LEE THOMAS WAI-HO (US)
MCCOMAS CASEY CAMERON (US)
SCHMIDT DARBY R (US)
GRAZIOTTO JOHN J (US)
WO2021127333A1 | 2021-06-24 | |||
WO2022150461A1 | 2022-07-14 |
US20190248764A1 | 2019-08-15 |
CLAIMS What is claimed is: 1. A compound of formula (Ia) or a pharmaceutically acceptable salt thereof, wherein R1 is heteroaryl optionally substituted by 1-5 independently selected R7; R2 is aryl, heteroaryl, cycloalkyl, heterocycloalkyl, C1-6 alkyl, or NRaRb, each R2 optionally substituted by 1-5 independently selected R8; R3 is each of R4 and R6 is independently selected from the group consisting of H, hydroxy, halogen, cyano, C1-6 alkyl, C1-6 haloalkyl, C1-6 alkoxy, C1-6 haloalkoxy, C1-6 alkylthio, and NRaRb; each of R7 and R8 are independently selected at each occurrence from the group consisting of hydroxy, halogen, cyano, C1-6 alkyl, C1-6 alkoxy, C1-6 alkylthio, C3-7 cycloalkyl, and NRaRb, wherein each C1-6 alkyl and C1-6 alkoxy are optionally substituted with substituents independently selected from the group consisting of halogen, hydroxyl, and C1-6 alkoxy, and each C3-7 cycloalkyl is optionally substituted with substituents independently selected from the group consisting of halogen, hydroxyl, C1-6 alkoxy and C1-6 alkyl; or when R1 or R2 is cycloalkyl or heterocycloalkyl, two R7 or two R8 can be taken together to form oxo, or any two R7 or two R8 can be taken together with the atoms to which they are attached to form an edge fused or spiro fused ring of 3-7 members, or a bridge of 1 to 3 carbons or a single bond, wherein the ring or bridge is optionally substituted with 1-3 substituents independently selected from the group consisting of halogen, hydroxyl, C1-6 haloalkyl, and C1-6 alkyl; R9 is C1-6 alkyl or C3-7 cycloalkyl, optionally substituted with 1-9 substituents independently selected from the group consisting of deuterium, halogen, C1-3 alkyl, hydroxyl, and C1-6 alkoxy, wherein C1-3 alkyl and C1-6 alkoxy are optionally substituted with 1-3 substituents independently selected from the group consisting of halogen and hydroxy; each R10 is selected independently from the group consisting of C1-6 alkyl, and C1-6 haloalkyl, optionally substituted with 1-5 substituents independently selected from the group consisting of deuterium, hydroxyl, C1-3 haloalkyl, C1-3 alkoxy and C1-3 alkyl; or two R10 on the same carbon can be taken together to form oxo; or any two R10 can be taken together with the atoms to which they are attached to form an edge fused or spiro fused ring of 3-7 members, or a bridge of 1 to 3 carbons or a single bond, wherein the ring or bridge is optionally substituted with 1-3 substituents independently selected from the group consisting of deuterium, halogen, hydroxyl, C1-6 haloalkyl, and C1-6 alkyl; each Ra and Rb is independently selected from H, C1-6 alkyl, –(CH2)0-2-C3-7 cycloalkyl, and 3- 7 membered heterocycloalkyl; m is 1 or 2; n is 1, 2, or 3; p is 0, 1, 2, 3, 4, 5, 6, 7, or 8; and wherein m + n is 2, 3, or 4. 2. The compound of claim 1 of formula (Ia) or a pharmaceutically acceptable salt thereof, wherein R1 is pyridyl optionally substituted by 1-5 independently selected R7; R2 is aryl, heteroaryl, cycloalkyl, heterocycloalkyl, C1-6 alkyl, or NRaRb, each R2 optionally substituted by 1-5 independently selected R8; R3 is each of R4 and R6 is H; each of R7 and R8 are independently selected at each occurrence from the group consisting of hydroxy, halogen, cyano, C1-6 alkyl, C1-6 alkoxy, C1-6 alkylthio, C3-7 cycloalkyl, and NRaRb, wherein each C1-6 alkyl and C1-6 alkoxy are optionally substituted with substituents independently selected from the group consisting of halogen, hydroxyl, and C1-6 alkoxy, and each C3-7 cycloalkyl is optionally substituted with substituents independently selected from the group consisting of halogen, hydroxyl, C1-6 alkoxy and C1-6 alkyl; R9 is C1-6 alkyl or C3-7 cycloalkyl, optionally substituted with 1-9 substituents independently selected from the group consisting of deuterium, halogen, C1-3 alkyl, hydroxyl, and C1-6 alkoxy, wherein C1-3 alkyl and C1-6 alkoxy are optionally substituted with 1-3 substituents independently selected from the group consisting of halogen and hydroxy; each R10 is selected independently from the group consisting of C1-6 alkyl, and C1-6 haloalkyl, optionally substituted with 1-5 substituents independently selected from the group consisting of deuterium, hydroxyl, C1-3 haloalkyl, C1-3 alkoxy and C1-3 alkyl; or two R10 on the same carbon can be taken together to form oxo; or any two R10 can be taken together with the atoms to which they are attached to form an edge fused or spiro fused ring of 3-7 members, or a bridge of 1 to 3 carbons or a single bond, wherein the ring or bridge is optionally substituted with 1-3 substituents independently selected from the group consisting of deuterium, halogen, hydroxyl, C1-6 haloalkyl, and C1-6 alkyl; each Ra and Rb is independently selected from H, C1-6 alkyl, –(CH2)0-2-C3-7 cycloalkyl, and 3- 7 membered heterocycloalkyl; and p is 0, 1, 2, 3, 4, 5, 6, 7, or 8. 3. The compound of claim 1 of formula (Ia) or a pharmaceutically acceptable salt thereof, wherein R1 is pyridyl optionally substituted by 1-5 independently selected R7; R2 is phenyl optionally substituted by 1-5 independently selected R8; R3 is each of R4 and R6 is H; each of R7 and R8 are independently selected at each occurrence from the group consisting of hydroxy, halogen, cyano, C1-6 alkyl, and C1-6 alkoxy; R9 is C1-6 alkyl or C3-7 cycloalkyl, optionally substituted with 1-9 substituents independently selected from the group consisting of deuterium, halogen, C1-3 alkyl, hydroxyl, and C1-6 alkoxy, wherein C1-3 alkyl and C1-6 alkoxy are optionally substituted with 1-3 substituents independently selected from the group consisting of halogen and hydroxy; each R10 is selected independently from the group consisting of C1-6 alkyl, and C1-6 haloalkyl, each optionally substituted with 1-5 deuterium; and p is 0, 1, 2, 3, 4, 5, 6, 7, or 8. 4. The compound of claim 1, wherein R1 is monocyclic heteroaryl optionally substituted by 1-5 independently selected R7. 5. The compound of claim 4, wherein R1 is monocyclic heteroaryl of 5-6 ring atoms with 1, 2 or 3 ring atoms selected independently from N, O, and S, wherein R1 is optionally substituted by 1-4 independently selected R7. 6. The compound of claim 5, wherein R1 is monocyclic nitrogen-containing heteroaryl of 5-6 ring atoms with 1, 2 or 3 ring heteroatoms selected from N only, wherein R1 is optionally substituted by 1-4 independently selected R7. 7. The compound of claim 6, wherein R1 is pyridine, pyrimidine, pyrazine, pyridazine, thiazole, oxazole, pyrrole, imidazole, or pyrazole, optionally substituted by 1-4 independently selected R7. 8. The compound of claim 5, wherein R1 is pyridine, thiazole, or pyrazole, optionally substituted by 1-4 independently selected R7. 9. The compound of claim 8, wherein R1 is pyridine, optionally substituted by 1-4 independently selected R7. 10. The compound of any one of claims 1-9, wherein R1 is 2-pyridyl, optionally substituted by 1-4 independently selected R7. 11. The compound of claim 6, wherein R1 is 12. The compound of claim 11, wherein R1 is stituted by 1-4 indepe 7 ndently selected R . 14. The compound of any one of claims 1-13, wherein R2 is aryl, heteroaryl, cycloalkyl, heterocycloalkyl, C1-6 alkyl, or NRaRb, each R2 optionally substituted by 1-5 independently selected R8, and wherein Ra and Rb of the R2 group are not both H. 15. The compound of claim 14, wherein R2 is aryl optionally substituted by 1-5 independently selected R8. 16. The compound of claim 15, wherein R2 is phenyl optionally substituted with 1-3 independently selected R8. 17. The compound of any one of claims 1-16, wherein each R8 is independently selected from H, halogen, cyano, C1-6 alkyl, C1-6 alkoxy, C1-6 haloalkyl, or C1-6 haloalkoxy. 18. The compound of claim 16, wherein R2 is 19. The compound of claim 18, wherein R2 is . 20. The compound of any one of claims 1-13, wherein R2 is heteroaryl, cycloalkyl, heterocycloalkyl, or NRaRb, each R2 optionally substituted by 1-5 independently selected R8, and wherein Ra and Rb of the R2 group are not both H. 21. The compound of any of claims 1-8 or 11-20, wherein R2 is heteroaryl or heterocycloalkyl, each R2 optionally substituted by 1-5 independently selected R8. 22. The compound of claim 21, wherein R2 is heteroaryl optionally substituted by 1-5 independently selected R8. 23. The compound of claim 22, wherein R2 is monocyclic heteroaryl optionally substituted by 1-5 independently selected R8. 24. The compound of claim 23, wherein R2 is monocyclic heteroaryl of 5-6 ring atoms with 1, 2 or 3 ring atoms selected independently from N, O, and S, wherein R2 is optionally substituted by 1-4 independently selected R8. 25. The compound of claim 24, wherein R2 is pyridine, pyrimidine, pyrazine, pyridazine, thiazole, oxazole, pyrrole, imidazole, or pyrazole, optionally substituted by 1-4 independently selected R8. 26. The compound of claim 25, wherein R2 is pyridine, pyrimidine, pyrazine, or pyrazole, optionally substituted by 1-4 independently selected R8. 27. The compound of claim 26, wherein R2 is pyridine, optionally substituted by 1-4 independently selected R8. 28. The compound of claim 25, wherein R2 is i 29. The compound of claim 28, wherein R2 is substituted. 30 The compound of claim 28, wherein R2 is 31. The compound of claim 20, wherein R2 is cycloalkyl optionally substituted by 1-5 independently selected R8. 32. The compound of claim 20, wherein R2 is C3-8 cycloalkyl optionally substituted with 1-5 independently selected R8. 33. The compound of claim 32, wherein R2 is cyclopropyl, cyclobutyl, cyclopentyl, or cyclohexyl, each optionally substituted with 1-3 independently selected R8. 34. The compound of any one of claims 31-33, wherein R2 is not substituted. 35. The compound of claim 33, wherein R2 is cyclopropyl. 36. The compound of claim 20, wherein R2 is heterocycloalkyl optionally substituted by 1-5 independently selected R8. 37. The compound of claim 36, wherein R2 is monocyclic heterocycloalkyl optionally substituted by 1-5 independently selected R8. 38. The compound of claim 37, wherein R2 is monocyclic heterocycloalkyl of 4-6 ring atoms with 1, 2 or 3 ring atoms selected independently from N, O, and S, wherein R2 is optionally substituted by 1-4 independently selected R8. 39. The compound of claim 38, wherein R2 is azetidine, oxetane, pyrrolidine, tetrahydrofuran, piperidine, piperazine, tetrahydropyran, or morpholine, optionally substituted by 1-4 independently selected R8. 40. The compound of claim 39, wherein R2 is azetidine, pyrrolidine, piperazine, or morpholine, optionally substituted by 1-4 independently selected R8. 41. The compound of any one of claims 36-40, wherein R2 contains a ring nitrogen atom and is bound to formula (I) at the ring nitrogen atom. 42. The compound of claim 40, wherein R2 is . 43. The compound of any one of claims 36-41, wherein R2 is not substituted. 44. The compound of claim 20, wherein R2 is NRaRb, each R2 optionally substituted by 1- 5 independently selected R8, and wherein Ra and Rb of the R2 group are not both H. 45. The compound of claim 44, wherein Ra is C1-6 alkyl, and Rb is C1-6 alkyl, C3-7 cycloalkyl, or 3-7 membered heterocycloalkyl. 46. The compound of claim 45, wherein Ra and Rb are each independently selected C1-6 alkyl. 47. The compound of claim 14, wherein R2 is C1-6 alkyl optionally substituted by 1-5 independently selected R8. 48. The compound of claim 47, wherein R2 is C1-6 alkyl optionally substituted by 1-5 independently selected halogens. 49. The compound of claim 48, wherein R2 is Me, Et, or CF3. 50. The compound of any one of claims 1-49, wherein m is 1 and n is 1. 51. The compound of any one of claims 1-50, wherein p is 0, 1, 2, 3, 4, 5, or 6. 52. The compound of claim 51, wherein each R10 is independently selected from the group consisting of C1-6 alkyl and C1-6 haloalkyl, each optionally substituted with 1-5 deuteriums. 53. The compound of claim 52, wherein each R10 is methyl. 54. The compound of claim 52 or 53, wherein p is 1, 2, 3, 4, 5, or 6. 55. The compound of claim 54, wherein R3 is substituted with an edge fused or spiro fused cyclopropane; or R3 includes a one or two carbon bridge; and R3 is optionally additionally substituted by 1-4 R10. 56. The compound of claim 55, wherein R3 is optionally additionally substituted by 1-4 R10. 57. The compound of claim 54, wherein R3 is optionally additionally substituted by 1-4 R10. 58. The compound of claim 57, wherein R3 is 59 The compound of any one of claims 54-57, wherein R3 is not substituted by any additional R10. 60. The compound of any one of claims 1-59, wherein R4 is H. 61. The compound of any one of claims 1-60, wherein R6 is H. 62. The compound of any one of claims 1-61, wherein R4 and R6 are H. 63. The compound of any one of claims 1-62, wherein each of R7 and R8 are independently selected at each occurrence from the group consisting of hydroxy, halogen, cyano, C1-6 alkyl, C1-6 alkoxy, and C3-7 cycloalkyl, wherein each C1-6 alkyl and C1-6 alkoxy is optionally substituted with 1-3 halogens. 64. The compound of any one of claims 1-63, wherein each R7 is independently selected at each occurrence from the group consisting of halogen, cyano, C1-6 alkyl, C1-6 alkoxy, and CF3. 65. The compound of any one of claims 1-64, wherein R9 is C1-6 alkyl, optionally substituted with 1-3 substituents independently selected from the group consisting of halogen, hydroxyl, and C1-6 alkoxy, or with 1-9 substituents selected from deuterium and halogen. 66. The compound of claim 65, wherein R9 is t-butyl, ethyl, or isopropyl, optionally substituted with 1-9 substituents selected from deuterium, hydroxy, and halogen or with 1-3 hydroxyl. 67. The compound of any one of claims 1-64, wherein R9 is C3-7 cycloalkyl, optionally substituted with 1-3 substituents independently selected from the group consisting of deuterium, halogen, hydroxyl, C1-3 alkyl, and C1-6 alkoxy, wherein C1-3 alkyl and C1-6 alkoxy are optionally substituted with 1-3 substituents independently selected from the group consisting of halogen and hydroxy. 68. The compound of claim 67, wherein R9 is cyclopropyl. 69. The compound of any one of claims 1-64, wherein R9 is Me, Et, t-butyl, isopropyl, cyclopropyl, isobutyl, neopentyl, F3C-CH2-, F3C-CH(CH3)-, F3C-C(CH3)2-, or FCH2- 70. The compound of any one of claims 1-64, wherein R9 is Me, Et, t-butyl, isopropyl, cyclopropyl, isobutyl, neopentyl, F3C-CH2-, F3C-CH(CH3)-, F3C-C(CH3)2-, or FCH2- wherein the variable definitions are as described in the specification and claims. 72. A compound of formula (Ic) wherein the variable definitions are as described in the specification and claims. 73. A compound of Formula (I), or any subformula thereof, selected from the compounds disclosed in the specification, or a pharmaceutically acceptable salt thereof. 74. A compound of any one of claims 1-73, wherein the compound achieves at least 50% of the maximal current obtained with 30 µM ML-SA1 in a patch clamp assay for TRPML1, and has an EC50 less than 1 µM. 75. A compound of any one of claims 1-74, wherein the compound achieves a maximal current obtained with 30 µM ML-SA1 in a patch clamp assay for TRPML1 which is at least 10 fold the maximal current achieved for any other TRPML. 76. A pharmaceutical composition comprising a pharmaceutically acceptable excipient and a compound of any one of claims 1-75. 77. A method of modulating TRPMLs, the method comprising administering to a patient in need thereof a therapeutically effective amount of a pharmaceutical composition of claim 76 or a compound of any one of claims 1-75. 78. A method of treating a disorder which can be treated by modulation of TRPMLs, the method comprising administering to a patient in need thereof a therapeutically effective amount of a pharmaceutical composition of claim 76 or a compound of any one of claims 1- 75. 79. A method of treating a disorder which can be treated by modulation of lysosomes, the method comprising administering to a patient in need thereof a therapeutically effective amount of a pharmaceutical composition of claim 76 or a compound of any one of claims 1- 75. 80. A method of treating a disorder selected from the group consisting of a ciliopathy, neurodegenerative disorder, lysosomal storage disorder, lysosomal transport disorder, glycogen storage disorder, cholesteryl ester storage disease, a muscular disease (e.g., muscular dystrophy), a disease related to aging (e.g., photo aging of the skin), macular degeneration (e.g., Stargardt’s or age related) and cancer (e.g., cancers of the blood, brain, bone, lung, liver, kidney, bladder, stomach, breast, prostate, ovary, testes, colon, pancreas, or skin), the method comprising administering to a patient in need thereof a therapeutically effective amount of a pharmaceutical composition of claim 76 or a compound of any one of claims 1-75. 81. The method of claim 80, wherein the disorder is a ciliopathy. 82. The method of claim 81, wherein the ciliopathy is selected from the group consisting of polycystic kidney disease, pancreatic cysts in polycystic kidney disease, Bardet-Biedl syndrome, nephronophthisis, Joubert Syndrome, Mecke-Gruber Syndrome, oral-facial-digital syndrome, Senior Loken Syndrome, Birt-Hogg-Dube syndrome, Leber’s congenital amaurosis, Alstrom syndrome, Jeune asphyxiating thoracic dystrophy, Ellis van Creveld syndrome, Sensenbrenner syndrome, and primary ciliary dyskinesia. 83. The method of claim 82, wherein the disorder is polycystic kidney disease 84. The method of claim 83 wherein the disorder is autosomal dominant polycystic kidney disease, autosomal recessive polycystic kidney disease, or pancreatic cysts associated with autosomal dominant polycystic kidney disease. 85. The method of claim 84, wherein the disorder is autosomal dominant polycystic kidney disease. 86. The method of claim 80, wherein the disorder is a neurodegenerative disorder. 87. The method of claim 86, wherein the neurodegenerative disorder is selected from the group consisting of Parkinson’s disease, GBA-Parkinson’s disease, LRRK2 Parkinson’s disease, Huntington’s disease, amyotrophic lateral sclerosis (ALS), Alzheimer’s disease, progressive supranuclear palsy, frontotemporal dementia, FTDP-17, corticobasal degeneration, Lewy body dementia, Pick’s disease, and multi system atrophy. 88. The method of claim 80, wherein the disorder is a lysosomal storage disorder. 89. The method of claim 88, wherein the lysosomal storage disorder is selected from the group consisting of Niemann-Pick disease, Gaucher’s disease, neuronopathic Gaucher’s disease, sphingolipidoses, Farber disease, Krabbe disease, Galactosialidosis, gangliosidoses, Gaucher Disease, Lysosomal acid lipase deficiency, sulfatidoses, mucopolysaccharidoses, mucolipidoses, lipidoses, and oligosaccharidoses. 90. The method of claim 89, wherein the lysosomal storage disorder is selected from the group consisting of sphingolipidoses, Farber disease, Krabbe disease, Galactosialidosis, Fabry disease, Schindler disease, beta-galactosidase disorder, GM1 gangliosidosis, GM2 gangliosidosis AB variant, GM2 gangliosidosis activator deficiency, Sandhoff disease, Tay- Sachs disease, Gaucher disease, lysosomal acid lipase deficiency, Niemann-Pick disease, metachromatic leukodystrophy, Saposin B deficiency, multiple sulfatase deficiency, Hurler syndrome, Scheie sundrome, Hurler-Scheie syndrome, Hunter syndrome, Sanfilippo syndrome, Morquio syndrome, Maroteaux-Lamy syndrome, Sly syndrome, hyaluronidase deficiency, sialidosis, I-cell disease, pseudo-Hurler polydystrophy, phosphotransferease deficiency, mucolipidin 1 deficiency, Santavuori-Haltia disease, Jansky-Bielchowsky disease, Batten-Spielmeyer-Vogt disease, Kufs disease, Finnish variant neuronal ceroid lipfuscinosis, late infantile variant neuronal ceroid lipfuscinosis, type 7 neuronal ceroid lipfuscinosis, northern epilepsy neuronal ceroid lipfuscinosis, Turkish late infantile neuronal ceroid lipfuscinosis, German/Serbian late infantile neuronal ceroid lipfuscinosis, congential cathepsin D deficiency, Wolman disease, alpha-mannosidosis, beta-mannosidosis, aspartylgluosaminuria, and fucosidosis. 91. The method of claim 90, wherein the lysosomal storage disorder is selected from the group consisting of Niemann-Pick disease, Gaucher’s disease, and neuronopathic Gaucher’s disease. 92. The method of claim 80, wherein the disorder is a lysosomal transport disease selected from the group consisting of cystinosis, pycnodysostosis, Salla disease, sialic acid storage disease, and infantile free sialic acid storage disease. 93. The method of claim 92, wherein the disorder is a glycogen storage disease selected from the group consisting of Pompe disease and Danon disease. |
Example 2. Synthesis of of isopropyl (S)-2-(5-cyclopropyl-4-(2-methyl-4- pivaloylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)ison icotinonitrile (Compound 104) Step 1.4-chloro-5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine At 0°C, to a suspension of NaH (11 g, 270 mmol) in DMF (500 mL) was added a solution of 4-chloro-5-iodo-7H-pyrrolo[2,3-d]pyrimidine (50 g, 180 mmol) in DMF (150 ml) dropwise. After being stirred at 0°C for 10 minutes, a solution of TsCl (50 g, 260 mmol) in DMF (150 ml) was added dropwise into the above reaction mixture. The resulting mixture was stirred at room temperature overnight. The reaction was poured into water (4 L) and filtered to give the product which was further dried under vacuum to give 4-chloro-5-iodo-7- tosyl-7H-pyrrolo [2,3-d]pyrimidine (73 g, 94%) as a light yellow solid. LC/MS ESI m/z: 434.2 (M+H) + . Step 2. tert-butyl (S)-4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3- methylpiperazine-1-carboxylate A mixture of 4-chloro-5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (50 g, 120 mmol) and tert-butyl-(S)-3-methylpiperazine-1-carboxylate (46 g, 230 mmol) in DIPEA (350 ml) was heated to 140 o C for 1.5 h. The mixture was concentrated, and the residue was purified by flash chromatography (silica gel, 0~30% ethyl acetate in petroleum ether) to afford tert- butyl(S)-4-(5-iodo-7-tosyl-7H-pyrrolo [2,3-d]pyrimidin- 4-yl)-3-methylpiperazine-1- carboxylate (52 g, 75%) as a white solid. LC/MS ESI m/z: 598.4 (M+H) + . Step 3. tert-butyl (S)-4-(5-cyclopropyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl )-3- methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-4-(5-iodo-7-tosyl-7H-pyrrolo [2,3-d]pyrimidin-4-yl)-3- methylpiperazine-1-carboxylate (39 g, 65 mmol) in toluene (400 mL) were added cyclopropylboronic acid (8.4 g, 98 mmol), K 2 CO 3 (117 g, 849 mmol) and 1,1'-bis (di-tert- butylphosphino)ferrocene palladium dichloride (2.0 g, 3.2 mmol). The resulting mixture was heated to 80 o C overnight. After cooling to room temperature, the reaction mixture was filtered. The reaction was partitioned between DCM and water, the organic layer was separated, and the aqueous layer was extracted with DCM twice. The combined organic layers were dried over Na 2 SO 4 , filtered, and concentrated. The residue was purified by flash chromatography (0~50% ethyl acetate in petroleum ether) to afford tert-butyl (S)-4-(5- cyclopropyl-7-tosyl -7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carbo xylate (22 g, 67% yield) as a white solid. LC/MS ESI m/z: 512.5(M+H) + . Step 4. tert-butyl (S)-4-(5-cyclopropyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3- methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-4-(5-cyclopropyl-7-tosyl-7H-pyrrolo [2,3-d]pyrimidin- 4-yl)-3-methylpiperazine-1-carboxylate (79 g, 160 mmol) in THF (500 ml) was added TBAF (400 ml, 1.0M in THF). The resulting mixture was stirred at room temperature overnight. After removal of solvent, the residue was diluted with H 2 O and extracted with DCM twice. The combined organic layers were dried over Na 2 SO 4 , filtered, and concentrated. The residue was purified by flash chromatography (0~50% ethyl acetate in petroleum ether) to afford tert- butyl (S)-4-(5-cyclopropyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-meth ylpiperazine-1- carboxylate (49 g, 88%) as light yellow solid. LC/MS ESI m/z: 358.5 (M+H) + . Step 5. tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5-cyclopropyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-4-(5-cyclopropyl-7H-pyrrolo [2,3-d]pyrimidin-4-yl)-3- methylpiperazine-1-carboxylate (18 g, 50 mmol) in DMF (180 mL) were added 2- bromoisonicotinonitrile (18 g, 100 mmol), CuI (4.8 g, 25 mmol), (+/-)-trans-1,2- diaminocyclohexane (1.7 g, 15 mmol), and K 3 PO 4 (32 g, 150 mmol). The resulting mixture was heated to 120 o C overnight. After cooling to room temperature, the reaction was filtered, and solvent was removed. The residue was purified by flash chromatography (0~30% EtOAc (with 50% DCM) in petroleum ether) to afford tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5- cyclopropyl- 7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carbox ylate (12 g, 51% yield) as a light yellow solid. LC/MS ESI m/z: 460.6 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.32 (s, 1H), 8.58 (d, J = 5.0 Hz, 1H), 8.50 (s, 1H), 7.77 (s, 1H), 7.33 (dd, J = 5.0, 1.2 Hz, 1H), 4.74 – 4.66 (m, 1H), 4.18 – 3.83 (m, 3H), 3.55 (t, J = 11.6 Hz, 1H), 3.39 – 3.09 (m, 2H), 2.06–1.99 (m, 1H), 1.50 (s, 9H), 1.24 (d, J = 6.5 Hz, 3H), 1.06 – 1.02 (m, 2H), 0.90 – 0.84 (m, 1H), 0.80 – 0.74 (m, 1H). Step 6. (S)-2-(5-cyclopropyl-4-(2-methylpiperazin-1-yl)-7H-pyrrolo[2 ,3-d] pyrimidin- 7-yl)isonicotinonitrile At 0 o C, to a solution of tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5-cyclopropyl-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (2.0 g, 4.4 mmol) in DCM (20 mL) was added TFA (0.9 mL, 13 mmol). The resulting mixture was stirred for 2 h then quenched with NaHCO3 (aq.) and extracted with DCM twice. The combined organic layers were dried over Na 2 SO 4 , filtered, and concentrated. The carried directly to the next step without further purification. LC/MS ESI m/z: 360 (M+H) + . Step 7. (S)-2-(5-cyclopropyl-4-(2-methyl-4-pivaloylpiperazin-1-yl)-7 H-pyrrolo [2,3- d]pyrimidin-7-yl)isonicotinonitrile At 0 o C, to a solution of (S)-2-(5-cyclopropyl-4- (2-methylpiperazin-1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (50 mg, 0.14 mmol) in DCM (5 mL) were added TEA (0.06 mL, 0.42 mmol) followed by pivaloyl chloride (34 mg, 0.28 mmol). The resulting mixture was stirred at that temperature for 20 minutes, then partitioned between DCM and water, and the organic layer was separated. The aqueous layer was extracted with DCM. The combined organic layer was washed with NaHCO 3 (aq.), dried over Na2SO4, filtered, and concentrated. The residue was purified by prep-HPLC to give (S)-2-(5- cyclopropyl-4-(2-methyl-4-pivaloylpiperazin-1-yl)-7H-pyrrolo [2,3-d]pyrimidin-7- yl)isonicotinonitrile (30 mg, 49%). LC/MS ESI m/z: 444 (M+H) + . 1 HNMR (400 MHz, CD 3 OD) δ 9.18 (s, 1H), 8.64 (d, J = 5.0 Hz, 1H), 8.46 (s, 1H), 7.85 (s, 1H), 7.53 (dd, J = 5.0, 1.2 Hz, 1H), 4.76 (s, 1H), 4.29 (m, 2H), 3.90 (d, J = 13.3 Hz, 1H), 3.66 – 3.58 (m, 1H), 3.49 – 3.38 (m, 2H), 2.14 – 2.07 (m, 1H), 1.34 (s, 9H), 1.19 (d, J = 6.6 Hz, 3H), 1.08 (dt, J = 8.1, 4.0 Hz, 2H), 0.88 (dd, J = 9.2, 4.3 Hz, 1H), 0.78 – 0.71 (m, 1H). The following compounds were prepared by an analogous procedure to the synthesis of compound 104 from the corresponding acid chlorides or acids using standard amide coupling reactions with coupling agents like HATU.
Example 3. Synthesis of 2-(5-(2-fluorophenyl)-4-(4-isobutyrylpiperazin-1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (Compound 106) Step 1. tert-butyl 4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl) piperazine-1- carboxylate To a solution of 4-chloro-5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (4.0 g, 9.2 mmol, prepared following the procedure outlined in compound 128) in EtOH (50 mL) were added tert-butyl piperazine-1-carboxylate (1.7 g, 9.2 mmol) and DIPEA (5.0 mL, 28 mmol), and the resulting mixture was heated to 100 o C overnight. The mixture was cooled to room temperature and concentrated. The residue was purified by flash chromatography (silica gel, 0~30%, ethyl acetate in petroleum ether) to afford tert-butyl 4-(5-iodo-7-tosyl-7H- pyrrolo[2,3-d]pyrimidin-4-yl)piperazine-1- carboxylate (4.5 g, 83%) as a white solid. LC/MS ESI m/z: 584 (M+H) + . Step 2. tert-butyl 4-(5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4- yl)piperazine-1-carboxylate A suspension of tert-butyl 4-[5-iodo-7-(4-methylbenzenesulfonyl) -7H-pyrrolo[2,3- d]pyrimidin-4-yl]piperazine-1-carboxylate (2.3 g, 4.0 mmol), (2-fluorophenyl)boronic acid (0.61 g, 4.4 mmol), K 2 CO 3 (1.1 g, 8.0 mmol ) and Pd(dppf)Cl 2 (0.29 g, 0.40 mmol) in dioxane-water (18 mL, v:v=5:1) was stirred at 95℃ under N 2 for 18h. After cooling to room temperature, the reaction mixture was partitioned between EtOAc and water. The organic layer was separated, and the aqueous layer was extracted with EtOAc twice. The combined organic phases were washed with brine, dried over anhydrous Na 2 SO 4 , filtered, and concentrated. The product was used in the next step without further purification. LC/MS ESI m/z: 552 (M+H) + Step 3. tert-butyl 4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)pipera zine- 1-carboxylate To a solution of tert-butyl 4-(5-(2-fluorophenyl)-7-tosyl- 7H-pyrrolo[2,3-d]pyrimidin- 4-yl)piperazine-1-carboxylate (1.8 g, 3.3 mmol) in THF (15 mL) was added TBAF (6.5 mL, 1.0M in THF). The resulting mixture was stirred at room temperature for 18h. After removal of solvent, the residue was dissolved in EtOAc, washed with water, and the aqueous layer was extracted with EtOAc twice. The combined organic phases were dried over anhydrous Na 2 SO 4 , filtered, and concentrated. The residue was purified by column chromatography on silica gel (0~60% EtOAc in petroleum ether) to give tert-butyl 4-[5-(2-fluorophenyl)-7H- pyrrolo[2,3-d] pyrimidin-4-yl]piperazine-1-carboxylate (1.2 g, 92%) as a white solid. LC/MS ESI m/z: 398 (M+H) + Step 4. tert-butyl 4-(7-(4-cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H-pyrrolo[2,3 - d]pyrimidin-4-yl)piperazine-1-carboxylate A suspension of tert-butyl 4-[5-(2-fluorophenyl)-7H-pyrrolo[2,3-d] pyrimidin-4- yl]piperazine-1-carboxylate (1.2 g, 3.0 mmol), 2-bromopyridine- 4-carbonitrile (0.66 g, 3.6 mmol), K 3 PO 4 (1.3 g, 6.0 mmol), CuI (0.17 g, 0.90 mmol) and trans-cyclohexane-1,2-diamine (0.10 g, 0.90 mmol) in DMF (30 mL) was stirred at 120℃ under N 2 for 18 h. After being cooled to room temperature, the solvent was removed. The residue was added to water and EtOAc. The organic layer was separated, and the aqueous layer was extracted with EtOAc twice. The combined organic phases were washed with brine, dried over anhydrous Na 2 SO 4 , filtered, and concentrated. The residue was purified by column chromatography on silica gel (0~60% EtOAc in petroleum ether) to give tert-butyl 4-[7-(4-cyanopyridin-2-yl)-5- (2- fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl]piperazine-1-c arboxylate (1.0 g, 2.0 mmol, 66%) as a white solid. LC/MS ESI m/z: 500 (M+H) + Step 5.2-(5-(2-fluorophenyl)-4-(piperazin-1-yl)-7H-pyrrolo[2,3-d] pyrimidin -7-yl) isonicotinonitrile To a solution of tert-butyl 4-[7-(4-cyanopyridin-2-yl)-5-(2-fluorophenyl) -7H- pyrrolo[2,3-d]pyrimidin-4-yl]piperazine-1-carboxylate (1.0 g, 2.0 mmol) in DCM (5.0 mL) was added TFA (4.5 mL, 60 mmol) and the reaction was stirred for 18 h at room temperature. The reaction mixture was quenched with NaHCO 3 (aq.) and extracted with DCM twice. The combined organic layers were washed with NaHCO 3 (aq.), dried over Na 2 SO 4 , filtered, and concentrated. The residue was used directly in next step without further purification. LC/MS ESI m/z: 400 (M+H) + . Step 6.2-(5-(2-fluorophenyl)-4-(4-isobutyrylpiperazin-1-yl)-7H-py rrolo[2,3-d] pyrimidin-7-yl)isonicotinonitrile To a solution of 2-(5-(2-fluorophenyl)-4-(piperazin-1-yl)-7H- pyrrolo[2,3-d] pyrimidin-7-yl) isonicotinonitrile (80 mg, 0.20 mmol) and TEA (0.14 mL, 1.0 mmol) in DCM (2.0 mL) was added 2-methylpropanoyl chloride (0.03 mL, 0.30 mmol). The resulting mixture was stirred at room temperature for 3 h. The mixture was diluted with water and DCM. The layers were separated, and the aqueous layer was extracted with DCM twice. The combined organic phases were washed with brine, dried over anhydrous Na 2 SO 4 , filtered, and concentrated. The residue was purified by prep-HPLC to give 2-(5-(2-fluorophenyl)-4-(4- isobutyrylpiperazin-1-yl)-7H-pyrrolo [2,3-d]pyrimidin-7-yl)isonicotinonitrile (12 mg, 12%) as a white solid. LC/MS ESI m/z: 470 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.39 (s, 1H), 8.62 (d, J = 5.0 Hz, 1H), 8.59 (s, 1H), 8.31 (s, 1H), 7.48 (td, J = 7.5, 1.7 Hz, 1H), 7.42 – 7.34 (m, 2H), 7.28 – 7.18 (m, 2H), 3.45 – 3.29 (m, 6H), 3.26 – 3.14 (m, 2H), 2.72 (dt, J = 13.5, 6.8 Hz, 1H), 1.08 (d, J = 6.8 Hz, 6H). The following compound was prepared by an analogous procedure to the synthesis of compound 106 from the corresponding acid chlorides. Example 4. Synthesis of (S)-2-(4-(4-(1-fluorocyclopropane-1-carbonyl)-2- methylpiperazin -1-yl)-5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-7- yl)isonicotinonitrile (Compound 115) Step 1. (S)-2-(4-(4-(1-fluorocyclopropane-1-carbonyl)-2-methylpipera zin-1-yl) -5-(2- fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonit rile To a solution of (S)-2-(5-(2-fluorophenyl)-4-(2-methylpiperazin-1-yl) -7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (50 mg, 0.12 mmol, prepared following the procedure outlined in the experimental of compound 102) in DMF (2 mL) were added DIPEA (0.1 mL, 0.60 mmol), 1-fluorocyclopropane-1-carboxylic acid (35 mg, 0.18 mmol) and HATU (91 mg, 0.24 mmol) respectively. The resulting reaction mixture was stirred at room temperature under N 2 overnight. The reaction mixture was partitioned between EtOAc and NaHCO 3 (aq.). The organic layer was separated, and the aqueous layer was extracted with EtOAc twice. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated. The residue was purified by flash column chromatography (silica gel, 0~30% EtOAc in petroleum ether), followed by prep-HPLC to provide (S)-2-(4-(4-(1- fluorocyclopropane-1-carbonyl)-2-methylpiperazin-1-yl)-5-(2- fluorophenyl)-7H-pyrrolo[2,3- d]pyrimidin-7-yl)isonicotinonitrile (14 mg, 24%) as a white solid. LC/MS ESI (m/z): 500 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.41 (s, 1H), 8.64 – 8.62 (m, 1H), 8.59 (s, 1H), 8.30 (s, 1H), 7.51 – 7.46 (m, 1H), 7.42 – 7.35 (m, 2H), 7.26 – 7.18 (m, 2H), 4.41 – 4.15 (m, 1H), 4.07 (d, J = 12.7 Hz, 1H), 3.88 (d, J = 13.2 Hz, 1H), 3.64 – 3.48 (m, 1H), 3.30 – 3.06 (m, 2H), 2.82 – 2.58 (m, 1H), 1.39 – 1.13 (m, 5H), 1.09 – 0.98 (m, 2H). The following compound was prepared by an analogous procedure to the synthesis of compound 115 from the corresponding acids. The acid (4,4,4-trifluoro-3,3-dimethylbutanoic acid) for compound 140 was prepared following the procedure outlined in the experimental of compound 141.
