CA-3018429-C - DEGRADATION OF CYCLIN-DEPENDENT KINASE 9 (CDK9) BY CONJUGATION OF CDK9 INHIBITORS WITH E3 LIGASE LIGAND AND METHODS OF USE

Abstract

The present application provides bifunctional compounds of Formula (I): Targeting Ligand or a pharmaceutically acceptable salt, hydrate, solvate, prodrag, stereoisomer, or tautomer thereof, which act as protein degradation inducing moieties for cyclin-dependent kinase 9 (CDK.9). The present application also relates to methods for the targeted degradation of CDK9 through the use of th e bifunctional compounds that link a ubiquitin ligase-binding moiety to a ligand that is capable of binding to CDK9 which can be utilized in the treatment of disorders modulated by CDK9.

Inventors

• Nathanael Gray
• Tinghu Zhang
• Calla M. OLSON
• Yanke Liang
• Nicholas KWIATKOWSKI

Assignees

• DANA-FARBER CANCER INSTITUTE, INC.

Dates

Publication Date

20260505

Application Date

20170421

Priority Date

20160422

Claims (1)

1. CLAIMS 1. A bifunctional compound of Formula X: (Targeting Ligand)-( Linker )-(Degron) (X), wherein: the Targeting Ligand is of Formula TL-I: wherein: A is 0, NRs, or NRsC(O); Bis S(O)t, 0, or NR6; Xis Nor CH; R1 is H, (C1-C4) alkyl, or (C1-C4) haloalkyl; R2 is H, (C1-C4) alkyl, or (C1-C4) haloalkyl; R3 is H, (C1-C4) alkyl, (C1-C4) haloalkyl, (C1-C4) alkoxy, or (C1-C4) haloalkoxy; R4 is (C1-C4) alkyl, (C1-C4) haloalkyl, (C1-C4) alkoxy, or (C1-C4) haloalkoxy; Rs is Hor (C1-C3) alkyl; R6 is Hor (C1-C3) alkyl; and tis 0, 1 , or 2, or 3, wherein the Targeting Ligand is bonded to the Linker via the -)- next to Cx ; the Linker is of Formula LO: or a stereoisomer thereof, wherein: 77 Date Re9ue/Date Received 2024-05-09 pl is an integer selected from Oto 12; p2 is an integer selected from 0 to 12; p3 is an integer selected from 1 to 6; each W is independently absent, CH2, 0, S, NH, or NR19; each R19 is independently C1-C3 alkyl; R20 is absent, CH=CH, CH=CH(CH2)1-3, or (CH2)1-JCH=CH, wherein R20 is bonded to the remainder of the Linker; Q is absent orNHC(O)CH2, wherein the Linker is covalently bonded to a Targeting Ligand via the -~- next to Z1, and covalently bonded to a Degron via the -~- next to Q; and the Degron is of Formula DI or D2: =((;1,,,z---n>;~ + 1 N-( NYJ(R15)v R13 0 0 (DI), wherein: Y is a bond, (CH2)1-6, (CH2)0-6-O, (CH2)0-6-C(O)NR11, (CH2)0-6-NR11C(O), (CH2)0-6-NH, or (CH2)0-6-NR12; Z is C(O) or C(R13)2; R11 is Hor C1-C6 alkyl; R12 is C1-C6 alkyl or C(O)-C1-C6 alkyl; each RB is independently Hor C1-C3 alkyl; 78 Date Re9ue/Date Received 2024-05-09 each R14 is independently C1-C3 alkyl; R1s is H, deuterium, C1-C3 alkyl, F, or Cl; each R16 is independently halogen, OH, C1-C6 alkyl, or C1-C6 alkoxy; q is 0, 1, or 2; and vis 0, 1, 2, or 3, or wherein: each R11 is independently C1-C3 alkyl; q' is 0, 1, 2, 3 or4; and R1s is Hor C1-C3 alkyl, wherein the Degron is bonded to the Linker via -i-, or a stereoisomer or pharmaceutically acceptable salt thereof. (D2), 2. The bifunctional compound of claim 1, wherein A is NH or NHC(O). 