US20080261961A1 - Kinase inhibitors useful for the treatment of myleoprolific diseases and other proliferative diseases - Google Patents

Kinase inhibitors useful for the treatment of myleoprolific diseases and other proliferative diseases Download PDF

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US20080261961A1
US20080261961A1 US12/105,376 US10537608A US2008261961A1 US 20080261961 A1 US20080261961 A1 US 20080261961A1 US 10537608 A US10537608 A US 10537608A US 2008261961 A1 US2008261961 A1 US 2008261961A1
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c6alkyl
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Daniel L. Flynn
Peter A. Petillo
Michael D. Kaufman
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Deciphera Pharmaceuticals LLC
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Definitions

  • the present invention relates to novel kinase inhibitors and modulator compounds useful for the treatment of various diseases. More particularly, the invention is concerned with such compounds, kinase/compound adducts, methods of treating diseases, and methods of synthesis of the compounds. Preferably, the compounds are useful for the modulation of kinase activity of C-Abl, c-Kit, VEGFR, PDGFR kinases, Flt-3, c-Met, FGFR, the HER family and disease polymorphs thereof.
  • proliferative diseases relevant to this invention include cancer, rheumatoid arthritis, atherosclerosis, and retinopathies.
  • Important examples of kinases which have been shown to cause or contribute to the pathogensis of these diseases include C-Abl kinase and the oncogenic fusion protein bcr-Abl kinase; c-Kit kinase, PDGF receptor kinase; VEGF receptor kinases; and Flt-3 kinase.
  • C-Abl kinase is an important non-receptor tyrosine kinase involved in cell signal transduction. This ubiquitously expressed kinase—upon activation by upstream signaling factors including growth factors, oxidative stress, integrin stimulation, and ionizing radiation—localizes to the cell plasma membrane, the cell nucleus, and other cellular compartments including the actin cytoskeleton (Van Etten, Trends Cell Biol. (1999) 9: 179). There are two normal isoforms of Abl kinase: Abl-1A and Abl-1B.
  • the N-terminal half of c-Abl kinase is important for autoinhibition of the kinase domain catalytic activity (Pluk et al, Cell (2002) 108: 247). Details of the mechanistic aspects of this autoinhibition have recently been disclosed (Nagar et al, Cell (2003) 112: 859).
  • the N-terminal myristolyl amino acid residue of Abl-1B has been shown to intramolecularly occupy a hydrophobic pocket formed from alpha-helices in the C-lobe of the kinase domain.
  • Such intramolecular binding induces a novel binding area for intramolecular docking of the SH2 domain and the SH3 domain onto the kinase domain, thereby distorting and inhibiting the catalytic activity of the kinase.
  • an intricate intramolecular negative regulation of the kinase activity is brought about by these N-terminal regions of c-Abl kinase.
  • An aberrant dysregulated form of c-Abl is formed from a chromosomal translocation event, referred to as the Philadelphia chromosome (P. C. Nowell et al, Science (1960) 132: 1497; J. D. Rowley, Nature (1973) 243: 290).
  • This abnormal chromosomal translocation leads aberrant gene fusion between the Abl kinase gene and the breakpoint cluster region (BCR) gene, thus encoding an aberrant protein called bcr-Abl (G. Q. Daley et al, Science (1990) 247: 824; M. L. Gishizky et al, Proc. Natl. Acad. Sci. USA (1993) 90: 3755; S. Li et al, J. Exp. Med. (1999) 189: 1399).
  • the bcr-Abl fusion protein does not include the regulatory myristolylation site (B.
  • CML chronic myeloid leukemia
  • CML is a malignancy of pluripotent hematopoietic stem cells.
  • the p210 form of bcr-Abl is seen in 95% of patients with CML, and in 20% of patients with acute lymphocytic leukemia and is exemplified by sequences such as e14a2 and e13a2.
  • the corresponding p190 form, exemplified by the sequence e1a2 has also been identified.
  • a p185 form has also been disclosed and has been linked to being causative of up to 10% of patients with acute lymphocytic leukemia.
  • C-KIT (Kit, CD117, stem cell factor receptor) is a 145 kDa transmembrane tyrosine kinase protein that acts as a type-III receptor (Pereira et al. J Carcin. (2005), 4: 19).
  • the c-KIT proto-oncocgene located on chromosome 4q11-21, encodes the c-KIT receptor, whose ligand is the stem cell factor (SCF, steel factor, kit ligand, mast cell growth factor, Morstyn G, et al. Oncology (1994) 51(2):205. Yarden Y, et al. Embo J (1987) 6(11):3341).
  • the receptor has tyrosine-protein kinase activity and binding of the ligands leads to the autophosphorylation of KIT and its association with substrates such as phosphatidylinositol 3-kinase (Pi3K).
  • Tyrosine phosphorylation by protein tyrosine kinases is of particular importance in cellular signalling and can mediate signals for major cellular processes, such as proliferation, differentiation, apoptosis, attachment, and migration.
  • Defects in KIT are a cause of piebaldism, an autosomal dominant genetic developmental abnormality of pigmentation characterized by congenital patches of white skin and hair that lack melanocytes.
  • Gain-of-function mutations of the c-KIT gene and the expression of phosphorylated KIT are found in most gastrointestinal stromal tumors and mastocytosis. Further, almost all gonadal seminomas/dysgerminomas exhibit KIT membranous staining, and several reports have clarified that some (10-25%) have a c-KIT gene mutation (Sakuma, Y. et al. Cancer Sci (2004) 95:9, 716). KIT defects have also been associated with testicular tumors including germ cell tumors (GCT) and testicular germ cell tumors (TGCT).
  • GCT germ cell tumors
  • TGCT testicular germ cell tumors
  • c-kit expression has been studied in hematologic and solid tumours, such as acute leukemias (Cortes J. et al. Cancer (2003) 97(11):2760) and gastrointestinal stromal tumors (GIST, Fletcher C. D. et al. Hum Pathol (2002) 33(5):459).
  • the clinical importance of c-kit expression in malignant tumors relies on studies with Gleevec® (imatinib mesylate, STI571, Novartis Pharma AG Basel, Switzerland) that specifically inhibits tyrosine kinase receptors (Lefevre G. et al. J Biol Chem (2004) 279(30):31769).
