Compounds, pharmaceutical compositions and methods of making compounds and methods of using same

Abstract

The present invention relates to compounds, pharmaceutical compositions and methods of making the compounds and methods of using the same. Compounds and pharmaceutically acceptable salts thereof are disclosed that are useful in the treatment of subjects in need thereof. The compounds disclosed herein can be inhibitors of ataxia telangiectasia and RAD-3 associated protein kinase (ATR). Pharmaceutical compositions comprising the compounds, or pharmaceutically acceptable salts thereof, and methods of making and using the same are also disclosed.

Description

[0001] This application is a divisional application of the invention patent application with application number 201980087223.7, international application date October 30, 2019, and invention name “Compounds, pharmaceutical compositions, methods for preparing compounds, and methods of use thereof”. Technical Field

[0002] The present invention relates to compounds and pharmaceutical compositions, their preparation and their use in treating diseases or conditions (e.g., cancer) and particularly those diseases or conditions (e.g., cancer) that are dependent on the activity of ataxia telangiectasia and RAD-3 related protein (ATR) kinase. Background Art

[0003] DNA damage continues to occur in cells due to environmental damage including ultraviolet radiation, X-rays and endogenous stress factors (such as hydrolysis of reactive oxygen and alkali). Cancer cells experience a higher rate of DNA damage, which is essentially induced by the higher rate of DNA replication in these cells. Several DNA damage response (DDR) pathways have evolved in a highly coordinated manner to help repair DNA damage and act as cell checkpoints to prevent DNA-damaged cells from replicating, allowing repair functions to occur before damaged DNA is passed to daughter cells. Each type of DNA repair pathway identified can sense and repair different but overlapping DNA damage types.

[0004] One major DDR protein that acts as a key cell cycle checkpoint is the ataxia telangiectasia mutated and rad3-related (ATR) kinase, which is related to the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family. ATR is activated by single-strand (ss) DNA damage caused by stalled replication forks or during nucleotide excision repair, but is also activated by double-strand breaks after DNA end resection during homologous recombination. ATR is recruited to sites of DNA damage by binding to the RPA protein, which, together with an auxiliary factor called ATR interacting protein (ATRIP), coats ssDNA. The ATR / ATRIP complex is then activated by recruiting additional factors in the 9-1-1 complex (RAD 9, RAD1, and HUS1), which subsequently recruits the TOPBP1 protein and represents a key step in the activation of the downstream phosphorylation cascade that leads to cell cycle arrest. The main target of ATR kinase is CHK1, which, when phosphorylated, targets cdc25 and Wee1, leading to inhibition of cyclin-dependent kinase activity and cell cycle arrest in S phase or G2 / M.

[0005] ATR has been identified as an important cancer target because it is essential for cell division. ATR-deficient mice are embryonically lethal, but adult mice with conditional ATR knockout are viable, with effects on rapidly proliferating tissues and stem cell populations. Mouse embryonic stem cells lacking ATR divide and double only 1-2 times before dying, indicating that ATR is required to maintain cell division. Interestingly, mice carrying a hypomorphic ATR mutation (which reduces ATR expression to 10% of normal levels) show reduced H-rasG12D-induced tumor growth with minimal effects on proliferating normal cells (e.g., bone marrow or intestinal epithelial cells). Cancer cells with high levels of replication stress due to oncogenic mutations, dysfunctional G1 / S checkpoint regulation (e.g., loss of p53 function), defects in other DNA repair pathways (e.g., ATM), or cancer cells affected by DNA damaging agents (e.g., radiation therapy or chemotherapeutic agents) are therefore more dependent on ATR for DNA repair and survival. Together, these results highlight the rationale for the selective sensitivity of proliferating tumor cells to ATR inhibition and the potential for a therapeutic window over healthy, proliferating cells.

[0006] New anticancer therapies, particularly those based on ATR inhibitors, are needed. Summary of the Invention

[0007] In one aspect, the present invention provides a compound of formula (I):

[0008]

[0009]

[0010] or a pharmaceutically acceptable salt thereof,

[0011] in

[0012] is a double bond, and each Y is independently N or CR 4 ;or is a single bond, and each Y is independently NR Y , carbonyl or C(R Y )2; where each R Y are independently H or optionally substituted C 1-6 alkyl;

[0013] R 1 is optionally substituted C 1-6 Alkyl or H;

[0014] R 2 is optionally substituted C 2-9 Heterocyclyl, optionally substituted C 1-6 Alkyl, optionally substituted C3-8 Cycloalkyl, optionally substituted C 2-9 Heterocyclyl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, optionally substituted C 1-9 Heteroaryl C 1-6 Alkyl, halogen, –N(R 5 )2. –OR 5 、–CON(R 6 )2、–SO2N(R 6 )2. –SO2R 5A or –Q–R 5B ;

[0015] R 3 is optionally substituted C 1-9 Heteroaryl or optionally substituted C 1-9 Heteroaryl C 1-6 alkyl;

[0016] Each R 4 are independently hydrogen, halogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkenyl or optionally substituted C 2-6 Alkynyl;

[0017] Each R 5 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl or –SO2R 5A ; or two R 5 Together with the atoms to which they are attached, they form an optionally substituted C 2-9 heterocyclic group;

[0018] Each R 5A are independently optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 6-10 aryl;

[0019] R 5B is hydroxy, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, –N(R 5 )2、–CON(R 6 )2、–SO2N(R 6)2. –SO2R 5A or optionally substituted alkoxy;

[0020] Each R 6 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkoxyalkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 1-9 heteroaryl; or two R 6 Together with the atoms to which they are attached, they form an optionally substituted C 2-9 heterocyclic group;

[0021] Q is optionally substituted C 2-9 Heterocyclylene, optionally substituted C 3-8 Cycloalkylene, optionally substituted C 1-9 Heteroarylene or optionally substituted C 6-10 an arylene group; and

[0022] X is hydrogen or halogen.

[0023] In some embodiments, is a double bond. In some embodiments, For a single bond.

[0024] In some embodiments, the compound is of formula (II):

[0025]

[0026] or a pharmaceutically acceptable salt thereof,

[0027] in

[0028] Each Y is independently N or CR 4 ; and the remaining variables are as described for formula (I).

[0029] In some embodiments, in the compound of formula (I) or (II):

[0030] Each Y is independently N or CR 4 ;

[0031] R 1 is H or optionally substituted C 1-6 alkyl;

[0032] R 2 is optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl, optionally substituted C2-9 Heterocyclyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, optionally substituted C 1-9 Heteroaryl C 1-6 Alkyl, –N(R 5 )2、–CON(R 6 )2、–SO2N(R 6 )2 or –SO2R 5A ;

[0033] R 3 is optionally substituted C 1-9 heteroaryl;

[0034] Each R 4 are independently hydrogen or optionally substituted C 1-6 alkyl;

[0035] Each R 5 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl or –SO2R 5A ; or two R 5 Together with the atoms to which they are attached, they form an optionally substituted C 2-9 heterocyclic group;

[0036] Each R 5A are independently optionally substituted C 1-6 Alkyl or optionally substituted C 3-8 cycloalkyl; and

[0037] Each R 6 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl or optionally substituted C 1-9 heteroaryl; or two R 6 Together with the atoms to which they are attached, they form an optionally substituted C 2-9 Heterocyclic group.

[0038] In some embodiments, the compound is of formula (Ia):

[0039]

[0040] or a pharmaceutically acceptable salt thereof, wherein all variables are as described herein.

[0041] In some embodiments, the compound is of Formula (Ib):

[0042]

[0043] or a pharmaceutically acceptable salt thereof, wherein all variables are as described herein. In some embodiments, the compound is of formula (IA):

[0044]

[0045] or a pharmaceutically acceptable salt thereof, wherein all variables are as described herein. In some embodiments, the compound is of formula (IA-a):

[0046]

[0047] or a pharmaceutically acceptable salt thereof, wherein all variables are as described herein. In some embodiments, the compound is of formula (IB):

[0048]

[0049] or a pharmaceutically acceptable salt thereof, wherein all variables are as described herein. In some embodiments, the compound is of formula (IB-a):

[0050]

[0051] or a pharmaceutically acceptable salt thereof, wherein all variables are as described herein. In some embodiments, the compound is of formula (IC):

[0052]

[0053] or a pharmaceutically acceptable salt thereof, wherein all variables are as described herein. In some embodiments, the compound is of formula (IC-a):

[0054]

[0055] or a pharmaceutically acceptable salt thereof, wherein all variables are as described herein. In some embodiments, the compound is of formula (ID):

[0056]

[0057] or a pharmaceutically acceptable salt thereof, wherein all variables are as described herein. In some embodiments, the compound is of formula (ID-a):

[0058]

[0059] or a pharmaceutically acceptable salt thereof, wherein all variables are as described herein.

[0060] In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), R 1 It is a methyl group.

[0061] In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), R 2 is optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl, optionally substituted C 2-9 Heterocyclyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, optionally substituted C 1-9 Heteroaryl C 1-6 Alkyl, –N(R 5 )2、–CON(R 6 )2、–SO2N(R 6 )2 or –SO2R 5A .

[0062] In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), R 2 is optionally substituted C 3-8 In some embodiments, R 2 A group of formula (A):

[0063]

[0064] in

[0065] n is 0, 1, 2, or 3; and

[0066] R 7 is hydrogen, alkylsulfonyl, cyano, –CON(R A )2、-SON(R A ) 2. optionally substituted C 1-9 heteroaryl, hydroxyl or alkoxy, wherein each R A are independently H or alkyl; or two R A Together with the atoms to which they are attached, they combine to form C 2-9 Heterocyclic group.

[0067] In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), R 2 is a group of formula (B):

[0068]

[0069] where R 7 is hydrogen, alkylsulfonyl, cyano, –CON(R A )2、-SON(R A ) 2. optionally substituted C 1-9 heteroaryl, hydroxyl or alkoxy, wherein each R A are independently H or alkyl; or two R A Together with the atoms to which they are attached, they combine to form C 2-9 Heterocyclic group.

[0070] In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), R 2 is an optionally substituted non-aromatic C 2-9 In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), R 2 is an optionally substituted non-aromatic bridging C 2-9 In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), R 2 is an optionally substituted non-aromatic spiro C 2-9 Heterocyclic group.

[0071] In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), R 2 QR 5B In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), Q is optionally substituted C 2-9In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), R 5B It is a hydroxyl group.

[0072] In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), R 2 for:

[0073]

[0074] –I, –SO2Me, –SO2Ph, –OMe, –OCH2CF3,

[0075]

[0076]

[0077] In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), R 3 is an optionally substituted monocyclic C 1-9 In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), R 3 is an optionally substituted monocyclic C containing two nitrogen atoms 1-9 In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), R 3 is a group of formula (C):

[0078]

[0079] wherein A is an optionally substituted monocyclic C 1-9 Heteroaryl ring.

[0080] In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), R3 is a group of formula (C1):

[0081]

[0082] where R 8 is hydrogen, halogen or optionally substituted C 1-6 alkyl.

[0083] In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), A is an optionally substituted monocyclic C containing two nitrogen atoms. 1-9 Heteroaryl ring.

[0084] In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), R 3 for:

[0085]

[0086] In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), R 3 for:

[0087]

[0088] In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), R 4 For hydrogen.

[0089] In some embodiments of any of Formulas (I), (II), (IA), (IA-a), (IB), (IB-a), (IC), (IC-a), (ID), and (ID-a), X is hydrogen.

[0090] In some embodiments, the compound is selected from the group consisting of Compound 1-152 (e.g., Compound 1-140) and pharmaceutically acceptable salts thereof (e.g., Compound 1-152 is selected from the group consisting of Compound 1-152 (e.g., Compound 1-140) and pharmaceutically acceptable salts thereof (e.g., Compound 1-152 is selected from the group consisting of Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, Compound 1-152, 147, 148, 150, 151, and pharmaceutically acceptable salts thereof).

[0091] In another aspect, the present invention provides a pharmaceutical composition comprising a compound of the present invention and a pharmaceutically acceptable excipient. In some embodiments, the compound of the present invention is isotopically deuterium-enriched.

[0092] In another aspect, the present invention provides a method of inhibiting ATR kinase in a cell by contacting the cell expressing ATR kinase with a compound of the present invention. In some embodiments, the cell is in vitro. In some embodiments, the cell is in a subject.

[0093] In another aspect, the present invention provides a method of treating a subject in need thereof, comprising administering to the subject an effective amount of a compound of the present invention or a pharmaceutical composition of the present invention.

[0094] In some embodiments, the subject is suffering from a disease or condition symptom of cellular hyperproliferation (e.g., the disease or condition is cancer or a premalignant or precancerous condition) and is in need of treatment thereof. In some embodiments, the cancer is an epithelial cancer, sarcoma, adenocarcinoma, leukemia, or melanoma.

[0095] In some embodiments, the cancer is an epithelial carcinoma selected from the group consisting of thyroid encephaloid carcinoma, familial thyroid encephaloid carcinoma, acinar carcinoma, acinar-shaped carcinoma, adenoid cystic carcinoma, adenoid cystic carcinoma, adenomatous carcinoma, adrenal cortical carcinoma, alveolar carcinoma, alveolar cell carcinoma, basal cell carcinoma, basaloid carcinoma, basosquamous cell carcinoma, bronchioalveolar carcinoma, bronchiolar carcinoma, bronchial carcinoma, medullary carcinoma, cholangiocarcinoma, choriocarcinoma, colloid carcinoma, comedo carcinoma, corpus carcinoma, cribriform carcinoma, armor carcinoma, cutaneous carcinoma, columnar carcinoma, columnar cell carcinoma, ductal carcinoma, sclerosing carcinoma. durum), embryonal carcinoma, encephaloid carcinoma, epiermoid carcinoma, carcinoma epitheliale adenoide, exophytic carcinoma, carcinoma ex ulcere, carcinoma fibrosum, gelatiniforni carcinoma, gelatinous carcinoma, giant cell carcinoma, carcinoma gigantocellulare, glandular carcinoma, granular cell carcinoma, pilostromal carcinoma, hematoid carcinoma, hepatocellular carcinoma, Hurthle cell carcinoma, hyaline carcinoma, hypernephroid carcinoma carcinoma), embryonal carcinoma, carcinoma in situ, intraepidermal carcinoma, intraepithelial carcinoma, Krompecher's carcinoma, Kulchitzky-cell carcinoma, large cell carcinoma, lenticular carcinoma, carcinoma lenticulare, lipomatous carcinoma, lymphoepithelial carcinoma, carcinoma medullare, medullary carcinoma, melanotic carcinomacarcinoma), carcinoma molle, mucinous carcinoma, carcinoma muciparum, carcinoma mucocellulare, mucoepidermoid carcinoma, carcinoma mucocellulare, mucous carcinoma, carcinoma myxomatodes, nasopharyngeal carcinoma, oat cell carcinoma, carcinoma ossificans, osteoid carcinoma, papillary carcinoma, periportal carcinoma, preinvasive carcinoma, prickle cell carcinoma, pultaceous carcinoma carcinoma, renal cell carcinoma, reserve cell carcinoma, carcinoma sarcomatodes, schneiderian carcinoma, scirrhous carcinoma, carcinoma scroti, signet-ring cell carcinoma, carcinoma simplex, small cell carcinoma, solanoid carcinoma, spheroidal cell carcinoma, spindle cell carcinoma, carcinoma spongiosum, squamous carcinoma, squamous cell carcinoma, string carcinoma, telangiectatic carcinoma telangiectaticum), carcinomate langiectodes, transitional cell carcinoma, nodular carcinomatuberosum), tuberous carcinoma, verrucous carcinoma, and carcinoma villosum.

[0096] In some embodiments, the cancer is a sarcoma selected from the group consisting of chondrosarcoma, fibrosarcoma, lymphosarcoma, melanosarcoma, myxosarcoma, osteosarcoma, Abernethy's sarcoma, liposarcoma, liposarcoma, alveolar soft part sarcoma, ameloblastic sarcoma, botryoid sarcoma, chloromasarcoma, choriocarcinoma, embryonal sarcoma, Wilms' tumor sarcoma, endometrial sarcoma, stromal sarcoma, Ewing's sarcoma, fascial sarcoma, fibroblastic sarcoma, giant cell sarcoma, granulocytic sarcoma, Hodgkin's sarcoma, idiopathic multiple pigmented hemorrhagic sarcoma, and idiopathic multiple pigmented hemorrhagic sarcoma. sarcoma), B-cell immunoblastic sarcoma, T-cell immunoblastic sarcoma, Jensen's sarcoma, Kaposi's sarcoma, Kupffer cell sarcoma, angiosarcoma, leukemic sarcoma, malignant mesenchymoma sarcoma, parosteal sarcoma, reticulocytic sarcoma, Rous sarcoma, serocysticsarcoma, synovial sarcoma, and telangiectaltic sarcoma.

[0097] In some embodiments, the cancer is a leukemia selected from the group consisting of non-lymphocytic leukemia, chronic lymphocytic leukemia, acute granulocytic leukemia, chronic myeloid leukemia, acute promyelocytic leukemia, adult T-cell leukemia, non-leukemic leukemia, a leukocythemic leukemia, basophylicleukemia, blast cell leukemia, bovine leukemia, chronic myelocytic leukemia, leukemia cutis, embryonal leukemia, eosinophilic leukemia, Gross' leukemia, hairy cell leukemia, hemoblastic leukemia, hemocytoblastic leukemia. leukemia), histiocytic leukemia, stem cell leukemia, acute monocytic leukemia, leukopenic leukemia, lymphatic leukemia, lymphoblastic leukemia, lymphocytic leukemia, lymphogenous leukemia, lymphoid leukemia, lymphosarcoma cell leukemia, mast cell leukemia, megakaryocytic leukemia, micromyeloblastic leukemia, monocytic leukemia, myeloblastic leukemia, myelocytic leukemia, myeloid granulocytic leukemia, myelomonocytic leukemia, Naegeli leukemia leukemia), plasma cell leukemia, multiple myeloma, plasmacytic leukemia, promyelocytic leukemia, Riedercell leukemia, Schilling's leukemia, stem cell leukemia, subleukemic leukemia, and undifferentiated cell leukemia.

[0098] In some embodiments, the cancer is a melanoma selected from the group consisting of acral-lentiginous melanoma, amelanotic melanoma, benign juvenile melanoma, Cloudman's melanoma, S91 melanoma, Harding-Passey melanoma, juvenile melanoma, lentigo maligna melanoma, malignant melanoma, nodular melanoma, subungual melanoma, and superficial spreading melanoma.

[0099] In some embodiments, the cancer is prostate cancer, thyroid cancer, cancer of the endocrine system, brain cancer, breast cancer, cervical cancer, colon cancer, head and neck cancer, liver cancer, kidney cancer, lung cancer, non-small cell lung cancer, melanoma, mesothelioma, ovarian cancer, sarcoma, gastric cancer, uterine cancer, medulloblastoma, ampullary cancer, colorectal cancer, or pancreatic cancer.

[0100] In some embodiments, the cancer is Hodgkin's disease, non-Hodgkin's lymphoma, multiple myeloma, neuroblastoma, glioma, glioblastoma multiforme, ovarian cancer, rhabdomyosarcoma, essential thrombocythemia, essential macroglobulinemia, primary brain tumor, cancer, malignant pancreatic insulinoma, malignant carcinoid tumor, bladder cancer, precancerous skin lesions, testicular cancer, lymphoma, thyroid cancer, esophageal cancer, genitourinary tract cancer, hypercalcemia of malignancy, endometrial cancer, adrenocortical cancer, pancreatic endocrine and exocrine neoplasms, medullary thyroid cancer, cerebral thyroid carcinoma, melanoma, colorectal cancer, papillary thyroid cancer, hepatocellular carcinoma, or prostate cancer.

[0101] In some embodiments, the subject is suffering from and in need of treatment for a premalignant condition.

[0102] The present invention is also described by the items listed below.

[0103] 1. A compound of formula (I):

[0104]

[0105] or a pharmaceutically acceptable salt thereof,

[0106] in

[0107] is a double bond, and each Y is independently N or CR 4 ;or is a single bond, and each Y is independently NR Y, carbonyl or C(R Y )2; where each R Y are independently H or optionally substituted C 1-6 alkyl;

[0108] R 1 is optionally substituted C 1-6 Alkyl or H;

[0109] R 2 is optionally substituted C 2-9 Heterocyclyl, optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl, optionally substituted C 2-9 Heterocyclyl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, optionally substituted C 1-9 Heteroaryl C 1-6 Alkyl, halogen, –N(R 5 )2. –OR 5 、–CON(R 6 )2、–SO2N(R 6 )2. –SO2R 5A or –Q–R 5B ;

[0110] R 3 is optionally substituted C 1-9 Heteroaryl or optionally substituted C 1-9 Heteroaryl C 1-6 alkyl;

[0111] Each R 4 are independently hydrogen, halogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkenyl or optionally substituted C 2-6 Alkynyl;

[0112] Each R 5 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl or –SO2R 5A ; or two R 5 Together with the atoms to which they are attached, they form an optionally substituted C 2-9 heterocyclic group;

[0113] Each R 5A are independently optionally substituted C 1-6Alkyl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 6-10 aryl;

[0114] R 5B is hydroxy, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, –N(R 5 )2、–CON(R 6 )2、–SO2N(R 6 )2. –SO2R 5A or optionally substituted alkoxy;

[0115] Each R 6 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkoxyalkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 1-9 heteroaryl; or two R 6 Together with the atoms to which they are attached, they form an optionally substituted C 2-9 heterocyclic group;

[0116] Q is optionally substituted C 2-9 Heterocyclylene, optionally substituted C 3-8 Cycloalkylene, optionally substituted C 1-9 Heteroarylene or optionally substituted C 6-10 an arylene group; and

[0117] X is hydrogen or halogen.

[0118] 2. The compound according to item 1, wherein For double bonds.

[0119] 3. The compound according to item 1, wherein For a single bond.

[0120] 4. The compound according to item 1, wherein the compound is a compound of formula (II):

[0121]

[0122] or a pharmaceutically acceptable salt thereof,

[0123] in

[0124] Each Y is independently N or CR 4 ;

[0125] R 1 is optionally substituted C 1-6 Alkyl or H;

[0126] R 2 is optionally substituted C 2-9 Heterocyclyl, optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl, optionally substituted C 2-9 Heterocyclyl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, optionally substituted C 1-9 Heteroaryl C 1-6 Alkyl, halogen, –N(R 5 )2. –OR 5 、–CON(R 6 )2、–SO2N(R 6 )2. –SO2R 5A or –Q–R 5B ;

[0127] R 3 is optionally substituted C 1-9 Heteroaryl or optionally substituted C 1-9 Heteroaryl C 1-6 alkyl;

[0128] Each R 4 are independently hydrogen, halogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkenyl or optionally substituted C 2-6 Alkynyl;

[0129] Each R 5 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl or –SO2R 5A ; or two R 5 Together with the atoms to which they are attached, they form an optionally substituted C 2-9 heterocyclic group;

[0130] Each R 5A are independently optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 6-10 aryl;

[0131] R 5B is hydroxy, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, –N(R 5 )2、–CON(R 6 )2、–SO2N(R 6 )2. –SO2R 5A or optionally substituted alkoxy;

[0132] Each R 6 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkoxyalkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 1-9 heteroaryl; or two R 6 Together with the atoms to which they are attached, they form an optionally substituted C 2-9 heterocyclic group;

[0133] Q is optionally substituted C 2-9 Heterocyclylene, optionally substituted C 3-8 Cycloalkylene, optionally substituted C 1-9 Heteroarylene or optionally substituted C 6-10 an arylene group; and

[0134] X is hydrogen or halogen.

[0135] 5. The compound according to item 1, wherein the compound is a compound of formula (Ia):

[0136]

[0137] or a pharmaceutically acceptable salt thereof.

[0138] 6. The compound according to item 1, wherein the compound is a compound of formula (IA):

[0139]

[0140] or a pharmaceutically acceptable salt thereof.

[0141] 7. The compound according to item 6, wherein the compound is a compound of formula (IA-a):

[0142]

[0143] or a pharmaceutically acceptable salt thereof.

[0144] 8. The compound according to item 1, wherein the compound is a compound of formula (IB):

[0145]

[0146] or a pharmaceutically acceptable salt thereof.

[0147] 9. The compound according to item 8, wherein the compound is a compound of formula (IB-a):

[0148]

[0149] or a pharmaceutically acceptable salt thereof.

[0150] 10. The compound according to item 1, wherein the compound is a compound of formula (IC):

[0151]

[0152] or a pharmaceutically acceptable salt thereof.

[0153] 11. The compound according to item 10, wherein the compound is a compound of formula (IC-a):

[0154]

[0155] or a pharmaceutically acceptable salt thereof.

[0156] 12. A compound as described in any one of items 1 to 11, wherein R 1 It is a methyl group.

[0157] 13. A compound as described in any one of items 1 to 12, wherein R 2 is optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl, optionally substituted C 2-9 Heterocyclyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, optionally substituted C 1-9 Heteroaryl C 1-6 Alkyl, –N(R 5 )2、–CON(R 6 )2、–SO2N(R 6 )2 or –SO2R 5A .

[0158] 14. A compound as described in any one of items 1 to 13, wherein each R 5A are independently optionally substituted C 1-6Alkyl or optionally substituted C 3-8 Cycloalkyl.

[0159] 15. A compound as described in any one of items 1 to 13, wherein each R 6 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl or optionally substituted C 1-9 heteroaryl; or two R 6 Together with the atoms to which they are attached, they form an optionally substituted C 2-9 Heterocyclic group.

[0160] 16. A compound as described in any one of items 1 to 15, wherein R 2 is optionally substituted C 3-8 Cycloalkyl.

[0161] 17. The compound according to item 16, wherein R 2 C 3-8 Cycloalkyl, which is optionally substituted with alkylsulfonyl, cyano, -CON(R A )2, hydroxy or alkoxy substituted, wherein each R A are independently H or alkyl; or R A Together with the atoms to which they are attached, they combine to form C 2-9 Heterocyclic group.

[0162] 18. The compound according to item 16, wherein R 2 A group of formula (A):

[0163]

[0164] in

[0165] n is 0, 1, 2, or 3; and

[0166] R 7 is hydrogen, alkylsulfonyl, cyano, –CON(R A )2、-SON(R A ) 2. optionally substituted C 1-9 heteroaryl, hydroxyl or alkoxy, wherein each R A are independently H or alkyl; or two R A Together with the atoms to which they are attached, they combine to form C 2-9 Heterocyclic group.

[0167] 19. A compound as described in any one of items 1 to 15, wherein R 2 is a group of formula (B):

[0168]

[0169] where R 7 is hydrogen, alkylsulfonyl, cyano, –CON(R A )2、-SON(R A ) 2. optionally substituted C 1-9 heteroaryl, hydroxyl or alkoxy, wherein each R A are independently H or alkyl; or two R A Together with the atoms to which they are attached, they combine to form C 2-9 Heterocyclic group.

[0170] 20. The compound according to item 18 or 19, wherein R 7 is alkylsulfonyl, cyano or –CON(R A )2.

[0171] 21. A compound as described in any one of items 1 to 12, wherein R 2 is optionally substituted C 1-6 alkyl.

[0172] 22. The compound according to item 21, wherein R 2 is an optionally substituted tertiary C 3-6 alkyl.

[0173] 23. A compound as described in any one of items 1 to 15, wherein R 2 is an optionally substituted non-aromatic C 2-9 Heterocyclic group.

[0174] 24. The compound according to item 23, wherein R 2 is an optionally substituted non-aromatic bridging C 2-9 Heterocyclic group.

[0175] 25. The compound according to item 23, wherein R 2 is an optionally substituted non-aromatic spiro C 2-9 Heterocyclic group.

[0176] 26. A compound as described in any one of items 1 to 15, wherein R 2 is optionally substituted C 3-8 Cycloalkyl.

[0177] 27. The compound according to item 26, wherein R 2 is an optionally substituted spiro C 3-8 Cycloalkyl.

[0178] 28. A compound as described in any one of items 1 to 12, wherein R 2 QR 5B .

[0179] 29. The compound according to item 28, wherein Q is an optionally substituted C 1-9 Heteroarylene.

[0180] 30. The compound according to item 28, wherein Q is an optionally substituted C 3-8 Cycloalkylene.

[0181] 31. The compound according to item 28, wherein Q is an optionally substituted C 2-9 Heterocyclylene.

[0182] 32. The compound according to item 28, wherein Q is an optionally substituted C 6-10 Arylene.

[0183] 33. A compound as described in any one of items 28 to 32, wherein R 5B is optionally substituted C 1-6 alkyl.

[0184] 34. A compound as described in any one of items 28 to 32, wherein R 5B It is a hydroxyl group.

[0185] 35. A compound as described in any one of items 28 to 32, wherein R 5B is optionally substituted C 6-10 Aryl.

[0186] 36. A compound as described in any one of items 28 to 32, wherein R 5B is optionally substituted C 1-9 Heteroaryl.

[0187] 37. A compound as described in any one of items 28 to 32, wherein R 5B N(R 5 )2.

[0188] 38. The compound according to item 37, wherein each R 5 For hydrogen.

[0189] 39. A compound as described in any one of items 28 to 32, wherein R 5B is an optionally substituted alkoxy group.

[0190] 38. A compound as described in any one of items 28 to 32, wherein R 5B For –SO2N(R 6 )2.

[0191] 39. The compound according to item 38, wherein each R 6 For hydrogen.

[0192] 40. A compound as described in any one of items 28 to 32, wherein R 5B for –SO2R 5A .

[0193] 41. The compound according to item 40, wherein R 5A is optionally substituted C 1-6 alkyl.

[0194] 42. A compound as described in any one of items 1 to 15, wherein R 2 for:

[0195]

[0196] –I, –SO2Me, –SO2Ph, –OMe, –OCH2CF3,

[0197]

[0198]

[0199] 43. The compound according to item 42, wherein R 2 for:

[0200]

[0201] –I, –SO2Me, –SO2Ph, –OMe, –OCH2CF3,

[0202]

[0203] 44. The compound according to item 42, wherein R 2 for:

[0204]

[0205] 45. The compound according to item 42, wherein R 2 for:

[0206]

[0207] –OCH2CF3,

[0208]

[0209] 46. ​​The compound according to item 42, wherein R 2 for:

[0210] 47. The compound according to item 42, wherein R 2 for:

[0211] 48. The compound according to item 42, wherein R 2 for:

[0212] 49. The compound according to item 42, wherein R 2 for:

[0213] 50. The compound according to item 42, wherein R 2 for:

[0214] 51. The compound according to item 42, wherein R 2 for:

[0215] 52. The compound according to item 42, wherein R 2 for:

[0216] 53. The compound according to item 42, wherein R 2 for:

[0217] 54. The compound according to item 42, wherein R 2 for:

[0218] 55. The compound according to item 42, wherein R 2 for:

[0219] 56. The compound according to item 42, wherein R 2 for:

[0220] 57. The compound according to item 42, wherein R 2 for:

[0221] 58. The compound according to item 42, wherein R 2 for:

[0222] 59. The compound according to item 42, wherein R 2 for:

[0223] 60. The compound according to item 42, wherein R 2 for:

[0224] 61. The compound according to item 42, wherein R 2 for:

[0225] 62. The compound according to item 61, wherein R 2 for:

[0226] 63. The compound according to item 42, wherein R 2 for:

[0227] 64. The compound according to item 42, wherein R 2 for:

[0228] 65. The compound according to item 42, wherein R 2 for:

[0229] 66. The compound according to item 42, wherein R 2 for:

[0230] 67. The compound according to item 42, wherein R 2 for:

[0231]

[0232] 68. The compound according to item 42, wherein R 2 for:

[0233]

[0234] 69. The compound according to item 42, wherein R 2 for:

[0235]

[0236] 70. A compound as described in any one of items 1 to 69, wherein R 3 is an optionally substituted monocyclic C 1-9 Heteroaryl.

[0237] 71. The compound according to item 70, wherein R 3is an optionally substituted monocyclic C containing two nitrogen atoms 1-9 Heteroaryl.

[0238] 72. The compound according to item 70, wherein R 3 is a group of formula (C):

[0239]

[0240] wherein A is an optionally substituted monocyclic C 1-9 Heteroaryl ring.

[0241] 73. The compound according to claim 70, wherein R 3 is a group of formula (C1):

[0242]

[0243] where R 8 is hydrogen, halogen or optionally substituted C 1-6 alkyl.

[0244] 74. The compound according to item 73, wherein R 8 is hydrogen or halogen.

[0245] 75. A compound as described in any one of items 72 to 74, wherein A is an optionally substituted monocyclic C containing two nitrogen atoms 1-9 Heteroaryl ring.

