyl-4-(2-(1-methyl- 1H -pyrazol-4-yl)-1-( phenylsulfonyl)-3-(prop-1-yn-1-yl)-1 H -pyrrolo[2,3-b]pyridin-4-yl)piperazin-1-carboxylate (crude, presumably 0.35 mmol) in THF (2 ml) and then stirred at 60°C for 2 hours. The reaction mixture was cooled, concentrated and immediately purified by prep-HPLC to give the title compound (23 mg, 16% yield) as a white solid. MS (ES+) C ₂₁ H ₂₄ N ₆ O ₂ necessary: 392, obtained: 393 [M+H] ⁺ .

C synthesis protocol

[00175] Intermediate E was prepared using the methods described in Synthesis Protocol A. Intermediate E can be selectively deprotected to give Intermediate N and then re-protected to give Intermediate P. Intermediate P can be further functionalized by metalation/borylation to give boronic acid/ester intermediate Q. Intermediate Q can be further functionalized by a palladium-mediated coupling reaction (eg, Suzuki, Stille, Sonogashira, or Negishi coupling) to give intermediate R. Double deprotection of compound R followed by a capping reaction such as amide bond formation or carbamate formation gave intermediate I. Final compounds J can be obtained by substitution, halogenation, or other capping reactions of intermediate I. As shown below, Compound 205 of Tables 1, 2, and 3 was prepared using Synthesis Protocol C.

Example 8 Synthesis of (1r,3r)-3-(4-(2-(2-methylthiazol-4-yl)-1 H -pyrrolo[2,3-b]pyridin-4-yl)piperazin-1-carbonyl)cyclobutanecarbonitrile

[00176] Step 1. Synthesis of tert-butyl-tert-butyl-4-(1H-pyrrolo[2,3-b]pyridin-4-yl)piperazine-1-carboxylate

[00177] Sodium hydroxide (170 ml, 2.0 M) was added to a solution of tert-butyl-4-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-4-yl)piperazine-1-carboxylate (50 g, 112.0 mmol) in MeOH (170 ml). Then the resulting mixture was heated at 70°C for 16 hours. After cooling to room temperature, the solid precipitate was collected by filtration, which was then dried to give the title compound. (30.0 g, 89%) as a white solid. MS (ES+) C_sixteenH₂₂N_fourO₂ needed: 302, received: 303 [M+H]⁺.

[00178] Step 2. Synthesis of t-buty-4-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-4-yl)piperazine-1-carboxylate

[00179] Sodium hydride (1.18 g, 49.5 mmol) was slowly added to a solution of tert-butyl 4-( 1H -pyrrolo[2,3-b]pyridin-4-yl)piperazine-1-carboxylate ( 10 g, 33 mmol) in DMF (150 ml) and stirred at 0° C. for 30 minutes. 2-(Trimethylsilyl)ethoxymethyl chloride (SEMCl) (5.5 g, 33 mmol) was added followed by stirring for an additional 2 hours. A largely clear reaction mixture was observed by LC-MS. The reaction was quenched with H ₂ O and extracted with EtOAc. The organic layer was washed with H ₂ O and brine, dried over Na ₂ SO ₄ and then concentrated to give the crude product, which was purified by silica gel flash chromatography eluting with petroleum ether/ethyl acetate (3:1) to give the title compound (12 .0 g, 84%) as a yellow solid. MS (ES+) C ₂₂ H ₃₆ N ₄ O ₃ Si necessary: 432, obtained: 433 [M+H] ⁺ .

[00180] Step 3. Synthesis of 4-(4-(tert-butoxycarbonyl)piperazin-1-yl)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridine- 2-ylboronic acid

[00181] LDA (29.5 g, 276 mmol, 2.0 M) was added dropwise to a solution of tert-butyl-4-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H- pyrrolo [2 ,3-b]pyridin-4-yl)piperazine-1-carboxylate (23 g, 53.1 mmol) in dry THF (300 ml) at -7°C followed by stirring at -78°C for 30 minutes . Triisopropyl borate (64.8 g, 345.0 mmol) was then added dropwise at -78°C. Next, the reaction mixture was stirred at -78°C for another 1 hour, using LC-MS observed the completion of the reaction. The cold bath was removed. The reaction was quenched with aqueous NH ₄ Cl and extracted with EA. The organic layer was washed with water and brine, dried over Na ₂ SO ₄ and then concentrated to give the title compound (17.66 g, 70%) as a yellow solid. MS (ES+) C ₂₂ H ₃₇ BN ₄ O ₅ Si necessary: 476, obtained: 477 [M+H] ⁺ .