  • c-MET is a unique receptor tyrosine kinase (RTK) located on chromosome 7p and activated via its natural ligand hepatocyte growth factor.
  • RTK receptor tyrosine kinase
  • c-MET is found mutated in a variety of solid tumors (Ma P. C. et al. Cancer Metastasis (2003) 22:309). Mutations in the tyrosine kinase domain are associated with hereditary papillary renal cell carcinomas (Schmidt L et al. Nat. Genet. (1997)16:68; Schmidt L, et al.
  • the TPR-MET oncogene is a transforming variant of the c-MET RTK and was initially identified after treatment of a human osteogenic sarcoma cell line transformed by the chemical carcinogen N-methyl-N′-nitro-N-nitrosoguanidine (Park M. et al. Cell (1986) 45:895).
  • the TPR-MET fusion oncoprotein is the result of a chromosomal translocation, placing the TPR3 locus on chromosome 1 upstream of a portion of the c-MET gene on chromosome 7 encoding only for the cytoplasmic region.
  • Studies suggest that TPR-MET is detectable in experimental cancers (e.g. Yu J. et al. Cancer (2000) 88:1801).
  • TPR-MET acts to activated wild-type c-MET RTK and can activate crucial cellular growth pathways, including the Ras pathway (Aklilu F. et al. Am J Physiol (1996) 271:E277) and the phosphatidylinositol 3-kinase (PI3K)/AKT pathway (Ponzetto C. et al. Mol Cell Biol (1993) 13:4600).
  • TPR-MET is ligand independent, lacks the CBL binding site in the juxtamembrane region in c-MET, and is mainly cytoplasmic.
  • c-Met immunohistochemical expression seems to be associated with abnormal ⁇ -catenin expression, and provides good prognostic and predictive factors in breast cancer patients.
  • kinases are regulated by a common activation/deactivation mechanism wherein a specific activation loop sequence of the kinase protein binds into a specific pocket on the same protein which is referred to as the switch control pocket.
  • a specific activation loop sequence of the kinase protein binds into a specific pocket on the same protein which is referred to as the switch control pocket.
  • Such binding occurs when specific amino acid residues of the activation loop are modified for example by phosphorylation, oxidation, or nitrosylation.
  • the binding of the activation loop into the switch pocket results in a conformational chance of the protein into its active form (Huse, M. and Kuriyan, J. Cell (109) 275)
  • Compounds of the present invention find utility in the treatment of mammalian cancers and especially human cancers including but not limited to malignant, melanomas, glioblastomas, ovarian cancer, pancreatic cancer, prostate cancer, lung cancers, breast cancers, kidney cancers, cervical carcinomas, metastasis of primary tumor sites, myeloproliferative diseases, leukemias, papillary thyroid carcinoma, non small cell lung cancer, mesothelioma, hypereosinophilic syndrome, gastrointestinal stromal tumors, colonic cancers, ocular diseases characterized by hyperproliferation leading to blindness including various retinopathies, rheumatoid arthritis, asthma, chronic obstructive pulmonary disorder, a disease caused by c-Abl kinase, oncogenic forms thereof, aberrant fusion proteins thereof and polymorphs thereof, or a disease caused by c-Kit, oncogenic forms thereof, aberrant fusion proteins thereof and polymorphs thereof.
  • Cycloalkyl refers to monocyclic saturated carbon rings taken from cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptanyl and cyclooctanyl;
  • Aryl refers to monocyclic or fused bicyclic ring systems characterized by delocalized ⁇ electrons (aromaticity) shared among the ring carbon atoms of at least one carbocyclic ring; preferred aryl rings are taken from phenyl, naphlthyl, tetrahydronaphthyl, indenyl, and indanyl;
  • Heteroaryl refers to monocyclic or fused bicyclic ring systems characterized by delocalized ⁇ electrons (aromaticity) shared among the ring carbon or heteroatoms including nitrogen, oxygen, or sulfur of at least one carbocyclic or heterocyclic ring; heteroaryl rings are taken from, but not limited to, pyrrolyl, furyl, thienyl, oxazolyl, thiazolyl, isoxazolyl, isothiazolyl, imidazolyl, pyrazolyl, oxadiazolyl, thiadiazolyl, triazolyl, tetrazolyl, pyridinyl, pyrimidinyl, pyrazinyl, pyridazinyl, triazinyl, indolyl, indolinyl, isoindolyl, isoindolinyl, indazolyl, benzofuranyl, benzothienyl, benzothiazolyl, be
  • Heterocyclyl refers to monocyclic rings containing carbon and heteroatoms taken from oxygen, nitrogen, or sulfur and wherein there is not delocalized ⁇ electrons (aromaticity) shared among the ring carbon or heteroatoms; heterocyclyl rings include, but are not limited to, oxetanyl, azetadinyl, tetrahydrofuranyl, pyrrolidinyl, oxazolinyl, oxazolidinyl, thiazolinyl, thiazolidinyl, pyranyl, thiopyranyl, tetrahydropyranyl, dioxalinyl, piperidinyl, morpholinyl, thiomorpholinyl, thiomorpholinyl S-oxide, thiomorpholinyl S-dioxide, piperazinyl, azepinyl, oxepinyl, diazepinyl, tropanyl, and homotropanyl;
  • Poly-aryl refers to two or more monocyclic or fused aryl bicyclic ring systems characterized by delocalized ⁇ electrons (aromaticity) shared among the ring carbon atoms of at least one carbocyclic ring wherein the rings contained therein are optionally linked together;
  • Poly-heteroaryl refers to two or more monocyclic or fused bicyclic systems characterized by delocalized ⁇ electrons (aromaticity) shared among the ring carbon or heteroatoms including nitrogen, oxygen, or sulfur of at least one carbocyclic or heterocyclic ring wherein the rings contained therein are optionally linked together, wherein at least one of the monocyclic or fused bicyclic rings of the poly-heteroaryl system is taken from heteroaryl as defined broadly above and the other rings are taken from either aryl, heteroaryl, or heterocyclyl as defined broadly above;
  • Poly-heterocyclyl refers to two or more monocyclic or fused bicyclic ring systems containing carbon and heteroatoms taken from oxygen, nitrogen, or sulfur and wherein there is not delocalized ⁇ electrons (aromaticity) shared among the ring carbon or heteroatoms wherein the rings contained therein are optionally linked, wherein at least one of the monocyclic or fused bicyclic rings of the poly-heteroaryl system is taken from heterocyclyl as defined broadly above and the other rings are taken from either aryl, heteroaryl, or heterocyclyl as defined broadly above;
  • Alkyl refers to straight or branched chain C1-C6alkyls
  • Halogen refers to fluorine, chlorine, bromine, and iodine
  • Alkoxy refers to —O-(alkyl) wherein alkyl is defined as above;
  • Alkoxylalkyl refers to -(alkyl)-O-(alkyl) wherein alkyl is defined as above;
  • Alkoxylcarbonyl refers to —C(O)O-(alkyl) wherein alkyl is defined as above;
  • CarboxylC1-C6alkyl refers to —C(O)-alkyl wherein alkyl is defined as above;
  • Substituted in connection with a moiety refers to the fact that a further substituent may be attached to the moiety to any acceptable location on the moiety.