[0246] 76. A compound as described in any one of items 1 to 75, wherein R 3 for:

[0247]

[0248] 77. The compound according to item 76, wherein R 3 for:

[0249]

[0250] 78. The compound according to item 76, wherein R 3 for:

[0251]

[0252] 79. The compound according to item 76, wherein R 3 for:

[0253]

[0254] 80. The compound according to item 76, wherein R 3 for:

[0255]

[0256] 81. A compound as described in any one of items 1 to 80, wherein R 4 For hydrogen.

[0257] 82. A compound as described in any one of items 1 to 80, wherein R 4 It is a halogen.

[0258] 83. A compound as described in any one of items 1 to 80, wherein R 4 is optionally substituted C 2-6 Alkenyl.

[0259] 84. The compound of any one of items 1 to 80, wherein X is hydrogen.

[0260] 85. A compound selected from the group consisting of Compounds 1-152 and pharmaceutically acceptable salts thereof.

[0261] 87. The compound of item 85, wherein the compound is selected from the group consisting of:

[0262] Compounds 1, 2, 3, 4, 5, 6, 7, 8, 24, 43, 45, 47, 48, 49, 52, 53, 55, 57, 58, 59, 61, 62, 63, 73, 74, 77, 80, 81, 82, 84, 86, 87, 92, 93, 94, 95, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110 , 111, 112, 113, 114, 115, 116, 118, 119, 120, 121, 122, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150, 151 and pharmaceutically acceptable salts thereof.

[0263] 88. The compound of claim 85, wherein the compound is selected from the group consisting of compounds 6, 8, 43, 48, 92, 126, 128, 130, 131, 141, 142, 143, 145, 150, and pharmaceutically acceptable salts thereof.

[0264] 89. The compound of claim 85, wherein the compound is selected from the group consisting of compounds 2, 4, 7, 47, 49, 63, 86, and pharmaceutically acceptable salts thereof.

[0265] 90. The compound of claim 85, wherein the compound is selected from the group consisting of compounds 57, 62, 73, 74, 80, 81, 82, 84, 87, 93, 94, 95, 99, 100, 106, 107, 108, 109, 111, 112, 113, 114, 115, 116, 118, 119, 120, 121, 122, 123, 135, 137, 138, 144, 146, 147, 148, 151 and pharmaceutically acceptable salts thereof.

[0266] 91. The compound of claim 85, wherein the compound is selected from the group consisting of compounds 57, 62, 87, 93, 94, 95, 99, 100, 106, 107, 108, 109, 111, 112, 113, 114, 115, 116, 118, 119, 120, 121, 122, 123, 135, 147, 148 and pharmaceutically acceptable salts thereof.

[0267] 92. The compound of claim 85, wherein the compound is selected from the group consisting of compounds 61, 105, 107, 110, 112, 113 and pharmaceutically acceptable salts thereof.

[0268] 93. The compound of claim 56, wherein the compound is selected from the group consisting of compounds 121, 122, and pharmaceutically acceptable salts thereof.

[0269] 94. The compound of claim 85, wherein the compound is selected from the group consisting of compounds 125, 127, 129, 138, 139, 140, 144, 146, 151 and pharmaceutically acceptable salts thereof.

[0270] 95. The compound of claim 85, wherein the compound is selected from the group consisting of compounds 58, 123, and pharmaceutically acceptable salts thereof.

[0271] 96. The compound of claim 85, wherein the compound is selected from the group consisting of compounds 1, 3, 5, 59, 77, 97, 98, 101, 102, 103, 104, 106, 114, 115, 132, 133 and pharmaceutically acceptable salts thereof.

[0272] 97. The compound of claim 85, wherein the compound is selected from the group consisting of compounds 45, 52, 55, and pharmaceutically acceptable salts thereof.

[0273] 98. The compound of claim 85, wherein the compound is Compound 1 or a pharmaceutically acceptable salt thereof.

[0274] 99. The compound of claim 85, wherein the compound is Compound 2 or a pharmaceutically acceptable salt thereof.

[0275] 100. The compound according to claim 85, wherein the compound is Compound 3 or a pharmaceutically acceptable salt thereof.

[0276] 101. The compound according to claim 85, wherein the compound is compound 4 or a pharmaceutically acceptable salt thereof.

[0277] 102. The compound according to claim 85, wherein the compound is Compound 5 or a pharmaceutically acceptable salt thereof.

[0278] 103. The compound according to claim 85, wherein the compound is Compound 6 or a pharmaceutically acceptable salt thereof.

[0279] 104. The compound according to claim 85, wherein the compound is Compound 7 or a pharmaceutically acceptable salt thereof.

[0280] 105. The compound according to claim 85, wherein the compound is Compound 8 or a pharmaceutically acceptable salt thereof.

[0281] 106. The compound according to claim 85, wherein the compound is Compound 9 or a pharmaceutically acceptable salt thereof.

[0282] 107. The compound according to claim 85, wherein the compound is compound 86 or a pharmaceutically acceptable salt thereof.

[0283] 108. The compound according to claim 85, wherein the compound is compound 99 or a pharmaceutically acceptable salt thereof.

[0284] 109. The compound according to claim 85, wherein the compound is Compound 100 or a pharmaceutically acceptable salt thereof.

[0285] 110. The compound according to claim 85, wherein the compound is compound 115 or a pharmaceutically acceptable salt thereof.

[0286] 111. The compound according to claim 85, wherein the compound is compound 120 or a pharmaceutically acceptable salt thereof.

[0287] 112. The compound according to claim 85, wherein the compound is compound 121 or a pharmaceutically acceptable salt thereof.

[0288] 113. The compound according to claim 85, wherein the compound is compound 125 or a pharmaceutically acceptable salt thereof.

[0289] 114. The compound according to claim 85, wherein the compound is compound 126 or a pharmaceutically acceptable salt thereof.

[0290] 115. The compound according to claim 85, wherein the compound is compound 138 or a pharmaceutically acceptable salt thereof.

[0291] 116. The compound according to claim 85, wherein the compound is compound 139 or a pharmaceutically acceptable salt thereof.

[0292] 117. The compound according to claim 85, wherein the compound is compound 140 or a pharmaceutically acceptable salt thereof.

[0293] 118. The compound according to claim 85, wherein the compound is compound 142 or a pharmaceutically acceptable salt thereof.

[0294] 119. The compound according to claim 85, wherein the compound is compound 144 or a pharmaceutically acceptable salt thereof.

[0295] 120. The compound according to claim 85, wherein the compound is compound 147 or a pharmaceutically acceptable salt thereof.

[0296] 121. The compound of claim 85, wherein the compound is compound 148 or a pharmaceutically acceptable salt thereof.

[0297] 122. The compound of claim 85, wherein the compound is Compound 150 or a pharmaceutically acceptable salt thereof.

[0298] 123. The compound according to claim 85, wherein the compound is compound 151 or a pharmaceutically acceptable salt thereof.

[0299] 124. A pharmaceutical composition comprising a compound as described in any one of items 1 to 123 and a pharmaceutically acceptable excipient.

[0300] 125. The pharmaceutical composition of claim 124, wherein the compound is isotopically deuterium-enriched.

[0301] 126. A method of inhibiting ATR kinase in a cell expressing ATR kinase, the method comprising contacting the cell with a compound according to any one of items 1 to 123.

[0302] 127. The method of claim 126, wherein the cells are in vitro.

[0303] 128. The method of claim 126, wherein the cell is in a subject.

[0304] 129. A method of treating a subject in need thereof, comprising administering to the subject a compound as described in any one of items 1 to 123 or a pharmaceutical composition as described in item 124 or 125.

[0305] 130. The method of claim 128 or 129, wherein the subject is suffering from a disease or condition characterized by cellular hyperproliferation and is in need of treatment thereof.

[0306] 131. The method of claim 130, wherein the disease or condition is cancer.

[0307] 132. The method of claim 131 , wherein the cancer is a solid tumor.

[0308] 133. The method of claim 131, wherein the cancer is an epithelial cancer, a sarcoma, an adenocarcinoma, a leukemia, or a melanoma.

[0309] 134. The method of claim 131, wherein the cancer is an epithelial cancer selected from the group consisting of thyroid brain-like epithelial carcinoma, familial thyroid brain-like epithelial carcinoma, acinar epithelial carcinoma, acinar epithelial carcinoma, adenoid cystic epithelial carcinoma, adenomatous epithelial carcinoma, adrenal cortical epithelial carcinoma, alveolar epithelial carcinoma, alveolar cell epithelial carcinoma, basal cell epithelial carcinoma, basaloid epithelial carcinoma, basosquamous cell epithelial carcinoma, bronchioalveolar epithelial carcinoma, bronchiolar epithelial carcinoma, bronchial epithelial carcinoma, medullary epithelial carcinoma, cholangiocarcinoma, chorionic villus epithelial carcinoma, Carcinoma of the skin, colloid carcinoma, comedo carcinoma, main carcinoma of the skin, cribriform carcinoma, armor carcinoma, cutaneous carcinoma, columnar carcinoma, columnar cell carcinoma, ductal carcinoma, sclerosing carcinoma, embryonal carcinoma, brain-like carcinoma, epidermoid carcinoma, adenoid carcinoma, exophytic carcinoma, ulcerative carcinoma, fibrocarcinoma, colloid carcinoma, gelatinous carcinoma, giant cell carcinoma, giant cell carcinoma, glandular carcinoma, granular cell carcinoma, pilostromal carcinoma, hematogenous carcinoma, hepatocellular carcinoma, Schütt cell carcinoma, hyalinoid carcinoma, adrenal carcinoma Epithelial carcinoma, infantile embryonal carcinoma, epithelial carcinoma in situ, intraepidermal epithelial carcinoma, intraepithelial epithelial carcinoma, Klebsiella pneumoniae epithelial carcinoma, Kurchitsky cell carcinoma, large cell epithelial carcinoma, lenticular carcinoma, lenticular carcinoma, lipomatous epithelial carcinoma, lymphoepithelial carcinoma, medullary epithelial carcinoma, melanotic epithelial carcinoma, soft epithelial carcinoma, mucinous epithelial carcinoma, mucinous epithelial carcinoma, mucoepidermoid epithelial carcinoma, mucinous epithelial carcinoma, myxomatous epithelial carcinoma, nasopharyngeal epithelial carcinoma, oat cell epithelial carcinoma, ossifying epithelial carcinoma, osteoid epithelial carcinoma, papillary epithelial carcinoma, periportal epithelial carcinoma carcinoma, preinvasive carcinoma, prickle cell carcinoma, mucus carcinoma, renal cell carcinoma, reserve cell carcinoma, sarcomatoid carcinoma, Schneider's carcinoma, scirrhous carcinoma, scrotal carcinoma, signet ring cell carcinoma, simple carcinoma, small cell carcinoma, potato carcinoma, spheroid cell carcinoma, spindle cell carcinoma, spongiform carcinoma, squamous cell carcinoma, squamous cell carcinoma, string carcinoma, telangiectatic carcinoma, angioectatic carcinoma, transitional cell carcinoma, nodular carcinoma, tubercular carcinoma, verrucous carcinoma, and villous carcinoma.

[0310] 135. The method of claim 131, wherein the cancer is a sarcoma selected from the group consisting of chondrosarcoma, fibrosarcoma, lymphosarcoma, melanosarcoma, myxosarcoma, osteosarcoma, Albernethy's sarcoma, liposarcoma, liposarcoma, alveolar soft part sarcoma, ameloblastic sarcoma, botryoid sarcoma, chloroma sarcoma, choriocarcinoma, embryonal sarcoma, Williams' tumor sarcoma, endometrial sarcoma, stromal sarcoma, Ewing's sarcoma, myelosarcoma, muscular sarcoma, ectopic ... Theming sarcoma, fibroblastic sarcoma, giant cell sarcoma, granulocytic sarcoma, Hodgkin's sarcoma, idiopathic multiple pigmented hemorrhagic sarcoma, B-cell immunoblastic sarcoma, T-cell immunoblastic sarcoma, Janssen's sarcoma, Kaposi's sarcoma, Kupffer cell sarcoma, angiosarcoma, leukemic sarcoma, malignant mesenchymal sarcoma, parosteal sarcoma, reticulum cell sarcoma, Rous sarcoma, serosal cystic sarcoma, synovial sarcoma, and telangiectatic sarcoma.

[0311] 136. The method of claim 131, wherein the cancer is a leukemia selected from the group consisting of non-lymphocytic leukemia, chronic lymphocytic leukemia, acute myeloid leukemia, chronic myeloid leukemia, acute promyelocytic leukemia, adult T-cell leukemia, non-leukemic leukemia, leukemic leukemia, basophilic leukemia, blast cell leukemia, bovine leukemia, chronic myelocytic leukemia, leukemia cutis, embryonal leukemia, eosinophilic leukemia, Gross' leukemia, hairy cell leukemia, hematopoietic leukemia, hematoblastic leukemia, histiocytic leukemia, stem cell leukemia, acute monocytic leukemia, leukemia, leukopenic leukemia, lymphocytic leukemia, lymphoblastic leukemia, lymphocytic leukemia, lymphoblastic leukemia, lymphoid leukemia, lymphosarcoma cell leukemia, mast cell leukemia, megakaryocytic leukemia, myeloblastic leukemia, monocytic leukemia, myeloblastic leukemia, myeloid leukemia, myeloid granulocytic leukemia, myelomonocytic leukemia, Negley's leukemia, plasma cell leukemia, multiple myeloma, plasma cell leukemia, promyelocytic leukemia, Liddle cell leukemia, Schilling's leukemia, stem cell leukemia, subleukemic leukemia and undifferentiated cell leukemia.

[0312] 137. The method of claim 136, wherein the cancer is chronic lymphocytic leukemia.

[0313] 138. The method of claim 131 , wherein the cancer is lymphoma.

[0314] 139. The method of claim 138, wherein the lymphoma is non-Hodgkin's lymphoma, Hodgkin's disease, diffuse large B-cell lymphoma, follicular lymphoma, mucosa-associated lymphoid tissue (MALT) lymphoma, small cell lymphocytic lymphoma-chronic lymphocytic leukemia, mantle cell lymphoma, mediastinal (thymic) large B-cell lymphoma, lymphoplasmacytic lymphoma-Waldenstrom's macroglobulinemia, peripheral T-cell lymphoma (PTCL), angioimmunoblastic T-cell lymphoma (AITL) / follicular T-cell lymphoma (FTCL), anaplastic large cell lymphoma (ALCL), enteropathy-associated T-cell lymphoma (EATL), adult T-cell leukemia / lymphoma (ATLL), or extranodal NK / T-cell lymphoma, nasal type.

[0315] 140. The method of claim 139, wherein the lymphoma is mantle cell lymphoma.

[0316] 141. The method of claim 131, wherein the cancer is a melanoma selected from the group consisting of acral lentiginous melanoma, amelanotic melanoma, benign juvenile melanoma, Claudemann's melanoma, S91 melanoma, Harper's melanoma, juvenile melanoma, lentigo maligna melanoma, malignant melanoma, nodular melanoma, subungual melanoma, and superficial spreading melanoma.

[0317] 142. The method of claim 131, wherein the cancer is prostate cancer, thyroid cancer, endocrine system cancer, brain cancer, breast cancer, cervical cancer, colon cancer, head and neck cancer, liver cancer, kidney cancer, lung cancer, non-small cell lung cancer, melanoma, mesothelioma, ovarian cancer, sarcoma, gastric cancer, uterine cancer, medulloblastoma, ampullary cancer, colorectal cancer, or pancreatic cancer.

[0318] 143. The method of claim 131 , wherein the cancer is prostate cancer.

[0319] 144. The method of claim 131, wherein the cancer is ampullary carcinoma.

[0320] 145. The method of claim 131 , wherein the cancer is colorectal cancer.

[0321] 146. The method of claim 131 , wherein the cancer is lung cancer.

[0322] 147. The method of claim 131 , wherein the cancer is non-small cell lung cancer.

[0323] 148. The method of claim 131 , wherein the cancer is ovarian cancer.

[0324] 149. The method of claim 131 , wherein the cancer is pancreatic cancer.

[0325] 150. The method of claim 131, wherein the cancer is Hodgkin's disease, non-Hodgkin's lymphoma, multiple myeloma, neuroblastoma, glioma, glioblastoma multiforme, ovarian cancer, rhabdomyosarcoma, essential thrombocythemia, essential macroglobulinemia, primary brain tumor, cancer, malignant pancreatic insulinoma, malignant carcinoid tumor, bladder cancer, precancerous skin lesions, testicular cancer, lymphoma, thyroid cancer, neuroblastoma, esophageal cancer, genitourinary tract cancer, malignant hypercalcemia, endometrial cancer, adrenocortical cancer, pancreatic endocrine and exocrine neoplasms, medullary thyroid cancer, cerebral thyroid carcinoma, melanoma, colorectal cancer, papillary thyroid cancer, hepatocellular carcinoma, or prostate cancer.

[0326] 151. The method of claim 129, wherein the subject is suffering from a premalignant condition and is in need of treatment thereof.

[0327] abbreviation

[0328] Abbreviations and terms commonly used in the fields of organic chemistry, medicinal chemistry, pharmacology, and medicine and familiar to practitioners in these fields are used herein. Representative abbreviations and definitions are provided below:

[0329] Ac is acetyl [CH3C(O)-], Ac2O is acetic anhydride; AcOH is acetic acid; APC is antigen presenting cell; aq. is aqueous; 9-BBN is 9-boronobicyclo[3.3.1]nonane; BINAP is (2,2'-bis(diphenylphosphine)-1,1'-binaphthyl); Bn is benzyl; BOC is tert-butyloxycarbonyl; CDI is carbonyldiimidazole; DCM is dichloromethane; DIAD is diisopropyl azodicarboxylate; DIBAL is diisobutylaluminum hydride; DIPEA is diisopropylethylamine; DMA is dimethylacetylamine amine; DMAP is 4-dimethylaminopyridine; DMF is N,N-dimethylformamide; DMSO is dimethyl sulfoxide; dppf is 1,1'-bis(diphenylphosphino)ferrocene; EDAC (or EDC) is 1-ethyl-3-[3-(dimethylamino)propyl]-carbodiimide hydrochloride; ESI is electrospray ionization mass spectrometry; Et2O is diethyl ether; Et3N is triethylamine; Et is ethyl; EtOAc is ethyl acetate; EtOH is ethanol; 3-F-Ph is 3-fluorophenyl; HATU is (1-[bis(dimethylamino)methylene ]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxide hexafluorophosphate; HCl is hydrochloric acid; HOBt is 1-hydroxybenzotriazole; HPLC is high performance liquid chromatography; LCMS is HPLC with mass spectrometry detection; LiHMDS is lithium bis(trimethylsilyl); LG is a leaving group; M is molar; mCPBA is meta-chloroperbenzoic acid; mmol is millimole; Me is methyl; MeCN is acetonitrile; MeOH is methanol; Ms is methylsulfonyl; MS is mass spectrometry; N is normal; NaHMDS S is sodium hexamethyldisilazide; NaOAc is sodium acetate; NaOtBu is sodium tert-butoxide; NMO is N-methylmorpholine N-oxide; NMP is N-methylpyrrolidone; NMR is nuclear magnetic resonance spectroscopy; Pd2(dba)3 is tris(dibenzylideneacetone)dipalladium; PdCl2(PPh3)2 is dichlorobis(triphenylphosphine)palladium; PG represents an unspecified protecting group; Ph is phenyl; PhMe is toluene; PPh3 is triphenylphosphine; PMB is p-methoxybenzyl; rt is room temperature; RBF is a round-bottom flask; RuPhos Pd G1 is chloro-(2-dicyclohexylphosphino-2',6'-diisopropoxy-1,1'-biphenyl)[2-(2-aminoethyl)phenyl]palladium(II); SEM is [2-(trimethylsilyl)ethoxy]methyl; SFC is supercritical fluid chromatography; S NAr is a nucleophilic aromatic substituent; TBAB is tetrabutylammonium bromide; TBAF is tetrabutylammonium fluoride; TBS is tert-butyldimethylsilyl; tBu is tert-butyl; Tf is trifluoromethanesulfonic acid; TFA is trifluoroacetic acid; THF is tetrahydrofuran; THP is tetrahydropyran; TLC is thin-layer chromatography; TMAD is tetramethylazodicarbonamide; TMS is trimethylsilyl; TPAP is tetrapropylammonium perruthenate; Ts is p-toluenesulfonyl; UPLC is ultra-performance liquid chromatography.

[0330] definition

[0331] As used herein, the term "abnormal" refers to different from normal. When used to describe enzyme activity, abnormal refers to activity that is greater than or less than the average of a normal control or a normal non-diseased control sample. Abnormal activity can refer to the amount of activity that causes the disease, wherein restoring the abnormal activity to a normal or disease-independent amount (e.g., by administering a compound or using a method as described herein) results in a reduction in the disease or one or more disease symptoms. Abnormal activity can be measured by measuring changes in the substrate of the enzyme in question; a difference greater than or equal to a 2-fold change in activity can be considered abnormal. Abnormal activity can also refer to an increased reliance on a specific signaling pathway due to a defect in a separate complementary pathway.

[0332] As used herein, the term "acyl" refers to the group -C(=O)-R, where R is alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl, or heterocyclyl. Acyl groups may be optionally substituted as described herein for each corresponding R group.

[0333] As used herein, the term "glandular epithelial carcinoma" refers to a malignant tumor arising from glandular cells that line organs in an organism. Non-limiting examples of glandular epithelial carcinomas include non-small cell lung cancer, prostate cancer, pancreatic cancer, esophageal cancer, and colorectal cancer.

[0334] As used herein, the term "alkanoyl" refers to a hydrogen or alkyl group attached to the parent molecule through a carbonyl group and is exemplified by formyl (i.e., a carboxaldehyde group), acetyl, propionyl, butyryl, and isobutyryl. Unsubstituted alkanoyl groups contain 1 to 7 carbon atoms. As described herein for alkyl groups, alkanoyl groups can be unsubstituted or substituted (e.g., optionally substituted C1-7 alkanoyl groups). A terminal "-acyl" group can be added to another group as defined herein, such as aryl, cycloalkyl, and heterocyclyl, to define "aroyl," "cycloalkanoyl," and "(heterocyclyl)acyl." These groups represent a carbonyl group substituted with an aryl, cycloalkyl, or heterocyclyl group, respectively. Each of "aroyl," "cycloalkanoyl," and "(heterocyclyl)acyl" can be optionally substituted as defined for "aryl," "cycloalkyl," or "heterocyclyl," respectively.

[0335] As used herein, the term "alkenyl" refers to a non-cyclic monovalent straight or branched hydrocarbon radical containing one, two, or three carbon-carbon double bonds. Non-limiting examples of alkenyl include vinyl, prop-1-enyl, prop-2-enyl, 1-methylvinyl, but-1-enyl, but-2-enyl, but-3-enyl, 1-methylprop-1-enyl, 2-methylprop-1-enyl, and 1-methylprop-2-enyl. As defined herein for alkyl, alkenyl may be optionally substituted.

[0336] As used herein, unless otherwise indicated, the term "alkoxy" refers to a chemical substituent of the formula -OR, wherein R is C 1-6 Alkyl. In some embodiments, the alkyl group may be further substituted as defined herein. The term "alkoxy" may be combined with other terms defined herein (e.g., aryl, cycloalkyl, or heterocyclyl) to define "arylalkoxy," "cycloalkylalkoxy," and "(heterocyclyl)alkoxy." These groups represent alkoxy groups substituted with aryl, cycloalkyl, or heterocyclyl, respectively. Each "arylalkoxy," "cycloalkylalkoxy," and "(heterocyclyl)alkoxy" may be optionally substituted as defined herein for each individual moiety.

[0337] As used herein, the term "alkoxyalkyl" refers to a chemical substituent of the formula -L-O-R, wherein L is C 1-6 Alkylene and R is C 1-6 Optionally substituted alkoxyalkyl is an alkoxyalkyl group that is optionally substituted as described herein for alkyl.

[0338] Unless otherwise indicated, as used herein, the term "alkyl" refers to a non-cyclic straight or branched chain saturated hydrocarbon group having 1 to 12 carbons when unsubstituted. In certain preferred embodiments, the unsubstituted alkyl group has 1 to 6 carbons. Alkyl groups are exemplified by methyl, ethyl, n-propyl and isopropyl, n-butyl, sec-butyl, isobutyl and tert-butyl, neopentyl, and the like, and may be optionally substituted (as valence permits) with one, two, three, or, in the case of alkyl groups having two or more carbon atoms, four or more substituents independently selected from the group consisting of amino, aryl, aryloxy, azido, cycloalkyl, cycloalkoxy, cycloalkenyl, cycloalkynyl, halo, heterocyclyl, (heterocyclyl)oxy, heteroaryl, hydroxy, nitro, thiol, silyl, cyano, alkylsulfonyl, alkylsulfinyl, alkylsulfenyl, =O, =S, -S02R (wherein R is amino or cycloalkyl), =NR' (wherein R' is H, alkyl, aryl or heterocyclyl). Each substituent may itself be unsubstituted or (as valence permits) substituted with an unsubstituted substituent as defined herein for each corresponding group.

[0339] As used herein, the term "alkylene" refers to a divalent alkyl group. Optionally substituted alkylene is an alkylene group that is optionally substituted as described herein for an alkyl group.

[0340] As used herein, the term "alkylamino" refers to a group having the formula -N(R N1 )2 or –NHR N1 A group wherein, as defined herein, R N1 is an alkyl group. The alkyl portion of the alkylamino group may be optionally substituted as defined for an alkyl group. Each optional substituent on a substituted alkylamino group may itself be unsubstituted or, where valence permits, substituted with an unsubstituted substituent as defined herein for each corresponding group.

[0341] As used herein, the term "alkylsulfenyl" refers to a group of the formula -S-(alkyl). As defined for an alkyl group, an alkylsulfenyl group may be optionally substituted.

[0342] As used herein, the term "alkylsulfinyl" refers to a group of the formula -S(O)-(alkyl). Alkylsulfinyl groups may be optionally substituted as defined for alkyl groups.

[0343] As used herein, the term "alkylsulfonyl" refers to a group of the formula -S(O)2-(alkyl). Alkylsulfonyl groups may be optionally substituted as defined for alkyl groups.

[0344] As used herein, the term "alkynyl" refers to a monovalent straight or branched chain hydrocarbon radical of 2 to 6 carbon atoms containing at least one carbon-carbon triple bond and is exemplified by ethynyl, 1-propynyl, etc. As defined for alkyl, alkynyl groups can be unsubstituted or substituted (e.g., optionally substituted alkynyl).

[0345] As used herein, the term "amino" refers to -N(R N1 )2, wherein, if the amino group is unsubstituted, the two R N1 are H; or, if amino is substituted, each R N1 are independently H, -OH, -NO2, -N(R N2 )2, -SO2OR N2 、-SO2R N2 、-SOR N2 、-COOR N2 , N-protecting group, alkyl, alkenyl, alkynyl, alkoxy, aryl, arylalkyl, aryloxy, cycloalkyl, cycloalkenyl, heteroalkyl or heterocyclyl, provided that at least one R N1 is not H, and each R N2is independently H, alkyl, or aryl. Each substituent may itself be unsubstituted or substituted with an unsubstituted substituent as defined herein for each corresponding group. In some embodiments, amino is unsubstituted amino (i.e., -NH2) or substituted amino (e.g., NHR N1 ), where R N1 are independently -OH, SO2OR N2 、-SO2R N2 、-SOR N2 、-COOR N2 , optionally substituted alkyl or optionally substituted aryl, and each R N2 Can be optionally substituted alkyl or optionally substituted aryl. In some embodiments, the substituted amino group can be an alkylamino group, wherein the alkyl group is optionally substituted as described herein for the alkyl group. In some embodiments, the amino group is -NHR N1 , where R N1 is an optionally substituted alkyl group.

[0346] As used herein, the term "aryl" refers to a monocyclic, bicyclic or polycyclic carbocyclic ring system having one or two aromatic rings. The aryl group may contain 6 to 10 carbon atoms. All atoms in the unsubstituted carbocyclic aryl are carbon atoms. Non-limiting examples of carbocyclic aryl groups include phenyl, naphthyl, 1,2-dihydronaphthyl, 1,2,3,4-tetrahydronaphthyl, fluorenyl, indanyl, indenyl, etc. The aryl group may be unsubstituted or substituted by 1, 2, 3, 4 or 5 substituents independently selected from the group consisting of: alkyl, alkenyl, alkynyl, alkoxy, alkylsulfinyl, alkylthiosulfenyl, alkylsulfonyl, amino, aryl, aryloxy, azido, cycloalkyl, cycloalkoxy, cycloalkenyl, cycloalkynyl, halo, heteroalkyl, heterocyclyl, (heterocyclyl)oxy, hydroxyl, nitro, thiol, silyl and cyano. Each substituent may itself be unsubstituted or substituted with an unsubstituted substituent as defined herein for each corresponding group.

[0347] As used herein, the term "arylalkyl" refers to an alkyl group substituted with an aryl group. As described herein, the aryl and alkyl portions can be optionally substituted as separate groups.

[0348] As used herein, the term "arylene" refers to a divalent aromatic radical. An optionally substituted arylene radical is an arylene radical that is optionally substituted as described herein for an aryl radical.

[0349] As used herein, unless otherwise indicated, the term "alkoxy" refers to a chemical substituent of the formula -OR, wherein R is an aryl group. In an optionally substituted aryloxy group, the aryl group is optionally substituted as described herein for an aryl group.

[0350] As used herein, the term "ATR inhibitor" refers to an agent that, when contacted with the enzyme ATR kinase, whether in vitro, in cell culture, or in vivo in an animal, reduces ATR kinase activity such that the measured ATR kinase IC is reduced. 50 For certain ATR inhibitors, the ATR kinase IC 50 It may be 100 nM or less (e.g., 10 nM or less or 1 nM or less) and may be as low as 100 pM or 10 pM. Preferably, the ATR kinase IC 50 In the range of 1 nM to 1 μM (eg, 1 nM to 750 nM, 1 nM to 500 nM, or 1 nM to 250 nM).

[0351] As used herein, the term "ATR kinase" refers to ataxia-telangiectasia and RAD-3-related protein kinase.

[0352] As used herein, the term "azido" refers to a -N3 group.

[0353] As used herein, the term "cancer" refers to all types of cancers, neoplasms, or malignancies found in mammals (e.g., humans), including leukemias, epithelial cancers, and sarcomas. Non-limiting examples of cancers that can be treated with the compounds or methods provided herein include prostate cancer, thyroid cancer, endocrine system cancer, brain cancer, breast cancer, cervical cancer, colon cancer, head and neck cancer, liver cancer, kidney cancer, lung cancer, non-small cell lung cancer, melanoma, mesothelioma, ovarian cancer, sarcoma, gastric cancer, uterine cancer, medulloblastoma, ampullary cancer, colorectal cancer, and pancreatic cancer. Additional non-limiting examples can include Hodgkin's disease, non-Hodgkin's lymphoma, multiple myeloma, neuroblastoma, glioma, glioblastoma multiforme, ovarian cancer, rhabdomyosarcoma, essential thrombocythemia, essential macroglobulinemia, primary brain tumors, carcinoma, malignant pancreatic insulinoma, malignant carcinoid tumor, bladder cancer, precancerous skin lesions, testicular cancer, lymphoma, thyroid cancer, neuroblastoma, esophageal cancer, genitourinary tract cancer, malignant hypercalcemia, endometrial cancer, adrenocortical cancer, pancreatic endocrine and exocrine neoplasms, medullary thyroid cancer, cerebral thyroid carcinoma, melanoma, colorectal cancer, papillary thyroid cancer, hepatocellular carcinoma, and prostate cancer.

[0354] As used herein, the term "carbocycle" refers to an optionally substituted C3-16 monocyclic, bicyclic or tricyclic structure in which the ring, which may be aromatic or non-aromatic, is formed by carbon atoms. Carbocyclic structures include cycloalkyl, cycloalkenyl, cycloalkynyl and certain aromatic groups.

[0355] As used herein, the term "carbonyl" refers to a -C(O)- group.