Example 5. Synthesis of (S)-2-(4-(4-isobutyryl-2-methylpiperazin-1-yl)-5-(pyridin-2- yl)- 7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (Compound 116) Step 1. tert-butyl (S)-3-methyl-4-(5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan -2-yl)-7- tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperazine-1-carboxyla te To a solution of tert-butyl (S)-4-(5-iodo-7-tosyl-7H-pyrrolo [2,3-d]pyrimidin-4-yl)-3- methylpiperazine-1-carboxylate (3.0 g, 5.0 mmol, prepared following the procedure outlined in compound 128) in dioxane (40 mL) were added 4,4,5,5-tetramethyl-1,3,2-dioxaborolane (2.9 mL, 20 mmol), X-Phos (0.24 g, 0.50 mmol), TEA (3.5 mL, 25 mmol) and Pd 2 (dba) 3 (0.46 g, 0.50 mmol). The resulting mixture was stirred at 95 o C overnight. After cooling to room temperature, the reaction was quenched with water and extracted with DCM twice. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated to afford tert-butyl (S)-3-methyl-4-(5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan- 2-yl)-7-tosyl- 7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperazine-1-carboxylate which was used directly in the next step without further purification. LC/MS ESI m/z: 598 (M+H) + . Step 2. tert-butyl (S)-3-methyl-4-(5-(pyridin-2-yl)-7-tosyl-7H-pyrrolo[2,3-d] pyrimidin-4-yl)piperazine-1-carboxylate To a solution of tert-butyl (S)-3-methyl-4-(5-(4,4,5,5-tetramethyl- 1,3,2-dioxaborolan- 2-yl)-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperazine-1-c arboxylate (3.0 g, 5.0 mmol) in dioxane (40 mL) and H 2 O (8 mL) were added 2-bromopyridine (0.96 mL, 10 mmol), K 2 CO 3 (3.5 g, 25 mmol) and Pd(dppf)Cl 2 (0.37 g, 0.50 mmol). The resulting mixture was heated to 90 o C overnight. After cooling to room temperature, the solvent was removed and the residue was purified by flash column chromatography (silica gel, 0~50%, ethyl acetate in petroleum ether) to afford tert-butyl (S)-3-methyl-4-(5-(pyridin-2-yl)-7-tosyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl) piperazine-1-carboxylate (2.0 g, 73%) as a yellow solid. LC/MS ESI m/z: 549 (M+H) + . Step 3. tert-butyl (S)-3-methyl-4-(5-(pyridin-2-yl)-7H-pyrrolo[2,3-d]pyrimidin- 4-yl) piperazine-1-carboxylate To a solution of tert-butyl (S)-3-methyl-4-(5-(pyridin-2-yl)-7-tosyl-7H- pyrrolo[2,3- d]pyrimidin-4-yl)piperazine-1-carboxylate (2.0 g, 3.6 mmol) in THF (15 mL) was added TBAF (14.5 mL, 1.0M in THF) and the resulting mixture was stirred at room temperature overnight. The reaction was quenched with water and extracted with EtOAc twice. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated. The residue was purified by flash column chromatography (silica gel, 0~10%, methanol in dichloromethane) to afford tert-butyl (S)-3-methyl-4-(5-(pyridin-2-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)piperazine-1-carboxylate (1.4 g, 97%) as a yellow solid. LC/MS ESI m/z: 395 (M+H) + . Step 4. tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5-(pyridin-2-yl)-7H-pyrrolo [2,3-d] pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-3-methyl-4-(5-(pyridin-2-yl)-7H-pyrrolo[2,3- d]pyrimidin-4-yl)piperazine-1-carboxylate (1.4 g, 3.5 mmol) in DMF (20 mL) were added 2- bromoisonicotinonitrile (1.3 g, 7.1 mmol), CuI (0.68 g, 3.5 mmol), trans-cyclohexane-1,2- diamine (0.41 g, 3.5 mmol) and K 3 PO 4 (2.26 g, 10.6 mmol). The resulting mixture was heated to 120 o C overnight. After cooling to room temperature. The reaction was partitioned between EtOAc, and water and the organic layer was separated. The aqueous layer was extracted with EtOAc twice, and the combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50%, ethyl acetate in petroleum ether) to afford tert-butyl (S)- 4-(7-(4-cyanopyridin-2-yl)-5-(pyridin-2-yl)-7H-pyrrolo[2,3-d ]pyrimidin-4-yl)-3- methylpiperazine-1-carboxylate (1.7 g, 96%) as a yellow solid. LC/MS ESI m/z: 497 (M+H) + . Step 5. (S)-2-(4-(2-methylpiperazin-1-yl)-5-(pyridin-2-yl)-7H-pyrrol o[2,3-d] pyrimidin-7-yl)isonicotinonitrile To a solution of tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5-(pyridin-2-yl) -7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (900 mg, 1.8 mmol) in DCM (5 mL) was added HCl (5 mL, 4M in dioxane). The resulting mixture was stirred at room temperature for 1 h. After removal of solvent, the residue was dissolved in DCM and washed with NaHCO 3 (aq.). The aqueous layer was extracted with DCM twice and the combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated. The residue was used directly in the next step without further purification. LC/MS ESI m/z: 397 (M+H) + . Step 6. (S)-2-(4-(4-isobutyryl-2-methylpiperazin-1-yl)-5-(pyridin-2- yl)-7H-pyrrolo [2,3-d]pyrimidin-7-yl)isonicotinonitrile At 0 o C, to a solution of (S)-2-(4-(2-methylpiperazin-1-yl)-5-(pyridin-2-yl) -7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (100 mg, 0.25 mmol) and TEA (0.17 mL, 1.2 mmol) in DCM (3 mL) was added isobutyryl chloride (0.05 mL, 0.5 mmol) and the resulting mixture was stirred at room temperature for 1 h. The reaction was quenched with water and extracted with DCM twice. The combined organic layers were washed with NaHCO 3 (aq.), brine, dried over Na 2 SO 4 , filtered, and concentrated. The residue was purified by prep-HPLC to afford (S)-2-(4-(4-isobutyryl-2-methylpiperazin-1-yl)-5-(pyridin-2- yl)-7H-pyrrolo[2,3- d]pyrimidin-7-yl)isonicotinonitrile (24 mg, 19%) as a light yellow solid. LC/MS ESI m/z: 467 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.40 (s, 1H), 8.82 – 8.68 (m, 1H), 8.64 (d, J = 4.9 Hz, 1H), 8.61 – 8.50 (m, 2H), 7.87 – 7.76 (m, 1H), 7.65 (t, J = 8.7 Hz, 1H), 7.42 (dd, J = 5.0, 1.0 Hz, 1H), 7.35 – 7.28 (m, 1H), 4.62 – 4.25 (m, 1H), 4.21 – 4.06 (m, 1H), 3.77 (d, J = 10.1 Hz, 1H), 3.52 (t, J = 15.0 Hz, 1H), 3.39 – 2.99 (m, 2H), 2.83 – 2.46 (m, 2H), 1.18 – 1.04 (m, 8H), 0.92 (d, J = 6.5 Hz, 1H). The following compounds were prepared by an analogous procedure to the synthesis of compound 116 from the corresponding acid chlorides and aryl halides. Example 6. Synthesis of 2-(5-(2-fluorophenyl)-4-((2S,5R)-4-isobutyryl-2,5- dimethylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)ison icotinonitrile (Compound 118) Step 1.5-bromo-4-chloro-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine At 0 o C, to a suspension of NaH (1 g, 26 mmol, 60% wt%) in anhydrous DMF (25 mL) was added 5-bromo-4-chloro-7H-pyrrolo[2,3-d]pyrimidine (5.0 g, 22 mmol) in portions. The resulting mixture was stirred at the same temperature for 20 minutes before 4- methylbenzenesulfonyl chloride (4.9 g, 26 mmol) was added in portions. After addition, the reaction was stirred at room temperature overnight. The reaction was poured into ice water and the precipitate was collected by filtration. The solid was dried under vacuum to provide 5-bromo-4-chloro-7-tosyl-7H- pyrrolo[2,3-d]pyrimidine (5.4 g, 65%) as a white solid. LC/MS ESI (m/z): 386, 388 (M+H) + . Step 2. tert-butyl (S)-4-(5-bromo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3 - methylpiperazine-1-carboxylate To a solution of 5-bromo-4-chloro-7-(4-methylbenzenesulfonyl)-7H- pyrrolo[2,3- d]pyrimidine (3.0 g, 7.8 mmol) in DIPEA (9.5 mL, 55 mmol) was added tert-butyl (S)-3- methylpiperazine-1-carboxylate (6.2 mg, 31 mmol). The resulting mixture was heated to 150 o C for 3 h under N 2 . After cooling to room temperature, the solvent was removed and the residue was purified by flash column chromatography to afford tert-butyl (S)-4-(5-bromo-7- tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-methyl piperazine-1-carboxylate (3.5 g, 83%) as a solid. LC/MS ESI m/z: 550, 552 (M+H) + . Step 3. tert-butyl (S)-3-methyl-4-(5-phenyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin- 4-yl) piperazine-1-carboxylate To a solution of tert-butyl (S)-4-(5-bromo-7-tosyl-7H-pyrrolo [2,3-d]pyrimidin-4-yl)- 3-methylpiperazine-1-carboxylate (1.5 g, 2.7 mmol) in dioxane (20 mL) and H 2 O (2 mL) were added phenylboronic acid (667 mg, 5.46 mmol), K 2 CO 3 (1.13 g, 8.19 mmol) and Pd(dppf)Cl 2 (200 mg, 0.27 mmol). The resulting mixture was stirred at 90 o C overnight under N 2 . After cooling to room temperature, the solvent was removed and the residue was purified by flash column chromatography (silica gel, 0~20%, ethyl acetate in petroleum ether) to afford tert-butyl (S)-3-methyl-4-(5-phenyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin- 4-yl) piperazine-1-carboxylate (1.4 g, 94%) as a yellow solid. LC/MS ESI m/z: 548 (M+H) + . Step 4. tert-butyl (S)-3-methyl-4-(5-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl) piperazine-1-carboxylate To a solution of tert-butyl (S)-3-methyl-4-(5-phenyl-7-tosyl-7H- pyrrolo[2,3- d]pyrimidin-4-yl)piperazine-1-carboxylate (1.40 g, 2.56 mmol) in THF (2 mL) was added TBAF (5.0 mL, 1.0 M in THF) and the resulting mixture was stirred at room temperature overnight. The reaction was quenched with water and extracted with EtOAc twice. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated. The residue was purified by flash column chromatography (silica gel, 0~60%, ethyl acetate in petroleum ether) to afford tert-butyl (S)-3-methyl-4-(5-phenyl-7H- pyrrolo[2,3-d]pyrimidin-4-yl)piperazine-1- carboxylate (900 mg, 90%) as a yellow solid. LC/MS ESI m/z: 394 (M+H) + . Step 5. tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5-phenyl-7H-pyrrolo[2,3-d] pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-3-methyl-4-(5-phenyl-7H-pyrrolo [2,3-d]pyrimidin-4- yl)piperazine-1-carboxylate (900 mg, 2.30 mmol) in DMF (20 mL) were added 2- bromoisonicotinonitrile (1.2 g, 6.6 mmol), trans-cyclohexane-1,2-diamine (377 mg, 3.31 mmol), CuI (628 mg, 3.31 mmol) and K 3 PO 4 (2.10 g, 9.93 mmol). The resulting mixture was heated to 120 o C overnight. After cooling to room temperature, the reaction mixture was partitioned between EtOAc, and water and the organic layer was separated. The aqueous layer was extracted with EtOAc twice. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated. The residue was purified by flash column chromatography (silica gel, 0~30%, ethyl acetate in petroleum ether) to afford tert-butyl (S)- 4-(7-(4-cyanopyridin-2-yl)-5-phenyl-7H-pyrrolo[2,3-d]pyrimid in-4-yl) -3-methylpiperazine- 1-carboxylate (800 mg, 71%) as a yellow solid. LC/MS ESI m/z: 496 (M+H) + . Step 6. (S)-2-(4-(2-methylpiperazin-1-yl)-5-phenyl-7H-pyrrolo[2,3-d] pyrimidin-7-yl) isonicotinonitrile At 0 o C, to a solution of tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl) -5-phenyl-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (800 mg, 1.62 mmol) in DCM (3 mL) was added HCl (10 mL, 4.0 M in dioxane). The resulting mixture was stirred at room temperature for 0.5 h. After removal of solvent, the residue was diluted with DCM, washed with NaHCO 3 (aq.), and the organic layer was extracted with DCM twice. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated to give (S)-2-(4-(2-methylpiperazin-1-yl)-5-phenyl-7H-pyrrolo[2,3-d] pyrimidin- 7-yl)isonicotinonitrile (500 mg, 78%). LC/MS ESI m/z: 396 (M+H) + . The product was used directly in the next step without further purification. Step 7. (S)-2-(4-(4-isobutyryl-2-methylpiperazin-1-yl)-5-phenyl-7H-p yrrolo[2,3-d] pyrimidin-7-yl)isonicotinonitrile At 0 o C, to a solution of (S)-2-(4-(2-methylpiperazin-1-yl)-5-phenyl-7H-pyrrolo[2,3-d] pyrimidin-7-yl)isonicotinonitrile (40 mg, 0.10 mmol) in DCM (3 mL) was added TEA (0.30 mL, 0.30 mmol), followed by isobutyryl chloride (0.02 mL, 0.2 mmol) dropwise. The resulting mixture was stirred at room temperature overnight. The reaction was quenched with water and extracted with DCM twice. The combined organic layers were washed with NaHCO 3 (aq.), dried over Na 2 SO 4 , filtered, and concentrated. The residue was purified by flash column chromatography (silica gel, 0~30%, ethyl acetate in petroleum ether) to give the product which was further purified by prep-HPLC to afford (S)-2-(4-(4-isobutyryl-2- methylpiperazin-1-yl)-5-phenyl-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (22 mg, 46%) as a white solid. LC/MS ESI m/z: 466 (M+H) + . 1 H NMR (400 MHz, CD 3 OD) δ 9.27 (s, 1H), 8.69 (d, J = 5.0 Hz, 1H), 8.54 (s, 1H), 8.23 (s, 1H), 7.59 – 7.55 (m, 3H), 7.50 (t, J = 7.6 Hz, 2H), 7.43 – 7.38 (m, 1H), 4.30 – 4.12 (m, 1.5H, rotamers), 3.88 (m, 1H), 3.67 – 3.50 (m, 1.5H, rotamers), 3.22 – 3.03 (m, 2H), 2.96 – 2.78 (m, 1H), 2.70 – 2.60 (m, 1H), 1.10 – 0.99 (m, 7.5H, rotamers), 0.87 (m, 1.5H, rotamers). The following compounds were prepared by an analogous procedure to the synthesis of compound 118 from the corresponding acid chlorides.
Example 7. Synthesis of (R)-2-(4-(4-isobutyryl-3-methylpiperazin-1-yl)-5-phenyl-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (Compound 119) Step 1. tert-butyl (R)-2-methyl-4-(5-phenyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin- 4- yl)piperazine-1-carboxylate To a solution of tert-butyl (R)-4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2- methylpiperazine-1-carboxylate (1.5 g, 2.1 mmol) in dioxane (10 mL) and water (180 mg,10 mmol) were added phenylboronic acid (490 mg, 4.0 mmol), K 2 CO 3 (1.4 g, 10 mmol) and Pd(dppf)Cl 2 (150 mg, 0.20 mmol). Then the resulting mixture was stirred at 80℃ under N 2 atmosphere overnight. After being cooled down to room temperature, the reaction mixture was filtered. The filtrate was partitioned between EtOAc and water, organic layer was separated, the aqueous layer was extracted with EtOAc twice, the combined organic layers were dried over Na 2 SO 4 , filtered and concentrated to afford crude product tert-butyl (R)-2- methyl-4-(5-phenyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)p iperazine-1-carboxylate (1.6 g) as a yellow solid. LC/MS ESI m/z: 548(M+H) + . Step 2. tert-butyl (R)-2-methyl-4-(5-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4- yl)piperazine-1-carboxylate To a solution of tert-butyl (R)-2-methyl-4-(5-phenyl-7-tosyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)piperazine-1-carboxylate (1.6 g) in THF (5 ml) was added TBAF (4.0 ml, 1.0 M in THF). The resulting mixture was stirred at room temperature overnight. After removal of solvent under reduced pressure, the residue was partitioned between EtOAc and water, organic layer was separated, the aqueous layer was extracted with EtOAc twice, the combined organic layers were dried over Na 2 SO 4 , filtered and concentrated to afford crude product which was further purified by flash column chromatography (30~80% EtOAc in petroleum ether) to afford tert-butyl (R)-2-methyl-4-(5-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4- yl)piperazine-1-carboxylate (790 mg, 97% yield in two steps) as a gray solid. LC/MS ESI m/z: 394 (M+H) + . Step 3. tert-butyl (R)-4-(7-(4-cyanopyridin-2-yl)-5-phenyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2-methylpiperazine-1-carboxylate To a solution of tert-butyl (R)-2-methyl-4-(5-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4- yl)piperazine-1-carboxylate (790 mg, 2.0 mmol) in DMF (5 mL) was added 2- bromopyridine-4-carbonitrile (730 mg, 4.0 mmol), CuI (110 mg, 0.60 mmol), trans-1,2- diaminocyclohexane (68 mg, 0.60 mmol) and K 3 PO 4 (1.3 g, 6.0 mmol). The resulting mixture was heated to 120 o C overnight under N 2 atmosphere. After being cooled down to room temperature, the reaction was partitioned between EtOAc and water, organic layer was separated, aqueous layer was extracted with EtOAc twice, the combined organic layers were washed with brine, dried over Na 2 SO 4 , filter and concentrated. The residue was purified by flash column chromatography (0~30% EtOAc in petroleum ether) to afford tert-butyl (R)-4- (7-(4-cyanopyridin-2-yl)-5-phenyl-7H-pyrrolo[2,3-d]pyrimidin -4-yl)-2-methylpiperazine-1- carboxylate (680 mg, 69% yield) as a white solid. LC/MS ESI m/z: 496 (M+H) + . Step 4. (R)-2-(4-(3-methylpiperazin-1-yl)-5-phenyl-7H-pyrrolo[2,3-d] pyrimidin-7- yl)isonicotinonitrile At 0 o C, to a solution of tert-butyl (R)-4-(7-(4-cyanopyridin-2-yl)-5-phenyl-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2-methylpiperazine-1-carboxyla te (490 mg, 1.0 mmol) in DCM (10 mL) was added HCl (15 mL, 4.0 M in dioxane), the resulting mixture was stirred at room temperature for 4 h. After removal of solvent, the residue was used to the next step directly. (R)-2-(4-(3-methylpiperazin-1-yl)-5-phenyl-7H-pyrrolo[2,3-d] pyrimidin-7- yl)isonicotinonitrile. (500 mg, contain solvent) LC/MS ESI m/z: 396 (M+H) + . Step 5. (R)-2-(4-(4-isobutyryl-3-methylpiperazin-1-yl)-5-phenyl-7H-p yrrolo[2,3- d]pyrimidin-7-yl)isonicotinonitrile At 0 o C, to a solution of (R)-2-(4-(3-methylpiperazin-1-yl)-5-phenyl-7H-pyrrolo[2,3- d]pyrimidin-7-yl)isonicotinonitrile. (94 mg, 0.20 mmol) in DCM (2 mL) was added TEA (0.11 mL, 80 mg, 0.80 mmol), followed by di-isobutyryl chloride (43 mg, 0.40 mmol) dropwise. The resulting mixture was stirred at room temperature for 1 h. The solvent was removed under reduced pressure. The residue was purified by prep-HPLC to afford (R)-2-(4- (4-isobutyryl-3-methylpiperazin-1-yl)-5-phenyl-7H-pyrrolo[2, 3-d]pyrimidin-7- yl)isonicotinonitrile (39 mg, 42%) as a white solid. LC/MS ESI m/z: 466 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.41 (s, 1H), 8.63 (dd, J = 5.0, 0.6 Hz, 1H), 8.59 (s, 1H), 8.23 (s, 1H), 7.63 – 7.53 (m, 2H), 7.52 – 7.44 (m, 2H), 7.44 – 7.34 (m, 2H), 4.86 – 4.14 (m, 1H), 4.06 – 3.72 (m, 2H), 3.66 – 3.21 (m, 1H), 3.16 – 2.34 (m, 4H), 1.39 – 0.97 (m, 9H). The following compound was prepared by the procedures similar to the synthesis of example above from the corresponding acyl chloride. Example 8. Synthesis of (R)-2-(5-cyclopropyl-4-(3-methyl-4-pivaloylpiperazin-1-yl)-7 H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (Compound 122) C ompound 122 At 0 o C, to a solution of (R)-2-(5-cyclopropyl-4-(3-methylpiperazin-1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (100 mg, 0.28 mmol) in DCM (3 mL) was added TEA (85 mg, 0.84 mmol), followed by pivaloyl chloride (67 mg, 0.56 mmol) dropwise. The resulting mixture was stirred at room temperature for 30 minutes. The reaction was quenched with ice water and extracted with DCM twice, The combined organic layers were washed with NaHCO 3 (aq.), dried over Na 2 SO 4 , filtered, concentrated, the residue was purified by flash chromatography (0~35% ethyl acetate in petroleum ether) to give solid product which was further purified by prep-HPLC to afford (R)-2-(5-cyclopropyl-4-(3- methyl-4-pivaloylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin- 7-yl)isonicotinonitrile (42 mg, 34%) as a white solid. LC/MS ESI m/z: 444 (M+H) + . 1 H NMR (400 MHz, CD 3 OD) δ 9.19 – 9.15 (m, 1H), 8.65 – 8.62 (m, 1H), 8.44 (s, 1H), 7.86 (d, 1H), 7.52 (dd, J = 5.0, 1.3 Hz, 1H), 4.82 – 4.76 (m, 1H), 4.53 – 4.48 (m, 1H), 4.40 – 4.26 (m, 1H), 4.15 – 4.10 (m, 1H), 3.72 – 3.46 (m, 1H), 3.44 – 3.38 (m, 1H), 3.16 – 3.06 (m, 1H), 2.11 – 2.05 (m, 1H), 1.32 (s, 9H), 1.30 – 1.25 (m, 3H), 1.12 – 1.06 (m, 2H), 0.95 – 0.89 (m, 1H), 0.75 – 0.69 (m, 1H).
Example 9. Synthesis of (R)-2-(4-(4-(2-fluoro-2-methylpropanoyl)-3-methylpiperazin-1 - yl)-5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isoni cotinonitrile (Compound 126) Step 1. tert-butyl (R)-4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2- methylpiperazine-1-carboxylate To a solution of 4-chloro-5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (50 g, 120 mmol) in EtOH (500 mL) was added tert-butyl (R)-2-methylpiperazine-1-carboxylate (27.7 g, 138 mmol). The resulting mixture was stirred at 90 o C under N 2 atmosphere for 16 h. After cooled down to room temperature, solvent was removed and the residue was quenched with H 2 O and EtOAc, organic layer was separated, the aqueous phase was extracted with EtOAc twice, the combined organic layers were dried over Na 2 SO 4 , filtered and concentrated, the residue was triturated with petroleum ether/EtOAc (10:1) and filtered to afford tert-butyl (R)- 4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2-methylp iperazine-1-carboxylate (48 g, 70%) as a light yellow solid. LC/MS ESI (m/z): 598 (M+H) + . Step 2. tert-butyl (R)-4- (5- (2-fluorophenyl) -7-tosyl-7H-pyrrolo [2,3-d]pyrimidin-4- yl) -2-methylpiperazine-1-carboxylate To a solution of tert-butyl (R)-4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl) -2- methylpiperazine-1-carboxylate (1.5 g, 2.5 mmol) in dioxane (50 mL) and water (5 mL) were added (2-fluorophenyl)boronic acid (385 mg, 2.75 mmol), K 3 PO 4 (1.0 g, 5.0 mmol), and Pd(dppf)Cl 2 (190 mg, 0.25 mmol), The resulting mixture was heated to 90 o C overnight. After being cooled down to room temperature, solvent was removed and the residue was purified by flash chromatography (silica gel, 0~60% EtOAc in petroleum ether) to afford tert-butyl (R)-4-(5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin -4-yl) -2-methylpiperazine-1- carboxylate (1.4 g, 97%) as a white solid. LC/MS ESI (m/z): 566 (M+H) + . Step 3. tert-butyl (R)-4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2 - methylpiperazine-1-carboxylate To a solution of tert-butyl (R)-4-(5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2-methylpiperazine-1-carboxylate (1.38 g, 2.44 mmol) in THF (30 mL) were added TBAF (15 mL, 1.0M in THF). The reaction mixture was stirred at room temperature overnight. The solvent was removed, and the residue was purified by flash column chromatography (silica gel, 0~64% EtOAc in petroleum ether) to afford tert-butyl (R)-4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2 -methylpiperazine-1- carboxylate (870 mg, 86%) as a colorless oil. LC/MS ESI (m/z): 412 (M+H) + . Step 4. tert-butyl (R)-4-(7-(4-cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H-pyrrolo [2,3- d]pyrimidin-4-yl)-2-methylpiperazine-1-carboxylate To the solution of tert-butyl (R)-4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4- yl)-2-methylpiperazine-1-carboxylate (870 mg, 2.1 mmol) in DMF (10 mL) were added CuI (460 mg, 2.1 mmol), K 3 PO 4 (900 mg, 4.2 mmol), trans-cyclohexane-1,2-diamine (480 mg, 4.2 mmol) and 2-bromoisonicotinonitrile (770 mg, 4.2 mmol) respectively. The resulting reaction mixture was stirred at 120℃ under N 2 overnight. After being cooled down to room temperature, the reaction mixture was partitioned between EtOAc and water, organic layer was separated, the aqueous layer was extracted with EtOAc twice, the combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography to afford tert-butyl (R)-4-(7-(4-cyanopyridin-2-yl)- 5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2-methyl piperazine-1-carboxylate (1.0 g, 92%) as white solid. LC/MS ESI m/z: 514 (M+H) + . Step 5. (R)-2-(5-(2-fluorophenyl)-4-(3-methylpiperazin-1-yl)-7H-pyrr olo[2,3- d]pyrimidin-7-yl)isonicotinonitrile At 0 o C, to a solution of tert-butyl (R)-4-(7-(4-cyanopyridin-2-yl)-5-(2-fluorophenyl)- 7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2-methylpiperazine-1-carbox ylate (900 mg, 1.7 mmol) in DCM (10 mL) was added TFA (3 mL). The resulting mixture was stirred at the same temperature for 2 h. The reaction was quenched with NaHCO 3 (aq.), extracted with DCM twice, the combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was used in the next step directly. LC/MS ESI m/z: 414.5 (M+H) + . Step 6. (R)-2-(4-(4-(2-fluoro-2-methylpropanoyl)-3-methylpiperazin-1 -yl)-5-(2- fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonit rile To the solution of (R)-2-(5-(2-fluorophenyl)-4-(3-methylpiperazin-1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (100 mg, 0.24 mmol) in DMF (4 mL) were added DIPEA (25 mg, 0.3 mmol), 2-fluoro-2-methylpropanoic acid (0.02 mL, 0.24 mmol) and HATU (180 mg, 0.48 mmol) respectively. The resulting reaction mixture was stirred at room temperature under N 2 overnight. The reaction mixture was partitioned between EtOAc and water, organic layer was separated, aqueous layer was extracted with EtOAc twice, the combined organic payers were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated under reduced pressure, the residue was purified by flash column chromatography to afford (R)-2-(4-(4-(2-fluoro-2-methylpropanoyl)-3-methylpiperazin-1 -yl)- 5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicoti nonitrile (12 mg, 10%) as a white solid. LC/MS ESI (m/z): 502.6 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.41 (s, 1H), 8.65 – 8.61 (m, 1H), 8.58 (s, 1H), 8.30 (s, 1H), 7.53 – 7.47 (m, 1H), 7.42 – 7.36 (m, 2H), 7.33 – 7.27 (m, 1H), 7.25 – 7.19 (m, 1H), 4.76 – 4.62 (m, 1H), 3.97 – 3.55 (m, 3H), 3.10 – 2.40 (m, 3H), 1.63 – 1.58 (m, 3H), 1.56 – 1.52 (m, 3H), 1.33 – 1.11 (m, 3H). The following compound was prepared by the procedure similar to the synthesis of example above from the corresponding acid.
Example 10. Synthesis of (S)-2-(4-(2-methyl-4-(1-methylcyclopropane-1- carbonyl)piperazin-1-yl)-5-(pyridin-2-yl)-7H-pyrrolo[2,3-d]p yrimidin-7- yl)isonicotinonitrile (Compound 127) C ompound 127 Step 1. (S)-2-(4-(2-methyl-4-(1-methylcyclopropane-1-carbonyl)pipera zin-1-yl)-5- (pyridin-2-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinoni trile To a solution of (S)-2-(4-(2-methylpiperazin-1-yl)-5-(pyridin-2-yl)-7H-pyrrol o[2,3- d]pyrimidin-7-yl)isonicotinonitrile (100 mg, 0.25 mmol) in DMF (3 mL) were added 1- methylcyclopropane-1-carboxylic acid (38 mg, 0.37 mmol), DIPEA (0.13 mL, 0.75 mmol) and HATU (190 mg, 0.50 mmol). The resulting mixture was stirred at room temperature overnight. The reaction was quenched with water, extracted with EtOAc twice, the combined organic layers were washed with NaHCO 3 (aq.) and brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by prep-HPLC to afford (S)-2-(4-(2-methyl-4-(1- methylcyclopropane-1-carbonyl)piperazin-1-yl)-5-(pyridin-2-y l)-7H-pyrrolo[2,3- d]pyrimidin-7-yl)isonicotinonitrile (27 mg, 21%) as a white solid. LC/MS ESI m/z: 479 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.40 (s, 1H), 8.74 (d, J = 4.3 Hz, 1H), 8.64 (dd, J = 5.0, 0.6 Hz, 1H), 8.60 (s, 1H), 8.59 (s, 1H), 7.84 (t, J = 7.3 Hz, 1H), 7.66 (d, J = 7.8 Hz, 1H), 7.42 (dd, J = 5.0, 1.3 Hz, 1H), 7.34 – 7.29 (m, 1H), 4.38 – 4.15 (m, 2H), 3.97 – 3.91 (m, 1H), 3.66 (d, J = 8.1 Hz, 1H), 3.21 – 2.77 (m, 3H), 1.29 (s, 3H), 1.02 (s, 3H), 0.94 – 0.86 (m, 2H), 0.62 – 0.50 (m, 2H).
Example 11. Synthesis of (S)-2-(4-(2-methyl-4-(1-methylcyclopropane-1- carbonyl)piperazin-1-yl)-5-phenyl-7H-pyrrolo[2,3-d]pyrimidin -7-yl)isonicotinonitrile (Compound 128) Step 1.4-chloro-5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine At 0℃, to a solution of 4-chloro-5-iodo-7H-pyrrolo[2,3-d]pyrimidine (200 g, 0.71 mol) and 4-methylbenzene-1-sulfonyl chloride (180 g, 0.93 mol) in acetone (2 L) was added dropwise 2M NaOH (0.53 L). After addition, the reaction was allowed to warm up to room temperature and stirred for another 3 hours. The precipitation was collected by filtration and washed with water twice and dried over oil pump.4-chloro-5-iodo-7-tosyl-7H-pyrrolo[2,3- d]pyrimidine (300 g, 95%) as an off white solid. LC/MS ESI (m/z): 434 (M+H) + . Step 2. tert-butyl (S)-4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3- methylpiperazine-1-carboxylate To a solution of 4-chloro-5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (90 g, 0.21 mol) in DIPEA (600 mL) was added tert-butyl (S)-3-methylpiperazine-1-carboxylate (81 g, 0.42 mol). The resulting mixture was heated to 140 o C for 3 h. After being cooled down to room temperature, solvent was removed and the residue was purified by flash column chromatography (silica gel, 0~30%, ethyl acetate in petroleum ether) to afford tert-butyl (S)- 4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylp iperazine-1-carboxylate (100 g, 73%) as a white solid. LC/MS ESI m/z: 598 (M+H) + . Step 3. tert-butyl (S)-3-methyl-4-(5-phenyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin- 4- yl)piperazine-1-carboxylate To a solution of tert-butyl (S)-4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3- methylpiperazine-1-carboxylate (30 g, 50 mmol) in dioxane-H 2 O (300 mL, V:V=5:1) were added phenylboronic acid (12.3 g, 101 mmol), K 2 CO 3 (20.8 g, 151 mmol) and Pd(dppf)Cl 2 (3.7 g, 5.0 mmol). The resulting mixture was heated to 90 o C overnight. After being cooled down to room temperature, solvent was filtered. The filtrate was concentrated and purified by flash column chromatography (silica gel, 0~30%, ethyl acetate in petroleum ether) to afford tert-butyl (S)-3-methyl-4-(5-phenyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin- 4-yl)piperazine-1- carboxylate (23 g, 84%) as a white solid. LC/MS ESI m/z: 548 (M+H) + . Step 4. (S)-4-(2-methylpiperazin-1-yl)-5-phenyl-7-tosyl-7H-pyrrolo[2 ,3-d]pyrimidine To a solution of tert-butyl (S)-3-methyl-4-(5-phenyl-7-tosyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)piperazine-1-carboxylate (23 g, 42 mmol) in DCM (200 mL) was added TFA (30 mL). The resulting mixture was stirred at room temperature for 2 h. After removal of solvent, the residue was diluted with DCM, washed with NaHCO 3 (aq.), the organic layer was extracted with DCM twice, the combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was used in the next step directly (S)-4- (2-methylpiperazin-1-yl)-5-phenyl-7-tosyl-7H-pyrrolo[2,3-d]p yrimidine. LC/MS ESI m/z: 448 (M+H) + . Step 5. (S)-(3-methyl-4-(5-phenyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin -4-yl)piperazin- 1-yl)(1-methylcyclopropyl)methanone To the solution of (S)-4-(2-methylpiperazin-1-yl)-5-phenyl-7-tosyl-7H-pyrrolo[2 ,3- d]pyrimidine (10.5 g, 23.4 mmol) in DMF (200 mL) were added DIPEA (12.2 mL, 70.5 mmol), 1-methylcyclopropane-1-carboxylic acid (3.5 g, 35 mmol) and HATU (1.1 g, 28 mmol) respectively. The resulting reaction mixture was stirred at room temperature under N 2 overnight. The reaction mixture was partitioned between EtOAc and water, organic layer was separated, aqueous layer was extracted with EtOAc twice, the combined organic payers were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated under reduced pressure. The residue was purified by flash column chromatography (silica gel, 0~30% EtOAc in petroleum) to afford (S)-(3-methyl-4-(5-phenyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin -4- yl)piperazin-1-yl)(1-methylcyclopropyl)methanone (9.6 g, 79%) as a solid. LC/MS ESI m/z: 530 (M+H) + . Step 6. (S)-(3-methyl-4-(5-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)pi perazin-1-yl)(1- methylcyclopropyl)methanone To a solution of (S)-(3-methyl-4-(5-phenyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin -4- yl)piperazin-1-yl)(1-methylcyclopropyl)methanone (9.8 g, 19 mmol) in THF (100 mL) was added TBAF (93 mL, 1.0 M in THF). The resulting mixture was stirred at room temperature overnight. The reaction was quenched with water, extracted with EtOAc twice, the combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~60%, ethyl acetate in petroleum ether) to afford (S)-(3-methyl-4-(5-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4- yl)piperazin-1-yl)(1-methylcyclopropyl)methanone (6.0 g, 87%) as a white solid. LC/MS ESI m/z: 376 (M+H) + . Step 7. (S)-2-(4-(2-methyl-4-(1-methylcyclopropane-1-carbonyl)pipera zin-1-yl)-5- phenyl-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile To a solution of (S)-(3-methyl-4-(5-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4- yl)piperazin-1-yl)(1-methylcyclopropyl)methanone (6.2 g, 26 mmol) in DMF (60 mL) were added 2-fluoroisonicotinonitrile (5.6 g, 46 mmol) and Cs 2 CO 3 (42.4 g, 131 mmol). The resulting mixture was heated to 40 o C for 3 h. After being cooled down to room temperature. The reaction was quenched with water, extracted with EtOAc twice, the combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~40%, ethyl acetate in petroleum ether) to give (S)-2-(4-(2-methyl-4-(1-methylcyclopropane-1-carbonyl)pipera zin-1-yl)-5- phenyl-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (6.2 g, 82%) as a white solid. LC/MS ESI m/z: 478 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.41 (s, 1H), 8.65 – 8.57 (m, 2H), 8.22 (s, 1H), 7.55 (d, J = 7.3 Hz, 2H), 7.46 (t, J = 7.5 Hz, 2H), 7.38 (dd, J = 13.2, 5.8 Hz, 2H), 4.29 – 4.05 (m, 2H), 3.83 (d, J = 12.9 Hz, 1H), 3.59 (d, J = 11.5 Hz, 1H), 3.14 (m, 3H), 1.27 (s, 3H), 0.92 (m, 5H), 0.56 (d, J = 3.3 Hz, 2H).
Example 12. Synthesis of (R)-2-(5-cyclopropyl-4-(4-(1-fluorocyclopropane-1-carbonyl)- 3-methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)ison icotinonitrile (Compound 129) Step 1.4-chloro-5-cyclopropyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine To a solution of 4-chloro-5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (5.8 g, 13 mmol) in toluene (50 mL) were added cyclopropylboronic acid (1.09 g, 12.7 mmol), K 2 CO 3 (24.0 g, 174 mmol) and Pd-118 (875 mg, 1.34 mmol). The resulting mixture was heated to 80 o C overnight. After being cooled down to room temperature, solvent was filtered. The filtrate was concentrated and purified by flash column chromatography (silica gel, 0~30%, ethyl acetate in petroleum ether) to give 3.6 g of 4-chloro-5-cyclopropyl-7-tosyl-7H- pyrrolo[2,3-d]pyrimidine (3.7 g, 77% yield) as a solid. LC/MS ESI m/z: 348 (M+H) + . Step 2. tert-butyl (R)-4-(5-cyclopropyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl )-2- methylpiperazine-1-carboxylate To a solution of 4-chloro-5-cyclopropyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (3.0 g, 8.7 mmol) in EtOH (60 mL) were added tert-butyl (R)-2-methylpiperazine-1-carboxylate (3.46 g, 17.3 mmol) and DIPEA (6.74 g, 52.2 mmol). The resulting mixture was heated to 100 o C overnight. After being cooled down to room temperature, solvent was removed and the residue was purified by flash column chromatography (silica gel, 0~30%, ethyl acetate in petroleum ether) to afford tert-butyl (R)-4-(5-cyclopropyl-7-tosyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2-methylpiperazine-1-carboxylate (3.0 g, 73%) as a white solid. LC/MS ESI m/z: 512 (M+H) + . Step 3. tert-butyl (R)-4-(5-cyclopropyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2- methylpiperazine-1-carboxylate To a solution of tert-butyl (R)-4-(5-cyclopropyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin- 4-yl)-2-methylpiperazine-1-carboxylate (3.0 g, 6.0 mmol) in THF (50 mL) was added TBAF (36 mL, 1.0M in THF). The resulting mixture was stirred at room temperature overnight. The reaction was quenched with water, extracted with EtOAc twice, the combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~60%, ethyl acetate in petroleum ether) to afford tert-butyl (R)-4-(5-cyclopropyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2- methylpiperazine-1-carboxylate (1.9 g, 88%) as a white solid. LC/MS ESI m/z: 358 (M+H) + . Step 4. tert-butyl (R)-4-(7-(3-cyanophenyl)-5-cyclopropyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2-methylpiperazine-1-carboxylate To a solution of tert-butyl (R)-4-(5-cyclopropyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2- methylpiperazine-1-carboxylate (1.2 g, 3.4 mmol) in DMF (15 mL) were added 2- bromoisonicotinonitrile (1.23 mg, 6.72 mmol), trans-cyclohexane-1,2-diamine (383 mg, 3.36 mmol), CuI (638 mg, 3.36 mmol) and K 3 PO 4 (2.14 g, 10.1 mmol). The resulting mixture was heated to 120 o C overnight. After being cooled down to room temperature. The reaction was partitioned between EtOAc and water, organic layer was separated, aqueous layer was extracted with EtOAc twice, the combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~30%, ethyl acetate in petroleum ether) to afford tert-butyl (R)-4-(7-(3- cyanophenyl)-5-cyclopropyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)- 2-methylpiperazine-1- carboxylate (1.4 g, 91%) as a solid. LC/MS ESI m/z: 459 (M+H) + . Step 5. (R)-2-(5-cyclopropyl-4-(3-methylpiperazin-1-yl)-7H-pyrrolo[2 ,3-d]pyrimidin- 7-yl)isonicotinonitrile At 0 o C, to a solution of tert-butyl (R)-4-(7-(3-cyanophenyl)-5-cyclopropyl-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2-methylpiperazine-1-carboxyla te (1.1 g, 2.5 mmol) in DCM (10 mL) was added HCl (8.0 mL, 4.0M in dioxane). The resulting mixture was stirred at room temperature for 4 h. The reaction mixture was concentrated to afford (R)-2-(5- cyclopropyl-4-(3-methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyri midin-7-yl)isonicotinonitrile (890 mg, 100%) as a solid which was used in the next step directly. LC/MS ESI (m/z): 359 (M+H) + . Step 6. (R)-2-(5-cyclopropyl-4-(4-(1-fluorocyclopropane-1-carbonyl)- 3- methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonic otinonitrile To a solution of (R)-2-(5-cyclopropyl-4-(3-methylpiperazin-1-yl)-7H-pyrrolo[2 ,3- d]pyrimidin-7-yl)isonicotinonitrile (60 mg, 0.17 mmol) in DMF (3 mL) were added 1- fluorocyclopropane-1-carboxylic acid (32 mg, 0.31 mmol), DIPEA (44 mg, 0.34 mmol) and HATU (129 mg, 0.34 mmol). The resulting mixture was stirred at room temperature overnight. The reaction was quenched with water, extracted with EtOAc twice, the combined organic layers were washed with NaHCO 3 (aq.) and brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~35%, ethyl acetate in petroleum ether) to give crude product which was further purified by prep- HPLC to afford (R)-2-(5-cyclopropyl-4-(4-(1-fluorocyclopropane-1-carbonyl)- 3- methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonic otinonitrile (28 mg, 38%) as a white solid. LC/MS ESI m/z: 446 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.35 – 9.29 (m, 1H), 8.59 (dd, J = 5.0, 0.8 Hz, 1H), 8.51 (s, 1H), 7.82 (d, J = 0.9 Hz, 1H), 7.35 (dd, J = 5.0, 1.3 Hz, 1H), 4.85 – 4.75 (m, 1H), 4.55 – 4.50 (m, 1H), 4.45 – 4.24 (m, 1H), 4.20 – 4.13 (m, 1H), 3.82 – 3.36 (m, 2H), 3.21 – 3.11 (m, 1H), 2.07 – 2.01 (m, 1H), 1.40 – 1.24 (m, 7H), 1.09 – 1.03 (m, 2H), 1.00 – 0.94 (m, 1H), 0.76 – 0.70 (m, 1H). The following compounds were prepared by the procedure similar to the synthesis of compound 129 from the corresponding acids.