  • salts embraces pharmaceutically acceptable salts commonly used to form alkali metal salts of free acids and to form addition salts of free bases.
  • the nature of the salt is not critical, provided that it is pharmaceutically-acceptable.
  • Suitable pharmaceutically-acceptable acid addition salts may be prepared from an inorganic acid or from an organic acid. Examples of such inorganic acids are hydrochloric, hydrobromic, hydroiodic, nitric, carbonic, sulfuric and phosphoric acid.
  • Appropriate organic acids may be selected from aliphatic, cycloaliphatic, aromatic, arylaliphatic, and heterocyclyl containing carboxylic acids and sulfonic acids, examples of which are formic, acetic, propionic, succinic, glycolic, gluconic, lactic, malic, tartaric, citric, ascorbic, glucuronic, maleic, fumaric, pyruvic, aspartic, glutamic, benzoic, anthranilic, mesylic, stearic, salicylic, p-hydroxybenzoic, phenylacetic, mandelic, embonic (pamoic), methanesulfonic, ethanesulfonic, benzenesulfonic, pantothenic, toluenesulfonic, 2-hydroxyethanesulfonic, sulfanilic, cyclohexylaminosulfonic, algenic, 3-hydroxybutyric, galactaric and
  • Suitable pharmaceutically-acceptable salts of free acid-containing compounds of Formula I include metallic salts and organic salts. More preferred metallic salts include, but are not limited to appropriate alkali metal (group Ia) salts, alkaline earth metal (group IIa) salts and other physiological acceptable metals. Such salts can be made from aluminum, calcium, lithium, magnesium, potassium, sodium and zinc.
  • Preferred organic salts can be made from primary amines, secondary amines, tertiary amines and quaternary ammonium salts, including in part, tromethamine, diethylamine, tetra-N-methylammonium, N,N′-dibenzylethylenediamine, chloroprocaine, choline, diethanolamine, ethylenediamine, meglumine(N-methylglucamine) and procaine.
  • prodrug refers to derivatives of active compounds which revert in vivo into the active form.
  • a carboxylic acid form of an active drug may be esterified to create a prodrug, and the ester is subsequently converted in vivo to revert to the carboxylic acid form. See Ettmayer et. al, J. Med. Chem (2004) 47: 2393 and Lorenzi et. al, J. Pharm. Exp. Therapeutic (2005) 883 for reviews.
  • Structural, chemical and stereochemical definitions are broadly taken from IUPAC recommendations, and more specifically from Glossary of Terms used in Physical Organic Chemistry (IUPAC Recommendations 1994) as summarized by P. Müller, Pure Appl. Chem., 66, 1077-1184 (1994) and Basic Terminology of Stereochemistry (IUPAC Recommendations 1996) as summarized by G. P. Moss Pure and Applied Chemistry, 68, 2193-2222 (1996). Specific definitions are as follows:
  • Atropisomers are defined as a subclass of conformers which can be isolated as separate chemical species and which arise from restricted rotation about a single bond.
  • Enatiomers are defined as one of a pair of molecular entities which are mirror images of each other and non-superimposable.
  • Diastereomers or diastereoisomers are defined as stereoisomers other than enantiomers. Diastereomers or diastereoisomers are stereoisomers not related as mirror images.
  • Diastereoisomers are characterized by differences in physical properties, and by some differences in chemical behavior towards achiral as well as chiral reagents.
  • Tautomerism is defined as isomerism of the general form
  • Tautomers are defined as isomers that arise from tautomerism, independent of whether the isomers are isolable.