[0356] As used herein, the term "epithelial cancer" refers to a malignant new growth composed of epithelial cells that tend to infiltrate surrounding tissues and produce metastases. Non-limiting examples of epithelial cancers that can be treated with the compounds or methods provided herein include, for example, thyroid brain-like epithelial cancer, familial thyroid brain-like epithelial cancer, acinar epithelial cancer, acinar epithelial cancer, adenoid cystic epithelial cancer, adenoid cystic epithelial cancer, adenomatous epithelial cancer, adrenal cortical epithelial cancer, alveolar epithelial cancer, alveolar cell epithelial cancer, basal cell epithelial cancer, basaloid epithelial cancer, basosquamous cell epithelial cancer, bronchioalveolar epithelial cancer, bronchiolar epithelial cancer, bronchial epithelial cancer, medullary epithelial cancer, cholangiocarcinoma, choriocarcinoma, Colloid carcinoma, comedo carcinoma, main epithelial carcinoma, cribriform carcinoma, armored carcinoma, cutaneous carcinoma, columnar carcinoma, columnar cell carcinoma, ductal carcinoma, sclerosing carcinoma, embryonal carcinoma, brain-like carcinoma, epidermoid carcinoma, adenoid carcinoma, exophytic carcinoma, ulcerative carcinoma, fibrocarcinoma, colloid carcinoma, gelatinous carcinoma, giant cell carcinoma, giant cell carcinoma, glandular carcinoma, granular cell carcinoma, pilostromal carcinoma, hematogenous carcinoma, hepatocellular carcinoma, Schütt cell carcinoma, hyalinoid carcinoma, adrenal carcinoma carcinoma, infantile embryonal carcinoma, carcinoma in situ, intraepidermal carcinoma, intraepithelial carcinoma, Klebsiella pneumoniae carcinoma, Kurchitsky cell carcinoma, large cell carcinoma, lenticular carcinoma, lenticular carcinoma, lipomatous carcinoma, lymphoepithelial carcinoma, medullary carcinoma, medullary carcinoma, melanotic carcinoma, soft cell carcinoma, mucinous carcinoma, mucinous carcinoma, mucocytic carcinoma, mucoepidermoid carcinoma, mucinous carcinoma, myxomatous carcinoma, myxomatous carcinoma, nasopharyngeal carcinoma, oat cell carcinoma, ossifying carcinoma, osteoid carcinoma, papillary carcinoma, periportal carcinoma carcinoma, preinvasive carcinoma, prickle cell carcinoma, mucus carcinoma, renal cell carcinoma, reserve cell carcinoma, sarcomatoid carcinoma, Schneider's carcinoma, scirrhous carcinoma, scrotal carcinoma, signet ring cell carcinoma, simple carcinoma, small cell carcinoma, potato carcinoma, spheroid cell carcinoma, spindle cell carcinoma, spongiform carcinoma, squamous cell carcinoma, squamous cell carcinoma, string carcinoma, telangiectatic carcinoma, angioectatic carcinoma, transitional cell carcinoma, nodular carcinoma, tubercular carcinoma, verrucous carcinoma, and villous carcinoma.

[0357] As used herein, the term "cyano" refers to a -CN group.

[0358] As used herein, unless otherwise indicated, the term "cycloalkenyl" refers to a non-aromatic carbocyclic group having at least one intracyclic double bond and 3 to 10 carbon atoms (e.g., C 3-10Cycloalkenyl). Non-limiting examples of cycloalkenyl include cycloprop-1-enyl, cycloprop-2-enyl, cyclobut-1-enyl, cyclobut-1-enyl, cyclobut-2-enyl, cyclopent-1-enyl, cyclopent-2-enyl, cyclopent-3-enyl, norbornen-1-yl, norbornen-2-yl, norbornen-5-yl, and norbornen-7-yl. As described for cycloalkyl, cycloalkenyl can be unsubstituted or substituted (e.g., optionally substituted cycloalkenyl).

[0359] As used herein, the term "cycloalkenylalkyl" refers to an alkyl group substituted by a cycloalkenyl group, each of which is as defined herein. The cycloalkenyl and alkyl moieties may be substituted as defined herein in their own right.

[0360] Unless otherwise indicated, as used herein, the term "alkoxy" refers to a chemical substituent of the formula -OR, wherein R is a cycloalkyl group. In some embodiments, the cycloalkyl group may be further substituted, as defined herein.

[0361] Unless otherwise indicated, as used herein, the term "cycloalkyl" refers to a cycloalkyl group having 3 to 10 carbon atoms (e.g., C 3-10 Cycloalkyl). Cycloalkyl groups may be monocyclic or bicyclic. Bicyclic cycloalkyl groups may be bicyclic [pq0] alkyl types, wherein each p and q are independently 1, 2, 3, 4, 5, 6 or 7, provided that the sum of p and q is 2, 3, 4, 5, 6, 7 or 8. Alternatively, bicyclic cycloalkyl groups may comprise bridged cycloalkyl structures, for example, bicyclic [pqr] alkyl, wherein r is 1, 2 or 3, and each p and q are independently 1, 2, 3, 4, 5 or 6, provided that the sum of p, q and r is 3, 4, 5, 6, 7 or 8. Cycloalkyl groups may be spirocyclic groups, for example, spiro [pq] alkyl, wherein each p and q are independently 2, 3, 4, 5, 6 or 7, provided that the sum of p and q is 4, 5, 6, 7, 8 or 9. Non-limiting examples of cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, 1-bicyclo[2.2.1.]heptyl, 2-bicyclo[2.2.1.]heptyl, 5-bicyclo[2.2.1.]heptyl, 7-bicyclo[2.2.1.]heptyl, and decalinyl. The cycloalkyl group can be unsubstituted or substituted (e.g., optionally substituted cycloalkyl) with 1, 2, 3, 4, or 5 substituents independently selected from the group consisting of alkyl, alkenyl, alkynyl, alkoxy, alkylsulfinyl, alkylthiooxylide, alkylsulfonyl, amino, aryl, aryloxy, azido, cycloalkyl, cycloalkoxy, cycloalkenyl, cycloalkynyl, halo, heteroalkyl, heterocyclyl, (heterocyclyl)oxy, heteroaryl, hydroxy, nitro, thiol, silyl, cyano, ═O, ═S, —S02R (wherein R is amino or cycloalkyl), ═NR′ (wherein R′ is H, alkyl, aryl, or heterocyclyl), or —CON(R) A)2(where each R A are independently H or alkyl or two R A Each substituent may itself be unsubstituted or substituted with an unsubstituted substituent as defined herein for each corresponding group.

[0362] As used herein, the term "cycloalkylalkyl" refers to an alkyl group substituted by a cycloalkyl group, each of which is as defined herein. The cycloalkyl and alkyl moieties may be optionally substituted as separate groups as described herein.

[0363] As used herein, the term "cycloalkylene" refers to a divalent cycloalkyl group. Optionally substituted cycloalkylene is an optionally substituted cycloalkylene group as described herein for cycloalkyl.

[0364] Unless otherwise indicated, as used herein, the term "cycloalkynyl" refers to a monovalent carbocyclic group having one or two carbon-carbon triple bonds and having 8 to 12 carbon atoms. The cycloalkynyl group may comprise a trans-ring bond or bridge. Non-limiting examples of cycloalkynyl groups include cyclooctynyl, cyclononynyl, cyclodecynyl, and cyclodecadiynyl. As defined for cycloalkyl, the cycloalkynyl group may be unsubstituted or substituted (e.g., an optionally substituted cycloalkynyl group).

[0365] "Disease" or "condition" refers to a state or health condition in a patient or subject that can be treated using the compounds or methods provided herein.

[0366] As used herein, the term "halo" refers to a halogen selected from bromo, chloro, iodo and fluoro.

[0367] As used herein, the term "heteroalkyl" refers to an alkyl, alkenyl, or alkynyl group that is interrupted once by one or two heteroatoms, twice independently each time by one or two heteroatoms, three times independently each time by one or two heteroatoms, or four times independently each time by one or two heteroatoms. Each heteroatom is independently O, N, or S. In some embodiments, the heteroatom is O or N. No heteroalkyl group contains two consecutive oxygen or sulfur atoms. The heteroalkyl group may be unsubstituted or substituted (e.g., optionally substituted heteroalkyl groups). When the heteroalkyl group is substituted and a substituent is bonded to a heteroatom, the substituent is selected based on the nature and valence of the heteroatom. Thus, the substituent bonded to the heteroatom (when valence permits) is selected from the group consisting of: =O, -N(R N2 )2, -SO2OR N3 、-SO2R N2 、-SOR N3 、-COOR N3 , N protecting group, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, cycloalkynyl, heterocyclic group or cyano group, wherein each R N2are independently H, alkyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl or heterocyclyl, and each R N3 In some embodiments, the present invention provides an alkyl radical, a cycloalkyl radical, a cycloalkenyl radical, a cycloalkynyl radical, an aryl radical or a heterocyclic radical. Each of these substituents can itself be unsubstituted or substituted by an unsubstituted substituent defined herein for each corresponding group. When heteroalkyl is substituted and a substituent is bonded to carbon, the substituent is selected from those described for the alkyl, provided that the carbon atom bonded to the heteroatom substituent is not Cl, Br or I. It should be understood that the carbon atom is located at the end of the heteroalkyl radical.

[0368] As used herein, the term "heteroarylalkyl" refers to an alkyl group substituted with a heteroaryl group, each of which is as defined herein. The heteroaryl and alkyl moieties may be optionally substituted as separate groups as described herein.

[0369] As used herein, the term "heteroarylene" refers to a divalent heteroaryl group. An optionally substituted heteroarylene group is an optionally substituted heteroarylene group as described herein for a heteroaryl group.

[0370] As used herein, the term "heteroaryloxy" refers to the structure -OR, in which R is a heteroaryl. As defined for a heterocyclyl group, a heteroaryloxy group may be optionally substituted.

[0371] As used herein, the term "heterocyclyl" refers to a monocyclic, bicyclic, tricyclic or tetracyclic ring system having a fused, bridged or spiral 3, 4, 5, 6, 7 or 8-membered ring, unless otherwise specified, the ring contains 1, 2, 3 or 4 heteroatoms independently selected from the group consisting of nitrogen, oxygen and sulfur. In some embodiments, a "heterocyclyl" is a monocyclic, bicyclic, tricyclic or tetracyclic ring system having a fused or bridged 5, 6, 7 or 8-membered ring, unless otherwise specified, the ring contains 1, 2, 3 or 4 heteroatoms independently selected from the group consisting of nitrogen, oxygen and sulfur. The heterocyclyl group may be aromatic or non-aromatic. Non-aromatic 5-membered heterocyclyls have 0 or 1 double bonds, non-aromatic 6 and 7-membered heterocyclyls have 0 to 2 double bonds, and non-aromatic 8-membered heterocyclyls have 0 to 2 double bonds and / or 0 or 1 carbon-carbon triple bonds. Unless otherwise specified, the heterocyclyl group contains 1 to 16 carbon atoms. Certain heterocyclic groups may contain up to 9 carbon atoms. Non-aromatic heterocyclic groups include pyrrolinyl, pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, homopiperidinyl, piperazinyl, pyridazinyl, oxazolidinyl, isoxazolinyl, morpholinyl, thiomorpholinyl, thiazolidinyl, isothiazolidinyl, thiazolidinyl, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothiophenyl, dihydrothiophenyl, dihydroindolinyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, pyranyl, dihydropyranyl, dithiazolyl, and the like. If the heterocyclic ring system has at least one aromatic resonance structure or at least one aromatic tautomer, such structure is an aromatic heterocyclic group (i.e., a heteroaryl group). Non-limiting examples of heteroaryl groups include benzimidazolyl, benzofuranyl, benzothiazolyl, benzothiophenyl, benzoxazolyl, furanyl, imidazolyl, indolyl, isoindolyl, isoquinolyl, isothiazolyl, isothiazolyl, isoxazolyl, oxadiazolyl, oxazolyl, purinyl, pyrrolyl, pyridinyl, pyrazinyl, pyrimidinyl, quinazolinyl, quinolinyl, thiadiazolyl (e.g., 1,3,4-thiadiazole), thiazolyl, thienyl, triazolyl, tetrazolyl, and the like. The term "heterocyclyl" also refers to heterocyclic compounds having a bridged polycyclic structure in which one or more carbon atoms and / or heteroatoms bridge two non-adjacent members of a monocyclic ring (e.g., quinuclidine, tropane, or diazabicyclo[2.2.2]octane). The term "heterocyclyl" includes bicyclic, tricyclic, and tetracyclic groups in which any of the above heterocyclic rings is fused with 1, 2, or 3 carbocyclic rings, such as an aryl ring, a cyclohexane ring, a cyclohexene ring, a cyclopentane ring, a cyclopentene ring, or another monocyclic heterocycle. Examples of fused heterocycles include 1,2,3,5,8,8a-hexahydroindole, 2,3-dihydrobenzofuran, 2,3-dihydroindole, and 2,3-dihydrobenzothiophene.The heterocyclyl group may be unsubstituted or substituted with 1, 2, 3, 4, or 5 substituents independently selected from the group consisting of alkyl, alkenyl, alkynyl, alkoxy, alkylsulfinyl, alkylthiooxy, alkylsulfonyl, amino, aryl, aryloxy, azido, cycloalkyl, cycloalkoxy, cycloalkenyl, cycloalkynyl, halo, heteroalkyl, heterocyclyl, (heterocyclyl)oxy, hydroxy, nitro, thiol, silyl, cyano, =O, =S, =NR' (wherein R' is H, alkyl, aryl, or heterocyclyl). Each substituent may itself be unsubstituted or substituted with an unsubstituted substituent as defined herein for each corresponding group.

[0372] As used herein, the term "heterocycloalkyl" refers to an alkyl group substituted with a heterocyclyl group, each of which is as defined herein. The heterocyclyl and alkyl moieties may be optionally substituted as separate groups as described herein.

[0373] As used herein, the term "heterocyclylene" refers to a divalent heterocyclyl group. An optionally substituted heterocyclylene group is an optionally substituted heterocyclylene group as described herein for a heterocyclyl group.

[0374] Unless otherwise indicated, as used herein, the term "(heterocyclyl)oxy" refers to a chemical substituent of the formula -OR, wherein R is heterocyclyl. (Heterocyclyl)oxy may be optionally substituted in the manner described for heterocyclyl.

[0375] As used interchangeably herein, the terms "hydroxyl" and "hydroxy" refer to an -OH group.

[0376] As used herein, the term "isotopically enriched" refers to a pharmaceutical agent having an isotopic content of an isotope at a predetermined position within a molecule that is at least 100 times greater than the natural abundance of that isotope. For example, a composition isotopically deuterium-enriched comprises an agent having an abundance of deuterium at at least one hydrogen atom position that is at least 100 times greater than the natural abundance of deuterium. Preferably, the isotopic deuterium enrichment is at least 1000 times greater than the natural abundance of deuterium. More preferably, the isotopic deuterium enrichment is at least 4000 times greater (e.g., at least 4750 times, e.g., up to 5000 times) than the natural abundance of deuterium.

[0377] As used herein, the term "leukemia" broadly refers to progressive malignant diseases of the blood-forming organs and is generally characterized by abnormal proliferation and development of white blood cells and their precursors in the blood and bone marrow. Leukemias are generally clinically classified based on: (1) the duration and characteristics of the disease: acute or chronic; (2) the cell types involved: myeloid (myeloid), lymphoid (lymphoid), or monocytic; and (3) whether the number of abnormal cells in the blood is increased or not, whether it is leukemic or non-leukemic (subleukemic). Exemplary leukemias that can be treated with the compounds or methods provided herein include, for example, acute non-lymphocytic leukemia, chronic lymphocytic leukemia, acute myeloid leukemia, chronic myeloid leukemia, acute promyelocytic leukemia, adult T-cell leukemia, non-leukemic leukemia, leukemic leukemia, basophilic leukemia, blast cell leukemia, bovine leukemia, chronic myelocytic leukemia, leukemia cutis, embryonal leukemia, eosinophilic leukemia, Gross' leukemia, hairy cell leukemia, hematopoietic leukemia, hematoblastic leukemia, histiocytic leukemia, stem cell leukemia, acute monocytic leukemia, , leukopenic leukemia, lymphocytic leukemia, lymphoblastic leukemia, lymphocytic leukemia, lymphoblastic leukemia, lymphoid leukemia, lymphosarcoma cell leukemia, mast cell leukemia, megakaryocytic leukemia, myeloblastic leukemia, monocytic leukemia, myeloblastic leukemia, myeloid leukemia, myeloid granulocytic leukemia, myelomonocytic leukemia, Negley's leukemia, plasma cell leukemia, multiple myeloma, plasma cell leukemia, promyelocytic leukemia, Liddle cell leukemia, Schilling's leukemia, stem cell leukemia, subleukemic leukemia and undifferentiated cell leukemia.

[0378] As used herein, the term "lymphoma" refers to cancers caused by cells of immune origin. Non-limiting examples of T-cell and B-cell lymphomas include non-Hodgkin's lymphoma and Hodgkin's disease, diffuse large B-cell lymphoma, follicular lymphoma, mucosa-associated lymphoid tissue (MALT) lymphoma, small cell lymphocytic lymphoma-chronic lymphocytic leukemia, mantle cell lymphoma, mediastinal (thymic) large B-cell lymphoma, lymphoplasmacytic lymphoma-Waldenstrom's macroglobulinemia, peripheral T-cell lymphoma (PTCL), angioimmunoblastic T-cell lymphoma (AITL) / follicular T-cell lymphoma (FTCL), anaplastic large cell lymphoma (ALCL), enteropathy-associated T-cell lymphoma (EATL), adult T-cell leukemia / lymphoma (ATLL), or extranodal NK / T-cell lymphoma nasal type.

[0379] As used herein, the term "melanoma" refers to a tumor arising from the melanocyte system of the skin and other organs. Melanomas that can be treated with the compounds or methods provided herein include, for example, acral-lentiginous melanoma, amelanotic melanoma, benign juvenile melanoma, Claudemann melanoma, S91 melanoma, Harper-Parkinson melanoma, juvenile melanoma, lentigo maligna melanoma, malignant melanoma, nodular melanoma, subungual melanoma, and superficial spreading melanoma.

[0380] As used herein, the term "nitro" refers to a -NO2 group.

[0381] As used herein, the term "oxo" refers to a divalent oxygen atom (eg, an oxo structure can be represented as =0).

[0382] As used herein, the term "phenyl" refers to a phenyl group.

[0383] As used herein, the term "pharmaceutical composition" refers to a composition containing a compound described herein formulated with a pharmaceutically acceptable excipient and manufactured or sold under the approval of a governmental regulatory agency as part of a therapeutic regimen for treating a disease in a mammal. The pharmaceutical composition can be formulated, for example, for oral administration in a unit dosage form (e.g., tablets, capsules, caplets, softgels, or syrups); for topical administration (e.g., in the form of a cream, gel, lotion, or ointment); for intravenous administration (e.g., in the form of a sterile solution without microparticles and in a solvent system suitable for intravenous use); or as any other formulation described herein.

[0384] As used interchangeably herein, the terms "pharmaceutically acceptable excipient" or "pharmaceutically acceptable carrier" refer to any ingredient other than a compound described herein that has non-toxic and non-inflammatory properties in a patient (e.g., a vehicle capable of suspending or dissolving the active compound). Excipients may include, for example, anti-adherents, antioxidants, binders, coatings, compression aids, disintegrants, dyes (colorants), softeners, emulsifiers, fillers (diluents), film formers or coatings, flavorings, fragrances, glidants (flow enhancers), lubricants, preservatives, printing inks, adsorbents, suspending or dispersing agents, sweeteners, or water of hydration. Exemplary excipients include, but are not limited to, butylated hydroxytoluene (BHT), calcium carbonate, calcium phosphate (dibasic), calcium stearate, cross-linked carboxymethylcellulose, cross-linked polyvinyl pyrrolidone, citric acid, crospovidone, cysteine, ethylcellulose, gelatin, hydroxypropyl cellulose, hydroxypropyl methylcellulose, lactose, magnesium stearate, maltitol, mannitol, methionine, methylcellulose, methylparaben, microcrystalline cellulose, polyethylene glycol, polyvinyl pyrrolidone, povidone, pregelatinized starch, propylparaben, retinyl palmitate, shellac, silicon dioxide, sodium carboxymethylcellulose, sodium citrate, sodium starch glycolate, sorbitol, starch (corn), stearic acid, stearic acid, sucrose, talc, titanium dioxide, vitamin A, vitamin E, vitamin C, and xylitol.

[0385] As used herein, the term "pharmaceutically acceptable salt" refers to salts that are suitable for use in contact with human and animal tissues without excessive toxicity, irritation, allergic response, etc., within the scope of sound medical judgment and commensurate with a reasonable benefit / risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, pharmaceutically acceptable salts are described in Berge et al., J. Pharmaceutical Sciences 66: 1-19, 1977 and Pharmaceutical Salts: Properties, Selection, and Use, (P.H. Stahl and C.G. Wermuth, eds.), Wiley-VCH, 2008. Salts can be prepared in situ during the final isolation and purification of the compounds described herein or separately by reacting the free base groups with suitable organic acids. Representative acid addition salts include acetate, adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, gluconate, dodecylsulfate, ethanesulfonate, fumarate, glucoheptonate, glycerophosphate, hemisulfate, heptanoate, hexanoate, hydrobromide, hydrochloride, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, toluenesulfonate, undecanoate, valerate, and the like. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like, as well as non-toxic ammonium, quaternary ammonium, and amine cations, including but not limited to ammonium, tetramethylammonium, tetraethylammonium, methylamine, dimethylamine, trimethylamine, triethylamine, ethylamine, and the like.

[0386] As used herein, the term "premalignant" or "precancerous" refers to a condition that is not malignant but can become malignant at any time. Non-limiting examples of premalignant conditions include myelodysplastic syndrome, colon polyps, actinic keratosis, cervical dysplasia, pulmonary metaplasia, and leukoplakia.

[0387] As used herein, the term "protecting group" refers to a group that is intended to protect a hydroxyl, amino, or carbonyl group from participating in one or more undesirable reactions during chemical synthesis. As used herein, the term "O-protecting group" refers to a group that is intended to protect a hydroxyl or carbonyl group from participating in one or more undesirable reactions during chemical synthesis. As used herein, the term "N-protecting group" refers to a group that is intended to protect a nitrogen-containing (e.g., amino, amido, heterocyclic NH, or hydrazine) group from participating in one or more undesirable reactions during chemical synthesis. Commonly used O-protecting groups and N-protecting groups are disclosed in Greene, "Protective Groups in Organic Synthesis," 3rd Edition (John Wiley & Sons, New York, 1999), which is incorporated herein by reference. Exemplary O-protecting and N-protecting groups include alkanoyl, aroyl, or carbamoyl groups, such as formyl, acetyl, propionyl, pivaloyl, tert-butylacetyl, 2-chloroacetyl, 2-bromoacetyl, trifluoroacetyl, trichloroacetyl, phthaloyl, o-nitrophenoxyacetyl, α-chlorobutyryl, benzoyl, 4-chlorobenzoyl, 4-bromobenzoyl, tert-butyldimethylsilyl, tri-isopropylsiloxymethyl, 4,4′-dimethoxytrityl, isobutyryl, phenoxyacetyl, 4-isopropylphenoxyacetyl, dimethylformamidinyl, and 4-nitrobenzoyl.

[0388] Exemplary O-protecting groups for protecting carbonyl-containing groups include, but are not limited to, acetal, acyl, 1,3-dithiane, 1,3-dioxane, 1,3-dioxolane, and 1,3-dithiolane.

[0389] Other O-protecting groups include, but are not limited to, substituted alkyl, aryl, and arylalkyl ethers (e.g., trityl, methylthiomethyl, methoxymethyl, benzyloxymethyl, silyloxymethyl, 2,2,2-trichloroethoxymethyl, tetrahydropyranyl, tetrahydrofuranyl, ethoxyethyl, 1-[2-(trimethylsilyl)ethoxy]ethyl, 2-trimethylsilylethyl, tert-butyl ether, p-chlorophenyl, p-methoxyphenyl, p-nitrophenyl, benzyl, p-methoxybenzyl, and nitrobenzyl); silyl ethers (e.g., silyl, trimethylsilyl, triethylsilyl, triisopropylsilyl, dimethylisopropylsilyl, tert-butyldimethylsilyl, tert-butyldiphenylsilyl, tribenzylsilyl, triphenylsilyl, and diphenylmethylsilyl); carbonates (e.g., methyl, methoxymethyl, 9-fluorenylmethyl, ethyl, 2,2,2-trichloroethyl, 2-(trimethylsilyl)ethyl, vinyl, allyl, nitrophenyl, benzyl, methoxybenzyl, 3,4-dimethoxybenzyl, and nitrobenzyl).

[0390] Other N-protecting groups include, but are not limited to, chiral auxiliaries such as protected or unprotected D-amino acids, L-amino acids, or D,L-amino acids (such as alanine, leucine, phenylalanine, etc.); sulfonyl-containing groups such as benzylsulfonyl, p-toluenesulfonyl, etc.; carbamate-forming groups such as benzyloxycarbonyl, p-chlorobenzyloxycarbonyl, p-methoxybenzyloxycarbonyl, p-nitrobenzyloxycarbonyl, 2-nitrobenzyloxycarbonyl, p-bromobenzyloxycarbonyl, 3,4-dimethoxybenzyloxycarbonyl, 3,5-dimethoxybenzyloxycarbonyl, 2,4-dimethoxybenzyloxycarbonyl, 4-methoxybenzyloxycarbonyl, 2-nitro-4,5-dimethoxybenzyloxycarbonyl, 3,4,5-trimethoxybenzyloxycarbonyl, 1-(p-biphenyl)-1,2-di ... such as 2-(trimethylsilyl)ethoxy]methyl; and silyl groups such as trimethylsilyl. Useful N-protecting groups are formyl, acetyl, benzoyl, pivaloyl, tert-butylacetyl, alanyl, phenylsulfonyl, benzyl, dimethoxybenzyl, [2-(trimethylsilyl)ethoxy]methyl (SEM), tetrahydropyranyl (THP), tert-butyloxycarbonyl (Boc) and benzyloxycarbonyl (Cbz).

[0391] The term "tautomer" refers to structural isomers that are often easily interchangeable by proton migration. Tautomers are different chemical species that can be identified by different spectral characteristics, but are generally not separable. Non-limiting examples of tautomers include keto-enols, enamines-imines, amides-imidic acids, nitroso-oximes, enones-alkynols, and amino acids-ammonium formate.

[0392] The term "sarcoma" generally refers to a tumor composed of a substance resembling embryonic connective tissue and generally composed of densely packed cells embedded in a fibrous or homogeneous mass. Non-limiting examples of sarcomas that can be treated with the compounds or methods provided herein include, for example, chondrosarcoma, fibrosarcoma, lymphosarcoma, melanosarcoma, myxosarcoma, osteosarcoma, Albernethy's sarcoma, liposarcoma, liposarcoma, alveolar soft part sarcoma, ameloblastic sarcoma, botryoid sarcoma, chloroma sarcoma, choriocarcinoma, embryonal sarcoma, Williams' tumor sarcoma, endometrial sarcoma, stromal sarcoma, Ewing's sarcoma, fascial sarcoma, , fibroblastic sarcoma, giant cell sarcoma, granulocytic sarcoma, Hodgkin's sarcoma, idiopathic multiple pigmented hemorrhagic sarcoma, B-cell immunoblastic sarcoma, T-cell immunoblastic sarcoma, Janssen's sarcoma, Kaposi's sarcoma, Kupffer cell sarcoma, angiosarcoma, leukemic sarcoma, malignant mesenchymal sarcoma, parosteal sarcoma, reticulum cell sarcoma, Rous sarcoma, serosal cystic sarcoma, synovial sarcoma, and telangiectatic sarcoma.

[0393] As used herein, the term "subject" refers to a human or non-human animal (e.g., a mammal) who has been determined by a qualified professional (e.g., a physician or nurse practitioner) to be suffering from or at risk for a disease or condition, with or without laboratory testing known in the art on a sample from the subject. Preferably, the subject is a human. Non-limiting examples of diseases and conditions include diseases whose symptoms are excessive cell proliferation, such as cancer.

[0394] As used herein, the terms "treatment" and "treating" refer to the medical management of a subject with the intent to modify, ameliorate, stabilize, prevent, or cure a disease or condition. This term includes active treatment (treatment involving amelioration of the disease or condition), causal treatment (treatment involving the cause of the relevant disease or condition), palliative treatment (treatment designed to relieve the symptoms of the disease or condition), preventive treatment (treatment involving minimization or partial or complete inhibition of the development of the relevant disease or condition), and supportive treatment (treatment used to supplement another therapy). DETAILED DESCRIPTION

[0395] In general, the present invention provides compounds, pharmaceutical compositions comprising the compounds, methods for preparing the compounds, and methods of use. The compounds of the present invention may be ATR kinase inhibitors. These compounds can be used to inhibit ATR kinase in cells (e.g., cells of a subject). The subject may need treatment for a disease or condition, such as a disease or condition characterized by excessive cell proliferation, such as cancer. The ATR kinase inhibitory activity of the compounds disclosed herein can be used to treat a subject in need of treatment for cancer. Non-limiting examples of cancers that can be treated using the compounds disclosed herein are provided in Foote et al., J. Med. Chem., 61:9889-9907, 2018; Wengner et al., Mol. Cancer Ther., doi: 10.1158 / 1535-7163.MCT-19-0019; and Dillon and Harrington, “Targeting ATR for Cancer Therapy: ATR-Targeted Drug Candidates”, in Targeting the DNA Damage Response for Anti-Cancer Therapy, ed. Pollard and Curtin; Humana Press, Cham (2018), pp. 99-127.

[0396] The present invention provides a compound of formula (I):

[0397]

[0398] or a pharmaceutically acceptable salt thereof,

[0399] in

[0400] is a double bond, and each Y is independently N or CR 4 ;or is a single bond, and each Y is independently NR Y , carbonyl or C(R Y )2; where each R Y are independently H or optionally substituted C 1-6 alkyl;

[0401] R 1 is optionally substituted C 1-6 Alkyl or H;

[0402] R 2 is optionally substituted C 2-9 Heterocyclyl, optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl, optionally substituted C 2-9 Heterocyclyl C1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, optionally substituted C 1-9 Heteroaryl C 1-6 Alkyl, halogen, –N(R 5 )2. –OR 5 、–CON(R 6 )2、–SO2N(R 6 )2. –SO2R 5A or –Q–R 5B ;

[0403] R 3 is optionally substituted C 1-9 Heteroaryl or optionally substituted C 1-9 Heteroaryl C 1-6 alkyl;

[0404] Each R 4 are independently hydrogen, halogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkenyl or optionally substituted C 2-6 Alkynyl;

[0405] Each R 5 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl or –SO2R 5A ; or two R 5 Together with the atoms to which they are attached, they form an optionally substituted C 2-9 heterocyclic group;

[0406] Each R 5A are independently optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 6-10 aryl;

[0407] R 5B is hydroxy, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, –N(R 5 )2、–CON(R 6 )2、–SO2N(R 6 )2. –SO2R 5A or optionally substituted alkoxy;

[0408] Each R 6 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkoxyalkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 1-9 heteroaryl; or two R 6 Together with the atoms to which they are attached, they form an optionally substituted C 2-9 heterocyclic group;

[0409] Q is optionally substituted C 2-9 Heterocyclylene, optionally substituted C 3-8 Cycloalkylene, optionally substituted C 1-9 Heteroarylene or optionally substituted C 6-10 an arylene group; and

[0410] X is hydrogen or halogen.

[0411] The compound of the present invention may be, for example, a compound of formula (II):

[0412]

[0413] or a pharmaceutically acceptable salt thereof,

[0414] in

[0415] Each Y is independently N or CR 4 ;

[0416] R 1 is optionally substituted C 1-6 Alkyl or H;

[0417] R 2 is optionally substituted C 2-9 Heterocyclyl, optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl, optionally substituted C 2-9 Heterocyclyl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, optionally substituted C 1-9 Heteroaryl C 1-6 Alkyl, halogen, –N(R 5 )2. –OR 5 、–CON(R 6 )2、–SO2N(R 6 )2. –SO2R 5Aor –Q–R 5B ;

[0418] R 3 is optionally substituted C 1-9 Heteroaryl or optionally substituted C 1-9 Heteroaryl C 1-6 alkyl;

[0419] Each R 4 are independently hydrogen, halogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkenyl or optionally substituted C 2-6 Alkynyl;

[0420] Each R 5 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl or –SO2R 5A ; or two R 5 Together with the atoms to which they are attached, they form an optionally substituted C 2-9 heterocyclic group;

[0421] Each R 5A are independently optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 6-10 aryl;

[0422] R 5B is hydroxy, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, –N(R 5 )2、–CON(R 6 )2、–SO2N(R 6 )2. –SO2R 5A or optionally substituted alkoxy;

[0423] Each R 6 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkoxyalkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 1-9 heteroaryl; or two R 6Together with the atoms to which they are attached, they form an optionally substituted C 2-9 heterocyclic group;

[0424] Q is optionally substituted C 2-9 Heterocyclylene, optionally substituted C 3-8 Cycloalkylene, optionally substituted C 1-9 Heteroarylene or optionally substituted C 6-10 an arylene group; and

[0425] X is hydrogen or halogen.