Example 13. Synthesis of (R)-2-(5-(2-fluorophenyl)-4-(4-isobutyryl-2-methylpiperazin- 1- yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (Compound 138) Step1.4-chloro-5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]p yrimidine To a solution of 4-chloro-5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (1.1 g, 2.5 mmol) in DMF (15 mL) and water (0.5 mL) were added (2-fluorophenyl)boronic acid (420 mg, 0.60 mmol), X-Phos (180 mg, 0.37 mmol), K 3 PO 4 (1.6 g, 7.5 mmol) and Pd 2 (dba) 3 (230 mg, 0.25 mmol), the resulting mixture was heated to 60 o C overnight. After being cooled down to room temperature, the reaction mixture was filtered, filtrate was partitioned between EtOAc and water, organic layer was separated, aqueous layer was extracted with EtOAc twice, the combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash chromatography (silica gel, 0~50% EtOAc in petroleum ether) to afford 4-chloro-5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrimid ine (600 mg, 60%). LC/MS ESI (m/z): 402 (M+H) + . Step 2. tert-butyl (R)-4-(5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin -4-yl)- 3-methylpiperazine-1-carboxylate A mixture of 4-chloro-5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrimid ine (600 mg, 1.49 mmol) and tert-butyl (R)-3-methylpiperazine-1-carboxylate (598 mg, 3.00 mmol) in DIEA (20 mL) was heated at 150°C for 3 hours. The reaction mixture was concentrated, and the residue was purified by column chromatography on silica gel (0~30% EtOAc in petroleum ether, V/V) to give the tert-butyl (R)-4-(5-(2-fluorophenyl)-7-tosyl-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (520 mg, 61%) as a yellow solid. LC/MS ESI (m/z): 566 (M+H) + . Step 3. tert-butyl (R)-4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3 - methylpiperazine-1-carboxylate To a solution of tert-butyl (R)-4-(5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate (500 mg, 0.88 mmol) in THF (10 mL) was added TBAF (5.0 mL, 1.0M in THF). The resulting mixture was stirred at room temperature for 12 h. The reaction mixture was partitioned between EtOAc and water, organic layer was separated, aqueous layer was extracted with EtOAc twice. The combined layers were washed with brine, dried over Na 2 SO 4 and concentrated. The residue was purified by column chromatography on silica gel (0~80% EtOAc in petroleum ether, V/V) to give the tert-butyl (R)-4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3 -methylpiperazine-1- carboxylate (100 mg, 27%) as a yellow solid. LC/MS ESI (m/z): 412 (M+H) + . Step 4. tert-butyl (R)-4-(7-(4-cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H-pyrrolo [2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate A mixture of tert-butyl (R)-4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)- 3-methylpiperazine-1-carboxylate (100 mg, 0.24 mmol), 2-bromopyridine-4-carbonitrile (89 mg, 0.49 mmol), CuI (23 mg, 0.12 mmol), trans-1,2-diaminocyclohexane (8.3 mg, 0.07 mmol) and K 3 PO 4 (150 mg, 0.73 mmol) in DMF (10 mL) was heated at 120°C for 12 hours. After being cooled down to room temperature, solvent was concentrated. The residue was purified by column chromatography on silica gel (0~40% EtOAc in petroleum ether, V/V) to give the tert-butyl (R)-4-(7-(4-cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H-pyrrolo [2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate (80 mg, 64%) as a white solid. LC/MS ESI (m/z): 514 (M+H) + . 1 H NMR (400 MHz, CD 3 OD) δ 9.30 (s, 1H), 8.70 (d, J = 5.0 Hz, 1H), 8.55 (s, 1H), 8.29 (s, 1H), 7.61 (dd, J = 5.0, 1.3 Hz, 1H), 7.54 (td, J = 7.5, 1.7 Hz, 1H), 7.50 – 7.43 (m, 1H), 7.34 (dd, J = 7.5, 6.5 Hz, 1H), 7.31 – 7.24 (m, 1H), 4.19 – 4.11 (m, 1H), 3.72 (d, J = 13.6 Hz, 1H), 3.49 (d, J = 11.7 Hz, 2H), 3.13 – 3.06 (m, 1H), 2.73 (br, 2H), 1.42 (s, 9H), 0.97 (d, J = 6.5 Hz, 3H). Step 5. (R)-2-(5-(2-fluorophenyl)-4-(2-methylpiperazin-1-yl)-7H-pyrr olo[2,3- d]pyrimidin-7-yl)isonicotinonitrile At 0 o C, to a solution of tert-butyl (R)-4-(7-(4-cyanopyridin-2-yl)-5-(2-fluorophenyl)- 7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carbox ylate (60 mg, 0.12 mmol) in DCM (10 mL) was added TFA (4 mL). The resulting mixture was stirred at the same temperature for 1 h. The reaction mixture was basified with NaHCO 3 (aq.) and extracted with DCM twice. The combined organic layers were washed with NaHCO 3 (aq.), dried over Na 2 SO 4 and concentrated to afford the (R)-2-(5-(2-fluorophenyl)-4-(2-methylpiperazin-1-yl)- 7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (40 mg, 83%) as a yellow solid which was used in the next step without further purification. LC/MS ESI m/z: 414 (M+H) + . Step 6. (R)-2-(5-(2-fluorophenyl)-4-(4-isobutyryl-2-methylpiperazin- 1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile At 0 o C, to a solution of (R)-2-(5-(2-fluorophenyl)-4-(2-methylpiperazin-1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (40 mg, 0.10 mmol) and TEA (30 mg, 0.30 mmol) in DCM (5 mL) was added di-isobutyryl chloride (12 mg, 0.12 mmol). The resulting mixture was stirred at room temperature for 20 minutes. The reaction was quenched with ice water and extracted with DCM twice. The combined layers were washed with NaHCO 3 (aq.) and brine, dried over Na 2 SO 4 and concentrated. The residue was purified by column chromatography on silica gel (0~40% EtOAc in petroleum ether, V/V) to give the crude product, which was purified by prep-HPLC to give the (R)-2-(5-(2-fluorophenyl)-4-(4- isobutyryl-2-methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidi n-7-yl)isonicotinonitrile (30 mg, 64%) as a white solid. LC/MS ESI (m/z): 484.1 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.41 (s, 1H), 8.63 (d, J = 5.0 Hz, 1H), 8.58 (d, J = 4.6 Hz, 1H), 8.29 (d, J = 5.9 Hz, 1H), 7.53 – 7.43 (m, 1H), 7.43 – 7.34 (m, 2H), 7.26 – 7.16 (m, 2H), 4.46 – 3.98 (m, 2H), 3.65 (t, J = 11.7 Hz, 1H), 3.44 (t, J = 10.8 Hz, 1H), 3.25 – 2.97 (m, 2H), 2.81 – 2.65 (m, 1H), 2.56 (br, 1H), 1.14 – 1.08 (m, 6H), 1.07 – 0.87 (m, 3H). The following compounds were prepared by the procedure analogous to the synthesis of compound 138 from the corresponding amines.
Example 14. Synthesis of (S)-2-(5-cyclopropyl-4-(2-methyl-4-(4,4,4-trifluoro-3,3- dimethylbutanoyl)piperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin- 7-yl)isonicotinonitrile (Compound 141) Step 1.3,3,3-trifluoro-2,2-dimethylpropan-1-ol At 0 o C , to a solution of 3,3,3-trifluoro-2,2-dimethylpropanoic acid (4.0 g, 26 mmol) in THF (20 mL) was added LAH (21 ml, 2.5M in THF) dropwise. The resulting mixture was stirred at room temperature overnight. The reaction was quenched with water, extracted with DCM twice, the combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated to afford 3,3,3-trifluoro-2,2-dimethylpropan-1-ol (2.5 g, 69%) as a colorless oil. 1 HNMR (400 MHz, CD 3 OD) δ 3.51 (s, 2H), 1.10 (s, 6H). Step 2.3,3,3-trifluoro-2,2-dimethylpropyl methanesulfonate At 0 o C, to a solution of 3,3,3-trifluoro-2,2-dimethylpropan-1-ol (2.5 g, 18 mmol) in DCM (15 ml) was added MsCl (4.0 g, 35 mmol) dropwise. The resulting mixture was stirred at the room temperature for 3 h. The reaction was quenched with ice water, extracted with DCM twice, the combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was used in the next step directly.3,3,3-trifluoro-2,2- dimethylpropyl methanesulfonate. as a colorless oil. 1 HNMR (400 MHz, CDCl 3 ) δ 4.15 (s, 2H), 3.05 (s, 3H), 1.23 (d, J = 0.5 Hz, 6H). Step 3.4,4,4-trifluoro-3,3-dimethylbutanenitrile To a solution of 3,3,3-trifluoro-2,2-dimethylpropyl methanesulfonate (4.0 g, crude) in DMSO (10 mL) was added NaCN (1.3 g, 27 mmol). The resulting mixture was stirred at 120 o C for 3 days. After being cooled down to room temperature, the reaction was quenched with NaHCO 3 (aq.), extracted with MTBE twice, the combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was used in the next step directly.4,4,4-trifluoro-3,3-dimethylbutanenitrile (1.5 g, 40%) as a colorless oil. 1 H NMR (400 MHz, CDCl 3 ) δ 2.56 (s, 2H), 1.32 (d, J = 6.3 Hz, 6H). Step 4.4,4,4-trifluoro-3,3-dimethylbutanoic acid To a solution of 4,4,4-trifluoro-3,3-dimethylbutanenitrile (1.5 g, 6.8 mmol) in EtOH (10 mL) was added NaOH (5.0 ml of 6.0M). The resulting mixture was stirred at 70 o C overnight. The reaction was quenched with water and adjusted to pH= 1 with concentrated HCl, extracted with EtOAc twice. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated to afford 4,4,4-trifluoro-3,3-dimethylbutanoic acid (450 mg, 45%) as a colorless oil. LC/MS ESI m/z: 169 (M-H)- Step 5. (S)-2-(5-cyclopropyl-4-(2-methyl-4-(4,4,4-trifluoro-3,3-dime thylbutanoyl) piperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinon itrile To a solution of (S)-2-(5-cyclopropyl-4-(2-methylpiperazin-1-yl)-7H-pyrrolo[2 ,3- d]pyrimidin-7-yl)isonicotinonitrile (100 mg, 0.28 mmol) in DMF (5 mL) were added 4,4,4- trifluoro-3,3-dimethylbutanoic acid (94 mg, 0.56 mmol), DIEA (110 mg, 0.84 mmol) and HATU (210 mg, 0.56 mmol). The resulting mixture was stirred at room temperature overnight. The reaction was quenched with NaHCO 3 (aq.), extracted with EtOAc twice, the combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50%, ethyl acetate in petroleum ether) to give crude product (80 mg) which was further purified by prep-HPLC to afford (S)-2-(5-cyclopropyl-4-(2-methyl-4-(4,4,4-trifluoro-3,3- dimethylbutanoyl)piperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin- 7-yl)isonicotinonitrile (35 mg, 40%) as a white solid. LC/MS ESI m/z: 512 (M+H) + . 1 HNMR(400 MHz, CDCl 3 ) δ 9.32 (s, 1H), 8.59 (d, J = 5.0 Hz, 1H), 8.52 (s, 1H), 7.80 (s, 1H), 7.35 (d, J = 4.2 Hz, 1H), 4.84 – 4.70 (m, 1H), 4.52 – 4.37 (m, 1H), 4.02 – 3.89 (m, 1.5H, rotamers), 3.68 – 3.45 (m, 2.5H, rotamers), 3.21 – 3.06 (m, 1H), 2.68 – 2.43 (m, 2H), 2.07 – 1.99 (m, 1H), 1.36 (s, 3H), 1.32 (d, J = 2.4 Hz, 3H), 1.23 (m, 3H), 1.07 – 1.01 (m, 2H), 0.93 – 0.85 (m, 1H), 0.82 – 0.75 (m, 1H). The following compounds were prepared by the procedures analogous to the synthesis of example above from the corresponding commercially available carboxylic acid.
Example 15. Synthesis of ethyl (S)-4-(7-(4-cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (Compound 142) Step 1. (S)-5-(2-fluorophenyl)-4-(2-methylpiperazin-1-yl)-7H-pyrrolo [2,3- d]pyrimidine To a solution of tert-butyl (S)-4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4- yl)-3-methylpiperazine-1-carboxylate (2.0 g, 5.1 mmol, prepared following the procedure described for compound 143) in DCM (10 mL) at 0 o C was added TFA (3.0 mL). The resulting mixture was stirred at 0 o C for 2 h. The reaction was quenched with NaHCO 3 (aq.) and extracted twice with DCM/IPA (85/15). The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was used in the next step directly. LC/MS ESI m/z: 312 (M+H) + . Step 2. (S)-1-(4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl )-3- methylpiperazin-1-yl)-2-methylpropan-1-one To the solution of (S)-5-(2-fluorophenyl)-4-(2-methylpiperazin-1-yl)-7H-pyrrolo [2,3- d]pyrimidine (2.0 g, 6.4 mmol)) in DMF (9 mL) were added DIPEA (2.5 g, 19 mmol), 2- methylpropanoic acid (0.59 mL, 6.4 mmol) and HATU (2.4 g, 6.4 mmol) respectively. The resulting reaction mixture was stirred at room temperature for 30 minutes. The reaction was quenched with NaHCO 3 (aq.) and extracted twice with DCM/IPA (85/15). The combined organic layers were dried over Na2SO4, filtered and concentrated. The residue was purified by flash column chromatography to afford crude product (S)-1-(4-(5-(2-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazin-1-yl)-2-meth ylpropan-1-one (2.0 g, 82%) as a solid. LC/MS ESI m/z: 382.6 (M+H) + . Step 3. (S)-2-(5-(2-fluorophenyl)-4-(4-isobutyryl-2-methylpiperazin- 1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)thiazole-5-carbonitrile To a solution of (S)-1-(4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl )-3- methylpiperazin-1-yl)-2-methylpropan-1-one (50 mg, 0.13 mmol) in DMF (3 mL) were added CuI (25 mg, 0.13 mmol), K 3 PO 4 (56 mg, 0.26 mmol), trans-N,N’- dimethylcyclohexane-1,2-diamine (37 mg, 0.26 mmol) and 2-bromo-1,3-thiazole-5- carbonitrile (50 mg, 0.26 mmol) respectively. The resulting reaction mixture was stirred at 90℃ under N 2 overnight. After cooling to room temperature, the reaction mixture was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography and Prep-HPLC to afford (S)-2-(5-(2-fluorophenyl)-4-(4-isobutyryl-2-methylpiperazin- 1-yl)-7H-pyrrolo[2,3- d]pyrimidin-7-yl)thiazole-5-carbonitrile (10 mg, 16%) as a white solid. LC/MS ESI m/z: 490 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 8.60 (d, J = 5.2 Hz, 1H), 8.14 – 8.04 (m, 2H), 7.49 – 7.38 (m, 2H), 7.31 – 7.27 (m, 1H), 7.25 – 7.19 (m, 1H), 4.61 – 4.52 (m, 0.5H, rotamers), 4.26 – 4.18 (m, 1H), 4.12 – 4.05 (m, 0.5H, rotamers), 3.76 – 3.61 (m, 1H), 3.59 – 3.42 (m, 1H), 3.27 – 2.97 (m, 2H), 2.78 – 2.46 (m, 2H), 1.16 – 1.04 (m, 8H), 0.94 – 0.90 (m, 1H). The following compound was prepared by the procedure analogous to the synthesis of compound 142 from the corresponding aryl halide. Example 16. Synthesis of (S)-2-(5-(2-fluorophenyl)-4-(4-isobutyryl-2-methylpiperazin- 1- yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-6-methylisonicotinonitr ile (Compound 143) Step 1. tert-butyl (S)-4-(7-(6-bromo-4-cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H - pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te To the solution of tert-butyl (S)-4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)- 3-methylpiperazine-1-carboxylate (1.0 g, 1.7 mmol, prepared following the procedure of compound 128) in dioxane (20 mL) and water (0.5 mL) were added Pd(dppf)Cl 2 (140 mg, 0.17 mmol), K 2 CO 3 (930 mg, 6.7 mmol) and (2-fluorophenyl)boronic acid (280 mg, 2.0 mmol). The resulting reaction mixture was stirred at 90℃ overnight. After cooling to room temperature, solvent was removed and the residue was purified by flash column chromatography (silica gel, 0~40%, ethyl acetate in petroleum ether) to obtain tert-butyl (S)- 4-(5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-y l)-3-methylpiperazine-1- carboxylate (810 mg, 85%) as a white solid. LC/MS ESI m/z: 566 (M+H) + . Step 2. tert-butyl (S)-4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3 - methylpiperazine-1-carboxylate To the solution of tert-butyl (S)-4-(5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate (570 mg, 1.0 mmol) in THF (4 mL) was added TBAF (4.0 mL, 1.0M in THF). The resulting reaction mixture was stirred at room temperature under N 2 atmosphere overnight. The reaction mixture was quenched with ice water and extracted twice with EtOAc. The combined organic layers were washed with water and brine, dried over Na 2 SO 4 , filtered, and concentrated under reduced pressure. The residue was purified by flash column chromatography (silica gel, 0~60%, ethyl acetate in petroleum ether) to obtain tert-butyl (S)-4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3 - methylpiperazine-1-carboxylate (330 mg, 80%) as a white solid. LC/MS ESI m/z: 412 (M+H) + . Step 3. tert-butyl (S)-4-(7-(6-bromo-4-cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H - pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te In a sealed tube, tert-butyl (S)-4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4- yl)-3-methylpiperazine-1-carboxylate (150 mg, 0.37 mmol), 2,6-dibromoisonicotinonitrile (190 mg, 0.73 mmol), K 3 PO 4 (160 mg, 0.73 mmol) and CuI (69 mg, 0.36 mmol) were mixed in dry DMF. Then (±)-trans-1,2-cyclohexanediamine (100 mg, 0.73 mmol) was added. The reaction was stirred at 90°C under N 2 atmosphere for 3.5 h. After cooling to room temperature, the reaction mixture was diluted with EtOAc, washed with 5% LiCl (aq.) and brine, dried over Na 2 SO 4 and concentrated. The residue was purified by flash column chromatography (silica gel, 0~11% EtOAc in petroleum ether) to provide tert-butyl (S)-4-(7- (6-bromo-4-cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H-pyrrolo[ 2,3-d]pyrimidin-4-yl)-3- methylpiperazine-1-carboxylate (120 mg, 55%) as a yellow foam. LC/MS ESI (m/z): 592 (M+H) + . Step 4. tert-butyl (S)-4-(7-(4-cyano-6-methylpyridin-2-yl)-5-(2-fluorophenyl)-7 H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te A mixture of tert-butyl (S)-4-(7-(6-bromo-4-cyanopyridin-2-yl)-5-(2-fluorophenyl)- 7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carbox ylate (120 mg, 0.20 mmol), methylboronic acid (98 mg, 1.6 mmol), Cs 2 CO 3 (200 mg, 0.61 mmol) and Pd(dppf)Cl 2 (20 mg, 0.027 mmol) in dioxane (3 mL) and H 2 O (0.6 mL) was stirred at 100°C under N 2 atmosphere overnight. After cooling to room temperature, the reaction mixture was diluted with EtOAc and DCM and filtered. The filtrate was purified by flash column chromatography (silica gel, 0~20% EtOAc in petroleum ether followed by Prep-HPLC to provide tert-butyl (S)-4-(7-(4-cyano-6-methylpyridin-2-yl)-5-(2-fluorophenyl)-7 H-pyrrolo[2,3-d]pyrimidin-4- yl)-3-methylpiperazine-1-carboxylate (23 mg, 21%) as a light yellow oil. LC/MS ESI (m/z): 528 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.16 (s, 1H), 8.56 (s, 1H), 8.29 (s, 1H), 7.46 (td, J = 7.6, 1.5 Hz, 1H), 7.37 (tdd, J = 7.2, 5.1, 1.8 Hz, 1H), 7.26 – 7.17 (m, 3H), 4.32 – 4.06 (m, 1H), 3.86 – 3.61 (m, 1H), 3.56 – 3.42 (m, 2H), 3.08 (td, J = 12.3, 2.5 Hz, 1H), 2.87 – 2.59 (m, 5H), 1.43 (s, 9H), 1.01 (d, J = 5.7 Hz, 3H). Step 5. (S)-2-(5-(2-fluorophenyl)-4-(2-methylpiperazin-1-yl)-7H-pyrr olo[2,3- d]pyrimidin-7-yl)-6-methylisonicotinonitrile To tert-butyl (S)-4-(7-(4-cyano-6-methylpyridin-2-yl)-5-(2-fluorophenyl)-7 H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (28 mg, 0.053 mmol) in DCM (3 mL) at room temperature was added TFA (0.50 mL) dropwise and stirred at room temperature for 2 h. The reaction mixture was then diluted with DCM and poured into saturated NaHCO 3 (aq.). The organic layer was dried over Na 2 SO 4 , filtered, and concentrated to dryness to give the desired crude product, which was used in the next step directly. LC/MS ESI (m/z): 428 (M+H) + . Step 6. (S)-2-(5-(2-fluorophenyl)-4-(4-isobutyryl-2-methylpiperazin- 1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)-6-methylisonicotinonitrile A mixture of (S)-2-(5-(2-fluorophenyl)-4-(2-methylpiperazin-1-yl)-7H-pyrr olo[2,3- d]pyrimidin-7-yl)-6-methylisonicotinonitrile (24 mg, 0.056 mmol) and Et 3 N (17 mg, 0.17 mmol) in dry DCM (2.5 mL) under N 2 atmosphere was cooled to 0°C for 10 min. Isobutyryl chloride (10 mg, 0.094 mmol) was added. The reaction was stirred at 0°C for 15 min. The mixture was diluted with DCM, washed with NaHCO 3 (aq.), dried over Na 2 SO 4 and concentrated. The residue was purified by Prep-HPLC to give (S)-2-(5-(2-fluorophenyl)-4-(4- isobutyryl-2-methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidi n-7-yl)-6- methylisonicotinonitrile (18 mg, 63%) as a white solid. LC/MS ESI (m/z): 498 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.16 (s, 1H), 8.58 (d, J = 5.0 Hz, 1H), 8.31 (d, J = 6.1 Hz, 1H), 7.48 (dt, J = 12.8, 6.4 Hz, 1H), 7.41 – 7.33 (m, 1H), 7.26 – 7.16 (m, 3H), 4.27 (m, 1H), 4.11 – 3.94 (m, 1H), 3.70 – 3.61 (m, 1H), 3.44 (m, 1H), 3.09 (m, 2H), 2.74 (m, 1H), 2.63 (s, 3H), 2.55 (td, J = 12.6, 2.6 Hz, 1H), 1.13 – 1.04 (m, 7H), 0.92 (m, 2H). Example 17. Synthesis of (S)-2-(4-(4-isobutyryl-2-methylpiperazin-1-yl)-5-(pyrrolidin -1- yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (Compound 144) Step 1. tert-butyl (S)-4-(5-iodo-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiper azine- 1-carboxylate To a solution of tert-butyl (S)-4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3- methylpiperazine-1-carboxylate (55 g, 110 mmol, prepared following the procedure described for compound 128) in THF (400 mL) at 0 o C was added TBAF (440 mL, 1.0M in THF). The resulting mixture was stirred at 0 o C for 1.5 h. The reaction was quenched with ice water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~10%, methanol in dichloromethane) to afford tert-butyl (S)-4- (5-iodo-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine- 1-carboxylate (37 g, 91%) as a white solid. LC/MS ESI m/z: 444 (M+H) + Step 2. tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)-5-iodo-7H-pyrrolo[2,3-d]pyri midin- 4-yl)-3-methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-4-(5-iodo-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3- methylpiperazine-1-carboxylate (2.0 g, 4.5 mmol) and 4-chloro-2-fluoropyridine (0.71 g, 5.4 mmol) in DMF (20 mL) was added Cs 2 CO 3 (2.9 g, 9.0 mmol). The resulting mixture was stirred at 60℃ for 18 h. After cooling to room temperature, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over anhydrous Na 2 SO 4 , filtered and concentrated. The residue was purified by column chromatography on silica gel (0~35% EtOAc in petroleum ether) to give tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)-5-iodo-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (1.5 g, 60%) as a white solid. LC/MS ESI m/z: 555 (M+H) + Step 3 tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)-5-(2-oxopyrrolidin-1-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te A mixture of tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)-5-iodo-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate (1.5 g, 2.7 mmol), pyrrolidin-2-one (0.62 mL, 8.1 mmol), K 3 PO 4 (1.5 g, 8.1 mmol), CuI (0.29 g, 1.4 mmol) and trans-N,N'- dimethyl-1,2-cyclohexanediamine (0.19 g, 1.4 mmol) in DMF (15 mL) was stirred at 90℃ under N 2 atmosphere overnight. After cooling to room temperature, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over anhydrous Na 2 SO 4 , filtered and concentrated. The residue was purified by column chromatography (0~50% EtOAc in petroleum ether) to give tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)-5-(2-oxopyrrolidin-1-yl)- 7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carbox ylate (0.60 g, 43%) as a white solid. LC/MS ESI m/z: 512 (M+H) + Step 4. tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)-5-(pyrrolidin-1-yl)-7H-pyrro lo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)-5-(2-oxopyrrolidin-1-yl)- 7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carbox ylate (600 mg, 1.2 mmol) in dry THF (5 mL) at 0ºC was added BH 3 /THF (12 mL, 1.0M in THF) dropwise. The resulting mixture was stirred for 3 h. The reaction was quenched with saturated NaHCO 3 (aq.) and extracted twice with EtOAc. The combined organic phases were washed with brine, dried over anhydrous Na 2 SO 4 , filtered and concentrated. The residue was purified by column chromatography on silica gel (0~50% EtOAc in petroleum ether) to give tert-butyl (S)-4-(7- (4-chloropyridin-2-yl)-5-(pyrrolidin-1-yl)-7H-pyrrolo[2,3-d] pyrimidin-4-yl)-3- methylpiperazine-1-carboxylate (300 mg, 51%) as a yellow solid. LC/MS ESI m/z: 498 (M+H) + Step 5. (S)-7-(4-chloropyridin-2-yl)-4-(2-methylpiperazin-1-yl)-5-(p yrrolidin-1-yl)- 7H-pyrrolo[2,3-d]pyrimidine To a solution of tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)-5-(pyrrolidin-1-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (300 mg, 0.60 mmol) in DCM (3 mL) was added TFA (0.89 mL, 12 mmol). The reaction was stirred at room temperature for 3h. After removal of solvent, the residue was used directly in next step without further purification. LC/MS ESI m/z: 398 (M+H) + . Step 6. (S)-1-(4-(7-(4-chloropyridin-2-yl)-5-(pyrrolidin-1-yl)-7H-py rrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazin-1-yl)-2-methylpropan-1-o ne To a solution of (S)-7-(4-chloropyridin-2-yl)-4-(2-methylpiperazin-1-yl)-5- (pyrrolidin-1-yl)-7H-pyrrolo[2,3-d]pyrimidine (230 mg, 0.58 mmol) and TEA (0.48 mL, 3.5 mmol) in DCM (5 mL) at 0 o C was added a solution of 2-methylpropanoyl chloride (0.090 mL, 0.87 mmol) in DCM (0.5 mL). The resulting mixture was stirred at 0 o C for 1 h. The mixture was quenched with NaHCO 3 (aq.) and extracted twice with DCM. The combined organic phases were washed with brine, dried over anhydrous Na 2 SO 4 , filtered and concentrated. The residue was purified by column chromatography on silica gel (0~50% EtOAc in petroleum ether) to give (S)-1-(4-(7-(4-chloropyridin-2-yl)-5-(pyrrolidin-1-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazin-1-yl)-2-meth ylpropan-1-one (90 mg, 33%) as a yellow solid. LC/MS ESI m/z: 468 (M+H) + . Step 7. (S)-2-(4-(4-isobutyryl-2-methylpiperazin-1-yl)-5-(pyrrolidin -1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile A mixture of (S)-1-(4-(7-(4-chloropyridin-2-yl)-5-(pyrrolidin-1-yl)-7H-py rrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazin-1-yl)-2-methylpropan-1-o ne (90 mg, 0.19 mmol), Zn(CN) 2 (68 mg, 0.57 mmol) and Pd(PPh 3 ) 4 (67 mg, 0.060 mmol) in DMF (2 mL) was stirred at 120℃ under N 2 atmosphere overnight. After cooling to room temperature, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic phases were washed with brine, dried over anhydrous Na 2 SO 4 , filtered and concentrated. The residue was purified by column chromatography on silica gel (0~50% EtOAc in petroleum ether) and Prep-HPLC to give (S)-2-(4-(4-isobutyryl- 2-methylpiperazin-1-yl)-5-(pyrrolidin-1-yl)-7H-pyrrolo[2,3-d ]pyrimidin-7- yl)isonicotinonitrile (30 mg, 34%) as a yellow solid. LC/MS ESI m/z: 459 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.35 (s, 1H), 8.57 (d, J = 5.0 Hz, 1H), 8.45 (s, 1H), 7.58 (s, 1H), 7.32 – 7.27 (m, 1H), 5.06 (d, J = 8.0 Hz, 1H), 4.56 (m, 1H), 4.26 (m, 1H), 4.05 – 3.69 (m, 1H), 3.64 – 3.31 (m, 2H), 3.21 (m, 2H), 3.11 – 2.75 (m, 4H), 2.03 – 1.90 (m, 4H), 1.25 – 0.99 (m, 9H). The following compound was prepared by the procedure similar to the synthesis of compound 144 from the corresponding acids. The acid (4,4,4-trifluoro-3,3-dimethylbutanoic acid) for compound 140 was prepared following the procedure outlined in the experimental of compound 141 Example 18. Synthesis of 2-(5-(2-fluorophenyl)-4-(4-isobutyryl-4,7-diazaspiro[2.5]oct an- 7-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (Compound 145) Step 1.4-chloro-5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrim idine To a solution of 4-chloro-5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (10 g, 23 mmol, prepared following the procedure of compound 128) in dioxane-H 2 O (100 mL, 5:1 v/v) were added (2-fluorophenyl)boronic acid (3.3 g, 23 mmol), K 3 PO 4 (9.8 g, 46 mmol) and Pd(dppf)Cl 2 (1.7 g, 2.3 mmol). The resulting mixture was heated to 60 o C overnight. After cooling to room temperature, the reaction was filtered. The filtrate was partitioned between EtOAc and water. The aqueous phase was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~30% EtOAc in petroleum ether) to give 4-chloro-5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrimid ine (7.0 g, 75% yield) as a solid. LC/MS ESI m/z: 402 (M+H) + . Step 2. tert-butyl 7-(5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-y l)-4,7- diazaspiro[2.5]octane-4-carboxylate To the solution of 4-chloro-5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrimid ine (550 mg, 2.2 mmol) in EtOH (6 mL) were added DIEA (0.66 mL, 4.0 mmol) and tert-butyl 4,7-diazaspiro[2.5]octane-4-carboxylate (440 mg, 2.1 mmol) respectively. The resulting reaction mixture was stirred at 100℃ under N 2 atmosphere overnight. After cooling to room temperature, solvent was removed. The crude product was purified by flash column chromatography (silica gel, 0~20%, ethyl acetate in petroleum ether) to afford tert-butyl 7-(5- (2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-4, 7-diazaspiro[2.5]octane-4- carboxylate (660 mg, 70%) as white solid. LC/MS ESI m/z: 578 (M+H) + . Step 3. tert-butyl 7-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-4,7- diazaspiro[2.5]octane-4-carboxylate To the solution of tert-butyl 7-(5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-4,7-diazaspiro[2.5]octane-4-carboxylate (660 mg, 1.6 mmol) in THF (10 mL) was added TBAF (6.5 mL, 1.0M in THF). The resulting reaction mixture was stirred at rt under N 2 atmosphere overnight. The reaction was quenched with ice water and extracted twice with EtOAc. The combined organic layers were washed with water, dried over Na 2 SO 4 , filtered, and concentrated under reduced pressure. The crude product was purified by flash column chromatography (silica gel, 0~70%, ethyl acetate in petroleum ether) to obtain tert- butyl 7-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-4,7-d iazaspiro[2.5]octane-4- carboxylate (410 mg, 62%) as a white solid. LC/MS ESI m/z: 424 (M+H) + . Step 4. tert-butyl 7-(7-(4-cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H-pyrrolo[2,3 - d]pyrimidin-4-yl)-4,7-diazaspiro[2.5]octane-4-carboxylate To a solution of tert-butyl 7-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)- 4,7-diazaspiro[2.5]octane-4-carboxylate (400 mg, 0.95 mmol) in DMF (5 mL) were added CuI (90 mg, 0.47 mmol), K 3 PO 4 (600 mg, 2.9 mmol), trans-cyclohexane-1,2-diamine (0.030 mL, 0.28 mmol) and 2-bromoisonicotinonitrile (350 mg, 1.9 mmol) respectively. The resulting reaction mixture was stirred at 80℃ under N 2 atmosphere overnight. After cooling to room temperature, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated under reduced pressure. The crude product was purified by flash column chromatography (silica gel, 0~20%, ethyl acetate in petroleum ether) to afford tert-butyl 7-(7-(4-cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H-pyrrolo[2,3 - d]pyrimidin-4-yl)-4,7-diazaspiro[2.5]octane-4-carboxylate (450 mg, 91%) as a white solid. LC/MS ESI m/z: 526 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.40 (s, 1H), 8.63 – 8.60 (m, 1H), 8.54 (s, 1H), 8.28 (s, 1H), 7.50 – 7.46 (m, 1H), 7.41 – 7.35 (m, 2H), 7.28 – 7.18 (m, 2H), 3.28 (s, 2H), 3.21 (s, 2H), 3.12 (s, 2H), 1.42 (s, 9H), 0.93 – 0.88 (m, 2H), 0.74 (s, 2H). Step 5.2-(5-(2-fluorophenyl)-4-(4,7-diazaspiro[2.5]octan-7-yl)-7H -pyrrolo[2,3- d]pyrimidin-7-yl)isonicotinonitrile To a solution of tert-butyl 7-(7-(4-cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-4,7-diazaspiro[2.5]octane-4-ca rboxylate (70 mg, 0.11 mmol) in DCM (1 mL) at 0 o C was added TFA (1.0 mL). The reaction was stirred at 0 o C for 1 h. The resulting mixture was basified with NaHCO 3 (aq.) and extracted twice with DCM. The combined organic layers were washed with NaHCO 3 (aq.), dried over Na 2 SO 4 , filtered and concentrated. The residue was used in the next step directly. LC/MS ESI m/z: 426 (M+H) + . Step 6.2-(5-(2-fluorophenyl)-4-(4-isobutyryl-4,7-diazaspiro[2.5]o ctan-7-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile To a solution of 2-(5-(2-fluorophenyl)-4-(4,7-diazaspiro[2.5]octan-7-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (50 mg, 0.12 mmol) in DCM (2 mL) at 0 o C was added TEA (0.050 mL, 0.36 mmol), followed by isobutyryl chloride (0.020 mL, 0.24 mmol). The resulting mixture was stirred at room temperature for 20 minutes. The reaction was quenched with ice water and extracted twice with DCM. The combined organic layers were washed with NaHCO 3 (aq.), dried over Na 2 SO 4 , filtered, concentrated, the residue was purified by Prep-HPLC to afford 2-(5-(2-fluorophenyl)-4-(4-isobutyryl-4,7- diazaspiro[2.5]octan-7-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)i sonicotinonitrile (32 mg, 53%) as a white solid. LC/MS ESI m/z: 496 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.40 (s, 1H), 8.63 (d, J = 5.0 Hz, 1H), 8.54 (s, 1H), 8.29 (s, 1H), 7.53 – 7.46 (m, 1H), 7.42 – 7.35 (m, 2H), 7.29 – 7.18 (m, 2H), 3.61 – 2.48 (m, 7H), 1.12 – 0.70 (m, 10H). Example 19. Synthesis of (S)-1-(4-(7-(3-chlorophenyl)-5-(diethylamino)-7H-pyrrolo[2,3 - d]pyrimidin-4-yl)-3-methylpiperazin-1-yl)-2-methylpropan-1-o ne (Compound 147) Step 1.4-chloro-7-(3-chlorophenyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimi dine To a mixture of 4-chloro-5-iodo-7H-pyrrolo[2,3-d]pyrimidine (10 g, 36 mmol), (3- chlorophenyl)boronic acid (11 g, 72 mmol) and Cu(OAc) 2 (10 g, 55 mmol) in DCM (300 mL) were added pyridine (18 mL, 220 mmol) and 4Å MS. The reaction was stirred under O 2 atmosphere at room temperature for 2 days. The resultant mixture was then treated with NH 4 OH (aq., 25%) and filtered through Celite. The filtrate was washed with water, dried over Na 2 SO 4 and concentrated to dryness. The crude solid product was triturated with EtOAc / petroleum ether (1:5, v/v) to give 4-chloro-7-(3-chlorophenyl)-5-iodo-7H-pyrrolo[2,3- d]pyrimidine (12 g, ~75% purity, 64%) as a brown solid. LC/MS ESI (m/z): 390 (M+H) + . Step 2. tert-butyl (S)-4-(7-(3-chlorophenyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimidin- 4-yl)- 3-methylpiperazine-1-carboxylate A mixture of 4-chloro-7-(3-chlorophenyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimidi ne (3.0 g, ~75% purity, 5.8 mmol) and tert-butyl (S)-3-methylpiperazine-1-carboxylate (3.0 g, 15 mmol) in DIPEA (6.5 mL, 39 mmol) was stirred at 140°C for 2.5 h. DIPEA was removed by rotary evaporation. The residue was purified by flash column chromatography (silica gel, 0~16% EtOAc in petroleum ether) to provide tert-butyl (S)-4-(7-(3-chlorophenyl)-5-iodo-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (2.6 g, 82%) as a light brown foam. LC/MS ESI (m/z): 554 (M+H) + . Step 3. methyl (S)-4-(4-(tert-butoxycarbonyl)-2-methylpiperazin-1-yl)-7-(3- chlorophenyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carboxylate To tert-butyl (S)-4-(7-(3-chlorophenyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimidin- 4-yl)-3- methylpiperazine-1-carboxylate (2.6 g, 4.7 mmol) in MeOH (20 mL) were added Pd(dppf)Cl 2 (0.29 g, 0.40 mmol ) and Et 3 N (2.0 mL, 14 mmol). The reaction was stirred under CO atmosphere at 70°C for 4 h. The resulting mixture was concentrated and purified by flash column chromatography (silica gel, 0~23% EtOAc in petroleum ether) to give methyl (S)-4- (4-(tert-butoxycarbonyl)-2-methylpiperazin-1-yl)-7-(3-chloro