  • pyridine ring may be optionally substituted with one or more R20 moieties;
  • each D is individually taken from the group consisting of C, CH, C—R20, N-Z3, N, O and S, such that the resultant ring is taken from the group consisting of triazolyl, isoxazolyl, isothiazolyl, oxazolyl, and thiadiazolyl;
  • E is selected from the group consisting of phenyl, pyridyl, and pyrimidinyl;
  • E may be optionally substituted with one or two R16 moieties
  • A is a ring system selected from the group consisting of phenyl, naphthyl, cyclopentyl, cyclohexyl, G1, G2, and G3;
  • G1 is a heteroaryl taken from the group consisting of pyrrolyl, furyl, thienyl, oxazolyl, thiazolyl, isoxazol-4-yl, isoxazol-5-yl, isothiazolyl, imidazolyl, pyrazolyl, oxadiazolyl, thiadiazolyl, triazolyl, tetrazolyl, pyrazinyl, pyridazinyl, triazinyl, pyridinyl, and pyrimidinyl;
  • G2 is a fused bicyclic heteroaryl taken from the group consisting of indolyl, indolinyl, isoindolyl, isoindolinyl, indazolyl, benzofuranyl, benzothienyl, benzothiazolyl, benzothiazolonyl, benzoxazolyl, benzoxazolonyl, benzisoxazolyl, benzisothiazolyl, benzimidazolyl, benzimidazolonyl, benztriazolyl, imidazopyridinyl, pyrazolopyridinyl, imidazolonopyridinyl, thiazolopyridinyl, thiazolonopyridinyl, oxazolopyridinyl, oxazolonopyridinyl, isoxazolopyridinyl, isothiazolopyridinyl, triazolopyridinyl, imidazopyr
  • G3 is a heterocyclyl taken from the group consisting of oxetanyl, azetadinyl, tetrahydrofuranyl, pyrrolidinyl, oxazolinyl, oxazolidinyl, imidazolonyl, pyranyl, thiopyranyl, tetrahydropyranyl, dioxalinyl, piperidinyl, morpholinyl, thiomorpholinyl, thiomorpholinyl S-oxide, thiomorpholinyl S-dioxide, piperazinyl, azepinyl, oxepinyl, diazepinyl, tropanyl, and homotropanyl;
  • the A ring may be optionally substituted with one or two R2 moieties;
  • X is selected from the group consisting of —O—, —S(CH 2 ) n —, —N(R3)(CH 2 ) n —, —(CH 2 ) p —, and wherein the carbon atoms of —(CH 2 ) n —, —(CH 2 ) p —, of X may be further substituted by oxo or one or more C1-C6alkyl moieties;
  • each respective sp2 hybridized carbon atom may be optionally substituted with a Z1 substituent;
  • each respective sp3 hybridized carbon atom may be optionally substituted with a Z2 substituent;
  • each respective nitrogen atom may be optionally substituted with a Z4 substituent;
  • each Z1 is independently and individually selected from the group consisting of C1-6alkyl, branched C3-C7alkyl, C3-C8cycloalkyl, halogen, fluoroC1-C6alkyl wherein the alkyl moiety can be partially or fully fluorinated, cyano, C1-C6alkoxy, fluoroC1-C6alkoxy wherein the alkyl moiety can be partially or fully fluorinated, —(CH 2 ) n OH, oxo, C1-C6alkoxyC1-C6alkyl, (R4) 2 N(CH 2 ) n —, (R3) 2 N(CH 2 ) n —, (R4) 2 N(CH 2 ) q N(R4)(CH 2 ) n —, (R4) 2 N(CH 2 ) q O(CH 2 ) n —, (R3) 2 NC(O)—, (R4) 2 NC(O)—, (R4)
  • each Z2 is independently and individually selected from the group consisting of aryl, C1-C6alkyl, C3-C8cycloalkyl, branched C3-C7alkyl, hydroxyl, hydroxyC1-C6alkyl-, cyano, (R3) 2 N—, (R4) 2 N—, (R4) 2 NC1-C6alkyl-, (R4) 2 NC2-C6alkylN(R4)(CH 2 ) n —, (R4) 2 NC2-C6alkylO(CH 2 ) n —, (R3) 2 NC(O)—, (R4) 2 NC(O)—, (R4) 2 NC(O)—C1-C6alkyl-, carboxyl, -carboxyC1-C6alkyl, C1-C6alkoxycarbonyl-, C1-C6alkoxycarbonylC1-C6alkyl-, (R3) 2 NSO 2 —, (R4) 2 NSO 2
  • each Z3 is independently and individually selected from the group consisting of H, C1-C6alkyl, branched C3-C7alkyl, C3-C8cycloalkyl, fluoroC1-C6alkyl wherein the alkyl moiety can be partially or fully fluorinated, hydroxyC2-C6alkyl-, C1-C6alkoxycarbonyl-, —C(O)R8, R5C(O)(CH 2 ) n —, (R4) 2 NC(O)—, (R4) 2 NC(O)C1-C6alkyl-, R8C(O)N(R4)(CH 2 ) q —, (R3) 2 NSO 2 —, (R4) 2 NSO 2 —, —(CH 2 ) q N(R3) 2 , and —(CH 2 ) q N(R4) 2 ;
  • each Z4 is independently and individually selected from the group consisting of C1-C6alkyl, branched C3-7alkyl, hydroxyC2-C6alkyl-, C1-C6alkoxyC2-C6alkyl-, (R4) 2 N—C2-C6alkyl-, (R4) 2 N—C2-C6alkylN(R4)—C2-C6alkyl-, (R4) 2 N—C2-C6alkyl-O—C2-C6alkyl-(R4) 2 NC(O)C1-C6alkyl-, carboxyC1-C6alkyl, C1-C6alkoxycarbonylC1-C6alkyl-, —C2-C6alkylN(R4)C(O)R8, R8-C( ⁇ NR3)—, —SO 2 R8, and —COR8;
  • each R2 is selected from the group consisting of H, C1-C6alkyl, branched C3-C8alkyl, R19 substituted C3-C8cycloalkyl-, fluoroC1-C6alkyl- wherein the alkyl is fully or partially fluorinated, halogen, cyano, C1-C6alkoxy-, and fluoroC1-C6alkoxy- wherein the alkyl group is fully or partially fluorinated, hydroxyl substituted C1-C6alkyl-, hydroxyl substituted branched C3-C8alkyl-, cyano substituted C1-C6alkyl-, cyano substituted branched C3-C8alkyl-, (R3) 2 NC(O)C1-C6alkyl-, and (R3) 2 NC(O)C3-C8 branched alkyl-;
  • each R3 is independently and individually selected from the group consisting of H, C1-C6alkyl, branched C3-C7alkyl, and C3-C8cycloalkyl;
  • each R4 is independently and individually selected from the group consisting of H, C1-C6alkyl, hydroxyC1-C6alkyl-, dihydroxyC1-C6alkyl-, C1-C6alkoxyC1-C6alkyl-, branched C3-C7alkyl, branched hydroxyC1-C6alkyl-, branched C1-C6alkoxyC1-C6alkyl-, branched dihydroxyC1-C6alkyl-, —(CH 2 ) p N(R7) 2 , —(CH 2 ) p C(O)N(R7) 2 , —(CH 2 ) n C(O)OR3, and R19 substituted C3-C8cycloalkyl-;
  • each R5 is independently and individually selected from the group consisting of
  • each R6 is independently and individually selected from the group consisting of C1-C6alkyl, branched C3-C7alkyl, and R19 substituted C3-C8cycloalkyl-;
  • each R7 is independently and individually selected from the group consisting of H, C1-C6alkyl, hydroxyC2-C6alkyl-, dihydroxyC2-C6alkyl-, C1-C6alkoxyC2-C6alkyl-, branched C3-C7alkyl, branched hydroxyC2-C6alkyl-, branched C1-C6alkoxyC2-C6alkyl-, branched dihydroxyC2-C6alkyl-, —(CH 2 ) n C(O)OR3, R19 substituted C3-C8cycloalkyl- and —(CH 2 ) n R17;
