WO2009030952A2

WO2009030952A2 - Phenylcarboxamide derivatives as inhibitors and effectors of the hedgehog pathway

Info

Publication number: WO2009030952A2
Application number: PCT/GB2008/050782
Authority: WO
Inventors: Benjamin Fauber; Alexander Hird; James Janetka; Daniel John Russell; Bin Yang
Original assignee: Astrazeneca Ab; Astrazeneca Uk Limited
Priority date: 2007-09-05
Filing date: 2008-09-04
Publication date: 2009-03-12
Also published as: PE20091092A1; UY31322A1; AR068376A1; WO2009030952A3; TW200916458A

Abstract

The present disclosure relates to heterocyclic amide compounds, which are useful for inhibiting the Hedgehog pathway, and their use in treating a disease or medical condition mediated alone or in part by Hedgehog pathway inhibition. Also disclosed are methods for manufacture of these compounds, pharmaceutical compositions including these compounds, and use of these compounds in the manufacture of medicaments for treating such diseases and medical conditions in a subject. (I)

Description

HETEROCYCLIC COMPOUNDS AND METHODS OF USE THEREOF-975

RELATED APPLICATIONS

This application claims priority under 35 U.S. C. § 119(e) to U.S. Provisional Application Nos. 60/970,107 filed on September 5, 2007 and 61/036,661, filed on March 14, 2008; the entire contents of each of which is hereby expressly incorporated by reference in their entireties.

BACKGROUND OF THE INVENTION

The Hedgehog pathway (HH pathway) is a well-studied pathway affecting numerous biological processes, such as embryogenesis, where the pathway is activated and mediates patterning of the embryo, cell differentiation and proliferation. This pathway has been conserved throughout evolution, and components of the pathway have been identified in many species including sea urchins, worms, flies, and mammals. Much of the current understanding about the HH pathway has come from studies in Drosophila. The human genome contains three hedgehog genes: Sonic (SHH), Indian (IHH) and Desert (DHH). Sonic Hedgehog is the most widely expressed of the three genes, and studies have shown that this gene plays a role in many aspects of embryogenesis.

The Sonic gene codes for the SHH protein ligand. All hedgehog proteins are secreted from the cell and bind to their common 12-pass transmembrane protein, PTCHl, whose function is to inhibit a 7-pass GPCR- like membrane protein called Smoothened (SMO). The binding of SHH to PTCHl relieves the inhibition on SMO, allowing translocation of SMO to the membrane followed by subsequent initiation of a signal transduction pathway (Varjosalo et al, J. Cell Sci. 120:3-6 (2007)). Recently, it has been shown that the localization of SMO to the membrane occurs specifically in the cilia of mammalian cells (Caspary et al., Dev. Cell 12:767-778 (2007)). Moreover, mutations in intraflagellar transport proteins result in dysfunctional SHH signaling and lead to developmental deformities analogous to those observed with SHH mutations. After the HH pathway is activated, a complex series of interactions downstream of SMO ultimately leads to the processing and translocation of the GLI transcription factors to the nucleus, where they act as transcriptional regulators. In vertebrates, there are three GLI genes (GLIl, GLI2, and GLI3) which are members of the zinc finger transcription factor family. GLIl and GLI2 act primarily as transcriptional activators, while GLI3 functions as a transcriptional repressor. The GLI2 gene is constitutively expressed and is believed to be the primary target for activation by SMO. In the presence of SHH ligand and activation of SMO, the GLI2 protein becomes stabilized and functions to up-regulate a number of genes identified as targets of the HH pathway, including GLIl, PTCH, BCL2, c-myc and IGF2. Of these genes, studies have indicated that GLIl appears to be the most reliable biological endpoint for measuring activation of the HH pathway.

One of the difficulties in targeting the HH pathway is the incomplete understanding of the signal transduction pathway and the lack of identification of positive pathway regulators. Cyclopamine is a well-established natural product antagonist of the HH pathway, which has been proven to be a valuable tool to modulate the HH pathway. Cyclopamine has been shown to directly bind to SMO and inhibit its activation, leading to downregulation of the pathway both in vitro and in vivo (Chen et al., Cancer Sci. 98:68-76 (2007); Mukherjee et al., Cancer Bio & Therapy 5:674-683 (2006)).

Recently, the linkage of the Hedgehog pathway to diseases, such as cancer, has been established. Activating mutations in either PTCH or SMO have been associated with basal cell carcinoma, medulloblastoma, and rhabdomyosarcoma. In addition, upregulation of the pathway, as measured by overexpression of SHH or upregulation of GLIl expression, has been associated with solid tumors including prostate, pancreas, upper digestive tract tumors and small cell lung cancer (Bak et al., Pharmacogenomica 4:411-429 (2003)). In addition, several transgenic or knockout/knock- in models have been developed by overexpression of pathway components in specific tissues or tissue specific knockout that lead to tumor formation in mice. For example, overexpression of constitutively active SMO in the mammary gland leads to increased proliferation, altered differentiation and ductal dysplasia (Moraes et al., Development 134:1231- 1242 (2007)). Mice heterozygous for PTCH form basal cell carcinoma when exposed to UV light (Aszterbaum et al. Nat. Med. 5:1285-1291 (1999)), and tissue specific overexpression of SHH in the pancreas leads to abnormal tubule structures that mimic human pancreatic cancer (Thayer et al., Nature 425:851-856 (2003)). In addition, several studies have reported expression of HH signaling components in human tumor tissues including, but not limited to, prostate, pancreas, ovarian, melanoma, breast, colon, lung, esophagus, stomach, biliary, hepatocellular and multiple myeloma.

The tumor microenvironment is a very important aspect of tumorogenesis, but it is unclear as to how growth factor signaling pathways influence the tumor microenvironment. These pathways may function in an autocrine manner, where the ligands are produced by the tumor cells and thus activate the signaling pathways within the tumor cell. However, during normal development, the HH pathway is thought to function in a paracrine manner where the reactive stromal cells produce the growth factors and send signals back to the developing tumor (Fan et al, Endocrinology 145:3961-3970 (2004).

In addition to effects on proliferation and differentiation, the HH pathway is also implicated in the process of angiogenesis, which results in the growth of new blood vessels from existing vasculature and remodeling smaller vessels into larger ones. All of these effects help to promote growth and survival of the tumor (Klagsbrun and D'Amore, Annu. Rev. Physiol. 53:217-239 (1991); Cherington et al., Adv. Cancer Res. 79:1-38 (2000)).

In addition, the HH pathway may play a role in the developing field of cancer stem cells. Stem cells are slowly replicating cells that have the ability to give rise to exact replicates of themselves, as well as a heterogeneous population of progeny cells. In the stem cell model of cancer, a rare subpopulation of cells have the ability to self-renew, yielding another malignant stem cell as well as non-tumorigenic cancer cells, thus increasing the heterogeneous cell population of the tumor. Recent studies have demonstrated in leukemia and several solid tumors including brain, prostate, pancreatic, colon and breast, that a small proportion of cancer cells have the capacity to proliferate extensively and form new heterogeneous tumors in vivo (Clarke et al. Cancer Res. 66:9339-9344 (2006). For example, in the pancreas, these cancer stem cells have also been reported to have a higher level of GLI expression (Li et al., Cancer Res. 67:1030-1037 (2007)). Compounds effectively inhibiting the Hedgehog pathway could thus be useful in decreasing cancer stem cell proliferation or differentiation activity.

SUMMARY OF THE INVENTION

Accordingly, novel compounds are provided that are potent inhibitors and effectors of the Hedgehog pathway and therefore possess the ability to prevent gene transcription effected by the GLI proteins. This inhibitory ability results in preventing or reducing cell differentiation, proliferation, and/or affecting stromal microenvironment modulation. The disclosed compounds are useful for treating diseases and medical conditions mediated alone or in part by Hedgehog pathway inhibition, and thus possess anti-proliferative (such as anti-cancer) activity. Such activity is useful in treating subjects having a PTCH loss-of function phenotype, a SMO gain-of- function phenotype or a Hedgehog gain-of- function phenotype.

One aspect of the invention provides a compound of formula I

I wherein

Ri, R2 and R3 are each independently selected from the group consisting of hydrogen, Ci-βalkyl, and halogen;

R4 is selected from the group consisting of Ci-βalkyl, haloCi-βalkyl, and halogen; each W is independently selected from the group consisting of CR₅, NR₅, N, O, and S, where R₅ is selected from the group consisting of hydrogen, Ci_6alkoxy, e.g., -OCH3, Ci-ealkoxyCi-βalkyl, Ci_₆alkoxycarbonyl, Ci_₆alkyl, e.g., -CH₃, amidino, amido, amino, e.g., aminoCi-₆alkyl, Ci_₆alkylcarbonyl, aryl, carboxamido, C₃_₈cycloalkyl, cyano, haloCi_₆alkyl, halogen, heterocyclyl, heterocyclylCi-_όalkyl, hydroxy, hydroxyCi_₆alkyl, nitro, sulfide, sulfϊnyl, sulfonamido, and sulfonyl, or two adjacent W atoms can be taken together with their R₅ substituents to form a fused second ring, wherein the second ring is optionally substituted with one or more R₅ substituents and is selected from the group consisting of aryl, C₃_₈cycloalkyl, 5- or 6-membered heteroaryl, and 5- or 6-membered heterocyclyl; at least one W is N; q is 0 or 1, where if q is 0 and two adjacent W atoms are taken together with their R₅ substituents to form a fused second ring, then one of the adjacent W atoms is N and the second ring is a 6-membered heterocyclyl, and if q is 0, and the ring comprised of the W atoms is 2-imidazolyl, R₅ is not an unsubstituted phenyl ring;

A is selected from the group consisting of CR₆, NR5, N, O, and S;

R₆ is selected from the group consisting of hydrogen, Ci_₆alkoxy, Ci_₆alkoxyCi_₆alkyl, Ci_₆alkoxycarbonyl, Ci_₆alkyl, Ci_₆alkyl, e.g., -CH₃, amidino, amido, amino, e.g., aminoCi_₆alkyl, Ci_₆alkylcarbonyl, aryl, carboxamido, C₃_₈cycloalkyl, cyano, haloCi galley 1, e.g. , trifluoromethyl, halogen, e.g., Cl, heterocyclyl, heterocyclylCi-όalkyl, heterocyclylCi-όalkoxy, e.g., 2- pyridylmethoxy, hydroxy, hydroxyCi galley 1, nitro, sulfϊnyl, sulfide, sulfonamido, and sulfonyl, or two adjacent A atoms can be taken together with their R₆ substituents to form a fused second ring, wherein the second ring is a 5- or 6-membered heterocyclyl, e.g. , forming a fused 2,3-dihydro-l,4-benzodioxine; at least one A is selected from the group consisting of NR₆, N, O, and S; p is 0 or 1, where if p is 0 and Ri, R2, and R₄ are each methyl, then A is not S; wherein the compound of formula I is not

or

, where L is selected from the group consisting of NH and CH, and if L is NH, then M is CH₂, and if L is CH then M is CH; and pharmaceutically acceptable salts thereof. Another aspect of the invention provides a compound of formula II:

II wherein,

A is selected from the group consisting of N and CRio;

X is selected from the group consisting of halogen and Ci-βalkyl;

Y is selected from the group consisting OfNR₅, O and S; each R₅ is independently selected from the group consisting of hydrogen, Ci-βalkyl and hydroxy Ci-βalkyl;

R₇ is selected from the group consisting of hydrogen, halogen, cyano, Ci-βalkyl, Ci-βhaloalkyl, amino, e.g., Ci_6alkylamino, Ci_6alkoxy, aryloxy, hydroxy, sulfonyl, sulfonamide, and heterocyclyl, wherein R₇ may be optionally substituted with one or more Rn;

R₈, R₉, and Ri₀ are each independently selected from the group consisting of hydrogen, Ci-βalkyl, e.g., -CH₃, halogen, e.g., Cl or F, Ci-βalkoxy, e.g., -OCH₃, amino, hydroxy, haloalkyl, cyano, sulfonyl, and sulfonamide; Rn may be selected from the group consisting of halogen, hydroxy, amino, Ci_₆alkyl, Ci-βalkoxy, aryl, and heterocyclyl, wherein Rn may be optionally substituted with one or more Ri 2; and

R12 may be selected from the group consisting of amino, cyano, hydroxy, Ci_6alkyl, cycloalkyl, and aryl, or pharmaceutically acceptable salts thereof.

In another aspect, the invention provides a compound of formula III

III wherein n is 0, 1, 2, or 3;

Z is a direct bond, NR_a, S and O, wherein R_a is selected from the group consisting of the group consisting of H, alkyl, and cycloalkyl

R₃ is selected from the group consisting of the group consisting of hydrogen, halogen, and alkyl; each Ri₄ is selected from the group consisting of the group consisting of hydrogen, halogen, hydroxyl, sulfide, carboxamide, Ci_6alkylcarbonyl, amino, alkyl, alkoxyl, alkoxycarbonyl, sulfinyl, sulfonyl, cyano, cycloalkyl, aryl or a heterocyclyl wherein each R₁₄ is optionally substituted with Ci_₆alkylcarbonyl, hydroxyl, hydroxy Ci_₆alkyl, halogen, amino, nitro, Ci_₆alkyl, sulfonyl, cyano, alkoxyl or heterocyclyl, such that R₁₄ is not unsubstituted phenyl when the imidazolyl ring to which the R14 is attached is 2-imidazolyl;

Ri5 is selected from the group consisting of the group consisting of -(CH)o-s-heterocycle, - (CH)₀-5-NRbRb, -(CH)o-5-hydroxy, -(CH)₀-5-Ci_6alkoxy, aryl and heterocyclyl, e.g., piperazine, wherein R15 is optionally substituted with Ri6, and each Rb is selected from the group consisting of the group consisting of H, alkyl, and cycloalkyl; and Ri6 is selected from the group consisting of the group consisting of halo, alkyl, alkoxy, alkylthio, wherein Ri6 is optionally substituted with aryl or heteroaryl, or a pharmaceutically acceptable salt thereof.