[0426] In some embodiments, in the compound of Formula (II), (I) or (Ib):

[0427] Each Y is independently N or CR 4 ;

[0428] R 1 is H or optionally substituted C 1-6 alkyl;

[0429] R 2 is optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl, optionally substituted C 2-9 Heterocyclyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, optionally substituted C 1-9 Heteroaryl C 1-6 Alkyl, –N(R 5 )2、–CON(R 6 )2、–SO2N(R 6 )2 or –SO2R 5A ;

[0430] R 3 is optionally substituted C 1-9 heteroaryl;

[0431] Each R 4 are independently H or optionally substituted C 1-6 alkyl;

[0432] Each R 5 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl or –SO2R 5A , where each R 5A are independently optionally substituted C 1-6Alkyl or optionally substituted C 3-8 Cycloalkyl; or two R 5 Together with the atoms to which they are attached, they form an optionally substituted C 2-9 heterocyclic group;

[0433] Each R 5A are independently optionally substituted C 1-6 Alkyl or optionally substituted C 3-8 cycloalkyl; and

[0434] Each R 6 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl or optionally substituted C 1-9 heteroaryl; or two R 6 Together with the atoms to which they are attached, they form an optionally substituted C 2-9 Heterocyclic group.

[0435] The compound of the present invention may be, for example, a compound of formula (Ia):

[0436]

[0437] or a pharmaceutically acceptable salt thereof, wherein Y, R 1 、R 2 、R 3 and R 4 As described in formula (I).

[0438] The compound of the present invention may be, for example, a compound of formula (Ib):

[0439]

[0440] or a pharmaceutically acceptable salt thereof, wherein Y, R 1 、R 2 、R 3 and R 4 As described in formula (I).

[0441] The compound of the present invention may be, for example, a compound of formula (IA):

[0442]

[0443] or a pharmaceutically acceptable salt thereof, wherein R 1 、R 2 、R 3 and R 4 As described in formula (I).

[0444] The compound of formula (IA) may be, for example, a compound of formula (IA-a):

[0445]

[0446] or a pharmaceutically acceptable salt thereof, wherein R 1 、R 2 、R 3 and R 4 As described in formula (I).

[0447] The compound of the present invention may be, for example, a compound of formula (IB):

[0448]

[0449] or a pharmaceutically acceptable salt thereof, wherein R 1 、R 2 、R 3 and R 4 As described in formula (I).

[0450] The compound of formula (IB) may be, for example, a compound of formula (IB-a):

[0451]

[0452] or a pharmaceutically acceptable salt thereof, wherein R 1 、R 2 、R 3 and R 4 As described in formula (I).

[0453] The compound of the present invention may be, for example, a compound of formula (IC):

[0454]

[0455]

[0456] or a pharmaceutically acceptable salt thereof, wherein R 1 、R 2 、R 3 and R 4 As described in formula (I).

[0457] The compound of formula (IC) may be, for example, a compound of formula (IC-a):

[0458]

[0459] or a pharmaceutically acceptable salt thereof, wherein R 1 、R 2 、R 3 and R 4 As described in formula (I).

[0460] The compound of the present invention may be, for example, a compound of formula (ID):

[0461]

[0462] or a pharmaceutically acceptable salt thereof, wherein R 1 、R 2 、R 3 and R 4 As described in formula (I).

[0463] The compound of formula (ID) may be, for example, a compound of formula (ID-a):

[0464]

[0465] or a pharmaceutically acceptable salt thereof, wherein R 1 、R 2 、R 3 and R 4 As described in formula (I).

[0466] Preferably, R 1 It is a methyl group.

[0467] In the compounds of the present invention, R 2 It can be, for example, optionally substituted C 3-8 Cycloalkyl. For example, R 2 It may be a group of formula (A):

[0468]

[0469] in

[0470] n is 0, 1, 2, or 3; and

[0471] R 7 is hydrogen, alkylsulfonyl, cyano, –CON(R A )2、-SON(R A ) 2. optionally substituted C 1-9 heteroaryl, hydroxyl or alkoxy, wherein each R A are independently H or alkyl; or two R A Together with the atoms to which they are attached, they combine to form C 2-9 Heterocyclic group.

[0472] In the compounds of the present invention, R 2 It can be, for example, optionally substituted C 1-6 Alkyl, for example, optionally substituted tert-C 3-6 Alkyl. For example, R 2 It may be a group of formula (B):

[0473]

[0474]

[0475] where R 7 is hydrogen, alkylsulfonyl, cyano, –CON(R A )2、-SON(R A ) 2. optionally substituted C 1-9 heteroaryl, hydroxyl or alkoxy, wherein each R A are independently H or alkyl; or two R A Together with the atoms to which they are attached, they combine to form C 2-9 Heterocyclic group.

[0476] In the compounds of the present invention, R 2 It can be, for example, an optionally substituted non-aromatic C 2-9 Heterocyclic group.

[0477] In the compounds of the present invention, R 2 It can be, for example:

[0478] –I, –SO2Me, –SO2Ph, –OMe, –OCH2CF3,

[0479]

[0480]

[0481] In the compounds of the present invention, R 3 It may be, for example, an optionally substituted monocyclic C 1-9 Heteroaryl. For example, R 3 It may be a group of formula (C):

[0482]

[0483] wherein A is an optionally substituted monocyclic C 1-9 Heteroaryl ring.

[0484] In some compounds of the present invention, A may be, for example, a group of formula (C1):

[0485]

[0486] where R 8 is hydrogen, halogen or optionally substituted C 1-6 alkyl.

[0487] In the compounds of the present invention, R 3 It can be, for example:

[0488]

[0489] In the compounds of the present invention, R 3 It can be, for example:

[0490]

[0491] In the compounds of the present invention, R 4 It may be, for example, hydrogen.

[0492] The compound of the present invention may be, for example, a compound listed in the following Table 1 or a pharmaceutically acceptable salt thereof.

[0493] Table 1

[0494]

[0495]

[0496]

[0497]

[0498]

[0499]

[0500]

[0501]

[0502]

[0503]

[0504] The present invention includes (where possible) individual diastereomers, enantiomers, epimers and atropisomers of the compounds disclosed herein, as well as mixtures of diastereomers and / or enantiomers thereof, including racemic mixtures. Although the specific stereochemistry disclosed herein is preferred, other stereoisomers, including diastereomers, enantiomers, epimers, atropisomers and mixtures thereof, may also be used to treat ATR-mediated diseases. Inactive or less active diastereomers and enantiomers may be useful, for example, in scientific research related to receptors and activation mechanisms.

[0505] It should be understood that certain molecules can exist in multiple tautomeric forms. Although only one tautomer may be indicated in the examples, the present invention includes all tautomers.

[0506] The invention also includes pharmaceutically acceptable salts of the compounds and pharmaceutical compositions comprising the compounds and a pharmaceutically acceptable carrier.The compounds are particularly useful, for example, in certain types of cancer and in slowing the progression of cancer once it develops in a patient.

[0507] The compounds disclosed herein can be used in pharmaceutical compositions comprising (a) a compound or a pharmaceutically acceptable salt thereof and (b) a pharmaceutically acceptable carrier. The compounds can be used in pharmaceutical compositions comprising one or more other active pharmaceutical ingredients. The compounds can also be used in pharmaceutical compositions in which a compound disclosed herein or a pharmaceutically acceptable salt thereof is the sole active ingredient.

[0508] Optical isomers-diastereomers-geometric isomers-tautomers

[0509] The compounds disclosed herein may contain, for example, one or more stereogenic centers and may exist as racemates, racemic mixtures, single enantiomers, individual diastereomers, and diastereomers and / or enantiomeric mixtures. The present invention includes all such isomeric forms of the compounds disclosed herein. It is intended that all possible stereoisomers (e.g., enantiomers and / or diastereomers) in the form of mixtures and as pure or partially purified compounds are included within the scope of the present invention (i.e., all possible combinations of stereogenic centers as pure compounds or in the form of mixtures).

[0510] Some of the compounds described herein may contain a bond that is rotationally hindered such that two separate rotamers or atropisomers can be separated and found to possess potentially advantageously different biological activities. It is intended that all possible atropisomers are included within the scope of the present invention.

[0511] Some of the compounds described herein may contain olefinic double bonds, and unless specified otherwise, are meant to include both E and Z geometric isomers.

[0512] Some of the compounds described herein may exist with different points of hydrogen attachment, known as tautomers. An example is a ketone and its enol form, known as keto-enol tautomers. Individual tautomers as well as mixtures thereof are encompassed by the present invention.

[0513] Compounds disclosed herein having one or more asymmetric centers can be separated into diastereomers, enantiomers, etc. by methods well known in the art.

[0514] Alternatively, enantiomers and other compounds with chiral centers can be synthesized by stereospecific synthesis using optically pure starting materials and / or reagents of known configuration.

[0515] Metabolites-Prodrugs

[0516] The present invention includes therapeutically active metabolites, wherein the metabolites themselves fall within the scope of the claims. The present invention also includes prodrugs, which are compounds that are converted to the claimed compounds upon or after administration to a patient. In some cases, the claimed chemical structures of the present application may themselves be prodrugs.

[0517] Isotopically enriched derivatives

[0518] The present invention includes molecules that are isotopically enriched at one or more positions within the molecule. Thus, deuterium-enriched compounds fall within the scope of the claims.

[0519] Methods for preparing the compounds of the present invention

[0520] The compounds of the present invention can be prepared using reactions and techniques known in the art as well as the reactions and techniques described herein.

[0521] Method A

[0522] The compounds of the present invention can be prepared as shown in Scheme A and described herein. Commercially available 4-cyano-7-azaindole can be hydrolyzed to the acid and esterified under standard conditions. Regiospecific chlorination at the 6-position can be achieved by oxidation of the 7-aza with an oxidizing agent (e.g., mCPBA) followed by chlorination with methanesulfonyl chloride. The indole nitrogen can be protected with a suitable protecting group (PG) such as SEM or THP. In the presence of an optionally palladium (0) or copper (I) catalyzed S N Under Ar conditions, 6-position chlorine can be replaced with appropriately substituted morpholine. Then, the ester can be derivatized by reducing to an alcohol by a suitable reducing agent (e.g., LiBH 4 or DIBAL-H), activated by forming a mesylate or iodo group and replaced with sodium methanesulfonate to form methyl sulfone. In the presence of a base and a phase-transfer catalyst, ethylene dibromide can be used to complete the cyclopropanation of the benzyl position. Then, the deprotection of azaindole obtains a key intermediate, which can be obtained by reacting the amine with an appropriate aryl iodide or heteroaryl iodide (R 3 -I) by palladium or copper catalyzed coupling to derivatize it to generate the compound of the present invention. 3 In the case of protecting groups to facilitate substitution reactions, the deprotection step may require the use of acid, base and / or fluoride conditions to provide the compounds of the present invention.

[0523] Plan A

[0524]

[0525] Method B

[0526] The compounds of the present invention can also be prepared as shown in Scheme B and described herein. Commercially available 4-chloro-7-azaindole can be activated as an affinity substitution by oxidation of the 7-aza group and methylation with dimethyl sulfate. Addition of an appropriately substituted morpholine followed by in situ elimination of methanol affords the 6-morpholinoazaindole. Aryl or heteroaryl groups (R) can then be added via copper-mediated arylation. 3 Depending on the nature of the heteroaryl group, it may be necessary to keep the protecting group in place prior to this coupling reaction. The 4-chloro group can be derivatized in a variety of different ways to provide compounds of the present invention. For example, palladium or copper mediated coupling can be used to obtain a 4-chloro group in R 2 Alternatively, if R 2 For substituted amine, then in S N Chloride displacement may occur under Ar conditions or under Buchwald-type coupling conditions. Sulfides may also be used to displace the 4-chloro group, which can be optionally oxidized to form a sulfone. 3 In the case of protecting groups, the deprotection step may require the use of acidic, basic and / or fluoride conditions to provide the compounds of the present invention.

[0527] Plan B

[0528]

[0529] Method C

[0530] The compounds of the present invention can be prepared from key intermediate A, which can be prepared as shown in Scheme C and described herein. Protected 5-aminopyrazoles can be prepared by condensing the appropriate aldehyde with hydrazine hydrate and acrylonitrile. This is then condensed with a dialkyl oxaloacetate in refluxing acetic acid to produce the substituted azaindazole. Activation of the hydroxyl group with trifluoromethanesulfonic anhydride followed by nucleophilic displacement with a morpholine derivative produces key intermediate A.

[0531] Plan C

[0532]

[0533] Method D

[0534] Intermediate A can be converted to compounds of the invention by converting the alkyl ester into a radical as shown in Scheme D and described herein. For example, intermediate A is treated with a reducing group (e.g., DIBAL-H, LiBH 4 or NaBH 4 ) to generate a primary alcohol, which can be activated with reagents such as MsCl or TsCl. Displacement of the leaving group with an alkyl sulfonate provides a benzyl sulfone, which can be alkylated with an alkyl halide under basic conditions. Deprotection and arylation are then performed as described in Method A to provide compounds of the invention.

[0535] Plan D

[0536]

[0537] Method E

[0538] The compounds of the present invention can be prepared from intermediate A as shown in Scheme E and described herein. Intermediate A can be treated with an alkylating agent such as methylmagnesium bromide to convert the alkyl ester group to a tertiary alcohol. This material can be deprotected and arylated as described in Method A to provide the compounds of the present invention.

[0539] Plan E

[0540]

[0541] Method F

[0542] The compounds of the present invention can be prepared by intermediate A as shown in Scheme F and as described herein. Intermediate A can be deprotected under acidic conditions and then arylated under copper catalysis. The ester group can then be reduced and optionally activated with an agent (such as methanesulfonyl chloride or toluenesulfonyl chloride) in the presence of lithium iodide. Sodium cyanide is then used to replace the aryl acetonitrile, an exemplary compound of the present invention. This type of compound can be alkylated with an alkyl halide in the presence of a base to provide a dialkylated aryl acetonitrile, which is a compound of the present invention. If RX is a dihaloalkane, a corresponding cyclic derivative will be formed in which two R groups form a 3-7 membered ring. Alternatively, primary alcohols can be coupled to cyanohydrins under Mitsunobu conditions to directly obtain nitrile derivatives. Nitriles can also be hydrolyzed to primary amides under alkaline conditions or in the presence of a metal catalyst to provide the compounds of the present invention.

[0543] Plan F

[0544]

[0545] Method G

[0546] The compounds of the present invention can be prepared as shown in Scheme G and described herein. N-protected 5,7-dichloro-3H-imidazo[4,5-b]pyridine can be treated with an arylboronic acid under palladium catalysis to install the appropriate R 2 In the presence of S optionally catalyzed by palladium (0) or copper (I) N Under Ar conditions, the second chloro substituent can be replaced with an appropriately substituted morpholine. Removal of the protecting group, followed by arylation, as described in Method A provides compounds of the present invention.

[0547] Plan G

[0548]

[0549] Method H

[0550] Compounds of the present invention can be prepared as shown in Scheme H and described herein. An alkyl Grignard reagent is added to the protected azaindole described in Method A to form a tertiary alcohol. Removal of the protecting group on the azaindole, followed by arylation, as described in Method A, provides compounds of the present invention.

[0551] Plan H

[0552]

[0553] Method I

[0554] The compounds of the present invention can be prepared from intermediate A as shown in Scheme 1 and described herein. The ester of intermediate A can be hydrolyzed to the corresponding acid and then treated with an amide using a suitable coupling reagent (e.g., EDC or HATU) under amide forming conditions. Deprotection of the azaindole then provides the key intermediate, which can be synthesized by reacting the intermediate with an appropriate aryl or heteroaryl iodide (R 3 -I) by palladium or copper catalyzed coupling to derivatize it to generate the compound of the present invention. 3 In the case of protecting groups to facilitate substitution reactions, the deprotection step may require the use of acid, base and / or fluoride conditions to provide the compounds of the present invention.

[0555] Plan I

[0556]

[0557] Method J

[0558] The compounds of the present invention can be prepared as shown in Scheme J and described herein. The ester intermediate of Method F can be hydrolyzed to the corresponding acid under standard conditions (e.g., aqueous LiOH or NaOH). This acid can be coupled with hydrazine using an activating agent (e.g., CDI or EDC) to generate an acylhydrazine. This can be formylated (R = H) or acylated (R = alkyl, aryl) to give a diacylhydrazine, which can be cyclized to give the compounds of the present invention. If cyclization is performed with POCl3, an oxadiazole is generated. If cyclization is performed with Lawesson reagent, a thiadiazole is generated. In R 3 In the case of protecting groups to facilitate these cyclizations, the deprotection step may require the use of acid, base and / or fluoride conditions to provide the compounds of the present invention.

[0559] Plan J

[0560]

[0561] Method K

[0562] The compounds of the present invention can be prepared as shown in Scheme K and described herein. N Under Ar conditions, 5-chloro-3H-[1,2,3]triazolo[4,5-b]pyridine can be replaced with an appropriately substituted morpholine. 3 -I) to derivatize the triazole nitrogen to install the appropriate R 3 Group. Regiospecific chlorination at position 7 can be achieved by 3-aza oxidation with an oxidizing agent (e.g., mCPBA) followed by chlorination with methanesulfonyl chloride. The 7-chloro group can be derivatized in a variety of different ways to provide compounds of the invention. For example, palladium or copper mediated coupling can be used to provide a regiospecific chlorination at position R. 2 Alternatively, if R 2 For substituted amine, then in S N Chloride displacement may occur under Ar conditions or under Buchwald-type coupling conditions. Sulfides may also be used to displace the 4-chloro group, which can be optionally oxidized to form a sulfone. 3 In the case of protecting groups to facilitate these cyclizations, the deprotection step may require the use of acid, base and / or fluoride conditions to provide the compounds of the present invention.

[0563] Plan K

[0564]

[0565] Method L

[0566] 2,6-Difluoro-4-iodopicolinyl can be formylated by metalation with a strong base and trapping with a suitable formylation agent such as ethyl formate. The resulting aldehyde can be condensed with an appropriately substituted pyrazole hydrazine to form the corresponding hydrazine, which can be cyclized to the azaindazole by heating to elevated temperatures. N Displacement of the fluorine substituent on the azaindazole by an appropriately substituted morpholine under Ar conditions provides key intermediate B. Protection of the pyrazole NH with a suitable protecting group affords key intermediate C, typically as a mixture of N-protected regioisomers.

[0567] Plan L

[0568]

[0569] Method M

[0570] The compounds of the present invention can be prepared as shown in Scheme M and described herein. The key intermediate C can be treated with an arylboronic acid under palladium catalysis to install the appropriate R 2 The protective group is removed to obtain the compound of the present invention.

[0571] Plan M

[0572]

[0573] Method N

[0574] The compounds of the present invention can be prepared as shown in Scheme N and described herein. The key intermediate C can be metalated with an alkyl lithium or alkyl magnesium halide to generate an aryl lithium or aryl magnesium bromide, which can be added to a suitable ketone to generate a tertiary alcohol derivative. In the case where the ketone contains one or more deuterium-enriched positions, the resulting product will also be isotopically deuterium-enriched. Removal of the protecting group provides the compounds of the present invention. Alternatively, this chemistry can be performed using the key intermediate B in the absence of a protecting group to directly provide the compounds of the present invention.

[0575] Plan N

[0576]

[0577] Method O

[0578] The compounds of the present invention can be prepared as shown in Scheme O and described herein. The key intermediate C can be treated with a carbon-, nitrogen-, or sulfur-based nucleophile to displace the iodide group and install the appropriate R 2 The protective group is removed to obtain the compound of the present invention.

[0579] Plan O

[0580]

[0581] Method P

[0582] Compounds of the present invention can be prepared as shown in Scheme P and described herein. Treatment with a brominating agent can introduce a bromine atom into the 3-position of the azaindazole ring, thereby providing compounds of the present invention. Treatment with an alkyl, vinyl, or arylstannane under Pd catalysis provides compounds of the present invention.

[0583] Plan P

[0584]

[0585] Method Q

[0586] Compounds of the present invention can be prepared as shown in Scheme Q and described herein. 2,6-Difluoro-4-iodonicotinaldehyde can be cyclized with hydrazine to form 6-fluoro-4-iodo-1H-pyrazolo[3,4-b]pyridine, which can then be reacted with a substituted morpholine. N Ar reaction. The intermediate can be reacted with 2-cyanopropane for a second S reaction under alkaline conditions. N Ar reaction to obtain a disubstituted azaindazole ring system. Ullmann coupling on the NH of the azaindazole followed by deprotection provides the compounds of the present invention.

[0587] Plan Q

[0588]

[0589] Method R

[0590] The compounds of the present invention can be prepared as shown in Scheme R and described herein. Intermediate C can be converted to a boronate reagent by treatment with bis(pinacolato)diboron, a palladium catalyst, and a base. This boronate can then be treated with an aryl halide or triflic acid under palladium catalysis to install the appropriate R 2 The protective group is removed to obtain the compound of the present invention.

[0591] Plan R

[0592]

[0593] Method S

[0594] The compounds of the present invention can be prepared as shown in Scheme R and described herein. Intermediate C can be chlorinated at the 5-position. The resulting intermediate can be treated with an aryl boronic acid or aryl boronic ester under palladium catalysis to install the appropriate R 2 The protective group is removed to obtain the compound of the present invention.

[0595] Plan S

[0596]

[0597] Method T

[0598] The compounds of the present invention can be prepared as shown in Scheme T and described herein. 2,6-difluoro-4-iodopyridine-3-carboxaldehyde can be treated with substituted morpholines to selectively displace the 6-fluoro substituent. Oxidation of the aldehyde is performed, followed by hydrazide formation with an appropriately protected heterocyclic hydrazine. The hydrazide can be cyclized under basic conditions to form an iodopyrazolopyridinone ring system. This intermediate can react with carbon, oxygen, or sulfur nucleophiles to form a cyclic iodine ring. N Ar substitution reactions, or preferably palladium catalysis, can be treated with arylboronic acids to install the appropriate R 2 Subsequent removal of the protecting group provides the compounds of the present invention.

[0599] Plan T

[0600]

[0601] Treatment

[0602] The compounds of the present invention may be used to treat an ATR kinase-mediated disease or condition in a subject by administering to the subject an effective amount of the compound of the present invention.

[0603] The symptom of the disease or condition can be excessive cell proliferation. For example, the disease or condition can be cancer. The cancer can be, for example, an epithelial carcinoma, a sarcoma, an adenocarcinoma, a lymphoma, a leukemia, or a melanoma. The cancer can be, for example, a solid tumor.

[0604] Non-limiting examples of cancer include prostate cancer, breast cancer, ovarian cancer, multiple myeloma, brain cancer, glioma, lung cancer, salivary gland cancer, gastric cancer, thymic epithelial cancer, thyroid cancer, leukemia, melanoma, lymphoma, stomach cancer, pancreatic cancer, kidney cancer, bladder cancer, colon cancer, and liver cancer.

[0605] Non-limiting examples of epithelial cancers include thyroid encephaloid carcinoma, familial thyroid encephaloid carcinoma, acinar carcinoma, acinar epithelial carcinoma, adenoid cystic epithelial carcinoma, adenomatous epithelial carcinoma, adrenal cortical carcinoma, alveolar epithelial carcinoma, alveolar cell carcinoma, basal cell carcinoma, basaloid epithelial carcinoma, basosquamous cell carcinoma, bronchioalveolar carcinoma, bronchiolar carcinoma, bronchial carcinoma, medullary carcinoma, cholangiocarcinoma, choriocarcinoma, colloid carcinoma, comedocarcinoma, and main Epithelial carcinoma, cribriform epithelial carcinoma, armor-like epithelial carcinoma, cutaneous epithelial carcinoma, columnar epithelial carcinoma, columnar cell epithelial carcinoma, ductal epithelial carcinoma, sclerosing epithelial carcinoma, embryonal epithelial carcinoma, brain-like epithelial carcinoma, epidermoid epithelial carcinoma, adenoid epithelial carcinoma, exophytic epithelial carcinoma, ulcerative epithelial carcinoma, fibrocarcinoma, colloid epithelial carcinoma, gelatinous epithelial carcinoma, giant cell epithelial carcinoma, glandular epithelial carcinoma, granular cell epithelial carcinoma, pilostromal epithelial carcinoma, hematogenous epithelial carcinoma, hepatocellular carcinoma, Schüttel cell epithelial carcinoma, hyalinoid epithelial carcinoma, adrenaloid epithelial carcinoma, infantile embryonal carcinoma, Carcinoma in situ, intraepidermal carcinoma, intraepithelial carcinoma, Klebsiella pneumoniae carcinoma, Kurtschitzky cell carcinoma, large cell carcinoma, lenticular carcinoma, lenticular carcinoma, lipomatous carcinoma, lymphoepithelial carcinoma, medullary carcinoma, medullary carcinoma, melanotic carcinoma, soft epithelial carcinoma, mucinous carcinoma, mucinous cell carcinoma, mucoepidermoid carcinoma, mucinous epithelial carcinoma, myxomatous carcinoma, myxomatous carcinoma, nasopharyngeal carcinoma, oat cell carcinoma, ossifying carcinoma, osteoid carcinoma, papillary carcinoma, periportal carcinoma, preinvasive carcinoma, prickle cell carcinoma, mucus cell carcinoma, renal cell carcinoma, reserve cell carcinoma, sarcomatoid carcinoma, Schneider's carcinoma, scirrhous carcinoma, scrotal carcinoma, signet ring cell carcinoma, simple carcinoma, small cell carcinoma, potato carcinoma, spheroid cell carcinoma, spindle cell carcinoma, spongiform carcinoma, squamous cell carcinoma, squamous cell carcinoma, string carcinoma, telangiectatic carcinoma, angioectatic carcinoma, transitional cell carcinoma, nodular carcinoma, tubercular carcinoma, verrucous carcinoma, and villous carcinoma.

[0606] Non-limiting examples of sarcomas include chondrosarcoma, fibrosarcoma, lymphosarcoma, melanosarcoma, myxosarcoma, osteosarcoma, Albernethy's sarcoma, liposarcoma, liposarcoma, alveolar soft part sarcoma, ameloblastic sarcoma, botryoid sarcoma, chloroma sarcoma, choriocarcinoma, embryonal sarcoma, Williams' tumor sarcoma, endometrial sarcoma, stromal sarcoma, Ewing's sarcoma, fascial sarcoma, fibroblastic sarcoma, giant cell sarcoma, granulocytic sarcoma, Hodgkin's sarcoma, idiopathic multiple pigmented hemorrhagic sarcoma, B-cell immunoblastic sarcoma, T-cell immunoblastic sarcoma, Janssen's sarcoma, Kaposi's sarcoma, Kupffer cell sarcoma, angiosarcoma, leukemic sarcoma, malignant mesenchymal sarcoma, parosteal sarcoma, reticulum cell sarcoma, Rous' sarcoma, serous cystic sarcoma, synovial sarcoma, and telangiectatic sarcoma.

[0607] Non-limiting examples of leukemias include acute non-lymphocytic leukemia, chronic lymphocytic leukemia, acute myeloid leukemia, chronic myeloid leukemia, acute promyelocytic leukemia, adult T-cell leukemia, non-leukemic leukemia, leukemic leukemia, basophilic leukemia, blast cell leukemia, bovine leukemia, chronic myelocytic leukemia, leukemia cutis, embryonal leukemia, eosinophilic leukemia, Gross' leukemia, hairy cell leukemia, hematopoietic leukemia, hematoblastic leukemia, histiocytic leukemia, stem cell leukemia, acute monocytic leukemia, leukopenic leukemia, Leukemia, lymphocytic leukemia, lymphoblastic leukemia, lymphocytic leukemia, lymphoblastic leukemia, lymphoid leukemia, lymphosarcoma cell leukemia, mast cell leukemia, megakaryocytic leukemia, myeloblastic leukemia, monocytic leukemia, myeloblastic leukemia, myeloid leukemia, myeloid granulocytic leukemia, myelomonocytic leukemia, Negley's leukemia, plasma cell leukemia, multiple myeloma, plasma cell leukemia, promyelocytic leukemia, Liddle cell leukemia, Schilling's leukemia, stem cell leukemia, subleukemic leukemia and undifferentiated cell leukemia.

[0608] Non-limiting examples of melanoma include acral-lentiginous melanoma, amelanotic melanoma, benign juvenile melanoma, Claudemann melanoma, S91 melanoma, Harrington-Persson melanoma, juvenile melanoma, lentigo maligna melanoma, malignant melanoma, nodular melanoma, subungual melanoma, and superficial spreading melanoma.

[0609] The compounds of the present invention can be administered by a route selected from the group consisting of oral, sublingual, buccal, transdermal, intradermal, intramuscular, parenteral, intravenous, intraarterial, intracranial, subcutaneous, intraorbital, intraventricular, intraspinal, intraperitoneal, intranasal, inhalation, intratumoral, and topical administration.

[0610] The methods of the present invention may include the step of identifying the subject as a candidate for ATR inhibitor therapy. For example, the subject may be identified as a candidate for ATR inhibitor therapy by determining: (i) whether the subject has a cancer with a defect in the ATM signaling cascade; (ii) whether the subject has a cancer, cancer cell, or cell with a genetic abnormality that expresses a cancer driver gene or oncogene; (iii) whether the subject has a cancer, cancer cell, or cell with one or more defects in proteins and genes involved in base excision repair; (iv) whether the subject has a cancer with a defect in a protein or gene involved in homologous recombination; (v) whether the subject has a cancer with a defect in a protein or gene associated with sensitivity to ATR inhibitors or genetic perturbations of ATR; or (vi) whether the subject has a cancer with a genetic or protein feature associated with sensitivity to ATR inhibitors.

[0611] The compounds, compositions, and methods described herein can be used to treat a subject suffering from a cancer in which the ATM signaling cascade is abnormal. For example, the abnormality in the ATM signaling cascade can be, for example, altered expression or activity of one or more of the following proteins / genes, including, but not limited to, ATM, p53, CHK2, MRE11, RAD50, NBS1, 53BP1, MDC1, H2AX, MCPH1 / BRIT1, CTIP, and SMC1. An abnormality in ATM signaling can be identified by a change in CHK2 phosphorylation of 20% or greater, which can indicate an abnormality in the ATM signaling cascade, or by an inability of cells to arrest in the G1 and S phases of the cell cycle in response to double-stranded DNA breaks.

[0612] The compounds, compositions and methods described can be used to treat cancer, cancer cells or subjects with cells that have abnormal expression of cancer driver protein oncogenes. For example, cancer cells may have genetic abnormalities that result in altered expression or activity of one or more of the following proteins / genes, including but not limited to KRAS, NRAS, HRAS, BRAF, MYC, MOS, E2F, CDC25A, CDC4, CDK2, CCNE1, CCNA1, DNAPK, APOBEC3, CDC6 and RB1.

[0613] The compounds, compositions, and methods described herein can be used to treat a subject having cancer, cancer cells, or cells with one or more abnormalities in proteins or genes involved in base excision repair. For example, the abnormality in a base excision repair protein can be an alteration in the expression of one or more of the following proteins / genes, including but not limited to UNG, SMUG1, MBD4, TDG, OGG1, MYH, NTH1, MPG, NEIL1, NEIL2, NEIL3 (DNA glycosylases); APE1, APEX2 (AP endonucleases); LIG1, LIG3 (DNA ligases I and III); XRCC1 (LIG3-affiliated); PNK, PNKP (polynucleotide kinases and phosphatases); PARP1, PARP2 (poly(ADP-ribose) polymerases); PolB, PolG (polymerases); FEN1 (endonuclease), or Aprataxin.

[0614] The compounds, compositions, and methods described herein can be used to treat a subject having cancer, cancer cells, or cells that have one or more abnormalities in proteins or genes involved in homologous recombination. For example, the abnormality in homologous recombination can be altered expression or activity of one or more of the following proteins / genes, including but not limited to: BRCA1, BRCA2, MRE11, RAD50, RAD51, RAD52, RAD54L, NBN, ATM, H2AX, PALB2, RPA, BRIP1, BARD1, ATR, ATRX, CHK1, CHK2, MDM2, MDM4, FANCA, FANCC, FANCD2, FANCE, FANCF, FANCG, and FANCL.

[0615] The compounds, compositions and methods described can be used to treat a subject having cancer, cancer cells or cells that have one or more abnormalities in proteins or genes associated with sensitivity to ATR inhibitors or genetic perturbations of the ATR signaling pathway. For example, a genetic abnormality associated with sensitivity to ATR inhibitors or genetic perturbations of ATR can be an altered expression or activity of one or more of the following proteins / genes, including but not limited to: ATR, CHK1, ERCC1, ERCC2, RAD17, RAD1, RAD9A, ERCC4, ATM, FANCE, GCP3, IDH1, PALB2, PMS2, ARID1A, SLX4, MSH4, RRM2, POLA, POLD1, RRM1, WEE1, CLSPN, PGBD5, XRCC1, XRCC3, XRCC5, KDM5D, CDC6, SLFN11, TLK1 and TLK2

[0616] Many methods are known in the art for determining whether a tumor has abnormalities in proteins or genes. For example, sequencing of the genomic DNA or mRNA products of each specified gene (e.g., UNG, PARP1, or LIG1) can be performed on a tumor sample to determine whether there are mutations that are expected to regulate the function or expression of the gene product. In addition to mutational inactivation, tumor cells can also regulate genes by methylating the promoter region, resulting in reduced gene expression. This is most commonly assessed using methylation-specific polymerase chain reaction (PCR) to quantify the methylation level of the promoter of the base excision repair gene of interest. Assays for DNA repair gene promoter methylation are commercially available.