3. The bifunctional compound of claim 1 or 2, wherein Bis S. 4. The bifunctional compound of any one of claims 1 to 3, wherein R1 is H. 5. The bifunctional compound of any one of claims 1 to 4, wherein R2 is H. 6. The bifunctional compound of any one of claims 1 to 5, wherein R3 is H. 7. The bifunctional compound of any one of claims 1 to 6, R4 is (C1-C4) alkyl. 79 Date Re9ue/Date Received 2024-05-09 8. The bifunctional compound of any one of claims 1 to 7, wherein Xis N. 9. The bifunctional compound of any one of claims 1 to 7, wherein Xis CH. 10. The bifunctional compound of claim 1, wherein the Targeting Ligand is of Formula TLIa, TL-lb, TL-le, TL-Id, TL-le, or TL-If: (TL-Ia), (TL-le), (TL-If). 80 Date Re9ue/Date Received 2024-05-09 11. The bifuncti onal compound of claim 1, wherein the Linker is selected from: T~ p1 (LI), (L2), (L3), (L4), TL~o~a~ p3 p1 p2 's, (LS), (L6), (L7), (L8), (L9), 81 Date Re9ue/Date Received 2024-05-09 (LIO), and (L11), wherein TL represents the Targeting Ligand. 12. The bifunctional compound of any one of claims 1 to 11, wherein the Degron is of FormulaDl: or a stereoisomer thereof, wherein: Y is a bond, (CH2)1-6, (CH2)0-6-O, (CH2)0-6-C(O)NRu, (CH2)0-6-NRuC(O), (CH2)0-6-NH, or (CH2)0-6-NR12; Z is C(O) or C(R13)2; Ru is Hor C1-C6 alkyl; R12 is C1-C6 alkyl or C(O)-C1-C6 alkyl; RB is H; each R14 is independently C1-C3 alkyl; R1s is H, deuterium, C1-C3 alkyl, F, or Cl; each R16 is independently halogen, OH, C1-C6 alkyl, or C1-C6 alkoxy; qis 0, 1, or 2; and vis 0, 1, 2, or 3, wherein the Degron is covalently bonded to the Linker via -l-. 82 Date Re9ue/Date Received 2024-05-09 13. The bifunctional compound of claim 12, wherein the Degron is of Formula Dla or Dlb: Y-~- O Yt aA}y~ (R10l, o~~ H\-{ ~ HN-( 1yJ 0 0 (Dla) or O O (Dlb). 14. The bifunctional compound of any one of claims 1 to 11, wherein the Degron is of FormulaD2: or a stereoisomer thereof, wherein: each R11 is independently C1-C3 alkyl; q' is 0, 1, 2, 3 or4; and R1s is H or C 1-C3 alkyl, (D2), wherein the Degron is covalently bonded to another moiety via -i-. 15. The bifunctional compound of claim 14, wherein the Degron is of Formula D2a or D2b: (D2a) or (D2b). 16. The bifunctional compound of claim 1, selected from: 83 Date Re9ue/Date Received 2024-05-09 ~N 0) J)-s HN S ~o o--./'-NHoo 0 ~~~N~o~o~ ~ t-N,H O H I "\.__)'= ,,,::, 0 , \" l~s HN S ~ o o--./'-o o o o l,,,J~N~o~o~ ~ J---N,H H I N~0 Date Re9ue /Date Received 2 024-05-09 .,.;;:: 0 , 84 ~N 0-1 J)-i HN S ~ ~ ~NH o -b=o N ~O ~ NH lo--::::: N 0 Date Re9ue /Date Received 2 024-05-09 0 ' 85 or a stereoisomer or pharmaceutically acceptable salt thereof. 17. The bifunctional compound of claim 16, which is 86 Date Re9ue/Date Received 2024-05-09 ~N 0~ J)-s 0~ 0 ~~JN/"-..../o~o~o~NH o o H ~I -tN; =H0 or a stereoisomer or pharmaceutically acceptable salt thereof. 