phenyl)-7H-pyrrolo[2,3- d]pyrimidine-5-carboxylate (2.1 g, 89%) as a light brown foam. LC/MS ESI (m/z): 486 (M+H) + . Step 4. (S)-4-(4-(tert-butoxycarbonyl)-2-methylpiperazin-1-yl)-7-(3- chlorophenyl)- 7H-pyrrolo[2,3-d]pyrimidine-5-carboxylic acid A solution of methyl (S)-4-(4-(tert-butoxycarbonyl)-2-methylpiperazin-1-yl)-7-(3- chlorophenyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carboxylate (2.1 g, 4.2 mmol) in THF (8 mL) / MeOH (8 mL) / H 2 O (4 mL) was treated with NaOH (0.68 g, 17 mmol) at 50°C for 1 h. The volatile solvents were removed by rotary evaporation. The residue was diluted with H 2 O, acidified with 1 N HCl (aq.) under ice-cooling and extracted with EtOAc. The organic layer was dried over Na 2 SO 4 and concentrated to provide (S)-4-(4-(tert-butoxycarbonyl)-2- methylpiperazin-1-yl)-7-(3-chlorophenyl)-7H-pyrrolo[2,3-d]py rimidine-5-carboxylic acid (1.8 g, 90%) as a pale yellow foam. LC/MS ESI (m/z): 472 (M+H) + . Step 5. tert-butyl (S)-4-(5-acetamido-7-(3-chlorophenyl)-7H-pyrrolo[2,3-d]pyrim idin- 4-yl)-3-methylpiperazine-1-carboxylate To (S)-4-(4-(tert-butoxycarbonyl)-2-methylpiperazin-1-yl)-7-(3- chlorophenyl)-7H- pyrrolo[2,3-d]pyrimidine-5-carboxylic acid (200 mg, 0.42 mmol) in toluene (6 mL) were added DPPA (140 mg, 0.51 mmol) and Et 3 N (86 mg, 0.85 mmol). The mixture was degassed and backfilled with N 2 and stirred at rt for 2.5 h. AcOH (1 mL) and Ac 2 O (1 mL) were then added, and the mixture was stirred at 60°C for 1 h. The reaction was quenched with NaHCO 3 (aq.) and extracted with EtOAc. The organic layer was dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50% EtOAc in petroleum ether) to provide tert-butyl (S)-4-(5-acetamido-7-(3-chlorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (170 mg, 82%) as a light yellow foam. LC/MS ESI (m/z): 485 (M+H) + . Step 6. tert-butyl (S)-4-(7-(3-chlorophenyl)-5-(N-ethylacetamido)-7H-pyrrolo[2, 3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate To tert-butyl (S)-4-(5-acetamido-7-(3-chlorophenyl)-7H-pyrrolo[2,3-d]pyrim idin-4- yl)-3-methylpiperazine-1-carboxylate (160 mg, 0.33 mmol) in dry DMF (2 mL) at 0°C under N 2 atmosphere was added NaH (80 mg, 60% in mineral oil, 2.0 mmol). The mixture was stirred at room temperature for 15 min. Then iodoethane (100 mg, 0.66 mmol) was added. The reaction was stirred at room temperature for 1 h and was then carefully poured into crushed ice. The resultant mixture was extracted with EtOAc, washed with LiCl (5% aq.) and brine, dried over Na 2 SO 4 , filtered and concentrated. Purification by flash column chromatography (silica gel, 0~30% EtOAc in petroleum ether) gave tert-butyl (S)-4-(7-(3- chlorophenyl)-5-(N-ethylacetamido)-7H-pyrrolo[2,3-d]pyrimidi n-4-yl)-3-methylpiperazine- 1-carboxylate (140 mg, 79%) as a light yellow foam. LC/MS ESI (m/z): 513 (M+H) + . Step 7. tert-butyl (S)-4-(7-(3-chlorophenyl)-5-(diethylamino)-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate To tert-butyl (S)-4-(7-(3-chlorophenyl)-5-(N-ethylacetamido)-7H-pyrrolo[2, 3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate (140 mg, 0.26 mmol) in dry THF (2 mL) at 0°C under N 2 atmosphere was added BH 3 -THF (5.0 mL, 1.0 M in THF) dropwise. The mixture was stirred at 0°C for 25 min and was then carefully quenched with MeOH. The solvent was removed by rotary evaporation. The residue was partitioned between EtOAc and brine. The organic layer was dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by prep-TLC (petroleum ether / EtOAc = 5:1, v/v) to provide tert-butyl (S)-4-(7-(3- chlorophenyl)-5-(diethylamino)-7H-pyrrolo[2,3-d]pyrimidin-4- yl)-3-methylpiperazine-1- carboxylate (100 mg, 76%) as a pale yellow oil. LC/MS ESI (m/z): 499 (M+H) + . Step 8. (S)-7-(3-chlorophenyl)-N,N-diethyl-4-(2-methylpiperazin-1-yl )-7H- pyrrolo[2,3-d]pyrimidin-5-amine A solution of tert-butyl (S)-4-(7-(3-chlorophenyl)-5-(diethylamino)-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate (100 mg, 0.20 mmol) in DCM (3 mL) was treated with TFA (1.0 mL) at room temperature for 1 h. The mixture was quenched with NaHCO 3 (aq.) and extracted with DCM. The organic layer was dried over Na 2 SO 4 , filtered and concentrated to dryness to provide (S)-7-(3-chlorophenyl)-N,N-diethyl-4-(2- methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-amine, which was used directly. LC/MS ESI (m/z): 399 (M+H) + . Step 9. (S)-1-(4-(7-(3-chlorophenyl)-5-(diethylamino)-7H-pyrrolo[2,3 -d]pyrimidin-4- yl)-3-methylpiperazin-1-yl)-2-methylpropan-1-one To (S)-7-(3-chlorophenyl)-N,N-diethyl-4-(2-methylpiperazin-1-yl )-7H-pyrrolo[2,3- d]pyrimidin-5-amine (80 mg, 0.20 mmol) in dry DCM (2.5 mL) was added Et 3 N (61 mg, 0.60 mmol). The mixture was cooled at 0°C under N 2 atmosphere for 10 min. Isobutyryl chloride (26 mg, 0.24 mmol) was then added. The reaction was stirred at 0°C for 45 min. The resultant mixture was diluted with DCM and washed with NaHCO 3 (aq.). The organic layer was dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by prep-HPLC to give (S)- 1-(4-(7-(3-chlorophenyl)-5-(diethylamino)-7H-pyrrolo[2,3-d]p yrimidin-4-yl)-3- methylpiperazin-1-yl)-2-methylpropan-1-one (67 mg, 71%) as a white solid. LC/MS ESI (m/z): 469 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 8.38 (s, 1H), 7.73 (s, 1H), 7.67 (d, J = 8.1 Hz, 1H), 7.43 (t, J = 8.1 Hz, 1H), 7.28 (d, J = 9.0 Hz, 1H), 6.79 (s, 1H), 5.25 (pair of br. s, 1H, rotamers), 4.50 (m, 2H), 3.86 (m, 1H), 3.64 – 3.31 (m, 2H), 3.24 – 2.78 (m, 6H), 1.16 (m, 9H), 1.03 (t, J = 7.0 Hz, 6H). Example 20. Synthesis of (S)-2-(5-cyclobutyl-4-(4-isobutyryl-2-methylpiperazin-1-yl)- 7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (Compound 150) C ompound 150 Step 1. tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5-iodo-7H-pyrrolo[2,3-d]pyrim idin- 4-yl)-3-methylpiperazine-1-carboxylate To a solution of tert-butyl 4-{5-cyclopropyl-7H-pyrrolo[2,3-d]pyrimidin-4- yl}piperidine-1-carboxylate (4.5 g, 10 mmol, prepared following the procedure described for compound 144) and 2-fluoropyridine-4-carbonitrile (1.8 g, 15 mmol) in DMF (60 mL) was added Cs 2 CO 3 (16 g, 50 mmol). The reaction was stirred at 40℃ for 18 h. After cooling to room temperature, the resulting mixture was filtered. The filtrate was diluted with ice water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by column chromatography on silica gel (0~40% ethyl acetate in petroleum ether) to give tert-butyl (S)-4-(7-(4- cyanopyridin-2-yl)-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3 -methylpiperazine-1- carboxylate (3.6 g, 66%). LC/MS(ESI)m/z: 546 (M+H) + Step 2. tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5-cyclobutyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate A mixture of tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5-iodo-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate (550 mg, 1.0 mmol), cyclobutylboronic acid (0.19 mL, 2.0 mmol), K 2 CO 3 (2.7 mg, 19 mmol) and Pd(dtbpf)Cl 2 (66 mg, 0.10 mmol) in toluene (50 mL) was stirred at 80℃ under N 2 atmosphere overnight. After cooling to room temperature, solvent was removed. The residue was purified by flash column chromatography (0~50% ethyl acetate in petroleum ether) to give tert-butyl (S)-4-(7-(4- cyanopyridin-2-yl)-5-cyclobutyl-7H-pyrrolo[2,3-d]pyrimidin-4 -yl)-3-methylpiperazine-1- carboxylate (100 mg, 21%) as a white solid. LC/MS ESI m/z: 474 (M+H) + Step 3. (S)-2-(5-cyclobutyl-4-(2-methylpiperazin-1-yl)-7H-pyrrolo[2, 3-d]pyrimidin-7- yl)isonicotinonitrile To a solution of tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5-cyclobutyl-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (100 mg, 0.21 mmol) in DCM (2.0 mL) at 0 o C was added TFA (0.31 mL, 4.2 mmol). The reaction was stirred at 0 o C for 3 h. The mixture was basified with NaHCO 3 (aq.) and extracted twice with DCM. The combined organic layers were washed with NaHCO 3 (aq.), dried over Na 2 SO 4 , filtered and concentrated. The residue was used directly in next step. LC/MS ESI m/z: 374 (M+H) + Step 4. (S)-2-(5-cyclobutyl-4-(4-isobutyryl-2-methylpiperazin-1-yl)- 7H-pyrrolo[2,3- d]pyrimidin-7-yl)isonicotinonitrile To a solution of (S)-2-(5-cyclobutyl-4-(2-methylpiperazin-1-yl)-7H-pyrrolo[2, 3- d]pyrimidin-7-yl)isonicotinonitrile (40 mg, 0.11 mmol) and TEA (0.070 mL, 0.53 mmol) in DCM (2 mL) was added a solution of 2-methylpropanoyl chloride (0.020 mL, 0.21 mmol) in DCM. The mixture was stirred at 0 o C for 1 h. The reaction was quenched with NaHCO 3 (aq.) and extracted twice with DCM. The combined organic phases were washed with brine, dried over anhydrous Na 2 SO 4 , filtered and concentrated. The residue was purified by Prep-HPLC to give (S)-2-(5-cyclobutyl-4-(4-isobutyryl-2-methylpiperazin-1-yl)- 7H-pyrrolo[2,3- d]pyrimidin-7-yl)isonicotinonitrile (20 mg, 42%) as a white solid. LC/MS(ESI)m/z: 444 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.34 (s, 1H), 8.62 (d, J = 4.9 Hz, 1H), 8.54 (s, 1H), 8.13 (d, J = 10.4 Hz, 1H), 7.36 (d, J = 4.9 Hz, 1H), 4.45 – 4.15 (m, 2H), 3.95 – 3.43 (m, 5H), 3.37 – 3.18 (m, 1H), 2.95 – 2.78 (m, 1H), 2.45 (m, 2H), 2.29 – 1.91 (m, 4H), 1.32 – 1.09 (m, 9H). Example 21. Synthesis of (S)-6-(5-(2-fluorophenyl)-4-(4-isobutyryl-2-methylpiperazin- 1- yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)pyrimidine-4-carbonitril e (Compound 152) C ompound 152 Step 1. (S)-1-(4-(7-(6-chloropyrimidin-4-yl)-5-(2-fluorophenyl)-7H-p yrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazin-1-yl)-2-methylpropan-1-o ne To a solution of (S)-1-(4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl )-3- methylpiperazin-1-yl)-2-methylpropan-1-one (38 mg, 0.10 mmol, prepared following the procedure described for compound 142) in DMF (1 mL) were added 4,6-dichloropyrimidine (30 mg, 0.20 mmol) and Cs 2 CO 3 (65 mg, 0.20 mmol) at 25°C. After 3 h, the reaction mixture was poured into H2O and extracted twice with EtOAc. The combined organic phases were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated under vacuo. The crude product was purification by silica gel column (SiO 2 , petroleum ether : EtOAc = 100 : 0 to 70 : 30). (S)-1-(4-(7-(6-chloropyrimidin-4-yl)-5-(2-fluorophenyl)-7H-p yrrolo[2,3-d]pyrimidin-4- yl)-3-methylpiperazin-1-yl)-2-methylpropan-1-one (38 mg, 77%) was obtained as a yellow solid. LC/MS ESI (m/z): 494 (M+H) + . Step 2. (S)-6-(5-(2-fluorophenyl)-4-(4-isobutyryl-2-methylpiperazin- 1-yl)-7H-pyrrolo[2,3- d]pyrimidin-7-yl)pyrimidine-4-carbonitrile To a solution of (S)-1-(4-(7-(6-chloropyrimidin-4-yl)-5-(2-fluorophenyl)-7H-p yrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazin-1-yl)-2-methylpropan-1-o ne (38 mg, 0.077 mmol) in DMF (1 mL) were added Zn(CN) 2 (70 mg, 0.60 mmol) and Pd(PPh 3 ) 4 (120 mg, 0.10 mmol) at 25°C. The mixture was degassed 3 times with N 2 , and then heated at 120°C for 2 h. After cooling to 25°C, the mixture was poured into H 2 O and extracted twice with EtOAc. The combined organic phases were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated in vacuo. The residue was purified by Prep-HPLC (0.1% formic acid as additive) to afford (S)-6-(5-(2-fluorophenyl)-4-(4-isobutyryl-2-methylpiperazin- 1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)pyrimidine-4-carbonitrile (16 mg, 43%) as a light yellow solid. LC/MS ESI (m/z): 485 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.64 (s, 1H), 9.11 (s, 1H), 8.59 (d, J = 4.7 Hz, 1H), 8.30 (d, J = 5.8 Hz, 1H), 7.48 – 7.38 (m, 2H), 7.26 – 7.17 (m, 2H), 4.53 – 3.99 (m, 2H), 3.75 – 3.56 (m, 1H), 3.55 – 3.34 (m, 1H), 3.30 – 2.91 (m, 2H), 2.83 – 2.63 (m, 1H), 2.61 – 2.42 (m, 1H), 1.19 – 0.85 (m, 9H). Example 22. Synthesis of 2-(5-cyclopropyl-4-((2S,5R)-4-(3,3-dimethylbutanoyl)-2,5- dimethylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)ison icotinonitrile (Compound 153) Step 1. tert-butyl (2R,5S)-4-(5-cyclopropyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin- 4-yl)- 2,5-dimethylpiperazine-1-carboxylate To a solution of 4-chloro-5-cyclopropyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (500 mg, 1.4 mmol, prepared following the procedure described for compound 129) in DIEA (1.0 mL) was added tert-butyl (2R,5S)-2,5-dimethylpiperazine-1-carboxylate (1.2 g, 5.8 mmol). The resulting mixture was stirred at 150 o C for 3 h. After cooling to room temperature, solvent was removed. The residue was purified by flash column chromatography (silica gel, 0~40%, ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(5-cyclopropyl-7-tosyl-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (600 mg , 80%) as a light yellow solid. LC/MS ESI m/z: 526 (M+H) + . Step 2. tert-butyl (2R,5S)-4-(5-cyclopropyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2, 5- dimethylpiperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-4-(5-cyclopropyl-7-tosyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate (600 mg, 1.1 mmol) in THF (3 mL) was added TBAF (5.0 mL, 1.0M in THF). The resulting mixture was stirred at room temperature overnight. The reaction was quenched with water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~60%, ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(5-cyclopropyl-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (400 mg, 92%) as a white solid. LC/MS ESI m/z: 372 (M+H) + . Step 3. tert-butyl (2R,5S)-4-(7-(4-cyanopyridin-2-yl)-5-cyclopropyl-7H-pyrrolo[ 2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-4-(5-cyclopropyl-7H-pyrrolo[2,3-d]pyrimidin-4- yl)-2,5-dimethylpiperazine-1-carboxylate (400 mg, 1.1 mmol) in DMF (5 mL) were added 2- bromoisonicotinonitrile (390 mg, 2.2 mmol), trans-N,N’-dimethylcyclohexane-1,2-diamine (46 mg, 0.32 mmol), CuI (120 mg, 0.65 mmol) and K 3 PO 4 (690 mg, 3.2 mmol). The reaction was stirred at 120 o C overnight. After cooled down to room temperature, the mixture was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50%, ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(7-(4-cyanopyridin-2-yl)-5- cyclopropyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpip erazine-1-carboxylate (350 mg, 68%) as a yellow solid. LC/MS ESI m/z: 474 (M+H) + . Step 4.2-(5-cyclopropyl-4-((2S,5R)-2,5-dimethylpiperazin-1-yl)-7H -pyrrolo[2,3- d]pyrimidin-7-yl)isonicotinonitrile To a solution of tert-butyl (2R,5S)-4-(7-(4-cyanopyridin-2-yl)-5-cyclopropyl-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (350 mg, 0.74 mmol) in DCM (5 mL) at 0 o C was added HCl (1.0 mL, 4.0M in dioxane). The resulting mixture was stirred at room temperature for 3 h. The reaction was then quenched with NaHCO 3 (aq.) and extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was used in the next step directly. LC/MS ESI m/z: 374 (M+H) + . Step 5.2-(5-cyclopropyl-4-((2S,5R)-4-(3,3-dimethylbutanoyl)-2,5-d imethylpiperazin- 1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile To a solution of 2-(5-cyclopropyl-4-((2S,5R)-2,5-dimethylpiperazin-1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (50 mg, 0.13 mmol) in DCM (5 mL) were added TEA (40 mg, 0.40 mmol) and 3,3-dimethylbutanoyl chloride (36 mg, 0.27 mmol). The resulting mixture was stirred at room temperature for 1 h. The reaction was quenched with water, extracted twice with DCM. The combined organic layers were washed with NaHCO 3 (aq.), dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50%, ethyl acetate in petroleum ether) to give crude product which was further purified by Prep-HPLC to afford 2-(5-cyclopropyl-4-((2S,5R)-4-(3,3- dimethylbutanoyl)-2,5-dimethylpiperazin-1-yl)-7H-pyrrolo[2,3 -d]pyrimidin-7- yl)isonicotinonitrile (35 mg, 60%) as a white solid. LC/MS ESI m/z: 472 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.31 (s, 1H), 8.59 (d, J = 4.9 Hz, 1H), 8.51 (d, J = 6.5 Hz, 1H), 7.82 (s, 1H), 7.37 – 7.33 (m, 1H), 4.96 (s, 1.5H, rotamers), 4.43 (d, J = 13.3 Hz, 0.5H, rotamers), 4.30 (s, 0.5H, rotamers), 3.89 – 3.62 (m, 3H), 3.38 (dd, J = 13.2, 2.3 Hz, 0.5H, rotamers), 2.52 (d, J = 13.7 Hz, 0.5H, rotamers), 2.39 (d, J = 14.0 Hz, 0.5H, rotamers), 2.19 (t, J = 14.1 Hz, 1H), 2.05 – 1.95 (m, 1H), 1.32 (d, J = 6.6 Hz, 1.5H, rotamers), 1.24 (d, J = 6.4 Hz, 1.5H, rotamers), 1.13 – 1.03 (m, 14H), 0.98 – 0.91 (m, 1H), 0.74 – 0.68 (m, 1H). The following compound was prepared by the procedures analogous to the synthesis of compound 153 using the corresponding acid chloride. Example 23. Synthesis of 2-(5-(2-fluorophenyl)-4-(7-isobutyryl-4,7-diazaspiro[2.5]oct an- 4-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (Compound 155) Step 1.2-(5-bromo-4-methoxy-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isoni cotinonitrile To a solution of 5-bromo-4-methoxy-7H-pyrrolo[2,3-d]pyrimidine (5.0 g, 22 mmol, prepared from MeONa and 5-bromo-4-chloro-7H-pyrrolo[2,3-d]pyrimidine) in DMF (25 mL) were added 2-fluoroisonicotinonitrile (5.4 g, 44 mmol) and Cs 2 CO 3 (36 g, 110 mmol). The resulting mixture was stirred at 50 o C for 5 h. The reaction was quenched with ice water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50%, ethyl acetate in petroleum ether) to afford 2-(5-bromo-4- methoxy-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (6.0 g, 83%) as a yellow solid. LC/MS ESI m/z: 330, 332 (M+H) + . Step 2.2-(5-bromo-4-hydroxy-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isoni cotinonitrile To a solution of 2-(5-bromo-4-methoxy-7H-pyrrolo[2,3-d]pyrimidin-7- yl)isonicotinonitrile (6.0 g, 18 mmol) in DMF (20 mL) were added 4-methylbenzenesulfonic acid (31 g, 180 mmol) and LiOH (7.7 g, 180 mmol). The resulting mixture was stirred at 110 o C for 2 h. The reaction was quenched with water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50%, ethyl acetate in petroleum ether) to afford 2-(5-bromo-4-hydroxy-7H-pyrrolo[2,3- d]pyrimidin-7-yl)isonicotinonitrile (5.5 g, 96%) as a yellow solid. LC/MS ESI m/z: 316, 318 (M+H) + . Step 3.2-(5-bromo-4-chloro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonic otinonitrile To a solution of POCl 3 (20 mL) was added 2-(5-bromo-4-hydroxy-7H-pyrrolo[2,3- d]pyrimidin-7-yl)isonicotinonitrile (5.5 g, 17 mmol). The resulting mixture was stirred at 120 o C under N 2 atmosphere overnight. The solvent was removed, the residue was poured into water and extracted twice with EtOAc. The combined organic layers were dried over Na 2 SO 4 , filtered and concentrated, the residue was purified by flash chromatography (silica gel, 0~30% EtOAc in petroleum ether) to afford 2-(5-bromo-4-chloro-7H-pyrrolo[2,3- d]pyrimidin-7-yl)isonicotinonitrile (5.0 g, 86%) as a light yellow solid. LC/MS ESI (m/z): 334,336 (M+H) + . Step 4.2-(5-bromo-4-fluoro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonic otinonitrile To a solution of 2-(5-bromo-4-chloro-7H-pyrrolo[2,3-d]pyrimidin-7- yl)isonicotinonitrile (500 mg, 1.5 mmol) in THF (5 mL) were added TBAF (5.0 ml, 1.0M in THF) at 0 o C. The resulting mixture was stirred at room temperature overnight. The reaction was quenched with ice water and extracted twice with EtOAc. The combined organic layers were dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50%, ethyl acetate in petroleum ether) to afford 2-(5-bromo-4- fluoro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (100 mg, 25%) as a light yellow solid. LC/MS ESI (m/z): 318, 320 (M+H) + . Step 5. tert-butyl 4-(5-bromo-7-(4-cyanopyridin-2-yl)-7H-pyrrolo[2,3-d]pyrimidi n-4- yl)-4,7-diazaspiro[2.5]octane-7-carboxylate A mixture of 2-(5-bromo-4-fluoro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicot inonitrile (100 mg, 0.31 mmol) and tert-butyl 4,7-diazaspiro[2.5]octane-7-carboxylate (270 mg, 1.3 mmol) was stirred at 150 o C under N 2 atmosphere for 3 h. After cooling to room temperature, the reaction was purified by flash column chromatography (silica gel, 0~50%, ethyl acetate in petroleum ether) to afford tert-butyl 4-(5-bromo-7-(4-cyanopyridin-2-yl)-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-4,7-diazaspiro[2.5]octane-7-carboxylate (80 mg, 50%) as a yellow solid. LC/MS ESI (m/z): 510, 512 (M+H) + . Step 6. tert-butyl 4-(7-(4-cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H-pyrrolo[2,3 - d]pyrimidin-4-yl)-4,7-diazaspiro[2.5]octane-7-carboxylate To a solution of tert-butyl 4-(5-bromo-7-(4-cyanopyridin-2-yl)-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-4,7-diazaspiro[2.5]octane-7-carboxylate (80 mg, 0.16 mmol) in 1.4- dioxane (5 mL) and H 2 O (1 ml) were added (2-fluorophenyl)boronic acid (44 mg, 0.31 mmol), K 2 CO 3 (65 mg, 0.47 mmol) and Pd(dppf)Cl 2 (4.0 mg, 0.020 mmol). The resulting mixture was heated to 90 o C overnight. After cooling to room temperature, solvent was removed and the residue was purified by flash column chromatography (silica gel, 0~50%, ethyl acetate in petroleum ether) to give crude product (100 mg) which was further purified by Prep-HPLC to afford tert-butyl 4-(7-(4-cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-4,7-diazaspiro[2.5]octane-7-ca rboxylate (70 mg, 80%) as a white solid. LC/MS ESI m/z: 526 (M+H) + . 1 HNMR(400 MHz, CDCl 3 ) δ 9.33 (s, 1H), 8.60 – 8.54 (m, 2H), 8.23 (s, 1H), 7.35 – 7.27 (m, 3H), 7.15 – 7.09 (m, 2H), 3.55 – 3.37 (m, 2H), 3.32 – 2.94 (m, 2H), 2.93 – 2.82 (m, 2H), 1.34 (s, 9H), 0.89 – 0.76 (m, 4H). Step 7.2-(5-(2-fluorophenyl)-4-(4,7-diazaspiro[2.5]octan-4-yl)-7H -pyrrolo[2,3- d]pyrimidin-7-yl)isonicotinonitrile To a solution of tert-butyl 4-(7-(4-cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-4,7-diazaspiro[2.5]octane-7-ca rboxylate (70 mg, 0.13 mmol) in DCM (4 mL) at 0 o C was added HCl (0.50 mL, 4.0M in dioxane). The resulting mixture was stirred at 0 o C for 1 h. The reaction was quenched with NaHCO 3 (aq.) and extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was used in the next step directly. LC/MS ESI m/z: 372 (M+H) + . Step 8.2-(5-(2-fluorophenyl)-4-(7-isobutyryl-4,7-diazaspiro[2.5]o ctan-4-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile To a solution of 2-(5-(2-fluorophenyl)-4-(4,7-diazaspiro[2.5]octan-4-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (0.13 mmol) in DCM (3 mL) at 0 o C were added TEA (49 mg, 0.49 mmol) and isobutyryl chloride (26 mg, 0.24 mmol) dropwise. The resulting mixture was stirred at room temperature for 20 min. The reaction was quenched with NaHCO 3 (aq.) and extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by Prep-HPLC to afford 2-(5-(2-fluorophenyl)-4-(7-isobutyryl-4,7-diazaspiro[2.5]oct an-4-yl)- 7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (20 mg, 35% over 2 steps) as a white solid. LC/MS ESI m/z: 496 (M+H) + . 1 HNMR(400 MHz, CDCl 3 ) δ 9.33 (s, 1H), 8.61 – 8.55 (m, 2H), 8.26 – 8.21 (m, 1H), 7.35 – 7.27 (m, 3H), 7.15 – 7.07 (m, 2H), 3.77 – 3.07 (m, 4H), 2.99 – 2.83 (m, 2H), 2.62 – 2.55 (m, 1H), 1.02 – 0.97 (m, 6H), 0.88 – 0.72 (m, 4H). The following compounds were prepared by the procedures analogous to the synthesis of compound 155 using the corresponding amine (tert-butyl 3,3-dimethylpiperazine-1- carboxylate) Example 24. Synthesis of (S)-2-(5-(2-fluorophenyl)-4-(4-isobutyryl-2-methylpiperazin- 1- yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)pyrimidine-4-carbonitril e (Compound 156) Step 1. (S)-2-(5-(2-fluorophenyl)-4-(4-isobutyryl-2-methylpiperazin- 1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)pyrimidine-4-carbonitrile To a solution of (S)-1-(4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl )-3- methylpiperazin-1-yl)-2-methylpropan-1-one (38 mg, 0.10 mmol, prepared following the procedure described for compound 142) in dioxane (1 mL) were added 2-bromopyrimidine- 4-carbonitrile (28 mg, 0.15 mmol), Pd 2 (dba) 3 (18 mg, 0.020 mmol), X-Phos (23 mg, 0.040 mmol) and Cs 2 CO 3 (65 mg, 0.20 mmol ) at 25°C. The mixture was degassed 3 times with N 2 and then stirred at 100°C for 2 h. After cooling to room temperature, the reaction mixture was poured into H 2 O and extracted twice with EtOAc. The combined organic phases were washed with brine, dried over Na 2 SO 4 , filtered and concentrated under vacuo. The crude product was purification by Prep-HPLC (0.1% formic acid as additive) to afford (S)-2-(5-(2- fluorophenyl)-4-(4-isobutyryl-2-methylpiperazin-1-yl)-7H-pyr rolo[2,3-d]pyrimidin-7- yl)pyrimidine-4-carbonitrile (31 mg, 66%) was obtained as a solid. LC/MS ESI (m/z): 485 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.17 (d, J = 4.8 Hz, 1H), 8.72 (s, 1H), 8.17 (d, J = 4.3 Hz, 1H), 7.54 (d, J = 4.7 Hz, 1H), 7.52 – 7.44 (m, 1H), 7.44 – 7.35 (m, 1H), 7.26 – 7.16 (m, 2H), 4.50 – 3.87 (m, 2H), 3.81 – 3.54 (m, 1H), 3.53 – 3.31 (m, 1H), 3.28 – 2.87 (m, 2H), 2.86 – 2.63 (m, 1H), 2.63 – 2.37 (m, 1H), 1.26 – 0.73 (m, 9H). Example 25. Synthesis of (S)-4-(5-(2-fluorophenyl)-4-(4-isobutyryl-2-methylpiperazin- 1- yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-1-methyl-1H-pyrrole-2-c arbonitrile (Compound 157) Step 1. (S)-4-(5-(2-fluorophenyl)-4-(4-isobutyryl-2-methylpiperazin- 1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)-1-methyl-1H-pyrrole-2-carbonit rile To a solution of (S)-1-(4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl )-3- methylpiperazin-1-yl)-2-methylpropan-1-one (95 mg, 0.25 mmol, prepared following the procedure of compound 142) and 4-bromo-1-methyl-1H-pyrrole-2-carbonitrile (92 mg, 0.50 mmol, prepared in three steps from commercially available methyl 4-bromo-1-methyl-1H- pyrrole-2-carboxylate by hydrolysis of ester mediated by sodium hydroxide, followed by conversion to a primary amide using ammonium chloride and dehydration to the nitrile using trifluoroacetic anhydride) in DMF (2 mL) were added CuI (47 mg, 0.25 mmol), trans-N,N’- dimethylcyclohexane-1,2-diamine (35 mg, 0.25 mmol) and K 3 PO 4 (530 mg, 2.5 mmol). The resulting mixture was stirred at 120℃ under N 2 atmosphere overnight. After cooling to room temperature, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted with EtOAc twice, the combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50%, ethyl acetate in petroleum ether) to give crude product which was further purified by prep-HPLC to afford (S)-4-(5-(2-fluorophenyl)-4-(4-isobutyryl-2- methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-1-met hyl-1H-pyrrole-2-carbonitrile (23 mg, 19% yield) as a white solid. LC/MS ESI (m/z): 486 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 8.51 (d, J = 2.5 Hz, 1H), 7.57 (s, 1H), 7.51 – 7.40 (m, 1H), 7.39 – 7.29 (m, 2H), 7.26 – 7.15 (m, 2H), 7.03 (s, 1H), 4.46 – 3.96 (m, 2H), 3.88 (s, 3H), 3.66 (t, J = 11.6 Hz, 1H), 3.45 (d, J = 13.1 Hz, 1H), 3.28 – 2.94 (m, 2H), 2.83 – 2.65 (m, 1H), 2.64 – 2.49 (m, 1H), 1.18 – 0.83 (m, 9H). Example 26. Synthesis of tert-butyl (S)-4-(1-(4-cyanopyridin-2-yl)-3-(2-fluorophenyl)- 1H-pyrrolo[3,2-c]pyridin-4-yl)-3-methylpiperazine-1-carboxyl ate (Compound 161) Step 1.3-bromo-1-tosyl-1H-pyrrolo[3,2-c]pyridine To a suspension of NaH (1.2 g, 30 mmol) in DMF (50 mL) at 0 o C were added 3- bromo-1H-pyrrolo[3,2-c]pyridine (5.0 g, 25 mmol). After stirring at 0 o C for 15 min, TsCl (5.3 g, 28 mmol) was added in portions. The resulting mixture was stirred at room temperature overnight under N 2 atmosphere. The mixture was quenched with ice water and was filtered. The filter cake was washed with water and dried under vacuum to provide 3- bromo-1-tosyl-1H-pyrrolo[3,2-c]pyridine (7.5 g, 84%) as a white solid. LC/MS ESI (m/z): 351 (M+H) + . Step 2.3-bromo-1-tosyl-1H-pyrrolo[3,2-c]pyridine 5-oxide To a solution of 3-bromo-13-bromo-1-tosyl-1H-pyrrolo[3,2-c]pyridine (7.0 g, 20 mmol) in DCM (70 mL) at 0 o C was added 3-chloroperoxybenzoic acid (5.2 g, 30 mmol) in portions. The resulting mixture was stirred at room temperature overnight. The reaction was quenched with NaHCO 3 (aq.) and extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~20 %, MeOH in DCM) to provide 3- bromo-1-tosyl-1H-pyrrolo[3,2-c]pyridine 5-oxide (4.0 g, 54%) as a light yellow solid. LC/MS ESI (m/z): 367, 369 (M+H) +. Step 3. tert-butyl (S)-4-(3-bromo-1-tosyl-1H-pyrrolo[3,2-c]pyridin-4-yl)-3- methylpiperazine-1-carboxylate To a solution of 3-bromo-1-tosyl-1H-pyrrolo[3,2-c]pyridine 5-oxide (300 mg, 0.80 mmol) in CHCl 3 (5 mL) at 0 o C were added tert-butyl (S)-3-methylpiperazine-1-carboxylate (390 mg, 1.9 mmol). After stirring at 0 o C for 10 min, TsCl (180 mg, 0.96 mmol) was added. The resulting mixture was stirred at room temperature overnight under N 2 atmosphere. The reaction was quenched with NaHCO 3 (aq.) and extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~40 %, ethyl acetate in petroleum ether) to provide tert-butyl (S)-4-(3-bromo-1-tosyl-1H-pyrrolo[3,2-c]pyridin-4-yl)- 3-methylpiperazine-1-carboxylate (47 mg, 10%) as a light yellow solid. LC/MS ESI (m/z): 549, 551 (M+H) +. Step 4. tert-butyl (S)-4-(3-(2-fluorophenyl)-1-tosyl-1H-pyrrolo[3,2-c]pyridin-4 -yl)-3- methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-4-(3-bromo-1-tosyl-1H-pyrrolo[3,2-c]pyridin-4-yl)-3- methylpiperazine-1-carboxylate (62 mg, 0.10 mmol) in dioxane (5 mL) and H 2 O (1 mL) were added (2-fluorophenyl)boronic acid (16 mg, 0.11 mmol), K 3 PO 4 (43 mg, 0.20 mmol) and Pd(dppf)Cl 2 (8.0 mg, 0.010 mmol). The resulting mixture was heated to 90 o C overnight. After cooling to room temperature, solvent was removed and the residue was purified by flash column chromatography (silica gel, 0~40%, ethyl acetate in petroleum ether) to afford tert-butyl (S)-4-(3-(2-fluorophenyl)-1-tosyl-1H-pyrrolo[3,2-c]pyridin-4 -yl)-3- methylpiperazine-1-carboxylate (51 mg, 80%) as a white solid. LC/MS ESI m/z: 565 (M+H) + . Step 5. tert-butyl (S)-4-(3-(2-fluorophenyl)-1H-pyrrolo[3,2-c]pyridin-4-yl)-3- methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-4-(3-(2-fluorophenyl)-1-tosyl-1H-pyrrolo[3,2- c]pyridin-4-yl)-3-methylpiperazine-1-carboxylate (50 mg, 0.090 mmol) in THF (1 mL) was added TBAF (1.0 mL, 1.0M in THF). The resulting mixture was stirred at room temperature overnight under N 2 atmosphere. The reaction was quenched with water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~60%, ethyl acetate in petroleum ether) to provide tert-butyl (S)-4-(3-(2-fluorophenyl)- 1H-pyrrolo[3,2-c]pyridin-4-yl)-3-methylpiperazine-1-carboxyl ate (35 mg, 96%) as a yellow solid. LC/MS ESI m/z: 411 (M+H) + . Step 6. tert-butyl (S)-4-(1-(4-cyanopyridin-2-yl)-3-(2-fluorophenyl)-1H-pyrrolo [3,2- c]pyridin-4-yl)-3-methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-4-(3-(2-fluorophenyl)-1H-pyrrolo[3,2-c]pyridin-4-yl)- 3-methylpiperazine-1-carboxylate (35 mg, 0.080 mmol) in DMF (5 mL) were added 2- fluoroisonicotinonitrile (20 mg, 0.16 mmol), and Cs 2 CO 3 (1.2 g, 8.3 mmol). The resulting mixture was heated to 50 o C overnight. After cooling to room temperature, solvent was removed and the residue was purified by flash column chromatography (silica gel, ethyl acetate in petroleum ether) to give crude product which was further purified by prep-HPLC to afford tert-butyl (S)-4-(1-(4-cyanopyridin-2-yl)-3-(2-fluorophenyl)-1H-pyrrolo [3,2-c]pyridin- 4-yl)-3-methylpiperazine-1-carboxylate (51 mg, 80%) as a white solid. LC/MS ESI m/z: 513 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 8.77 (d, J = 4.9 Hz, 1H), 8.23 (d, J = 5.9 Hz, 1H), 7.88 (d, J = 5.8 Hz, 1H), 7.71 (d, J = 13.5 Hz, 2H), 7.53 – 7.44 (m, 2H), 7.42 – 7.35 (m, 1H), 7.24 – 7.17 (m, 2H), 3.47 (s, 1H), 3.12 – 2.86 (m, 6H), 1.42 (s, 9H), 0.91 (d, J = 4.7 Hz, 3H). Step 7. (S)-2-(3-(2-fluorophenyl)-4-(2-methylpiperazin-1-yl)-1H-pyrr olo[3,2- c]pyridin-1-yl)isonicotinonitrile To a solution of tert-butyl (S)-4-(1-(4-cyanopyridin-2-yl)-3-(2-fluorophenyl)-1H- pyrrolo[3,2-c]pyridin-4-yl)-3-methylpiperazine-1-carboxylate (130 mg, 0.24 mmol) in DCM (2 mL) at 0 o C was added TFA (1 mL). The resulting mixture was stirred at 0 o C for 1.5 h. The reaction was quenched with NaHCO 3 (aq.). The aqueous layer was extracted with DCM twice. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was used in the next step directly. LC/MS ESI m/z: 413 (M+H) + . Step 8. (S)-2-(3-(2-fluorophenyl)-4-(4-isobutyryl-2-methylpiperazin- 1-yl)-1H- pyrrolo[3,2-c]pyridin-1-yl)isonicotinonitrile To a solution of (S)-2-(3-(2-fluorophenyl)-4-(2-methylpiperazin-1-yl)-1H- pyrrolo[3,2-c]pyridin-1-yl)isonicotinonitrile (98 mg, 0.24 mmol) in DCM (3 mL) at 0 o C were added dropwise TEA (0.060 mL, 0.48 mmol) and isobutyryl chloride (0.040 mL, 0.36 mmol). The resulting mixture was stirred at room temperature for 1.5 h. The reaction was quenched with ice water and extracted twice with DCM. The combined organic layers were washed with NaHCO 3 (aq.), dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, ethyl acetate in petroleum ether) to give crude product which was further purified by prep-HPLC to afford (S)-2-(3-(2-fluorophenyl)-4-(4- isobutyryl-2-methylpiperazin-1-yl)-1H-pyrrolo[3,2-c]pyridin- 1-yl)isonicotinonitrile (43 mg, 36%) as a white solid. LC/MS ESI m/z: 483 (M+H) + . 1 HNMR (400 MHz, CDCl 3 ) δ 8.77 (d, J = 4.9 Hz, 1H), 8.25 – 8.20 (m, 1H), 7.90 (s, 1H), 7.72 (d, J = 11.9 Hz, 2H), 7.48 (dd, J = 21.6, 5.9 Hz, 2H), 7.42 – 7.36 (m, 1H), 7.20 (dd, J = 17.9, 8.3 Hz, 2H), 3.57 – 2.71 (m, 8H), 1.13 – 1.06 (m, 6H), 1.03 (d, J = 6.1 Hz, 1.5H, rotamers), 0.83 (d, J = 6.3 Hz, 1.5H, rotamers). Example 27. Synthesis of (S)-2-(5-(azetidin-1-yl)-4-(4-(2-hydroxy-2-methylpropanoyl)- 2- methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonic otinonitrile (Compound 162) C ompound 162 Step 1. (S)-2-(5-(azetidin-1-yl)-4-(2-methylpiperazin-1-yl)-7H-pyrro lo[2,3- d]pyrimidin-7-yl)isonicotinonitrile To a solution of tert-butyl (S)-4-(5-(azetidin-1-yl)-7-(4-cyanopyridin-2-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (100 mg, 0.21 mmol, prepared following the procedure of compound 144, substituting azetidin-2-one for pyrrolidin-2-one in the third step) in DCM (2 mL) at 0 o C was added TFA (0.47 mL, 6.3 mmol). The reaction was stirred at 0 o C for 3 h. The reaction was quenched with saturated of NaHCO 3 solution and extracted twice with EtOAc. The combined organic phases were washed with brine, dried over anhydrous Na 2 SO 4 , filtered and concentrated. The residue was used directly in next step without further purification. LC/MS ESI m/z: 375 (M+H) + . Step 2. (S)-2-(5-(azetidin-1-yl)-4-(4-(2-hydroxy-2-methylpropanoyl)- 2- methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonic otinonitrile A mixture of 2-hydroxy-2-methylpropanoic acid (21 mg, 0.20 mmol), HATU (85 mg, 0.22 mmol) and DIEA (0.15 mL, 0.93 mmol) in DMF (3 mL) was stirred at room temperature for 0.5 h. (S)-2-(5-(azetidin-1-yl)-4-(2-methylpiperazin-1-yl)-7H-pyrro lo[2,3-d]pyrimidin-7- yl)isonicotinonitrile (70 mg, 0.18 mmol) was then added. After 2.5 h, the reaction mixture was quenched with NaHCO 3 (aq.) and extracted twice with EtOAc. The combined organic phases were washed with brine, dried over anhydrous Na 2 SO 4 , filtered and concentrated. The residue was purified by prep-HPLC to obtain (S)-2-(5-(azetidin-1-yl)-4-(4-(2-hydroxy-2- methylpropanoyl)-2-methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]py rimidin-7- yl)isonicotinonitrile (30 mg, 35%) as a yellow solid. LC/MS ESI m/z: 461 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.32 (s, 1H), 8.57 (d, J = 5.0 Hz, 1H), 8.45 (s, 1H), 7.49 (s, 1H), 7.30 (d, J = 4.9 Hz, 1H), 5.06 (s, 1H), 4.34 (d, J = 19.5 Hz, 3H), 4.18 (d, J = 13.5 Hz, 1H), 3.83 (q, J = 6.9 Hz, 2H), 3.66 (q, J = 6.9 Hz, 2H), 3.60 – 3.38 (m, 2H), 3.22 (s, 1H), 2.29 (p, J = 6.9 Hz, 2H), 1.55 (d, J = 8.3 Hz, 6H), 1.16 (d, J = 4.8 Hz, 3H). Example 28. Synthesis of (S)-2-(5-(ethyl(propyl)amino)-4-(4-isobutyryl-2- methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonic otinonitrile (Compound 163)