[00182] Step 4. Synthesis of tert-butyl-4-(2-(2-methylthiazol-4-yl)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b] pyridin-4-yl)piperazine-1-carboxylate

[00183] 4-Bromo-2-methylthiazole mixture (600 mg, 3.36 mmol), (4-(4-(ethoxycarbonyl)piperazin-1-yl)-1-((2-(trimethylsilyl)ethoxy)methyl) -1 H -pyrrolo[2,3-b]pyridin-2-yl)boronic acid (1.60 g, 3.36 mmol), Pd(dppf)Cl ₂ (245 mg, 336 μmol) and triethylamine (1, 01 g, 10.0 mmol) in dioxane (20 ml) and H ₂ O (5 ml) was stirred at 70°C for 2 hours After that, the reaction mixture was cooled and concentrated. The residue was purified on a silica gel column (petroleum ether/ethyl acetate = 2/1) to give the title compound as a yellow solid (1.5 g, 84%). MS (ES+) C ₂₆ H ₃₉ N ₅ O ₃ SSi required: 529, obtained: 530 [M+H] ⁺ .

[00184] Step 5. Synthesis of 2-methyl-4-(4-(piperazin-1-yl)-1H-pyrrolo[2,3-b]pyridin-2-yl)thiazole

[00185] TFA (5 ml) was added to a solution of tert-butyl-4-(2-(2-methylthiazol-4-yl)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H- pyrrolo [2 ,3-b]pyridin-4-yl)piperazine-1-carboxylate (1.5 g, 2.83 mmol) in DCM (5 ml) and then the solution was stirred at 40°C for 12 h. Next, the solution was concentrated at 40-50°C. The residue was purified on a reverse phase column and then triturated with CH ₃ OH (15 mL) to give the title compound as a white solid (620 mg, 73%). MS (ES+) C ₁₅ H ₁₇ N ₅ S needed: 299, obtained: 300 [M+H] ⁺ .

[00186] Step 6. Synthesis of (1s,3s)-3-(4-(2-(2-methylthiazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-4-yl)piperazin-1 -carbonyl)cyclobutyl-4-methylbenzenesulfonate

[00187] HATU (306 mg, 805 µmol) was added to a mixture of 2-methyl-4-(4-(piperazin-1-yl)-1 H -pyrrolo[2,3-b]pyridin-2-yl)thiazole ( 201 mg, 671 µmol), (1s,3s)-3-(tosyloxy)cyclobutanecarboxylic acid (200 mg, 738 µmol) and DIEA (260 mg, 2.01 mmol) in DMF (5 ml) and then stirred at room temperature temperature for 16 hours. The reaction mixture was diluted with ethyl acetate and washed with water and brine. The organic layer was dried, filtered and concentrated. The residue was purified on a silica gel column (MeOH/EtOAc = 1/10) to give the title compound (226 mg, 55%) as a colorless oil. MS (ES+) C ₂₇ H ₂₉ N ₅ O ₄ S ₂ needed: 551, 552 [M+H] ⁺ obtained.

[00188] Step 7. Synthesis of (1r,3r)-3-(4-(2-(2-methylthiazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-4-yl)piperazin-1 -carbonyl)cyclobutanecarbonitrile

Tetraethylammonium cyanide (32 mg, 2.05 µmol) was added to a mixture of (1s,3s)-3-(4-(2-(2-methylthiazol-4-yl)-1H- pyrrolo [2,3-b]pyridine -4-yl)piperazin-1-carbonyl)cyclobutyl-4-methylbenzenesulfonate (226 mg, 409 μmol) in CH ₃ CN (10 ml) and then stirred at 80°C for 16 h. The reaction mixture was cooled and concentrated. The residue was immediately purified by prep-HPLC to give the title compound (44.3 mg, 36%) as a white solid. MS (ES+) C ₂₁ H ₂₂ N ₆ OS required: 406, obtained 407 [M+H] ⁺ .

Example 9 Synthesis of Other Exemplary Compounds

[00189] Table 2 indicates that Synthesis Protocol A, B, or C described in this disclosure was used to synthesize the various compounds described herein. Blank values indicate that a different synthesis scheme than that of Synthesis Protocols A, B, or C was used, and that the synthesis scheme for such a compound is set forth in the examples.