[0617] The expression level of a gene can be assessed by directly quantifying the levels of mRNA and protein products of each gene using standard techniques (e.g., quantitative reverse transcriptase-coupled polymerase chain reaction (RT-PCR), RNA-Seq for gene expression, and immunohistochemistry (IHC) for protein expression. Gene amplification or deletion, which results in abnormal overexpression or underexpression of a protein (respectively), can also be measured by FISH (fluorescence in situ hybridization) analysis using probes specific for the gene of interest.

[0618] The methods described above (gene sequence, promoter methylation, and mRNA expression) can also be used to characterize the status (e.g., expression or mutation) of other genes or proteins of interest, such as tumor-expressed DNA-damaging oncogenes or defects in cellular DNA repair pathways.

[0619] The compounds, compositions, and methods described herein can be used to treat subjects suffering from cancers whose genetic characteristics are associated with sensitivity to ATR inhibitors. In some embodiments, the genetic characteristics are one or more of the following: cells having an alternative mechanism of telomere lengthening (ALT) characterized by cell transformation or protein expression in the absence of HTERT and / or ATRX mRNA; the presence of C-loops or partially double-stranded and circular extrachromosomal telomeric repeats (ECTRs); the presence of telomeres of varying lengths and positive staining for ALT-associated promyelocytic leukemia (PML) nucleosomes (APBs).

[0620] There are several methods for determining ALT signatures in cells. Non-limiting examples of these methods include: HTERT and ATRX expression can be measured by Western blot, immunohistochemistry (IHC), or by mRNA expression (qRT-PCR) analysis; the presence of C-loops can be measured in PCR analysis; the presence of telomeres of varying lengths can be measured by telomere restriction fragment analysis (TRF), which measures the heterogeneous range of telomere lengths in a cell population using the length distribution of terminal restriction fragments; and staining for the presence of APB can be accomplished using IHC by co-staining with probes for telomeric DNA and PML protein.

[0621] Pharmaceutical composition

[0622] The compounds used in the methods described herein are preferably formulated into pharmaceutical compositions for administration to human subjects in a biocompatible form suitable for in vivo administration. Pharmaceutical compositions generally comprise a compound as described herein and a pharmaceutically acceptable excipient. Certain pharmaceutical compositions may comprise one or more additional pharmaceutically active agents as described herein.

[0623] The compounds described herein may also be used in the form of free bases; in the form of salts, zwitterions, solvates; or as prodrugs or pharmaceutical compositions thereof. All forms are within the scope of the present invention. As will be appreciated by those skilled in the art, the compounds, their salts, zwitterions, solvates, prodrugs or pharmaceutical compositions may be administered to the patient in a variety of forms, depending on the route of administration selected. The compounds used in the methods described herein may be administered, for example, orally, parenterally, buccally, sublingually, nasally, rectally, by patch, pump or transdermal administration, and pharmaceutical compositions may be formulated accordingly. Parenteral administration includes intravenous, intraperitoneal, subcutaneous, intramuscular, transepithelial, nasal, intrapulmonary, intrathecal, rectal and topical administration. Parenteral administration may be performed by continuous infusion over a selected period of time.

[0624] For human use, the compounds of the present invention can be administered alone or in admixture with a pharmaceutical carrier selected with respect to the intended route of administration and standard pharmaceutical practice. Therefore, the pharmaceutical compositions used according to the present invention can be formulated in a conventional manner using one or more physiologically acceptable carriers comprising excipients and adjuvants that facilitate processing of the compounds of the present invention into pharmaceutically acceptable preparations.

[0625] The present invention also includes pharmaceutical compositions that may contain one or more pharmaceutically acceptable carriers. When making the pharmaceutical compositions of the present invention, the active ingredient is typically mixed with an excipient, diluted by the excipient or enclosed in such a carrier in the form of, for example, a capsule, pouch, paper, or other container. When the excipient acts as a diluent, it can be a solid, semisolid, or liquid material (normal saline) that acts as a vehicle, carrier, or medium for the active ingredient. Thus, the composition can be in the form of tablets, powders, lozenges, sachets, cachets, elixirs, suspensions, emulsions, solutions, syrups, and soft and hard gelatin capsules. As is known in the art, the type of diluent can vary depending on the intended route of administration. The resulting composition may contain additional agents, such as preservatives.

[0626] Excipient or carrier is selected based on mode of administration and approach. Suitable pharmaceutical carriers and pharmaceutical necessities for pharmaceutical preparations are described in Remington: The Science and Practice of Pharmacy, 21st edition, Gennaro, ed., Lippincott Williams & Wilkins (2005) and USP / NF (United States Pharmacopoeia / National Formulary), a reference well known in the art. Examples of suitable excipients include lactose, dextrose, sucrose, sorbitol, mannitol, starch, gum arabic, calcium phosphate, alginate, tragacanth gum, gelatin, calcium silicate, microcrystalline cellulose, polyvinyl pyrrolidone, cellulose, water, syrup and methylcellulose. Preparations may additionally include: lubricants, such as talc, magnesium stearate and mineral oil; wetting agents; emulsifiers and suspending agents; preservatives, such as methyl hydroxybenzoate and propyl hydroxybenzoate; sweeteners; and flavorings. Other exemplary excipients are described in Handbook of Pharmaceutical Excipients, 6th edition, Rowe et al., eds., Pharmaceutical Press (2009).

[0627] These pharmaceutical compositions can be manufactured in a conventional manner, for example, by conventional mixing, dissolving, granulating, making dragees, grinding, emulsifying, encapsulating, embedding or lyophilizing processes. Methods for making formulations well known in the art are found in, for example, Remington: The Science and Practice of Pharmacy, 21st edition, Gennaro ed., Lippincott Williams & Wilkins (2005) and Encyclopedia of Pharmaceutical Technology, J. Swarbrick and J. C. Boylan ed., 1988-1999, Marcel Dekker, New York. The correct formulation depends on the selected route of administration. The formulations and preparations of such compositions are well known to those skilled in the art of pharmaceutical formulation. When preparing the formulation, the active compound can be ground to provide an appropriate particle size before combining with other ingredients. If the active compound is substantially insoluble, it can be ground to a particle size of less than 200 mesh. If the active compound is substantially water-soluble, the particle size can be adjusted by grinding to provide a substantially uniform distribution in the formulation, for example, about 40 mesh.

[0628] dose

[0629] The dosage of the compound used in the methods described herein, or a pharmaceutically acceptable salt or prodrug thereof, or a pharmaceutical composition thereof, can vary depending on many factors, such as: the pharmacodynamic properties of the compound; the mode of administration; the age, health, and weight of the recipient; the nature and extent of symptoms; the frequency of treatment and the type of concurrent treatment (if any); and the clearance rate of the compound in the animal to be treated. One skilled in the art can determine the appropriate dosage based on the above factors. The compound used in the methods described herein can be initially administered at an appropriate dosage, which can be adjusted as needed based on clinical response. In general, a suitable daily dose of the compound of the invention will be the lowest dose effective to produce a therapeutic effect. Such an effective dosage will generally depend on the factors described above.

[0630] The compounds of the present invention can be administered to the patient in a single dose or multiple doses. When multiple doses are administered, the dosage can be separated from each other by, for example, 1-24 hours, 1-7 days, 1-4 weeks, or 1-12 months. The compound can be administered according to a schedule or can be administered without a predetermined schedule. For example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 times a day; every 2 days, every 3 days, every 4 days, every 5 days, or every 6 days; 1, 2, 3, 4, 5, 6, or 7 times a week; 1, 2, 3, 4, 5, or 6 times a month; or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 times a year. It should be understood that for any particular subject, the specific dosage regimen should be adjusted over time according to the professional judgment of the individual who needs to administer or supervise the administration of the composition.

[0631] Although the attending physician ultimately decides the appropriate amount and dosage regimen, an effective amount of the compounds of the present invention may be, for example, a total daily dose of any compound described herein, for example, between 0.05 mg and 3000 mg. Alternatively, the amount of the dosage can be calculated using the patient's weight. Such dosage ranges may include, for example, between 10-1000 mg (e.g., 50-800 mg). In some embodiments, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950 or 1000 mg of compound is administered.

[0632] In the method of the present invention, the time period over which multiple doses of the compounds of this invention are administered to a patient can vary. For example, in some embodiments, the dosage of the compounds of this invention is administered to a patient over a period of 1-7 days, 1-12 weeks, or 1-3 months. In some embodiments, the compound is administered to a patient over a period of, for example, 4-11 months or 1-30 years. In some embodiments, the compound is administered to a patient at the onset of symptoms. In any of these embodiments, the amount of the compound administered can vary over the administration period. When the compound is administered daily, it can be administered, for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 times a day.

[0633] preparation

[0634] Using any of the methods described herein, compounds identified as being able to treat any of the conditions described herein can be administered to a patient or animal in unit dosage form together with a pharmaceutically acceptable diluent, carrier, or excipient. Compounds for such therapy can be produced and isolated by any standard technique known in the art of pharmaceutical chemistry. Conventional pharmaceutical practice can be used to provide suitable formulations or compositions to administer the identified compounds to a patient suffering from a disease or condition. Administration can be initiated before the patient has symptoms.

[0635] Exemplary routes of administration for a compound of the invention (e.g., a compound of the invention) or a pharmaceutical composition thereof include oral, sublingual, buccal, transdermal, intradermal, intramuscular, parenteral, intravenous, intraarterial, intracranial, subcutaneous, intraorbital, intraventricular, intraspinal, intraperitoneal, intranasal, inhalation, and topical administration. The compound is ideally administered with a pharmaceutically acceptable carrier. Pharmaceutical formulations of the compounds described herein formulated for treating the conditions described herein are also part of the present invention.

[0636] Preparations for oral administration

[0637] Pharmaceutical compositions contemplated by the present invention include those formulated for oral administration ("oral dosage forms"). Oral dosage forms can be in the form of, for example, tablets, capsules, liquid solutions or suspensions, powders, liquid or solid crystals, which contain the active ingredient mixed with non-toxic pharmaceutically acceptable excipients. These excipients can be, for example, inert diluents or fillers (e.g., sucrose, sorbitol, sugar, mannitol, microcrystalline cellulose, starch (including potato starch), calcium carbonate, sodium chloride, lactose, calcium phosphate, calcium sulfate, or sodium phosphate); granulating and disintegrants (e.g., cellulose derivatives (including microcrystalline cellulose), starch (including potato starch), cross-linked sodium carboxymethylcellulose, alginates, or alginic acid); binders (e.g., sucrose, glucose, sorbitol, gum arabic, alginic acid, sodium alginate, gelatin, starch, pregelatinized starch, microcrystalline cellulose, magnesium aluminum silicate, sodium carboxymethylcellulose, methylcellulose, hydroxypropyl methylcellulose, ethylcellulose, polyvinyl pyrrolidone, or polyethylene glycol); and lubricants, glidants, and anti-adherents (e.g., magnesium stearate, zinc stearate, stearic acid, silicon dioxide, hydrogenated vegetable oils, or talc). Other pharmaceutically acceptable excipients may be colorants, flavorings, plasticizers, humectants, buffers, and the like.

[0638] Formulations for oral administration may also be presented as chewable tablets, hard gelatin capsules (where the active ingredient is mixed with an inert solid diluent (e.g., potato starch, lactose, microcrystalline cellulose, calcium carbonate, calcium phosphate or kaolin)) or soft gelatin capsules (where the active ingredient is mixed with water or an oil medium (e.g., peanut oil, liquid paraffin or olive oil). Powders, granules and pills can be prepared using the ingredients mentioned above under tablets and capsules in a conventional manner using, for example, a mixer, fluidized bed equipment or spray drying equipment.

[0639] The controlled release formulation for oral use can be constructed to release the active drug by controlling the dissolution and / or diffusion of the active drug substance. Any of a plurality of strategies can be adopted to obtain a curve of controlled release and target plasma concentration relative to time. In one example, controlled release is obtained by appropriately selecting various formulation parameters and ingredients (including, for example, various types of controlled release compositions and coatings). Examples include single or multiple unit tablets or capsule compositions, oil solutions, suspensions, emulsions, microcapsules, microspheres, nanoparticles, patches, and liposomes. In some embodiments, the composition comprises a biodegradable, pH, and / or temperature-sensitive polymer coating.

[0640] Dissolving or diffusion controlled release can be achieved by tablets, capsules, pills or granular preparations of suitable coating compounds or by incorporating compound into suitable matrix.Controlled release coating can include coating materials mentioned above and / or such as shellac, beeswax, sugar wax, castor wax, carnauba wax, stearyl alcohol, glyceryl monostearate, glyceryl distearate, glyceryl palmitostearate, ethylcellulose, acrylic resin, dl-polylactic acid, cellulose acetate butyrate, polyvinyl chloride, polyvinyl acetate, vinyl pyrrolidone, polyethylene, polymethacrylate, methyl methacrylate, 2-hydroxy methylacrylate, methacrylate hydrogel, 1,3-butylene glycol, ethylene glycol methacrylate and / or polyethylene glycol.In controlled release matrix preparation, matrix material can also include such as hydrated methylcellulose, carnauba wax and stearyl alcohol, carbomer 934, silicone, tristearin, methyl acrylate-methyl methacrylate, polyvinyl chloride, polyethylene and / or halogenated fluorocarbon.

[0641] Liquid forms in which the compounds and compositions of the invention can be incorporated for oral administration include aqueous solutions, suitably flavored syrups, aqueous or oily suspensions, and emulsions flavored with edible oils (e.g., cottonseed oil, sesame oil, coconut oil, or peanut oil), as well as elixirs and similar pharmaceutical vehicles.

[0642] Preparations for parenteral administration

[0643] The compounds described herein for use in the methods of the present invention can be administered as described herein in pharmaceutically acceptable parenteral (e.g., intravenous or intramuscular) formulations. Pharmaceutical formulations can also be administered parenterally (intravenously, intramuscularly, subcutaneously, etc.) in dosage forms or formulations containing conventional non-toxic pharmaceutically acceptable carriers and adjuvants. Specifically, formulations suitable for parenteral administration include: aqueous and non-aqueous sterile injection solutions, which may contain antioxidants, buffers, antibacterial agents, and solutes that make the formulation isotonic with the blood of the intended recipient; and aqueous and non-aqueous sterile suspensions, which may contain suspending agents and thickening agents. For example, to prepare such compositions, the compounds of the present invention can be dissolved or suspended in a liquid vehicle that is acceptable for parenteral administration. Acceptable vehicles and solvents that can be used are water (adjusted to a suitable pH by adding an appropriate amount of hydrochloric acid, sodium hydroxide, or a suitable buffer), 1,3-butanediol, Ringer's solution, and isotonic sodium chloride solution. Aqueous formulations may also contain one or more preservatives, such as methylparaben, ethylparaben, or n-propylparaben.Additional information on parenteral formulations can be found, for example, in the United States Pharmacopoeia-National Formulary (USP-NF), which is incorporated herein by reference.

[0644] Parenteral formulations can be any of the five general types of preparations identified by the USP-NF as suitable for parenteral administration:

[0645] (1) “Drug injection”: a liquid preparation of a drug substance (e.g., a compound of the present invention) or its solution;

[0646] (2) "Injectables": a drug substance (e.g., a compound of the present invention) in the form of a dry solid that is to be combined with an appropriate sterile vehicle for parenteral administration in the form of a pharmaceutical injection;

[0647] (3) “Drug injectable emulsion”: a liquid preparation of a drug substance (e.g., a compound of the present invention) dissolved or dispersed in a suitable emulsion medium;

[0648] (4) "Drug injectable suspension": a liquid preparation of a drug substance (e.g., a compound of the present invention) suspended in a suitable liquid medium; and

[0649] (5) "Injectable suspension": a drug substance (eg, a compound of the present invention) in the form of a dry solid to be combined with an appropriate sterile vehicle for parenteral administration in the form of a pharmaceutical injectable suspension.

[0650] The exemplary formulations of parenteral administration are included in the solution of the compound prepared in the water suitably mixed with a surfactant (for example, hydroxypropyl cellulose). Dispersion can also be prepared in glycerol, liquid polyethylene glycol, DMSO and its mixture with or without alcohol and in oil. Under common storage and use conditions, these preparations can contain preservatives to prevent microbial growth. For selecting and preparing the conventional procedures and composition of suitable formulations, for example, Remington:TheScienceandPracticeofPharmacy, the 21st edition, Gennaro compiled, Lippincott Williams&Wilkins (2005) and the United States Pharmacopeia:TheNationalFormulary (USP36NF31) published in 2013.

[0651] Preparations for parenteral administration can, for example, comprise excipients, sterile water or saline, polyalkylene glycols (e.g., polyethylene glycol), oils of plant origin, or hydrogenated naphthalenes. Biocompatible biodegradable lactide polymers, lactide / glycolide copolymers, or polyoxyethylene-polyoxypropylene copolymers can be used to control the release of the compound. Other potential parenteral delivery systems for the compound include ethylene-vinyl acetate copolymer particles, osmotic pumps, implantable infusion systems, and liposomes. Preparations for inhalation can contain excipients (e.g., lactose) or can be aqueous solutions containing, for example, polyoxyethylene-9-lauryl ether, hepatocholate, and deoxycholate, or can be oily solutions administered in the form of nasal drops or as a gel.

[0652] Parenteral formulations can be formulated for rapid release or sustained / extended release of the compound. Exemplary formulations for parenteral release of the compound include aqueous solutions, reconstituted powders, co-solvent solutions, oil / water emulsions, suspensions, oil-based solutions, liposomes, microspheres, and polymer gels.

[0653] combination

[0654] The compounds of the present invention may be administered to a subject in combination with one or more additional agents, such as:

[0655] (a) cytotoxic agents;

[0656] (b) antimetabolites;

[0657] (c) an alkylating agent;

[0658] (d) anthracyclines;

[0659] (e) antibiotics;

[0660] (f) antimitotic agents;

[0661] (g) Hormone therapy;

[0662] (h) signal transduction inhibitors;

[0663] (i) gene expression regulators;

[0664] (j) apoptosis inducers;

[0665] (k) angiogenesis inhibitors;

[0666] (1) immunotherapeutic agents;

[0667] (m) DNA damage repair inhibitors;

[0668] or

[0669] Its combination.

[0670] The cytotoxic agent can be, for example, actinomycin D, alemtuzumab, alitretinoin, allopurinol, hexamethylmelamine, amifostine, amphotericin, amsacrine, arsenic trioxide, asparaginase, azacitidine, azathioprine, Bacille Calmette-Guérin, or amphetamine. Calmette-Guérin (BCG), bendamustine, bexarotene, bevacuzimab, bleomycin, bortezomib, busulfan, capecitabine, carboplatin, carfilzomib, carmustine, cetuximab, cisplatin, chlorambucil, cladribine, clofarabine, colchicine, crisantaspase, cyclophosphamide, cyclosporine, cytarabine, cytochalasin B, dacarbazine, dactinomycin, darbepoetin alfa, dasatinib, daunorubicin, 1-dehydrotestosterone, denileukin, dexamethasone, dexrazoxane, dihydroxy anthracin dione dione), disulfiram, docetaxel, doxorubicin, emetine, epirubicin, erlotinib, epigallocatechin gallate, epoetin alfaalfa), estramustine, ethidium bromide, etoposide, everolimus, filgrastim, finasunate, floxuridine, fludarabine, 5-fluorouracil (5-FU), fulvestrant, ganciclovir, geldanamycin, gemcitabine, glucocorticoids, gramicidin D, histrelin acetate, hydroxyurea, ibritumomab, idarubicin, ifosfamide, imatinib, irinotecan, interferon, interferon alfa-2a, interferon alfa-2b, ixabepilone, lactate dehydrogenase A (LDH-A), lenalidomide, letrozole, leucovorin, levamisole, lidocaine, lomustine, nitrogen mustard, melphalan, 6-mercaptopurine, mescaline sodium, methotrexate, methoxsalen, metoprine, metronidazole, mithramycin, mitomycin C, mitoxantrone, nandrolone, nelarabine, nilotinib, nofetumomab, oprelvekin, oxaliplatin, paclitaxel, pemetrexed, pentostatin, palifermin, pamidronate, pegaspargase, pegfilgrastim, pemetrexed disodium, plicamycin, porfimer sodium, procaine, procarbazine, propranolol, puromycin, quinacrine, radicicol, radioisotopes, raltitrexed, rapamycin, rasburicase, salinosporamide A A), sargramostim, sunitinib, temozolomide, teniposide, tetracaine, 6-thioguanine, thiotepa, topotecan, toremifene, trastuzumab, treosulfan, tretinoin, valrubicin, vinblastine, vincristine, vindesine, vinorelbine, zoledronate, or a combination thereof.

[0671] The antimetabolite can be, for example, methotrexate, 6-mercaptopurine, 6-thioguanine, cytarabine, 5-fluorouracil dacarbazine, cladribine, pemetrexed, gemcitabine, capecitabine, hydroxyurea, mercaptopurine, fludarabine, pralatrexate, clofarabine, cytarabine, decitabine, floxuridine, nelarabine, trimetrexate, thioguanine, pentostatin, or a combination thereof.

[0672] The alkylating agent can be, for example, mechlorethamine, thiotepa, chlorambucil, melphalan, carmustine (BSNU), lomustine (CCNU), cyclophosphamide, busulfan, dibromomannitol, streptozotocin, mitomycin C, cis-dichlorodiamine platinum (II) (DDP), cisplatin, altretamine, cyclophosphamide, ifosfamide, altretamine, altretamine, procarbazine, dacarbazine, temozolomide, streptozocin, carboplatin, cisplatin, oxaliplatin, uramustine, bendamustine, trabectedin, semustine, or a combination thereof.

[0673] The anthracycline can be, for example, daunorubicin, doxorubicin, aclarubicin, adoxorubicin, amrubicin, annamycin, carrubicin, epirubicin, idarubicin, mitoxantrone, valrubicin, or a combination thereof.

[0674] The antibiotic can be, for example, dactinomycin, bleomycin, mithramycin, anthramycin (AMC), ampicillin, bacampicillin, carbenicillin, cloxacillin, dicloxacillin, flucloxacillin, mezlocillin, nafcillin, oxacillin, piperacillin, pivampicillin, pivmecillin, ticarcillin, aztreonam, imipenem, doripenem, ertapenem, meropenem, cephalosporins, clarithromycin, dirithromycin, roxithromycin, telithromycin, lincomycin, pristinamycin, quinupristin, amikacin, gentamicin, kanamycin, neomycin, netilmicin, paromomycin, tobramycin, streptomycin, sulfamethoxazole, sulfamethoxazole, oxazole, sulfisoxazole, demeclocycline, minocycline, oxytetracycline, tetracycline, penicillin, amoxicillin, cephalexin, erythromycin, clarithromycin, azithromycin, ciprofloxacin, levofloxacin, ofloxacin, doxycycline, clindamycin, metronidazole, tigecycline, chloramphenicol, metronidazole, tinidazole, nitrofurantoin, vancomycin, teicoplanin, telavancin, linezolid, cycloserine, rifamycin, polymyxin B, bacitracin, viomycin, capreomycin, quinolone, daunorubicin, doxorubicin, 4'-deoxydoxorubicin, epirubicin, idarubicin, plicamycin, mitomycin C, mitoxantrone, or a combination thereof.

[0675] The antimitotic agent can be, for example, vincristine, vinblastine, vinorelbine, docetaxel, estramustine, ixabepilone, paclitaxel, a maytansinoid, a dolastatin, a cryptophycin, or a combination thereof.

[0676] The signal transduction inhibitor can be, for example, imatinib, trastuzumab, erlotinib, sorafenib, sunitinib, temsirolimus, vemurafenib, lapatinib, bortezomib, cetuximab, panitumumab, matuzumab, gefitinib, STI 571, rapamycin, flavopiridol, imatinib mesylate, vatalanib, semaxinib, motesanib, axitinib, afatinib, bosutinib, crizotinib, cabozantinib, dasatinib, entrectinib, pazopanib, lapatinib, vandetanib, or a combination thereof.

[0677] The gene expression regulator can be, for example, siRNA, shRNA, antisense oligonucleotide, HDAC inhibitor, or a combination thereof. The HDAC inhibitor can be, for example, trichostatin A, trapoxin B, valproic acid, vorinostat, belinostat, LAQ824, panobinostat, entinostat, tacedinaline, mocetionstat, givinostat, resminostat, abexinostat, quisinostat, rocilinostat, practinostat, CHR-3996, butyric acid, phenylbutyric acid, 4SC202, romidepsin, sirtinol, cambinol, EX-527, nicotinamide, or a combination thereof. The antisense oligonucleotide may be, for example, custirsen, apatorsen, AZD9150, trabadersen, EZN-2968, LErafAON-ETU, or a combination thereof. The siRNA may be, for example, ALN-VSP, CALAA-01, Atu-027, SPC2996, or a combination thereof.

[0678] Hormone therapy can be, for example, a luteinizing hormone-releasing hormone (LHRH) antagonist. Hormone therapy can be, for example, firmagon, leuprorelin, goserelin, buserelin, flutamide, bicalutamide, ketoconazole, aminoglutethimide, prednisone, hydroxyprogesterone caproate, medroxyprogesterone acetate, megestrol acetate, diethylstilbestrol, ethinyl estradiol, tamoxifen, testosterone propionate, fluoxymesterone, flutamide, raloxifene, droloxifene, iodoxyfene, 4-hydroxytamoxifen, troxifene, keoxifene, LY117018, onapristone, toremifene citrate (toremifine citrate), megestrol acetate, exemestane, fadrozole, vorozole, letrozole, anastrozole, nilutamide, tripterelin, histerelin, abiraterone, medroxyprogesterone acetate, diethylstilbestrol, premarin, fluoxymesterone, tretinoin, fenretinide, troxacitabine, or a combination thereof.

[0679] The apoptosis-inducing agent can be, for example, recombinant human TNF-related apoptosis-inducing ligand (TRAIL), camptothecin, bortezomib, etoposide, tamoxifen, or a combination thereof.

[0680] The angiogenesis inhibitor can be, for example, sorafenib, sunitinib, pazopanib, everolimus, or a combination thereof.

[0681] Immunotherapeutic agents can be, for example, monoclonal antibodies, cancer vaccines (e.g., dendritic cell (DC) vaccines), oncolytic viruses, cytokines, adoptive T cell therapy, Bacillus Calmette-Guérin (BCG), GM-CSF, thalidomide, lenalidomide, pomalidomide, imiquimod, or a combination thereof. Monoclonal antibodies can be, for example, anti-CTLA4, anti-PD1, anti-PD-L1, anti-LAG3, anti-KIR, or a combination thereof. The monoclonal antibody can be, for example, alemtuzumab, trastuzumab, ibritumomab tiuxetan, brentuximab vedotin, trastuzumab, adotrastuzumab-emtansine, blinatumomab, bevacizumab, cetuximab, pertuzumab, panitumumab, ramucirumab, obinutuzumab, ofatumumab, rituximab, pertuzumab, tositumomab, gemtuzumab ozogamicin, tositumomab, or a combination thereof. Cancer vaccines can be, for example, Sipuleucel-T, BioVax ID, NeuVax, DCVax, SuVaxM, hsp110 chaperone protein complex vaccine, CDX-1401, MIS416, CDX-110, GVAX Pancreas, HyperAcute TM Pancreas, GTOP-99 or Imprime The oncolytic virus may be, for example, talimogene laherparepvec. The cytokine may be, for example, IL-2, IFNα, or a combination thereof. The adoptive T cell therapy may be, for example, tisagenlecleucel, axicabtagene ciloleucel, or a combination thereof.

[0682] DNA damage repair inhibitors can be, for example, PARP inhibitors, cell checkpoint kinase inhibitors, or combinations thereof. PARP inhibitors can be, for example, olaparib, rucaparib, veliparib (ABT-888), niraparib (ZL-2306), iniparib (BSI-201), talazoparib (BMN 673), 2X-121, CEP-9722, KU-0059436 (AZD2281), PF-01367338, or combinations thereof. The cellular checkpoint kinase inhibitor can be, for example, MK-1775 or AZD1775, AZD7762, LY2606368, PF-0477736, AZD0156, GDC-0575, ARRY-575, CCT245737, PNT-737, or a combination thereof.

[0683] Example

[0684] The following examples are intended to illustrate the present invention. They are not intended to limit the present invention in any way.

[0685] Example 1. Preparation of compounds

[0686] Compound 1

[0687] Step 1. A suspension of 4-chloro-7-azaindole (25 g) in DMA (140 mL) was purged with vacuum / N2 gas (3 cycles). Zinc powder (1.07 g), zinc cyanide (11.26 g), dppf (2.72 g) and Pd2(dba)3 (2.39 g) were then added. The mixture was purged with vacuum / N2 gas (3 cycles) and heated to 120°C for 4 h. The reaction mixture was cooled to 100°C and water (428 mL) was added within 30 min. The mixture was then cooled to rt within 2 h. The crude product was filtered and washed with water (2 x 95 mL), then added to 3N HCl (150 mL), and the mixture was stirred at rt for 2 h. Insoluble matter was removed by filtration. A 50% aqueous NaOH solution was added to the filtrate until pH 12 was reached. Filtration and drying gave 1H-pyrrolo[2,3-b]pyridine-4-carbonitrile (11.6 g) as a tan solid.

[0688] Step 2. A mixture of 1H-pyrrolo[2,3-b]pyridine-4-carbonitrile (10.4 g) and NaOH (29 g) in water (100 mL) and EtOH (100 mL) was heated to reflux for 18 h. After cooling to rt, the mixture was treated with concentrated hydrochloric acid to a pH of about 2. The solid was collected by filtration and dried under high vacuum to give 1H-pyrrolo[2,3-b]pyridine-4-carboxylic acid (11.8 g) as a tan solid.

[0689] Step 3. at 0 ° C, thionyl chloride (12.4 mL) was added dropwise into EtOH (120 mL), and the mixture was stirred at rt for 30 min, then 1H-pyrrolo [2,3-b] pyridine -4- carboxylic acid (12.0 g) was added, and the reaction mixture was heated to reflux for 8 h. After cooling to rt, the solvent was removed under reduced pressure. The residue thus obtained was suspended in water (150 mL) and the pH was adjusted to pH 9 with saturated K CO aqueous solution. The mixture was extracted with EtOAc (2 × 150 mL). The combined extracts were washed with brine, dried over MgSO4, filtered and concentrated to dryness to obtain 1H-pyrrolo [2,3-b] pyridine -4- ethyl formate (10.5 g) as a tan solid.

[0690] Step 4. To a mixture of ethyl 1H-pyrrolo[2,3-b]pyridine-4-carboxylate (9.5 g) in EtOAc (95 mL) was added mCPBA (15.5 g) in portions at 0°C. The reaction mixture was allowed to warm to rt and stirred for 3 h. The precipitate was filtered, washed with EtOAc (3×30 mL), and the residue was dried under high vacuum to give 4-(ethoxycarbonyl)-1H-pyrrolo[2,3-b]pyridine 7-oxide (8.8 g) as a light yellow solid.

[0691] Step 5. To a solution of 4-(ethoxycarbonyl)-1H-pyrrolo[2,3-b]pyridine 7-oxide (25.5 g) in DMF (250 mL) was added methanesulfonyl chloride (11.5 mL) dropwise. The mixture was then heated to 80 ° C for 1 h, then allowed to cool to rt, and additional methanesulfonyl chloride (11.5 mL) was added. The mixture was heated at 80 ° C for 1 h again. After cooling to 0 ° C, the reaction mixture was poured into ice water (480 mL) with vigorous stirring. The mixture was then stirred at 0 ° C for 2 h. The precipitate was filtered and washed with water (3 × 200 mL). The residue was dried under high vacuum to obtain 6-chloro-1H-pyrrolo[2,3-b]pyridine-4-carboxylic acid ethyl ester (25.0 g) as a beige solid, which was used in subsequent steps without further purification.

[0692] Step 6. At 0 ° C, NaH (6.68 g) was added to a solution of ethyl 6-chloro-1H-pyrrolo[2,3-b]pyridine-4-carboxylate (25 g) in DMF (250 mL) over 45 min, followed by stirring at 0 ° C for 1 h. SEM-Cl (23.6 mL) was added over 20 minutes, and the mixture was stirred at 0 ° C for 1 h. Water (300 mL) was slowly added and the mixture was extracted with EtOAc (2×200 mL), then washed with brine, dried over MgSO 4 , filtered and concentrated to dryness. The residue was purified by silica gel flash chromatography (15-30% EtOAc / hexane) to give ethyl 6-chloro-1-(((2-trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridine-4-carboxylate (32.4 g) as an orange oil.