  • each R8 is independently and individually selected from the group consisting of C1-C6alkyl, branched C3-C7alkyl, fluoroC1-C6alkyl- wherein the alkyl moiety is partially or fully fluorinated, R19 substituted C3-C8cycloalkyl-, —OH, C1-C6alkoxy, —N(R3) 2 , and —N(R4) 2 ;
  • each R10 is independently and individually selected from the croup consisting of —CO 2 H, —CO 2 C1-C6alkyl, —C(O)N(R4) 2 , OH, C1-C6alkoxy, and —N(R4) 2 ;
  • each R16 is independently and individually selected from the group consisting of H, C1-C6alkyl, branched C3-C7alkyl, R19 substituted C3-C8cycloalkyl-, halogen, fluoroC1-C6alkyl- wherein the alkyl moiety can be partially or fully fluorinated, cyano, hydroxyl, C1-C6alkoxy, fluoroC1-C6alkoxy- wherein the alkyl moiety can be partially or fully fluorinated, —N(R3) 2 , —N(R4) 2 , R3 substituted C2-C3alkynyl- and nitro;
  • each R17 is independently and individually selected from the group consisting of H, C1-C6alkyl, branched C3-C7alkyl, R19 substituted C3-C8cycloalkyl-, halogen, fluoroC1-C6alkyl- wherein the alkyl moiety can be partially or Filly fluorinated, cyano, hydroxyl, C1-C6alkoxy, fluoroC1-C6alkoxy- wherein the alkyl moiety can be partially or fully fluorinated, —N(R3) 2 , —N(R4) 2 , and nitro;
  • each R19 is independently and individually selected from the group consisting of H, OH and C1-C6alkyl;
  • each R20 is independently and individually selected from the group consisting of C1-C6alkyl, branched C3-C7alkyl, R19 substituted C3-C8cycloalkyl-, halogen, fluoroC1-C6alkyl- wherein the alkyl moiety can be partially or fully fluorinated, cyano, hydroxyl, C1-C6alkoxy, fluoroC1-C6alkoxy- wherein the alkyl moiety can be partially or fully fluorinated, —N(R3) 2 , —N(R4) 2 , —N(R3)C(O)R3, —C(O)N(R3) 2 and nitro and wherein two R4 moieties independently and individually taken from the group consisting of C1-C6alkyl, branched C3-C6alkyl, hydroxyalkyl-, and alkoxyalkyl and attached to the same nitrogen heteroatom may cyclize to form a C3-C7 heterocycly
  • A is any possible isomer of pyrazole.
  • A is selected from the group consisting of any possible isomer of phenyl and pyridine.
  • the invention includes methods of modulating kinase activity of a variety of kinases, e.g. C-Abl kinase, bcr-Abl Kinase, Flt-3, VEGFR-2 kinase mutants, c-Met, c-Kit, PDGFR and the HER family of kinases.
  • the kinases may be wildtype kinases, oncogenic forms thereof, aberrant fusion proteins thereof or polymorphs of any of the foregoing.
  • the method comprises the step of contacting the kinase species with compounds of the invention and especially those set forth in sections section 1.
  • the kinase species may be activated or unactivated, and the species may be modulated by phosphorylations, sulfation, fatty acid acylations glycosylations, nitrosylation, cystinylation (i.e. proximal cysteine residues in the kinase react with each other to form a disulfide bond) or oxidation.
  • the kinase activity may be selected from the group consisting of catalysis of phospho transfer reactions, inhibition of phosphorylation, oxidation or nitrosylation of said kinase by another enzyme, enhancement of dephosphorylation, reduction or denitrosylation of said kinase by another enzyme, kinase cellular localization, and recruitment of other proteins into signaling complexes through modulation of kinase conformation.
  • the methods of the invention also include treating individuals suffering from a condition selected from the group consisting of cancer and hyperproliferative diseases.
  • These methods comprise administering to such individuals compounds of the invention, and especially those of section 1, said diseases including, but not limited to, malignant melanomas, glioblastomas, ovarian cancer, pancreatic cancer, prostate cancer, lung cancers, breast cancers, kidney cancers, cervical carcinomas, metastasis of primary tumor secondary sites, myeloproliferative diseases, leukemias, papillary thyroid carcinoma, non small cell lung cancer, mesothelioma, hypereosinophilic syndrome, gastrointestinal stromal tumors, colonic cancers, ocular diseases characterized by hyperproliferation leading to blindness including various retinopathies including diabetic retinopathy and age-related macular degeneration, rheumatoid arthritis, asthma, chronic obstructive pulmonary disorder, mastocytosis, mast cell leukemia, a disease caused by c-Abl kin
  • compositions may include an additive selected from the group consisting of adjuvants, excipients, diluents, and stabilizers.
  • ureas of general formula 1 can be readily prepared by the union of amines of general formula 2 with isocyanates 3 or isocyanate surrogates, for example trichloroethyl carbamates (4) or isopropenyl carbamates (5).
  • Preferred conditions for the preparation of compounds of general formula 1 involve heating a solution of 4 or 5 with 2 in the presence of a tertiary base such as diisopropylethylamine, triethylamine or N-methylpyrrolidine in a solvent such as dimethylformamide, dimethylsulfoxide, tetrahydrofuran or 1,4-dioxane at a temperature between 50 and 100° C. for a period of time ranging from 1 hour to 2 days.
  • a tertiary base such as diisopropylethylamine, triethylamine or N-methylpyrrolidine
  • a solvent such as dimethylformamide, dimethylsulfoxide, tetrahydrofur
  • isocyanates 3 can be prepared from amines A-NH 2 6 with phosgene, or a phosgene equivalent such as diphosgene, triphosgene, or N,N-dicarbonylimidazole.
  • Trichloroethyl carbamates 4 and isopropenyl carbamates 5 are readily prepared from amines A-NH 2 , (6) by acylation with trichloroethyl chloroformate or isopropenyl chloroformate by standard conditions familiar to those skilled in the art.