Table 2. Synthesis protocols used for exemplary compounds

No. Synthesis protocol 1 A 2 A 3 A four A five A 6 A 7 A 8 A nine A 10 A eleven A 12 A 13 A fourteen A 15 A sixteen A 17 A eighteen A nineteen A 20 A 21 A 22 A 23 A 24 A 25 A 26 A 27 A 29 A thirty A 31 A 32 A 33 A 34 A 35 A 36 A 37 A 38 B 39 A 40 A 41 A 42 A 43 A 44 A 45 A 46 A 47 A 48 A 49 A 50 B 51 A 52 A 53 A 54 A 55 B 56 A 57 A 58 A 59 A 60 A 61 A 62 A 63 A 64 A 65 A 66 A 67 A 68 B 69 A 70 A 71 A 72 A 73 A 74 A 75 A 76 A 77 A 78 A 79 A 80 A 81 A 82 A 83 A 84 A 85 A 86 A 87 A 88 A 89 A 90 A 91 A 92 A 93 A 94 A 95 A 96 A 97 A 98 A 99 B one hundred A 101 A 102 A 103 A 104 A 105 A 106 A 107 A 108 A 109 A 110 A 111 B 112 A 113 A 114 A 115 B 116 A 117 A 118 A 119 A 120 A 121 B 122 A 123 C 124 A 125 A 126 A 127 A 128 A 129 B 130 B 131 A 132 B 133 A 134 A 135 A 136 B 137 B 138 A 139 A 140 B 141 A 142 A 143 A 144 A 145 A 146 A 147 A 148 B 149 A 150 A 151 A 152 A 153 A 154 A 155 A 156 A 157 A 158 A 159 A 160 A 161 A 162 A 163 A 164 A 165 A 166 A 167 A 168 A 169 A 170 A 171 A 172 A 173 A 174 A 175 A 177 A 178 B 179 A 180 A 181 A 182 A 183 A 184 A 185 A 186 B 187 B 188 A 189 A 190 A 191 A 192 A 194 A 195 A 196 A 197 A 198 A 199 B 200 B 201 B 202 A 203 A 204 A 205 C 206 A 207 B 208 B 209 A 210 A 211 A 212 A 213 A 214 A 215 B 216 B 217 B 218 A 219 A 220 A 221 A 222 A 223 A 224 A 225 A 226 A 227 A 228 B 229 A 230 A 231 A 232 A 233 A 234 A 235 A 236 A 237 B 238 A 239 A 240 A 241 A 242 A 243 A 244 A 245 B 246 A 247 A 248 A 249 A 250 A 251 A 252 A 253 A 254 A 255 B 256 B 257 B 258 B 259 A 260 A 261 A 262 A 263 A 264 A 265 A 266 A 267 B 268 A 269 A 270 A 271 A 272 A 273 A 274 B 275 A 276 B 277 A 278 A 279 A 280 A 281 A 282 A 283 A 284 B 285 B 286 A 287 A 288 B 289 B 290 B 291 A 292 A 293 B 294 B 295 B 296 B 297 B 299 C 300 A 301 A 302 A 303 B 304 A 305 A 306 A 307 A 308 B 309 A 310 A 311 A 312 A 313 A 314 A 315 A 316 A 317 A 318 B 319 A 320 B 321 B 322 A 323 A 324 A 325 A 326 A 327 A 328 A 329 A 330 B 331 B 332 B 333 A 334 A 335 A 336 A 337 B 338 A 339 B 340 B 341 B 342 B 343 A 344 B 345 A 346 A 347 B 348 A 349 A 350 B 351 A 352 A 353 A 354 A 355 A 356 B 357 B 358 A 359 A 360 B 361 A 362 A 363 B 364 A 365 B 366 B 367 B 368 B 369 B 370 B 371 A 372 A 373 A 374 B 375 B 376 B 377 A 378 A 379 A 380 A 381 A 382 A 383 A 384 A 385 A 386 A 387 A 388 A 389 A 390 A 391 B 392 A 393 A 394 B 395 B 396 A 397 B 398 A 399 A 400 A 401 A 402 A 403 A 404 B 405 A 406 A 407 B 408 A 409 A 410 A 412 B 413 B 414 B 415 A 416 A 417 A 418 A 420 A 421 A 422 A 423 A 424 A 425 A 426 B 427 A 428 A 429 A 430 A 431 A 432 A 433 A 434 B 436 A 437 A 438 A 439 A 440 B 441 B 442 A 443 B 444 A 445 A 446 A 447 A 448 A 449 B 450 A 451 A 452 A 453 A 454 A 455 A 456 A 457 A 458 A 459 A 460 A 461 A 462 A 463 A 464 A 465 B 466 A 467 A 468 A 469 A 470 B 471 A 472 A 473 A 474 A 475 A 476 A 477 A 478 A 479 A

Example 10 ALK Binding Assays

[00190] Binding assays were performed using LANTHASCREEN® technology (ThermoFisher Scientific). LANTHASCREEN® is a displacement competitive binding assay in which the estimated steady state binding site occupancy is measured using a time-resolved fluorescence energy transfer (TR-FRET) readout between a fluorescent indicator and a europium (Eu) labeled kinase-specific antibody. , or expression label (eg GST) of interest. Substitution of an indicator with a compound of the present disclosure reduces TR-FRET and is directly proportional to the TR-FRET between indicator and antibody. The indicator was used at a concentration equal to or close to its Kd for the kinase. The Eu labeled antibody was typically used in excess to ensure sampling of all competent protein capable of binding the indicator.

[00191] Mutant ALK2 labeled at the N-terminus with GST (ALK2 R206H Carna Bioscience (09-148) or ALK2 R206H ThermoFisher (PV6232)), Eu labeled anti-GST antibody (ThermoFisher), and Kinase Tracer 178 ( ThermoFisher).

[00192] In all cases, the kinase (2-5 nM) was mixed with a mixture of Eu labeled antibody (4-10 nM) and an indicator (50 nM) was incubated with test compound titrations prepared in 100% DMSO (final 1% DMSO) for 30 minutes at room temperature. All reagents and compounds were dissolved in Kinase Buffer A (ThermoFisher) to reach the final concentration. Plates were read on an EnVision® PerkinElmer multichannel plate reader or BioTek Synergy Neo plate reader and the signal in the assay was represented as TR-FRET emission ratio (λ _ex 330 nm, λ ^em 662 nm and λ ^em 665 nm). This reading was normalized to 0% and 100% inhibited control wells, plotted against inhibitor concentration, and fitted to a 4-parameter log dose-response curve.