Step 1. tert-butyl (S)-4-(5-bromo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3- methylpiperazine-1-carboxylate To a solution of 5-bromo-4-chloro-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (17 g, 43 mmol, prepared following a similar procedure described for compound 128) in DIPEA (30 mL) was added tert-butyl (S)-3-methylpiperazine-1-carboxylate (22 g, 110 mmol). The resulting mixture was stirred at 150 o C for 2.5 h. After cooling to room temperature, solvent was removed and the residue was purified by flash column chromatography (silica gel, 0~20%, ethyl acetate in petroleum ether) to afford tert-butyl (S)-4-(5-bromo-7-tosyl-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (20 g, 86%) as a white solid. LC/MS ESI m/z: 550, 552 (M+H) + . Step 2. tert-butyl (S)-4-(5-bromo-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3- methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-4-(5-bromo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)- 3-methylpiperazine-1-carboxylate (15 g, 27 mmol) in THF (30 mL) was added TBAF (64 mL, 1.0M in THF). The resulting mixture was stirred at room temperature for 4h. The reaction was quenched with water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50%, ethyl acetate in petroleum ether) to afford tert-butyl (S)-4-(5-bromo-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3- methylpiperazine-1-carboxylate (9.3 g, 86%) as a white solid. LC/MS ESI m/z: 396, 398 (M+H) + . Step 3. tert-butyl (S)-4-(5-bromo-7-(4-chloropyridin-2-yl)-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-4-(5-bromo-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3- methylpiperazine-1-carboxylate (9.3 g, 23 mmol) in DMF (100 mL) were added 2-bromo-4- chloropyridine (9.0 g, 47 mmol), CuI (4.5 g, 23 mmol), trans-N,N’-dimethylcyclohexane-1,2- diamine (5.0 g, 35 mmol) and K 3 PO 4 (10 g, 47 mmol). The resulting mixture was heated to 100 o C for 3 h. After cooling to room temperature, the reaction was quenched with water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~15%, ethyl acetate in petroleum ether) to afford tert-butyl (S)- 4-(5-bromo-7-(4-chloropyridin-2-yl)-7H-pyrrolo[2,3-d]pyrimid in-4-yl)-3-methylpiperazine- 1-carboxylate (9.8 g, 82%) as a white solid. LC/MS ESI m/z: 507, 509 (M+H) + . Step 4. methyl (S)-4-(4-(tert-butoxycarbonyl)-2-methylpiperazin-1-yl)-7-(4- chloropyridin-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carboxylat e To a solution of tert-butyl (S)-4-(5-bromo-7-(4-chloropyridin-2-yl)-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate (9.8 g, 19 mmol) in MeOH (80 mL) were added Pd(dppf)Cl 2 (1.4 g, 1.9 mmol) and TEA (5.3 mL, 39 mmol). The resulting mixture was stirred at 50 o C overnight under CO atmosphere. After cooling to room temperature, solvent was removed and the residue was purified by flash column chromatography (silica gel, 0~15%, ethyl acetate in petroleum ether) to afford methyl (S)-4- (4-(tert-butoxycarbonyl)-2-methylpiperazin-1-yl)-7-(4-chloro pyridin-2-yl)-7H-pyrrolo[2,3- d]pyrimidine-5-carboxylate (8.7 g, 92%) as a white solid. LC/MS ESI m/z: 487 (M+H) + . Step 5. (S)-4-(4-(tert-butoxycarbonyl)-2-methylpiperazin-1-yl)-7-(4- chloropyridin-2- yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carboxylic acid To a solution of methyl (S)-4-(4-(tert-butoxycarbonyl)-2-methylpiperazin-1-yl)-7-(4- chloropyridin-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carboxylat e (8.7 g, 18 mmol) in MeOH (90 mL) and H 2 O (10 mL) was added NaOH (1.4 g, 36 mmol). The resulting mixture was stirred at 80 o C overnight. After cooling to room temperature, the reaction was concentrated. The residue was treated with H 2 O and acidified to pH 5 with HCl (aq.). The precipitate was collected by filtration to afford (S)-4-(4-(tert-butoxycarbonyl)-2-methylpiperazin-1-yl)-7-(4- chloropyridin-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carboxylic acid (5.1 g, 60%) as a white solid. LC/MS ESI m/z: 473 (M+H) + . Step 6. tert-butyl (S)-4-(5-acetamido-7-(4-chloropyridin-2-yl)-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate To a solution of (S)-4-(4-(tert-butoxycarbonyl)-2-methylpiperazin-1-yl)-7-(4- chloropyridin-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carboxylic acid (400 mg, 0.84 mmol) in toluene (8 mL) were added TEA (0.40 mL, 2.5 mmol) and DPPA (460 mg, 1.7 mmol). The resulting mixture was stirred at room temperature for 2 h. Ac 2 O (4 mL) was added, and the resulting mixture was heated to 60 o C for 2 h. After cooling to room temperature, the reaction was quenched with NaHCO 3 (aq.) and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, ethyl acetate in petroleum ether) to afford tert-butyl (S)-4-(5-acetamido-7-(4-chloropyridin-2-yl)-7H-pyrrolo[2,3-d ]pyrimidin-4- yl)-3-methylpiperazine-1-carboxylate (350 mg, 86%) as a light yellow solid. LC/MS ESI m/z: 486 (M+H) + . Step 7. tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)-5-(N-propylacetamido)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te To a suspension of NaH (40 mg, 1.0 mmol) in THF (8 mL) at 0 o C were added tert- butyl (S)-4-(5-acetamido-7-(4-chloropyridin-2-yl)-7H-pyrrolo[2,3-d ]pyrimidin-4-yl)-3- methylpiperazine-1-carboxylate (250 mg, 0.50 mmol). After stirring at 0 o C for 15 min, 1- iodopropane (13 mg, 0.75 mmol) was added. The resulting mixture was stirred at room temperature overnight under N 2 atmosphere. The reaction was quenched with ice water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, ethyl acetate in petroleum ether) to afford tert-butyl (S)-4-(7-(4- chloropyridin-2-yl)-5-(N-propylacetamido)-7H-pyrrolo[2,3-d]p yrimidin-4-yl)-3- methylpiperazine-1-carboxylate (190 mg, 70%) as a light yellow solid. LC/MS ESI m/z: 528 (M+H) + . Step 8. tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)-5-(ethyl(propyl)amino)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te To a solution of tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)-5-(N-propylacetamido)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (190 mg, 0.36 mmol) in THF (1 mL) at 0 o C were added BH 3 -THF (3.0 mL, 1.0 M in THF) dropwise. After stirring at room temperature for 1 h, the reaction was quenched with ice water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~35%, ethyl acetate in petroleum ether) to afford tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)- 5-(ethyl(propyl)amino)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-me thylpiperazine-1-carboxylate (110 mg, 57%) as a colorless oil. LC/MS ESI m/z: 514 (M+H) + . Step 9. tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5-(ethyl(propyl)amino)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te To a solution of tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)-5-(ethyl(propyl)amino)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (110 mg, 0.20 mmol) in DMF (5 mL) were added Zn(CN) 2 (140 mg, 1.2 mmol) and Pd(PPh 3 ) 4 (120 mg, 0.10 mmol). The resulting reaction mixture was stirred at 120℃ under N 2 atmosphere overnight. After cooling to room temperature, the reaction mixture was concentrated under reduced pressure. The residue was purified by flash column chromatography (silica gel, ethyl acetate in petroleum ether) and to afford tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5- (ethyl(propyl)amino)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-meth ylpiperazine-1-carboxylate (100 mg, 97%) as a yellow solid. LC/MS ESI m/z: 505 (M+H) + . Step 10. (S)-2-(5-(ethyl(propyl)amino)-4-(2-methylpiperazin-1-yl)-7H- pyrrolo[2,3- d]pyrimidin-7-yl)isonicotinonitrile To a solution of tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5-(ethyl(propyl)amino)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (100 mg, 0.20 mmol) in DCM (1 mL) at 0 o C was added TFA (1 mL). The resulting mixture was stirred at the same temperature for 1.5 h. The reaction was quenched with NaHCO 3 (aq.). The aqueous layer was extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was used in the next step directly. LC/MS ESI m/z: 405 (M+H) + . Step 11. (S)-2-(5-(ethyl(propyl)amino)-4-(4-isobutyryl-2-methylpipera zin-1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile To a solution of (S)-2-(5-(ethyl(propyl)amino)-4-(2-methylpiperazin-1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (80 mg, 0.20 mmol) in DCM (3 mL) at 0 o C were added dropwise TEA (0.060 mL, 0.46 mmol) and isobutyryl chloride (0.030 mL, 0.30 mmol). The resulting mixture was stirred at room temperature for 30 minutes. The reaction was quenched with ice water and extracted twice with DCM. The combined organic layers were washed with NaHCO 3 (aq.) and brine, dried over Na2SO4, filtered and concentrated. The residue was purified by flash column chromatography (silica gel, ethyl acetate in petroleum ether) to give crude product which was further purified by prep-HPLC to afford (S)-2-(5-(ethyl(propyl)amino)-4-(4-isobutyryl-2-methylpipera zin-1-yl)-7H-pyrrolo[2,3- d]pyrimidin-7-yl)isonicotinonitrile (19 mg, 41%) as a yellow solid. LC/MS ESI m/z: 475 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.38 (s, 1H), 8.58 (d, J = 4.9 Hz, 1H), 8.44 (s, 1H), 7.62 (s, 1H), 7.30 (d, J = 4.7 Hz, 1H), 5.23 (d, J = 44.4 Hz, 1H), 4.69 – 4.30 (m, 2H), 3.97 (d, J = 10.8 Hz, 0.5H, rotamers), 3.76 (d, J = 13.7 Hz, 0.5H, rotamers), 3.59 (d, J = 11.8 Hz, 0.5H, rotamers), 3.42 – 3.01 (m, 6H), 2.92 – 2.78 (m, 1.5H), 1.57 – 1.50 (m, 2H), 1.25 – 1.13 (m, 8H), 1.06 (d, J = 4.9 Hz, 1H), 0.98 – 0.88 (m, 6H). The following compounds were prepared by procedures analogous to the synthesis of compound 163 from the corresponding acid chloride or acid anhydride. Example 29. Synthesis of 2-(4-((S)-4-(3,3-dimethylbutanoyl)-2-methylpiperazin-1-yl)-5 - ((R)-2-methylmorpholino)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)iso nicotinonitrile (Compound 165) Step 1. tert-butyl (S)-4-(5-bromo-7-(4-chloropyridin-2-yl)-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-4-(5-bromo-7-(4-chloropyridin-2-yl)-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate (600 mg, 1.2 mmol, prepared following the procedure described for compound 163) in DMF (15 mL) were added CuI (110 mg, 0.59 mmol), 6-methylmorpholin-3-one (410 mg, 3.5 mmol), K 3 PO 4 (500 mg, 2.4 mmol) and trans- N,N’-dimethylcyclohexane-1,2-diamine (340 mg, 2.4 mmol) at 25°C. The mixture was degassed 3 times with N 2 and then stirred at 95°C for 12 h. The mixture was cooled to 25°C, poured into H 2 O and extracted twice with EtOAc. The combined organic phases were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated under vacuo. The crude product was purified by silica gel column (SiO 2 , petroleum ether : EtOAc = 5 : 1 to 4 : 1) to afford tert- butyl (3S)-4-(7-(4-chloropyridin-2-yl)-5-(2-methyl-5-oxomorpholino )-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate (60 mg, 9%) as a solid. LC/MS ESI (m/z): 542 (M+H) + . Step 2. tert-butyl (3S)-4-(7-(4-chloropyridin-2-yl)-5-(2-methylmorpholino)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te To a solution of tert-butyl (3S)-4-(7-(4-chloropyridin-2-yl)-5-(2-methyl-5- oxomorpholino)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpipe razine-1-carboxylate (60 mg, 0.11 mmol ) in THF(5 mL) was added BH 3 -THF(1.0 mL, 1.0M in THF) at 0°C under N 2 atmosphere. The mixture was warmed to 25°C and stirred for 2 h. The reaction was quenched by addition of MeOH (10 mL) at 0°C and concentrated in vacuo. The crude product was purification by silica gel column (SiO 2 , petroleum ether : EtOAc = 50 : 1 to 40 : 1) to afford tert-butyl (3S)-4-(7-(4-chloropyridin-2-yl)-5-(2-methylmorpholino)-7H-p yrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate (40 mg , 68%) as a solid. LC/MS ESI (m/z): 528 (M+H) + . Step 3. tert-butyl (3S)-4-(7-(4-cyanopyridin-2-yl)-5-(2-methylmorpholino)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te To a solution of tert-butyl (3S)-4-(7-(4-chloropyridin-2-yl)-5-(2-methylmorpholino)- 7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carbox ylate (40 mg, 0.076 mmol) in DMF (3 mL) were added Zn(CN) 2 (53 mg, 0.45 mmol) and Pd(PPh 3 ) 4 (44 mg, 0.038 mmol) at 25°C. The mixture was degassed 3 times with N 2 and then stirred at 120°C for 3 h. The mixture was poured into H 2 O and extracted twice with EtOAc. The combined organic phases were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated in vacuo. The crude product was purification by silica gel column (SiO 2 , petroleum ether : EtOAc = 50 : 1 to 30 : 1) and Prep-HPLC (with 0.1% formic acid) to afford tert-butyl (3S)-4-(7-(4-cyanopyridin-2- yl)-5-(2-methylmorpholino)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)- 3-methylpiperazine-1- carboxylate (10 mg, 25%) as a yellow solid. LC/MS ESI (m/z): 519 (M+H) + . Step 4. tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5-((R)-2-methylmorpholino)-7H - pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te The racemate tert-butyl (3S)-4-(7-(4-cyanopyridin-2-yl)-5-(2-methylmorpholino)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (10 mg, 0.019 mmol) was separate by chiral Prep-HPLC (IA-H 4.6*250mm IPA+0.05%DEA 40% 8min). The longer retention time peak labeled as tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5-((R)-2- methylmorpholino)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylp iperazine-1-carboxylate (2.0 mg, 0.004 mmol) was obtained as a white solid. LC/MS ESI (m/z): 519 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.30 (s, 1H), 8.52 (d, J = 4.8 Hz, 1H), 8.39 (s, 1H), 7.57 (s, 1H), 7.25 (d, J = 5.0 Hz, 1H), 4.98 (s, 1H), 4.29 – 4.04 (m, 2H), 3.93 – 3.69 (m, 4H), 3.43 – 3.30 (m, 2H), 3.28 – 3.11 (m, 2H), 2.80 (m, 1H), 2.55 – 2.33 (m, 2H), 1.43 (s, 9H), 1.10 – 1.05 (m, 3H), 0.83 – 0.76 (m, 3H). Scale-up using 2.0 g of tert-butyl (S)-4-(5-bromo-7-(4-chloropyridin-2-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te following the synthetic route described above gave 30 mg of tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5-((R)-2- methylmorpholino)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylp iperazine-1-carboxylate. Step 5.2-(5-((R)-2-methylmorpholino)-4-((S)-2-methylpiperazin-1-y l)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile To a solution of tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5-((R)-2- methylmorpholino)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylp iperazine-1-carboxylate (30 mg, 0.058 mmol) in DCM (5 mL) at 0°C was added HCl (0.072 mL, 4.0M in dioxane). The mixture was warmed up to 25°C and stirred for 4 h. The mixture was quenched with NaHCO 3 (aq.) and extracted twice with EtOAc. The combined organic phases were washed with brine, dried over Na 2 SO 4 , filtered and concentrated in vacuo.2-(5-((R)-2-methylmorpholino)-4-((S)- 2-methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)ison icotinonitrile (20 mg, 83%) was obtained as a yellow solid. LC/MS ESI m/z: 419 (M+H) + . Step 6.2-(4-((S)-4-(3,3-dimethylbutanoyl)-2-methylpiperazin-1-yl) -5-((R)-2- methylmorpholino)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotin onitrile To a solution of 2-(5-((R)-2-methylmorpholino)-4-((S)-2-methylpiperazin-1-yl) -7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (20 mg, 0.048 mmol) in DCM (4 mL) at 0°C was added Et 3 N (9.7 mg, 0.096 mmol), followed by 3,3-dimethylbutanoyl chloride (8.0 mg, 0.053 mmol). The mixture was stirred at 0°C for 1 h. The reaction was quenched with NaHCO 3 (aq.) and extracted twice with EtOAc. The combined organic phases were washed with brine, dried over Na 2 SO 4 , filtered and concentrated in vacuo. The crude product was purified by Prep-HPLC to afford 2-(4-((S)-4-(3,3-dimethylbutanoyl)-2-methylpiperazin-1-yl)- 5-((R)-2-methylmorpholino)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)i sonicotinonitrile (10 mg, 40%) as a yellow solid. LC/MS ESI m/z: 517 (M+H) + .1H NMR (400 MHz, CDCl 3 ) δ 9.30 (s, 1H), 8.52 (d, J= 5.0 Hz, 1H), 8.40 (d, J = 6.7 Hz, 1H), 7.59 (d, J = 8.4 Hz, 1H), 7.26 (d, J = 5.0 Hz, 1H), 5.06 (d, J = 48.9 Hz, 1H), 4.51 (dd, J= 35.9, 13.4 Hz, 1H), 4.34 – 4.07 (m, 1H), 3.98 – 3.87 (m, 1.5H), 3.85 – 3.65 (m, 2.5H, rotamers), 3.53 (dd, J= 13.3, 3.1 Hz, 0.5 H), 3.47 – 3.30 (m, 2H), 3.25 – 3.12 (m, 1.5H, rotamers), 3.03 (dd, J = 12.9, 2.6 Hz, 0.5H, rotamers), 2.74 – 2.60 (m, 0.5H, rotamers), 2.56 – 2.36 (m, 2H), 2.34 – 2.22 (m, 1.5H, rotamers), 2.16 – 2.09 (m, 0.5H, rotamers), 1.28 – 1.20 (m, 3H), 1.20 – 1.11 (m, 3H), 1.02 (d, J = 5.9 Hz, 9H). Example 30. Synthesis of 1-((2R,5S)-4-(5-(2-fluorophenyl)-7-(4-fluoropyridin-2-yl)-7H - pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazin-1-yl)-2- methylpropan-1-one (Compound 167) C ompound 167 Step 1.1-((2R,5S)-4-(5-(2-fluorophenyl)-7-(4-fluoropyridin-2-yl)- 7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazin-1-yl)-2-methylpropan -1-one To a solution of 4-((2S,5R)-2,5-dimethylpiperazin-1-yl)-5-(2-fluorophenyl)-7- (4- fluoropyridin-2-yl)-7H-pyrrolo[2,3-d]pyrimidine (100 mg, 0.24 mmol, prepared following the procedure described for compound 169) and TEA (0.19 mL, 1.4 mmol) in DCM (5 mL) was added a solution of 2-methylpropanoyl chloride (0.060 mL, 0.59 mmol) in DCM. The resulting mixture was stirred at 0ºC for 1 h. The reaction was quenched with NaHCO 3 (aq.) and extracted twice with DCM. The combined organic phases were washed with brine, dried over anhydrous Na 2 SO 4 , filtered and concentrated. The residue was purified by flash chromatography (0~50% ethyl acetate in petroleum ether) to give 1-[(2R,5S)-4-[5-(2- fluorophenyl)-7-(4-fluoropyridin-2-yl)-7H-pyrrolo[2,3-d]pyri midin-4-yl]-2,5- dimethylpiperazin-1-yl]-2-methylpropan-1-one (25 mg, 21%) as a white solid. LC/MS ESI m/z: 491 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 8.80 (d, J = 10.5 Hz, 1H), 8.56 (d, J = 4.7 Hz, 1H), 8.43 (dd, J = 8.5, 5.7 Hz, 1H), 8.31 (d, J = 3.3 Hz, 1H), 7.55 – 7.45 (m, 1H), 7.37 (dd, J = 13.0, 6.1 Hz, 1H), 7.21 (dd, J = 18.2, 8.6 Hz, 2H), 6.96 (t, J = 5.5 Hz, 1H), 4.74 – 4.29 (m, 1H), 4.06 (dd, J = 39.9, 5.2 Hz, 1H), 3.68 (m, 1H), 3.35 (d, J = 13.3 Hz, 1H), 3.21 – 2.73 (m, 2H), 2.58 (dt, J = 16.7, 8.6 Hz, 1H), 1.27 (d, J = 6.6 Hz, 1.5H, rotamers), 1.16 – 1.07 (m, 5.5H, rotamers), 1.04 – 0.80 (m, 5H). Example 31. Synthesis of 1-((2R,5S)-4-(7-(4-chloropyridin-2-yl)-5-(2-fluorophenyl)-7H - pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazin-1-yl)-2- methylpropan-1-one (Compound 168) Step 1. tert-butyl (2R,5S)-4-(7-(4-chloropyridin-2-yl)-5-(2-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate To a solution of tert-butyl (2R,5S)-4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin- 4-yl)-2,5-dimethylpiperazine-1-carboxylate (340 mg, 0.80 mmol, prepared following the procedure outlined in compound 169) and 4-chloro-2-fluoropyridine (210 mg, 1.6 mmol) in DMF (5 mL) was added Cs2CO3 (1.0 g, 3.2 mmol). The resulting mixture was stirred at 60℃ for 18 h. After cooling to room temperature, the reaction mixture was poured into water and extracted twice with EtOAc. The combined organic phases were washed with brine, dried over anhydrous Na 2 SO 4 , filtered and concentrated. The residue was purified by column chromatography on silica gel (0~40% EtOAc in petroleum ether) to give tert-butyl (2R,5S)-4- (7-(4-chloropyridin-2-yl)-5-(2-fluorophenyl)-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5- dimethylpiperazine-1-carboxylate (370 mg, 86%) as a white solid. LC/MS(ESI)m/z: 537(M+H) + Step 2.7-(4-chloropyridin-2-yl)-4-((2S,5R)-2,5-dimethylpiperazin- 1-yl)-5-(2- fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidine To a solution of tert-butyl (2R,5S)-4-(7-(4-chloropyridin-2-yl)-5-(2-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (300 mg, 0.56 mmol) in DCM (3 mL) was added TFA (1.0 mL, 14 mmol). The resulting mixture was stirred at 0ºC for 3 h. After removal of solvent, the residue was used directly to next step without further purification. LC/MS ESI m/z: 437 (M+H) + . Step 3.1-((2R,5S)-4-(7-(4-chloropyridin-2-yl)-5-(2-fluorophenyl)- 7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazin-1-yl)-2-methylpropan -1-one To a solution of 7-(4-chloropyridin-2-yl)-4-((2S,5R)-2,5-dimethylpiperazin-1- yl)-5- (2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidine (240 mg, 0.55 mmol) and TEA (0.46 mL, 3.3 mmol) in DCM (5.0 mL) at 0 o C was added a solution of 2-methylpropanoyl chloride (0.14 mL, 1.4 mmol) in DCM. The resulting mixture was stirred at the same temperature for 1 h. The mixture was quenched with NaHCO 3 (aq.) and extracted twice with DCM. The combined organic phases were washed with brine, dried over anhydrous Na 2 SO 4 , filtered and concentrated. The residue was purified by Prep-HPLC to give 1-((2R,5S)-4-(7-(4- chloropyridin-2-yl)-5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyri midin-4-yl)-2,5- dimethylpiperazin-1-yl)-2-methylpropan-1-one (70 mg, 25%) as a white solid. LC/MS(ESI)m/z: 507 (M+H) + , 1 H NMR (400 MHz, CDCl 3 ) δ 9.04 (s, 1H), 8.57 (d, J = 4.9 Hz, 1H), 8.37 (d, J = 5.3 Hz, 1H), 8.27 (d, J = 3.4 Hz, 1H), 7.49 (dd, J = 13.2, 6.3 Hz, 1H), 7.36 (dd, J = 12.9, 6.1 Hz, 1H), 7.20 (dt, J = 12.0, 8.5 Hz, 3H), 4.72 – 4.31 (m, 1H), 4.06 (m, 1H), 3.68 (m, 1H), 3.35 (d, J = 13.5 Hz, 1H), 3.22 – 2.73 (m, 2H), 2.64 – 2.50 (m, 1H), 1.30 – 1.07 (m, 6H), 1.05 – 0.80 (m, 6H).
Example 32. Synthesis of 1-((2R,5S)-4-(5-(2-fluorophenyl)-7-(4-fluoropyridin-2-yl)-7H - pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazin-1-yl)-2- hydroxy-2-methylpropan- 1-one (Compound 169) Step 1. tert-butyl (2R,5S)-4-(5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrim idin- 4-yl)-2,5-dimethylpiperazine-1-carboxylate A mixture of tert-butyl (2R,5S)-4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)- 2,5-dimethylpiperazine-1-carboxylate (3.1 g, 5.0 mmol, prepared following a similar procedure described for compound 128), (2-fluorophenyl)boronic acid (0.84 g, 6.0 mmol), K 2 CO 3 (1.4 g, 10 mmol) and Pd(dppf)Cl 2 (0.36 g, 0.50 mmol) in dioxane-water (30 mL, 5:1 v/v) was stirred at 90℃ under N 2 atmosphere for 18 h. After cooling to room temperature, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic phases were washed with brine, dried over anhydrous Na 2 SO 4 , filtered and concentrated. The residue was purified by column chromatography on silica gel (0~30% EtOAc in petroleum ether) to give tert-butyl (2R,5S)-4-(5-(2- fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-d imethylpiperazine-1- carboxylate (2.7 g, 93%) as a white solid. LC/MS ESI m/z: 580 (M+H) + Step 2. tert-butyl (2R,5S)-4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-y l)- 2,5-dimethylpiperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-4-(5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate (2.7 g, 4.7 mmol) in THF (20 mL) was added TBAF (12 mL, 1.0M in THF). The resulting mixture was stirred at room temperature overnight. The reaction was poured into water and extracted twice with EtOAc. The combined organic phases were washed water and brine, dried over anhydrous Na 2 SO 4 , filtered and concentrated. The residue was purified by column chromatography on silica gel (0~70% ethyl acetate in petroleum ether) to give tert-butyl (2R,5S)-4-(5-(2-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (1.8 g, 91%) as a white solid. LC/MS ESI m/z: 426 (M+H) + Step 3. tert-butyl (2R,5S)-4-(5-(2-fluorophenyl)-7-(4-fluoropyridin-2-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate A mixture of tert-butyl (2R,5S)-4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4- yl)-2,5-dimethylpiperazine-1-carboxylate (550 mg, 1.3 mmol), 2-bromo-4-fluoropyridine (680 mg, 3.9 mmol), K 3 PO 4 (820 mg, 3.9 mmol), CuI (120 mg, 0.64 mmol) and trans-N,N’- dimethylcyclohexane-1,2-diamine (280 mg, 1.9 mmol) in DMF (20 mL) was stirred at 90℃ under N 2 atmosphere overnight. After cooling to room temperature, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic phases were washed with brine, dried over anhydrous Na 2 SO 4 , filtered and concentrated. The residue was purified by column chromatography on silica gel (0~40% ethyl acetate in petroleum ether) to give tert-butyl (2R,5S)-4-(5-(2-fluorophenyl)-7-(4- fluoropyridin-2-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dim ethylpiperazine-1-carboxylate (580 mg, 86%) as a white solid. LC/MS ESI m/z: 521 (M+H) + . Step 4.4-((2S,5R)-2,5-dimethylpiperazin-1-yl)-5-(2-fluorophenyl)- 7-(4-fluoropyridin- 2-yl)-7H-pyrrolo[2,3-d]pyrimidine To a solution of tert-butyl (2R,5S)-4-(5-(2-fluorophenyl)-7-(4-fluoropyridin-2-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (580 mg, 1.1 mmol) in DCM (5 mL) was added TFA (1.7 mL, 22 mmol), the reaction was stirred at 0ºC for 2 h. After removal of solvent, the residue was used directly in next step. LC/MS ESI m/z: 421 (M+H) + . Step 5.1-((2R,5S)-4-(5-(2-fluorophenyl)-7-(4-fluoropyridin-2-yl)- 7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazin-1-yl)-2-hydroxy-2-me thylpropan-1-one To a solution of 4-((2S,5R)-2,5-dimethylpiperazin-1-yl)-5-(2-fluorophenyl)-7- (4- fluoropyridin-2-yl)-7H-pyrrolo[2,3-d]pyrimidine (210 mg, 0.50 mmol) in DMF (5.0 mL) were added DIEA (0.33 mL, 2.0 mmol), 2-hydroxy-2-methylpropanoic acid (62 mg, 0.60 mmol) and HATU (230 mg, 0.60 mmol). The resulting mixture was stirred at room temperature for 30 minutes. The reaction was quenched with NaHCO 3 (aq.) and extracted twice with EtOAc. The combined organic phases were washed with brine, dried over anhydrous Na 2 SO 4 , filtered and concentrated. The residue was purified by column chromatography on silica gel (0~50% ethyl acetate in petroleum ether) and Prep-HPLC to give 1-((2R,5S)-4-(5-(2-fluorophenyl)-7-(4-fluoropyridin-2-yl)-7H -pyrrolo[2,3-d]pyrimidin- 4-yl)-2,5-dimethylpiperazin-1-yl)-2-hydroxy-2-methylpropan-1 -one (70 mg, 28%) as a white solid. LC/MS ESI m/z: 507 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 8.80 (dd, J = 10.9, 1.9 Hz, 1H), 8.57 (s, 1H), 8.43 (dd, J = 8.6, 5.7 Hz, 1H), 8.32 (s, 1H), 7.51 (t, J = 6.3 Hz, 1H), 7.40 – 7.33 (m, 1H), 7.27 – 7.13 (m, 2H), 7.01 – 6.87 (m, 1H), 4.46 (m, 2H), 4.06 – 3.81 (m, 1H), 3.58 – 2.52 (m, 3H), 1.48 (m, 9H), 0.92 (pair of s, 3H, rotamers). Example 33. Synthesis of (S)-6-(5-(2-fluorophenyl)-4-(4-isobutyryl-2-methylpiperazin- 1- yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)pyridazine-4-carbonitril e (Compound 171) Step 1. tert-butyl (S)-4-(7-(5-chloropyridazin-3-yl)-5-(2-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te To a solution of tert-butyl (S)-4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4- yl)-3-methylpiperazine-1-carboxylate (160 mg, 0.40 mmol, prepared following a similar procedure described for compound 128) in THF (2 mL) was added NaH (64 mg, 0.16 mmol, 60% wt) at 0ºC. The resulting mixture was stirred for 20 min under N 2 atmosphere before 3,5-dichloropyridazine (120 mg, 0.80 mmol) was added. After stirring at room temperature overnight, the reaction was quenched with NH 4 Cl (aq.) and diluted with EtOAc. The organic layer was washed with brine, dried over Na 2 SO 4 , filter and concentrated. The residue was purified by flash column chromatography (silica gel, 0~40% EtOAc in petroleum ether) to afford tert-butyl (S)-4-(7-(5-chloropyridazin-3-yl)-5-(2-fluorophenyl)-7H-pyrr olo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate (72 mg, 34% yield) as a white solid. LC/MS ESI (m/z): 524 (M+H) + . The regioisomer tert-butyl (S)-4-(7-(6-chloropyridazin-4- yl)-5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-me thylpiperazine-1-carboxylate (72 mg, 34%) was also obtained as a white solid. LC/MS ESI (m/z): 524 (M+H) + . Step 2. (S)-7-(5-chloropyridazin-3-yl)-5-(2-fluorophenyl)-4-(2-methy lpiperazin-1-yl)- 7H-pyrrolo[2,3-d]pyrimidine To a solution of tert-butyl (S)-4-(7-(5-chloropyridazin-3-yl)-5-(2-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (72 mg, 0.14 mmol) in DCM (5 mL) at 0 o C was added TFA (1.0 mL). The resulting mixture was stirred at the room temperature for 1 h. The reaction mixture was basified with NaHCO 3 (aq.) and extracted twice with DCM. The combined organic layers were washed with NaHCO 3 (aq.), dried over Na 2 SO 4 and concentrated to afford the (S)-7-(5-chloropyridazin-3-yl)-5-(2-fluorophenyl)-4- (2-methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidine (50 mg, 88%) as a yellow solid which was used in the next step without further purification. LC/MS ESI m/z: 424 (M+H) + Step 3. (S)-1-(4-(7-(5-chloropyridazin-3-yl)-5-(2-fluorophenyl)-7H-p yrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazin-1-yl)-2-methylpropan-1-o ne To a solution of (S)-7-(5-chloropyridazin-3-yl)-5-(2-fluorophenyl)-4-(2- methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidine (50 mg, 0.11 mmol) and TEA (36 mg, 0.30 mmol) in DCM (5 mL) at 0 o C was added isobutyryl chloride (25 mg, 0.24 mmol). The resulting mixture was stirred at room temperature for 20 minutes. The reaction was quenched with ice water and extracted twice with DCM. The combined layers were washed with NaHCO 3 (aq.) and brine, dried over Na 2 SO 4 and concentrated. The residue was purified by column chromatography on silica gel (0~40% EtOAc in petroleum ether, V/V) to give (S)-1- (4-(7-(5-chloropyridazin-3-yl)-5-(2-fluorophenyl)-7H-pyrrolo [2,3-d]pyrimidin-4-yl)-3- methylpiperazin-1-yl)-2-methylpropan-1-one (51 mg, 90%) as a yellow solid LC/MS ESI m/z: 494 (M+H) + Step 4. (S)-6-(5-(2-fluorophenyl)-4-(4-isobutyryl-2-methylpiperazin- 1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)pyridazine-4-carbonitrile To a solution of (S)-1-(4-(7-(5-chloropyridazin-3-yl)-5-(2-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazin-1-yl)-2-meth ylpropan-1-one (51 mg, 0.10 mmol) in DMF (5 mL) was added Zn(CN) 2 (49 mg, 0.40 mmol) and Pd(PPh 3 ) 4 (53 mg, 0.040 mmol). The mixture was stirred at 120°C under N 2 atmosphere for 3 h. After cooling to room temperature, the reaction mixture was diluted with EtOAc, washed with brine, dried over Na 2 SO 4 , filter and concentrated. The residue was purified by flash column chromatography (silica gel, 0~40% EtOAc in petroleum ether) to provide a crude product which was further purified by Prep-HPLC to afford (S)-6-(5-(2-fluorophenyl)-4-(4-isobutyryl-2- methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)pyrida zine-4-carbonitrile (20 mg, 40% yield) as a yellow solid. LC/MS ESI (m/z): 485 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.77 (s, 1H), 9.23 (s, 1H), 8.58 – 8.53 (m, 1H), 8.51 – 8.47 (m, 1H), 7.51 – 7.46 (m, 1H), 7.42 – 7.38 (m, 1H), 7.22 – 7.18 (m, 2H), 4.48 – 4.04 (m, 2H), 3.69 – 3.61 (m, 1H), 3.51 – 3.43 (m, 1H), 3.25 – 3.02 (m, 2H), 2.77 – 2.66 (m, 1H), 2.58 – 2.48 (m, 1H), 1.11 – 0.91 (m, 9H). Example 34. Synthesis of 2-(5-(2-fluorophenyl)-4-(7-(2-hydroxy-2-methylpropanoyl)- 4,7-diazaspiro[2.5]octan-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-7- yl)isonicotinonitrile (Compound 174) Step 1.2-(5-(2-fluorophenyl)-4-(7-(2-hydroxy-2-methylpropanoyl)-4 ,7- diazaspiro[2.5]octan-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)i sonicotinonitrile To a solution of 2-(5-(2-fluorophenyl)-4-(4,7-diazaspiro[2.5]octan-4-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (60 mg, 0.16 mmol, prepared following the procedure described for compound 155) in DMF (4 mL) were added 2-hydroxy-2- methylpropanoic acid (29 mg, 0.28 mmol), DIEA (55 mg, 0.42 mmol) and HATU (84 mg, 0.23 mmol). The resulting mixture was stirred at room temperature overnight. The reaction was quenched with NaHCO 3 (aq.) and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50%, ethyl acetate in petroleum ether) to give crude product which was further purified by prep-HPLC to afford 2-(5-(2- fluorophenyl)-4-(7-(2-hydroxy-2-methylpropanoyl)-4,7-diazasp iro[2.5]octan-4-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (20 mg, 38%) as a white solid. LC/MS ESI m/z: 512 (M+H) + . 1 HNMR(400 MHz, CDCl 3 ) δ 9.32 (s, 1H), 8.61 (s, 1H), 8.57 (d, J = 4.9 Hz, 1H), 8.26 (s, 1H), 7.37 – 7.34 (m, 1H), 7.33 – 7.27 (m, 2H), 7.15 – 7.08 (m, 2H), 4.06 – 3.90 (m, 1H), 3.81 – 3.63 (m, 2H), 3.44 – 3.25 (m, 1H), 3.02 – 2.86 (m, 2H), 1.34 (s, 6H), 0.94 – 0.70 (m, 4H). The following compounds were prepared by the procedures similar to the synthesis of compound 174 from the corresponding amine (tert-butyl 3,3-dimethylpiperazine-1- carboxylate).