In an additional aspect the invention provides a pharmaceutical composition comprising one or more of the compounds described herein, formulated together with one or more pharmaceutically acceptable carriers.

Another aspect of the invention pertains to a method for inhibiting the Hedgehog pathway comprising administering to a subject, e.g., a subject in need thereof, a therapeutically effective amount of one or more of the compounds described herein, or a pharmaceutical composition described herein, such that the Hedgehog pathway is inhibited.

In another aspect, the invention provides a method of reducing cell proliferation, differentiation and/or affecting stromal microenvironment modulation comprising administering to a subject, e.g., a subject in need thereof, a therapeutically effective amount of one or more of the compounds described herein, or a pharmaceutical composition described herein, thereby reducing cell proliferation, differentiation and/or affecting stromal microenvironment modulation in the subject.

DETAILED DESCRIPTION OF THE INVENTION

The present disclosure relates to heterocyclic amide compounds, which are useful for inhibiting the Hedgehog pathway, and their use in treating a disease or medical condition mediated alone or in part by Hedgehog pathway inhibition. Also disclosed are methods for manufacture of these compounds, pharmaceutical compositions including these compounds, and use of these compounds in the manufacture of medicaments for treating such diseases and medical conditions in a subject.

It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the invention as claimed. Moreover, the present invention, including compounds, methods, and pharmaceutical compositions will be described with reference to the following definitions that, for convenience, are set forth below: Unless otherwise specified, the chemical groups refer to their unsubstituted and substituted forms.

The term "aldehyde" or "formyl" as used herein refers to the radical -CHO.

The term "alkenyl" as used herein refers to an unsaturated straight or branched hydrocarbon having at least one carbon-carbon double bond, such as a straight or branched group of 2-12, 2-10, or 2-6 carbon atoms, referred to herein as C2-Ci2alkenyl, C_2-Ci₀alkenyl, and C2- C_όalkenyl, respectively. Exemplary alkenyl groups include, but are not limited to, vinyl, allyl, butenyl, pentenyl, hexenyl, butadienyl, pentadienyl, hexadienyl, 2-ethylhexenyl, 2-propyl-2- butenyl, 4-(2-methyl-3-butene)-pentenyl, etc.

The term "alkoxy" as used herein refers to an alkyl group attached to an oxygen (-0- alkyl-). Exemplary alkoxy groups include, but are not limited to, groups with an alkyl, alkenyl or alkynyl group of 1-12, 1-8, or 1-6 carbon atoms, referred to herein as

Ci-Csalkoxy, and Ci-C_όalkoxy, respectively. Exemplary alkoxy groups include, but are not limited to methoxy, ethoxy, etc. Similarly, exemplary "alkenoxy" groups include, but are not limited to vinyloxy, allyloxy, butenoxy, etc.

The term "alkyl" as used herein refers to 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 Ci- Cπalkyl, Ci-Cioalkyl, and Ci-C_όalkyL respectively. Exemplary alkyl groups include, but are not limited to, methyl, ethyl, propyl, isopropyl, 2-methyl-l -propyl, 2-methyl-2-propyl, 2-methyl-l - butyl, 3 -methyl- 1 -butyl, 2-methyl-3 -butyl, 2,2-dimethyl-l -propyl, 2-methyl-l -pentyl, 3-methyl- 1-pentyl, 4-methyl-l -pentyl, 2-methyl-2-pentyl, 3 -methy 1-2 -pentyl, 4-methy 1-2 -pentyl, 2,2- dimethyl-l -butyl, 3,3-dimethyl-l-butyl, 2-ethyl-l -butyl, butyl, isobutyl, t-butyl, pentyl, isopentyl, neopentyl, hexyl, heptyl, octyl, etc.

Alkyl groups can optionally be substituted with or interrupted by at least one group selected from the group consisting of alkoxy, alkyl, alkenyl, alkynyl, amide, amino, aryl, arylalkyl, carbamate, carboxy, cyano, cycloalkyl, ester, ether, formyl, halogen, haloalkyl, heteroaryl, heterocyclyl, hydroxyl, ketone, nitro, sulfide, sulfonamide, and sulfonyl.

The term "alkynyl" as used herein refers to an unsaturated straight or branched hydrocarbon having at least one carbon-carbon triple bond, such as a straight or branched group of 2-12, 2-8, or 2-6 carbon atoms, referred to herein as C₂-Ci₂alkynyl, C₂-C₈alkynyl, and C₂- Cόalkynyl, respectively. Exemplary alkynyl groups include, but are not limited to, ethynyl, propynyl, butynyl, pentynyl, hexynyl, methylpropynyl, 4-methyl-l-butynyl, 4-propyl-2-pentynyl, and 4-butyl-2-hexynyl, etc.

The term "amide" or "amido" as used herein refers to a radical of the form -R₃C(O)N(Rb)-, -RaC(O)N(Rb)R₀-, or -C(O)NR_bR_c, wherein R_b and R_c are each independently selected from the group consisting of alkoxy, alkyl, alkenyl, alkynyl, amide, amino, aryl, arylalkyl, carbamate, carboxy, cyano, cycloalkyl, ester, ether, formyl, halogen, haloalkyl, heteroaryl, heterocyclyl, hydrogen, hydroxyl, ketone, and nitro. The amide can be attached to another group through the carbon, the nitrogen, Rb, R_c, or R_a. The amide also may be cyclic, for example R_b and R_c, R_a and R_b, or R_a and R_c may be joined to form a 3- to 12-membered ring, such as a 3- to 10-membered ring or a 5- to 6-membered ring. The term "carboxamido" refers to the structure -C(O)NR_bRc.

The term "amidino" as used herein refers to a radical of the form -C(=NR)NR'R" where R, R', and R" can each independently be selected from the group consisting of alkyl, alkenyl, alkynyl, amide, aryl, arylalkyl, cyano, cycloalkyl, haloalkyl, heteroaryl, heterocyclyl, hydroxyl,ketone and nitro.

The term "amine" or "amino" as used herein refers to a radical of the form -NRdR₅, -N(Rd)Re-, or -R₆N(Rd)Rf- where Rd, Re, and Rf are independently selected from the group consisting of alkoxy, alkyl, alkenyl, alkynyl, amide, amino, aryl, arylalkyl, carbamate, cycloalkyl, ester, ether, formyl, halogen, haloalkyl, heteroaryl, heterocyclyl, hydrogen, hydroxyl, ketone, and nitro. The amino can be attached to the parent molecular group through the nitrogen, Rd, R_e or Rf. The amino also may be cyclic, for example any two of Rd, Re or Rf may be joined together or with the N to form a 3- to 12-membered ring, e.g., morpholino or piperidinyl. The term amino also includes the corresponding quaternary ammonium salt of any amino group, e.g., -[Nf(Rd)(Re)(Rf)]+. Exemplary amino groups include aminoalkyl groups, wherein at least one of Rd, R_e, or Rf is an alkyl group. In specific embodiments, the amino group is a Ci_6alkylamino group.

The term "aryl" as used herein refers to a mono-, bi-, or other multi-carbocyclic, aromatic ring system. The aryl group can optionally be fused to one or more rings selected from the group consisting of aryls, cycloalkyls, and heterocyclyls. The aryl groups of this invention can be substituted with groups selected from the group consisting of alkoxy, alkyl, alkenyl, alkynyl, amide, amino, aryl, arylalkyl, carbamate, carboxy, cyano, cycloalkyl, ester, ether, formyl, halogen, haloalkyl, heteroaryl, heterocyclyl, hydroxyl, ketone, nitro, sulfide, sulfonamide, and sulfonyl. Exemplary aryl groups include, but are not limited to, phenyl, tolyl, anthracenyl, fluorenyl, indenyl, azulenyl, and naphthyl, as well as benzo-fused carbocyclic moieties such as 5,6,7, 8-tetrahydronaphthyl.

The term "arylalkyl" as used herein refers to an aryl group having at least one alkyl substituent, e.g. -aryl-alkyl-. Exemplary arylalkyl groups include, but are not limited to, arylalkyls having a monocyclic aromatic ring system, wherein the ring comprises 6 carbon atoms. For example, "phenylalkyl" includes phenylQalkyl, benzyl, 1-phenylethyl, 2-phenylethyl, etc.

The term "carbamate" as used herein refers to a radical of the form -RgOC(O)N(Ri₁)-,

-RgOC(O)N(Ri₁)Ri., ^or -OC(O)NRi₁Rj, wherein Rg Rj₁ and Rj are each independently selected from the group consisting of alkoxy, aryloxy, alkyl, alkenyl, alkynyl, amide, amino, aryl, arylalkyl, carbamate, carboxy, cyano, cycloalkyl, ester, ether, formyl, halogen, haloalkyl, heteroaryl, heterocyclyl, hydroxyl, ketone, nitro, sulfide, sulfonyl, and sulfonamide. Exemplary carbamates include, but are not limited to, arylcarbamates or heteroaryl carbamates, e.g., wherein at least one of R_g Rj₁ and Rj are independently selected from the group consisting of aryl or heteroaryl, such as phenyl and pyridinyl.

The term "carbonyl" as used herein refers to the radical -C(O)-.

The term "carboxamido" as used herein refers to the radical -C(O)NRR', where R and R' may be the same or different. R and R' may be selected from the group consisting of, for example, alkyl, aryl, arylalkyl, cycloalkyl, formyl, haloalkyl, heteroaryl and heterocyclyl.

The term "carboxy" as used herein refers to the radical -COOH or its corresponding salts, e.g. -COONa, etc.

The term "cyano" as used herein refers to the radical -CN.

The term "cycloalkoxy" as used herein refers to a cycloalkyl group attached to an oxygen.

The term "cycloalkyl" as used herein refers to a monovalent saturated or unsaturated cyclic, bicyclic, or bridged bicyclic hydrocarbon group of 3-12, 3-8, 4-8, or 4-6 carbons, referred to herein, e.g., as "C₄_₈cycloalkyl," derived from a cycloalkane. Exemplary cycloalkyl groups include, but are not limited to, cyclohexanes, cyclohexenes, cyclopentanes, cyclopentenes, cyclobutanes and cyclopropanes. Cycloalkyl groups may be substituted with alkoxy, alkyl, alkenyl, alkynyl, amide, amino, aryl, arylalkyl, carbamate, carboxy, cyano, cycloalkyl, ester, ether, formyl, halogen, haloalkyl, heteroaryl, heterocyclyl, hydroxyl, ketone, nitro, sulfide, sulfonamide, and sulfonyl. Cycloalkyl groups can be fused to other cycloalkyl, aryl, or heterocyclyl groups.

The term "ether" refers to a radical having the structure -RiO-R_1n-, where Ri and R_m can independently be alkyl, aryl, cycloalkyl, heterocyclyl, or ether. The ether can be attached to the parent molecular group through Ri or R_m. Exemplary ethers include, but are not limited to, alkoxyalkyl and alkoxyaryl groups. Ether also includes polyethers, e.g., where one or both of Ri and R_m are ethers.

The terms "halo" or "halogen" or "Hal" as used herein refer to F, Cl, Br, or I.

The term "haloalkyl" as used herein refers to an alkyl group substituted with one or more halogen atoms.

The term "heteroaryl" as used herein refers to a mono-, bi-, or other multi-cyclic, aromatic ring system containing one or more heteroatoms, for example 1 to 4 heteroatoms, such as nitrogen, oxygen, and sulfur. Heteroaryls can be substituted with one or more substituents including alkoxy, alkyl, alkenyl, alkynyl, amide, amino, aryl, arylalkyl, carbamate, carboxy, cyano, cycloalkyl, ester, ether, formyl, halogen, haloalkyl, heteroaryl, heterocyclyl, hydroxyl, ketone, nitro, sulfide, sulfonamide, and sulfonyl. Heteroaryls can also be fused to non-aromatic rings. Illustrative examples of heteroaryl groups include, but are not limited to, pyridinyl, pyridazinyl, pyrimidyl, pyrazyl, triazinyl, pyrrolyl, pyrazolyl, imidazolyl, (1,2,3,)- and (1,2,4)- triazolyl, pyrazinyl, pyrimidilyl, tetrazolyl, furyl, thienyl, isoxazolyl, thiazolyl, furyl, phenyl, isoxazolyl, and oxazolyl. Exemplary heteroaryl groups include, but are not limited to, a monocyclic aromatic ring, wherein the ring comprises 2 to 5 carbon atoms and 1 to 3 heteroatoms.

The terms "heterocycle," "heterocyclyl," or "heterocyclic" as used herein refer to a saturated, partially unsaturated, or unsaturated 4-12 membered ring containing at least one heteroatom independently selected from the group consisting of nitrogen, oxygen, and sulfur. Unless otherwise specified, the heteroatom may be carbon or nitrogen linked, a -CH2- group can optionally be replaced by a -C(O)-, and a ring sulfur atom may be optionally oxidized to form a sulfϊnyl or sulfonyl group. Heterocycles can be aromatic (heteroaryls) or non-aromatic. Heterocycles can be substituted with one or more substituents including alkoxy, alkyl, alkenyl, alkynyl, amide, amino, aryl, arylalkyl, carbamate, carboxy, cyano, cycloalkyl, ester, ether, formyl, halogen, haloalkyl, heteroaryl, heterocyclyl, hydroxyl, hydroxyalkyl, ketone, nitro, sulfide, sulfonamide, and sulfonyl. In certain embodiments, the heterocycles are substituted with a methyl or hydroxyethyl.