[00193] The results of this assay are shown in Table 3 in the column labeled "Binding Assay", where "A" is an IC ₅₀ that is less than or equal to 10 nM; "B" is an IC ₅₀ that is greater than 10 nM and less than or equal to 50 nM; and "C" is an IC ₅₀ that is greater than 50 nM. Empty values in the table indicate that a particular compound was not tested in this assay.

Example 11 Cellular Assay of ALK2-R206H Activity in a Cell

A. Cell line HEK293-ALK2-R206H

[00194] A stable HEK293-based cell line (ATCC, cat. no. CRL1573) expressing human ALK2 R206H cDNA (synthesized with GeneScript, Piscataway, NJ) and a C-terminal FLAG tag was generated by lentivirus transduction followed by blastidin selection (Life) Technologies, cat # A1113902) at 10 µg/mL for > 2 weeks. This cell line was named HEK293-ALK2-R206H.

b. Measurement of Smad1-Ser463/Ser465 Phosphorylation with AlphaLISA

[00195] HEK293-ALK2-R206H cells were grown, harvested, and then resuspended in serum-free phenol red-free high glucose DMEM (Life Technologies, catalog # 31053). The medium also contained 50 units/ml penicillin and 50 μg/ml streptomycin (Life Technologies, cat. no. 15070-063). HEK293-ALK2-R206H cells were then seeded in white opaque 384-well microplates (2 x 10 ⁴ /well) (OptiPlate-384, PerkinElmer, Waltham, MA, Cat # 6007299) overnight (>16 hours) at 37° C, 5% CO ₂ for use in the analysis.

[00196] Test compounds were first diluted to 4 mM or 0.4 mM and then serially diluted 3-fold to 10 different concentrations using DMSO. Each compound concentration was further diluted 40-fold with phenol red-free DMEM (Life Technologies, Cat # 31053). Then 2 μl of the diluted compounds were dispensed into microplate wells containing HEK293-ALK2-R206H cells in duplicate. In this way, each compound was tested at 10 doses (3-fold serial dilution with a maximum concentration of 10 μM or 1 μM). Liquid handling was performed using the Bravo Automated Liquid Handling Platform (Agilent Technologies). DMSO without compound was used as a negative control. The positive control was 1 μM LDN193189, a known bone morphogenetic protein (BMP inhibitor).

[00197] After 2-3 hours of incubation with test compound or control, cells were lysed and signal developed using the ALPHASCREEN® SUREFIRE® SMAD1 (p-Ser463/465) kinase cell assay kit (PerkinElmer, catalog # TGRSM1S10K) according to the protocol recommended manufacturer. Microplates were read using an ENVISION® Perkin Elmer plate reader (emission 520-620 nM). The signal reflected the content of phospho-Ser/463/465-Smad1 in the lysate. Raw data were plotted using DMSO negative and LDN193189 positive controls as 0% and 100% inhibition, respectively. A 10-point dose-response curve was used to calculate IC ₅₀ values.

[00198] The results of this assay are shown in Table 3 in the column labeled "Cell Assay", where "A" is an IC ₅₀ that is less than or equal to 100 nM; "B" is an IC ₅₀ that is greater than 100 nM and less than or equal to 500 nM; "C" is an IC ₅₀ that is greater than 500 nM. Empty values in the table indicate that a particular compound was not tested in this assay.

[00199] Table 3 uses the following designations.

[00200] For the data in the Binding Assay column: ≤ 10 nM = A; ≥ 10-50 nM = B; > 50 nM = C; and blank values in the table indicate that the particular compound was not tested in this assay.

[00201] For the data in the cell line column: ≤ 100 nM = A; ≥ 100-500 nM = B; > 500 nM = C; and blank values in the table indicate that the particular compound was not tested in this assay.

Table 3. ALK2 inhibitory activity of exemplary compounds according to the present disclosure