Example 35. Synthesis of 1-((2R,5S)-4-(7-(3,5-difluorophenyl)-5-(3-methylpyrazin-2-yl )- 7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazin-1-yl) -3-methylbutan-1-one (Compound 177) Step 1. tert-butyl (2R,5S)-4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2 ,5- dimethylpiperazine-1-carboxylate To a solution of 4-chloro-5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (12 g, 28 mmol, prepared following the procedure described for compound 128) in DIPEA (15 mL) was added tert-butyl (2R,5S)-2,5-dimethylpiperazine-1-carboxylate (9.0 g, 42 mmol). The resulting mixture was heated to 150 o C for 3 h under N 2 atmosphere. After cooling to room temperature, solvent was removed and the residue was purified by flash column chromatography (silica gel, 0~30%, ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2 ,5-dimethylpiperazine-1- carboxylate (16 g, 94%) as a light yellow solid. LC/MS ESI m/z: 612 (M+H) + . Step 2. tert-butyl (2R,5S)-2,5-dimethyl-4-(5-(4,4,5,5-tetramethyl-1,3,2-dioxabo rolan- 2-yl)-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperazine-1-c arboxylate To a solution of tert-butyl (2R,5S)-4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4- yl)-2,5-dimethylpiperazine-1-carboxylate (2.0 g, 3.2 mmol) in dioxane (20 mL) were added 4,4,5,5-tetramethyl-1,3,2-dioxaborolane (1.7 g, 13 mmol), TEA (2.2 mL, 16 mmol), X-Phos (0.31 g, 0.65 mmol) and Pd 2 (dba) 3 (0.30 g, 0.32 mmol). The resulting mixture was stirred at 95 o C overnight. After cooling to room temperature, the reaction was quenched with water and extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated to afford crude tert-butyl (2R,5S)-2,5-dimethyl-4-(5- (4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-7-tosyl-7H-pyr rolo[2,3-d]pyrimidin-4- yl)piperazine-1-carboxylate as a brown oil, which was used in the next step directly. LC/MS ESI m/z: 612 (M+H) + . Step 3. tert-butyl (2R,5S)-2,5-dimethyl-4-(5-(3-methylpyrazin-2-yl)-7-tosyl-7H- pyrrolo[2,3-d]pyrimidin-4-yl)piperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-2,5-dimethyl-4-(5-(4,4,5,5-tetramethyl-1,3,2- dioxaborolan-2-yl)-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)p iperazine-1-carboxylate (2.0 g, 3.2 mmol, theoretical) in dioxane (20 mL) and H 2 O (4 mL) were added 2-chloro-3- methylpyrazine (0.92 g, 7.2 mmol), K 2 CO 3 (2.5 g, 18 mmol) and Pd(dppf)Cl 2 (0.26 g, 0.36 mmol). The resulting mixture was heated to 90 o C overnight. After cooling to room temperature, solvent was removed and the residue was purified by flash column chromatography (silica gel, 0~50%, ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-2,5-dimethyl-4-(5-(3-methylpyrazin-2-yl)-7-tosyl-7H- pyrrolo[2,3-d]pyrimidin-4- yl)piperazine-1-carboxylate (1.3 g, 62 %) as a yellow solid. LC/MS ESI m/z: 578 (M+H) + . Step 4. tert-butyl (2R,5S)-2,5-dimethyl-4-(5-(3-methylpyrazin-2-yl)-7H-pyrrolo[ 2,3- d]pyrimidin-4-yl)piperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-2,5-dimethyl-4-(5-(3-methylpyrazin-2-yl)-7-tosyl- 7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperazine-1-carboxylate (1.3 g, 2.2 mmol) in THF (10 mL) was added TBAF (10 mL, 1.0M in THF). The resulting mixture was stirred at room temperature for 2 h. The reaction was quenched with water and extracted twice with EtOAc. The combined organic layers were washed with NH 4 Cl (aq.), dried over Na 2 SO 4 , filtered and concentrated to afford crude tert-butyl (2R,5S)-2,5-dimethyl-4-(5-(3-methylpyrazin-2-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)piperazine-1-carboxylate (950 mg, 99 %) as a brown solid. LC/MS ESI m/z: 424 (M+H) + . Step 5. tert-butyl (R)-4-(7-(3,5-difluorophenyl)-5-(pyridin-2-yl)-7H-pyrrolo[2, 3- d]pyrimidin-4-yl)-2-methylpiperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-2,5-dimethyl-4-(5-(3-methylpyrazin-2-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)piperazine-1-carboxylate (480 mg, 1.1 mmol) in DMF (5 mL) were added 1,3-difluoro-5-iodobenzene (310 mg, 1.3 mmol), trans-N,N’- dimethylcyclohexane-1,2-diamine (71 mg, 0.50 mmol), CuI (210 mg, 1.1 mmol) and K 3 PO 4 (700 mg, 3.3 mmol). The resulting mixture was heated to 120 o C overnight. After cooling to room temperature, the reaction was quenched with water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~30%, ethyl acetate in petroleum ether) to give crude product which was further purified by Prep- HPLC to afford tert-butyl (2R,5S)-4-(7-(3,5-difluorophenyl)-5-(3-methylpyrazin-2-yl)-7 H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (780 mg, 84 %) as a white solid. LC/MS ESI m/z: 536 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 8.57 – 8.51 (m, 3H), 7.49 – 7.43 (m, 3H), 6.84 (t, J = 8.7 Hz, 1H), 4.09 (m, 2H), 3.31 (m, 2H), 3.09 (s, 1H), 2.95 – 2.66 (m, 1H), 2.53 (s, 3H), 1.43 (s, 9H), 1.02 – 0.97 (m, 6H). Step 6.7-(3,5-difluorophenyl)-4-((2S,5R)-2,5-dimethylpiperazin-1- yl)-5-(3- methylpyrazin-2-yl)-7H-pyrrolo[2,3-d]pyrimidine To a solution of tert-butyl (2R,5S)-4-(7-(3,5-difluorophenyl)-5-(3-methylpyrazin-2- yl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine- 1-carboxylate (650 mg, 1.2 mmol) in DCM (3 mL) at 0 o C was added TFA (2.0 mL). The resulting mixture was stirred at the room temperature for 1.5 h. The reaction was quenched with NaHCO 3 (aq.). The aqueous layer was extracted with DCM twice. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was used in the next step directly. LC/MS ESI m/z: 436 (M+H) + . Step 7.1-((2R,5S)-4-(7-(3,5-difluorophenyl)-5-(3-methylpyrazin-2- yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazin-1-yl)-3- methylbutan-1-one To a solution of 7-(3,5-difluorophenyl)-4-((2S,5R)-2,5-dimethylpiperazin-1-yl )-5-(3- methylpyrazin-2-yl)-7H-pyrrolo[2,3-d]pyrimidine (100 mg, 0.23 mmol) in DCM (3 mL) at 0 o C were added dropwise TEA (0.060 mL, 0.46 mmol) and 3-methylbutanoyl chloride (0.040 mL, 0.34 mmol). The resulting mixture was stirred at room temperature for 1.5 h. The reaction was quenched with ice water and extracted twice with DCM. The combined organic layers were washed with NaHCO 3 (aq.) and brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, ethyl acetate in petroleum ether) to give crude product which was further purified by Prep-HPLC to afford 1-((2R,5S)-4-(7-(3,5-difluorophenyl)-5-(3-methylpyrazin-2-yl )-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazin-1-yl)-3-methylbutan- 1-one (33 mg, 27%) as a white solid. LC/MS ESI m/z: 520 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 8.58 – 8.50 (m, 3H), 7.47 (t, J = 7.1 Hz, 3H), 6.85 (t, J = 8.6 Hz, 1H), 4.52 (pair of s, 1H, rotamers), 3.98 (s, 1H), 3.88 (d, J = 13.5 Hz, 0.5H, rotamers), 3.50 (d, J = 13.1 Hz, 0.5H, rotamers), 3.27 – 3.19 (m, 2H), 2.98 – 2.92 (m, 0.5H, rotamers), 2.54 (s, 3H), 2.39 (d, J = 14.7 Hz, 0.5H, rotamers), 2.32 – 2.25 (m, 0.5H, rotamers), 2.13 – 2.03 (m, 2.5H, rotamers), 1.18 (d, J = 6.6 Hz, 1.5H, rotamers), 1.08 (d, J = 6.6 Hz, 1.5H, rotamers), 0.98 – 0.91 (m, 7.5H, rotamers), 0.86 (d, J = 6.6 Hz, 1.5H, rotamers). The following compounds were prepared by the procedures analogous to the synthesis of compound 177 from the corresponding acid chlorides and aryl halides. Example 36. Synthesis of 2-(5-(2-fluorophenyl)-4-((2R,5S)-4-isobutyryl-2,5- dimethylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)ison icotinonitrile (Compound 201) Compound 201 Step 1.4-Chloro-5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrim idine To a solution of 4-chloro-5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (1.1 g, 2.5 mmol, prepared following the procedure outlined for compound 230) in DMF (15 mL) and water (0.5 mL) were added (2-fluorophenyl)boronic acid (420 mg, 0.60 mmol), X-Phos (180 mg, 0.37 mmol), K 3 PO 4 (1.6 g, 7.5 mmol) and Pd 2 (dba) 3 (230 mg, 0.25 mmol). The resulting mixture was heated at 60 o C overnight. After cooling to room temperature, the reaction mixture was filtered, and the filtrate was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50% ethyl acetate in petroleum ether) to afford 4-chloro-5-(2- fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (600 mg, 60%). LC/MS ESI (m/z): 402 (M+H) + . Step 2. tert-Butyl (2S,5R)-4-(5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrim idin- 4-yl)-2,5-dimethylpiperazine-1-carboxylate To a solution of 4-chloro-5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrimid ine (300 mg, 0.74 mmol) in DIPEA (0.40 mL, 2.2 mmol) was added tert-butyl (2S,5R)-2,5- dimethylpiperazine-1-carboxylate (240 mg, 1.1 mmol). The resulting mixture was heated at 150℃ for 2 h. After cooling to room temperature, the solvent was removed and the residue was purified by flash column chromatography (silica gel, 0~20% ethyl acetate in petroleum ether) to afford tert-butyl (2S,5R)-4-(5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrim idin- 4-yl)-2,5-dimethylpiperazine-1-carboxylate (320 mg, 74%) as a white solid. LC/MS ESI (m/z): 580 (M+H) + . Step 3.4-((2R,5S)-2,5-Dimethylpiperazin-1-yl)-5-(2-fluorophenyl)- 7-tosyl-7H- pyrrolo[2,3-d]pyrimidine To a solution of tert-butyl (2S,5R)-4-(5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate (320 mg, 0.55 mmol) in DCM (3 mL) was added HCl (1.0 mL, 4.0 M in dioxane). The resulting mixture was stirred at room temperature for 2 h. After removal of solvent, the residue was used in the next step directly. LC/MS ESI (m/z): 480 (M+H) + . Step 4.1-((2S,5R)-4-(5-(2-Fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d] pyrimidin-4-yl)- 2,5-dimethylpiperazin-1-yl)-2-methylpropan-1-one To a solution of 4-((2R,5S)-2,5-dimethylpiperazin-1-yl)-5-(2-fluorophenyl)-7- tosyl- 7H-pyrrolo[2,3-d]pyrimidine (260 mg, 0.54 mmol) and TEA (0.38 mL, 2.7 mmol) in DCM (3 mL) at 0℃ was added isobutyryl chloride (0.12 mL, 1.1 mmol). After 1 h, the reaction was partitioned between DCM and water. The aqueous layer was extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50% ethyl acetate in petroleum ether) to afford 1-((2S,5R)-4-(5-(2-fluorophenyl)-7-tosyl-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazin-1-yl)-2- methylpropan-1-one (290 mg, 95%) as a white solid. LC/MS ESI (m/z): 550 (M+H) + . Step 5.1-((2S,5R)-4-(5-(2-Fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidi n-4-yl)-2,5- dimethylpiperazin-1-yl)-2-methylpropan-1-one To a solution of 1-((2S,5R)-4-(5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazin-1-yl)-2-methylpropan -1-one (290 mg, 0.52 mmol) in THF (3 mL) was added TBAF (2.1 mL, 1.0 M in THF). After 2 h, the reaction was diluted with water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~60% ethyl acetate in petroleum ether) to afford 1-((2S,5R)-4- (5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dim ethylpiperazin-1-yl)-2- methylpropan-1-one (200 mg, 97%) as a white solid. LC/MS ESI (m/z): 396 (M+H) + . Step 6.2-(5-(2-Fluorophenyl)-4-((2R,5S)-4-isobutyryl-2,5-dimethyl piperazin-1-yl)- 7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile To a solution of 1-((2S,5R)-4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin- 4-yl)- 2,5-dimethylpiperazin-1-yl)-2-methylpropan-1-one (200 mg, 0.50 mmol) in DMF (10 mL) were added 2-fluoroisonicotinonitrile (120 mg, 1.0 mmol) and Cs 2 CO 3 (1.6 g, 5.1 mmol). The resulting mixture was stirred at 50℃ for 1 h. After cooling to room temperature, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50% ethyl acetate in petroleum ether) to give crude product which was further purified by prep-HPLC to afford 2-(5-(2-fluorophenyl)-4-((2R,5S)-4-isobutyryl-2,5-dimethylpi perazin-1- yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (27 mg, 10%) as a white solid. LC/MS ESI (m/z): 498 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.34 (s, 1H), 8.56 (d, J = 4.9 Hz, 1H), 8.51 (d, J = 6.0 Hz, 1H), 8.23 (d, J = 4.6 Hz, 1H), 7.43 (dd, J = 13.9, 6.9 Hz, 1H), 7.35 – 7.28 (m, 2H), 7.20 – 7.10 (m, 2H), 4.60 (br. s, ~0.5H), 4.34 (br. s, ~0.5H), 4.05 (br. s, ~0.5H), 3.95 (br. s, ~0.5H), 3.78 (d, J = 16 Hz, ~0.5H), 3.48 (d, J = 16 Hz, ~0.5H), 3.27 (m, 1H), 3.16 – 3.02 (m, 1H), 2.80 – 2.37 (m, 2H), 1.21 (d, J = 6.6 Hz, 2H), 1.10 – 1.01 (m, 5H), 0.99 – 0.89 (m, 4H), 0.76 (d, J = 6.6 Hz, 1H); several peaks and their integrations are fractions of protons on account of presence of rotomers. Example 37. Synthesis of 2-(5-cyclopropyl-4-((S)-4-((R)-2-fluoro-3,3-dimethylbutanoyl )- 2-methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)ison icotinonitrile (Compound 202) and 2-(5-cyclopropyl-4-((S)-4-((S)-2-fluoro-3,3-dimethylbutanoyl )-2- methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonic otinonitrile (Compound 203) Ms Step 1. N-(3,3-Dimethylbut-1-yn-1-yl)-N-methylmethanesulfonamide To a suspension of CuCl 2 (65 mg, 0.49 mmol), N-methylmethanesulfonamide (660 mg, 6.1 mmol) and Na2CO3 (520 mg, 4.9 mmol) in toluene (12 mL) under O2 atmosphere was added pyridine (430 mg, 4.9 mmol). After stirring at 70 o C for 15 min, a solution of 3,3- dimethylbut-1-yne (200 mg, 2.4 mmol) in toluene (12 mL) was added dropwise. After stirring at 70 o C for 4 h, the reaction was cooled to room temperature and the solvent was removed. The residue was purified by flash chromatography (silica gel, ethyl acetate in petroleum ether) to afford N-(3,3-dimethylbut-1-yn-1-yl)-N-methylmethanesulfonamide (230 mg, 50%). Step 2.2-Fluoro-N,3,3-trimethyl-N-(methylsulfonyl)butanamide To a solution of N-(3,3-dimethylbut-1-yn-1-yl)-N-methylmethanesulfonamide (180 mg, 1.0 mmol) in MeCN (15 mL) and water (5 mL) was added SelectFluor (710 mg, 2.0 mmol). After stirring at room temperature for 2 h, the solvent was removed and the residue was purified by flash chromatography (silica gel) to afford 2-fluoro-N,3,3-trimethyl-N- (methylsulfonyl)butanamide (80 mg, 36%). Step 3.2-(5-Cyclopropyl-4-((S)-4-((R)-2-fluoro-3,3-dimethylbutano yl)-2- methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonic otinonitrile and 2-(5- cyclopropyl-4-((S)-4-((S)-2-fluoro-3,3-dimethylbutanoyl)-2-m ethylpiperazin-1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile A mixture of (S)-2-(5-cyclopropyl-4-(2-methylpiperazin-1-yl)-7H-pyrrolo[2 ,3- d]pyrimidin-7-yl)isonicotinonitrile (110 mg, 0.31 mmol, prepared following the procedure outlined for compound 264) and 2-fluoro-N,3,3-trimethyl-N-(methylsulfonyl)butanamide (70 mg, 0.31 mmol) in THF (5 mL) was stirred at 80 o C for 12 h. After cooling to room temperature, the solvent was removed and the residue was purified by flash chromatography (silica gel, 0~50% ethyl acetate in petroleum ether) and prep-HPLC to afford two isomers: Peak 1 was assigned as 2-(5-cyclopropyl-4-((S)-4-((R)-2-fluoro-3,3-dimethylbutanoyl )-2- methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonic otinonitrile compound 202 (5.0 mg, 3.0%) without additional confirmation. The material was isolated as a white solid. LC/MS ESI (m/z): 476 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.32 (s, 1H), 8.58 (d, J = 4.9 Hz, 1H), 8.52 (s, 1H), 7.80 (d, J = 0.8 Hz, 1H), 7.35 (dd, J = 5.0, 1.3 Hz, 1H), 5.00 – 4.83 (m, 1H), 4.83 – 4.61 (m, 1H), 4.44 – 4.37 (m, 1H), 4.22 (d, J = 12.8 Hz, ~0.5 H), 4.02 – 3.88 (m, 1H), 3.75 – 3.54 (m, 2H), 3.45 – 3.38 (m, ~0.5 H), 3.25 – 3.17 (m, 1H), 2.05 – 2.01 (m, 1H), 1.32 (d, J = 6.6 Hz, ~1.5 H), 1.20 (d, J = 6.7 Hz, ~1.5 H), 1.11 and 1.10 (pair of s, 9H), 1.06 – 1.02 (m, 2H), 0.89 – 0.85 (m, 1H), 0.80 – 0.74 (m, 1H); several peaks and their integrations are fractions of protons on account of presence of rotomers. Peak 2 was assigned as 2-(5-cyclopropyl-4-((S)-4-((S)-2-fluoro-3,3- dimethylbutanoyl)-2-methylpiperazin-1-yl)-7H-pyrrolo[2,3-d]p yrimidin-7- yl)isonicotinonitrile compound 203 (5.0 mg, 0.3%) without additional confirmation. The material was isolated as a white solid. LC/MS ESI (m/z): 476 (M+H) + . 1 H NMR(400 MHz, CDCl 3 ) δ 9.32 (s, 1H), 8.58 (d, J = 5.0 Hz, 1H), 8.51 (d, J = 2.2 Hz, 1H), 7.80 (d, J = 2.5 Hz, 1H), 7.35 (m, 1H), 4.98 – 4.67 (m, 2H), 4.49 – 4.39 (m, 1H), 4.20 – 4.10 (m, 1H), 4.05 – 3.92 (m, 1H), 3.63 – 3.45 (m, 2H), 3.23 – 3.10 (m, 1H), 2.05 – 1.99 (m, 1H), 1.30 (d, J = 6.7 Hz, ~1.5H), 1.21 (d, J = 6.7 Hz, ~1.5H), 1.13 and 1.09 (pair of s, 9H), 1.06 – 1.02 (m, 2H), 0.89 – 0.86 (m, 1H), 0.80 – 0.75 (m, 1H); several peaks and their integrations are fractions of protons on account of presence of rotomers.
Example 38. Synthesis of 1-((2R,5S)-4-(7-(3-chlorophenyl)-5-(trifluoromethyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazin-1-yl)-2, 2-dimethylpropan-1-one (Compound 204) Step 1.4-Chloro-7-(3-chlorophenyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimi dine To a solution of 4-chloro-5-iodo-7H-pyrrolo[2,3-d]pyrimidine (10 g, 36 mmol) in DCM (400 mL) were added (3-chlorophenyl)boronic acid (8.7 g, 72 mmol), 4Å molecular sieves (5.0 g), Cu(OAc) 2 (16 g, 89 mmol) and pyridine (17 mL, 210 mmol). The resulting mixture was stirred at room temperature under O 2 atmosphere for 48 hours. The reaction was then quenched with aq. NH 4 OH (30 mL) in an ice water bath and filtered. The filtrate was extracted twice with DCM twice. The combined organic layers were dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~30% ethyl acetate in petroleum ether) to afford 4-chloro-7-(3-chlorophenyl)-5-iodo- 7H-pyrrolo[2,3-d]pyrimidine (7.5 g, 54%) as a white solid. LC/MS ESI (m/z): 390 (M+H) + . Step 2. tert-Butyl (2R,5S)-4-(7-(3-chlorophenyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimi din- 4-yl)-2,5-dimethylpiperazine-1-carboxylate To a solution of 4-chloro-7-(3-chlorophenyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimidi ne (5.0 g, 13 mmol) in DIPEA (50 mL) was added tert-butyl (2R,5S)-2,5-dimethylpiperazine-1- carboxylate (5.5 g, 26 mmol). After stirring at 150 o C for 2 h under N 2 , the reaction was concentrated and purified by flash column chromatography (silica gel, 0~20% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(7-(3-chlorophenyl)-5-iodo-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate (7.0 g, 89%) as a white solid. LC/MS ESI (m/z): 568 (M+H) + . Step 3. tert-Butyl (2R,5S)-4-(7-(3-chlorophenyl)-5-(trifluoromethyl)-7H-pyrrolo [2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-4-(7-(3-chlorophenyl)-5-iodo-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate (1.0 g, 1.8 mmol) in DMF (10 mL) were added methyl 2,2-difluoro-2-(fluorosulfonyl)acetate (1.1 g, 5.6 mmol) and CuI (38 mg, 0.20 mmol). The resulting mixture was heated at 80 o C overnight. After cooling to room temperature, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~30% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(7-(3-chlorophenyl)-5-(trifluoromethyl)-7H-pyrrolo [2,3-d]pyrimidin-4-yl)-2,5- dimethylpiperazine-1-carboxylate (600 mg, 67%) as a white solid. LC/MS ESI (m/z): 510 (M+H) + . Step 4.7-(3-Chlorophenyl)-4-((2S,5R)-2,5-dimethylpiperazin-1-yl)- 5- (trifluoromethyl)-7H-pyrrolo[2,3-d]pyrimidine To a solution of tert-butyl (2R,5S)-4-(7-(3-chlorophenyl)-5-(trifluoromethyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (480 mg, 0.94 mmol) in DCM (2 mL) was added TFA (2 mL). The resulting mixture was stirred at room temperature for 2 h. After removal of solvent, the residue was diluted with DCM and washed with NaHCO 3 (aq.). The organic layer was washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was used in the next step directly. LC/MS ESI (m/z): 410 (M+H) + . Step 5. tert-Butyl (2R,5S)-4-(7-(3-chlorophenyl)-5-(trifluoromethyl)-7H-pyrrolo [2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate To a solution of 7-(3-chlorophenyl)-4-((2S,5R)-2,5-dimethylpiperazin-1-yl)-5- (trifluoromethyl)-7H-pyrrolo[2,3-d]pyrimidine (180 mg, 0.44 mmol) in DCM (10 mL) at 0 o C were added TEA (55 mg, 0.54 mmol) and pivaloyl chloride (130 mg, 1.2 mmol). The resulting mixture was stirred at room temperature for 2 h. The reaction was diluted with DCM and washed with brine. The aqueous layer was extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50% ethyl acetate in petroleum ether) to give crude product which was further purified by prep- HPLC to afford 1-((2R,5S)-4-(7-(3-chlorophenyl)-5-(trifluoromethyl)-7H-pyrr olo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazin-1-yl)-2,2-dimethylpr opan-1-one (92 mg, 43%) as a white solid. LC/MS ESI (m/z): 494 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 8.53 (s, 1H), 7.76 – 7.69 (m, 2H), 7.61 – 7.56 (m, 1H), 7.52 – 7.41 (m, 2H), 4.78 – 4.54 (m, 2H), 4.40 – 3.91 (m, 1H), 3.83 – 3.49 (m, 3H), 1.34 (s, 9H), 1.28 – 1.05 (m, 6H). Example 39. Synthesis of 1-((2R,5S)-4-(5-cyclopropyl-7-(3,5-difluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazin-1-yl)-2, 2-dimethylpropan-1-one (Compound 205) Step 1.4-Chloro-5-cyclopropyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine To a solution of 4-chloro-5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (5.8 g, 13 mmol, prepared following the procedure outlined for compound 230) in toluene (50 mL) were added cyclopropylboronic acid (1.1 g, 13 mmol), K 2 CO 3 (24 g, 170 mmol) and Pd(dtbpf)Cl 2 (880 mg, 1.3 mmol). The resulting mixture was heated at 80 o C overnight. After cooling to room temperature, the reaction mixture was filtered and concentrated. Purification by flash column chromatography (silica gel, 0~30% ethyl acetate in petroleum ether) afforded 4-chloro-5-cyclopropyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (3.6 g, 77% yield) as a solid. LC/MS ESI (m/z): 348 (M+H) + . Step 2.4-Chloro-5-cyclopropyl-7H-pyrrolo[2,3-d]pyrimidine To a solution of 4-chloro-5-cyclopropyl-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (3.6 g, 10 mmol) in THF (50 mL) at 0 o C was added TBAF (20 mL, 1.0 M in THF). After stirring at 0 o C for 5 h, the reaction was diluted with water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~10% methanol in dichloromethane) to afford 4-chloro-5-cyclopropyl-7H-pyrrolo[2,3-d]pyrimidine (1.8 g, 90%) as a white solid. LC/MS ESI (m/z): 194 (M+H) + . Step 3.4-Chloro-5-cyclopropyl-7-(3,5-difluorophenyl)-7H-pyrrolo[2 ,3-d]pyrimidine To a solution of 4-chloro-5-cyclopropyl-7H-pyrrolo[2,3-d]pyrimidine (780 mg, 4.0 mmol) in DCM (20 mL) were added (3,5-difluorophenyl)boronic acid (1.3 g, 8.0 mmol), pyridine (1.6 mL, 20 mmol) and Cu(OAc) 2 (3.2 g, 16 mmol). The resulting mixture was stirred at room temperature under O 2 atmosphere for 48 h. The reaction was quenched with aq. NH 4 OH and filtered. The filtrate was washed with water and brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~30% ethyl acetate in petroleum ether) to afford 4-chloro-5-cyclopropyl-7-(3,5- difluorophenyl)-7H-pyrrolo[2,3-d]pyrimidine (400 mg, 33%) as a solid. LC/MS ESI (m/z): 306 (M+H) + . Step 4. tert-Butyl (2R,5S)-4-(5-cyclopropyl-7-(3,5-difluorophenyl)-7H-pyrrolo[2 ,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-2,5-dimethylpiperazine-1-carboxylate (220 mg, 1.0 mmol) in DIEA (0.33 mL, 2.0 mmol) was added tert-butyl (2R,5S)-4-(5-cyclopropyl-7-(3,5- difluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethy lpiperazine-1-carboxylate (150 mg, 0.50 mmol). The resulting mixture was stirred at 150℃ for 1 h. After cooling to room temperature, DIEA was removed and the residue was purified by column chromatography (silica gel, 0~30% ethyl acetate in petroleum ether) to give tert-butyl (2R,5S)-4-(5-cyclopropyl-7-(3,5-difluorophenyl)-7H-pyrrolo[2 ,3-d]pyrimidin-4-yl)-2,5- dimethylpiperazine-1-carboxylate (220 mg, 91%) as a white solid. LC/MS ESI (m/z): 484 (M+H) + . Step 5.5-Cyclopropyl-7-(3,5-difluorophenyl)-4-((2S,5R)-2,5-dimeth ylpiperazin-1-yl)- 7H-pyrrolo[2,3-d]pyrimidine To a solution of tert-butyl (2R,5S)-4-(5-cyclopropyl-7-(3,5-difluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (220 mg, 0.45 mmol) in DCM (3.0 mL) was added HCl (2.3 mL, 4.0 M in dioxane). After 2 h, the mixture was concentrated, and the residue was used directly into the next step. LC/MS ESI (m/z): 384 (M+H) + . Step 6.1-((2R,5S)-4-(5-Cyclopropyl-7-(3,5-difluorophenyl)-7H-pyrr olo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazin-1-yl)-2,2-dimethylpr opan-1-one To a solution of 5-cyclopropyl-7-(3,5-difluorophenyl)-4-((2S,5R)-2,5- dimethylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidine (80 mg, 0.21 mmol) and TEA (0.14 mL, 1.0 mmol) in DCM (2.0 mL) in an ice water bath was added 2,2-dimethylpropanoyl chloride (0.05 mL, 0.42 mmol). After 1 h, the reaction was quenched with water and extracted twice with DCM. The combined organic layers were dried over anhydrous Na 2 SO 4 , filtered and concentrated. The residue was purified by prep-HPLC to give 1-((2R,5S)-4-(5- cyclopropyl-7-(3,5-difluorophenyl)-7H-pyrrolo[2,3-d]pyrimidi n-4-yl)-2,5-dimethylpiperazin- 1-yl)-2,2-dimethylpropan-1-one (50 mg, 51%) as a white solid. LC/MS ESI (m/z): 468 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 8.44 (s, 1H), 7.39 – 7.32 (m, 2H), 6.94 (d, J = 0.8 Hz, 1H), 6.77 (m, 1H), 5.02 – 4.91 (m, 1H), 4.71 (br. s, 1H), 4.37 – 4.04 (br. s, 1H), 3.86 – 3.72 (m, 2H), 3.69 – 3.41 (m, 1H), 2.07 – 1.98 (m, 1H), 1.34 (s, 9H), 1.25 (m, 3H), 1.14 (m, 3H), 1.07 – 1.02 (m, 2H), 0.91 – 0.84 (m, 1H), 0.69 – 0.63 (m, 1H). The following compound was prepared by a procedure analogous to the synthesis of compound 205 from the corresponding arylboronic acid. Example 40. Synthesis of 2-(4-((2S,5R)-2,5-dimethyl-4-pivaloylpiperazin-1-yl)-5- (trifluoromethyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotin onitrile (Compound 207) Compound 207 Step 1. tert-Butyl (2R,5S)-2,5-dimethyl-4-(7-tosyl-5-(trifluoromethyl)-7H-pyrro lo[2,3- d]pyrimidin-4-yl)piperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4- yl)-2,5-dimethylpiperazine-1-carboxylate (26 g, 43 mmol, prepared following the procedure outlined for compound 230) in DMF (50 mL) were added methyl 2,2-difluoro-2- (fluorosulfonyl)acetate (24 g, 130 mmol) and CuI (8.0 g, 43 mmol). The resulting mixture was heated at 80 o C overnight. After cooling to room temperature, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~30% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-2,5-dimethyl-4-(7-tosyl-5- (trifluoromethyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperazine -1-carboxylate (13 g, 55%) as a yellow oil. LC/MS ESI (m/z): 554 (M+H) + . Step 2. tert-Butyl (2R,5S)-2,5-dimethyl-4-(5-(trifluoromethyl)-7H-pyrrolo[2,3-d ]pyrimidin-4- yl)piperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-2,5-dimethyl-4-(7-tosyl-5-(trifluoromethyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)piperazine-1-carboxylate (12 g, 22 mmol) in THF (10 mL) was added TBAF (42 mL, 1.0 M in THF). After 2 h, the reaction was diluted with water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-2,5-dimethyl-4-(5-(trifluoromethyl)-7H-pyrrolo[2,3-d ]pyrimidin-4-yl)piperazine-1- carboxylate (7.5 g, 87%) as a yellow oil. LC/MS ESI (m/z): 400 (M+H) + . Step 3. tert-Butyl (2R,5S)-4-(7-(4-cyanopyridin-2-yl)-5-(trifluoromethyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate To a solution of tert-butyl (2R,5S)-2,5-dimethyl-4-(5-(trifluoromethyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)piperazine-1-carboxylate (1.2 g, 3.0 mmol) in DMF (200 ml) were added Cs 2 CO 3 (2.0 g, 6.0 mmol) and 2-fluoroisonicotinonitrile (1.1 g, 9.0 mmol) at 25°C. The resulting mixture was heated to 50°C and stirred for 2 h. After cooling to room temperature, the reaction mixture was poured into H 2 O (100 ml) and extracted with EtOAc (3 x 100 mL). The combined organic phases were washed twice with NH 4 Cl (aq.) and brine, dried over Na 2 SO 4 , filtered, and concentrated in vacuo. The crude product was purified by flash column chromatography (silica gel, 0~30% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(7-(4-cyanopyridin-2-yl)-5-(trifluoromethyl)-7H-py rrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate (1.4 g, 92%) as a white solid. LC/MS ESI (m/z): 502 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.27 (d, J = 0.9 Hz, 1H), 8.60 (d, J = 5.0 Hz, 1H), 8.57 (s, 1H), 8.50 (s, 1H), 7.43 – 7.39 (m, 1H), 4.52 (s, 1H), 4.31 (s, 1H), 3.76 – 3.63 (m, 2H), 3.59 – 3.52 (m, 1H), 3.41 (d, J = 13.3 Hz, 1H), 1.42 (s, 9H),1.09 (d, J = 6.6 Hz, 3H), 1.03 (d, J = 6.8 Hz, 3H). Step 4.2-(4-((2S,5R)-2,5-Dimethylpiperazin-1-yl)-5-(trifluorometh yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile To a solution of tert-butyl (2R,5S)-4-(7-(4-cyanopyridin-2-yl)-5-(trifluoromethyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (1.4 g, 2.8 mmol) in THF (30 mL) was added HCl in dioxane (4.0 mL, 4.0 M in dioxane). After 16 h, the reaction mixture was concentrated in vacuo to give 1.5 g of 2-(4-((2S,5R)-2,5-dimethylpiperazin-1- yl)-5-(trifluoromethyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)ison icotinonitrile as a HCl salt which was used in the next step without further purification. LC/MS ESI (m/z): 402 (M+H) + . Step 5.2-(4-((2S,5R)-2,5-Dimethyl-4-pivaloylpiperazin-1-yl)-5-(tr ifluoromethyl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile To a solution of 2-(4-((2S,5R)-2,5-dimethylpiperazin-1-yl)-5-(trifluoromethyl )-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (60 mg, 0.15 mmol) and TEA (0.10 ml, 0.75 mmol) in DCM (10 mL) at 0 o C was added pivaloyl chloride (22 mg, 0.18 mmol). After 20 minutes, the reaction was quenched with ice water and extracted twice with DCM. The combined layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by column chromatography on silica gel (0~30% ethyl acetate in petroleum ether) to give the crude product. The crude product was further purified by prep- HPLC to give the 2-(4-((2S,5R)-2,5-dimethyl-4-pivaloylpiperazin-1-yl)-5-(trif luoromethyl)- 7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (45 mg, 62%) as a white solid. LC/MS ESI (m/z): 486 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.34 (s, 1H), 8.72 – 8.65 (m, 2H), 8.59 (s, 1H), 7.49 (dd, J = 5.0, 1.3 Hz, 1H), 4.76 – 4.56 (m, 2H), 4.16 (br. s, 1H), 3.86 – 3.57 (m, 2H), 3.52 (d, J = 13.4 Hz, 1H), 1.34 (s, 9H), 1.24 – 1.07 (m, 6H). The following compounds were prepared by procedures analogous to the synthesis of compound 207 from the corresponding carboxylic acid chloride. Example 41. Synthesis of (S)-2-(4-(4-isobutyryl-2-methylpiperazin-1-yl)-5-(pyridin-2- yl)-5H-pyrrolo[3,2-d]pyrimidin-7-yl)isonicotinonitrile (Compound 211) Compound 211 Step 1.7-Bromo-4-chloro-5-((2-(trimethylsilyl)ethoxy)methyl)-5H-p yrrolo[3,2- d]pyrimidine. To a solution of 7-bromo-4-chloro-5H-pyrrolo[3,2-d]pyrimidine (2.0 g, 8.6 mmol) in DMF (20 mL) at 0 o C were added NaH (410 mg, 17 mmol, 60 wt% in mineral oil) in portions followed by SEM-Cl (1.6 g, 9.5 mmol) dropwise. The resulting mixture was stirred at 0 o C for 30 min and then at room temperature for 2 h. The reaction was then quenched with ice water and extracted twice with EtOAc. The combined organic layers were dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (0~10% ethyl acetate in petroleum ether) to afford 7-bromo-4-chloro-5-((2- (trimethylsilyl)ethoxy)methyl)-5H-pyrrolo[3,2-d]pyrimidine (2.8 g, 90%) as a solid. LC/MS ESI (m/z): 362, 364 (M+H) + . Step 2. tert-Butyl (S)-4-(7-bromo-5-((2-(trimethylsilyl)ethoxy)methyl)-5H-pyrro lo[3,2- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate. To a solution of 7-bromo-4-chloro-5-((2-(trimethylsilyl)ethoxy)methyl)-5H- pyrrolo[3,2-d]pyrimidine (2.8 g, 7.8 mmol) in DIPEA (5 mL) was added tert-butyl (S)-3- methylpiperazine-1-carboxylate (3.1 g, 16 mmol). The resulting mixture was heated at 140 o C for 1.5 h. After cooling to room temperature, solvent was removed and the residue was purified by flash column chromatography (silica gel, 0~15% ethyl acetate in petroleum ether) to afford tert-butyl (S)-4-(7-bromo-5-((2-(trimethylsilyl)ethoxy)methyl)-5H-pyrro lo[3,2- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate (2.9 g, 72%) as a solid. LC/MS ESI (m/z): 526, 528 (M+H) + . Step 3. (S)-(4-(4-(tert-Butoxycarbonyl)-2-methylpiperazin-1-yl)-5-(( 2- (trimethylsilyl)ethoxy)methyl)-5H-pyrrolo[3,2-d]pyrimidin-7- yl)boronic acid. To a solution of tert-butyl (S)-4-(7-bromo-5-((2-(trimethylsilyl)ethoxy)methyl)-5H- pyrrolo[3,2-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (2.9 g, 5.5 mmol) in THF (15 mL) at -70 o C were added triisopropyl borate (4.2 g, 23 mmol) followed by n-butyllithium (9.0 ml, 2.5 M in hexane) dropwise. The resulting mixture was stirred at -70 o C for 1 h. The reaction was then quenched with aq. NH 4 Cl solution carefully and extracted twice with EtOAc. The combined organic layers were dried over Na 2 SO 4 , filtered, and concentrated to afford the crude product which was used in the next step directly. Step 4. tert-Butyl (S)-4-(7-(4-chloropyridin-2-yl)-5-((2-(trimethylsilyl)ethoxy )methyl)- 5H-pyrrolo[3,2-d]pyrimidin-4-yl)-3-methylpiperazine-1-carbox ylate To a solution of (S)-(4-(4-(tert-butoxycarbonyl)-2-methylpiperazin-1-yl)-5-(( 2- (trimethylsilyl)ethoxy)methyl)-5H-pyrrolo[3,2-d]pyrimidin-7- yl)boronic acid (from step 3, 5.5 mmol) in dioxane (13 mL) and H 2 O (2 mL) were added 2-bromo-4-chloropyridine (1.3 g, 6.6 mmol), K 2 CO 3 (6.5 g, 47 mmol) and Pd(dppf)Cl 2 (570 mg, 0.78 mmol). The resulting mixture was heated at 90 o C overnight under N 2 . After cooling to room temperature, solvent was removed and the residue was purified by flash column chromatography (silica gel, 0~40% ethyl acetate in petroleum ether) to afford tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)- 5-((2-(trimethylsilyl)ethoxy)methyl)-5H-pyrrolo[3,2-d]pyrimi din-4-yl)-3-methylpiperazine- 1-carboxylate (1.0 g, 32% over two steps) as an oil. LC/MS ESI (m/z): 559 (M+H) + . Step 5. tert-Butyl (S)-4-(7-(4-chloropyridin-2-yl)-5H-pyrrolo[3,2-d]pyrimidin-4 -yl)-3- methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)-5-((2- (trimethylsilyl)ethoxy)methyl)-5H-pyrrolo[3,2-d]pyrimidin-4- yl)-3-methylpiperazine-1- carboxylate (1.0 g, 1.8 mmol) in THF (10 mL) was added TBAF (20 mL, 1.0 M in THF). The resulting mixture was heated at 55 o C for 2 h. The reaction was then quenched with water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated to afford tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)- 5H-pyrrolo[3,2-d]pyrimidin-4-yl)-3-methylpiperazine-1-carbox ylate (700 mg, 91%) as a solid. LC/MS ESI (m/z): 429 (M+H) + . Step 6. tert-Butyl (S)-4-(7-(4-chloropyridin-2-yl)-5-(5-nitropyridin-2-yl)-5H- pyrrolo[3,2-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te To a solution of tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)-5H-pyrrolo[3,2- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate (700 mg, 1.6 mmol) in DMF (10 mL) were added 2-fluoro-5-nitropyridine (690 mg, 4.9 mmol) and Cs 2 CO 3 (2.1 g, 6.5 mmol). The resulting mixture was heated at 100 o C for 2 h. After cooling to room temperature, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~60%, ethyl acetate in petroleum ether) to afford tert-butyl (S)-4-(7-(4-chloropyridin-2- yl)-5-(5-nitropyridin-2-yl)-5H-pyrrolo[3,2-d]pyrimidin-4-yl) -3-methylpiperazine-1- carboxylate (800 mg, 89%) as a solid. LC/MS ESI (m/z): 551 (M+H) + . Step 7. tert-Butyl (S)-4-(5-(5-aminopyridin-2-yl)-7-(4-chloropyridin-2-yl)-5H- pyrrolo[3,2-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te To a solution of tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)-5-(5-nitropyridin-2-yl)-5H- pyrrolo[3,2-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (700 mg, 1.3 mmol) in EtOH (10 mL) and H 2 O (5 mL) were added NH 4 Cl (680 mg, 13 mmol) and Fe (710 mg, 13 mmol). The resulting mixture was heated at 60 o C overnight. After cooling to room temperature, the reaction was filtered, and the filtrate was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~80% ethyl acetate in petroleum ether) to afford tert-butyl (S)- 4-(5-(5-aminopyridin-2-yl)-7-(4-chloropyridin-2-yl)-5H-pyrro lo[3,2-d]pyrimidin-4-yl)-3- methylpiperazine-1-carboxylate (490 mg, 74%) as a solid. LC/MS ESI (m/z): 521 (M+H) + . Step 8. tert-Butyl (S)-4-(7-(4-chloropyridin-2-yl)-5-(pyridin-2-yl)-5H-pyrrolo[ 3,2- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-4-(5-(5-aminopyridin-2-yl)-7-(4-chloropyridin-2-yl)- 5H-pyrrolo[3,2-d]pyrimidin-4-yl)-3-methylpiperazine-1-carbox ylate (300 mg, 0.58 mmol) in THF (10 mL) was added isopentyl nitrite (270 mg, 2.3 mmol). The resulting mixture was heated at 55 o C for overnight. After cooling to room temperature, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~70%, ethyl acetate in petroleum ether) to afford tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)-5- (pyridin-2-yl)-5H-pyrrolo[3,2-d]pyrimidin-4-yl)-3-methylpipe razine-1-carboxylate (200 mg, 68%) as a solid. LC/MS ESI (m/z): 506 (M+H) + . Step 9. tert-Butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5-(pyridin-2-yl)-5H-pyrrolo[3 ,2- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-4-(7-(4-chloropyridin-2-yl)-5-(pyridin-2-yl)-5H- pyrrolo[3,2-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (150 mg, 0.30 mmol) in DMF (10 mL) were added Pd(PPh 3 ) 4 (170 mg, 0.15 mmol) and Zn(CN) 2 (250 mg, 2.1 mmol). The resulting mixture was heated at 120 o C overnight. After cooling to room temperature, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~60% ethyl acetate in petroleum ether) to afford tert-butyl (S)-4-(7-(4-cyanopyridin-2- yl)-5-(pyridin-2-yl)-5H-pyrrolo[3,2-d]pyrimidin-4-yl)-3-meth ylpiperazine-1-carboxylate (120 mg, 81%) as a solid. LC/MS ESI (m/z): 497 (M+H) + . Step 10. (S)-2-(4-(2-Methylpiperazin-1-yl)-5-(pyridin-2-yl)-5H-pyrrol o[3,2- d]pyrimidin-7-yl)isonicotinonitrile To a solution of tert-butyl (S)-4-(7-(4-cyanopyridin-2-yl)-5-(pyridin-2-yl)-5H- pyrrolo[3,2-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (30 mg, 0.06 mmol) in DCM (3 mL) was added TFA (0.3 mL). The resulting mixture was stirred at room temperature for 1 h. The reaction was quenched with NaHCO 3 (aq.) and extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was used in the next step directly. LC/MS ESI (m/z): 397 (M+H) + . Step 11. (S)-2-(4-(4-Isobutyryl-2-methylpiperazin-1-yl)-5-(pyridin-2- yl)-5H- pyrrolo[3,2-d]pyrimidin-7-yl)isonicotinonitrile To a solution of (S)-2-(4-(2-methylpiperazin-1-yl)-5-(pyridin-2-yl)-5H-pyrrol o[3,2- d]pyrimidin-7-yl)isonicotinonitrile (20 mg, 0.05 mmol) in DCM (3 mL) at 0 o C were added TEA (0.10 mL) and isobutyryl chloride (20 mg, 0.19 mmol). After 1 h, the reaction was partitioned between DCM and water. The aqueous layer was extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by prep-HPLC to afford (S)-2-(4-(4-isobutyryl-2- methylpiperazin-1-yl)-5-(pyridin-2-yl)-5H-pyrrolo[3,2-d]pyri midin-7-yl)isonicotinonitrile (10 mg, 43%) as a white solid. LC/MS ESI (m/z): 467 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.04 (s, 1H), 8.70 (s, 1H), 8.68 (d, J = 5.0 Hz, 1H), 8.63 (d, J = 7.5 Hz, 1H), 8.57 (br. s, 1H), 7.82 (m, 1H), 7.33 – 7.29 (m, 2H), 7.20 (m, 1H), 4.28 (br. s, ~0.5H), 4.14 (d, J = 16 Hz, ~0.5H), 3.97 (d, J = 12 Hz, ~0.5H), 3.86 (br. s, ~0.5H), 3.65 (d, J = 12 Hz, ~0.5H), 3.56 (d, J = 12 Hz, ~0.5H), 3.43 (d, J = 12 Hz, ~0.5H), 3.28 (d, J = 16 Hz, ~0.5H), 3.10 (m, 1H), 3.05 – 2.70 (m, 1H), 2.74 – 2.59 (m, 1H), 2.42 (m, 1H), 1.02 (m, 7.5H), 0.80 (d, J = 6.5 Hz, 1.5H); several peaks and their integrations are fractions of protons on account of presence of rotomers. The following compounds were prepared by the procedure analogous to the synthesis of compound 211 from the corresponding aryl fluoride (1,2-difluoro-4-nitrobenzene) and chiral amine.