[0693] Step 7. To a solution of ethyl 6-chloro-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridine-4-carboxylate (32.3 g) in toluene (150 mL) was added (R)-3-methylmorpholine (12.4 mL), BINAP (3.4 g) and cesium carbonate (89 g). The mixture was degassed (vacuum / argon, 3 cycles) and palladium acetate (1.0 g) was added, and the reaction mixture was degassed again and then heated to 120° C. for 4 hours. After cooling to rt, the mixture was diluted with EtOAc (500 mL), filtered through a pad of celite and washed with EtOAc (2×250 mL). The filtrate was concentrated to dryness under reduced pressure and purified by silica gel chromatography (0-40% EtOAc / hexanes) to give (R)-ethyl 6-(3-methylmorpholino)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridine-4-carboxylate (26 g) as a yellow oil.

[0694] Step 8. To a solution of (R)-6-(3-methylmorpholino)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridine-4-carboxylic acid ethyl ester (4.9 g) in THF (80 mL) was added MeOH (0.048 mL). The reaction mixture was heated to 65 ° C, and then a solution of 2M LiBH4 in THF (9 mL) was added dropwise over 1 h. The reaction mixture was stirred at 65 ° C for 18 h. After cooling to rt, acetone (2 mL) was added and stirred at rt for 30 min. The mixture was diluted with 1:1 saturated NH4Cl aqueous solution / water (100 mL) and extracted with EtOAc (2×100 mL). The combined organic extracts were washed with brine, dried over MgSO4, filtered and concentrated to dryness. The residue was purified by silica gel chromatography (5-50% EtOAc / hexanes) to give (R)-(6-(3-methylmorpholino)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-4-yl)methanol (3.9 g) as a yellow gum.

[0695] Step 9. To a solution of (R)-(6-(3-methylmorpholino)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-4-yl)methanol (7.5 g) in dichloromethane (70 mL) at 0°C was added triethylamine (2.8 mL) followed by methanesulfonyl chloride (1.55 mL). The reaction mixture was stirred at rt for 90 min then diluted with dichloromethane (100 mL) and water (100 mL). The layers were partitioned and the aqueous layer was extracted with dichloromethane (100 mL). The combined organic extracts were washed with brine, dried over MgSO4, filtered and concentrated to dryness to give (R)-(6-(3-methylmorpholino)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-4-yl)methyl methanesulfonate (9 g) as a yellow gum which was used in the subsequent step without further purification.

[0696] Step 10. To a solution of (R)-(6-(3-methylmorpholino)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-4-yl)methyl methanesulfonate (9 g) in dioxane (80 mL) was added LiI (5.3 g). The mixture was heated to 100 °C under argon for 2.5 h. After cooling to rt, the mixture was diluted with EtOAc (100 mL) and water (100 mL). The layers were partitioned and the aqueous layer was extracted with EtOAc (80 mL). The combined organic extracts were washed with 2M sodium bisulfite (80 mL), water (80 mL), brine (80 mL), dried over MgSO4, filtered and concentrated to give (R)-(4-(4-iodomethyl)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methylmorpholine (9.6 g) as a dark oil which was used as such in the subsequent step without further purification.

[0697] Step 11. To a solution of (R)-4-(4-iodomethyl)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methylmorpholine (9.6 g) in DMF (80 mL) was added sodium methanesulfonate (2.4 g). The reaction mixture was stirred at rt for 18 h. The reaction mixture was EtOAc (100 mL) and water (100 mL), and each layer was distributed and the aqueous layer was extracted with EtOAc (80 mL). The combined organic extracts were washed with sodium thiosulfate aqueous solution (80 mL), water (80 mL) and brine, dried over MgSO4, filtered and concentrated. The residue was purified by silica gel chromatography (10-90% EtOAc / hexanes) to provide (R)-3-methyl-4-(4-((methylsulfonyl)methyl)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)morpholine (7.5 g) as a gray-green gum.

[0698] Step 12. To a solution of (R)-3-methyl-4-(4-((methylsulfonyl)methyl)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)morpholine (7.5 g) in toluene (80 mL) was added TBAB (1 g) and 50% NaOH (36 mL) followed by 1,2-dibromoethane (2 mL). The mixture was heated to 65° C. for 18 h. Additional 1,2-dibromoethane (16 mL) was then added via syringe pump over 18 h while the mixture was stirred at 65° C. The reaction mixture was aged at 65° C. for an additional 18 h and then cooled to rt. The reaction mixture was diluted with EtOAc (200 mL) and water (150 mL), the layers were partitioned, and the aqueous layer was extracted with EtOAc (100 mL). The combined organic extracts were washed with brine, dried over MgSO₄, and concentrated to dryness under reduced pressure. The residue was purified by silica gel chromatography (10-80% EtOAc / hexanes) to give (R)-3-methyl-4-(4-(1-(methylsulfonyl)cyclopropyl)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)morpholine (5.4 g) as a yellow foam.

[0699] Step 13. To a solution of (R)-3-methyl-4-(4-(1-(methylsulfonyl)cyclopropyl)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)morpholine (5.4 g) in dichloromethane (50 mL) was added TFA (18 mL) at 0°C. The reaction mixture was warmed to rt and stirred for 18 h. Toluene (40 mL) was added and the mixture was concentrated. The residue was diluted with dioxane (40 mL) and the pH of the mixture was adjusted to pH 10 by adding 3N NaOH. The mixture was heated to 80°C for 3 h and then cooled to rt. The mixture was diluted with EtOAc (150 mL) and water (150 mL). The layers were partitioned and the aqueous layer was extracted with EtOAc (100 mL). The combined organic extracts were washed with brine, dried over MgSO4, filtered and concentrated to dryness. The residue was purified by silica gel chromatography (30-100% EtOAc / hexanes) to provide (R)-3-methyl-4-(4-(1-(methylsulfonyl)cyclopropyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)morpholine (1.65 g) as a light yellow foam.

[0700] Step 14. At 0 ° C, cesium carbonate (9.43 g) was added to a solution of 3-iodo-1H-pyrazole (2.5 g) in DMF (25 mL). SEM-Cl (2.8 mL) was then added within 15 min. The mixture was stirred at rt for 18 h. Water (60 mL) was slowly added and the mixture was distributed with Et2O (60 mL). The aqueous layer was extracted with Et2O (30 mL), and the combined organic extracts were washed with water (3 × 50 mL), brine, dried over MgSO4, filtered and concentrated to dryness. The residue was purified by silica gel chromatography (0-30% EtOAc / hexane) to obtain 3-iodo-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazole (3.3 g) as a colorless liquid. 1H-NMR showed that the ratio of the two regioisomers was 1: 1.

[0701] Step 15. To (R)-3-methyl-4-(4-(1-(methylsulfonyl)cyclopropyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)morpholine (100 mg), 3-iodo-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazole (145 mg), cesium carbonate (244 mg), and L-proline (21 mg) in a microwave vessel was added NMP (1 mL) followed by CuBr (20 mg). The vessel was capped and degassed (vacuum / argon, 3 cycles) and then heated to 150° C. for 4 h. After cooling to rt, the reaction mixture was quenched with 20 mL of NH4Cl:HO:NH4OH (4:3:1) and EtOAc (15 mL), filtered through celite, and extracted with ethyl acetate (2×150 mL). The combined organic extracts were washed with brine, dried over MgSO4, filtered, and concentrated to dryness. The residue was purified by silica gel chromatography (20-100% EtOAc / hexanes) to afford (R)-3-methyl-4-(4-(1-(methylsulfonyl)cyclopropyl)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrol-3-yl)-1H-pyrrolo[2,3-b]pyridin-6-yl)morpholine (25 mg) as a mixture of regioisomers.

[0702] Step 16. To a solution of (R)-3-methyl-4-(4-(1-(methylsulfonyl)cyclopropyl)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-6-yl)morpholine (25 mg) in dichloromethane (1 mL) was added TFA (0.2 mL). The reaction mixture was stirred at rt for 18 h. Toluene (10 mL) was added and the volatiles were removed under reduced pressure. The residue was dissolved in dioxane (3 mL) and saturated aqueous NaHCO3 (3 mL), and the mixture was heated to 65°C for 18 h and then to 80°C for 18 h. After cooling to rt, the mixture was extracted with dichloromethane (2×15 mL). The combined organic extracts were washed with brine, dried over MgSO4, filtered and concentrated to dryness. The residue was purified by silica gel chromatography (20-100% EtOAc / hexanes) to give the desired product. The residue was suspended in CH3CN (1 mL) and water (1 mL) and lyophilized to give (R)-3-methyl-4-(4-(1-(methylsulfonyl)cyclopropyl)-1-(1H-pyrazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-6-yl)morpholine (15 mg) as a light yellow foam. 1 H NMR (400MHz, CDCl3): δ7.66 (d; J=3.74Hz; 1H); 7.62 (d; J=2.36Hz; 1H); 6.98 (s ; 1H); 6.78 (s; 1H); 6.59 (d; J=3.76Hz; 1H); 4.32-4.37 (m; 1H); 4.05-4.09 (m; 1 H);3.87-3.91(m;1H);3.83-3.84(m;2H);3.64-3.71(m;1H);3.28-3.35(m;1H) ); 2.83 (s; 3H); 1.93-1.96 (m; 2H); 1.39-1.42 (m; 2H); 1.29 (d; J=6.71Hz; 3H). MS:[M+1]:402.2.

[0703] Intermediate A

[0704]

[0705] Step 1. In 30 minutes, to a cold (0 ℃) solution of acrylonitrile (12.4 mL) in THF (75 mL), hydrazine hydrate (8.7 mL) was added dropwise to keep the internal temperature below 10 ℃. The resulting mixture was stirred in an ice bath for 30 minutes, then warmed to rt for 3 hours. The mixture was cooled in an ice bath again, and 2,4-dimethoxybenzaldehyde (31 g) was added in 10 minutes. The resulting mixture was stirred in an ice bath for 25 minutes, warmed to rt for 1 hour, then concentrated in vacuo and placed under high vacuum with stirring overnight to remove water.

[0706] The resulting residue was dissolved in n-BuOH (70 mL) and treated with NaOMe (20.4 g) to give a dark coloration and exotherm. The mixture was heated to reflux for 1 h, cooled to room temperature and poured into brine. EtOAc was added and the organic layer was separated, washed with brine, dried over MgSO4, filtered through a celite pad and concentrated in vacuo. The material was placed under high vacuum to remove residual n-BuOH. The process was repeated on the same scale, and the combined material was purified on silica gel (eluted with 1:1 EtOAc / hexane) to give 35 g of 1-(2,4-dimethoxybenzyl)-1H-pyrazole-5-amine.

[0707] Step 2. to 1- (2,4- dimethoxybenzyl) -1H- pyrazole -5- amine (14g) in AcOH (140mL) solution of diethyl oxaloacetate sodium salt (16.1g). The resulting suspension is placed in an oil bath and heated to reflux for 2h. The reactant is cooled in an ice bath and then slowly added to 440mL of cold water by a dropping funnel under rapid stirring. The resulting suspension is stirred for 2 hours, filtered, rinsed with water and air-dried overnight to obtain 19.2g of 1- (2,4- dimethoxybenzyl) -6- hydroxy -1H- pyrazolo [3,4-b] pyridine -4- ethyl formate as a yellow solid.

[0708] Step 3. At 0 ° C, pyridine (1.8 mL) was added to a suspension of 1- (2,4-dimethoxybenzyl) -6-hydroxy -1H- pyrazolo [3,4-b] pyridine -4-carboxylic acid ethyl ester (11.0 g) in acetonitrile (100 mL), followed by trifluoromethane (3.8 mL) at a rate such that the internal temperature was maintained below 5 ° C. The reaction mixture was warmed to room temperature within 1 h, quenched with water (100 mL) and extracted with dichloromethane (2 × 100 mL). The combined organic extracts were washed with brine, dried over MgSO4, decompressed and concentrated to dryness under reduced pressure to give 10 g of 1- (2,4-dimethoxybenzyl) -6- (((trifluoromethyl) sulfonyl) oxy) -1H- pyrazolo [3,4-b] pyridine -4-carboxylic acid ethyl ester as a yellow solid, which was used in subsequent steps without further purification.

[0709] Step 4. To a solution of crude ethyl 1-(2,4-dimethoxybenzyl)-6-(((trifluoromethyl)sulfonyl)oxy)-1H-pyrazolo[3,4-b]pyridine-4-carboxylate (10 g) in DMF (100 mL) at 0°C was added (R)-3-methylmorpholine (6.8 g) and pyridine (2.0 mL). The reaction mixture was stirred at room temperature for 5 days and then diluted with water (100 mL) and EtOAc (120 mL). The layers were partitioned and the aqueous layer was extracted with EtOAc (100 mL). The combined organic extracts were washed with brine, dried over MgSO4, filtered and concentrated in vacuo to dryness. The residue was purified by ISCO CombiFlash (120 g column) eluting with 10-100% EtOAc / hexanes to afford 5.8 g of (R)-ethyl 6-(3-methylmorpholino)-1H-pyrazolo[3,4-b]pyridine-4-carboxylate (Intermediate A) as a yellow gum. LCMS (+ESI): m / z = 441.1 [M+H]+.

[0710] Compound 2

[0711] Step 1. At -78 ° C, to a solution of intermediate A (400 mg) in THF (4 mL) was added MeMgBr (3M / Et2O, 1 mL), and the reaction mixture was warmed to room temperature. The reaction mixture was quenched with cooled saturated NH4Cl aqueous solution and extracted with EtOAc (2 × 30 mL). The combined organic layer was washed with brine, dried over MgSO4, decompressed and concentrated to dryness under reduced pressure. The residue was purified by ISCO CombiFlash (40 g column) (eluted with 10-100% EtOAc / hexane) to give 380 mg of (R) -2- (1- (2,4-dimethoxybenzyl) -6- (3-methylmorpholino) -1H- pyrazolo [3,4-b] pyridin-4-yl) propan-2-ol as a yellow oil.

[0712] Step 2. To a solution of (R)-2-(1-(2,4-dimethoxybenzyl)-6-(3-methylmorpholino)-1H-pyrazolo[3,4-b]pyridin-4-yl)propan-2-ol (380 mg) in dichloromethane (4 mL) was added TFA (1.36 mL) and the solution was stirred for 18 h at room temperature. The volatiles were removed under reduced pressure and the residue was suspended in EtOAc (30 mL) and washed with saturated NaHCO3 aqueous solution. The aqueous layer was extracted with EtOAc (20 mL), and the combined organic layers were washed with brine, dried over MgSO4, filtered and concentrated under reduced pressure to dryness to give 160 mg of (R)-2-(6-(3-methylmorpholino)-1H-pyrazolo[3,4-b]pyridin-4-yl)propan-2-ol.

[0713] Step 3. A microwave vial was charged with (R)-2-(6-(3-methylmorpholino)-1H-pyrazolo[3,4-b]pyridin-4-yl)propan-2-ol (160 mg), SEM-protected 3-iodopyrazole (376 mg), Cs2CO3 (475 mg), L-proline (13 mg), CuBr (13 mg), and NMP (3 mL). The vessel was then capped and degassed (vacuum / argon, 3 cycles) and heated to 150°C for 18 h. After cooling to room temperature, the reaction mixture was diluted with EtOAc (50 mL) and then purified by ISCO CombiFlash (24 g column) eluting with 10-100% EtOAc / hexanes to afford 100 mg of (R)-2-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)propan-2-ol as a yellow gum. 1H-NMR and LCMS showed two regioisomers of the SEM N-protected pyrazole.

[0714] Step 4. To a solution of (R)-2-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)propan-2-ol (100 mg) in dichloromethane (1 mL) was added TFA (0.211 mL) and the reaction mixture was stirred for 18 h at room temperature. Toluene (10 mL) was added and the volatiles were removed under reduced pressure. The flask was placed under high vacuum to remove residual TFA. The residue was dissolved in dioxane (3 mL) and 1 N NaOH (1 mL) was added. The reaction mixture was heated to reflux for 3 h, cooled to room temperature, and then diluted with EtOAc (20 mL) and water (20 mL). The layers were partitioned, and the aqueous layer was extracted with EtOAc (10 mL). The combined organic layers were washed with brine, dried over MgSO4, decompressed and concentrated to dryness under reduced pressure. The residue was adsorbed on silica gel for purification by ISCO CombiFlash (12 g column) (eluted with 40-100% EtOAc / hexanes). The desired product fractions were combined and concentrated to dryness. The residue was diluted in CH3CN (1 mL) and water (1 mL) for lyophilization to give 22 mg of the desired product (R)-2-(6-(3-methylmorpholino)-1-(1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)propan-2-ol as a colorless foam. Purity by HPLC at 254 nm: 93.0%, 1HNMR (400MHz, CDCl3): δ8.12 (s; 1H); 7.63 (d; J=2.10Hz; 1H); 6.83 (s; 1H); 6.72 (s; 1H); 4.45-4.49 (m; 1H); 4.02-4.09 (m; 2H) ); 3.77-3.86 (m; 3H); 3.66 (td; J = 11.90; 3.16Hz; 1H); 3.39 (td; J = 12.73; 3.87Hz; 1H); 1.73 (s; 6H); 1.35 (d; J = 6.74Hz; 3H).

[0715] Compound 3

[0716] Step 1. To a solution of intermediate A (3.4 g) in THF (35 mL) was added MeOH (0.062 mL). The reaction mixture was heated to 65 ° C, and then a solution of 2M LiBH4 in THF (5.8 mL) was added dropwise over 1 h. The reaction mixture was stirred at 65 ° C for 4 h and then cooled to room temperature. Acetone (1 mL) was added and stirred at room temperature for 30 min. The mixture was diluted with 1: 1 saturated NH4Cl aqueous solution / water (80 mL) and EtOAc (80 × 100 mL). The layers were distributed and the aqueous layer was extracted with EtOAc (40 mL). The combined organic extracts were washed with brine, dried over MgSO4, decompressed and concentrated to dryness under reduced pressure. The residue was purified by ISCO CombiFlash (80 g column) eluting with 30-100% EtOAc / hexanes to afford (R)-(1-(2,4-dimethoxybenzyl)-6-(3-methylmorpholino)-1H-pyrazolo[3,4-b]pyridin-4-yl)methanol and (R)-(1-(2,4-dimethoxybenzyl)-6-(3-methylmorpholino)-2H-pyrazolo[3,4-b]pyridin-4-yl)methanol (a separable mixture of positional isomers) as colorless foams.

[0717] Step 2. To a solution of (R)-(1-(2,4-dimethoxybenzyl)-6-(3-methylmorpholino)-2H-pyrazolo[3,4-b]pyridin-4-yl)methanol (600 mg) in dichloromethane (7 mL) was added triethylamine (0.141 mL) followed by methanesulfonyl chloride (0.254 mL) at 0°C. The reaction mixture was stirred at room temperature for 90 min and then diluted with dichloromethane (40 mL) and water (40 mL). The layers were partitioned, the aqueous layer was extracted with dichloromethane (30 mL), and the combined organic extracts were washed with brine, dried over MgSO4, filtered, and concentrated to dryness to give 700 mg of (R)-(1-(2,4-dimethoxybenzyl)-6-(3-methylmorpholino)-2H-pyrazolo[3,4-b]pyridin-4-yl)methyl methanesulfonate, which was used in the subsequent step without further purification.

[0718] Step 3. To a solution of (R)-(1-(2,4-dimethoxybenzyl)-6-(3-methylmorpholino)-2H-pyrazolo[3,4-b]pyridin-4-yl)methyl methanesulfonate (700 mg) in dioxane (7 mL) was added LiI (393 mg). The mixture was heated to 50 ° C under argon for 2.5 h. After cooling to room temperature, the mixture was diluted with EtOAc (50 mL) and water (50 mL). The layers were partitioned and the aqueous layer was extracted with EtOAc (30 mL). The combined organic extracts were washed with 2M sodium bisulfite (50 mL), water (50 mL), and brine (50 mL), then dried over MgSO4, filtered, and concentrated to dryness under reduced pressure to give 760 mg of (R)-4-(2-(2,4-dimethoxybenzyl)-4-(iodomethyl)-2H-pyrazolo[3,4-b]pyridin-6-yl)-3-methylmorpholine, which was used in the subsequent step without further purification.

[0719] Step 4. To a solution of (R)-4-(2-(2,4-dimethoxybenzyl)-4-(iodomethyl)-2H-pyrazolo[3,4-b]pyridin-6-yl)-3-methylmorpholine (790 mg) in DMF (8 mL) was added sodium methanesulfonate (190 mg). The reaction mixture was stirred at room temperature for 2 h and then diluted with EtOAc (40 mL) and water (40 mL). The layers were distributed and the aqueous layer was extracted with EtOAc (30 mL). The combined organic extracts were washed with aqueous sodium thiosulfate (50 mL), water (50 mL) and brine, then dried over MgSO4, filtered and concentrated to dryness under reduced pressure. The residue was absorbed onto silica gel for purification by Isco CombiFlash (40 g column) eluting with 30-100% EtOAc / hexanes to afford 640 mg of (R)-4-(2-(2,4-dimethoxybenzyl)-4-((methylsulfonyl)methyl)-2H-pyrazolo[3,4-b]pyridin-6-yl)-3-methylmorpholine as a colorless foam.

[0720] Step 5. To a solution of (R)-4-(1-(2,4-dimethoxybenzyl)-4-((methylsulfonyl)methyl)-2H-pyrazolo[3,4-b]pyridin-6-yl)-3-methylmorpholine (640 mg) in toluene (3 mL) was added TBAB (45 mg) and 1,2-dibromoethane (0.156 mL) followed by 50% NaOH (2.9 mL). The reaction mixture was heated to 60° C. for 2 h. Additional 1,2-dibromoethane (0.5 mL) was added and the mixture was heated again at 60° C. for 18 h. After cooling to rt, the mixture was diluted with EtOAc (30 mL) and water (25 mL), the layers were partitioned, and the aqueous layer was extracted with EtOAc (20 mL). The combined organic extracts were washed with brine, dried over MgSO 4 , reduced pressure, and concentrated to dryness under reduced pressure. The residue was adsorbed onto silica gel for purification by ISCO CombiFlash (24 g column) eluting with 30-100% EtOAc / hexanes to afford 510 mg of (R)-4-(1-(2,4-dimethoxybenzyl)-4-(1-methylsulfonyl)cyclopropyl)-2H-pyrazolo[3,4-b]pyridin-6-yl)-3-methylmorpholine as a light yellow foam.

[0721] Step 6. (R)-3-methyl-4-(4-(1-(methylsulfonyl)cyclopropyl)-1H-pyrazolo[3,4-b]pyridin-6-yl)morpholine: To a solution of (R)-4-(1-(2,4-dimethoxybenzyl)-4-(1-methylsulfonyl)cyclopropyl)-2H-pyrazolo[3,4-b]pyridin-6-yl)-3-methylmorpholine (510 mg) in dichloromethane (5 mL) was added TFA (1.6 mL) at 0°C. The reaction mixture was allowed to warm to room temperature and stirred for 5 h. Toluene (10 mL) was added to the reaction mixture, and the volatiles were removed in vacuo, then co-evaporated with toluene (10 mL). The residue was dissolved in EtOAc (50 mL) and saturated aqueous NaHCO3 (40 mL) with vigorous stirring. The layers were partitioned, and the aqueous layer was extracted with EtOAc (30 mL). The combined extracts were washed with brine, dried over MgSO4, filtered and concentrated to dryness in vacuo to give 350 mg of (R)-3-methyl-4-(4-(1-(methylsulfonyl)cyclopropyl)-1H-pyrazolo[3,4-b]pyridin-6-yl)morpholine as a light yellow foam which was used in the next step without further purification.

[0722] Step 7. A microwave tube was charged with (R)-3-methyl-4-(4-(1-(methylsulfonyl)cyclopropyl)-1H-pyrazolo[3,4-b]pyridin-6-yl)morpholine (160 mg), pyrazole (310 mg), CsCO (390 mg), L-proline (11 mg), CuBr (11 mg), and NMP (2 mL). The vessel was capped and degassed (vacuum / argon, 3 cycles), then heated to 150°C for 18 h. After cooling to room temperature, the reaction mixture was diluted with EtOAc (20 mL) and NH4Cl:HO:NH4OH (4:3:1, 20 mL), then filtered through celite. The layers were separated, and the aqueous layer was extracted with EtOAc (20 mL). The combined organic layers were washed with brine, dried over MgSO4, filtered, and concentrated in vacuo to dryness. The residue was absorbed onto silica gel for purification by ISCO CombiFlash (24 g column) eluting with 20-100% EtOAc / hexanes to afford (R)-3-methyl-4-(4-(1-(methylsulfonyl)cyclopropyl)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-5-yl)-1H-pyrazolo[3,4-b]pyridin-6-yl)morpholine and the corresponding SEM-pyrazole regioisomer.

[0723] Step 8. To a solution of (R)-3-methyl-4-(4-(1-(methylsulfonyl)cyclopropyl)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-5-yl)-1H-pyrazolo[3,4-b]pyridin-6-yl)morpholine (37 mg) in dichloromethane (1 mL) was added TFA (0.319 mL) and the reaction mixture was stirred for 18 h. Toluene (10 mL) was added and the volatiles were removed under reduced pressure. The residue was dissolved in dioxane (3 mL) and saturated aqueous NaHCO3 solution (3 mL), and the mixture was heated to 65°C for 4 h and then to 80°C for 18 h. After cooling to room temperature, the mixture was extracted with dichloromethane (2×15 mL) and the combined organic extracts were washed with brine, dried over MgSO4, filtered and concentrated to dryness. The residue was purified by flash chromatography on silica gel (eluting with EtOAc and 5% MeOH / EtOAc). The resulting residue was suspended in CHCN (2 mL) and water (2 mL) and lyophilized to afford 23 mg of (R)-3-methyl-4-(4-(1-(methylsulfonyl)cyclopropyl)-1-(1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-6-yl)morpholine as a light yellow foam. 1 HNMR (400MHz, CDCl3): δ8.11 (s; 1H); 7.70 (d; J = 2.26Hz; 1H); 6.93 (d; J = 2.26Hz; 1H); 6.84 (s; 1H); 4.41-4.43 (m; 1H); 4.06-4.09 (m; 2H) );3.77-3.87(m;2H);3.61-3.68(m;1H);3.33-3.40(m;1H);2.85(s;3H);1.97-2.00(m;2H);1.41-1.44(m;2H);1.35(d;J=6.78Hz;3H). [M+1]:m / z 403.1.

[0724] Compound 4

[0725] Step 1. At 0 ° C, TFA (20 mL) was added to a solution of intermediate A (5.8 g, 13.167 mmol) in dichloromethane (60 mL). The reaction mixture was warmed to room temperature and stirred for 18 h. Toluene (60 mL) was added, volatiles were removed in vacuo, and co-evaporated with toluene (20 mL). The residue was dissolved in dichloromethane (300 mL) and then treated with saturated NaHCO3 aqueous solution (200 mL) under vigorous stirring. The layers were separated and the aqueous layer was extracted with dichloromethane (150 mL). The combined extracts were washed with brine, dried over MgSO4, filtered and concentrated in vacuo to dryness to obtain 3.8 g of (R)-6-(3-methylmorpholino)-1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid ethyl ester as a yellow solid, which was used in the next step without further purification.

[0726] Step 2. A mixture of (R)-ethyl 6-(3-methylmorpholino)-1H-pyrazolo[3,4-b]pyridine-4-carboxylate (3.8 g), pyrazole (6.37 g), CsCO (10.7 g), L-proline (300 mg), CuBr (292 mg) and NMP (40 mL) was degassed (vacuum / argon, 3 cycles) and heated to 150° C. for 18 h. After cooling to room temperature, the reaction mixture was diluted with 10% citric acid to adjust the pH to approximately 6-7, and EtOAc (350 mL) was added. The mixture was filtered through celite and washed with EtOAc. The layers were partitioned, and the aqueous layer was extracted with EtOAc (150 mL). The combined organic layers were washed with brine, dried over MgSO , filtered, and concentrated in vacuo to dryness. The residue was purified by flash chromatography on silica gel eluting with 0-10% MeOH in dichloromethane to afford 3.6 g of (R)-6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid and its SEM regioisomer as a yellow oil.

[0727] Step 3. To a solution of (R)-6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid (3.6 g) in DMF (36 mL) was added potassium carbonate (2.7 g) followed by iodomethane (0.6 mL). The reaction mixture was stirred at room temperature for 18 h. EtOAc (50 mL) and water (50 mL) were added, the layers were separated, and the aqueous layer was extracted with EtOAc (40 mL). The combined organic layers were washed with brine, dried over MgSO4, filtered, and concentrated in vacuo to dryness. The residue was purified by ISCO CombiFlash (80 g column) eluting with 0-70% EtOAc / hexanes to afford 2.2 g of (R)-methyl 6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridine-4-carboxylate as a yellow solid.

[0728] Step 4. To a solution of (R)-methyl 6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridine-4-carboxylate (2.2 g) in THF (20 mL) and MeOH (0.038 mL) was added lithium borohydride (3.4 mL). The mixture was heated to 65° C. for 4 h and then cooled to room temperature. Acetone (1 mL) was added and stirred for 30 min. The mixture was diluted with (1:1) NHCl / water (50 mL) and then extracted with EtOAc (2×40 mL). The combined organic layers were washed with brine, dried over MgSO4, filtered and concentrated to dryness in vacuo to afford 2 g of (R)-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)methanol which was used without further purification.

[0729] Step 5. To a solution of (R)-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)methanol (2 g) in dichloromethane (20 mL) was added EtN (0.69 mL) followed by MsCl (0.38 mL) at 0°C. The reaction was then stirred at room temperature for 2 h. The mixture was diluted with dichloromethane (60 mL) and water (60 mL). The layers were partitioned and the aqueous layer was extracted with dichloromethane (30 mL). The combined organic layers were washed with brine, dried over MgSO4, filtered and concentrated in vacuo to afford 2.3 g of (R)-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)methyl methanesulfonate, which was used in the next step without further purification.

[0730] Step 6. To a solution of (R)-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)methyl methanesulfonate (2.3 g) in DMF (18 mL) was added NaCN (325 mg) at room temperature. The reaction mixture was stirred for 18 h and then diluted with EtOAc (40 mL) and water (40 mL). The layers were partitioned and the aqueous layer was extracted with EtOAc (35 mL). The combined organic layers were washed with brine, dried over MgSO4, filtered and concentrated in vacuo. The residue was purified by ISCO CombiFlash (24 g column) eluting with 20-100% EtOAc / hexanes to afford 440 mg of (R)-2-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)acetonitrile.

[0731] Step 7. To a solution of (R)-2-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)acetonitrile (430 mg) in THF (5 mL) was added iodomethane (0.148 mL) at 0°C, followed by potassium tert-butoxide (2.37 mL) dropwise over 10 min. The reaction mixture was stirred at 0°C for 1 h, then poured into saturated aqueous NH4Cl and extracted with EtOAc (2×35 mL). The combined organic layers were washed with brine, dried over MgSO4, filtered, and concentrated in vacuo to dryness. The residue was adsorbed onto silica gel for purification by ISCO CombiFlash (24 g Gold SiO2 column) eluting with 10-90% EtOAc / hexanes to afford 140 mg of (R)-2-methyl-2-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)propanenitrile.

[0732] Step 8. To a solution of (R)-2-methyl-2-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)propionitrile (90 mg) in EtOH / H2O (2 mL / 0.4 mL) was added hydrogenated (dimethylphosphinyl-kP) [hydrogen bis(dimethylphosphinyl-kP)] platinum(II) (4 mg). The mixture was heated to 80°C, then cooled and concentrated to dryness. The residue was adsorbed onto silica for purification by ISCO CombiFlash (12 g Gold SiO2 column) eluting with 30-100% EtOAc / hexanes to afford 82 mg of (R)-2-methyl-2-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)propanamide as a colorless solid.