Heterocycles also include bicyclic, tricyclic, and tetracyclic groups in which any of the above heterocyclic rings is fused to one or two rings independently selected from the group consisting of aryls, cycloalkyls, and heterocycles. Exemplary heterocycles include acridinyl, benzimidazolyl, benzofuryl, benzothiazolyl, benzothienyl, benzoxazolyl, biotinyl, cinnolinyl, dihydrofuryl, dihydroindolyl, dihydropyranyl, dihydrothienyl, dithiazolyl, furyl, homopiperidinyl, imidazolidinyl, imidazolinyl, imidazolyl, indolyl, isoquinolyl, isothiazolidinyl, isothiazolyl, isoxazolidinyl, isoxazolyl, morpholinyl, oxadiazolyl, oxazolidinyl, oxazolyl, piperazinyl, piperidinyl, pyranyl, pyrazolidinyl, pyrazinyl, pyrazolyl, pyrazolinyl, pyridazinyl, pyridyl, pyrimidinyl, pyrimidyl, pyrrolidinyl, pyrrolidin-2-onyl, pyrrolinyl, pyrrolyl, quinolinyl, quinoxaloyl, tetrahydrofuryl, tetrahydroisoquinolyl, tetrahydropyranyl, tetrahydroquinolyl, tetrazolyl, thiadiazolyl, thiazolidinyl, thiazolyl, thienyl, thiomorpholinyl, thiopyranyl, and triazolyl. In certain embodiments, the heterocycle is aromatic. In certain other embodiments, the heterocycle is partially or fully saturated. In particular embodiments, the heterocycle is imidazolyl.

The term "heterocyclylalkoxy" as used herein refers to a heterocyclyl attached to an alkoxy group.

The term "heterocyclyloxyalkyl" refers to a heterocyclyl attached to an oxygen (-O-), which is attached to an alkyl group.

The terms "hydroxy" and "hydroxyl" as used herein refers to the radical -OH.

The term "hydroxyalkyl" as used herein refers to a hydroxy radical attached to an alkyl group.

The term "imidazolyl," as used herein, is art-recognized and includes all isomeric forms of substituted or unsubstituted imidazolyl. For example, the term "imidazolyl" includes 1- imidazolyl, 2-imidazolyl, 3-imidazolyl, 4-imidazolyl, and 5-imidazolyl, each of which may be substituted by 1 to 3 substituents. Such substituents may include halogen, e.g., F, hydroxyl, alkyl, e.g. , methyl, alkoxyl, alkoxycarbonyl, sulfinyl, sulfonyl, cyano, cycloalkyl, aryl or a heterocycle.

The term "nitro" as used herein refers to the radical -NO2. The term "phenyl" as used herein refers to a 6-membered carbocyclic aromatic ring. The phenyl group can also be fused to a cyclohexane or cyclopentane ring. Phenyl can be substituted with one or more substituents including alkoxy, alkyl, alkenyl, alkynyl, amide, amino, aryl, arylalkyl, carbamate, carboxy, cyano, cycloalkyl, ester, ether, formyl, halogen, haloalkyl, heteroaryl, heterocyclyl, hydroxyl, ketone, nitro, sulfide, sulfonamide, and sulfonyl.

The term "sulfonamide" as used herein refers to a radical having the structure -N(R_r)-

S(O)2-R_S~ ^or -S(O)2-N(R_r)R_s, where R_r, and R_s can be, for example, hydrogen, alkyl, aryl, cycloalkyl, and heterocyclyl. Exemplary sulfonamides include alkylsulfonamides (e.g. , where R_s is alkyl), arylsulfonamides (e.g., where R_s is aryl), cycloalkyl sulfonamides (e.g., where R_s is cycloalkyl), and heterocyclyl sulfonamides (e.g., where R_s is heterocyclyl), etc.

The term "sulfonyl" as used herein refers to a radical having the structure R_uSθ2-, where R₁₁ can be alkyl, aryl, cycloalkyl, and heterocyclyl, e.g., alkylsulfonyl. The term "alkylsulfonyl" as used herein refers to an alkyl group attached to a sulfonyl group.

The term "sulfide" as used herein refers to the radical having the structure R₂S-, where R₂ can be alkoxy, alkyl, alkenyl, alkynyl, amide, amino, aryl, arylalkyl, carbamate, carboxy, cycloalkyl, ester, ether, formyl, haloalkyl, heteroaryl, heterocyclyl, and ketone. The term "alkylsulfide" as used herein refers to an alkyl group attached to a sulfur atom. Exemplary sulfides include "thio," which as used herein refers to an -SH radical.

The term "pharmaceutically acceptable carrier" as used herein refers to any and all solvents, dispersion media, coatings, isotonic and absorption delaying agents, and the like, that are compatible with pharmaceutical administration. The use of such media and agents for pharmaceutically active substances is well known in the art. The compositions may also contain other active compounds providing supplemental, additional, or enhanced therapeutic functions.

The term "pharmaceutical composition" as used herein refers to a composition comprising at least one compound as disclosed herein formulated together with one or more pharmaceutically acceptable carriers.

The term "pharmaceutically acceptable salt(s)" as used herein refers to salts of acidic or basic groups that may be present in compounds used in the present compositions. Compounds included in the present compositions that are basic in nature are capable of forming a wide variety of salts with various inorganic and organic acids. The acids that may be used to prepare pharmaceutically acceptable acid addition salts of such basic compounds are those that form nontoxic acid addition salts, i.e., salts containing pharmacologically acceptable anions, including but not limited to malate, oxalate, chloride, bromide, iodide, nitrate, sulfate, bisulfate, phosphate, acid phosphate, isonicotinate, acetate, lactate, salicylate, citrate, tartrate, oleate, tannate, pantothenate, bitartrate, ascorbate, succinate, maleate, gentisinate, fumarate, gluconate, glucaronate, saccharate, formate, benzoate, glutamate, methanesulfonate, ethanesulfonate, benzenesulfonate,j9-toluenesulfonate and pamoate (i.e., 1,1 '-methylene -bis-(2-hydroxy-3 - naphthoate)) salts. Compounds included in the present compositions that include an amino moiety may form pharmaceutically acceptable salts with various amino acids, in addition to the acids mentioned above. Compounds included in the present compositions that are acidic in nature are capable of forming base salts with various pharmacologically acceptable cations. Examples of such salts include alkali metal or alkaline earth metal salts and, particularly, calcium, magnesium, sodium, lithium, zinc, potassium, and iron salts.

The term "subject" is intended to include organisms, e.g., prokaryotes and eukaryotes, which are capable of suffering from proliferative disorders, e.g., cancer, and which are mediated alone or in part by the Hedgehog pathway. Examples of subjects include mammals, e.g., humans, dogs, cows, horses, pigs, sheep, goats, cats, mice, rabbits, rats, and transgenic non- human animals. In certain embodiments, the subject is a human, e.g., a human suffering from, at risk of suffering from, or potentially capable of suffering from cancer. In certain embodiments the subject possesses a PTCH loss-of function phenotype, a SMO gain-of- function phenotype or a Hedgehog gain-of- function phenotype.

The compounds of the disclosure may contain one or more chiral centers (e.g., some of which may be explicitly designated as such by the inclusion of bond orientation/designation) and/or double bonds and, therefore, exist as stereoisomers, such as geometric isomers, enantiomers or diastereomers. The term "stereoisomers" when used herein consist of all geometric isomers, enantiomers or diastereomers. These compounds may be designated by the symbols "R" or "S," depending on the configuration of substituents around the stereogenic carbon atom. The present invention encompasses various stereoisomers of these compounds and mixtures thereof. Stereoisomers include enantiomers and diastereomers. Mixtures of enantiomers or diastereomers may be designated "(±)" in nomenclature, but the skilled artisan will recognize that a structure may denote a chiral center implicitly. Individual stereoisomers of compounds of the present invention can be prepared synthetically from commercially available starting materials that contain asymmetric or stereogenic centers, or by preparation of racemic mixtures followed by resolution methods well known to those of ordinary skill in the art. These methods of resolution are exemplified by (1) attachment of a mixture of enantiomers to a chiral auxiliary, separation of the resulting mixture of diastereomers by recrystallization or chromatography and liberation of the optically pure product from the auxiliary, (2) salt formation employing an optically active resolving agent, or (3) direct separation of the mixture of optical enantiomers on chiral chromatographic columns. Stereoisomeric mixtures can also be resolved into their component stereoisomers by well known methods, such as chiral-phase gas chromatography, chiral-phase high performance liquid chromatography, crystallizing the compound as a chiral salt complex, or crystallizing the compound in a chiral solvent. Stereoisomers can also be obtained from stereomerically-pure intermediates, reagents, and catalysts by well known asymmetric synthetic methods.

Geometric isomers can also exist in the compounds of the present invention. The present invention encompasses the various geometric isomers and mixtures thereof resulting from the arrangement of substituents around a carbon-carbon double bond or arrangement of substituents around a carbocyclic ring. Substituents around a carbon-carbon double bond are designated as being in the "Z" or "E" configuration wherein the terms "Z" and "£"' are used in accordance with IUPAC standards. Unless otherwise specified, structures depicting double bonds encompass both the "E" and "Z" isomers.

Substituents around a carbon-carbon double bond alternatively can be referred to as "cis" or "trans," where "cis" represents substituents on the same side of the double bond and "trans" represents substituents on opposite sides of the double bond. The arrangement of substituents around a carbocyclic ring are designated as "cis" or "trans." The term "cis" represents substituents on the same side of the plane of the ring and the term "trans" represents substituents on opposite sides of the plane of the ring. Mixtures of compounds wherein the substituents are disposed on both the same and opposite sides of plane of the ring are designated "cis/trans."

The compounds of the invention can exist in solvated as well as unsolvated forms such as, for example, hydrated forms. In one embodiment, the compound is amorphous. In one embodiment, the compound is a polymorph. In another embodiment, the compound is in a crystalline form. /. Compounds of the Invention

Disclosed herein are compounds of formula I

I wherein

Ri, R2 and R3 are each independently selected from the group consisting of hydrogen, Ci_₆alkyl, and halogen;

R₄ is selected from the group consisting of Ci_₆alkyl, haloCi_₆alkyl, and halogen; each W is independently selected from the group consisting of CR5, NR5, N, O, and S, where R₅ is selected from the group consisting of hydrogen, Ci_₆alkoxy, e.g., -OCH₃, Ci-ealkoxyCi-βalkyl, Ci_₆alkoxycarbonyl, Ci_₆alkyl, e.g., -CH₃, amidino, amido, amino, e.g., aminoCi-₆alkyl, Ci_₆alkylcarbonyl, aryl, carboxamido, C₃_₈Cycloalkyl, cyano, haloCi_₆alkyl, halogen, heterocyclyl, heterocyclylCi-_όalkyl, hydroxy, hydroxyCi_₆alkyl, nitro, sulfide, sulfϊnyl, sulfonamido, and sulfonyl, or two adjacent W atoms can be taken together with their R₅ substituents to form a fused second ring, wherein the second ring is optionally substituted with one or more R₅ substituents and is selected from the group consisting of aryl, C₃_₈Cycloalkyl, 5- or 6-membered heteroaryl, and 5- or 6-membered heterocyclyl; at least one W is N; q is 0 or 1, where if q is 0 and two adjacent W atoms are taken together with their R₅ substituents to form a fused second ring, then one of the adjacent W atoms is N and the second ring is a 6-membered heterocyclyl, and A is selected from the group consisting of CRβ, NRs, N, O, and S;

Re is selected from the group consisting of hydrogen, Ci-₆alkoxy, Ci-₆alkoxyCi_₆alkyl, Ci_₆alkoxycarbonyl, Ci-₆alkyl, Ci_₆alkyl, e.g., -CH₃, amidino, amido, amino, e.g., aminoCi_₆alkyl, Ci_₆alkylcarbonyl, aryl, carboxamido, C₃_₈cycloalkyl, cyano, haloCi_₆alkyl, e.g. , trifluoromethyl, halogen, e.g., Cl, heterocyclyl, heterocyclylCi-όalkyl, heterocyclylCi-όalkoxy, e.g., 2- pyridylmethoxy, hydroxy, hydroxyCi_6alkyl, nitro, sulfinyl, sulfide, sulfonamido, and sulfonyl, or two adjacent A atoms can be taken together with their Re substituents to form a fused second ring, wherein the second ring is a 5- or 6-membered heterocyclyl, e.g. , forming a fused 2,3-dihydro-l,4-benzodioxine; at least one A is selected from the group consisting of NRβ, N, O, and S; p is 0 or 1, where if p is 0 and Ri, R2, and R₄ are each methyl, then A is not S; wherein the compound of formula I is not

, where L is selected from the group consisting of NH and CH, and if L is NH, then M is CH₂, and if L is CH then M is CH; and pharmaceutically acceptable salts thereof. In certain embodiments, if q is 0, and the ring comprised of the W atoms is 2-imidazolyl, R5 is not an unsubstituted phenyl ring. In certain embodiments, one of the five A groups is N. In certain embodiments, R5 is H, CH3, OrNH₂ In certain embodiments, two adjacent W atoms are not taken together with their R₅ substituents to form a fused second ring. In particular embodiments, if q is 0, then four W atoms are not N. In another particular embodiment, the ring comprised of W atoms is an imidazole. In another particular embodiment, the ring comprised of A atoms is a 3-pyridyl.