No. Binding analysis cell line 1 B C 2 A C 3 B four B five B 6 A B 7 A A 8 A B nine A 10 B eleven A B 12 A B 13 A B fourteen C 15 B sixteen B 17 B eighteen B nineteen A B 20 A 21 A B 22 B 23 A B 24 A B 25 A 26 A B 27 A 29 A A thirty A A 31 B 32 B B 33 B B 34 A B 35 A B 36 A 37 A A 38 A A 39 A B 40 A B 41 A B 42 B 43 C 44 B 45 A A 46 A A 47 A 48 A B 49 A B 50 A A 51 A B 52 B B 53 A A 54 A B 55 A B 56 A B 57 A 58 C 59 A B 60 A B 61 A 62 B 63 B 64 A B 65 A A 66 A B 67 A B 68 A A 69 A A 70 A A 71 A B 72 B 73 A 74 B 75 A A 76 A A 77 A A 78 A 79 A 80 A 81 B 82 A C 83 B 84 B 85 A 86 A A 87 B 88 A 89 A A 90 A A 91 A B 92 A 93 A A 94 A 95 A 96 A A 97 A B 98 A B 99 A one hundred A B 101 B 102 A B 103 A B 104 A B 105 A B 106 B 107 B 108 B 109 A A 110 B 111 A B 112 A A 113 A A 114 A A 115 A A 116 A A 117 A A 118 A B 119 C 120 A B 121 A A 122 A B 123 A B 124 A A 125 A A 126 A A 127 B B 128 A B 129 A A 130 A A 131 B C 132 A A 133 A B 134 A B 135 A B 136 A A 137 A A 138 A 139 A A 140 A A 141 A 142 A 143 A 144 A C 145 A A 146 A A 147 A A 148 A B 149 A B 150 A B 151 A B 152 A B 153 A B 154 A 155 A C 156 A 157 C 158 A 159 A A 160 A A 161 A A 162 A A 163 A 164 A 165 B 166 B 167 A A 168 A 169 A A 170 A A 171 A B 172 A B 173 A B 174 A B 175 A B 177 A A 178 A B 179 A B 180 A B 181 A 182 B 183 A A 184 A 185 A B 186 A B 187 A A 188 A A 189 A A 190 A A 191 A B 192 A B 194 A A 195 A A 196 B 197 A A 198 A B 199 A A 200 A A 201 A A 202 A A 203 A A 204 A B 205 A A 206 B 207 A A 208 A A 209 A B 210 A B 211 C 212 A A 213 A B 214 A B 215 A B 216 A 217 A 218 A A 219 A A 220 B C 221 A B 222 A 223 B 224 A C 225 A B 226 B 227 A B 228 A A 229 A 230 A 231 A A 232 A A 233 A B 234 A B 235 A 236 A 237 A 238 A 239 C 240 B 241 A A 242 A A 243 A A 244 A A 245 A A 246 A 247 A 248 A A 249 A A 250 A A 251 A B 252 A A 253 B 254 A B 255 A A 256 A A 257 A A 258 A A 259 A B 260 A A 261 A 262 A A 263 A A 264 A A 265 A A 266 A A 267 A A 268 A A 269 A A 270 A A 271 A A 272 A A 273 A B 274 A A 275 A A 276 A A 277 A A 278 A A 279 A A 280 A A 281 A B 282 A A 283 A B 284 A A 285 A A 286 A B 287 A B 288 A A 289 A A 290 A A 291 A A 292 A B 293 A 294 A A 295 A A 296 A A 297 A A 299 A A 300 A B 301 A B 302 A A 303 A A 304 A A 305 A B 306 A 307 A B 308 A A 309 C 310 A A 311 A A 312 A A 313 A B 314 A 315 A A 316 A A 317 A B 318 A 319 B 320 A B 321 A A 322 A A 323 A A 324 A B 325 A A 326 A A 327 A 328 A A 329 A A 330 A A 331 A A 332 A B 333 A B 334 A B 335 A A 336 A B 337 A A 338 B 339 B 340 A A 341 A A 342 A A 343 A A 344 A A 345 A A 346 A 347 A A 348 A C 349 A A 350 A A 351 A B 352 A B 353 B 354 A A 355 A A 356 A A 357 A A 358 A B 359 A A 360 A 361 B 362 A A 363 A A 364 B 365 A A 366 A A 367 A A 368 A A 369 A A 370 A A 371 A A 372 A A 373 B 374 A A 375 A A 376 A A 377 A A 378 A B 379 A 380 A A 381 A A 382 A A 383 A A 384 B 385 A A 386 A A 387 A A 388 A B 389 A A 390 A A 391 A 392 A A 393 C 394 A A 395 A A 396 A A 397 A A 398 A A 399 A B 400 A 401 A A 402 A 403 A A 404 B 405 A 406 B 407 A A 408 A B 409 A 410 B 412 A A 413 A A 414 A A 415 A B 416 A A 417 A A 418 A A 420 A B 421 A A 422 A A 423 A A 424 A A 425 A A 426 A B 427 A A 428 A A 429 A A 430 A 431 A A 432 A A 433 A A 434 A A 436 A A 437 A A 438 A A 439 A A 440 A A 441 A A 442 A A 443 A 444 A A 445 A A 446 A A 447 A A 448 A 449 A A 450 A B 451 A A 452 A A 453 A A 454 B 455 A A 456 A A 457 A 458 A A 459 A A 460 A A 461 A B 462 A A 463 A 464 A B 465 A 466 A A 467 A A 468 A A 469 A A 470 A A 471 A 472 A A 473 A A 474 A A 475 A A 476 A A 477 A A 478 A A 479 A A

Inclusion by reference

[00202] All publications and patents mentioned in the present invention are hereby incorporated by reference in their entirety as if each individual publication or patent were specifically and separately marked as incorporated by reference.