Example 42. Synthesis of 1-((2R,5S)-4-(5-cyclopropyl-7-(3-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazin-1-yl)-2, 2-dimethylpropan-1-one (Compound 214) Compound 214 Step 1.4-Chloro-7-(3-fluorophenyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimi dine To a solution of 4-chloro-5-iodo-7H-pyrrolo[2,3-d]pyrimidine (6.0 g, 22 mmol) in DCM (60 mL) were added (3-fluorophenyl)boronic acid (6.0 g, 43 mmol), 4Å molecular sieves (3.0 g), Cu(OAc) 2 (16 g, 86 mmol) and pyridine (10 g, 130 mmol). The resulting mixture was stirred at 30℃ under O 2 atmosphere for 2 days. The reaction was then quenched with aq. NH 4 OH (10 mL) in an ice water bath and filtered. The filtrate was extracted twice with DCM. The combined organic layers were dried over Na 2 SO 4 , filtered and concentrated. The residue was triturated with petroleum ether to afford 4-chloro-7-(3-fluorophenyl)-5-iodo- 7H-pyrrolo[2,3-d]pyrimidine (5.0 g, 62%) as a solid. LC/MS ESI (m/z): 374 (M+H) + . Step 2. tert-Butyl (2R,5S)-4-(7-(3-fluorophenyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimi din- 4-yl)-2,5-dimethylpiperazine-1-carboxylate To a solution of 4-chloro-7-(3-fluorophenyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimidi ne (1.0 g, 2.7 mmol) in DIPEA (3 mL) was added tert-butyl (2R,5S)-2,5-dimethylpiperazine-1- carboxylate (1.1 g, 5.4 mmol). The resulting reaction mixture was heated at 140℃ under N 2 for 2 h. After cooling to room temperature, solvent was removed and the residue was purified by flash column chromatography (silica gel, 0~30% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(7-(3-fluorophenyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimi din-4-yl)-2,5- dimethylpiperazine-1-carboxylate (1.0 g, 68%) as a solid. LC/MS ESI (m/z): 552 (M+H) + . Step 3. tert-Butyl (2R,5S)-4-(5-cyclopropyl-7-(3-fluorophenyl)-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-4-(7-(3-fluorophenyl)-5-iodo-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate (250 mg, 0.45 mmol) in toluene (5 mL) were added cyclopropylboronic acid (57 mg, 0.67 mmol), K 2 CO 3 (1.2 g, 9.0 mmol) and PdCl 2 (dtbpf) (14 mg, 0.02 mmol). The resulting mixture was heated at 90 o C overnight. After cooling to room temperature, solvents were removed and the residue was purified by flash column chromatography (silica gel, 0~40% ethyl acetate in petroleum ether) to afford tert- butyl (2R,5S)-4-(5-cyclopropyl-7-(3-fluorophenyl)-7H-pyrrolo[2,3-d ]pyrimidin-4-yl)-2,5- dimethylpiperazine-1 carboxylate (170 mg, 81%) as a white solid. LC/MS ESI (m/z): 466 (M+H) + . Step 4.5-Cyclopropyl-4-((2S,5R)-2,5-dimethylpiperazin-1-yl)-7-(3- fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidine To a solution of tert-butyl (2R,5S)-4-(5-cyclopropyl-7-(3-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (170 mg, 0.36 mmol) in DCM (3 mL) was added TFA (1.0 mL). The resulting mixture was stirred at room temperature for 2 h. After the removal of solvent, the residue was used in the next step directly. LC/MS ESI (m/z): 366 (M+H) + . Step 5.1-((2R,5S)-4-(5-Cyclopropyl-7-(3-fluorophenyl)-7H-pyrrolo[ 2,3-d]pyrimidin- 4-yl)-2,5-dimethylpiperazin-1-yl)-2,2-dimethylpropan-1-one To a solution of 5-cyclopropyl-4-((2S,5R)-2,5-dimethylpiperazin-1-yl)-7-(3- fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidine (130 mg, 0.36 mmol) and TEA (0.10 mL, 1.1 mmol) in DCM (2 mL) at 0℃ was added pivaloyl chloride (0.10 mL, 0.72 mmol). After stirring at room temperature for 1 h, the reaction was partitioned between DCM and water. The aqueous layer was extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by prep- HPLC to afford 1-((2R,5S)-4-(5-cyclopropyl-7-(3-fluorophenyl)-7H-pyrrolo[2, 3-d]pyrimidin- 4-yl)-2,5-dimethylpiperazin-1-yl)-2,2-dimethylpropan-1-one (51 mg, 31%) as a white solid. LC/MS ESI (m/z): 450 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 8.37 (s, 1H), 7.43 – 7.37 (m, 3H), 6.99 – 6.94 (m, 1H), 6.90 (s, 1H), 4.93 – 4.88 (m, 1H), 4.65 (br. s, 1H), 4.17 (br. s, 1H), 3.74 – 3.49 (m, 3H), 2.00 – 1.94 (m, 1H), 1.28 (s, 9H), 1.21 (br. s, 3H), 1.07 (br. s, 3H), 0.98 – 0.94 (m, 2H), 0.83 – 0.78 (m, 1H), 0.63 – 0.58 (m, 1H). The following compound was prepared by a procedure analogous to the synthesis of compound 214 from the corresponding chiral amine. Example. Synthesis of (S)-1-(4-(5-(azetidin-1-yl)-7-(3-fluorophenyl)-7H-pyrrolo[2, 3- d]pyrimidin-4-yl)-3-methylpiperazin-1-yl)-2,2-dimethylpropan -1-one (Compound 216) C ompound 216 Step 1.4-Chloro-7-(3-fluorophenyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimi dine To a solution of 4-chloro-5-iodo-7H-pyrrolo[2,3-d]pyrimidine (6.0 g, 22 mmol) in DCM (60 mL) were added (3-fluorophenyl)boronic acid (6.0 g, 43 mmol), 4Å molecular sieves (3.0 g), Cu(OAc) 2 (16 g, 86 mmol) and pyridine (10 g, 130 mmol). The resulting mixture was heated at 30℃ under O 2 atmosphere for 2 days. The reaction was quenched with aq. NH 4 OH (10 mL) in an ice water bath and filtered. The filtrate was extracted twice with DCM. The combined organic layers were dried over Na 2 SO 4 , filtered and concentrated. The residue was triturated with petroleum ether to afford 4-chloro-7-(3-fluorophenyl)-5-iodo-7H- pyrrolo[2,3-d]pyrimidine (5.0 g, 62%) as a solid. LC/MS ESI (m/z): 374 (M+H) + . Step 2. tert-Butyl (S)-4-(7-(3-fluorophenyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimidin- 4-yl)- 3-methylpiperazine-1-carboxylate To a solution of 4-chloro-7-(3-fluorophenyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimidi ne (1.0 g, 2.7 mmol) in DIPEA (3 mL) was added tert-butyl (S)-3-methylpiperazine-1-carboxylate (1.1 g, 5.4 mmol). The resulting reaction mixture was heated at 140℃ under N 2 for 2 h. After cooling to room temperature, solvent was removed and the residue was purified by flash column chromatography (silica gel, 0~30% ethyl acetate in petroleum ether) to afford tert- butyl (S)-4-(7-(3-fluorophenyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimidin- 4-yl)-3- methylpiperazine-1-carboxylate (800 mg, 68%) as a solid. LC/MS ESI (m/z): 538 (M+H) + . Step 3. tert-Butyl (S)-4-(7-(3-fluorophenyl)-5-(2-oxoazetidin-1-yl)-7H-pyrrolo[ 2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-4-(7-(3-fluorophenyl)-5-iodo-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate (600 mg, 1.1 mmol) in DMF (5 mL) were added azetidin-2-one (320 mg, 1.1 mmol), trans-N,N ’ -dimethylcyclohexane-1,2-diamine (160 mg, 1.1 mmol), CuI (210 mg, 1.1 mmol) and K 3 PO 4 (710 mg, 3.4 mmol). The resulting mixture was heated at 90 o C overnight. After cooling to room temperature, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~70% ethyl acetate in petroleum ether) to afford tert-butyl (S)-4-(7-(3-fluorophenyl)-5-(2- oxoazetidin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylp iperazine-1-carboxylate (300 mg, 56%) as a solid. LC/MS ESI (m/z): 481(M+H) + . Step 4. tert-Butyl (S)-4-(5-(azetidin-1-yl)-7-(3-fluorophenyl)-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-4-(7-(3-fluorophenyl)-5-(2-oxoazetidin-1-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxyla te (250 mg, 0.52 mmol) in THF (5 mL) were added RhHCO(PPh 3 ) 3 (130 mg, 0.14 mmol) and PhSiH 3 (220 mg, 2.1 mmol) dropwise. The resulting mixture was heated at 40 o C for 1 h. After cooling to room temperature, the reaction was quenched in an ice water bath and extracted twice with EtOAc. The combined organic layers were dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~70% ethyl acetate in petroleum ether) to afford tert-butyl (S)-4-(5-(azetidin-1-yl)-7-(3-fluorophenyl)-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate (200 mg, 68%) as a solid. LC/MS ESI (m/z): 467 (M+H) + . Step 5. (S)-5-(Azetidin-1-yl)-7-(3-fluorophenyl)-4-(2-methylpiperazi n-1-yl)-7H- pyrrolo[2,3-d]pyrimidine To a solution of tert-butyl (S)-4-(5-(azetidin-1-yl)-7-(3-fluorophenyl)-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate (80 mg, 0.17 mmol) in DCM (5 mL) was added TFA (0.50 mL). The resulting mixture was stirred at room temperature for 1 h. The reaction was quenched with NaHCO 3 (aq.) and extracted twice with DCM. The combined organic layers were dried over Na 2 SO 4 , filtered, and concentrated to afford (S)-5-(azetidin-1- yl)-7-(3-fluorophenyl)-4-(2-methylpiperazin-1-yl)-7H-pyrrolo [2,3-d]pyrimidine (60 mg, 97%) as a solid. LC/MS ESI (m/z): 367 (M+H) + . (S)-1-(4-(5-(Azetidin-1-yl)-7-(3-fluorophenyl)-7H-pyrrolo[2, 3-d]pyrimidin-4-yl)-3- methylpiperazin-1-yl)-2,2-dimethylpropan-1-one To a solution of (S)-5-(azetidin-1-yl)-7-(3-fluorophenyl)-4-(2-methylpiperazi n-1-yl)- 7H-pyrrolo[2,3-d]pyrimidine (60 mg, 0.16 mmol) in DCM (5 mL) at 0 o C were added TEA (0.15 mL) and pivaloyl chloride (58 mg, 0.48 mmol). The resulting mixture was stirred at room temperature for 1 h. The reaction was then partitioned between DCM and water. The aqueous layer was extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~30%, ethyl acetate in petroleum ether) to give crude product which was further purified by prep-HPLC to afford (S)-1-(4-(5-(azetidin-1-yl)-7-(3- fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-3-methylpiper azin-1-yl)-2,2- dimethylpropan-1-one (40 mg, 55%) as a solid. LC/MS ESI (m/z): 451 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 8.33 (s, 1H), 7.49 – 7.44 (m, 2H), 7.41 – 7.35 (m, 1H), 6.96 – 6.90 (m, 1H), 6.57 (s, 1H), 5.00 – 4.92 (m, 1H), 4.27 (d, J = 13.2 Hz, 2H), 4.03 (d, J = 12 Hz, 1H), 3.74 (app. q, J = 6.9 Hz, 2H), 3.57 (app. q, J = 6.8 Hz, 2H), 3.52 – 3.45 (m, 1H), 3.40 – 3.32 (m, 1H), 3.18 – 3.09 (m, 1H), 2.27 – 2.19 (m, 2H), 1.27 (s, 9H), 1.07 (d, J = 6.7 Hz, 3H). The following compounds were prepared by procedures analogous to the synthesis of compound 216 from the corresponding boronic acids, chiral amine, and acid chlorides. Example 43. Synthesis of 3-(4-((2S,5R)-2,5-dimethyl-4-pivaloylpiperazin-1-yl)-5- (trifluoromethyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)benzonitri le (Compound 222) Compound 222 Step 1.3-(4-((2S,5R)-4-Isobutyryl-2,5-dimethylpiperazin-1-yl)-5-( trifluoromethyl)- 7H-pyrrolo[2,3-d]pyrimidin-7-yl)benzonitrile To a solution of tert-butyl (2R,5S)-2,5-dimethyl-4-(5-(trifluoromethyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)piperazine-1-carboxylate (1.0 g, 2.5 mmol, prepared following the procedure outlined for compound 207) in DMF (10 mL) were added 3-iodobenzonitrile (1.2 g, 5.0 mmol), CuI (480 mg, 2.5 mmol), K 3 PO 4 (1.6 g, 7.5 mmol) and trans-N,N′- dimethylcyclohexane-1,2-diamine (71 mg, 0.50 mmol). The mixture was degassed 3 times with N 2 and was then heated at 90°C for 12 h. The mixture was cooled to room temperature, poured into H 2 O (50 mL) and extracted with EtOAc (100 mL). The organic phase was washed with brine, dried over Na2SO4, filtered, and concentrated in vacuo. The crude product was purified by column chromatography (silica gel, 0~20% ethyl acetate in petroleum ether) to give tert-butyl (2R,5S)-4-(7-(3-cyanophenyl)-5-(trifluoromethyl)-7H-pyrrolo[ 2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate (600 mg, 48%) as an white solid. LC/MS ESI (m/z): 501(M+H) + . Step 2.3-(4-((2S,5R)-2,5-Dimethylpiperazin-1-yl)-5-(trifluorometh yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)benzonitrile To a solution of tert-butyl (2R,5S)-4-(7-(3-cyanophenyl)-5-(trifluoromethyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (600 mg, 1.2 mmol) in DCM (5 mL) at 0 o C was added HCl (1.0 mL, 4.0 M in dioxane). The resulting mixture was stirred at room temperature for 2 h. The reaction was then basified with NaHCO 3 (aq.) to pH 8 and extracted twice with DCM. The combined organic layers were dried over Na 2 SO 4 , filtered, and concentrated in vacuo. The crude product was used in the next step directly. LC/MS ESI (m/z): 401 (M+H) + . Step 3.3-(4-((2S,5R)-2,5-Dimethyl-4-pivaloylpiperazin-1-yl)-5-(tr ifluoromethyl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)benzonitrile To a solution of 3-(4-((2S,5R)-2,5-dimethylpiperazin-1-yl)-5-(trifluoromethyl )-7H- pyrrolo[2,3-d]pyrimidin-7-yl)benzonitrile (200 mg, 0.50 mmol) in DCM (10.0 mL) at 0 o C was added DIEA (0.16 mL, 1.0 mmol) and pivaloyl chloride (92 mg, 0.76 mmol). After 1 h, the reaction was quenched with water and extracted twice with DCM. The combined organic phases were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated in vacuo. The crude product was purified by prep-HPLC to give 3-(4-((2S,5R)-2,5-dimethyl-4- pivaloylpiperazin-1-yl)-5-(trifluoromethyl)-7H-pyrrolo[2,3-d ]pyrimidin-7-yl)benzonitrile (130 mg, 54%). LC/MS ESI (m/z): 485 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 8.52 (s, 1H), 8.07 (m, 1H), 7.96 (m, 1H), 7.76 (m, 1H), 7.74 – 7.65 (m, 2H), 4.79 – 4.54 (m, 2H), 4.15 (br. s, 1H), 3.78 (dd, J = 16, 4.0 Hz, 1H), 3.68 (br. s, 1H), 3.54 (d, J = 13.4 Hz, 1H), 1.34 (s, 9H), 1.24 – 1.07 (m, 6H). The following compounds were prepared by procedures analogous to the synthesis of compound 222 from the corresponding aryl halides and carboxylic acid.
Example 44. Synthesis of 1-((2R,5S)-4-(3-(azetidin-1-yl)-1-(3-fluorophenyl)-1H- pyrrolo[3,2-c]pyridin-4-yl)-2,5-dimethylpiperazin-1-yl)-2,2- dimethylpropan-1-one (Compound 226) Step 1. tert-Butyl (2R,5S)-4-(1-(3-fluorophenyl)-3-iodo-1H-pyrrolo[3,2-c]pyridi n-4- yl)-2,5-dimethylpiperazine-1-carboxylate To a solution of 1-(3-fluorophenyl)-3-iodo-1H-pyrrolo[3,2-c]pyridine 5-oxide (450 mg, 1.3 mmol, prepared following the procedure outlined for compound 228) in DCM (10 mL) were added tert-butyl (2R,5S)-2,5-dimethylpiperazine-1-carboxylate (1.3 g, 6.4 mmol), DIPEA (0.90 mL, 5.1 mmol) and PyBrop (1.2 g, 2.5 mmol). After stirring at room temperature over multiple days, the reaction was partitioned between DCM and water. The aqueous layer was extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated, the residue was purified by flash column chromatography (silica gel, 0~20% ethyl acetate in petroleum ether) to afford tert- butyl (2R,5S)-4-(1-(3-fluorophenyl)-3-iodo-1H-pyrrolo[3,2-c]pyridi n-4-yl)-2,5- dimethylpiperazine-1-carboxylate (250 mg, 36%) as a yellow solid. LC/MS ESI (m/z): 551 (M+H) + . Step 2. tert-Butyl (2R,5S)-4-(1-(3-fluorophenyl)-3-(2-oxoazetidin-1-yl)-1H- pyrrolo[3,2-c]pyridin-4-yl)-2,5-dimethylpiperazine-1-carboxy late To a solution of tert-butyl (2R,5S)-4-(1-(3-fluorophenyl)-3-iodo-1H-pyrrolo[3,2- c]pyridin-4-yl)-2,5-dimethylpiperazine-1-carboxylate (200 mg, 0.36 mmol) in DMF (5 mL) were added azetidin-2-one (100 mg, 1.4 mmol), CuI (34 mg, 0.18 mmol), trans-N,N’- dimethylcyclohexane-1,2-diamine (51 mg, 0.36 mmol) and K 3 PO 4 (150 mg, 0.72 mmol). The resulting mixture was stirred at 90℃ overnight. After cooling to room temperature, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~55% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(1-(3- fluorophenyl)-3-(2-oxoazetidin-1-yl)-1H-pyrrolo[3,2-c]pyridi n-4-yl)-2,5-dimethylpiperazine- 1-carboxylate (160 mg, 90%) as a yellow solid. LC/MS ESI (m/z): 494 (M+H) + . Step 3. tert-Butyl (2R,5S)-4-(3-(azetidin-1-yl)-1-(3-fluorophenyl)-1H-pyrrolo[3 ,2- c]pyridin-4-yl)-2,5-dimethylpiperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-4-(1-(3-fluorophenyl)-3-(2-oxoazetidin-1-yl)-1H- pyrrolo[3,2-c]pyridin-4-yl)-2,5-dimethylpiperazine-1-carboxy late (160 mg, 0.32 mmol) in THF (5 mL) at 0℃ were added RhHCO(PPh 3 ) 3 (29 mg, 0.032 mmol) and PhSiH 3 (0.20 mL, 1.6 mmol) dropwise. After stirring at room temperature for 1 h under N 2 , the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50% ethyl acetate in petroleum ether) to give crude product which was further purified by prep- HPLC to afford tert-butyl (2R,5S)-4-(3-(azetidin-1-yl)-1-(3-fluorophenyl)-1H-pyrrolo[3 ,2- c]pyridin-4-yl)-2,5-dimethylpiperazine-1-carboxylate (85 mg, 55%) as a white solid. LC/MS ESI (m/z): 480 (M+H) + . Step 4. tert-Butyl (2R,5S)-4-(3-(azetidin-1-yl)-1-(3-fluorophenyl)-1H-pyrrolo[3 ,2- c]pyridin-4-yl)-2,5-dimethylpiperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-4-(3-(azetidin-1-yl)-1-(3-fluorophenyl)-1H- pyrrolo[3,2-c]pyridin-4-yl)-2,5-dimethylpiperazine-1-carboxy late (33 mg, 0.070 mmol) in DCM (2 mL) at 0℃ was added TFA (1 mL). After stirring at 0℃ for 1 h, the reaction was quenched with NaHCO 3 (aq.) and extracted twice with DCM. The combined organic layers were dried over Na 2 SO 4 , filtered and concentrated. The residue was used in the next step directly. LC/MS ESI (m/z): 380 (M+H) + . Step 5.1-((2R,5S)-4-(3-(Azetidin-1-yl)-1-(3-fluorophenyl)-1H-pyrr olo[3,2-c]pyridin- 4-yl)-2,5-dimethylpiperazin-1-yl)-2,2-dimethylpropan-1-one To a solution of 3-(azetidin-1-yl)-4-((2S,5R)-2,5-dimethylpiperazin-1-yl)-1-( 3- fluorophenyl)-1H-pyrrolo[3,2-c]pyridine (26 mg, 0.070 mmol) and TEA (0.10 mL, 0.21 mmol) in DCM (2 mL) at 0℃ was added pivaloyl chloride (0.10 mL, 0.14 mmol) dropwise. After stirring at 0℃ for 1 h, the reaction was partitioned between DCM and water. The aqueous layer was extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by prep- HPLC to afford 1-((2R,5S)-4-(3-(azetidin-1-yl)-1-(3-fluorophenyl)-1H-pyrrol o[3,2-c]pyridin- 4-yl)-2,5-dimethylpiperazin-1-yl)-2,2-dimethylpropan-1-one (7.8 mg, 22%) as a yellow solid. LC/MS ESI (m/z): 464 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 7.88 (d, J = 5.9 Hz, 1H), 7.50 – 7.43 (m, 1H), 7.27 (m, 1H), 7.19 (dt, J = 9.8, 2.2 Hz, 1H), 7.05 (td, J = 8.2, 2.0 Hz, 1H), 6.98 (d, J = 5.9 Hz, 1H), 6.62 (s, 1H), 4.96 (br. s, 1H), 4.68 (br. s, 1H), 4.24 (br. s, 1H), 3.97 (q, J = 6.8 Hz, 2H), 3.77 – 3.48 (m, 5H), 2.29 (app. p, J = 6.9 Hz, 2H), 1.35 (s, 9H), 1.30 – 1.18 (m, 3H), 1.03 – 0.87 (br. s, 3H). The following compound was prepared by a procedure analogous to the synthesis of compound 226 from the corresponding chiral amine. Example 45. Synthesis of (S)-1-(4-(3-cyclopropyl-1-(3-fluorophenyl)-1H-pyrrolo[3,2- c]pyridin-4-yl)-3-methylpiperazin-1-yl)-2,2-dimethylpropan-1 -one (Compound 228) Step 1.1-(3-Fluorophenyl)-3-iodo-1H-pyrrolo[3,2-c]pyridine A mixture of 3-iodo-1H-pyrrolo[3,2-c]pyridine (2.9 g, 12 mmol), (3- fluorophenyl)boronic acid (4.9 g, 35 mmol), Cu(OAc) 2 (5.8 g, 30 mmol) and pyridine (5.7 mL, 71 mmol) in DCM (50 mL) was stirred at room temperature for 48 h under an atmosphere of oxygen. The reaction mixture was then treated with aq. ammonium hydroxide and filtered. The filtrate was extracted twice with DCM. The combined layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by column chromatography on silica gel (0~30% ethyl acetate in petroleum ether) to give 1-(3- fluorophenyl)-3-iodo-1H-pyrrolo[3,2-c]pyridine (1.5 g, 37%) as a solid. LC/MS ESI (m/z): 339 (M+H) + . Step 2.1-(3-Fluorophenyl)-3-iodo-1H-pyrrolo[3,2-c]pyridine 5-oxide To a solution of 1-(3-fluorophenyl)-3-iodo-1H-pyrrolo[3,2-c]pyridine (1.5 g, 4.4 mmol) in DCM (20 mL) at 0 o C was added 3-chloroperoxybenzoic acid (1.1 g, 6.6 mmol) in portions. The resulting mixture was stirred at room temperature overnight. The reaction was quenched with NaHCO 3 (aq.) and extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~20 % MeOH in DCM) to provide 1- (3-fluorophenyl)-3-iodo-1H-pyrrolo[3,2-c]pyridine 5-oxide (920 mg, 61%) as a light yellow solid. LC/MS ESI (m/z): 355 (M+H) + . Step 3. tert-Butyl (S)-4-(1-(3-fluorophenyl)-3-iodo-1H-pyrrolo[3,2-c]pyridin-4- yl)-3- methylpiperazine-1-carboxylate To a solution of 1-(3-fluorophenyl)-3-iodo-1H-pyrrolo[3,2-c]pyridine 5-oxide (450 mg, 1.3 mmol) in DCM (10 mL) were added tert-butyl (S)-3-methylpiperazine-1-carboxylate (1.3 g, 6.4 mmol), DIPEA (0.90 mL, 5.1 mmol) and PyBrop (1.2 g, 2.5 mmol). After stirring for 3 days, the reaction was partitioned between DCM and water. The aqueous layer was extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~20% ethyl acetate in petroleum ether) to afford tert-butyl (S)-4-(1-(3- fluorophenyl)-3-iodo-1H-pyrrolo[3,2-c]pyridin-4-yl)-3-methyl piperazine-1-carboxylate (250 mg, 36%) as a yellow solid. LC/MS ESI (m/z): 537 (M+H) + . Step 4. tert-Butyl (S)-4-(3-cyclopropyl-1-(3-fluorophenyl)-1H-pyrrolo[3,2-c]pyr idin- 4-yl)-3-methylpiperazine-1-carboxylate To a solution of tert-butyl (S)-4-(1-(3-fluorophenyl)-3-iodo-1H-pyrrolo[3,2-c]pyridin- 4-yl)-3-methylpiperazine-1-carboxylate (50 mg, 0.093 mmol) in toluene (5 mL) were added cyclopropylboronic acid (32 mg, 0.37 mmol), K 2 CO 3 (260 mg, 1.9 mmol) and Pd-118 (6.0 mg, 0.01 mmol). The resulting mixture was stirred at 80℃ overnight. After cooling to room temperature, the reaction was concentrated and the residue was purified by flash column chromatography (silica gel, 0~20% ethyl acetate in petroleum ether) to afford tert-butyl (S)- 4-(3-cyclopropyl-1-(3-fluorophenyl)-1H-pyrrolo[3,2-c]pyridin -4-yl)-3-methylpiperazine-1- carboxylate (30 mg, 71%) as a yellow oil. LC/MS ESI (m/z): 451 (M+H) + . Step 5. (S)-3-Cyclopropyl-1-(3-fluorophenyl)-4-(2-methylpiperazin-1- yl)-1H- pyrrolo[3,2-c]pyridine To a solution of tert-butyl (S)-4-(3-cyclopropyl-1-(3-fluorophenyl)-1H-pyrrolo[3,2- c]pyridin-4-yl)-3-methylpiperazine-1-carboxylate (30 mg, 0.067 mmol) in DCM (1 mL) was added HCl (0.50 mL, 4.0 M in dioxane). The resulting mixture was stirred at room temperature for 2 h. After removal of solvent, the residue was used in the next step directly. LC/MS ESI (m/z): 351 (M+H) + . Step 6. (S)-1-(4-(3-Cyclopropyl-1-(3-fluorophenyl)-1H-pyrrolo[3,2-c] pyridin-4-yl)-3- methylpiperazin-1-yl)-2,2-dimethylpropan-1-one To a solution of (S)-3-cyclopropyl-1-(3-fluorophenyl)-4-(2-methylpiperazin-1- yl)-1H- pyrrolo[3,2-c]pyridine (23 mg, 0.066 mmol) and TEA (0.050 mL, 0.32 mmol) in DCM (2 mL) at 0 o C was added pivaloyl chloride (0.020 mL, 0.13 mmol). After stirring at room temperature for 1 h, the reaction was partitioned between DCM and water. The aqueous layer was extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by prep-HPLC to afford (S)-1-(4-(3-cyclopropyl-1-(3-fluorophenyl)-1H-pyrrolo[3,2-c] pyridin-4-yl)-3- methylpiperazin-1-yl)-2,2-dimethylpropan-1-one (6.3 mg, 22%) as a white solid. LC/MS ESI (m/z): 435 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 7.98 (d, J = 5.9 Hz, 1H), 7.40 (m, 1H), 7.16 (m, 1H), 7.10 – 7.06 (m, 2H), 6.78 (m, 1H), 6.78 (s, 1H), 3.97 – 3.80 (m, 3H), 3.65 – 3.47 (m, 3H), 3.07 (m, 1H), 2.43 (m, 1H), 1.27 (s, 9H), 0.99 (d, J = 6.2 Hz, 3H), 0.96 – 0.91 (m, 2H), 0.77 – 0.72 (m, 1H), 0.55 – 0.50 (m, 1H). The following compound was prepared by the procedure analogous to the synthesis of compound 228 from the corresponding chiral amine.
Example 46. Synthesis of 2-(4-((2S,5R)-2,5-dimethyl-4-pivaloylpiperazin-1-yl)-5-(2- fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonit rile (Compound 230) Compound 230 Step 1.4-Chloro-5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine To a solution of 4-chloro-5-iodo-7H-pyrrolo[2,3-d]pyrimidine (200 g, 0.71 mol) and 4-methylbenzene-1-sulfonyl chloride (180 g, 0.93 mol) in acetone (2 L) at 0 o C was added 2.0M NaOH (0.53 L) dropwise. After complete addition, the reaction was allowed to warm up to room temperature and stirred for another 3 h. The resulting precipitate was collected by filtration, washed twice with water and dried in vacuo to afford 4-chloro-5-iodo-7-tosyl-7H- pyrrolo[2,3-d]pyrimidine (300 g, 95 %) as an off-white solid. LC/MS ESI (m/z): 434 (M+H) + . Step 2. tert-Butyl (2R,5S)-4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2 ,5- dimethylpiperazine-1-carboxylate To a solution of 4-chloro-5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (10 g, 23 mmol) in DIPEA (100 mL) was added tert-butyl (2R,5S)-2,5-dimethylpiperazine-1- carboxylate (9.9 g, 46 mmol). The resulting mixture was stirred at 150 o C for 2 h. After cooling to room temperature, the reaction was concentrated and purified by flash column chromatography (silica gel, 0~30% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2 ,5-dimethylpiperazine-1- carboxylate (13 g, 92%) as a yellow solid. LC/MS ESI (m/z): 612 (M+H) + . Step 3. tert-Butyl (2R,5S)-4-(5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrim idin- 4-yl)-2,5-dimethylpiperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4- yl)-2,5-dimethylpiperazine-1-carboxylate (6.0 g, 9.8 mmol) in dioxane (60 mL) and H 2 O (10 mL) were added (2-fluorophenyl)boronic acid (1.7 g, 12 mmol), K 2 CO 3 (4.1 g, 29 mmol) and Pd(dppf)Cl 2 (0.72 g, 0.98 mmol). The resulting mixture was stirred at 90℃ overnight. After cooling to room temperature, the reaction was concentrated and the residue was purified by flash column chromatography (silica gel, 0~30% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3-d]pyrim idin-4-yl)-2,5- dimethylpiperazine-1-carboxylate (5.5 g, 97%) as a yellow solid. LC/MS ESI (m/z): 580 (M+H) + . Step 4. tert-Butyl (2R,5S)-4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-y l)- 2,5-dimethylpiperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-4-(5-(2-fluorophenyl)-7-tosyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate (3.0 g, 5.2 mmol) in THF (15 mL) was added TBAF (31 mL, 1.0 M in THF). After stirring at room temperature for 2 h, the reaction was diluted with water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~60% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-y l)-2,5- dimethylpiperazine-1-carboxylate (2.0 g, 90%) as a yellow solid. LC/MS ESI (m/z): 426 (M+H) + . Step 5. tert-Butyl (2R,5S)-4-(7-(4-cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate To a solution of tert-butyl (2R,5S)-4-(5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin- 4-yl)-2,5-dimethylpiperazine-1-carboxylate (300 mg, 0.70 mmol) in DMF (10 mL) were added 2-fluoroisonicotinonitrile (170 mg, 1.4 mmol) and Cs 2 CO 3 (690 mg, 2.1 mmol). The resulting mixture was stirred at 50℃ overnight. After cooling to room temperature, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~20% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(7-(4- cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrim idin-4-yl)-2,5- dimethylpiperazine-1-carboxylate (320 mg, 86%) as a yellow solid. LC/MS ESI (m/z): 528 (M+H) + . Step 6.2-(4-((2S,5R)-2,5-Dimethylpiperazin-1-yl)-5-(2-fluoropheny l)-7H-pyrrolo[2,3- d]pyrimidin-7-yl)isonicotinonitrile To a solution of tert-butyl (2R,5S)-4-(7-(4-cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (320 mg, 0.60 mmol) in THF (5 mL) was added HCl (3.0 mL, 4.0 M in dioxane). After stirring at room temperature overnight, the reaction was partitioned between DCM and water. The aqueous layer was extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~10% MeOH in DCM) to afford 2-(4-((2S,5R)-2,5-dimethylpiperazin-1-yl)-5-(2- fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonit rile (190 mg, 73%) as a pink solid. LC/MS ESI (m/z): 428 (M+H) + . Step 7.2-(4-((2S,5R)-2,5-Dimethyl-4-pivaloylpiperazin-1-yl)-5-(2- fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile To a solution of 2-(4-((2S,5R)-2,5-dimethylpiperazin-1-yl)-5-(2-fluorophenyl) -7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (90 mg, 0.21 mmol) and TEA (0.090 mL, 0.63 mmol) in DCM (3 mL) at 0 o C was added pivaloyl chloride (0.050 mL, 0.42 mmol). After stirring at room temperature for 1 h, the reaction was partitioned between DCM and water. The aqueous layer was extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by prep-HPLC to afford 2-(4-((2S,5R)-2,5-dimethyl-4-pivaloylpiperazin-1-yl)-5-(2- fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonit rile (65 mg, 61%) as a white solid. LC/MS ESI (m/z): 512 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.34 (s, 1H), 8.56 (d, J = 5.0 Hz, 1H), 8.51 (s, 1H), 8.23 (s, 1H), 7.43 (m, 1H), 7.34 (dd, J = 5.0, 1.3 Hz, 1H), 7.30 (m, 1H), 7.22 – 7.08 (m, 2H), 4.45 (br. s, 1H), 4.25 – 3.86 (br. s, 1H), 3.63 (m, 1H), 3.37 (d, J = 12.9 Hz, 1H), 3.22 (m, 1H), 3.01 – 2.35 (br. s, 1H), 1.17 (s, 9H), 1.11 (m, 3H), 0.85 (br. s, 3H). The following compounds were prepared by procedures analogous to the synthesis of compound 230 from the corresponding boronic acids and acid chlorides. For some analogs, the cyclobutyl group was introduced by coupling of the corresponding aryl bromide with cyclobutylboronic acid (Pd-118, K 2 CO 3 (20 eq.), 80 o C in toluene). For compound 239, the corresponding carboxylic acid was synthesized following procedures described in US patent US20190248809). Example 47. Synthesis of 1-((2R,5S)-4-(7-(4-fluoropyridin-2-yl)-5-methyl-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazin-1-yl)-2, 2-dimethylpropan-1-one (Compound 244) Compound 244 Step 1. tert-Butyl (2R,5S)-2,5-dimethyl-4-(5-methyl-7-tosyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)piperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-4-(5-iodo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4- yl)-2,5-dimethylpiperazine-1-carboxylate (4.0 g, 6.7 mmol, prepared following the procedure outlined for compound 230) in dioxane (50 mL) and H 2 O (10 mL) were added 2,4,6- trimethyl-1,3,5,2,4,6-trioxatriborinane (1.7 g, 13 mmol), K2CO3 (2.8 g, 20 mmol) and Pd(dppf)Cl 2 (490 mg, 0.67 mmol). The resulting mixture was heated at 70 o C overnight. After cooling to room temperature, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50% ethyl acetate in petroleum ether) to afford tert- butyl (2R,5S)-2,5-dimethyl-4-(5-methyl-7-tosyl-7H-pyrrolo[2,3-d]py rimidin-4-yl)piperazine- 1-carboxylate (2.0 g, 61%) as a white solid. LC/MS ESI (m/z): 500 (M+H) + . Step 2. tert-Butyl (2R,5S)-2,5-dimethyl-4-(5-methyl-7H-pyrrolo[2,3-d]pyrimidin- 4- yl)piperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-2,5-dimethyl-4-(5-methyl-7-tosyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)piperazine-1-carboxylate (2.0 g, 4.0 mmol) in THF (20 mL) was added TBAF (24 mL, 1.0 M in THF). After 5 h, the reaction was diluted with water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~80% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-2,5-dimethyl-4-(5- methyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperazine-1-carboxyl ate (1.2 g, 87%) as a white solid. LC/MS ESI (m/z): 346 (M+H) + . Step 3. tert-Butyl (2R,5S)-4-(7-(4-fluoropyridin-2-yl)-5-methyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-2,5-dimethyl-4-(5-methyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)piperazine-1-carboxylate (100 mg, 0.30 mmol) in DMF (5 mL) were added 2-bromo-4-fluoropyridine (67 mg, 0.60 mmol), trans-N,N’-dimethylcyclohexane-1,2-diamine (6.0 mg, 0.04 mmol), CuI (7.6 mg, 0.04 mmol) and K 3 PO 4 (190 mg, 0.90 mmol). The resulting mixture was heated at 120 o C overnight. After cooling to room temperature, the reaction was diluted with water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(7-(4-fluoropyridin-2-yl)-5-methyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate (110 mg, 90%) as a white solid. LC/MS ESI (m/z): 441 (M+H) + . Step 4.4-((2S,5R)-2,5-Dimethylpiperazin-1-yl)-7-(4-fluoropyridin- 2-yl)-5-methyl-7H- pyrrolo[2,3-d]pyrimidine tert-Butyl (2R,5S)-4-(7-(4-fluoropyridin-2-yl)-5-methyl-7H-pyrrolo[2,3- d]pyrimidin- 4-yl)-2,5-dimethylpiperazine-1-carboxylate (110 mg, 0.25 mmol) in DCM (5 mL) was treated with TFA (2.0 mL). The resulting mixture was stirred at room temperature for 2 h. After removal of solvent, the residue was diluted with DCM and washed with NaHCO 3 (aq.). The organic layer was extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was used in the next step directly. LC/MS ESI (m/z): 341 (M+H) + . Step 5.1-((2R,5S)-4-(7-(4-Fluoropyridin-2-yl)-5-methyl-7H-pyrrolo [2,3-d]pyrimidin- 4-yl)-2,5-dimethylpiperazin-1-yl)-2,2-dimethylpropan-1-one To a solution of 4-((2S,5R)-2,5-dimethylpiperazin-1-yl)-7-(4-fluoropyridin-2- yl)-5- methyl-7H-pyrrolo[2,3-d]pyrimidine (70 mg, 0.21 mmol) in DCM (10 mL) at 0 o C were added TEA (55 mg, 0.54 mmol) and pivaloyl chloride (32 mg, 0.27 mmol). After stirring at room temperature for 2 h, the reaction was diluted with DCM and washed with brine. The aqueous layer was extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50% ethyl acetate in petroleum ether) to give crude product which was further purified by prep-HPLC to afford 1-((2R,5S)-4-(7-(4-fluoropyridin- 2-yl)-5-methyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethyl piperazin-1-yl)-2,2- dimethylpropan-1-one (15 mg, 17%) as a white solid. LC/MS ESI (m/z): 425 (M+H) + . 1 H NMR (400 MHz, CD 3 OD) δ 8.68 (d, J = 11.2 Hz, 1H), 8.50 – 8.40 (m, 2H), 8.03 (s, 1H), 7.09 (t, J = 5.7 Hz, 1H), 4.72 (m, 1H), 4.57 (m, 1H), 4.39 – 4.08 (br. s, 1H), 3.86 – 3.51 (m, 3H), 2.50 (s, 3H), 1.34 (s, 9H), 1.26 (m, 3H), 1.13 (br. s, 3H). The following compounds were prepared by procedures analogous to the synthesis of compound 244 from the corresponding boronic acids and acid chlorides. In one instance, the cyclopropyl group was introduced by Suzuki coupling with cyclopropylboronic acid (Pd-118, K 2 CO 3 (20 eq.), 80 o C in toluene). For some analogs, the cyclobutyl group was introduced by Suzuki coupling of cyclobutylboronic acid and the corresponding aryl bromides. For compound 256, compound 262, compound 258, and compound 251 the corresponding carboxylic acid was synthesized following procedures described in US patent US20190248809).