Another embodiment of the invention provides a compound of formula II:

II wherein,

A is selected from the group consisting of N and CRio;

X is selected from the group consisting of halogen and Ci-βalkyl;

Y is selected from the group consisting OfNR₅, O and S, e.g., NR₅ and S; each R₅ is independently selected from the group consisting of hydrogen, Ci_₆alkyl (e.g., methyl) and hydroxy Ci_₆alkyl (e.g., hydroxymethyl), e.g., hydrogen and Ci_₆alkyl;

R₇ is selected from the group consisting of hydrogen, halogen, cyano, Ci_₆alkyl, Ci-όhaloalkyl, amino, e.g., Ci_6alkylamino, Ci_6alkoxy, aryloxy, hydroxy, sulfonyl, sulfonamide, and heterocyclyl, wherein R₇ may be optionally substituted with one or more Ri i ;

Rs, R₉, and Rio are each independently selected from the group consisting of hydrogen, Ci-₆alkyl, e.g., -CH₃, halogen, e.g., Cl or F, Ci-βalkoxy, e.g., -OCH₃, amino, hydroxy, haloalkyl, cyano, sulfonyl, and sulfonamide;

Rn may be selected from the group consisting of halogen, hydroxy, amino, Ci_₆alkyl, Ci_₆alkoxy, aryl, and heterocyclyl, wherein Rn may be optionally substituted with one or more Ri 2; and

R12 may be selected from the group consisting of amino, cyano, hydroxy, Ci_6alkyl, cycloalkyl, and aryl, or pharmaceutically acceptable salts thereof. In certain embodiments, R₇ is selected from the group consisting of the group consisting of 2-pyridylmethoxy, (l-methyl-4-piperidyl)methoxy, (3-cyanophenyl)methoxy, [(2S)-l-methylpyrrolidin-2-yl]methoxy, [(2R)-l-methylpyrrolidin-2- yljmethoxy, 2-dimethylaminoethoxy, 2-thienyl, 3-diethylaminopropoxy, 4-(2- dimethylaminoethyl)piperazin- 1 -yl, 4-(2-hydroxyethyl)piperazin- 1 -yl, 4-(2- pyridylmethyl)piperazin-l-yl, 4-(cyclopropylmethyl)piperazin-l-yl, chloro, cyano, fluoro, hydrogen, isobutoxy, morpholino, phenoxy, trifluoromethyl, 4-methylpiperazin- 1 -yl, [2- (dimethylamino)ethyl]methylamino, (2-morpholin-4-ylethyl)amino, 2-hydroxyethylamino, piperazin-lyl, 2-(dimethylamino)ethylamino, [(2S)-l-ethylpyrrolidin-2-yl]methylamino, (1- methylpyrrolidin-3-yl)methoxy, (l-methylpiperidin-2-yl)methoxy), 2-morpholin-4-ylethoxy, 2- pyrrolidin-1-ylethoxy, (l-methylpiperidin-3-yl)methoxy), (2S)-l-methylpiperidin-2-yl]methoxy, (2R)- 1 -methylpiperidin-2-yl]methoxy, (3 S)- 1 -methylpiperidin-3-yl]methoxy, (3R)- 1 - methylpiperidin-3-yl]methoxy, methyl, and any combination thereof. For example, in specific embodiments, R₇ is selected from the group consisting of the group consisting of (l-methyl-4- piperidyl)methoxy, [(2S)-l-methylpyrrolidin-2-yl]methoxy, trifluoromethyl, (1-methylpiperidin- 2-yl)methoxy), (l-methylpiperidin-3-yl)methoxy), methyl, and any combination thereof. In a particular embodiment of formula II, the compound has the formula:

In another embodiment, the invention provides a compound of formula III

III wherein n is 0, 1, 2, or 3 (e.g., n is 2 or 3);

R₃ is selected from the group consisting of the group consisting of hydrogen, halogen, and alkyl; each Ri₄ is selected from the group consisting of the group consisting of hydrogen, halogen, hydroxyl, sulfide, carboxamide, Ci_6alkylcarbonyl, amino, alkyl, alkoxyl, alkoxycarbonyl, sulfinyl, sulfonyl, cyano, cycloalkyl, aryl or a heterocyclyl wherein each R_ϊ4 is optionally substituted with Ci_₆alkylcarbonyl, hydroxyl, hydroxy Ci_₆alkyl (e.g., hydroxymethyl ), halogen, amino, nitro, Ci_6alkyl, (e.g., methyl) sulfonyl, cyano, alkoxyl or heterocyclyl, such that Ri₄ is not unsubstituted phenyl when the imidazolyl ring to which the R₁₄ is attached is 2- imidazolyl;

Ri5 is selected from the group consisting of the group consisting of -(CH)o-s-heterocycle, e.g., -(CH)₀-2-heterocycle, -(CH)o-5-NR_bR_b, e.g., -(CH)o-₂-NR_bRb, -(CH)₀-₅-hydroxy, e.g., -(CH)₀- ₂-hydroxy, -(CH)o-5-Ci_6alkoxy, e.g., -(CH)o-₂-Ci_6alkoxy, aryl and heterocyclyl, e.g., piperazine, wherein R₁5 is optionally substituted with Ri6, and each Rb is selected from the group consisting of the group consisting of H, alkyl, and cycloalkyl; and

Ri6 is selected from the group consisting of the group consisting of halo, alkyl, alkoxy, alkylthio, wherein Ri6 is optionally substituted with aryl or heteroaryl, or a pharmaceutically acceptable salt thereof. In certain embodiments, Ri₄ is H, hydroxyCi-₆alkyl, e.g., hyrdoxymethyl, or Ci_₆alkyl, e.g., methyl.

Compounds and compositions of the invention are also useful in the manufacture of a medicament for inhibiting the Hedgehog pathway in a subject in need thereof. One embodiment provides for the use of disclosed compounds and compositions in the manufacture of a medicament for reducing cell differentiation, proliferation, and/or affecting stromal microenvironment modulation in a subject in need thereof. Another embodiment provides for the use of disclosed compounds and compositions in the manufacture of a medicament for treating a disease or medical condition mediated alone or in part by Hedgehog pathway inhibition in a subject in need thereof. A. Additional Compounds of the Invention Disclosed herein are compounds of formula IV

IV wherein

Rr, R2' and R3' are each independently selected from hydrogen, Ci_₆alkyl, and halogen;

R₄' is selected from Ci_₆alkyl, haloCi_₆alkyl, and halogen; each W is independently selected from CR5', NR₅-, N, O, and S, where R5' is selected from hydrogen, Ci-₆alkoxy, Ci-₆alkoxyCi_₆alkyl, Ci_₆alkoxycarbonyl, Ci_₆alkyl, amidino, amido, amino, aryl, carboxamido, C₃_₈cycloalkyl, cyano, haloCi_₆alkyl, halogen, heterocyclylCi-_όalkyl, hydroxy, hydroxyCi_6alkyl, nitro, sulfide, sulfonamido, and sulfonyl, or two adjacent W atoms can be taken together to form a fused second ring, wherein the second ring is optionally substituted with one or more R₅ substituents and is selected from aryl, C3-8cycloalkyl, 5- or 6-membered heteroaryl, and 5- or 6-membered heterocyclyl; at least one W is N; q' is 0 or 1, where if q' is 0 and two adjacent W atoms are taken together to form a fused second ring, then one of the adjacent W atoms is N and the second ring is a 6-membered heteroaryl or a 6- membered heterocyclyl, and if q' is 0, then four W atoms are not N;

A' is selected from CR₆, NR₆, N, O, and S;

R₆' is selected from hydrogen, Ci_₆alkoxy, Ci-₆alkoxyCi_₆alkyl, Ci_₆alkoxycarbonyl, Ci-₆alkyl, amidino, amido, amino, aryl, carboxamido, C₃_₈cycloalkyl, cyano, haloCi_₆alkyl, halogen, heterocyclylCi_₆alkyl, hydroxy, hydroxyCi_₆alkyl, nitro, sulfide, sulfonamido, and sulfonyl, or two adjacent A' atoms can be taken together to form a fused second ring, wherein the second ring is selected from a 5- or 6-membered heteroaryl and a 5- or 6-membered heterocyclyl; at least one A' is selected from NRs-, N, O, and S; p' is 0 or 1, where if p' is 0 and Rr, Rr, and R₄' are each methyl, then A' is not S; wherein the compound of formula IV is not

, where L' is selected from NH and CH, and if L' is NH, then M' is CH₂, and if L' is CH then M' is CH; and pharmaceutically acceptable salts thereof.

In one embodiment, R₁-, Rr and R₃' are each hydrogen. In another embodiment, R₄' is chloro. In another embodiment, R₅' is selected from hydrogen, Ci_₆alkoxycarbonyl, Ci_₆alkyl, and amino.

In one embodiment, two adjacent W atoms are taken together to form a 6,6-fused bicyclic heteroaryl having at least one N heteroatom. In another embodiment, two adjacent W atoms are taken together to form a 5,6-fused bicyclic heteroaryl having at least one N heteroatom.

In a further embodiment, two W are N and q' is 1, such as a pyrazinyl. In one embodiment, the compound of formula (I) is N-[3-(5-aminopyrazin-2-yl)-4-chloro-phenyl]-2- methyl-6-(trifluoromethyl)pyridine-3-carboxamide. In another embodiment, at least one W is N and q is 0. In a further embodiment, the compound of formula I comprises an imidazolyl or a thiazolyl, such as a compound selected from N-[4-chloro-3-(l,5-dimethylimidazol-2-yl)phenyl]- 2-methyl-6-(trifluoromethyl)pyridine-3-carboxamide, N-[4-chloro-3-(l-methylimidazol-2- yl)phenyl]-2-methyl-6-(trifluoromethyl)pyridine-3-carboxamide, and methyl 2-[2-chloro-5-[[2- methyl-β-^ifluoromethy^pyridine-S-carbonyljaminojphenyljl^-thiazole-S-carboxylate.

In one embodiment, one A' is N and p' is 1. In another embodiment, one Rβ' is Ci_₆alkyl and one Rβ' is haloCi_₆alkyl.

In some embodiments, the invention relates to a compound of formula V:

V or pharmaceutically acceptable salts thereof wherein, A' is selected from N and CRi r; X' is selected from halogen and Ci_₆alkyl; Y' is selected from NR5' and S; R₅' is selected from hydrogen and Ci_₆alkyl;

R_O', and R₇' are each independently selected from hydrogen and Ci_₆alkyl; Ry is selected from hydrogen, halogen, Ci_₆alkyl, Ci_₆alkoxy, aryloxy, and heterocyclyl, wherein R₉' may be optionally substituted with one or more R12 ;

Rδ', Rio', and Ri r are each independently selected from hydrogen, halogen, and Ci_6alkoxy; Ri2' may be selected from halogen, amino, Ci_6alkyl, aryl, and heterocyclyl, wherein R12 may be optionally substituted with one or more R13; and Ri3> may be selected from cyano, Chalky 1, cycloalkyl, and aryl. In further embodiments, R5' and Rβ> are both methyl and R₇' is hydrogen.

In further embodiments, R₉' is selected from 2-pyridylmethoxy, (l-methyl-4-piperidyl)methoxy, (3-cyanophenyl)methoxy, [(2S)-l-methylpyrrolidin-2-yl]methoxy, 2-dimethylaminoethoxy, 2- thienyl, 3-diethylaminopropoxy, 4-(2-dimethylaminoethyl)piperazin-l-yl, 4-(2- hydroxy ethyl)piperazin- 1 -yl, 4-(2-pyridylmethyl)piperazin- 1 -yl, 4-(cyclopropylmethyl)piperazin- 1-yl, chloro, cyano, fluoro, hydrogen, isobutoxy, methyl, methyl, morpholino, phenoxy, trifluoromethyl, and methyl.

B. Synthetic Schemes

Compounds of formula I can be synthesized from the general synthetic methods described below in Schemes 1-3. It is to be understood that compounds of formula I, such as those synthesized according to the general methods below, may themselves be further derivatized to form other compounds of formula I. The following schemes are meant to be exemplary only, and one of ordinary skill in the art would recognize viable combinations thereof.

Shown in Scheme 1 , aryl nitro-boronate 1 can be reduced to aniline 2 using a variety of conditions such as iron chloride and hydrazine or catalytic hydrogenation. Amide bond formation to yield compound 4 can be effected by reaction with acid chloride 3 and a base, such as pyridine. Alternatively, reaction of aniline 2 with carboxylic acid 3 utilizing standard amide forming conditions such as, for example, HATU or EDCI and base such as Hunig's Base or N- methylmorpholine. Reaction of the resulting boronate 4 with an aryl or heterocyclic electrophile 5 via transition metal mediated coupling such as, for example, Suzuki conditions (Pd(Ph₃ )₄, CS₂CO₃) yields compounds of Formula I.

Scheme 1

Another route to compounds of Formula I is outlined in Scheme 2, which follows an identical series of transformations as Scheme 1, except that the starting nitro derivative 6 is an aryl or heterocyclic halide or triflate rather than boronate 1. The final transformation involves reacting electrophile 8 and boronate 9 under transition metal, such as Pd(O), mediated conditions, such as coupling of either boronate 9 in a Suzuki coupling or aryl/heteroaryl zinc 9 in a Negishi cross-coupling.

Scheme 2

LG=Br, I, OTf (i)

In addition, compounds of Formula I can be synthesized from a variety of other methods (Scheme 3) utilizing aryl alkynes 11, nitriles 12, or aldehydes/ketones/acids 13 as starting points to the Z ring of Formula I. For example, alkynes are useful precursors to rings such as, for example, triazoles (Bock et al. Eur. J. Org. Chem. 51-68 (2006)) and pyrazoles (Fulton et al. Eur. J. Org. Chem. 1479-1492 (2005)) by reaction with azido and diazo reagents, respectively. Nitriles are useful as starting materials to thiazoles and other heterocycles (Collier, S. J.; Langer, P., Science of Synthesis, 19:411 (2004)). Aldehydes and ketones can be used as precursors to a variety of heterocycles (Nakamura, et al., J. Med. Chem. 46:5416-5427 (2003)) including, but not limited to, imidazoles, benzimidazoles, and quinoxalines . Carboxylic acids and derivatives thereof can be converted to a variety of heterocycles such as, for example, benzimidazoles or benzothiazoles. Scheme 3

1 1

R'=H, OH, alkyl

//. Pharmaceutical Compositions

The present disclosure also provides pharmaceutical compositions comprising compounds as disclosed herein formulated together with one or more pharmaceutically acceptable carriers. These formulations include those suitable for oral, rectal, topical, buccal and parenteral {e.g., subcutaneous, intramuscular, intradermal, or intravenous) administration, although the most suitable form of administration in any given case will depend on the degree and severity of the condition being treated and on the nature of the particular compound being used. In one embodiment, the compound or pharmaceutical composition is administered to a subject such as a warm-blooded animal. In another embodiment, the warm-blooded animal is a mammal, such as a human.