Equivalents

[00203] In the claims, singular forms may mean one or more than one, unless otherwise noted or otherwise apparent from the context. Claims or descriptions that include "or" between one or more members of a group are considered satisfactory if one, more than one, or all of the members of the group are present in, used in, or otherwise relevant to the represented product or process if not noted to the contrary or otherwise not apparent from the context. The present disclosure includes embodiments in which exactly one member of the group is present in, used in, or otherwise related to the represented product or process. The present disclosure includes embodiments in which more than one or all of the members of the group are present in, used in, or otherwise related to the represented product or process.

[00204] Moreover, the present disclosure covers all variations, combinations, and permutations in which one or more limitations, elements, amendments, and descriptive terms of one or more of the stated claims are introduced in another claim. For example, any claim that is dependent on another claim may be modified to include one or more of the limitations presented in any other claim that is dependent on the same main claim. If the elements are presented as lists, for example in the Markush group format, each subgroup of elements is also open and any element(s) may be removed from the group. It should be understood that, as a general rule, if a disclosure or aspects of the present disclosure are mentioned/referred to as containing specific elements and/or features, certain embodiments of the present disclosure or aspects of the present disclosure consist, or essentially consist, of such elements and/or features. For the sake of simplicity, such embodiments have not been specifically set forth verbatim in this specification. If ranges are provided, endpoints are included. Moreover, unless otherwise noted or otherwise apparent from the context and understood by those skilled in the art, values that are expressed as ranges can take on any particular value or subrange within the specified ranges in various embodiments of the present disclosure, up to tenths. units of the lower limit of the range, unless the context clearly indicates otherwise.

[00205] Those skilled in the art will recognize or be able to ascertain using no more than routine experimentation that many equivalents of specific embodiments of the disclosure are described and claimed herein. Such equivalents are intended to be covered by the following claims.

Claims (145)

1. Compound of formula (I):

or a pharmaceutically acceptable salt thereof, wherein: ring A is selected from phenyl, a 5-6 membered monocyclic heteroaryl containing 1-3 ring heteroatoms selected from O, N, and S, quinolinyl, and an 8-10 membered bicyclic heterocyclyl containing 1-3 ring heteroatoms selected from O , N, and S, where only one ring of the specified bicyclic heterocyclyl is aromatic; each R ¹ is independently selected from halo - F or Cl, cyano, C ₁ -C ₄ alkyl, -O-(C ₁ -C ₃ alkyl), -C(O)-(C ₁ -C ₂ alkyl), -C (O)-N(R ⁸ )-(C ₂ alkyl), -N(R ⁸ ) ₂ , -N(R ⁸ )-C(O)-(C ₁ alkyl), -S(O) _p -( C ₁ -C ₂ alkyl), -O-(C ₁ alkylene)-C(O)-O-(C ₁ alkyl), -O-(C ₂ alkylene)-N(R ⁸ ) ₂ , -O-( C ₁ alkylene) -C (O) -N (R ⁸ ) ₂ , -Si (R ⁹ ) (C ₁ -C ₄ alkyl) ₂ , C ₃ -C ₆ carbocyclyl, -O- (C ₀ or C ₂ alkylene )-(C ₄ carbocyclyl), -(C ₁ alkylene)-phenyl, -O-(C ₀ -C ₁ alkylene)-phenyl, 4-6, 9- or 10-membered heterocyclyl containing 1-3 ring heteroatoms, selected from N or O, -C(O)-azetidinyl, -O-(C ₀ -C ₂ alkylene)-pyrrolidinyl and -O-(C ₁ alkylene)-C(O)-4-6-membered heterocyclyl containing 1-2 N atoms, where: any specified alkyl portion of R ¹ is optionally substituted with one to three substituents independently selected from fluoro, cyano, hydroxyl, and —O—(C ₁ alkyl); and any said carbocyclyl, said phenyl or said heterocyclyl moiety of R ¹ is optionally substituted with one to three substituents independently selected from fluoro, C ₁ -C ₃ alkyl, C ₂ -C ₃ haloalkyl, cyano, hydroxyl, -O-(C ₁ alkyl) , oxetanyl, -N(R ⁸ ) ₂ and -N(R ⁸ )-C(O)-O-(C ₁ or C ₄ alkyl); R ² is a bond or -O-; R ³ is selected from C ₁ -C ₆ alkyl, -(C ₀ -C ₃ alkylene)-(C ₃ -C ₆ carbocyclyl) and -(C ₀ -C ₁ alkylene)-(4-6-membered monocyclic O-containing or 4-membered S-containing heterocyclyl), where: the carbon atom of said monocyclic heterocyclyl is the point of attachment of said monocyclic heterocyclyl; any specified alkyl portion of R ³ is optionally substituted with one to three substituents independently selected from fluoro, cyano, C ₁ alkyl, -O-(C ₁ -C ₄ alkyl), -O-(C ₆ cycloalkyl), and -S(O) _p -(C ₁ -C ₂ alkyl); and any specified carbocyclyl or specified heterocyclyl portion of R ³ is optionally substituted with one to four substituents independently selected from fluoro, cyano, oxo, hydroxyl, C ₁ alkyl and -O-(C ₁ -C ₂ alkyl); R ⁴ is selected from hydrogen, C ₁ -C ₂ alkyl, C ₃ alkynyl, -C(O)-(C ₂ alkyl), halogen and cyano, where: any specified alkyl part of R ⁴ is optionally substituted by hydroxyl; each R ⁸ is independently selected from hydrogen and C ₁ alkyl; each R ⁹ is independently selected from hydroxyl; n is 0, 1, 2, or 3; and p is 1 or 2. 2. A compound according to claim 1 or a pharmaceutically acceptable salt thereof, wherein ring A is selected from phenyl, 5-membered monocyclic heteroaryl, 6-membered monocyclic heteroaryl, 9-membered bicyclic heterocyclyl, and 10-membered bicyclic heterocyclyl, wherein said heteroaryl and heterocyclyl contains 1-3 ring heteroatoms selected from O, N and S. 3. A compound according to claim 1 or 2, or a pharmaceutically acceptable salt thereof, wherein ring A is selected from phenyl, pyrrolyl, pyrazolyl, imidazolyl, thiazolyl, isothiazolyl, oxazolyl, isoxazolyl, thiophenyl, 1,2,4-thiadiazolyl, 1,3, 4-thiadiazolyl, 1,2,3-triazolyl, pyridinyl, pyrimidinyl, pyrazinyl,