Example 48. Synthesis of 2-(5-cyclopropyl-4-((2S,5R)-4-(2-methoxy-2- methylpropanoyl)-2,5-dimethylpiperazin-1-yl)-7H-pyrrolo[2,3- d]pyrimidin-7- yl)isonicotinonitrile (Compound 264) Compound 264 Step 1. tert-Butyl (2R,5S)-4-(7-(4-cyanopyridin-2-yl)-5-cyclopropyl-7H-pyrrolo[ 2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-4-[5-bromo-7-(4-cyanopyridin-2-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl]-2,5-dimethylpiperazine-1-carbo xylate (1500 mg, 2.9 mmol, prepared following a similar procedure outlined for compound 268 using 2- fluoroisonicotinonitrile instead) in toluene (15 mL) were added cyclopropylboronic acid (500 mg, 5.9 mmol), dipotassium carbonate (8.1 g, 59 mmol) and Pd-118 (380 mg, 0.60 mmol ). After heating at 80℃ overnight, the reaction mixture was cooled to room temperature and filtered. The filtrate was concentrated and purified by flash column chromatography to afford tert-butyl (2R,5S)-4-(7-(4-cyanopyridin-2-yl)-5-cyclopropyl-7H-pyrrolo[ 2,3-d]pyrimidin-4- yl)-2,5-dimethylpiperazine-1-carboxylate (1000 mg, 73%) as a solid. LC/MS ESI (m/z): 474 (M+H) + . Step 2.2-(5-Cyclopropyl-4-((2S,5R)-2,5-dimethylpiperazin-1-yl)-7H -pyrrolo[2,3- d]pyrimidin-7-yl)isonicotinonitrile To a solution of tert-butyl (2R,5S)-4-(7-(4-cyanopyridin-2-yl)-5-cyclopropyl-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (1000 mg, 2.1 mmol) in THF (8 mL) at 0℃ was added HCl (4.0 mL, 4.0 M in dioxane). The resulting mixture was stirred at room temperature for 2 h. The reaction mixture was then basified with NaHCO 3 (aq.) and extracted twice with DCM. The combined organic layers were washed with NaHCO 3 (aq.), dried over Na 2 SO 4 , filtered and concentrated. The residue was used in the next step directly. LC/MS ESI (m/z): 374 (M+H) + . Step 3.2-(5-Cyclopropyl-4-((2S,5R)-4-(2-methoxy-2-methylpropanoyl )-2,5- dimethylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)ison icotinonitrile To a solution of 2-(5-cyclopropyl-4-((2S,5R)-2,5-dimethylpiperazin-1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (100 mg, 0.27 mmol) in DMF (8 mL) at 0℃ were added DIPEA (70 mg, 0.54 mmol), 2-methoxy-2-methylpropanoic acid (38 mL, 0.32 mmol) and HATU (120 mg, 0.32 mol). After stirring at room temperature for 2 h, the reaction was quenched with NaHCO 3 (aq.) and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered, concentrated. The residue was purified by prep-HPLC to afford 2-(5-cyclopropyl-4-((2S,5R)-4-(2-methoxy-2- methylpropanoyl)-2,5-dimethylpiperazin-1-yl)-7H-pyrrolo[2,3- d]pyrimidin-7- yl)isonicotinonitrile (60 mg, 47%) as an off-white solid. LC/MS ESI (m/z): 474 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.25 (s, 1H), 8.52 (d, J = 5.0 Hz, 1H), 8.44 (d, J = 4.6 Hz, 1H), 7.74 (d, J = 3.3 Hz, 1H), 7.28 (d, J = 5.0 Hz, 1H), 5.23 (m, ~0.5H), 4.96 – 4.82 (m, 1H), 4.76 (m, ~0.5H), 4.48 – 4.33 (m, 1H), 3.93 – 3.64 (m, ~2.5H), 3.38 (m, ~0.5H), 3.29 (s, ~1.5H), 3.19 (s, ~1.5H), 1.94 (m, 1H), 1.48 – 1.38 (m, 6H), 1.31 – 1.17 (m, 3H), 1.08 – 1.00 (m, 3H), 1.00 – 0.94 (m, 2H), 0.89 (m, 1H), 0.65 (m, 1H); several peaks and their integrations are fractions of protons on account of presence of rotomers. The following compounds were prepared by procedures analogous to the synthesis of compound 264 from the corresponding carboxylic acids, chiral amines and boronic acids.
Example 49. Synthesis of 2-(5-(azetidin-1-yl)-4-((2S,5R)-4-(2-methoxy-2- methylpropanoyl)-2,5-dimethylpiperazin-1-yl)-7H-pyrrolo[2,3- d]pyrimidin-7- yl)isonicotinonitrile (Compound 268)
Compound 268 Step 1.5-Bromo-4-chloro-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine To a solution of 5-bromo-4-chloro-7H-pyrrolo[2,3-d]pyrimidine (100 g, 0.43 mol) and 4-methylbenzenesulfonyl chloride (120 g, 0.65 mol) in acetone (1.5 L) at 0 o C was added 2.0 M NaOH (0.33 L) dropwise. After the addition, the reaction was allowed to warm up to room temperature and stirred for another 3 h. The resulting precipitate was collected by filtration, washed twice with water twice and dried in vacuo to afford 5-bromo-4-chloro-7- tosyl-7H-pyrrolo[2,3-d]pyrimidine (160 g, 96 %) as an off-white solid. LC/MS ESI (m/z): 386, 388 (M+H) + . Step 2. tert-Butyl (2R,5S)-4-(5-bromo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)- 2,5- dimethylpiperazine-1-carboxylate To a solution of 5-bromo-4-chloro-7-tosyl-7H-pyrrolo[2,3-d]pyrimidine (17 g, 44 mmol) in DIPEA (200 mL) was added tert-butyl (2R,5S)-2,5-dimethylpiperazine-1- carboxylate (19 g, 88 mmol). The resulting mixture was stirred at 150 o C for 2 h. After cooling to room temperature, the reaction was concentrated and purified by flash column chromatography (silica gel, 0~30% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(5-bromo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)- 2,5-dimethylpiperazine-1- carboxylate (20 g, 80%) as a white solid. LC/MS ESI (m/z): 564, 566 (M+H) + . Step 3. tert-Butyl (2R,5S)-4-(5-bromo-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,5- dimethylpiperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-4-(5-bromo-7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4- yl)-2,5-dimethylpiperazine-1-carboxylate (20 g, 37 mmol) in THF (200 mL) was added TBAF (180 mL, 1.0 M in THF). After 3 h, the reaction was diluted with water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~80% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(5-bromo-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate(13 g, 90%) as a white solid. LC/MS ESI (m/z): 410, 412 (M+H) + . Step 4. tert-Butyl (2R,5S)-4-(5-bromo-7-(4-chloropyridin-2-yl)-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-4-(5-bromo-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,5- dimethylpiperazine-1-carboxylate (13 g, 32 mmol) in DMF (150 mL) were added 4-chloro-2- fluoropyridine (8.3 g, 64 mmol) and Cs 2 CO 3 (52 g, 160 mmol). The resulting mixture was heated at 60 o C overnight. After cooling to room temperature, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~40% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(5-bromo-7-(4-chloropyridin- 2-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazin e-1-carboxylate (7.8 g, 47%) as a white solid. LC/MS ESI (m/z): 521, 523 (M+H) + . Step 5. tert-Butyl (2R,5S)-4-(7-(4-chloropyridin-2-yl)-5-(2-oxoazetidin-1-yl)-7 H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate To a solution of tert-butyl (2R,5S)-4-(5-bromo-7-(4-chloropyridin-2-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (7.3 g, 14 mmol) in DMF (70 mL) were added azetidin-2-one (2.0 g, 28 mmol), trans-N,N’-dimethylcyclohexane- 1,2-diamine (1.6 g, 14 mmol), CuI (2.7 g, 14 mmol) and K 3 PO 4 (8.9 g, 42 mmol). The resulting mixture was heated at 90 o C overnight. After cooling to room temperature, the reaction was diluted with water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(7-(4-chloropyridin-2-yl)-5-(2-oxoazetidin-1-yl)-7 H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (4.8 g, 67%) as a white solid. LC/MS ESI (m/z): 512 (M+H) + . Step 6. tert-Butyl (2R,5S)-4-(5-(azetidin-1-yl)-7-(4-chloropyridin-2-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate To a solution of tert-butyl (2R,5S)-4-(7-(4-chloropyridin-2-yl)-5-(2-oxoazetidin-1-yl)- 7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-ca rboxylate (2.0 g, 3.9 mmol) in THF (20 mL) at 0 o C were added RhHCO(PPh 3 ) 3 (370 mg, 0.40 mmol) and PhSiH 3 (2.2 g, 20 mmol) dropwise. After stirring at room temperature overnight under N 2 , the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc twice. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~35% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(5-(azetidin-1-yl)-7-(4- chloropyridin-2-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dim ethylpiperazine-1-carboxylate (1.4 g, 72%) as a yellow solid. LC/MS ESI (m/z): 498 (M+H) + . Step 7. tert-Butyl (2R,5S)-4-(5-(azetidin-1-yl)-7-(4-cyanopyridin-2-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate To a solution of tert-butyl (2R,5S)-4-(5-(azetidin-1-yl)-7-(4-chloropyridin-2-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (1.3 g, 2.6 mmol) in DMF (15 mL) were added Zn(CN) 2 (1.5 g, 13 mmol) and Pd(PPh 3 ) 4 (1.5 g, 1.3 mmol). The resulting mixture was heated at 120 o C overnight. After cooling to room temperature, the solvent was removed and the residue was purified by flash column chromatography (silica gel, 0~60% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(5-(azetidin-1-yl)- 7-(4-cyanopyridin-2-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,5 -dimethylpiperazine-1- carboxylate (710 mg, 55%) as a yellow solid. LC/MS ESI (m/z): 489 (M+H) + . Step 8.2-(5-(Azetidin-1-yl)-4-((2S,5R)-2,5-dimethylpiperazin-1-yl )-7H-pyrrolo[2,3- d]pyrimidin-7-yl)isonicotinonitrile To a solution of tert-butyl (2R,5S)-4-(5-(azetidin-1-yl)-7-(4-cyanopyridin-2-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (710 mg, 1.5 mmol) in DCM (10 mL) at 0 o C was added TFA (3.0 mL). The resulting mixture was stirred at 0 o C for 2 h. After removal of solvent, the residue was diluted with DCM and washed with NaHCO 3 (aq.). The aqueous layer was extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was used in the next step directly. LC/MS ESI (m/z): 389 (M+H) + . Step 9.2-(5-(Azetidin-1-yl)-4-((2S,5R)-4-(2-methoxy-2-methylpropa noyl)-2,5- dimethylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)ison icotinonitrile To a solution of 2-(5-(azetidin-1-yl)-4-((2S,5R)-2,5-dimethylpiperazin-1-yl)- 7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (70 mg, 0.18 mmol) in DMF (10 mL) were added TEA (55 mg, 0.54 mmol), 2-methoxy-2-methylpropanoic acid (260 mg, 2.2 mmol) and HATU (840 mg, 2.2 mmol). After 2 h, the residue was diluted with EtOAc and washed with NaHCO 3 (aq.). The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50% ethyl acetate in petroleum ether) to give crude product which was further purified by prep-HPLC to afford 2-(5-(azetidin-1- yl)-4-((2S,5R)-4-(2-methoxy-2-methylpropanoyl)-2,5-dimethylp iperazin-1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (33 mg, 37%) as a yellow solid. LC/MS ESI (m/z): 489 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.35 (s, 1H), 8.58 (d, J = 5.0 Hz, 1H), 8.44 (d, J = 4.2 Hz, 1H), 7.47 (d, J = 8.7 Hz, 1H), 7.30 (d, J = 5.0 Hz, 1H), 5.33 – 5.13 (m, ~1.5H), 4.77 (br. s, ~0.5H), 4.48 (m, 1H), 4.18 (d, J = 14.2 Hz, ~0.5H), 3.99 (m, 1H), 3.92 – 3.78 (m, ~2.5H), 3.68 – 3.49 (m, ~3H), 3.35 (s, ~1.5H), 3.25 (s, ~1.5H), 2.31 (m, 2H), 1.55 – 1.40 (m, 6H), 1.26 – 1.20 (m, 3H), 1.07 – 0.95 (m, 3H); several peaks and their integrations are fractions of protons on account of presence of rotomers. The following compounds were prepared by procedures analogous to the synthesis of compound 268 from the corresponding acids or acid chlorides and chiral amines.4-Chloro-5- iodo-7H-pyrrolo[2,3-d]pyrimidine was used for the synthesis of compound 275 and compound 276.
Example 50. Synthesis of 1-((2R,5S)-4-(5-(azetidin-1-yl)-7-(3-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazin-1-yl)-2- methoxy-2-methylpropan- 1-one (Compound 277) Compound 277 Step 1. tert-Butyl (2R,5S)-4-(5-bromo-7-(3-fluorophenyl)-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-4-(5-bromo-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,5- dimethylpiperazine-1-carboxylate (1.7 g, 4.2 mmol) in DMF (20 mL) were added 1-fluoro-3- iodobenzene (1.9 g, 8.3 mmol), trans-N,N’-dimethylcyclohexane-1,2-diamine (480 mg, 4.2 mmol), CuI (790 mg, 4.2 mmol) and K 3 PO 4 (2.7 g, 12 mmol). The resulting mixture was heated at 90 o C overnight. After cooling to room temperature, the reaction was diluted with water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(5-bromo-7-(3-fluorophenyl)-7H-pyrrolo[2,3-d]pyrim idin-4-yl)-2,5- dimethylpiperazine-1-carboxylate (1.7 g, 46%) as a white solid. LC/MS ESI (m/z): 504, 506 (M+H) + . Step 2. tert-Butyl (2R,5S)-4-(7-(3-fluorophenyl)-5-(2-oxoazetidin-1-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate To a solution of tert-butyl (2R,5S)-4-(5-bromo-7-(4-chloropyridin-2-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (1.7 g, 3.4 mmol) in DMF (20 mL) were added azetidin-2-one (480 mg, 6.8 mmol), trans-N,N’- dimethylcyclohexane-1,2-diamine (390 mg, 3.4 mmol), CuI (650 mg, 3.4 mmol) and K 3 PO 4 (2.2 g, 10 mmol). The resulting mixture was heated at 90 o C overnight. After cooling to room temperature, the reaction was diluted with water and extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(7-(3-fluorophenyl)-5-(2- oxoazetidin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimet hylpiperazine-1-carboxylate (1.4 g, 84%) as a yellow solid. LC/MS ESI (m/z): 495 (M+H) + . Step 3. tert-Butyl (2R,5S)-4-(5-(azetidin-1-yl)-7-(3-fluorophenyl)-7H-pyrrolo[2 ,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-4-(7-(3-fluorophenyl)-5-(2-oxoazetidin-1-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (1.3 g, 3.4 mmol) in THF (20 mL) at 0 o C were added RhHCO(PPh 3 ) 3 (370 mg, 0.40 mmol) and PhSiH 3 (2.2 g, 20 mmol) dropwise. After stirring at room temperature overnight under N 2 , the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~35% ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(5-(azetidin-1-yl)-7-(3-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (850 mg, 52%) as a yellow solid. LC/MS ESI (m/z): 481 (M+H) + . Step 5.5-(Azetidin-1-yl)-4-((2S,5R)-2,5-dimethylpiperazin-1-yl)-7 -(3-fluorophenyl)- 7H-pyrrolo[2,3-d]pyrimidine To a solution of tert-butyl (2R,5S)-4-(5-(azetidin-1-yl)-7-(4-cyanopyridin-2-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (850 mg, 1.8 mmol) in DCM (10 mL) at 0 o C was added TFA (3.0 mL). The resulting mixture was stirred at 0 o C for 2 h. After removal of solvent, the residue was diluted with DCM and washed with NaHCO 3 (aq.). The aqueous layer was extracted twice with DCM. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was used in the next step directly. LC/MS ESI (m/z): 381 (M+H) + . Step 6.2-(5-(Azetidin-1-yl)-4-((2S,5R)-4-(2-methoxy-2-methylpropa noyl)-2,5- dimethylpiperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)ison icotinonitrile To a solution of 2-(5-(azetidin-1-yl)-4-((2S,5R)-2,5-dimethylpiperazin-1-yl)- 7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (70 mg, 0.18 mmol) in DMF (10 mL) were added TEA (55 mg, 0.54 mmol), 2-methoxy-2-methylpropanoic acid (260 mg, 2.2 mmol) and HATU (840 mg, 2.2 mmol). After 2 h, the residue was diluted with EtOAc and washed with NaHCO 3 (aq.). The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50% ethyl acetate in petroleum ether) to give crude product which was further purified by prep-HPLC to 1-((2R,5S)-4-(5-(azetidin- 1-yl)-7-(3-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2, 5-dimethylpiperazin-1-yl)-2- methoxy-2-methylpropan-1-one (24 mg, 27%) as a white solid. LC/MS ESI (m/z): 481 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 8.38 (d, J = 3.3 Hz, 1H), 7.57 – 7.53 (m, 2H), 7.45 (m, 1H), 7.00 (t, J = 8.2 Hz, 1H), 6.64 (d, J = 8.7 Hz, 1H), 5.28 (m, 1H), 5.16 (br. s, ~0.5H), 4.78 (br. s, ~0.5H), 4.49 (m, 1H), 4.17 (d, J = 14.0 Hz, ~0.5H), 3.99 (m, 1H), 3.88 – 3.76 (m, ~2.5H), 3.67 – 3.52 (m, 3H), 3.35 (s, ~1.5H), 3.25 (s, ~1.5H), 2.31 (m, 2H), 1.55 – 1.45 (m, 6H), 1.25 (m, 3H), 1.02 (m, 3H); several peaks and their integrations are fractions of protons on account of presence of rotomers. The following compounds were prepared by procedures analogous to the synthesis of compound 277 from the corresponding acids, aryl halides and lactam.
Example 51. Synthesis of 2-(5-(2-fluorophenyl)-4-((2S,5R)-4-isobutyryl-2-methyl-5- (methyl-d 3 )piperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isoni cotinonitrile (Compound 281) Compound 281 Step 1. Ethyl (R,E)-2-((tert-butylsulfinyl)imino)acetate To a solution of ethyl 2-oxoacetate (6.4 g, 63 mmol) in CH 2 Cl 2 (300 mL) were added (R)-2-methylpropane-2-sulfinamide (7.6 g, 63 mmol) and 4 Å molecular sieves (20 g). After 72 h, the mixture was filtered through a bed of Celite and washed with EtOAc. The filtrate was dried over Na 2 SO 4 , filtered and concentrated. The residue was purified with flash column chromatography (silica gel, 0~20% ethyl acetate in petroleum ether) to afford ethyl (R,E)-2- ((tert-butylsulfinyl)imino)acetate (7.2 g, 56%) as a colorless oil. Step 2. Ethyl ((R)-tert-butylsulfinyl)-D-alaninate-3,3,3-d 3 To a solution of ethyl (R,E)-2-((tert-butylsulfinyl)imino)acetate (6.2 g, 30 mmol) in DCM (400 mL) and THF (120 mL) at -78 o C was added BF 3 ·Et 2 O (7.4 mL, 60 mmol) dropwise under N 2 atmosphere. The resulting mixture was stirred at -78 ℃ for 5 min and treated with CD 3 MgI (1.0 M in Et 2 O, 60 mL, 60 mmol) dropwise. After stirring at -78 o C for 10 min, the reaction was quenched with NaHCO 3 (aq.) and partitioned between EtOAc and brine. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~50%, ethyl acetate in petroleum ether) to afford ethyl ((R)-tert-butylsulfinyl)-D-alaninate-3,3,3-d 3 (1.4 g, 21% yield, dr = 97/3) as a white solid. LC/MS ESI (m/z): 225 (M+H) + . The configuration was verified by 1 H NMR (J. Org. Chem.1999, 64, 3396-3397). Step 3. Ethyl D-alaninate-3,3,3-d 3 To a solution of ethyl ((R)-tert-butylsulfinyl)-D-alaninate-3,3,3-d 3 (1.4 g, 6.2 mmol) in MeOH (30 mL) was added HCl (5.0 mL, 4.0 M in dioxane). The resulting mixture was stirred at room temperature under N 2 for 2 h. The solvents were removed under vacuum to afford ethyl D-alaninate-3,3,3-d 3 , as a white solid (1.0 g crude HCl salt). LC/MS ESI (m/z): 121 (M+H) + . Step 4. Ethyl (tert-butoxycarbonyl)-D-alaninate-3,3,3-d 3 To a solution of ethyl D-alaninate-3,3,3-d 3 (1.0 g crude HCl salt) in MeOH (30 mL) were added TEA (1.7 mL, 12 mmol) and Boc 2 O (1.5 g, 6.9 mmol). The resulting mixture was stirred at room temperature under N 2 for 2 h. The reaction was partitioned between EtOAc and NH 4 Cl (aq.). The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated to afford crude product ethyl (tert-butoxycarbonyl)-D-alaninate-3,3,3-d 3 (1.4 g crude) as a white solid. LC/MS ESI (m/z): 221 (M+H) + . Step 5. (tert-Butoxycarbonyl)-D-alanine-3,3,3-d 3 To a solution of ethyl (tert-butoxycarbonyl)-D-alaninate-3,3,3-d 3 (1.4 g crude) in EtOH (20 mL) and H 2 O (10 mL) in an ice bath was added LiOH (310 mg, 13 mmol). The resulting mixture was stirred at room temperature under N 2 for 1 h. The reaction was partitioned between EtOAc and brine. The aqueous layer was acidified by HCl (1.0 M) to pH 3 and extracted twice with EtOAc. The organic layer was washed with brine, dried over Na 2 SO 4 , filtered, and concentrated to afford (tert-butoxycarbonyl)-D-alanine-3,3,3-d 3 (900 mg, 75% yield over three steps) LC/MS ESI (m/z): 193 (M+H) + . Step 6. Methyl N-benzyl-N-((tert-butoxycarbonyl)-D-alanyl-3,3,3-d 3 )-L-alaninate To a solution of (tert-butoxycarbonyl)-D-alanine-3,3,3-d 3 (900 mg, 4.7 mmol) and methyl benzyl-L-alaninate hydrochloride (1.2 g, 5.2 mmol) in DMF (20 mL) were added DIPEA (2.4 g, 19 mmol) and HATU (2.7 g, 7.0 mmol). The resulting mixture was stirred at room temperature under N 2 overnight. The reaction was partitioned between EtOAc and aqueous NaHCO 3 . The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash column chromatography (silica gel, 0~60%, ethyl acetate in petroleum ether) to afford methyl N-benzyl-N-((tert-butoxycarbonyl)-D-alanyl-3,3,3-d 3 )-L- alaninate (1.4 g, 81% yield) as a yellow solid. LC/MS ESI (m/z): 368 (M+H) + . Step 7. Methyl N-(D-alanyl-3,3,3-d 3 )-N-benzyl-L-alaninate To a solution of methyl N-benzyl-N-((tert-butoxycarbonyl)-D-alanyl-3,3,3-d 3 )-L- alaninate (1.4 g, 3.8 mmol) in DCM (20 mL) at 0 o C was added TFA (10 mL). The resulting mixture was stirred at room temperature under N 2 for 3 h. The solvent of the reaction was removed under vacuum to afford crude product methyl N-(D-alanyl-3,3,3-d 3 )-N-benzyl-L- alaninate (1.5 g crude TFA salt) as a yellow solid. LC/MS ESI (m/z): 268 (M+H) + . Step 8. (3R,6S)-1-Benzyl-6-methyl-3-(methyl-d 3 )piperazine-2,5-dione A solution of methyl N-(D-alanyl-3,3,3-d 3 )-N-benzyl-L-alaninate (1.5 g crude TFA salt) in MeOH (10 mL) was heated at 70 ℃ under N 2 for 4 h. The reaction mixture was then partitioned between EtOAc and brine aqueous. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered, and concentrated to afford (3R,6S)-1-benzyl-6-methyl-3-(methyl-d 3 )piperazine-2,5-dione (1.0 g crude) as a yellow solid. LC/MS ESI (m/z): 236 (M+H) + . Step 9. tert-Butyl (2R,5S)-4-benzyl-5-methyl-2-(methyl-d 3 )piperazine-1-carboxylate A solution of (3R,6S)-1-benzyl-6-methyl-3-(methyl-d 3 )piperazine-2,5-dione (1.0 g crude) in THF (10 mL) in an ice bath under N 2 was treated with LiAlH 4 (1.0 M in THF, 20 mL) dropwise. The reaction mixture was stirred at 70℃ for 3 h. The reaction mixture was carefully quenched with 20% NaOH (20 mL) and the resulting mixture was used in the next step directly. LC/MS ESI (m/z): 208 (M+H) + . The solution was then treated with Boc 2 O (1.7 g, 7.6 mmol). After stirring at room temperature overnight, the reaction mixture was filtered. The residue was purified by flash column chromatography (silica gel, 0~10%, ethyl acetate in petroleum ether) to afford tert- butyl (2R,5S)-4-benzyl-5-methyl-2-(methyl-d 3 )piperazine-1-carboxylate (990 mg, 85% yield dr = 90/10) as a colorless oil. LC/MS ESI (m/z): 308 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 7.37 – 7.28 (m, 4H), 7.26 – 7.21 (m, 1H), 4.17 (d, J = 3.9 Hz, 1H), 3.69 – 3.57 (m, 2H), 3.46 (d, J = 13.6 Hz, 1H), 3.30 (dd, J = 13.0, 3.7 Hz, 1H), 2.92 (dd, J = 10.9, 5.9 Hz, 1H), 2.69 (dd, J = 11.7, 4.4 Hz, 1H), 2.19 (dd, J = 11.7, 1.9 Hz, 1H), 1.46 (s, 9H), 0.98 (d, J = 6.5 Hz, 3H). Step 10. tert-Butyl (2R,5S)-5-methyl-2-(methyl-d3)piperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-4-benzyl-5-methyl-2-(methyl-d 3 )piperazine-1- carboxylate (550 mg, 1.7 mmol) in MeOH (15 mL) was added Pd (200 mg, 10% on carbon(wet)). After stirring at room temperature for 2 h under H 2 atmosphere (~0.1 MPa), the reaction was filtered and the filtrate was concentrated to afford tert-butyl (2R,5S)-5-methyl-2- (methyl-d 3 )piperazine-1-carboxylate (320 mg, 82%) as a yellow oil. LC/MS ESI (m/z): 218 (M+H) + . Step 11.2-(4-Chloro-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonic otinonitrile To a solution of 4-chloro-5-iodo-7H-pyrrolo[2,3-d]pyrimidine (7.0 g, 25 mmol) and 2-fluoroisonicotinonitrile (18 g, 150 mmol) in CH 3 CN (70 mL) was added Cs 2 CO 3 (12 g, 38 mmol). The resulting mixture was stirred at 25℃ under N 2 for 72 h. Crude product was collected by filtration, washed with water and CH 3 CN to afford 2-(4-chloro-5-iodo-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (9.0g , 94%) as a light brown solid. LC/MS ESI (m/z): 382 (M+H) + . Step 12.2-(4-Chloro-5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin -7- yl)isonicotinonitrile To a solution of 2-(4-chloro-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7- yl)isonicotinonitrile (600 mg, 1.6 mmol) in dioxane (25 mL) and water (2 drop) were added (2-fluorophenyl)boronic acid (290 mg, 2.0 mmol), K 2 CO 3 (1.1 g, 7.9 mmol) and Pd(dppf)Cl 2 (130 mg, 0.16 mmol). The resulting mixture was stirred at 80 o C overnight. After cooling to room temperature, solvent was removed and the residue was purified by flash column chromatography (silica gel, 0~30% ethyl acetate in petroleum) to afford 2-(4-chloro-5-(2- fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonit rile (150 mg, 27%) as a white solid. LC/MS ESI (m/z): 350 (M+H) + . Step 13. tert-Butyl (2R,5S)-4-(7-(4-cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-5-methyl-2-(methyl-d3)piperazi ne-1-carboxylate To a solution of tert-butyl (2R,5S)-5-methyl-2-(methyl-d 3 )piperazine-1-carboxylate (30 mg, 0.13 mmol) in DIPEA (3 mL) was added 2-(4-chloro-5-(2-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (72 mg, 0.20 mmol). The resulting mixture was stirred at 150℃ for 2 h. After cooling to room temperature, the reaction was concentrated and the residue was purified by flash column chromatography (silica gel, 0~30%, ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(7-(4-cyanopyridin-2- yl)-5-(2-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-5-me thyl-2-(methyl-d 3 )piperazine- 1-carboxylate (30 mg, 41%) as a yellow solid. LC/MS ESI (m/z): 531 (M+H) + . Step 14.2-(5-(2-Fluorophenyl)-4-((2S,5R)-2-methyl-5-(methyl-d3)pi perazin-1-yl)-7H- pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile To a solution of tert-butyl (2R,5S)-4-(7-(4-cyanopyridin-2-yl)-5-(2-fluorophenyl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-5-methyl-2-(methyl-d 3 )piperazine-1-carboxylate (15 mg, 0.028 mmol) in DCM (2 mL) at 0 o C was added TFA (0.50 mL, 6.7 mmol). After stirring at 0 o C for 1 h, the reaction was basified with NaHCO 3 (aq.) to pH 8 and extracted twice with DCM. The combined organic layers were dried over Na 2 SO 4 , filtered and concentrated. The residue was used directly in the next step. LC/MS ESI (m/z): 431 (M+H) + . Step 15.2-(5-(2-Fluorophenyl)-4-((2S,5R)-4-isobutyryl-2-methyl-5- (methyl- d3)piperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicoti nonitrile To a solution of 2-(5-(2-fluorophenyl)-4-((2S,5R)-2-methyl-5-(methyl-d 3 )piperazin-1- yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile (10 mg, 0.023 mmol) and TEA (0.02 mL, 0.11 mmol) in DCM (2 mL) at 0 o C was added isobutyryl chloride (5.0 mg, 0.046 mmol). After stirring at room temperature for 1 h, the reaction was partitioned between DCM and water. The aqueous layer was extracted twice with DCM. The combined organic layers were washed with NaHCO3 (aq.) and brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by prep-HPLC to afford 2-(5-(2-fluorophenyl)-4-((2S,5R)-4-isobutyryl- 2-methyl-5-(methyl-d 3 )piperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isoni cotinonitrile (2.3 mg, 19%) as a white solid. LC/MS ESI (m/z): 501 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.34 (s, 1H), 8.56 (d, J = 5.0 Hz, 1H), 8.51 (d, J = 6.1 Hz, 1H), 8.23 (d, J = 4.7 Hz, 1H), 7.43 (m, 1H), 7.36 – 7.29 (m, 2H), 7.19 – 7.11 (m, 2H), 4.64 – 4.30 (m, 1H), 4.05 – 3.70 (m, ~1.5H), 3.55 – 3.05 (m, 3H), 2.75 – 2.45 (m, ~1.5H), 1.09 – 1.01 (m, 6H), 1.00 – 0.95 (m, 3H); several peaks and their integrations are fractions of protons on account of presence of rotomers. Example 52. Synthesis of 2-(4-((2S,5R)-4-(2-methoxy-2-methylpropanoyl)-2,5- dimethylpiperazin-1-yl)-5-phenyl-7H-pyrrolo[2,3-d]pyrimidin- 7-yl)isonicotinonitrile (Compound 282) Compound 282 Step 1. tert-Butyl (2R,5S)-4-(7-(4-cyanopyridin-2-yl)-5-phenyl-7H-pyrrolo[2,3- d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carboxylate To a solution of tert-butyl (2R,5S)-4-(5-bromo-7-(4-cyanopyridin-2-yl)-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (1.5 g, 2.9 mmol, prepared following a similar procedure outlined for compound 268 using 2- fluoroisonicotinonitrile) in dioxane (40 mL) and H 2 O (8 mL) were added phenylboronic acid (0.71 g, 5.8 mmol), K 2 CO 3 (1.2 g, 8.7 mmol) and Pd(dppf)Cl 2 (0.21 g, 0.29 mmol). The resulting mixture was stirred at 80℃ overnight. After cooling to room temperature, the reaction was concentrated and the residue was purified by flash column chromatography (silica gel, 0~20%, ethyl acetate in petroleum ether) to afford tert-butyl (2R,5S)-4-(7-(4- cyanopyridin-2-yl)-5-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl) -2,5-dimethylpiperazine-1- carboxylate (1.00 g, 69%) as a yellow solid. LC/MS ESI (m/z): 510 (M+H) + . Step 2.2-(4-((2S,5R)-2,5-Dimethylpiperazin-1-yl)-5-phenyl-7H-pyrr olo[2,3- d]pyrimidin-7-yl)isonicotinonitrile To a solution of tert-butyl (2R,5S)-4-(7-(4-cyanopyridin-2-yl)-5-phenyl-7H- pyrrolo[2,3-d]pyrimidin-4-yl)-2,5-dimethylpiperazine-1-carbo xylate (1.0 g, 2.0 mmol) in THF (10 mL) was added HCl in dioxane (10 mL, 4.0 M). After stirring at room temperature overnight, the reaction was concentrated, and the residue was used directly in the next step. LC/MS ESI (m/z): 410 (M+H) + . Step 3.2-(4-((2S,5R)-4-(2-Methoxy-2-methylpropanoyl)-2,5-dimethyl piperazin-1-yl)- 5-phenyl-7H-pyrrolo[2,3-d]pyrimidin-7-yl)isonicotinonitrile To a solution of 2-(4-((2S,5R)-2,5-dimethylpiperazin-1-yl)-5-phenyl-7H-pyrrol o[2,3- d]pyrimidin-7-yl)isonicotinonitrile (100 mg, 0.24 mmol) in DMF (3 mL) were added 2- methoxy-2-methylpropanoic acid (0.040 mL, 0.29 mmol), HATU (190 mg, 0.48 mmol) and DIPEA (0.20 mL, 1.2 mmol). After 4 h, the reaction was partitioned between EtOAc and water. The aqueous layer was extracted twice with EtOAc. The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by prep-HPLC to afford 2-(4-((2S,5R)-4-(2-methoxy-2-methylpropanoyl)-2,5- dimethylpiperazin-1-yl)-5-phenyl-7H-pyrrolo[2,3-d]pyrimidin- 7-yl)isonicotinonitrile (50 mg, 40%) as a white solid. LC/MS ESI (m/z): 510 (M+H) + . 1 H NMR (400 MHz, CDCl 3 ) δ 9.35 (s, 1H), 8.55 (d, J = 5.0 Hz, 1H), 8.52 (s, 1H), 8.16 (d, J = 5.2 Hz, 1H), 7.50 (t, J = 7.0 Hz, 2H), 7.40 (m, 2H), 7.32 (m, 2H), 5.09 (br. s, ~0.5H), 4.57 (br. s, ~0.5H), 4.25 – 3.69 (m, 2H), 3.47 – 3.05 (m, ~5.5H), 2.60 (m, ~0.5H), 1.45 – 1.25 (m, ~7.5H), 1.02 (d, J = 6.7 Hz, ~1.5H), 0.96 (d, J = 6.7 Hz, ~1.5H), 0.74 (d, J = 6.7 Hz, ~1.5H); several peaks and their integrations are fractions of protons on account of presence of rotomers. The following compound was prepared by the procedure analogous to the synthesis of compound 282 from the corresponding carboxylic acid. Example 53. Fluorescent TRPML assays. TRPML1 Assay Cell Culture HEK-293 Trex cells were stably transfected with a construct consisting of the human coding sequence for TRPML1 cloned into the tet-inducible plasmid pCDNA5 T/O. Mutations were introduced into the TRPML1 sequence to facilitate expression on the cell surface (Silvia Vergarajauregui, Rosa Puertollano Traffic.2006 Mar; 7(3): 337–353). Briefly, the cells are cultured in 150 mm round tissue culture dishes containing 20 mL of media. The day before the assay the cells are rinsed with DPBS -Ca -Mg and then treated briefly with Trypsin-EDTA. The Trypsin-EDTA is diluted with growth media, and cells are counted. 38 x 10^6 cells are re-plated into 150 mm round tissue culture dishes in media containing 0.5ug/mL doxycycline to induce expression of hTRPML1. Dye Loading The day of the experiment cells are lifted from the plates as above and collected by centrifugation. The cells are then suspended in dye loading buffer consisting of Ringer’s solution supplemented with 0.1% Pluronic Acid and 1 micromolar Fluo4-AM dye. Cells are loaded for ~60 minutes in the dark with occasional mixing. The cells are collected by centrifugation, the loading media aspirated, and the cells resuspended in 25 mL Ringer’s solution and incubated ~60 minutes in the dark. The cells are again collected by centrifugation, rinsed in Ringer’s Solution and resuspended to 0.2 x10^6 cells / mL in modified Ringer’s solution containing 10 mM calcium. Compound Assay Plates Compounds are dissolved to a concentration of 10 millimolar with DMSO. Compound plates are created by dispensing compounds into 384 well black wall clear bottom plates (Greiner 781091). Positive and negative controls are included on each plate. Typically, different amounts of each compound are tested ranging from 100 nanoMoles (20 micromolar final concentration) decreasing in half-log steps to 31 picoMoles (6 nanomolar final concentration). Each concentration is typically tested in triplicate. Assay 50 microliters of dye-loaded cells are dispensed into each well of the compound assay plate created above. The fluorescence in each well is then determined with an excitation wavelength of 480 nM and an emission wavelength of 540 nM using either a Molecular Devices SpectraMax multimode plate reader or a Hamamatsu FDSS/uCell plate imager. Analysis and Statistics The resulting fluorescence for each well is exported as an ascii file and loaded into our LIMS for analysis. The percent activity of each compound at each concentration is determined by comparison to the positive and negative control wells included in each plate. TRPML2 and TRPML3 Assays Assays for TRPML2 and TRPML3 were performed as above for TRPML1, by substituting the appropriate TRPML2 or TRPML3 subtype for the TRPML1. EC 50 values were calculated using a non-linear regression of Prism. The EC 50 determined for each compound using the assay is summarized in Table 3 below. The compound numbers correspond to those shown in Table 1. In the table, “A” indicates an EC50 of less than 100 nM, “B” indicates an EC50 range from 100 nM to 500 nM; “C” indicates an EC 50 range from 500 nM to 2 µM; and “D” indicates an EC 50 greater than 2 µM. Table 3. Efficacy of exemplary compounds of the invention EQUIVALENTS It will be recognized that one or more features of any embodiments disclosed herein may be combined and/or rearranged within the scope of the invention to produce further embodiments that are also within the scope of the invention. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be within the scope of the present invention. Although the invention has been described and illustrated in the foregoing illustrative embodiments, it is understood that the present disclosure has been made only by way of example, and that numerous changes in the details of implementation of the invention can be made without departing from the spirit and scope of the invention, which is limited only by the claims that follow. Features of the disclosed embodiments can be combined and/or rearranged in various ways within the scope and spirit of the invention to produce further embodiments that are also within the scope of the invention. Those skilled in the art will recognize, or be able to ascertain, using no more than routine experimentation, numerous equivalents to the specific embodiments described specifically in this disclosure. Such equivalents are intended to be encompassed in the scope of the following claims. All patents, patent applications and publications cited herein are hereby incorporated by reference in their entirety. The disclosures of these publications in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art as known to those skilled therein as of the date of the invention described and claimed herein.