18. A pharmaceutical composition comprising the bifunctional compound of any one of claims 12 to 17, or a stereoisomer or pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier. 19. Use of the compound or a stereoisomer of pharmaceutically acceptable salt thereof of any one of claims 12 to 17 for treating or preventing a disease, wherein the disease is cancer or a proliferation disease, or wherein the disease is lung cancer, colon cancer, breast cancer, prostate cancer, liver cancer, brain cancer, kidney cancer, ovarian cancer, stomach cancer, skin cancer, bone cancer, gastric cancer, pancreatic cancer, glioma, glioblastoma, hepatocellular carcinoma, papillary renal carcinoma, head and neck squamous cell carcinoma, leukemia, lymphoma, myeloma, or a solid tumor, or wherein the disease is a proliferation disease and the proliferation disease is inflammation, arthritis, rheumatoid arthritis, spondyloarthropathies, gouty arthritis, osteoarthritis, juvenile arthritis, systemic lupus erythematosus (SLE), a skin-related condition, psoriasis, eczema, bums, dermatitis, neuroinflammation, allergy, pain, neuropathic pain, fever, a pulmonary disorder, lung inflammation, adult respiratory distress syndrome, pulmonary sarcoidosis, asthma, silicosis, chronic pulmonary inflammatory disease, chronic obstructive pulmonary disease (COPD), cardiovascular disease, arteriosclerosis, myocardial infarction, thrombosis, congestive heart failure, cardiac reperfusion injury, restenosis, cardiomyopathy, stroke, reperfusion injury, renal 87 Date Re9ue/Date Received 2024-05-09 reperfusion injury, ischemia, a neurodegenerative disorder, liver disease, nephritis, a gastrointestinal condition, inflammatory bowel disease, Crohn's disease, gastritis, irritable bowel syndrome, ulcerative colitis, an ulcerative disease, gastric ulcers, a viral or bacterial infection, sepsis, septic shock, gram negative sepsis, malaria, meningitis, HIV infection, cachexia secondary to infection or malignancy, cachexia secondary to acquired immune deficiency syndrome (AIDS), AIDS, ARC, pneumonia, herpes virus, myalgias due to infection, influenza, an autoimmune disease, graft vs. host reaction and allograft rejections, osteoporosis, multiple sclerosis, colorectal cancer, epithelial cell-derived neoplasia, basal cell carcinoma, adenocarcinoma, lip cancer, mouth cancer, esophageal cancer, small bowel cancer, bladder cancer, cervical cancer, squamous cell and/or basal cell cancers, renal cell carcinoma, chronic myelogenous leukemia (CML), acute myeloid leukemia (AML), acute promyelocytic leukemia (APL), angiogenesis, metastasis, a central nervous system disorder, Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, spinal cord injury, peripheral neuropathy, or B-Cell Lymphoma. 88 Date Re9ue/Date Received 2024-05-09