4. A compound according to claim 1 or 2, or a pharmaceutically acceptable salt thereof, wherein ring A is selected from

where: X is selected from O, N and S(O) _p ; Y is CH or N; W is selected from CH, N, S and O; Z is selected from CH, NH, S and O; and p is 1 or 2. 5. A compound according to claim 1 or 2, or a pharmaceutically acceptable salt thereof, wherein ring A is selected from

R ^1B is selected from hydrogen, halogen - F or Cl, cyano, C ₁ -C ₄ alkyl, -O- (C ₁ -C ₃ alkyl), -C (O) - (C ₁ -C ₂ alkyl), -N (R ⁸ )-C(O)-(C ₁ alkyl), -S(O) _p -(C ₁ -C ₂ alkyl), C ₃ -C ₆ cycloalkyl and 4-6 membered heterocyclyl containing 1-3 ring heteroatoms selected from N or O, where: any specified alkyl portion of R ^1B is optionally substituted with one to three substituents independently selected from fluoro and cyano; any specified cycloalkyl or specified heterocyclyl part of R ^1B is optionally substituted with one to three substituents independently selected from fluoro, -N(R ⁸ ) ₂ , C ₁ -C ₃ alkyl, oxetanyl, and C ₂ -C ₃ haloalkyl; p is 1 or 2; and if R ^1B is hydrogen then n1 is 0, 1, 2 or 3 and if R ^1B is not hydrogen then n1 is 0, 1 or 2. 6. The compound according to claim 1 or 2, or a pharmaceutically acceptable salt thereof, where ring A is selected from

R ^1B is selected from hydrogen, C ₁ -C ₄ alkyl, C ₃ -C ₆ cycloalkyl, -(C ₁ alkylene)-phenyl, 4-6, 9- or 10-membered heterocyclyl containing 1-3 ring heteroatoms selected from N or O and -S(O) _P -(C ₁ -C ₂ alkyl), where: any specified alkyl portion of R ^1B is optionally substituted with one to three substituents independently selected from fluoro and cyano; p is 1 or 2; each R ¹ is independently selected from C ₁ -C ₄ alkyl, C ₃ -C ₆ cycloalkyl, halogen - F or Cl, cyano and -N(R ⁸ ) ₂ where: any specified alkyl portion of R ^1B is optionally substituted with one to three substituents independently selected from fluoro and cyano; each R ⁸ is independently selected from C ₁ alkyl; and if R ^1B is hydrogen then n1 is 0, 1, 2 or 3 and if R ^1B is not hydrogen then n1 is 0, 1 or 2. 7. A compound according to claim 1 or 2, or a pharmaceutically acceptable salt thereof, wherein ring A is selected from

each R ¹ is independently selected from C ₁ -C ₄ alkyl, C ₃ -C ₆ cycloalkyl, -O-(C ₁ -C ₃ alkyl), -C(O)-azetidinyl and cyano, where: any specified alkyl portion of R ¹ is optionally substituted with one to three substituents independently selected from fluoro, hydroxyl and cyano. 8. The compound according to claim 1 or 2, or a pharmaceutically acceptable salt thereof, where ring A is selected from

each R ¹ is independently selected from C ₁ -C ₄ alkyl optionally substituted with one to three substituents independently selected from fluoro, hydroxyl and cyano. 9. A compound according to claim 1 or 2, or a pharmaceutically acceptable salt thereof, wherein ring A is selected from