Formulations suitable for oral administration may be presented in discrete units, such as capsules, cachets, lozenges, or tablets, each containing a predetermined amount of the compound as powder or granules; as a solution or a suspension in an aqueous or non-aqueous liquid; or as an oil-in-water or water-in-oil emulsion. As indicated, such formulations may be prepared by any suitable method of pharmacy which includes the step of bringing into association the active compound and the carrier or excipient (which may constitute one or more accessory ingredients). The carrier must be acceptable in the sense of being compatible with the other ingredients of the formulation and must not be deleterious to the recipient. The carrier may be a solid or a liquid, or both, and may be formulated with the compound as a unit-dose formulation, for example, a tablet, which may contain from about 0.05% to about 95% by weight of the active compound. Other pharmacologically active substances may also be present, including other compounds. The formulations of the invention may be prepared by any of the well known techniques of pharmacy involving admixing the components.

For solid compositions, conventional nontoxic solid carriers include, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talc, cellulose, glucose, sucrose, magnesium carbonate, and the like. Liquid pharmacologically administrable compositions can, for example, be prepared by dissolving, dispersing, etc., an active compound as described herein and optional pharmaceutical adjuvants in an excipient, such as, for example, water, saline, aqueous dextrose, glycerol, ethanol, and the like, to thereby form a solution or suspension. In general, suitable formulations may be prepared by uniformly and intimately admixing the active compound with a liquid or finely divided solid carrier, or both, and then, if necessary, shaping the product. For example, a tablet may be prepared by compressing or molding a powder or granules of the compound, optionally with one or more accessory ingredients. Compressed tablets may be prepared by compressing, in a suitable machine, the compound in a free-flowing form, such as a powder or granules optionally mixed with a binder, lubricant, inert diluent and/or surface active/dispersing agent(s). Molded tablets may be made by molding, in a suitable machine, the powdered compound moistened with an inert liquid diluent. Formulations suitable for buccal (sub-lingual) administration include lozenges comprising a compound in a flavored base, usually sucrose and acacia or tragacanth, and pastilles comprising the compound in an inert base such as gelatin and glycerin or sucrose and acacia.

Formulations of the present invention suitable for parenteral administration comprise sterile aqueous preparations of the compounds, which are approximately isotonic with the blood of the intended recipient. These preparations are administered intravenously, although administration may also be effected by means of subcutaneous, intramuscular, or intradermal injection. Such preparations may conveniently be prepared by admixing the compound with water and rendering the resulting solution sterile and isotonic with the blood. Injectable compositions according to the invention may contain from about 0.1 to about 5% w/w of the active compound.

Formulations suitable for rectal administration are presented as unit-dose suppositories. These may be prepared by admixing the compound with one or more conventional solid carriers, for example, cocoa butter, and then shaping the resulting mixture.

Formulations suitable for topical application to the skin may take the form of an ointment, cream, lotion, paste, gel, spray, aerosol, or oil. Carriers and excipients which may be used include Vaseline, lanoline, polyethylene glycols, alcohols, and combinations of two or more thereof. The active compound is generally present at a concentration of from about 0.1% to about 15% w/w of the composition, for example, from about 0.5% to about 2%.

The amount of active compound administered may be dependent on the subject being treated, the subject's weight, the manner of administration and the judgment of the prescribing physician. For example, a dosing schedule may involve the daily or semi-daily administration of the encapsulated compound at a perceived dosage of about 10 μg to about 100 mg. In another embodiment, intermittent administration, such as on a monthly or yearly basis, of a dose of the encapsulated compound may be employed. Encapsulation facilitates access to the site of action and allows the administration of the active ingredients simultaneously, in theory producing a synergistic effect. In accordance with standard dosing regimens, physicians will readily determine optimum dosages and will be able to readily modify administration to achieve such dosages.

A therapeutically effective amount of a compound or composition disclosed herein can be measured by the therapeutic effectiveness of the compound. Compounds of the invention may be administered in a dose of about 1 μg/kg to about 200 mg/kg daily; such as from about 1 μg/kg to about 150 mg/kg, from about 1 mg/kg to about 200 mg/kg, from about 1 μg/kg to about 100 mg/kg, from about 1 μg/kg to about 1 mg/kg, from about 50 μg/kg to about 200 mg/kg, from about 10 μg/kg to about 1 mg/kg, from about 10 μg/kg to about 100 μg/kg, from about 100 μg to about 10 mg/kg, and from about 500 μg/kg to about 50 mg/kg. The dosages, however, may be varied depending upon the requirements of the patient, the severity of the condition being treated, and the compound being used. In one embodiment, the therapeutically effective amount of a disclosed compound is sufficient to establish a maximal plasma concentration ranging from about 0.001 μM to about 100 μM, e.g., from about 1 μM to about 20 μM. Preliminary doses as, for example, determined according to animal tests, and the scaling of dosages for human administration is performed according to art-accepted practices.

Toxicity and therapeutic efficacy can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD_5O (the dose lethal to 50% of the population) and the ED₅O (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50. Compositions that exhibit large therapeutic indices are preferable.

The therapeutically effective dose can be estimated initially from cell culture assays. A dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (i.e., the concentration of the therapeutic which achieves a half-maximal inhibition of symptoms) as determined in cell culture assays or animal models. Levels in plasma may be measured, for example, by high performance liquid chromatography. The effects of any particular dosage can be monitored by a suitable bioassay. Examples of dosages are: about 0.1 x IC50, about 0.5 x IC50, about 1 x IC50, about 5 x IC50, 10 x IC50, about 5Ox IC50, and about 100 x IC₅₀.

Data obtained from the cell culture assays or animal studies can be used in formulating a range of dosage for use in humans. Therapeutically effective dosages achieved in one animal model may be converted for use in another animal, including humans, using conversion factors known in the art (see, e.g., Freireich et al., Cancer Chemother. Reports 50(4):219-244 (1966) and Table 1 for Equivalent Surface Area Dosage Factors). Table 1

The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED₅O with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. Generally, a therapeutically effective amount may vary with the subject's age, condition, and sex, as well as the severity of the medical condition in the subject. The dosage may be determined by a physician and adjusted, as necessary, to suit observed effects of the treatment.

One embodiment provides administration of a compound of formula I to a subject in conjunction with radiation treatment. In another embodiment, a compound as disclosed herein, or a pharmaceutically acceptable salt or hydrate thereof, is administered in combination with one or more therapeutic agents. The therapeutic agent can be administered separately, sequentially or simultaneously with the compound disclosed herein. Dosage ranges for combination therapies may be commensurate with that of monotherapy.

The therapeutic agent(s) can provide additive or synergistic value relative to the administration of the compound alone. The therapeutic agent can be, for example, selected from the group consisting of:

(i) antiproliferative/antineoplastic drugs and combinations thereof, as used in medical oncology, such as alkylating agents (for example, cis-platin, carboplatin, cyclophosphamide, nitrogen mustard, melphalan, chlorambucil, busulphan and nitrosoureas); antimetabolites (for example, antifolates such as fluoropyrimidines (like 5-fluorouracil and tegafur), raltitrexed, methotrexate, cytosine arabinoside and hydroxyurea); antitumor antibiotics (for example, anthracyclines like adriamycin, bleomycin, doxorubicin, daunomycin, epirubicin, idarubicin, mitomycin-C, dactinomycin and mithramycin); antimitotic agents (for example, vinca alkaloids like vincristine, vinblastine, vindesine and vinorelbine and taxoids like taxol and taxotere); and topoisomerase inhibitors (for example, epipodophyllotoxins like etoposide and teniposide, amsacrine, topotecan and camptothecin);

(ii) cytostatic agents such as antiestrogens (for example, tamoxifen, toremifene, raloxifene, droloxifene and iodoxyfene), estrogen receptor down regulators (for example, fulvestrant), antiandrogens (for example, bicalutamide, flutamide, nilutamide and cyproterone acetate), LHRH antagonists or LHRH agonists (for example, goserelin, leuprorelin and buserelin), progestogens (for example, megestrol acetate), aromatase inhibitors (for example, anastrozole, letrozole, vorazole and exemestane) and inhibitors of 5α-reductase such as finasteride;

(iii) agents which inhibit cancer cell invasion (for example, metalloproteinase inhibitors like marimastat and inhibitors of urokinase plasminogen activator receptor function);

(iv) inhibitors of growth factor function: for example, such inhibitors include growth factor antibodies, growth factor receptor antibodies (for example, the anti-erbb2 antibody trastuzumab [Herceptin™] and the anti-erbbl antibody cetuximab [C225]) , farnesyl transferase inhibitors, MEK inhibitors, tyrosine kinase inhibitors and serine/threonine kinase inhibitors, inhibitors of the epidermal growth factor family (for example, EGFR family tyrosine kinase inhibitors such as N-(3-chloro-4-fluorophenyl)-7-methoxy-6-(3-morpholinopropoxy)quinazolin- 4-amine (gefϊtinib, AZDl 839), N-(3-ethynylphenyl)-6,7-bis(2-methoxyethoxy)quinazolin-4- amine (erlotinib, OSI-774) and 6-acrylamido-N-(3-chloro-4-fluorophenyl)-7-(3- morpholinopropoxy)quinazolin-4-amine (CI 1033)), inhibitors of the platelet-derived growth factor family and inhibitors of the hepatocyte growth factor family;

(v) antiangiogenic agents such as those which inhibit the effects of vascular endothelial growth factor, (for example, the anti-vascular endothelial cell growth factor antibody bevacizumab [Avastin™], compounds such as those disclosed in International Patent Applications WO 97/22596, WO 97/30035, WO 97/32856 and WO 98/13354) and compounds that work by other mechanisms (for example, linomide, inhibitors of integrin αvβ3 function and angiostatin);

(vi) vascular damaging agents such as Combretastatin A4 and compounds disclosed in International Patent Applications WO 99/02166, WO00/40529, WO 00/41669, WOO 1/92224, WO02/04434 and WO02/08213; (vii) antisense therapies, for example, those which are directed to the targets listed above, such as ISIS 2503, an anti-ras antisense;

(viii) gene therapy approaches, including for example, approaches to replace aberrant genes such as aberrant p53 or aberrant BRCAl or BRCA2, GDEPT (gene-directed enzyme pro-drug therapy), approaches such as those using cytosine deaminase, thymidine kinase or a bacterial nitroreductase enzyme and approaches to increase patient tolerance to chemotherapy or radiotherapy such as multi-drug resistance gene therapy;

(ix) immunotherapy approaches, including for example ex vivo and in vivo approaches to increase the immunogenicity of patient tumor cells, such as transfection with cytokines such as interleukin 2, interleukin 4 or granulocyte-macrophage colony stimulating factor, approaches to decrease T-cell energy, approaches using transfected immune cells such as cytokine-transfected dendritic cells, approaches using cytokine-transfected tumor cell lines and approaches using anti-idiotypic antibodies;

(x) cell cycle inhibitors, including for example, CDK inhibitiors (e.g., flavopiridol) and other inhibitors of cell cycle checkpoints (e.g., checkpoint kinase); inhibitors of aurora kinase and other kinases involved in mitosis and cytokinesis regulation (e.g., mitotic kinesins); and histone deacetylase inhibitors; and

(xi) endothelin antagonists, including endothelin A antagonists, endothelin B antagonists and endothelin A and B antagonists; for example ZD4054 and ZD 1611 (WO 96/40681), atrasentan and YM598.

Compounds of formula I can be useful as pharmaceutical tools in the development and standardization of in vitro and in vivo test systems for evaluating the effects of Hedgehog pathway inhibition in laboratory animals such as cats, dogs, rabbits, monkeys, rats and mice, as part of the search for new therapeutic agents.

///. Methods of Use

In certain embodiments, the compounds and compositions of the invention can be useful in methods for inhibiting the Hedgehog pathway. Disclosed herein are methods for reducing cell differentiation, proliferation, and/or affecting stromal microenvironment modulation comprising administering a therapeutically effective amount of a compound of the invention to a subject in need thereof. Inhibiting the Hedgehog pathway provides useful methods for treating diseases or medical conditions mediated alone or in part by this pathway. These diseases include cancer and other proliferative diseases.

While the primary focus has been on cancer, Hedgehog antagonists have also been shown to reduce the symptoms of psoriasis (Tas et al. Dermatology 209:126-131 (2004)). Psoriasis is a chronic skin disorder typically characterized by skin lesions and plaques, and is currently understood to be autoimmune disease, though its etiology is not well defined. As such, compounds of the invention are expected to have a beneficial effect on subjects having psoriasis.

Accordingly, one embodiment provides a method for inhibiting the Hedgehog pathway comprising administering to a subject in need thereof a therapeutically effective amount of a disclosed compound or pharmaceutical composition. Another embodiment provides a method of reducing cell proliferation, differentiation and/or affecting stromal microenvironment modulation comprising administering to a subject in need thereof a therapeutically effective amount of a disclosed compound or pharmaceutical composition. In one embodiment, the cell is a stromal cell. In another embodiment, the cell is a cancer cell. In a further embodiment, the cell is a stem cell, such as a cancer stem cell.

In one embodiment, stromal microenvironment modulation comprises vascular modulation. In another embodiment, stromal microenvironment modulation comprises downregulation of the Hedgehog pathway in stromal cells. In a further embodiment, the stromal cell is a fibroblast.

In one embodiment, cell proliferation, differentiation and/or stromal microenvironment modulation are prevented by administering to a subject in need thereof a therapeutically effective amount of a disclosed compound or pharmaceutical composition. As used herein, "prevention" or "preventing" refers to a reduction of the risk of acquiring a given disease or disorder.

Also disclosed are methods for treating a disease or medical condition mediated alone or in part by Hedgehog pathway inhibition comprising administering to a subject in need thereof a therapeutically effective amount of a compound or composition as disclosed herein.