[0733] Step 9. To a solution of (R)-2-methyl-2-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)propanamide (81 mg) in dichloromethane (2 mL) was added TFA (0.30 mL) and the reaction mixture was stirred at room temperature for 18 h. Additional TFA (0.5 mL) was added and the mixture was stirred for 6 h. Toluene (10 mL) was added and the volatiles were removed under reduced pressure. The residue was diluted in 5 mL of MeOH / water (85:15) and stirred at room temperature for 18 h. The volatiles were removed under reduced pressure, and the residue was dissolved in EtOAc (25 mL) and treated with saturated NaHCO3 aqueous solution (20 mL). The layers were partitioned, and the aqueous layer was extracted with EtOAc (20 mL). The combined organic layers were washed with brine, dried over MgSO 4 , filtered, and concentrated to dryness in vacuo. The residue was absorbed onto silica gel for purification by ISCO CombiFlash (12 g Gold SiO 2 column) eluting with 80-100% EtOAc / hexanes to afford 23 mg of (R)-2-methyl-2-(6-(3-(methylmorpholino)-1-(1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)propanamide as a colorless foam. 1 H NMR (400MHz, DMSO): δ12.80 (s; 1H); 7.90 (s; 1H); 7.83 (s; 1H); 7.06 (s; 1H); 7 .02 (s; 1H); 6.76-6.77 (m; 1H); 6.65 (s; 1H); 4.47-4.50 (m; 1H); 4.06 (d; J=13. 56Hz; 1H); 3.99 (d; J = 11.46Hz; 1H); 3.78 (d; J = 11.34Hz; 1H); 3.63-3.66 (m; 1H ); 3.47-3.53 (m; 1H); 3.17-3.23 (m; 1H); 1.54 (s; 6H); 1.22 (d; J=6.68Hz; 3H). MS(+ESI):m / z370.2.

[0734] Compound 5

[0735] Step 1. To a solution of (R)-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)methanol (115 mg) from Example 4, Step 5, and 2-hydroxyisobutyronitrile (0.07 mL) in anhydrous toluene (10 mL) were added tributylphosphine (0.2 mL) and TMAD (133.6 mg) and the resulting mixture was stirred at room temperature for 1 h, then diluted with water and extracted with EtOAc. The organic extracts were dried and concentrated to dryness, then purified by Combi-Flash (12 g column) eluting with 10-80% EtOAc / hexanes to afford 110 mg of (R)-2-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)acetonitrile as a light yellow oil.

[0736] Step 2. To a solution of (R)-2-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)acetonitrile (68 mg) in toluene (2 mL) was added tetrabutylammonium bromide (9.66 mg) and 50% NaOH (0.5 mL), followed by 1,5-dibromopentane (0.027 mL). The mixture was heated to 65° C. for 2 h, then diluted with water and extracted with EtOAc. The combined organic extracts were dried over NaSO4, concentrated to dryness and purified by Combi-Flash (4 g column) eluting with 20-80% EtOAc / hexanes to give 54 mg of (R)-1-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)cyclohexane-1-carbonitrile as a light yellow oil.

[0737] Step 3. To a solution of (R)-1-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)cyclohexane-1-carbonitrile (54 mg) in dichloromethane (2 mL) was added TFA (0.27 mL). The reaction mixture was stirred at room temperature for 18 h and then concentrated under reduced pressure. The residue was dissolved in 5 mL of MeOH / H2O) (85:15) and stirred at room temperature for 18 h and concentrated. The residue was dissolved in EtOAc (25 mL) and saturated NaHCO3 aqueous solution (25 mL). Each layer was distributed, and the aqueous layer was extracted with EtOAc (10 mL). The combined organic layers were washed with brine, dried over MgSO4, filtered and concentrated. The residue was absorbed onto silica gel for purification by ISCO CombiFlash (4 g column) eluting with 30-100% EtOAc / n-hexane to afford 11 mg of (R)-1-(6-(3-methylmorpholino)-1-(1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)cyclohexane-1-carbonitrile as an off-white foam. 1 HNMR (400MHz, CDCl3): δ1.37 (d; 3H); 1.96 (d; 5H); 2.09 (t; 2H); 2.29 (d; 2H); 3.39 (td; 1H); 3.65 (td; 1 H); 3.87-3.77 (m; 2H); 4.08 (d; 3H); 4.49 (d; 1H); 6.82 (s; 1H); 6.99 (d; 1H); 7.80 (d; 1H); 8.22 (s; 1H).

[0738] Compound 6

[0739] Step 1. at 0 DEG C, in 30min, to the suspension of mechanically stirred 4-chloro-1H-pyrrolo-[2,3-b]pyridine (35g) in EtOAc (600mL) mCPBA (51.41g) was added in batches. Then the reaction mixture was stirred at rt for 18h, and the solid was collected by filtration and washed with n-heptane (350mL). The residue was dried under high vacuum to obtain 62g of 4-chloro-1H-pyrrolo-[2,3-b]pyridine 7-oxide 3-chlorobenzoate as a gray solid.

[0740] Step 2. To a mixture of 4-chloro-1H-pyrrolo[2,3-b]pyridine 7-oxide 3-chlorobenzoate (30g) in acetonitrile (300mL) was added dimethyl sulfate (9.6mL), and the reaction mixture was heated to 60°C for 18h. After cooling to rt, (R)-3-methylphosphine (14g) was added, followed by diisopropylethylamine (48.2mL), and the reaction mixture was heated to 60°C for 18h. After cooling to rt, volatiles were removed in vacuo, and the residue was purified by silica gel column chromatography (eluted with 10-40% EtOAc / hexane) to give 12g of (R)-4-(4-chloro-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methylmorpholine as a light grey solid.

[0741] Step 3. A mixture of (R)-4-(4-chloro-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methylmorpholine (11.64 g), iodine pyrazole (15.11 g), CuI (81 mg), trans-N,N-dimethylcyclohexane-1,2-diamine (0.66 mL) and K3PO4 (17.23 g) in dioxane (110 mL) was purged with argon three times and heated to 110°C for 18 h. The mixture was cooled and filtered through a silica gel pad eluted with EtOAc (700 mL). The filtrate was concentrated in vacuo to dryness and then purified by flash chromatography on silica gel eluted with 10-25% EtOAc / hexane. The pure fractions were combined and concentrated to give 19.3 g.

[0742] (R)-4-(4-chloro-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methylmorpholine as a mixture of SEM regioisomers.

[0743] Step 4. To a solution of (R)-4-(4-chloro-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methylmorpholine (5.0 g), bis(pinacolato)diboron (4.25 g), Pd2(dba)3 (510 mg), and tricyclohexylphosphine (780 mg) in dioxane (70 mL) was added potassium acetate (3.32 g). The mixture was purged with argon and heated to 100°C overnight, then cooled, diluted with ethyl acetate, and filtered through a pad of celite. The filtrate was concentrated to dryness and resubmitted to reaction conditions. After overnight, the reaction mixture was diluted with ethyl acetate, filtered through a pad of celite, and concentrated to dryness. Purification by column chromatography (eluting with 0-50% ethyl acetate / hexanes) gave 4.38 g of (R)-3-methyl-4-(4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-6-yl)morpholine as a yellow powder.

[0744] Step 5. To a dram containing (R)-3-methyl-4-(4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-6-yl)morpholine (106 mg), 2-bromophenylmethylsulfone (93 mg), [1,1'-bis(diphenylphosphino)ferrocene]dichloropalladium(II) (10 mg) was added dioxane (1 mL) and 2N NaCO (250 μL). The mixture was evacuated, purged with argon (3x), and heated at 120°C for 24 h before being cooled and partitioned between water and ethyl acetate. The organic phase was separated and the aqueous phase was extracted three times with ethyl acetate. The combined organic layers were washed with brine, dried over NaSO, filtered, and concentrated. The crude material was purified on a Redisep Gold Column (12 g) using 0-100% ethyl acetate / hexanes to afford 76 mg of (R)-3-methyl-4-(4-(2-(methylsulfonyl)phenyl)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-6-yl)morpholine.

[0745] Step 6. To a solution of (R)-3-methyl-4-(4-(2-(methylsulfonyl)phenyl)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-6-yl)morpholine (76 mg) in dichloromethane (2 mL) was added TFA (0.45 mL). The reaction was stirred at room temperature overnight, then concentrated and redissolved in 85 / 15 MeOH / HO and stirred for an additional 4 h. The reaction mixture was concentrated and partitioned between ethyl acetate and water. The organic layer was separated, and the aqueous layer was extracted with ethyl acetate (3x). The combined organic layers were washed with brine, dried over NaSO, filtered, and concentrated. The crude material was purified on a Redisep column (24 g) eluting with 40-60% ethyl acetate / hexanes to afford 58 mg of (R)-3-methyl-4-(4-(2-(methylsulfonyl)phenyl)-1-(1H-pyrazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-6-yl)morpholine. 1 HNMR(d6-DMSO)δ12.7(s,1H),8.2(d 1H),7.8(m,1H),7.7(m,2H),7.6(m1H),7.5(m 1H),7.0(s,1H),6.7(s,1H),4.3(m,1H),4.0(m,1H),3.7(m,2H),3.5(m,1H),3.2(m,1H),2.9(s,3H),1.2(d 3H).

[0746] Compound 7

[0747] Step 1. To a solution of 4-chloro-3-methyl-1H-pyrrolo[2,3-b]pyridine 7-oxide 3-chlorobenzoate (508 mg) in acetonitrile (10 mL) was added 3-chlorobenzoic acid (275 mg) and dimethyl sulfate (0.29 mL), and the reaction was heated at 60° C. for 36 h. After cooling, (R)-3-methylmorpholine (423 mg) and DIPEA (1.45 mL) were added, and the reaction was heated at 60° C. for 26 h. The reaction mixture was concentrated and purified by silica gel chromatography using 40 to 100% ethyl acetate / hexane to give 243 mg of (R)-4-(4-chloro-3-methyl-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methylmorpholine.

[0748] Step 2. To a 100 mL flask containing (R)-4-(4-chloro-3-methyl-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methylmorpholine (2.08 g) was added a solution of 3-iodo-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazole (2.79 g) in dioxane (20 mL). Argon was bubbled through the mixture and ground K3PO4 (2.9 g) was added followed by trans-N,N'-dimethylcyclohexane-1,2-diamine (111 mg) and CuI (15 mg). The reaction was heated at 100°C for 44 h and then filtered through celite and rinsed with ethyl acetate. The filtrate was washed with water and the organic layer was dried over Na2SO4, filtered and concentrated. Purification on a Redisep Gold column (80 g) eluting with 0-100% ethyl acetate in hexanes afforded 2.53 g of (R)-3-methyl-4-(6-(1-(methylsulfonyl)cyclopropyl)-2-((1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)sulfanyl)pyrimidin-4-yl)morpholine as a mixture of regioisomers.

[0749] Step 3. To a solution of (R)-4-(4-chloro-3-methyl-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-6-yl)-3-methylmorpholine (138 mg) in THF (1 mL) was added isobutyronitrile (350 μL) followed by LiHMDS (1 M in THF, 2.7 mL). The mixture was heated in a microwave at 100° C. for 15 min, then cooled and partitioned between saturated aqueous NH4Cl solution and ethyl acetate. The aqueous layer was extracted 3× with ethyl acetate and the combined organic layers were washed with brine, dried over Na2SO4, filtered and concentrated. Purification on a Redisep Gold column (24 g) using 0-100% ethyl acetate / hexanes afforded 136 mg of (R)-2-methyl-2-(3-methyl-6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-4-yl)propanenitrile as an oil.

[0750] Step 4. To a solution of (R)-2-methyl-2-(3-methyl-6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-4-yl)propionitrile (135 mg) in dichloromethane (1 mL) was added TFA (250 μL). The reaction was stirred at room temperature for 3 days, then concentrated and partitioned between ethyl acetate and saturated aqueous NaHCO3. The organic layer was separated, and the aqueous layer was extracted with ethyl acetate (3x). The combined organic layers were dried over Na2SO4, filtered, and concentrated. Purification on a Redisep Gold column (12 g) using 30-100% ethyl acetate / hexanes afforded 15 mg of (R)-2-methyl-2-(3-methyl-6-(3-methylmorpholino)-1-(1H-pyrazol-3-yl)-1H-pyrrolo[2,3-b]pyridin-4-yl)propanenitrile. 1 H NMR(d6-DMSO)δ12.7(s,1H),7.8(s,1H),7.6(s,1H),6.9(s,1H),6.6(s,1H),5.7(s,1H),4.4(m ,1H),4.0(m,1H),3.9(m,1H),3.8(m,1H),3.7(m,1H),3.5(m,1H),3.2(m,1H),2.6(s,3H),1.2(d 3H).

[0751] Compound 8

[0752] Step 1. To a solution of 5,7-dichloro-3H-imidazo[4,5-b]pyridine (457 mg) and 2-(chloromethoxy)ethyltrimethylsilane (516 μL) in DMF (8 mL) was added diisopropylethylamine (509 μL) and the mixture was stirred at room temperature for 1 h. Water and Et2O were added and the phases were separated. The aqueous phase was extracted with Et2O (2x), and the combined organic extracts were washed with brine and dried over Na2SO4, filtered and evaporated under reduced pressure. The crude mixture was purified using silica gel chromatography (eluting with 0 to 70% EtOAc / hexanes) to afford 473 mg of 2-[((5,7-dichloroimidazo[4,5-b]pyridin-3-yl)methoxy]ethyltrimethylsilane (temporarily partitioned) and 120 mg of 2-[(5,7-dichloroimidazo[4,5-b]pyridin-1-yl)methoxy]ethyltrimethylsilane (temporarily partitioned). Major isomers: 1H NMR (400 MHz, CDCl3) δ 8.22 (s, 1H), 7.35 (s, 1H), 5.64 (s, 2H), 3.69–3.48 (m, 2H), 0.99–0.85 (m, 2H), -0.04 (s, 9H). LCMS: 318.12 (M+H). Minor isomer: 1 HNMR (400MHz, CDCl3) δ8.21(s,1H),7.30(s,1H),5.74(s,2H),3.68–3.42(m,2H),1.05–0.84(m,2H),-0.07(s,9H). LCMS:319.97(M+H). LCMS:318.25(M+H).

[0753] Step 2. To a solution of 2-[(5,7-dichloroimidazo[4,5-b]pyridin-3-yl)methoxy]ethyl-trimethylsilane (90 mg), K 3 PO 4 (2M, 424 μL) and (2-methylsulfonylphenyl)boronic acid (68 mg) in dioxane (1 mL) was added Pd(dppf)Cl 2 · C 2 Cl 2 (31 mg) under nitrogen and stirred at 80° C. overnight. Water and EtOAc were added and the phases were separated. The aqueous phase was extracted with EtOAc (2×) and the combined organic extracts were washed with brine, dried over Na 2 SO 4 , filtered and evaporated under reduced pressure. The crude mixture was purified using silica gel chromatography (eluting with 0 to 100% EtOAc / hexanes) to provide 2-[[7-chloro-5-(2-methylsulfonylphenyl)imidazo[4,5-b]pyridin-3-yl]methoxy]ethyl-trimethylsilane as a 1:1 mixture of regioisomers. 1 HNMR(400MHz, CDCl3)δ8.22(dd,J=7.7,1.6Hz,1H),8.14(s,1H),7.79–7.64(m,2H),7.41(dd,J=7.3,1 .6Hz,1H),7.33(s,1H),5.67(s,2H),3.77–3.63(m,2H),3.03(s,3H),1.04–0.91(m,2H),-0.03(s,9H). LCMS:437.94(M+H).

[0754] Step 3. to 2-[[7-chloro-5-(2-methylsulfonylphenyl)imidazo[4,5-b]pyridinyl-3-yl]methoxy]ethyl-trimethylsilane (640mg) in anhydrous dioxane (1mL) solution was added cesium carbonate (952mg), RuPhos PdG1 methyl tert-butyl ether adduct (119mg) and (3R)-3-methylmorpholine (332μL). The mixture was purged with nitrogen and then heated to 100°C in a sealed vial for 16h. Water and EtOAc were added and the phases were separated. The aqueous phase was extracted with EtOAc (2x), and the combined organic extracts were washed with brine, then dried over Na2SO4, filtered and evaporated under reduced pressure. The residue was taken up in DMSO and purified using reverse phase chromatography to give 490 mg of trimethyl-[2-[[5-[(3R)-3-methylmorpholin-4-yl]-7-(2-methylsulfonylphenyl)imidazo[4,5-b]pyridin-3-yl]methoxy]ethyl]silane. 1 H NMR (400MHz, CDCl3) δ8.21 (dd, J=7.9, 1.4Hz, 1H), 7.95 (s, 1H), 7.68 (td, J=7.5, 1.4Hz, 1H), 7.59 (td, J=7 .7,1.5Hz,1H),7.52(dd,J=7.5,1.4Hz,1H),6.62(s,1H),5.56(d,J=2.3Hz,2H),5.06(s,1H),4.33(d,J=13 .2Hz,1H),4.03(dd,J=11.4,3.6Hz,1H),3.93(dd,J=11.4,3.1Hz,1H),3.84–3.71(m,2H),3.63–3.53(m,2 H),3.49(td,J=6.5,5.5,3.8Hz,1H),3.32(s,3H),1.34(d,J=6.7Hz,3H),0.97–0.83(m,2H),-0.06(s,9H). LCMS:505.19(M+H).

[0755] Step 4. to trimethyl-[2-[[5-[(3R)-3-methylmorpholine-4-yl]-7-(2-methylsulfonylphenyl)imidazo[4,5-b]pyridin-3-yl]methoxy]ethyl]silane (55 mg) in dichloromethane (1 mL) was slowly added TFA (250 μL), and the mixture was stirred at room temperature overnight. Additional TFA (250 μL) was added and the mixture was stirred over the weekend. Volatiles were removed under reduced pressure, and the crude residue was dissolved in EtOAc and treated with saturated NaHCO solution, and the layers were separated. The water layer was extracted with EtOAc (2x), and the combined organic extracts were dried over sodium sulfate, filtered and concentrated. The residue was purified using reverse phase chromatography to give 31 mg of (3R)-3-methyl-4-[7-(2-methylsulfonylphenyl)-3H-imidazo[4,5-b]pyridin-5-yl]morpholine. 1 H NMR(400MHz, CDCl3)δ8.23(dd,J=7.9,1.4Hz,1H),7.74(s,1H),7.70(td,J=7.5,1.4Hz, 1H),7.63(td,J=7.7,1.5Hz,1H),7.48(dd,J=7.5,1.4Hz,1H),6.73(s,1H),4.25(q,J=7. 0Hz,1H),4.02(dd,J=11.4,3.6Hz,1H),3.92–3.84(m,1H),3.80(d,J=2.1Hz,2H),3.64(t d,J=11.7,3.0Hz,1H),3.27(td,J=12.5,3.8Hz,1H),2.97(s,3H),1.27(d,J=6.7Hz,3H). LCMS:374.08(M+H).

[0756] Step 5. Under nitrogen, to a solution of (3R)-3-methyl-4-[5-(2-methylsulfonylphenyl)-3H-imidazo[4,5-b]pyridin-7-yl]morpholine (290 mg), 2-[(3-iodopyrazol-1-yl)methoxy]ethyl-trimethyl-silane (510 mg), 3-(1,1-difluoroethyl)benzenesulfinic acid (54 mg) and cesium carbonate (634 mg) in NMP (3.5 mL) was added copper bromide (45 mg) and the mixture was heated at 120° C. overnight. The mixture was cooled, treated with saturated aqueous NH4Cl solution, water and ammonium hydroxide (4:1:3), and extracted with EtOAc. The aqueous phase was extracted with EtOAc (2×), and the combined organic phases were washed with brine, dried over Na2SO4, filtered, and concentrated. The crude product was purified using reverse phase chromatography to afford 220 mg of trimethyl-[2-[[3-[5-[(3R)-3-methylmorpholin-4-yl]-7-(2-methylsulfonylphenyl)imidazo[4,5-b]pyridin-3-yl]pyrazol-1-yl]methoxy]ethyl]silane as a mixture of regioisomers. LCMS: 569.38 (M+H).

[0757] Step 6. to trimethyl-[2-[[3-[5-[(3R)-3-methylmorpholine-4-yl]-7-(2-methylsulfonylphenyl)imidazo[4,5-b]pyridin-3-yl]pyrazol-1-yl]methoxy]ethyl]silane (14 mg) in dichloromethane (1 mL) was added TFA (56 μL) and the mixture was stirred at room temperature overnight. Volatiles were removed under reduced pressure, and the mixture was dissolved in dioxane (1 mL) and basified to pH about 10 using 3N NaOH, and heated at 80 ° C for 3h. The mixture was distributed between EtOAc and water. The aqueous phase was extracted with EtOAc (2x), and the combined organic extracts were washed with brine, dried over Na2SO4, filtered and concentrated. The residue was taken up in DMSO and purified using reverse phase chromatography to give 3.7 mg of (3R)-3-methyl-4-[7-(2-methylsulfonylphenyl)-3-(1H-pyrazol-3-yl)imidazo[4,5-b]pyridin-5-yl]morpholine. 1H NMR (400MHz, DMSO-d6) δ13.03(s,1H),8.47(s,1H),8.14(dd,J=7.8,1.5Hz,1H),7.96(d ,J=2.3Hz,1H),7.80(dtd,J=21.7,7.5,1.5Hz,2H),7.52(dd,J=7.4,1.5Hz,1H),6.97(d ,J=2.2Hz,1H),6.79(s,1H),4.42–4.32(m,1H),3.99(d,J=11.8Hz,2H),3.82–3.65(m,2 H), 3.54 (td, J = 11.7, 3.0 Hz, 1H), 3.19 (s, 3H), 3.18–3.07 (m, 1H), 1.19 (d, J = 6.6 Hz, 3H). LCMS:438.94(M+H).

[0758] Intermediate C

[0759] Step 1. To a solution of 3-aminopyrazole (24.7 g, 297 mmol) in 6N HCl (181 mL) at -5°C was added 1 M NaNO aqueous solution (300 mL, 297 mmol). A solution of SnCl (113 g, 595 mmol) in concentrated HCl (510 mL) was then added dropwise, and the resulting mixture was stirred at room temperature for 2 h. The solvent was evaporated under reduced pressure to give 3-hydrazinylidene-3H-pyrazole as a light brown solid, which was used as is without further purification. 1 HNMR (400MHz, DMSO-d6, δppm): 9.90 (s, 3H), 7.65 (d, J = 2.4Hz, 1H), 5.81 (d, J = 2.3Hz, 1H).

[0760] Step 2. 500mL frame dried RBF is loaded with 2,6-difluoro-4-iodopyridine (17g, 70.5mmol) and anhydrous THF (255mL). The yellow reaction mixture is cooled to -78 ° C, and commercially available LDA (1.0M in THF / hexane, 84.7mL, 84.7mmol) is added dropwise so as to keep the internal temperature below -68 ° C. The light brown solution is stirred at -78 ° C for 1 hour, and ethyl formate (8.5mL, 105.678mmol) is then added in 10min. The reaction is monitored by TLC and completed after 30min. Formic acid (5.3mL, 140.5mmol) is added dropwise, and the mixture is stirred at -78 ° C for 10min, then diluted with EtOAc (150mL). The mixture is warmed to 0 ° C and water (100mL) is added. Each layer is separated, and the aqueous layer is extracted with EtOAc (150mL). The combined organic layers were washed with brine, dried over Na 2 SO 4 , filtered and concentrated in vacuo to afford 19 g of 2,6-difluoro-4-iodo-pyridine-3-carbaldehyde as a light brown solid. 1 H NMR: (400MHz, CDCl3), δ10.11 (s, 1H), 7.54 (d; J=2.87Hz; 1H).

[0761] Step 3. add 2,6-difluoro-4-iodo-pyridine-3-carboxaldehyde (4.4g, 16.3mmol) to the suspension of 3-hydrazide-3H-pyrazole (12.5g, 94.3mmol) in 95%EtOH (70mL) and stir the mixture at rt for 15min.Then most of the volatiles are removed under reduced pressure.The orange mixture is dissolved in EtOAc and NaHCO3 and stirred at rt for 15 minutes, resulting in a violent evolution of gas. Each phase is separated and the aqueous phase is extracted 3 times with EtOAc.The organic extracts merged are washed with water and salt water, then dried over MgSO4, filtered and evaporated under reduced pressure to obtain (E)-3-((2-(1H-pyrazol-3-yl)hydrazide)methyl)-2,6-difluoro-4-iodopyridine (5.5g, 15.9mmol) as a yellow / orange solid. 1 HNMR(400MHz, DMSO-d6)12.02(s,1H),10.89(s,1H),7.92(s,1H),7.82(d,1H),7.54(s,1H),5.97(s,1H).

[0762] Step 4. A solution of (E)-3-((2-(1H-pyrazol-3-yl)hydrazinylidene)methyl)-2,6-difluoro-4-iodopyridine (8.6 g, 24.7 mmol) in NMP (115 mL) was divided into 20 mL batches and heated in a microwave reactor at 200 °C for 20 min. The combined mixture was then added dropwise to water with vigorous stirring to give a cloudy mixture, which was stirred at rt for 5 min and then cooled to 0 °C. The precipitate was filtered, washed with water and dried on a Buchner funnel for 1 h and under reduced pressure for 1 h to give 6-fluoro-4-iodo-1-(1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridine (6.8 g, 20.7 mmol) as a light brown powder. 1 H NMR (400MHz, DMSO-d6) δ13.13(s,1H),8.29(s,1H),7.95(t,1H),7.71(d,1H),6.67(t,1H).

[0763] Step 5. A solution of 6-fluoro-4-iodo-1-(1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridine (6.8 g, 20.7 mmol) and (R)-3-methylmorpholine (1.24 mL, 7.23 mmol) in DMSO (35 mL) was sealed in a thick-walled tube and heated to 120 ° C for 45 min. The mixture was then added dropwise to a conical flask filled with water under vigorous stirring. The turbid mixture was stirred at rt for 5 min, then at 0 ° C for 20 min. The precipitation was filtered on a Buchner funnel, and the precipitation was washed with water and dried overnight on a Buchner funnel to obtain (R)-4-(4-iodo-1-(1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-6-yl)-3-methylmorpholine (6.9 g, 16.8 mmol), intermediate B.

[0764] Step 6. add 2-(chloromethoxy)ethyltrimethylsilane (1.04mL, 5.8mmol) in the solution of intermediate B (2.00g, 4.88mmol) in DMF (20mL), then add diisopropylethylamine (1.28mL, 7.3mmol), and stir the gained mixture for 40min.Mixture is distributed between EtOAc and water, and aqueous phase is extracted with EtOAc (2x).The organic layer water (2x) and salt water washing that merge are then through Na SO Dry, filter and evaporate. Purification by silica gel chromatography (gradient 0 to 80% EtOAc / hexanes) gave 2-[[3-[4-iodo-6-[(3R)-3-methylmorpholin-4-yl]pyrazolo[3,4-b]pyridin-1-yl]pyrazol-1-yl]methoxy]ethyltrimethylsilane (0.67 g, 1.25 mmol) and 2-[[5-[4-iodo-6-[(3R)-3-methylmorpholin-4-yl]pyrazolo[3,4-b]pyridin-1-yl]pyrazol-1-yl]methoxy]ethyltrimethylsilane (0.17 g, 0.31 mmol).

[0765] Compound 86

[0766] Step 1. 2,6-difluoro-4-iodo-pyridine-3-carboxaldehyde (1.76 g, 6.54 mmol) in DME (15 mL) was dissolved in a round-bottom flask and hydrazine hydrate (535 μL, 65% purity, 7.1 mmol) was added. The reaction mixture was stirred at rt for 4 h. Water was added to the heterogeneous yellow solution and stirred at rt for 30 min. The resulting solid was then collected by filtration, rinsed with water and vacuum dried overnight to obtain 6-fluoro-4-iodo-1H-pyrazolo[3,4-b]pyridine.

[0767] Step 2. 6-Fluoro-4-iodo-1H-pyrazolo[3,4-b]pyridine (2.18 g, 8.29 mmol) was dissolved in DMSO (30 mL) in a RBF. To this solution was added (3R)-3-methylmorpholine (3.43 g, 33.94 mmol, 3.85 mL), and the reaction mixture was stirred at 120°C overnight before slowly cooling to rt. Water was slowly added over 5-10 minutes, and the flask was placed in an ice bath, and the solution was stirred for 1 hour. The resulting solid was then collected by filtration, washed with water, and dried under vacuum for 1 hour, then dried under vacuum overnight to yield (3R)-4-(4-iodo-1H-pyrazolo[3,4-b]pyridin-6-yl)-3-methylmorpholine (2.12 g, 6.16 mmol).

[0768] Step 3. 6-Fluoro-4-iodo-1H-pyrazolo[3,4-b]pyridine (1.54 g, 5.86 mmol) in DMF (40 mL) was dissolved in a RBF and cooled to 0°C. To this solution was added 60 wt% sodium hydride (281.0 mg, 7.03 mmol, 60% purity), and the reaction mixture was stirred at 0°C for 30 minutes. SEM-Cl (1.46 g, 8.78 mmol, 1.55 mL) was then added, and the solution was stirred at 0°C for 5 minutes, then returned to room temperature and stirred for an additional hour. Saturated NH4Cl was added, followed by water, and the mixture was stirred for 30 minutes. The resulting solid was collected by filtration and dried under vacuum overnight to give 2-[(6-fluoro-4-iodo-pyrazolo[3,4-b]pyridin-2-yl)methoxy]ethyl-trimethyl-silane as a mixture of SEM regioisomers.

[0769] Step 4. 2-[[4-iodo-6-[(3R)-3-methylmorpholin-4-yl]pyrazolo[3,4-b]pyridin-1-yl]methoxy]ethyl-trimethylsilane (103 mg, 217.11 μmol) in THF (1 mL) was dissolved in a RBF. To this solution was added 2-methylpropionitrile (150.15 mg, 2.17 mmol, 195 μL) followed by LiHMDS (1 M, 1.09 mL). Under microwave irradiation, the reaction mixture was stirred at 20 ° C for 15 min and then heated to 100 ° C for 12 min. Water and EtOAc were added and the phases were separated. The aqueous phase was extracted a second time with EtOAc. The combined organic phases were washed with saturated brine solution, then dried over MgSO4, filtered and evaporated under reduced pressure. The crude product was purified using a 15.5 g Gold C18 Isco column and a 10 to 100% water / MeCN eluent to afford 2-methyl-2-[6-[(3R)-3-methylmorpholin-4-yl]-1-(2-trimethylsilylethoxymethyl)pyrazolo[3,4-b]pyridin-4-yl]propionitrile.

[0770] Step 5. In a RBF was dissolved 2-methyl-2-[6-[(3[R)-3-methylmorpholin-4-yl]-1-(2-trimethylsilylethoxymethyl)pyrazolo[3,4-b]pyridin-4-yl]propionitrile (690 mg, 1.66 mmol) in DCM (30 mL) and TFA (3.80 mL, 50 mmol) was added. The reaction mixture was stirred at rt overnight and then the volatiles were removed in vacuo. The crude product was dissolved in 1 mL of DMSO and purified using a 15.5 g Gold C18 Isco column and 5 to 100% water / MeCN eluent to give 2-methyl-2-[6-[(3R)-3-methylmorpholin-4-yl]-1H-pyrazolo[3,4-b]pyridin-4-yl]propionitrile.

[0771] Step 6. A solution of 2-methyl-2-[6-[(3[R)-3-methylmorpholin-4-yl]-1H-pyrazolo[3,4-b]pyridin-4-yl]propionitrile (100 mg, 0.35 mmol), 5-iodo-3-methyl-1-tetrahydropyran-2-yl-pyrazole (205 mg, 0.7 mmol), cesium carbonate (285 mg, 0.87 mmol), (1S,2S)-N1,N2-dimethylcyclohexane-1,2-diamine (100 mg, 0.70 mmol) in NMP (1.2 mL) was flushed with nitrogen for 5 minutes, followed by the addition of copper iodide (67 mg, 0.35 mmol). The mixture was heated to 120° C. for 16 hours. Water was added, the mixture was stirred for 30 minutes, and the resulting solid was collected by filtration and dried under vacuum for 1 hour. This solid was then dissolved in 1 mL of DMSO and purified by reverse phase chromatography (5 to 100% water / MeCN over 20 CV) to afford 2-methyl-2-[6-[(3[R)-3-methylmorpholin-4-yl]-1-(5-methyl-2-tetrahydropyran-2-yl-pyrazol-3-yl)pyrazolo[3,4-b]pyridin-4-yl]propanenitrile.

[0772] Step 7. In a round-bottom flask, 2-methyl-2-[6-[(3[R)-3-methylmorpholin-4-yl]-1-(5-methyl-2-tetrahydropyran-2-yl-pyrazol-3-yl)pyrazolo[3,4-b]pyridin-4-yl]propionitrile (42 mg, 93 μmol) was dissolved in MeOH (0.5 mL). To this solution was added HCl in MeOH (1.25 M, 112 μL), and the reaction mixture was stirred at 60°C for 1 h. The volatiles were evaporated under reduced pressure, and the crude product was purified using a 15.5 g Gold C18 Isco column and a 5 to 100% water / MeCN eluent to provide Compound 86. 1 H NMR (400MHz, DMSO-d6) δ12.51(s,1H),8.27(s,1H),6.73(s,1H),6.49(d,J=2. 0Hz,1H),4.46(s,1H),4.09–4.00(m,1H),3.97(dd,J=11.4,3.5Hz,1H),3.76( d,J=11.4Hz,1H),3.64(dd,J=11.5,3.1Hz,1H),3.49(td,J=11.9,3.1Hz,1H), 3.19(td,J=12.6,3.8Hz,1H),2.30(s,3H),1.85(s,6H),1.20(d,J=6.7Hz,3H).