  • Preferred conditions for the preparation of 4 and 5 include include treatment of compound 6 with the appropriate chloroformate in the presence of pyridine in an aprotic solvent such as dichloromethane or in the presence of aqueous hydroxide or carbonate in a biphasic aqueous/ethyl acetate solvent system.
  • compounds of formula 1 can also be prepared from carboxylic acids 7 by the intermediacy of in-situ generated acyl azides (Curtius rearrangement) as indicated in Scheme 3.
  • Preferred conditions for Scheme 3 include the mixing of acid 7 with amine 2 and diphenylphosphoryl azide in a solvent such as 1,4-dioxane or dimethylformamide in the presence of base, such as triethylamine and raising the temperature of the reaction to about 80-120° C. to affect the Curtius rearrangement.
  • Isocyanates 8 can be prepared from general amines 2 by standard synthetic methods. Suitable methods for example, include reaction of 2 with phosgene, or a phosgene equivalent such as diphosgene, triphosgene, or N,N-dicarbonylimidazole. In addition to the methods above for converting amines 2 into isocynates 8, the isocyanates 8 can also be prepared in situ by the Curtius rearrangement and variants thereof.
  • isocycanates 8 need not be isolated, but may be simply generated in situ. Accordingly, acid 9 can be converted to compounds of formula 1 either with or without isolation of 8. Preferred conditions for the direct conversion of acid 9 to compounds of formula 1 involve the mixing of acid 9, amine A-NH 2 6, diphenylphosphoryl azide and a suitable base, for example triethylamine, in an aprotic solvent, for example dioxane. Heating said mixture to a temperature of between 80 and 120° C. provides the compounds of formula 1.
  • compounds of formula 1 can also be prepared from amines 2 by first preparing stable isocyanate equivalents, such as carbamates (Scheme 5).
  • carbamates include trichloroethyl carbamates (10) and isopropenyl carbamates (11) which are readily prepared from amine 2 by reaction with trichloroethyl chloroformate or isopropenyl chloroformate respectively using standard conditions familiar to those skilled in the art. Further reaction of carbamates 10 or 11 with amine A-NH 2 6 provides compounds of formula 1.
  • certain carbamates can also be prepared from acid 9 by Curtius rearrangement and trapping with an alcoholic co-solvent. For example, treatment of acid 9 (Scheme 5) with diphenylphosphoryl azide and trichloroethanol at elevated temperature provides trichloroethyl carbamate 10.
  • Z4-substituted pyrazol-5-yl amines 14 are available by the condensation of hydrazines 12 and beta-keto nitrites 13 in the presence of a strong acid. Preferred conditions for this transformation are by heating in ethanolic HCl. Many such hydrazines 12 are commercially available. Others can be prepared by conditions familiar to those skilled in the art, for example by the diazotization of amines followed by reduction or, alternately from the reduction of hydrazones prepared from carbonyl precursors.
  • pyrazole acids 19 and 20 Another preferred method for constructing Z4-substituted pyrazoles is illustrated by the general preparation of pyrazole acids 19 and 20. (Scheme 7), aspects of of general acid A-CO 2 H 7 (Scheme 3).
  • pyrazole 5-carboxylic esters 17 and 18 can be prepared by the alkylation of pyrazole ester 16 with Z4-X 15, wherein X represents a leaving group on a Z4 moiety such as a halide, triflate, or other sulfonate.
  • Preferred conditions for the alkylation of pyrazole 16 include the use of strong bases such as sodium hydride, potassium tert-butoxide and the like in polar aprotic solovents such as dimethylsulfoxide, dimethylformamide or tetrahydrofuran.
  • Z4-substituted pyrazoles 17 and 18 are isomers of one another and can both be prepared in the same reactions vessel and separated by purification methods familiar to those skilled in the art.
  • the esters 17 and 18 in turn can be converted to acids 19 and 20 using conditions familiar to those skilled in the art, for example saponification in the case of ethyl esters, hydrogenation in the case of benzyl esters or acidic hydrolysis in the case of tert-butyl esters.
  • Scheme 8 illustrates the preparation of pyrazole amine 25, a further example of general amine A-NH 2 6.
  • Acid-catalyzed condensation of R2-substituted hydrazine 21 with 1,1,3,3-tetramethoxypropane 22 provides R2-substituted pyrazole 23.
  • R2-substituted pyrazole 23 can also be prepared by direct alkylation of pyrazole.
  • Pyrazole 23 can be regioselectively nitrated to provide nitro-pyrazole 24 by standard conditions familiar to those skilled in the art.
  • hydrogenation of nitro-pyrazole 24 employing a hydrogenation catalyst, such as palladium or nickel provides pyrazole amine 25, an example of general amine A-NH 2 6.
  • keto-ester 26 can be reacted with N,N-dimethylformamide dimethyl acetal to provide 27.
  • Reaction of 27 with either 21 or 28 (wherein P is an acid-labile protecting group) in the presence of acid provides 29 or 30.
  • both 29 and 30 can be obtained from the same reaction and can be separated by standard chromatographic conditions.
  • esters 29 and 30 can be converted to acids 31 and 32 respectively as previously described in Scheme 7.
  • NH-pyrazole 34 can be prepared by reaction of acrylate 33 with hydrazine (Scheme 10). Alkylation of 34 with R2-X 35 as described above for Scheme 7 provides mixtures of pyrazole esters 36 and 37 which are separable by standard chromatographic techniques. Further conversion of esters 36 and 37 to acids 38 and 39 can be accomplished as described above in Scheme 7.
  • General amines 6 containing an isoxazole ring can be prepared as described in Scheme 11.
  • reaction of keto-nitrile 9 with hydroxylamine can provide both the 5-aminoisoxazole 40 and 3-aminoisoxazole 41.
  • Preferred conditions for the formation of 5-aminoisoxazole 40 include the treatment of 9 with hydroxylamine in the presence of aqueous sodium hydroxide, optionally in the presence of an alcoholic co-solvent at a temperature between 15 and 100° C.
  • Preferred conditions for the formation of 3-aminoisoxazole 41 include the treatment of 9 with hydroxylamine hydrochloride in a polar solvent such as water, an alcohol, dioxane or a mixture thereof at a temperature between 15 and 100° C.