each R ¹ is independently selected from C ₁ -C ₄ alkyl and cyano, where: any specified alkyl portion of R ¹ is optionally substituted with one to three substituents independently selected from fluoro, hydroxyl and cyano. 10. Connection according to any one of paragraphs. 1-4 or a pharmaceutically acceptable salt thereof, where each R ¹ is independently selected from tetrahydropyranyl, tetrahydrofuranyl, 3,6-dihydro-2H--pyranyl, piperidinyl, piperazinyl, oxetanyl, cyano, C ₁ -C ₄ alkyl, -S(O )-(C ₁ -C ₂ alkyl), -S(O) ₂ -(C ₁ -C ₂ alkyl), -C(O)-(C ₁ -C ₂ alkyl), -C(O)-azetidinyl, -O-(C ₁ -C ₃ alkyl), halogen - F or Cl, C ₃ -C ₆ cycloalkyl, -O-(C ₄ cycloalkyl), -N (CH ₃ ) ₂ , Si(CH ₃ ) ₂ OH, -NH-C(O)-CH ₃ , -O-(C ₀ -C ₁ alkylene)-phenyl and morpholinyl, where said piperidinyl is optionally substituted with one substituent selected from oxetanyl, -O-(C ₁ alkyl), C ₁ -C ₃ alkyl and C ₂ -C ₃ haloalkyl, or one or two substituents independently selected from fluoro; said tetrahydropyranyl or tetrahydrofuranyl is optionally substituted with one substituent selected from hydroxyl and -O-(C ₁ alkyl); said oxetanyl is optionally substituted with one substituent selected from C ₁ -C ₃ alkyl; said piperazinyl is optionally substituted with one substituent selected from C ₁ -C ₃ alkyl and fluoro; any specified cycloalkyl part of R ¹ is optionally substituted with one substituent selected from cyano and hydroxyl; any specified alkyl portion of R ¹ is optionally substituted with one to three substituents independently selected from fluoro, cyano, hydroxyl, and —O—(C ₁ alkyl). 11. The connection according to any one of paragraphs. 1-4 or 10 or a pharmaceutically acceptable salt thereof, wherein R ³ is selected from C ₁ -C ₆ alkyl, -(C ₀ -C ₃ alkylene) -(C ₃ -C ₆ carbocyclyl) and -(C ₀ -C ₁ alkylene )-(4-6-membered monocyclic O-containing or 4-membered S-containing heterocyclyl), where: any specified alkyl portion of R ³ is optionally substituted with one to three substituents independently selected from fluoro and cyano; and any said carbocyclyl or said heterocyclyl portion of R ³ is optionally substituted with one to four substituents independently selected from fluoro, cyano, hydroxyl, C ₁ alkyl, -O-(C ₁ -C ₂ alkyl). 12. Compound selected from any of the following compounds:

or a pharmaceutically acceptable salt thereof. 13. The connection, which is

or a pharmaceutically acceptable salt thereof. 14. The connection, which is

or a pharmaceutically acceptable salt thereof. 15. The connection, which is

or a pharmaceutically acceptable salt thereof. 16. Pharmaceutical composition for the treatment or alleviation of progressive fibrodysplasia ossificans or diffuse glioma of the brainstem, containing at least one compound selected from the compounds according to any one of paragraphs. 1-15 and their pharmaceutically acceptable salts, and at least one pharmaceutically acceptable excipient. 17. The use of a compound selected from the compounds according to any one of paragraphs. 1-15 and their pharmaceutically acceptable salts, for the treatment or alleviation of progressive fibrodysplasia ossificans in a subject in need thereof. 18. Use according to claim 17, wherein the subject has a mutation in the ALK2 gene that results in the expression of an ALK2 enzyme having at least one amino acid modification selected from L196P, PF197-8L, R202I, R206H, Q207E, R258S, R258G, G328A , G328W, G328E, G328R, G356D and R375P. 19. Use according to claim 18, wherein the ALK2 enzyme has the amino acid modification R206H. 20. The use of a compound selected from the compounds according to any one of paragraphs. 1-15 and their pharmaceutically acceptable salts, for the treatment or alleviation of diffuse brainstem glioma in a subject in need thereof. 21. Use according to claim 20, wherein the subject has a mutation in the ALK2 gene that results in the expression of an ALK2 enzyme having at least one amino acid modification selected from R206H, G328V, G328W, G328E, and G356D. 22. Use according to claim 21, wherein the ALK2 enzyme has the amino acid modification R206H. 23. The use of a compound selected from the compounds according to any one of paragraphs. 1-15 and their pharmaceutically acceptable salts, to inhibit aberrant ALK2 activity in a subject in need thereof. 24. Use according to claim 23, wherein the aberrant ALK2 activity is caused by a mutation in the ALK2 gene that results in the expression of an ALK2 enzyme having at least one amino acid modification selected from L196P, PF197-8L, R202I, R206H, Q207E, R258S, R258G , G328A, G328V, G328W, G328E, G328R, G356D and R375P. 25. Use according to claim 24, wherein the ALK2 enzyme has the amino acid modification R206H. 26. Use according to claim 25, wherein the subject suffers from progressive fibrodysplasia ossificans or diffuse brainstem glioma.