[0773] Compound 99

[0774] Step 1. A solution of 2-[[5-[4-iodo-6-[(3[R)-3-methylmorpholine-4-yl]pyrazolo[3,4-b]pyridin-1-yl]pyrazol-1-yl]methoxy]ethyl-trimethylsilane (500 mg, 0.92 mmol) in THF (8 mL) was cooled to -78 ° C and slowly treated with nBuLi (2.5 M, 0.48 mL). The mixture was stirred for 40 min. A solution of tetrahydropyran-3-one (27 μ L, 2.78 mmol) in 1.5 mL THF was then added to the mixture. The flask was removed from the dry ice bath and continued to stir for 1 h. The mixture was then quenched with saturated NH4Cl solution and EtOAc was added, and each phase was separated. The aqueous phase was extracted twice more with EtOAc, and the combined organic extracts were washed with saturated brine solution, then dried over Na2SO4, filtered and evaporated under reduced pressure to give 3-[6-[(3R)-3-methylmorpholin-4-yl]-1-[2-(2-trimethylsilylethoxymethyl)pyrazol-3-yl]pyrazolo[3,4-b]pyridin-4-yl]tetrahydropyran-3-ol.

[0775] Step 2. A solution of 3-[6-[(3[R)-3-methylmorpholin-4-yl]-1-[2-(2-trimethylsilylethoxymethyl)pyrazol-3-yl]pyrazolo[3,4-b]pyridin-4-yl]tetrahydropyran-3-ol (168 mg, 0.325 mmol), triethylsilane (291 mg, 2.50 mmol, 0.4 mL), DCM (1 mL), and TFA (5.96 g, 52.3 mmol, 4 mL) was stirred at rt for 10 min. The volatiles were removed under reduced pressure, and the residue was purified by reverse phase chromatography to give a mixture of Compound 99 and Compound 100, which was separated by SFC.

[0776] Compound 121

[0777] Step 1. a solution of intermediate C (200mg, 0.37mmol) in THF (4mL) was cooled to -78°C and slowly processed with nBuLi (2.5M, 0.19mL). The mixture was stirred for 40min, and a solution of 8-oxabicyclo [3.2.1] octan-3-one (27 μL, 1.2mmol) in 0.4mL THF was then added. The flask was then removed from a dry ice bath and warmed to rt in 1.5h. The mixture was then quenched with saturated NH4Cl solution and extracted with EtOAc. Aqueous phase was extracted twice more with EtOAc, and the organic extracts merged were washed with saturated brine solution, then through Na2SO4 drying, filtered and evaporated under reduced pressure. The residue was not further purified and was used in the next step.

[0778] Step 2. A solution of 3-[6-[(3R)-3-methylmorpholin-4-yl]-1-[2-(2-trimethylsilylethoxymethyl)pyrazol-3-yl]pyrazolo[3,4-b]pyridin-4-yl]-8-oxabicyclo[3.2.1]octan-3-ol (100 mg, 0.18 mmol) and triethylsilane (0.23 mL, 1.42 mmol) in DCM (1 mL) was treated with TFA (2.3 mL, 30 mmol) at rt and stirred for 10 min. The volatiles were removed under reduced pressure and the residue was purified using silica gel chromatography (eluting with 0-10% MeOH) followed by reverse phase chromatography (eluting with 0-100% MeCN / HO) to give Compound 121. 1 H NMR(400MHz,DMSO-d6)δ12.79(s,1H),8.04(s,1H),7.83(s,1H),6.80(s,1H),6 .78(s,1H),5.33(s,1H),4.49–4.40(m,3H),4.05–3.91(m,2H),3.77(d,J=11.4H z,1H),3.64(dd,J=11.5,3.1Hz,1H),3.49(td,J=11.7,2.9Hz,1H),3.23–3.11( m,1H),2.43–2.31(m,4H),1.81(dd,J=20.9,11.5Hz,4H),1.20(d,J=6.6Hz,3H).

[0779] Compound 125

[0780] Step 1. At rt, to a solution of 2-amino-3-bromopyridine (1.0 g, 5.8 mmol) in DCM (10 mL), di-tert-butyl dicarbamate (2.65 g, 12.1 mmol) and DMAP (35 mg, 0.29 mmol) were added, followed by the slow addition of EtN (1.8 mL, 12.9 mmol). The reaction mixture was stirred at rt for 18 h, then distributed between water (50 mL) and DCM (40 mL). The aqueous layer was extracted with DCM (40 mL) and the combined organic layer was washed with salt water, dried over MgSO, filtered, and concentrated in vacuo. Residue was adsorbed on silica gel to purify by Combi-Flash (80 g Gold SiO) (eluted from 100% hexane to 35% EtOAc / hexane) in 25 min to obtain 1.8 g of (3-bromopyridin-2-yl) di-tert-butyl dicarbamate as a colorless solid. MS (+ESI) m / z 395.1 / 397.1 (M+Na)

[0781] Step 2. (3-bromopyridin-2-yl) di-tert-butyl diaminoformate (150mg, 0.40mmol), bis(pinacolato) diboron (204mg, 0.80mmol) and potassium acetate (120mg, 1.21mmol) are dissolved in anhydrous DMF (1mL), followed by dissolving Pd(dppf)Cl2CH2Cl2 (33mg, 0.04mmol). The reactant is purged with argon and then heated to 85°C for 16h. The mixture is diluted with EtOAc and filtered through a diatomaceous earth pad. Volatiles are evaporated to obtain (tert-butoxycarbonyl) (3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolane-2-yl) pyridin-2-yl) tert-butyl carbamate, which is used without further purification.

[0782] Step 3. 2-[[3-[4-iodo-6-[(3R)-3-methylmorpholin-4-yl]pyrazolo[3,4-b]pyridin-1-yl]pyrazol-1-yl]methoxy]ethyltrimethylsilane (120 mg, 0.22 mmol), K3PO4 (142 mg, 0.66 mmol), Pd(dppfCl2)CH2Cl2 (9 mg, 0.011 mmol) and tert-butyl (tert-butoxycarbonyl)(3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridin-2-yl)carbamate (186 mg, 0.44 mmol) were dissolved in anhydrous DMF (2 mL). The reaction was purged with argon and heated to 85°C for 16 h. The product was purified by combiflash (C18, 26 g) using 5-100% MeCN in H2O (0.1% formic acid) for 20 min to give tert-butyl (R)-(tert-butoxycarbonyl)(3-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)pyridin-2-yl)carbamate (35 mg).

[0783] Step 4. To a solution of tert-butyl (R)-(tert-butoxycarbonyl)(3-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)pyridin-2-yl)carbamate (35 mg, 0.05 mmol) in DCM (1.5 mL) was added TFA (0.40 mL, 5.2 mmol) and Et3SiH (0.03 mL, 0.17 mmol) and the reaction was stirred for 1.5 h. The volatiles were evaporated and the residue was purified by combi-flash (SiO2, 4 g) using 0-100% hexanes in EtOAc over 15 min to give (R)-3-(6-(3-methylmorpholino)-1-(1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)pyridin-2-amine (18 mg).

[0784] Compound 126

[0785] Step 1. A microwave tube was charged with (R)-4-(4-iodo-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-6-yl)-3-methylmorpholine (Intermediate C, 700 mg, 1.30 mmol), (2-(N-(tert-butyl)sulfamoyl)phenyl)boronic acid (492 mg, 1.68 mmol), 2M KCO (2 mL, 4 mmol), Pd(PPh) (75 mg, 0.065 mmol) and dioxane (7 mL). The tube was sealed and flushed with N (vacuum / N, 3 cycles). The mixture was heated to 100 °C for 5 h. LCMS showed the reaction was complete. After cooling to rt, the mixture was diluted with EtOAc (40 mL) and water (40 mL). The layers were separated and the aqueous layer was extracted with EtOAc (70 mL). The combined organic layers were washed with brine, dried over MgSO4, filtered and concentrated to dryness. The residue was adsorbed onto silica gel for purification by ISCO CombiFlash (40 g column, SiO2 Gold) eluting with 20-100% EtOAc / hexanes to afford 700 mg of (R)-N-(tert-butyl)-2-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)benzenesulfonamide.

[0786] Step 2. To a solution of (R)-N-(tert-butyl)-2-(6-(3-methylmorpholino)-1-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-3-yl)-1H-pyrazolo[3,4-b]pyridin-4-yl)benzenesulfonamide (700 mg, 1.12 mmol) and triethylsilane (0.68 mL, 4.26 mmol) in DCM (10 mL) was added TFA (9 mL, 118 mmol) at rt. The reaction mixture was stirred at rt for 4 h. The volatiles were removed in vacuo and the residue was dissolved in TFA (10 mL). The mixture was stirred at rt for 18 h, then heated to 40 ° C for 1 h, and heated to 50 ° C for 1 h. The volatiles were removed under reduced pressure and co-evaporated with DCM (3x). The residue was adsorbed on silica gel for purification by ISCO CombiFlash (24 g column GoldSiO ) (eluted with 30-100% EtOAc / hexane). The desired product fractions were combined and concentrated under reduced pressure to dryness. The residue was dissolved in CH CN (3 mL) and water (5 mL) for lyophilization to give 350 mg of (R) -2- (6- (3-methylmorpholino) -1- (1H- pyrazol-3-yl) -1H- pyrazolo [3, 4-b] pyridin-4-yl) benzenesulfonamide as a light yellow foam. + ESI [M + 1]: 440.2. Purity by HPLC at 254 nm: > 99%, 10-90% CH CN / H O (+ 0.1% formic acid) in 20 min. 1 HNMR (400MHz, DMSO): δ12.83 (s; 1H); 8.11-8.13 (m; 1H); 7.86 (s; 1H); 7.68-7.72 (m; 2H); 7.61 (s; 1H); 7.50-7.52 (m; 1H); 7.42 (s; 2H); 6.83 (s; 1H); 6.80 (s; 1H); 4 .33-4.38(m; 1H); 4.08(d; J=13.32Hz; 1H); 3.97-4.00(m; 1H); 3.73-3.76(m; 1H); 3.64-3.68 (m; 1H); 3.49-3.55 (m; 1H); 3.15-3.21 (m; 1H); 1.22 (d; J=6.61Hz; 3H).

[0787] Compound 138

[0788] Step 1. (3R)-4-[4-iodo-1-[2-[(4-methoxyphenyl)methyl]pyrazol-3-yl]pyrazolo[3,4-b]pyridin-6-yl]-3-methylmorpholine (500 mg, 0.943 mmol), bis(pinacolato)diboron (359 mg, 1.41 mmol) and potassium acetate (324 mg, 3.30 mmol) were combined in DMF (5 mL) and degassed by bubbling N2 through the mixture with sonication for 10 min. Pd(dppf)Cl2.DCM (69 mg, 0.0943 mmol) was then added and the mixture was degassed again for 5 minutes. The reaction was then heated to 95°C for 2 h. The mixture was cooled to rt and partitioned between EtOAc and water (3 volumes each). The organic layer was washed with water (2×3 volumes), dried over Na2SO4 and concentrated to dryness. The product was then purified by combiflash (0-100% EtOAc / hex).

[0789] Step 2. To a solution of (3R)-4-[1-[2-[(4-methoxyphenyl)methyl]pyrazol-3-yl]-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrazolo[3,4-b]pyridin-6-yl]-3-methyl-morpholine (220 mg, 0.415 mmol) and 3-bromo-6-(trifluoromethyl)pyridin-2-amine (200 mg, 0.830 mmol) in DMF (9 mL) was added aqueous KCO (1.1 mL, 1.24 mmol) followed by Pd(dppf)Cl-DCM complex (68 mg, 0.083 mmol). The reaction was heated to 110° C. in a microwave for 10 minutes. The mixture was cooled to rt and partitioned between EtOAc and water (3 volumes each). The organic layer was washed with water (2 x 3 volumes), dried over Na2SO4 and concentrated to dryness. The product was then purified by combiflash (0-100% EtOAc / hex).

[0790] Step 3. 3-[1-[2-[(4-methoxyphenyl)methyl]pyrazol-3-yl]-6-[(3R)-3-methylmorpholin-4-yl]pyrazolo[3,4-b]pyridin-4-yl]-6-(trifluoromethyl)pyridin-2-amine (120 mg, 0.213 mmol) was dissolved in trifluoroacetic acid (3.0 mL, 0.21 mmol) and the reaction was stirred for 2 h. The reaction was evaporated to dryness, the residue was taken up in DMSO (1 mL), and the product was purified by reverse phase combiflash (5-95% MeCN / water). +ESI [M+1]: 445.0. Purity by HPLC at 254 nm: >99%, 10-90% CH3CN / H2O (+0.1% formic acid) within 20 min. 1 HNMR(400MHz,DMSO-d6)δ12.81(s,1H),7.84(br m,2H),7.72(d,J=7.5Hz,1H),7.09(d,J=7.5Hz,1H),6.86–6.77(m,2H),6.45(s,2H),4.48(s,1H),4.11(d,J=13.4Hz,1H),4.07–3 .93(m,1H),3.75(d,J=11.3Hz,1H),3.64(d,J=9.8Hz,1H),3.49(t,J=11.1Hz,1H),3.20(t,J=12.6Hz,1H),1.20(d,J=6.9Hz,3H).

[0791] Compound 139

[0792] Step 1. To a solution of [1-[2-[(4-methoxyphenyl)methyl]pyrazol-3-yl]-6-[(3R)-3-methylmorpholin-4-yl]pyrazolo[3,4-b]pyridin-4-yl]boronic acid (250 mg, 0.558 mmol) and 3-bromo-6-methylpyridin-2-amine (0.33 mL, 1.12 mmol) in DMF (9 mL) was added KCO (1.1 mL, 1.67 mmol) and flushed with nitrogen, followed by the addition of Pd(dppf)Cl-DCM complex (91 mg, 0.11 mmol). The reaction was heated in a microwave at 100 ° C for 10 minutes, then the mixture was cooled to rt and partitioned between EtOAc and water (3 volumes each). The organic layer was washed with water (2×3 volumes), dried over NaSO and concentrated to dryness. The product was then purified by combiflash (0-100% EtOAc / hex).

[0793] Step 2. 3-[1-[2-[(4-Methoxyphenyl)methyl]pyrazol-3-yl]-6-[(3R)-3-methylmorpholin-4-yl]pyrazolo[3,4-b]pyridin-4-yl]-6-methyl-pyridin-2-amine (250 mg, 0.490 mmol) was dissolved in trifluoroacetic acid (4.0 mL, 0.49 mmol) and the reaction was heated to 60° C. and monitored by UPLC-MS. After 1 h, the reaction was cooled to rt and evaporated to dryness the next day. The product was purified by reverse phase combiflash (5-95% MeCN / water). +ESI[M+1]: 391.0. Purity by HPLC at 254 nm: >99%, 10-90% CH3CN / H2O (+0.1% formic acid) within 20 min. 1 HNMR(400MHz,DMSO-d6)δ12.81(s,1H),7.84(br,2H),7.59(br,1H),6.82–6.7 6(m,2H),6.68(s,1H),4.46(s,1H),4.09(d,J=13.3Hz,1H),3.97(d,J=10.2Hz ,1H),3.75(d,J=11.3Hz,1H),3.64(d,J=11.8Hz,1H),3.49(t,J=10.6Hz,1H), 3.19(t,J=13.0Hz,1H),2.55–2.50(m,3H),2.38(s,3H),1.22(d,J=6.6Hz,3H).

[0794] Compound 149

[0795] Step 1. To a solution of intermediate C (690 mg, 1.28 mmol) in chloroform (10 mL) was added N-chlorosuccinimide (170 mg, 1.27 mmol) and stirred overnight at rt. The solution was heated to 65 ° C for 1 h, and then 138 mg of additional N-chlorosuccinimide was added and stirred at 65 ° C for 2 h. The solvent was removed under reduced pressure, and the residue was purified by silica gel chromatography (eluting with 0-100% EtOAc / hexanes) to give 2-[[5-[5-chloro-4-iodo-6-[(3[R)-3-methylmorpholin-4-yl]pyrazolo[3,4-b]pyridin-1-yl]pyrazol-1-yl]methoxy]ethyl-trimethyl-silane (240 mg).

[0796] Step 2. To a solution of 2-[[5-[5-chloro-4-iodo-6-[(3R)-3-methylmorpholin-4-yl]pyrazolo[3,4-b]pyridin-1-yl]pyrazol-1-yl]methoxy]ethyl-trimethyl-silane (107 mg, 0.187 mmol) and 4,4,5,5-tetramethyl-2-[2-(trifluoromethyl)phenyl]-1,3,2-dioxaborolane (0.33 mL, 0.382 mmol) in 1,4-dioxane (1 mL) was added K 3 PO 4 (0.50 mL, 0.560 mmol). The vial was flushed with nitrogen, then Pd(dppf)Cl 2 (30 mg, 0.0373 mmol) was added and heated to 110° C. under microwave for 3 h. The solution was diluted with water and DCM and filtered on a phase separator. The aqueous phase was washed twice with DCM and the combined organic extracts were evaporated under reduced pressure. The product was used in the next step without further purification.

[0797] Step 3. To a solution of unpurified 2-[[5-[5-chloro-6-[(3R)-3-methylmorpholin-4-yl]]-4-[2-(trifluoromethyl)phenyl]pyrazolo[3,4-b]pyridin-1-yl]pyrazol-1-yl]methoxy]ethyl-trimethylsilane (110 mg, 0.186 mmol) in DCM (1 mL) was added 0.2 mL of triethylsilane and 1 mL of TFA. The resulting solution was stirred at rt for 1 h, and the solvent was removed under reduced pressure. The residue was purified using reverse phase chromatography (eluting with 0-100% MeCN / HO) followed by additional purification using normal phase chromatography (eluting with 0-10% MeOH / DCM) to give the desired product as a 1:1 mixture of atropisomers, which was used in bioassays. Further purification using chiral SFC afforded two separated atropisomers (4.0 mg, 6.8% and 4.7 mg, 8.0%, respectively).Mass spectrum: m / z: 463.2.

[0798] Compound 150

[0799] Step 1. 2,6-difluoro-4-iodo-pyridine-3-carboxaldehyde (9.00g, 33.5mmol) is dissolved in DMSO (330mL), and (3R)-3-methylmorpholine (3.8mL, 33.3mmol) is added. The solution is heated at 120 ° C for 2h. The solution is cooled and added dropwise to water (1.5L) with vigorous stirring. Ice is then added, and the suspension is stirred for another 2h. The solid is filtered and dried under house vacuum for 15h. The gained beige solid (10.9g) is dissolved in minimum DCM and purified by silica gel chromatography (0 to 100% EtOAc / hexane gradient) to obtain 2-fluoro-4-iodo-6-[(3R)-3-methylmorpholine-4-yl] pyridine-3-carboxaldehyde (6.36g, 18.16mmol) as a beige solid.

[0800] Step 2. at rt, to 2-fluoro-4-iodo-6-[(3R)-3-methylmorpholine-4-yl]pyridine-3-carboxaldehyde (5.86g, 16.7mmol) in the solution of tert-butyl alcohol (20mL) and water (6.5mL), add 2-methyl-2-butene (82mL, 164mmol), sodium chlorite (7.56g, 83.6mmol) and sodium dihydrogen phosphate (2.64g, 16.9mmol). The gained mixture is stirred for 15h at rt. Slowly add saturated sodium sulfite aqueous solution, add formic acid subsequently until reaching acidic pH. Add EtOAc and each phase is separated. Aqueous phase is extracted 3 times with EtOAc, and the organic extract merged is through MgSO drying, filter and reduced pressure vaporization, obtain beige solid. This material is ground 30 minutes in EtO, then filter, obtain 2.06g pale white solid. The filtrate was concentrated and purified on a 100 g C18 column using a 0 to 100% MeCN / water gradient to afford an additional 2.83 g of beige solid for a total of 4.89 g of 2-fluoro-4-iodo-6-[(3[R)-3-methylmorpholin-4-yl]pyridine-3-carboxylic acid.

[0801] Step 3. To a solution of 2-fluoro-4-iodo-6-[(3[R)-3-methylmorpholin-4-yl]pyridine-3-carboxylic acid (4.89 g, 13.4 mmol) in DMF (67 mL) was added azobenzenium-[2-[(4-methoxyphenyl)methyl]pyrazol-3-yl]ammonium dichloride (4.65 g, 16.0 mmol) followed by 2,6-lutidine (12 mL, 100 mmol). HATU (6.17 g, 16.2 mmol) was then added and the reaction mixture was stirred at rt for 1 h. The solution was then added dropwise to water (400 mL) with vigorous stirring to give a suspension, which was stirred for 1 h and then filtered. The resulting solid was dried in vacuo for 15 h to give 2-fluoro-4-iodo-N′-[2-[(4-methoxyphenyl)methyl]pyrazol-3-yl]-6-[(3[R)-3-methylmorpholin-4-yl]pyridine-3-carbohydrazide (7.48 g, 13.2 mmol) as a beige solid.

[0802] Step 4. 2-Fluoro-4-iodo-N'-[2-[(4-methoxyphenyl)methyl]pyrazol-3-yl]-6-[(3R)-3-methylmorpholin-4-yl]pyridine-3-carbohydrazide (2.00 g, 3.53 mmol) was dissolved in DMF (70 mL) and NaH (285 mg, 7.13 mmol) was added. The mixture was stirred at rt for 10 minutes and then slowly heated to 60°C over 30 minutes. Water, brine and EtOAc were added and the phases were separated. The aqueous phase was extracted three times with EtOAc and the combined organics were dried over MgSO4, filtered and evaporated under reduced pressure. The resulting material was purified by silica gel chromatography (0 to 10% MeOH / DCM gradient) to afford 4-iodo-1-[2-[(4-methoxyphenyl)methyl]pyrazol-3-yl]-6-[(3R)-3-methylmorpholin-4-yl]-2H-pyrazolo[3,4-b]pyridin-3-one (1.19 g, 2.18 mmol) as a brown solid.

[0803] Step 5. To a solution of 4-iodo-1-[2-[(4-methoxyphenyl)methyl]pyrazol-3-yl]-6-[(3R)-3-methylmorpholin-4-yl]-2H-pyrazolo[3,4-b]pyridin-3-one (100 mg, 0.183 mmol) and 2-trifluoromethylphenylboronic acid (87 mg, 0.43 mmol) in 1,4-dioxane (1.8 mL) was added KCO (0.28 mL, 0.55 mmol). The mixture was flushed with nitrogen for 5 minutes, then Pd(dppf)Cl (30 mg, 0.037 mmol) was added, and then heated to 110° C. under microwave irradiation for 15 minutes. Water and DCM were added, and the phases were separated. The aqueous phase was extracted three times with DCM, and the organic extracts were combined, dried over MgSO4, filtered, and evaporated under reduced pressure to give 1-[2-[(4-methoxyphenyl)methyl]pyrazol-3-yl]-6-[(3[R)-3-methylmorpholin-4-yl]-4-[2-(trifluoromethyl)phenyl]-2H-pyrazolo[3,4-b]pyridin-3-one (103 mg, 0.182 mmol) as a dark solid. The material was used in the next step without purification.

[0804] Step 6. The unpurified material from Step 5 was dissolved in trifluoroacetic acid (2.0 mL) and stirred at 60° C. for 1.5 h, then concentrated in vacuo. The resulting material was dissolved in DMSO (1 mL) and purified by silica gel chromatography (0 to 100% MeCN / water gradient) to afford 6-[(3R)-3-methylmorpholin-4-yl]-1-(1H-pyrazol-5-yl)-4-[2-(trifluoromethyl)phenyl]-2H-pyrazolo[3,4-b]pyridin-3-one (35 mg, 0.079 mmol) as a beige solid. 1 H NMR (400MHz, DMSO-d6) δ12.60(s,1H),10.86(s,1H),7.84(d,J=7.8Hz,1H),7.79–7.75(m,1H),7.7 3(t,J=7.5Hz,1H),7.65(t,J=7.6Hz,1H),7.47(d,J=7.0Hz,1H),6.76(s,1H),6.48(d,J=5.5Hz,1H) ,4.44–4.33(m,1H),4.12–4.03(m,1H),4.01–3.91(m,1H),3.73(d,J=11.4Hz,1H),3.65(dd,J=11. 4,2.7Hz,1H),3.57–3.46(m,1H),3.17(td,J=12.7,12.2,3.5Hz,1H),1.20(dd,J=10.9,6.6Hz,3H).

[0805] Example 2. ATR / ATRIP Enzyme Assay

[0806] ATR kinase activity was detected using the AlphaScreen system to measure phosphorylation of the substrate protein p53. Recombinant, purified ATR / ATRIP (Eurofins catalog number 14-953) was mixed at a final concentration of 0.63 nM in assay buffer (50 mM Hepes pH 7.4, 0.1 mM vanadate, 0.5 mM DTT, 0.1 mM EGTA, 5 mM MnCl2, 0.01% Brij-30, 1% glycerol, 0.05% BSA) with serially diluted compounds in 10% DMSO. The final DMSO concentration was 1.25%. A premix of GST-tagged p53 (full length, Enzo Life Sciences catalog number BML-FW9370) and 5′-adenosine triphosphate (ATP) (Sigma-Aldrich catalog number 10519979001, Roche Diagnostic) in assay buffer was added to the enzyme:compound mixture to a final concentration of 25 nM GST-p53 and 3 μM ATP. The reaction was allowed to proceed for 1 hour at room temperature and then terminated by the addition of a premix of 1:3000 final dilution of phosphorylated p53 (Ser 15) antibody (New England Biolabs catalog number 9284S), glutathione donor beads (PerkinElmer Life Sciences catalog number 6765301) at a final bead concentration of 14.3 μg / mL and protein A acceptor beads (PerkinElmer Life Sciences catalog number 670137) at a final bead concentration of 14.3 μg / mL in buffer (60 mM EDTA in 50 mM Tris, pH 7.4, and 0.1% BSA). The plate was incubated for 4 hours in the dark at room temperature and read on a BMG Polarstar using an AlphaScreen dedicated filter. The assay was performed in a 96-well format using white polypropylene half-area plates (Costar catalog number 3693). IC 50 Values ​​were determined using a 4-parameter fitting algorithm.

[0807] Example 3. ATR determination in Hela cells

[0808] HeLa S3 cells were plated in a 384-well format at a density of 16K cells per 25 μL well in regular culture medium F-12K 10% FBS and incubated overnight at 37°C, 5% CO2. The culture medium was then replaced with 20 μL of Opti-MEM (phenol red-free) per well, and 5 μL of serially diluted compounds were added to the assay plate at a final DMSO concentration of 0.5%. The cells and compounds were incubated at room temperature for 20 minutes, followed by the addition of 5 μL of gemcitabine at a final concentration of 1.5 μM. The plates were incubated at 37°C, 5% CO2 for 3.5 to 4 hours. The culture medium was removed, and the cells were lysed in 15 μL of PerkinElmer lysis buffer for 10-20 minutes; 4 μL of the lysate was then transferred to a 384-format proxi white plate (PerkinElmer Life Sciences catalog number 6008280). CHK1 phosphorylation at Ser345 was quantified using Alphascreen SureFire CHK1 p-Ser345 (PerkinElmer Life Sciences Cat. No. TGRCHK1S10K) and Alphascreen protein A. (PerkinElmer Life Sciences Cat. No. 67060617C). Plates were read on Envision using AlphaScreen dedicated filters. 50 Values ​​were determined using a 4-parameter fitting algorithm.

[0809] Table 2 shows exemplary prepared compounds and their activities in the ATR / ATRIP enzymatic assay.

[0810] Table 2

[0811]

[0812]

[0813]

[0814]

[0815]

[0816]

[0817]

[0818]

[0819]

[0820]

[0821]

[0822]

[0823]

[0824]

[0825] In Table 2, the Method column indicates the preparation method described above that was used to prepare the compound.

[0826] Exemplary prepared compounds and their ATR inhibitory activities in the HeLa S3 whole cell assay are shown in Table 3 below.

[0827] Table 3

[0828]

[0829]

[0830]

[0831]

[0832]

[0833]

[0834]

[0835]

[0836]

[0837]

[0838]

[0839] In Table 3, the Method column indicates the preparation method described above that was used to prepare the compound.

[0840] Other implementation plans

[0841] Various modifications and variations of the described invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in conjunction with specific embodiments, it will be understood that the invention as claimed should not be unduly limited to those specific embodiments. Indeed, various modifications of the described manner for carrying out the invention that would be apparent to those skilled in the art are intended to be within the scope of the invention.

[0842] Other embodiments are within the claims.

Claims

1. A compound of formula (I): or a pharmaceutically acceptable salt thereof, in is a double bond, and each Y is independently N or CR 4 ;or is a single bond, and each Y is independently NR Y , carbonyl or C(R Y )2; where each R Y are independently H or optionally substituted C 1-6 alkyl; R 1 is optionally substituted C 1-6 Alkyl or H; R 2 is optionally substituted C 2-9 Heterocyclyl, optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl, optionally substituted C 2-9 Heterocyclyl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, optionally substituted C 1-9 Heteroaryl C 1-6 Alkyl, halogen, –N(R 5 )2. –OR 5 、–CON(R 6 )2、–SO2N(R 6 )2. –SO2R 5A or –Q–R 5B ; R 3 is optionally substituted C 1-9 Heteroaryl or optionally substituted C 1-9 Heteroaryl C 1-6 alkyl; Each R 4 are independently hydrogen, halogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkenyl or optionally substituted C 2-6 Alkynyl; Each R 5 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl or –SO2R 5A ; or two R 5 Together with the atoms to which they are attached, they form an optionally substituted C 2-9 heterocyclic group; Each R 5A are independently optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 6-10 aryl; R 5B is hydroxy, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, –N(R 5 )2、–CON(R 6 )2、–SO2N(R 6 )2. –SO2R 5A or optionally substituted alkoxy; Each R 6 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkoxyalkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 1-9 heteroaryl; or two R 6 Together with the atoms to which they are attached, they form an optionally substituted C 2-9 heterocyclic group; Q is optionally substituted C 2-9 Heterocyclylene, optionally substituted C 3-8 Cycloalkylene, optionally substituted C 1-9 Heteroarylene or optionally substituted C 6-10 an arylene group; and X is hydrogen or halogen.

2. The compound according to claim 1, wherein the compound is a compound of formula (II): or a pharmaceutically acceptable salt thereof, in Each Y is independently N or CR 4 ; R 1 is optionally substituted C 1-6 Alkyl or H; R 2 is optionally substituted C 2-9 Heterocyclyl, optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl, optionally substituted C 2-9 Heterocyclyl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, optionally substituted C 1-9 Heteroaryl C 1-6 Alkyl, halogen, –N(R 5 )2. –OR 5 、–CON(R 6 )2、–SO2N(R 6 )2. –SO2R 5A or –Q–R 5B ; R 3 is optionally substituted C 1-9 Heteroaryl or optionally substituted C 1-9 Heteroaryl C 1-6 alkyl; Each R 4 are independently hydrogen, halogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkenyl or optionally substituted C 2-6 Alkynyl; Each R 5 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl or –SO2R 5A ; or two R 5 Together with the atoms to which they are attached, they form an optionally substituted C 2-9 heterocyclic group; Each R 5A are independently optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 6-10 aryl; R 5B is hydroxy, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, –N(R 5 )2、–CON(R 6 )2、–SO2N(R 6 )2. –SO2R 5A or optionally substituted alkoxy; Each R 6 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkoxyalkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 1-9 heteroaryl; or two R 6 Together with the atoms to which they are attached, they form an optionally substituted C 2-9 heterocyclic group; Q is optionally substituted C 2-9 Heterocyclylene, optionally substituted C 3-8 Cycloalkylene, optionally substituted C 1-9 Heteroarylene or optionally substituted C 6-10 an arylene group; and X is hydrogen or halogen.

3. The compound according to claim 1, wherein the compound is a compound of formula (IB): or a pharmaceutically acceptable salt thereof.

4. The compound according to claim 1, wherein the compound is a compound of formula (IB-a): or a pharmaceutically acceptable salt thereof.

5. The compound according to claim 1, wherein the compound is a compound of formula (Ia): or a pharmaceutically acceptable salt thereof.

6. The compound according to claim 1, wherein the compound is a compound of formula (IA): or a pharmaceutically acceptable salt thereof.

7. The compound according to claim 1, wherein the compound is a compound of formula (IA-a): or a pharmaceutically acceptable salt thereof.

8. The compound according to claim 1, wherein the compound is a compound of formula (IC): or a pharmaceutically acceptable salt thereof.

9. The compound according to claim 1, wherein the compound is a compound of formula (IC-a): or a pharmaceutically acceptable salt thereof.

10. The compound of claim 1, wherein R 1 It is a methyl group.

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