  • a polar solvent such as water, an alcohol, dioxane or a mixture thereof at a temperature between 15 and 100° C.
  • Amines 2 useful for the invention can be synthesized according to methods commonly known to those skilled in the art.
  • Amines of general formula 2 contain three rings and can be prepared by the stepwise union of three monocyclic subunits as illustrated in the following non-limiting Schemes.
  • Scheme 12 illustrates one mode of assembly in which an E-containing subunit 42 is combined with the central pyridine ring 43 to provide the bicyclic intermediate 44.
  • the “M” moiety of 42 represents a hydrogen atom of a heteroatom on the X linker that participates in a nucleophilic aromatic substitution reaction with monocycle 43.
  • M may also represent a suitable counterion (for example potassium, sodium, lithium, or cesium) within an alkoxide, sulfide or amide moiety.
  • the “M” group can represent a metallic species (for example, copper, boron, tin, zirconium, aluminum, magnesium, lithium, silicon, etc.) on a carbon atom of the X2 moiety that can undergo a transition-metal-mediated coupling with monocycle 43.
  • the “Y” group of monocyclic species 42 is an amine or an amine surrogate, such as an amine masked by a protecting group (“P” in formula 45), a nitro group, or a carboxy acid or ester that can be used to prepare an amine via known rearrangement.
  • suitable protecting groups “P” include but are not limited to tert-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz), and acetamide.
  • the products of Scheme 11 will be amine surrogates such as 45 or 46 that can be converted to amine 2 by a deprotection, reduction or rearrangement (for example, Curtius rearrangement) familiar to those skilled in the all.
  • the “LG” of monocycle 43 represents a moiety that can either be directly displaced in a nucleophilic substitution reaction (with or without additional activation) or can participate in a transition-mediated union with fragment 42.
  • the W group of monocycle 43 or bicycle 44 represents a moiety that allows the attachment of the pyrazole.
  • the “W” group represents a halogen atom that will participate in a transition-metal-mediated coupling with a pre-formed heterocyclic reagent (for example a boronic acid or ester, or heteroaryl stannane) to give rise to amine 2.
  • the “W” group of 43 and 44 represents a functional group that can be converted to a five-membered heterocycle by an annulation reaction.
  • Non-limiting examples of such processes would include the conversion of a cyano, formyl, carboxy, acetyl, or alkynyl moiety into a pyrazole moiety. It will be understood by those skilled in the art that such annulations may in fact be reaction sequences and that the reaction arrows in Scheme 11 may represent either a single reaction or a reaction sequence. Additionally, the “W” group of 44 may represent a leaving group (halogen or triflate) that can be displaced by a nucleophilic nitrogen atom of a pyrazole ring.
  • Scheme 13 illustrates the preparation of pyrazole 51, an example of general amine 2.
  • commercially available 3-fluoro-4-aminophenol (47) is reacted with potassium tert-butoxide and 2,4-dichloropyridine 48 to provide chloropyridine 49.
  • the preferred solvent for this transformation is dimethylacetamide at a temperature between 80 and 100° C.
  • a palladium catalyst preferably tetrakis(triphenylphosphine)palladium
  • Scheme 14 illustrates a non-limiting example of Scheme 12 wherein the “W” group is a leaving group for nucleophilic aromatic substitution.
  • amine 53 an example of general amine 2
  • Preferred conditions include the use of polar aprotic solvents such as 1-methyl-2-pyrrolidinone, dimethylacetamide, or dimethylsulfoxide in the presence of non-nucleophilic bases such as potassium carbonate, sodium hydride, 1,8-diaza-bicyclo[5.4.0]undec-7-ene (DBU), and the like.
  • Preferred temperatures are from ambient temperature up to about 250° C. and may optionally include the use of microwave irradiation or sonication.
  • the general methods of scheme 14 can be used to prepare additional triazole isomers by employing either 1,2,4-triazole 52, or alternatively, by employing 1,2,3-triazole in place of 52.
  • Scheme 15 illustrates the preparation of amine 55 and 56, non-limiting examples of general amine of formula 2, by way of an annulation sequence according to general Scheme 12.
  • Conversion of chloropyridine 49 into alkyne 53 can be accomplished by Sonogashira cross-coupling with trimethylsilylacetylene, followed by aqueous hydrolysis of the trimethylsilyl group, conditions familiar to those skilled in the art.
  • Further reaction of alkyne 53 with azidomethyl pivalate (54) in the presence of copper sulfate and sodium ascorbate provides the N-pivaloylymethyl triazole amine 55. (see Loren, et. al. Synlett, (2005), 2847).
  • Deprotection under standard conditions, preferably dilute aqueous sodium hydroxide, provides 56.
  • the amine 55 can be used directly to produce ureas of formula 1 prior to the removal of the N-pivaloylmethyl protecting group.
  • the general intermediate 40 can be converted by palladium-mediated Stille-coupling into oxazoles 57 or 59 by reaction with the tributylstannanes 58 (see: Cheng et al., Biorg. Med. Chem. Lett., 2006, 2076) or 60 (Aldrich Chemical).
  • Preferred palladium catalysts for the Stille reactions include dichlorobis(triplhenylphosphine)palladium, dichloro[11′-bis(diphenylphosphino)ferrocene]palladium and tetrakis(triphenylphosphine)palladium.
  • isoxazoles 61 and 63 can be obtained by the palladium-catalyzed reaction of 40 with 4-isoxazoleboronic acid pinacol ester 62 (Frontier Scientific) or tributylstannane 64 (see: Sakamoto, et al. Tetrahedron, 1991, 5111).
  • amines of general formula 2 containing an isothiazole ring can also be prepared by the methods described above.
  • Scheme 17 shows a non-limiting example wherein a palladium-catalyzed Stille reaction of trimethylstannane 65 (see: Wentland, et al. J. Med. Chem., 1993, 1580) with 40 can provide isothiazole 67.
  • palladium-catalyzed Suzuki-cross coupling between 40 and the boronate ester 66 gives rise to isothiazole amine 68.