In one embodiment, "treatment" or "treating" refers to an amelioration of a disease or disorder, or at least one discernible symptom thereof. In another embodiment, "treatment" or "treating" refers to an amelioration of at least one measurable physical parameter, not necessarily discernible by the patient. In yet another embodiment, "treatment" or "treating" refers to inhibiting the progression of a disease or disorder, either physically, e.g. , stabilization of a discernible symptom, physiologically, e.g. , stabilization of a physical parameter, or both. In yet another embodiment, "treatment" or "treating" refers to delaying the onset of a disease or disorder.

In one embodiment, the disease or medical condition mediated alone or in part by Hedgehog pathway inhibition is associated with cancer. Exemplary diseases and conditions include, but are not limited to, basal cell carcinoma, medulloblastoma, rhabdomyosarcoma, sarcoma, lymphoma, leukemia, glioblastoma, cancers of the prostate, pancreas, ovary, melanoma, breast, colon, lung, esophagus, gastric, biliary, hepatocellular and multiple myeloma. Thus, compounds and compositions of the invention possess anti -proliferative activity, such as anticancer activity.

In another embodiment, the disease or medical condition is psoriasis. In a further embodiment, psoriasis can be treated by administering a compound of the invention in combination with one or more anti -psoriasis agents. in one embodiment, the subject is characterized as having a phenotype selected from the group consisting of a PTCH loss-of function phenotype, a SMO gain-of- function phenotype, and a Hedgehog gain-of- function phenotype.

EXEMPLIFICATION

The following descriptions of experiments, procedures, examples, and intermediates are intended to exemplify embodiments of the invention, and are in no way intended to be limiting.

The compounds of the present invention can be prepared in a number of ways well known to one skilled in the art of organic synthesis. More specifically, compounds of the invention may be prepared using the reactions and techniques described herein. In the description of the synthetic methods described below, it is to be understood that all proposed reaction conditions, including choice of solvent, reaction atmosphere, reaction temperature, duration of the experiment and workup procedures, can be chosen to be the conditions standard for that reaction, unless otherwise indicated. It is understood by one skilled in the art of organic synthesis that the functionality present on various portions of the molecule should be compatible with the reagents and reactions proposed. Substituents not compatible with the reaction conditions will be apparent to one skilled in the art, and alternate methods are therefore indicated. The starting materials for the examples are either commercially available or are readily prepared by standard methods from known materials. In the following examples, the conditions are as follows, unless stated otherwise:

(i) temperatures are given in degrees Celsius (⁰C); operations are carried out at room temperature (RT) or ambient temperature, such as a range of about 18-25 ⁰C, unless otherwise stated; (ii) solutions are dried over anhydrous sodium sulfate or magnesium sulfate, for example; evaporation organic of organic solvent is carried out using a rotary evaporator under reduced pressure (e.g., about 4.5 - 30 mmHg) with a bath temperature of, for example, up to about 60 ⁰C; (iii) chromatography refers to flash chromatography on silica gel; thin layer chromatography (TLC) was carried out on silica gel plates; (iv) in general, the course of reactions was followed by TLC or liquid chromatography/mass spectroscopy (LC/MS), and reaction times are given for illustration only; (v) final products have been analyzed using proton nuclear magnetic resonance (NMR) spectra and/or mass spectra data; (vi) yields are given for illustration only and are not necessarily those that can be obtained by diligent process development; preparations can be repeated if more material is desired; (vii) when given, nuclear magnetic resonance (NMR) data is in the form of delta (δ) values for major diagnostic protons, given in part per million (ppm) relative to tetramethylsilane (TMS) as an internal standard, determined at either 300 or 400 MHz in de-DMSO;

(viii) chemical symbols have their usual meanings in the art; (ix) solvent ratio is given in volume:volume (v/v) terms; (x) purification of the compounds can be carried out using one or more of the following methods: a) flash chromatography on normal-phase silica gel; b) flash chromatography on silica gel using Isco Combiflash^® separation system: RediSep normal phase flash column at a flow rate such as 20-80 mL/min (ISCO MPLC);

c) flash chromatography on silica gel using Biotage^® separation system;

d) Gilson semiprep HPLC separation system: for example, YMC pack ODS-AQ column, 100x20 mm, S 5μm 12 nm, water (0.1% trifluoroacetic acid) and acetonitrile (0.1% trifluoroacetic acid) as solvents or water (10 mM ammonium acetate containing 5% acetontitrile) and acetonitrile, 10- 20 min run; and

e) crystalization or recrystalization using standard techniques.

Abbreviations used herein denote the following compounds, reagents and substituents: ammonium acetate (NH₄OAc), acetonitrile (MeCN), <9-(7-azabenzotriazol-l-yl)-N,N,N',N'- tetramethyluronium hexafluorophosphate (HATU), N,N-diisopropylethylamine or Hunig's Base (DIPEA), triethylamine (TEA), dimethylacetamide (DMA), ethylene glycol dimethyl ether (DME), diethyl ether (Et₂O), dimethylformamide (DMF), dimethylsulfoxide (DMSO), ethanol (EtOH), methanol (MeOH), tetrahydrofuran (THF), N-(3-dimethylaminopropy I)-N- ethylcarbodiimide (EDCI), fetal bovine serum (FBS), l-hydroxy-7-azabenzotriazole (HOAt), Sonic Hedgehog (shh ligand), para-nitrophenol (pNp), phosphate-buffered saline (PBS), methylene chloride or CH₂Cl₂ (DCM), ethyl acetate (EtOAc), sodium sulfate (Na₂SO₄), magnesium sulfate (MgSO₄), sodium hydroxide (NaOH), lithium hydroxide (LiOH), hydrogen chloride (HCl), hydrogen (H₂), cesium carbonate (Cs₂COs), potassium carbonate (K₂COs), sodium carbonate (Na₂COs), sodium bicarbonate (NaHCOs), potassium bicarbonate (KHCO3), tetrakis(triphenylphosphine) palladium (0) [Pd(PPh₃ )₄], ammonium chloride (NH₄Cl), sodium borohydride (NaBH₄), N,N-dimethylpyridin-4- amine (DMAP), ammonium hydroxide (NH₄OH), 1, 2-dichloroethane (DCE), potassium acetate (KOAc), N-methylpyrrolidinone (NMP), acetic acid (AcOH), methyl-fert-butyl ether (MTBE), diisopropyl azodicarboxylate (DIAD), 2,2'- bis(diphenylphosphino)- 1 , 1 '-binaphthyl (BINAP), tris(dibenzyideneacetone)dipalladium (Pd₂dba₃), [l,r-bis(diphenylphosphino)ferrocene]dichloropalladium(II) [PdCl₂(dppf)], sodium hydride (NaH), and sodium iodide (NaI). Example 1

N-[4-chloro-3-(l,5-dimethyl-lH-imidazol-2-yl)phenyl]-2-methyl-6-(trifluoromethyl)pyridine-3- carboxamide

IA. 5-amino-2-chlorophenylboronic acid

In a 250 mL round-bottomed flask were added 2-chloro-5-nitrophenylboronic acid (5.0 g, 24.83 mmol), iron(III) chloride (8.04 g, 2.48 mmol, 5% in silica gel), activated carbon (2.086 g, 173.81 mmol) and MeOH (124 mL) to give a suspension. The reaction was heated to 75 ⁰C for 20 min before hydrazine monohydrate (9.55 g, 297.96 mmol) was added. The reaction was stirred at 70 ⁰C for 3h. The reaction mixture was filtered and concentrated in vacuo to afford the crude product, which was purified by ISCO MPLC (10% MeOH/DCM) to give the title compound (3.8 g, 90% yield).

Alternatively, 5-amino-2-chlorophenylboronic acid can be synthesized using the following procedure:

In a 500 mL round-bottomed flask was combined 2-chloro-5-nitrophenylboronic acid (10.0 g, 49.66 mmol), iron (2.7 g, 496.6 mmol), and NH₄Cl (26.6 g, 496.6 mmol) in EtOH (100 mL) to give a black suspension. The reaction mixture was diluted with water (100 mL) and heated to 55 ⁰C for 0.5h. After filtration through a pad of silica gel, the filtrate was concentrated under reduced pressure to remove the EtOH. The remaining aqueous suspension was filtered to afford the title compound as a solid (5.4 g, 64% yield). ¹H NMR (DMSOd₆) δ 5.06 (s, 2 H), 6.51 (dd, 1 H), 6.94 (d, 1 H), 7.01 (d, 1 H). MS (M+H⁺) = 172.

IB. [2-chloro-5-({[2-methyl-6-(trifluoromethyl)pyridin-3-yl]carbonyl}amino)phenyl]boronic acid

In a 100 mL round-bottomed flask was placed 5-amino-2-chlorophenylboronic acid (2.500 g, 14.59 mmol) in pyridine (25 mL) to give a solution. To the solution was added 2- methyl-6-(trifluoromethyl)nicotinoyl chloride (3.26 g, 14.59 mmol). The reaction was stirred at RT for Ih. After concentration in vacuo, the crude product was purified by ISCO MPLC (10% MeOH/DCM) to give the title compound (4.5 g, 86%). MS (M+H⁺) = 359.

1C. N- [4-chloro-3-(l ,5-dimethylimidazol-2-yl)phenyl] -2-methyl-6-(trifluoromethyl)pyridine-3- carboxamide

In a 20 mL tube was added boronic acid (0.12 g, 0.33 μmol), Cs₂CO₃ (0.22 g, 0.67μmol), 2-bromo-l,5-dimethyl-lH-imidazole (0.12 g, 0.67μmol) in dioxane (8 mL) and water (2 mL) to give a suspension. Nitrogen was bubbled into the tube for about 15 min before Pd(PPh₃ )₄ (0.039 g, 0.03 μmol) was added. The reaction mixture was heated in microwave oven for 20 min at 100 ⁰C. The reaction was concentrated in vacuo and then 1 mL of DMSO was added to dissolve the residue. After filtration, the crude sample was purified by Gilson ΗPLC to give the title compound (24.7 mg, 18%). ¹H NMR (DMSO-d₆) δ 2.24 (s, 3 H), 2.64 (s, 3 H), 3.38 (s, 3 H), 6.84 (s, 1 H), 7.63 (s, 1 H), 7.82 (s, 1 H), 7.90 (s, 2 H), 8.21 (s, 1 H), 10.89 (s, 1 H). MS (M+H⁺) = 409.

The following Examples 2-6 were prepared in a similar fashion to Example 1 utilizing commercially available starting materials:

Example 7

N-[4-methyl-3-(4-methyl-lH-imidazol-2-yl)phenyl]-4-(2-pyridylmethoxy)benzamide

7A. N-(4-methyl-S-(4, 4, 5, 5-tetramethyl-l,3,2-dioxaborolan-2-yl)phenyl)-4-(pyridin-2- ylmethoxy)benzamide

In a 500 mL round-bottomed flask was dissolved 4-(pyridin-2-ylmethoxy)benzoic acid (1.50 g, 6.54 mmol), 4-methyl-3-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2-yl)aniline (1.525 g, 6.54 mmol), and DIPEA (2.286 mL, 13.09 mmol) in DMF (10.0 mL) to give a brown solution. The solution was cooled to 0 ⁰C and HATU (2.61 g, 6.87 mmol) was added slowly. After the reaction mixture was warmed to RT, it was stirred for an additional 1.5h. The reaction mixture was diluted with water (200 mL) and stirred for another 0.5h. The solid was collected by filtration and was washed with EtOAc (50 mL) to give the title compound as a white solid (2.0 g, 69% yield). ¹H NMR (DMSOd₆) B 1.31 (s, 12 H), 2.43 (s, 3 H), 5.28 (s, 2 H), 7.14 (d, 3 H), 7.37 (dd, 1 H), 7.54 (d, 1 H), 7.86 (m, 2 H), 7.97 (m, 3 H), 8.60 (d, 1 H), 10.04 (s, 1 H). MS (M+H⁺) = 445. 7B. N-[4-methyl-3-(4-methyl-lH-imidazol-2-yl)phenyl]-4-(2-pyridylmethoxy)benzamide

The title compound was prepared using a similar procedure in the preparation of N- [3- (l,5-dimethylimidazol-2-yl)-4-methyl-phenyl]-2-methyl-6-(trifiuoromethyl)pyridine-3- carboxamide (Example 57) (33% yield). ¹H NMR (DMSOd₆) δ 2.35 (s, 3 H), 2.36 (s, 3 H), 5.34 (s, 2 H), 7.20 (m, 2 H), 7.46 (m, 2 H), 7.56 (s, 1 H), 7.63 (d, 1 H), 7.82 (dd, 1 H), 7.99 (m, 2 H), 8.18 (d, 1 H), 8.66 (s, 1 H), 10.40 (s, 1 H), 14.34 (m, 1 H), 14.48 (s, 1 H). MS (M+ H⁺) = 399.

The following Examples 8-9 were prepared in a similar fashion to Example 7 utilizing commercially available starting materials:

Example 10

N-[4-chloro-3-(lH-imidazol-2-yl)phenyl]-2-methyl-6-(trifluoromethyl)pyridine-3- carboxamide

1OA. 2-(2-chloro-5-nitrophenyl)-lH-imidazole

In a 200 mL round-bottomed flask was added NH₄OH (12 mL, 308.17 mmol) and 2- chloro-5-nitrobenzaldehyde (2.0 g, 10.8 mmol) in EtOH (12 mL) to give a colorless suspension. After cooling to 0 ⁰C, oxalaldehyde (1.854 mL, 16.17 mmol) was added dropwise and the mixture was heated under microwave for Ih at 90 ⁰C. The mixture was extracted with DCM (2 X 30 mL) after dilution with water (40 mL). The combined organic phase was concentrated in vacuo and purified by ISCO MPLC (EtOAc/hexane) to give the title compound (0.4 g, 16% yield). ¹U NMR (DMSO-d₆) δ 7.17 (s, 1 H), 7.39 (s, 1 H), 7.87 (d, 1 H), 8.21 (dd, 1 H), 8.64 (d, 1 H), 12.61 (s, 1 H). LCMS (M + H⁺) = 224.