Description

DEGRADATION OF CYCLIN-DEPENDENT KINASE 9 (CDK9) BY CONJUGATION OF CDK9 INIDBITORS WITH E3 LI GASE LIGAND AND METHODS OF USE RELATED APPLICATION This application claims priority to, and the benefit of, U.S. Provisional Application 5 No. 62/326,581, filed on April 22, 2016. BACKGROUND Ubiquitin-Proteasome Pathway (UPP) is a critical pathway that regulates proteins and degrades misfolded or abnormal proteins. UPP is central to multiple cellular processes, and if defective or imbalanced, leads to pathogenesis of a variety of diseases. The covalent 10 attachment of ubiquitin to specific protein substrates is achieved through the action of E3 ubiquitin ligases. These ligases comprise over 500 different proteins and are categorized into multiple classes defined by the structural element of their E3 functional activity. For example, cereblon (CRBN) interacts with damaged DNA binding protein 1 and forms an E3 ubiquitin ligase complex with Cullin 4 in which the proteins recognized by CRBN are 15 ubiquitinated and degraded by proteasomes. Various immunomodulatory drugs (IMiDs), e.g. thalidomide and lenalidomide, binds to CRBN and modulates CRBN's role in the ubiquitination and degradation of protein factors involved in maintaining regular cellular function. Bifunctional compounds composed of a target protein-binding moiety and an E3 20 ubiquitin ligase-binding moiety have been shown to induce proteasome-mediated degradation of selected proteins. These drug-like molecules offer the possibility of temporal control over protein expression, and could be useful as biochemical reagents for the treatment of diseases. Cyclin-dependent kinase is a kinase family integrating multiple signaling pathways to control either cell cycle or gene transcription. CDKl, 2, 4 and 6 are the critical enzymes that 25 drive cell cycle transition. For example, CDKl is a key determinant of mitotic progression, CDK2 regulates DNA replication in S phase, and CDK4/6 drives the cell cycle from GO or 1 Date Rer;ue/Date Received 2023-07-28 WO 2017/185023 PCT/0S2017/028924 Gl to S pha..,;;;e by phosphorylation on Rb protein to activate expression of genes involved in cel1 cycle control. CDK7, 9 and 12 are known enzymes that regulate the transcription instead of directly promoting cell cycles. CDK7 is the enzymatic component of TFIIH complex which is responsible for regulating transcription initiation, and CDK9 and CDK12 regulate 5 transcription elongation and processing. Deregulation of CDKs has been shcnvn to have a significant impact on the cell state and is frequently identified as oncogenic. Numerous selective or pan-CDK small molecule inhibitors have been identified, however, most of the known inhibitors have failed in clinic trials due to the lack of high systemic drug concentration. More recently, the development of 10 a CDK7 covalent inhibitor, IHZ1, has demonstrated that irreversible binders are supeiior to reversible CDK binders. Alternative strategies to inhibit cyclin-dependent kinases, such as CDK9, are needed. At present, swtable compounds ,vith alternative mechanisms of action targeting CDK9 are not available. The present application addresses the need. SUMMARY The present application relates to novel bifunctional compotmds, wfoch function to recruit targeted proteins to E3 ubiquitin ligase for degradation, and methods of preparation and uses thereof. The bifunctional compound is of Formula X: ( Targeting Ligand)-( Linker)-( Degron J (X), 20 wherein: the Targeting Ligand is capable of binding to a targeted protein, such as a cyclindependent kinase (e.g., CDK9); the Linker is a group that covalently binds to the Targeting Ligand and the Degron; and 25 the Degron is capable of binding to a ubiquitin ligase, such as an E3 ubiquitin liga,;;;e (e.g., cereblon). The present application also relates to targeted degradation of proteins through the use ofbifunctional compounds, including bifunctiona1 compounds that link an E3 ubiquitin ligase-binding rnoiety to a ligand that binds the targeted proteins. TI1e present application also relates to a bi functional compound of Formula I: 2 WO 2017/185023 PCT/0S2017/028924 N.::::::-t"' A ';,...r"'"'""'\ R,~! (_}~-( Degron) ::z-B R3~0 ~ m Targeting Ligand or an enantiomer, dia.<;tereomer, stereoisomer, or pharmaceutically acceptable salt thereof, wherein: R1, R2, R3, R4, A, B, and X are each as defined herein; the Linker is a group that covalently binds to Cx and the Degron; the Degron is capable of binding to a ubiquitin ligase, such as an E3 ubiquitin ligase (e.g., cereblon); and the Targeting Ligand is capable of binding to a targeted protein, such as CDK9. The present application further relates to a Degron of Formula Dl: )-~! 141 ~15 z-~~-lo=\. N)r,Jl· _,:T·(Rrn)v N ✓ I R13 0 0 (D1), or an enantiomer, diastereomer, or stereoisomer thereof: wherein Y, Z, RB, Ru, R1s, R16, v, and q are each ac;_;: defined herein. The present application further relates to a Linker of Formula LO: or an enantiomer, dia.<