  • reaction mixture was purified directly by reverse phase chromatography (MeCN (w/0.1% TFA)/H 2 O (w/0.1% TFA)) to afford 1-(3-tert-butyl-1-methyl-1H-pyrazol-5-yl)-3-(2-fluoro-4-(2-(oxazol-2-yl)pyridin-4-yloxy)phenyl)urea of 96.8% purity.
  • Abl kinase Activity of Abl kinase (SEQ ID NO:1) was determined by following the production of ADP from the kinase reaction through coupling with the pyruvate kinase/lactate dehydrogenase system (e.g., Schindler, et al. Science (2000) 289, 1938-1942). In this assay, the oxidation of NADH (thus the decrease at A 340nm was continuously monitored spectrophometrically. The reaction mixture (100 ⁇ l) contained Abl kinase (1 nM.
  • IC 50 values were calculated from a series of percent inhibition values determined at a range of inhibitor concentrations using software routines as implemented in the GraphPad Prism software package.
  • T3 15I Abl kinase (SEQ ID NO:2) was determined by following the production of ADP from the kinase reaction through coupling with the pyruvate kinase/lactate dehydrogenase system (e.g., Schindler, et al. Science (2000) 289, 1938-1942). In this assay, the oxidation of NADH (thus the decrease at A 340nm ) was continuously monitored spectrophometrically. The reaction mixture (100 ⁇ l) contained Abl kinase (4.4 nM.
  • M315I Abl from deCode Genetics peptide substrate (EAIYAAPFAKKK, 0.2 mM), MgCl 2 (10 mM), pyruvate kinase (4 units), lactate dehydrogenase (0.7 units), phosphoenol pyruvate (1 mM), and NADH (0.28 mM) in 90 mM Tris buffer containing 0.2% octyl-glucoside and 1% DMSO, pH 7.5. Test compounds were incubated with T315I Abl (SEQ ID NO:2) and other reaction reagents at 30° C. for 1 h before ATP (500 ⁇ M) was added to start the reaction.
  • the absorption at 340 nm was monitored continuously for 2 hours at 30° C. on Polarstar Optima plate reader (BMG).
  • the reaction rate was calculated using the 1.0 to 2.0 h time frame. Percent inhibition was obtained by comparison of reaction rate with that of a control (i.e. with no test compound).
  • IC 50 values were calculated from a series of percent inhibition values determined at a range of inhibitor concentrations using software routines as implemented in the GraphPad Prism software package.
  • c-Kit kinase Activity of c-Kit kinase (SEQ ID NO:9) was determined by following the production of ADP from the kinase reaction through coupling with the pyruvate kinase/lactate dehydrogenase system (e.g.. Schindler, et al. Science (2000) 289, 1938-1942). In this assay, the oxidation of NADH (thus the decrease at A340 nm) was continuously monitored spectrophometrically.
  • the reaction mixture (100 ⁇ l) contained c-Kit (cKIT residues T544-V976, from ProQinase, 5.4 nM), polyE4Y (1 mg/ml), MgCl2 (10 mM), pyruvate kinase (4 units), lactate dehydrogenase (0.7 units), phosphoenol pyruvate (1 mM), and NADH (0.28 mM) in 90 mM Tris buffer containing 0.2% octyl-glucoside and 1% DMSO, pH 7.5. Test compounds were incubated with C-Met (SEQ ID NO:9) and other reaction reagents at 22° C.
  • C-Met SEQ ID NO:9
  • ATP 200 ⁇ M
  • ATP 200 ⁇ M
  • the absorption at 340 nm was monitored continuously for 0.5 hours at 30° C. on Polarstar Optima plate reader (BMG).
  • BMG Polarstar Optima plate reader
  • the reaction rate was calculated using the 0 to 0.5 h time frame. Percent inhibition was obtained by comparison of reaction rate with that of a control (i.e. with no test compound).
  • IC50 values were calculated from a series of percent inhibition values determined at a range of inhibitor concentrations using software routines as implemented in the GraphPad Prism software package.
  • C-Met kinase (SEQ ID NO:10) was determined by following the production of ADP from the kinase reaction through coupling with the pyruvate kinase/lactate dehydrogenase system (e.g., Schindler, et al. Science (2000) 289, 1938-1942). In this assay, the oxidation of NADH (thus the decrease at A340 nm) was continuously monitored spectrophometrically.
  • the reaction mixture (100 ⁇ l) contained C-Met (c-Met residues: 956-1390, from Invitrogen, catalogue #PV3143, 6 nM), polyE4Y (1 mg/ml), MgCl2 (10 mM), pyruvate kinase (4 units), lactate dehydrogenase (0.7 units), phosphoenol pyruvate (1 mM), and NADH (0.28 mM) in 90 mM Tris buffer containing 0.25 mM DTT, 0.2% octyl-glucoside and 1% DMSO, pH 7.5. Test compounds were incubated with C-Met (SEQ ID NO:10) and other reaction reagents at 22° C.
  • ATP 100 ⁇ M
  • BMG Polarstar Optima plate reader
  • biochemical IC 50 Values of other compounds disclosed herein are at least 10 ⁇ M against Abl enzyme.
  • BaF3 cells Parental or transfected with the following: wild type p210 BCR-Abl and T315I p210 BCR-Abl was obtained from Professor Richard Van Etten (New England Medical Center, Boston, Mass.). Briefly, cells were grown in RPMI 1640 supplemented with 10% characterized fetal bovine serum (HyClone, Logan, Utah) at 37 degrees Celsius, 5% CO 2 , 95% humidity. Cells were allowed to expand until reaching 80% saturation at which point they were subcultured or harvested for assay use.
  • test compound was dispensed into a 96 well black clear bottom plate (Coming, Coming, N.Y.). For each cell line, three thousand cells were added per well in complete growth medium. Plates were incubated for 72 hours at 37 degrees Celsius, 5% CO 2 , 95% humidity. At the end of the incubation period Cell Titer Blue (Promega, Madison, Wis.) was added to each well and an additional 4.5 hour incubation at 37 degrees Celsius, 5% CO 2 , 95% humidity was performed. Plates were then read on a BMG Fluostar Optima (BMG, Durham, N.C.) using an excitation of 544 nM and an emission of 612 nM. Data was analyzed using Prism software (Graphpad, San Diego. Calif.) to calculate IC50's.

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