1OB. N-[4-chloro-3-(lH-imidazol-2-yl)phenyl]-2-methyl-6-(trifluoromethyl)pyridine-3- carboxamide

In a 75 mL round-bottomed flask was combined 2-(2-chloro-5-nitrophenyl)-lH-imidazole (0.30 g, 1.34 mmol) and FeCl₃ in silica gel (0.869 g, 0.27 mmol) in MeOH (6.71 mL) to give a colorless suspension. The mixture was heated 75 ⁰C for 20 min before hydrazine (0.972 mL, 20.12 mmol) was added. The reaction was allowed to stir for another 3h. After cooling to RT, the reaction was filtered and concentrated in vacuo to give 4-chloro-3-(lH-imidazol-2-yl)aniline. This crude product was diluted in DCM (1 mL) to give a colorless solution. To the solution was added pyridine (1 mL) followed by 2-methyl-6-(trifluoromethyl)nicotinoyl chloride (0.040 g, 0.18 mmol) and the reaction was stirred at RT overnight. The reaction mixture was concentrated in vacuo and purified by Gilson HPLC (MeCN/10 mM NH₄OAc in water) to give the title compound (0.025 g, 36% yield). ¹H NMR (DMSO-d₆) δ 2.65 (s, 3 H), 7.08 (s, 1 H), 7.29 (s, 1 H), 7.56 (d, 1 H), 7.75 (dd, 1 H), 7.90 (d, 1 H), 8.21 (m, 2 H), 10.83 (s, 1 H), 12.30 (d, 1 H). LCMS (M + H⁺) = 381.

Example 11

N-[4-chloro-3-(8-methyl-l,7-diazabicyclo[4.3.0]nona-2,4,6,8-tetraen-9-yl)phenyl]-2- methyl-6-(trifluoromethyl)pyridine-3-carboxamide

HA. 4-chloro-3-(2-methylimidazo[l,2-a]pyridin-3-yl)aniline

In a 50 mL vial was added 5-amino-2-chlorophenylboronic acid (0.15 g, 0.88 mmol), 3- bromo-2-methylimidazo[l,2-a]pyridine (0.240 g, 1.14 mmol), and CS₂CO₃ (0.713 g, 2.19 mmol) in dioxane (4 mL) to give a yellow suspension. The reaction mixture was diluted with water (0.80 mL) and after bubbling in nitrogen for 10 min, Pd(PPlIs)₄ (0.303 g, 0.26 mmol) was added. The reaction was heated using a microwave at 100 ⁰C for 20 min. The solvents were removed under reduced pressure and the residue was purified by ISCO MPLC (EtOAc/hexane) to give the title compound (0.11 g, 49% yield). ¹H NMR (DMSOd₆) δ 2.27 (s, 3 H), 5.47 (s, 2 H), 6.64 (d, 1 H), 6.72 (dd, 1 H), 6.86 (t, 1 H), 7.24 (m, 2 H), 7.52 (m, 1 H), 7.78 (d, 1 H). MS (M+H⁺) = 258.

1 IB. N-[4-chloro-3-(8-methyl-l , 7-diazabicyclo[4.3.0]nona-2,4,6,8-tetraen-9-yl)phenyl]-2- methyl-6-(trifluoromethyl)pyridine-3-carboxamide

In a 50 mL round-bottomed flask was dissolved 4-chloro-3-(2-methylimidazo[l,2- a]pyridin-3-yl)aniline (0.104 g, 0.40 mmol) in pyridine (1.342 mL) to give a colorless solution. The solution was cooled to 0 ⁰C, and 2-methyl-6-(trifluoromethyl)nicotinoyl chloride (0.09 g, 0.40 mmol) was added. After stirring at 0 ⁰C for 5 min, the reaction was concentrated under reduced purified by ISCO MPLC (EtOAc/DCM) to give the title compound (0.10 g, 60% yield). ¹H NMR (DMSOd₆) δ 2.30 (s, 3 H), 2.65 (s, 3 H), 6.90 (t, 1 H), 7.29 (m, 1 H), 7.57 (d, 1 H), 7.73 (d, 1 H), 7.90 (m, 4 H), 8.22 (d, 1 H), 10.90 (s, 1 H). MS (M+H⁺) = 445.

Example 12

N-[4-chloro-3-(l,5-dimethylimidazol-2-yl)phenyl]-2-methoxy-pyridine-3-carboxamide

12A. 4-Chloro-3-(l,5-dimethylimidazol-2-yl)aniline

In a 35 mL vial was placed 5-amino-2-chlorophenylboronic acid (0.7 g, 4.08 mmol), 2- bromo-l,5-dimethyl-lH-imidazole (1.072 g, 6.13 mmol), and KOAc (1.203 g, 12.25 mmol) in dioxane (8 mL) to give a yellow suspension. The reaction mixture was diluted with water (2.0 mL) and after bubbling in nitrogen for 10 min, Pd(PPlIs)₄ (0.472 g, 0.41 mmol) was added. The reaction was heated using a microwave at 100 ⁰C for 85 min. After concentration in vacuo, the residue was purified by ISCO MPLC (10% MeOH in DCM) to give the product (0.45 g, 50% yield). ¹H NMR (DMSO-d₆) δ 2.19 (s, 3 H), 3.30 (s, 3 H), 5.41 (s, 2 H), 6.56 (d, 1 H), 6.66 (m, 2 H), 7.16 (d, 1 H). MS (M+H⁺) = 222.

12B. N-[4-chloro-3-(l,5-dimethylimidazol-2-yl)phenyl]-2-methoxy-pyridine-3-carboxamide

In a 10 mL vial was dissolved 4-chloro-3-(l,5-dimethyl-lH-imidazol-2-yl)aniline (0.06 g, 0.27 mmol), 2-methoxynicotinic acid (0.27 mmol), and HATU (0.103 g, 0.27 mmol) in DMF (1.0 mL) to give a brown solution. HATU (0.103 g, 0.27 mmol) was added. The reaction was stirred at RT for 72 h and then concentrated in vacuo. The residue purified by Gilson HPLC (MeCN /10 mM NH₄OAc in water). Collected fractions were concentrated to give the product (0.033 g, 34% yield). ¹H NMR (DMSO-d₆) δ 2.23 (s, 3 H), 3.35 (s, 3 H), 3.97 (s, 3 H), 6.77 (s, 1 H), 7.15 (dd, 1 H), 7.58 (d, 1 H), 7.87 (m, 2 H), 8.04 (dd, 1 H), 8.34 (dd, 1 H), 10.43 (s, 1 H). MS (M+H⁺) = 357.

The following Examples 13-22 were prepared in a similar fashion to Example 12 utilizing commercially available starting materials:

Example 23

N-[4-chloro-3-(l,5-dimethylimidazol-2-yl)phenyl]-3-methoxy-benzamide

In a 10 mL vial was dissolved 4-chloro-3-(l,5-dimethyl-lH-imidazol-2-yl)aniline (0.04 mg, 0.18 μmol) in DCM (0.5 mL) to give a colorless solution. The solution was cooled to 0 ⁰C before 3-methoxybenzoyl chloride (0.03 g, 0.18 μmol) was added and the reaction mixture was then diluted with pyridine (0.5 mL). After stirring overnight and concentration under reduced pressure , the residue was dissolved in DMSO (1 mL), and purified by Gilson HPLC (MeCN/10 mM NH₄OAc in water) to give the title compound (0.017 g). ¹H NMR (DMSO-d₆) δ 2.23 (s, 3 H), 3.36 (s, 3 H), 3.84 (s, 3 H), 6.77 (s, 1 H), 7.17 (dt, 1 H), 7.46 (m, 2 H), 7.56 (m, 2 H), 7.92 (m, 2 H), 10.44 (s, 1 H). MS (M+H⁺) = 356.

The following Examples 24-33 were prepared in a similar fashion to Example 22 utilizing commercially available starting materials:

Example 34

N-[4-chloro-3-(l,5-dimethylimidazol-2-yl)phenyl]-6-[4-(2-hydroxyethyl)piperazin-l-yl]pyridine-

3-carboxamide

In a 10 mL vial was combined 6-chloro-N-(4-chloro-3-(l,5-dimethyl-lH-imidazol-2- yl)phenyl)nicotinamide (0.15 g, 0.42 mmol) and 2-(piperazin-l-yl)ethanol (0.271 g, 2.08 mmol) in DME (2.0 mL) to give a white suspension. The reaction was stirred at 90 ⁰C overnight. After concentration in vacuo, the residue was purified by Gilson HPLC (MeCN/10 mM NH₄OAc in water) to give the title compound (0.062 g, 33%). ¹H NMR (DMSOd₆) δ 2.23 (s, 3 H), 2.43 (t, 2 H), 2.52 (s, 4 H), 3.35 (s, 3 H), 3.54 (t, 2 H), 3.62 (m, 4 H), 4.46 (s, 1 H), 6.77 (s, 1 H), 6.91 (d, 1 H), 7.55 (d, 1 H), 7.89 (m, 2 H), 8.06 (dd, 1 H), 8.72 (d, 1 H), 10.20 (s, 1 H). MS (M+H⁺) = 455.

The following Examples 35-44 were prepared in a similar fashion to Example 34 utilizing commercially available starting materials:

Example 45

N-[4-chloro-3-(l,5-dimethyl-lH-imidazol-2-yl)phenyl]-6-(2-methylpropoxy)pyridine-3- carboxamide

In a 10 mL vial was added 6-chloro-N-(4-chloro-3-(l,5-dimethyl-lH-imidazol-2- yl)phenyl)nicotinamide (0.12 mg, 0.33 μmol), 2-methylpropan-l-ol (0.148 g, 1.99 μmol), and sodium tert-butoxide (0.383 mg, 3.99 μmol) in t-BuOH (3 mL) to give a white suspension. The reaction was stirred 95 ⁰C overnight. After cooling down to RT, the mixture was diluted with water (15 mL) and DCM (15 mL). The aqueous layer was extracted with DCM (2 X 10 mL), and the combined organic layers were concentrated in vacuo. The crude product was purified by Gilson HPLC (MeCN/10 mM NH₄OAc in water) to give the title compound (0.043 g, 32% yield). ¹H NMR (DMSOd₆) δ 0.98 (d, 6 H), 2.06 (m, 1 H), 2.23 (s, 3 H), 3.35 (s, 3 H), 4.12 (d, 2 H), 6.77 (s, 1 H), 6.96 (d, 1 H), 7.59 (m, 1 H), 7.90 (m, 2 H), 8.22 (dd, 1 H), 8.76 (d, 1 H), 10.45 (s, 1 H). MS (M+H⁺) = 399.

The following Examples 46-56 were prepared in a similar fashion to Example 45 utilizing commercially available starting materials:

Example 57

N-[3-(l,5-dimethylimidazol-2-yl)-4-methyl-phenyl]-2-methyl-6-(trifluoromethyl)pyridine-3- carboxamide

57A. 2-methyl-N-(4-methyl-3-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2-yl)phenyl)-6- (trifluoromethyl)nicotinamide

In a 100 mL round-bottomed flask was dissolved 4-methyl-3-(4,4,5,5-tetramethyl-l,3,2- dioxaborolan-2-yl)aniline (2.0 g, 8.58 mmol) in DCM (15.0 mL) to give a colorless solution and the solution was diluted with pyridine (15 mL). The solution was cooled to 0 ⁰C before 2- methyl-6-(trifluoromethyl)nicotinoyl chloride (1.918 g, 8.58 mmol) was added. After stirring at 0 ⁰C for 2h, the solvent was removed under reduced pressure and the residue was diluted with Et₂θ (10 mL). The suspension was stirred for 10 min, filtered, and dried to afford the title compound as a solid (2.1 g, 58% yield). ¹H NMR (DMSOd₆) δ 1.31 (s, 12 H), 2.44 (s, 3 H), 2.63 (s, 3 H), 7.19 (d, 1 H), 7.75 (dd, 1 H), 7.94 (m, 2 H), 8.16 (d, 1 H), 10.53 (s, 1 H). MS (M+H⁺) = 421.

57B. N-[3-(l,5-dimethylimidazol-2-yl)-4-methyl-phenyl]-2-methyl-6-(trifluoromethyl)pyridine-3- carboxamide

In a 10 mL vial was placed 2-methyl-N-(4-methyl-3-(4,4,5,5-tetramethyl-l,3,2- dioxaborolan-2-yl)phenyl)-6-(trifluoromethyl)nicotinamide (0.1 g, 0.24 mmol), CS2CO3 (0.194 g, 0.59 mmol), and 2-bromo- 1,5 -dimethyl- lH-imidazole (0.062 g, 0.36 mmol) in dioxane (4 mL) to give a colorless suspension. The reaction mixture was diluted with water (1 mL). Nitrogen was bubbled through the mixture for 20 min before Pd(PPh₃ )₄ (0.041 g, 0.04 mmol) was added and the reaction was heated to 100 ⁰C using a microwave for 40 min. After concentration in vacuo, the residue was diluted with EtOAc (10 mL) and water (10 mL). The aqueous layer was extracted with EtOAc (2 X 10 mL). The combined organic layers were dried (Na2SO₄) and concentrated in vacuo to give the crude product that was purified by ISCO MPLC (10% MeOH in DCM) to give the title compound (0.035 g, 38% yield). ¹H NMR (DMSO-d₆) δ 2.13 (s, 3 H), 2.23 (s, 3 H), 2.64 (s, 3 H), 3.34 (s, 3 H), 6.76 (s, 1 H), 7.33 (s, 1 H), 7.65 (s, 2 H), 7.89 (s, IH), 8.18 (s, 1 H), 10.63 (s, 1 H). MS (M+H⁺) = 389.

Example 58

N-[4-chloro-3-(l,2-dimethyl-lH-imidazol-5-yl)phenyl]-6-{[(2S)-l-methylpyrrolidin-2- yl]methoxy}pyridine-3-carboxamide Chiral

58A. (S)-6-((l-methylpyrrolidin-2-yl)methoxy)nicotinic acid To a solution of (S)-(I -methylpyrro Ii din-2-yl)methanol (4.39 g, 38.08 mmol) and 6- chloronicotinic acid (1.0 g, 6.35 mmol) was slowly added solid sodium tert-butoxide (7.32 g, 76.16 mmol). The reaction was stirred at 95 ⁰C for 8h then cooled to RT, diluted with water and adjusted pH to 5-6 with HCl, extracted with EtOAc. The aqueous layer was concentrated to dryness to afford the title compound. MS (M+H⁺) = 237.

58B. (S)-2-chloro-5-(6-((l-methylpyrrolidin-2-yl)methoxy)nicotinamido)phenylboronic acid

(S)-6-((l -methylpyrro lidin-2-yl)methoxy)nicotinic acid (1.0 g, 4.23 mmol) was dissolved in SOCI₂ (50 mL) followed by the addition of a few drops of DMF and then stirred overnight at RT. After concentration in vacuo, the residue was redissolved in DCM, concentrated and then placed under high vacuum to give 6-{[(25)-l-methylpyrrolidin-2-yl]methoxy}pyridine-3- carbonyl chloride. To a solution of this crude acid chloride in dichloromethane (20 mL) and pyridine (20ml) was added 5-amino-2-chlorophenylboronic acid (0.66 g, 3.85 mmol). The solution was stirred at RT overnight and then concentrated in vacuo to dryness and then purified by ISCO MPLC (10-20% MeOH/DCM with 3% NH₄OH) to afford the title compound as a white solid (1.20 g, 80 %). MS (M+H⁺) 390.

58C. (S)-N-(4-chloro-S-(l -methyl-1 H-imidazol-4-yl)phenyl)-6-((l -methylpyrrolidin-2- yl)methoxy)nicotinamide

To a solution of 4-bromo-l -methyl- lH-imidazole (165 mg, 1.03 mmol), (S)-2-chloro-5- (6-((l-methylpyrrolidin-2-yl)methoxy)nicotinamido)phenylboronic acid (200 mg, 0.51 mmol), and KOAc (151 mg, 1.54 mmol) in dioxane (3 mL) and water (1 mL) was added solid Pd(PPlIs)₄ (59.3 mg, 0.05 mmol). Nitrogen gas was bubbled through the solution for 10 min and then placed in the microwave for 4h at 130 ⁰C. The water layer was removed followed by concentration of the dioxane. The crude residue was purified by Gilson HPLC (5-75% MeCN/0.1% TFA in water). The combined fractions containing product were concentrated and repurifϊed using Gilson (5-95% MeCN/lOmM NH₄OAc in water) to give the title compound (12.40 mg, 4.69 %). ¹H NMR (DMSO-d₆) δ 1.87 (m, 1 H), 2.02 (m, 2 H), 2.28 (m, 1 H), 2.92 (d, 3 H), 3.11 (m, 1 H), 3.62 (m, 1 H), 3.83 (m, 1 H), 3.94 (s, 3 H), 4.71 (m, 2 H), 7.08 (d, 1 H), 7.67 (d, 1 H), 7.92 (dd, 1 H), 8.10 (s, 1 H), 8.30 (d, 1 H), 8.40 (dd, 1 H), 8.91 (d, 1 H), 9.24 (s, 1 H), 10.92 (s, I H), 11.15 ( br s, I H). MS (M+H⁺) = 426. Examples 59-61 were prepared in a similar fashion to Example 58 utilizing commercially available starting materials:

Examples 62-63 were obtained by the purification of Example 51 using a chiral HPLC separation (Chiralpak AD/ 20 μ column, 50 x 500 mm; 100% ethanohmethanol (1:1), 0.1 % diethylamine, 120 mL/min):

Examples 64-65 were obtained by the purification of Example 54 using a chiral HPLC separation (Chiralpak AD/20 μ column, 50 x 500 mm; 100% ethanol:methanol (1:1), 0.1 % diethylamine, 120 mL/min):

Example 66 was prepared in a similar fashion to Example 1 utilizing commercially available starting materials:

Example 67

Hedgehog pathway cellular differentiation assay

[001] The ability of compounds of the invention to inhibit the Hedgehog pathway can be determined by the following cell differentiation assay.

[002] C3H10T1/2 cells were plated into 384 well plates at a concentration of 5000 cells/well in DMEM/10% FBS. The following day the media was changed to 20% conditioned media (low serum media DMEM/2%FBS + Shh ligand). Compounds were solubilized in 100% DMSO to a concentration of 1OmM and then serially diluted three fold in 100% DMSO. The highest concentration in the cell plate was 30μM and the lowest was 3nM. The compounds were then added to the cells. Cell plates were incubated with the compound for 72 hours and then assayed for alkaline phosphatase production using pNp as a substrate. Briefly, after 72 hours of incubation, the media was aspirated from the cells and washed with 30 μl of PBS. PBS was aspirated off the cells and 15 μl of Ix RIPA cell lysis buffer is added on to the cells. The cell plates are then incubated at -80 ⁰C for 30 minutes to insure proper cell lysis. The plates were then thawed back to room temperature. The substrate solution containing pNp at lmg/mL in diethanolamine buffer pH 9.8 was then added onto the lysed cells. The plates were incubated at 30 ⁰C for color development and read at an absorbance of 405 nm. The percent inhibition and IC50 value was then calculated from the absorbance data using standard procedures. When tested in the above assay, exemplary compounds showed an IC50 of less than about 30 μM. For example, the following results were obtained as shown in Table 2. TABLE 2

Percent inhibition at 3 μM for all examples disclosed herein according to the assay describe above are shown in Table 3.

TABLE 3

Incorporation By Reference

The entire contents of all patents, published patent applications and other references cited herein are hereby expressly incorporated herein in their entireties by reference.

Equivalents

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, numerous equivalents to the specific procedures described herein. Such equivalents were considered to be within the scope of this invention and are covered by the following claims. The contents of all references, issued patents, and published patent applications cited throughout this application are hereby incorporated by reference.

Claims

WHAT IS CLAIMED IS:

1. A compound of formula I

I wherein

Ri, R₂ and R3 are each independently selected from the group consisting of hydrogen, Ci-βalkyl, and halogen;

R₄ is selected from the group consisting of Ci-βalkyl, haloCi-βalkyl, and halogen; each W is independently selected from the group consisting of CR₅, NR₅, N, O, and S, where R₅ is selected from the group consisting of hydrogen, Ci_₆alkoxy, Ci-₆alkoxyCi_₆alkyl, Ci_₆alkoxycarbonyl, Ci_₆alkyl, amidino, amido, amino, Ci_₆alkylcarbonyl, aryl, carboxamido, C₃. scycloalkyl, cyano, haloCi_₆alkyl, halogen, heterocyclyl, heterocyclylCi-_όalkyl, hydroxy, hydroxyCi_₆alkyl, nitro, sulfide, sulfϊnyl, sulfonamido, and sulfonyl, or two adjacent W atoms can be taken together with their R₅ substituents to form a fused second ring, wherein the second ring is optionally substituted with one or more R₅ substituents and is selected from the group consisting of aryl, C₃_₈cycloalkyl, 5- or 6-membered heteroaryl, and 5- or 6-membered heterocyclyl; at least one W is N; q is 0 or 1, where if q is 0 and two adjacent W atoms are taken together with their R₅ substituents to form a fused second ring, then one of the adjacent W atoms is N and the second ring is a 6-membered heterocyclyl, and if q is 0, and the ring comprised of the W atoms is 2-imidazolyl, R5 is not an unsubstituted phenyl ring;

A is selected from the group consisting of CRβ, NRβ, N, O, and S;

Re is selected from the group consisting of hydrogen, Ci_₆alkoxy, Ci_₆alkoxyCi_₆alkyl, Ci_₆alkoxycarbonyl, Ci_₆alkyl, amidino, amido, amino, Ci_₆alkylcarbonyl, aryl, carboxamido, C₃. scycloalkyl, cyano, haloCi-βalkyl, halogen, heterocyclyl, heterocyclylCi-_δalkyl, heterocyclylCi. βalkoxy, hydroxy, hydroxyCi_6alkyl, nitro, sulfϊnyl, sulfide, sulfonamido, and sulfonyl, or two adjacent A atoms can be taken together with their Re substituents to form a fused second ring, wherein the second ring is a 5- or 6-membered heterocyclyl; at least one A is selected from the group consisting of NRβ, N, O, and S; p is 0 or 1, where if p is 0 and R₁, R2, and R₄ are each methyl, then A is not S; wherein the compound of formula I is not

, where L is selected from the group consisting of NH and CH, and if L is NH, then M is CH₂, and if L is CH then M is CH; and pharmaceutically acceptable salts thereof.

2. A compound of formula II:

II wherein,

A is selected from the group consisting of N and CRio;

X is selected from the group consisting of halogen and Ci_₆alkyl;

Y is selected from the group consisting OfNR₅, O and S, e.g., NR₅ and S; each R₅ is independently selected from the group consisting of hydrogen, Ci_₆alkyl and hydroxyCi-_δalkyl;

R₇ is selected from the group consisting of hydrogen, halogen, cyano, Ci_₆alkyl, Ci-όhaloalkyl, amino, e.g., Ci_6alkylamino, Ci_6alkoxy, aryloxy, hydroxy, sulfonyl, sulfonamide, and heterocyclyl, wherein R₇ may be optionally substituted with one or more Rn;

Rs, R₉, and Rio are each independently selected from the group consisting of hydrogen, Ci_6alkyl, halogen, Ci_6alkoxy, amino, hydroxy, haloalkyl, cyano, sulfonyl, and sulfonamide; Rn may be selected from the group consisting of halogen, hydroxy, amino, Ci_₆alkyl, Ci_6alkoxy, aryl, and heterocyclyl, wherein Rn may be optionally substituted with one or more Ri 2; and

3. The compound of claim 2, wherein the compound has the formula:

4. The compound of claim 2, wherein R₇ is selected from the group consisting of the group consisting of 2-pyridylmethoxy, (l-methyl-4-piperidyl)methoxy, (3-cyanophenyl)methoxy, [(2S)- 1 -methylpyrrolidin-2-yl]methoxy, [(2R)- 1 -methylpyrrolidin-2-yl]methoxy, 2- dimethylaminoethoxy, 2-thienyl, 3-diethylaminopropoxy, 4-(2-dimethylaminoethyl)piperazin-l- yl, 4-(2-hydroxyethyl)piperazin-l-yl, 4-(2-pyridylmethyl)piperazin-l-yl, 4- (cyclopropylmethyl)piperazin-l-yl, chloro, cyano, fluoro, hydrogen, isobutoxy, morpholino, phenoxy, trifluoromethyl, 4-methylpiperazin-l-yl, [2-(dimethylamino)ethyl]methylamino, (2- morpholin-4-ylethyl)amino, 2-hydroxyethylamino, piperazin-lyl, 2-(dimethylamino)ethylamino, [(2S)-l-ethylpyrrolidin-2-yl]methylamino, (l-methylpyrrolidin-3-yl)methoxy, (1- methylpiperidin-2-yl)methoxy), 2-morpholin-4-ylethoxy, 2-pyrrolidin-l-ylethoxy, (1- methylpiperidin-3-yl)methoxy), (2S)-l-methylpiperidin-2-yl]methoxy, (2R)-l-methylpiperidin- 2-yl]methoxy, (3 S)- 1 -methylpiperidin-3 -yljmethoxy, (3R)-I -methylpiperidin-3-yl]methoxy, methyl, and any combination thereof.

5. A compound of formula III

III wherein n is 0, 1, 2, or 3;

R₃ is selected from the group consisting of the group consisting of hydrogen, halogen, and alkyl; each Ri₄ is selected from the group consisting of the group consisting of hydrogen, halogen, hydroxyl, sulfide, carboxamide, Ci_6alkylcarbonyl, amino, alkyl, alkoxyl, alkoxycarbonyl, sulfinyl, sulfonyl, cyano, cycloalkyl, aryl or a heterocyclyl wherein each R_ϊ4 is optionally substituted with Ci_₆alkylcarbonyl, hydroxyl, hydroxy Ci_₆alkyl, halogen, amino, nitro, Ci-₆alkyl, sulfonyl, cyano, alkoxyl or heterocyclyl, such that R₁₄ is not unsubstituted phenyl when the imidazolyl ring to which the Ri₄ is attached is 2-imidazolyl;

Ri₅ is selected from the group consisting of the group consisting of -(CH)₀_₅-heterocycle, - (CH)₀-5-NRbRb, -(CH)o-5-hydroxy, -(CH)₀-5-Ci_6alkoxy, aryl and heterocyclyl, e.g., piperazine, wherein R15 is optionally substituted with Ri6, and each Rb is selected from the group consisting of the group consisting of H, alkyl, and cycloalkyl; and

Ri6 is selected from the group consisting of the group consisting of halo, alkyl, alkoxy, alkylthio, wherein Ri6 is optionally substituted with aryl or heteroaryl, or a pharmaceutically acceptable salt thereof.

6. The compound of claim 5, wherein Ri₄ is H, hydroxyCi_₆alkyl, or Ci_₆alkyl.

7. A pharmaceutical composition comprising one or more of the compounds according to claims 1, 2, or 5, formulated together with one or more pharmaceutically acceptable carriers.

8. A method for inhibiting the Hedgehog pathway comprising administering to a subject a therapeutically effective amount of one or more of the compounds according to claims 1, 2, or 5, or a pharmaceutical composition according to claim 7, such that the Hedgehog pathway is inhibited.

9. A method of reducing cell proliferation, differentiation and/or affecting stromal microenvironment modulation comprising administering to a subject a therapeutically effective amount of one or more of the compounds according to claims 1, 2, or 5, or a pharmaceutical composition according to claim 7, thereby reducing cell proliferation, differentiation and/or affecting stromal microenvironment modulation in the subject.

10. The method of claim 9, wherein the cell is a stromal cell.

11. The method of claim 9, wherein the cell is a cancer cell.

12. The method of claim 9, wherein the cell is a stem cell.

13. The method of claim 12, where the stem cell is a cancer stem cell.