Compositions and methods for treating cdk4/6-mediated cancer

Abstract

Methods for designing heterobifunctional small molecules which selectively degrade/disrupt CDK4/6 and compositions and methods of using such degraders/disruptors to treat CDK4/6-mediated cancer are provided.

What is claimed is: 
     
         1 . A bivalent compound comprising a cyclin-dependent kinase 4/6 (CDK4/6) ligand conjugated to a degradation/disruption tag. 
     
     
         2 . The bivalent compound of  claim 1 , wherein the CDK4/6 ligand is a CDK4/6 inhibitor. 
     
     
         3 . The bivalent compound of  claim 2 , wherein the CDK4/6 ligand is selected from the group consisting of abemaciclib, palbociclib, ribociclib, trilaciclib, G1T38, SHR6390, and analogs thereof. 
     
     
         4 . The bivalent compound of any one of  claims 1 - 3 , wherein the CDK4/6 ligand is bound to CDK4/6. 
     
     
         5 . The bivalent compound of any one of  claims 1 - 4 , wherein the degradation/disruption tag is selected from the group consisting of pomalidomide, thalidomide, lenalidomide, VHL-1, adamantane, and analogs thereof. 
     
     
         6 . The bivalent compound of any one of  claims 1 - 5 , wherein the degradation/disruption tag binds to a ubiquitin ligase or serves as a hydrophobic group that leads to CDK4 or CDK6 protein misfolding. 
     
     
         7 . The bivalent compound of any one of  claims 1 - 6 , wherein the CDK4/6 ligand is conjugated to the degradation/disruptor tag through a linker. 
     
     
         8 . The bivalent compound of any one of  claims 1 - 7 , wherein the bivalent compound has the structure of formula I: 
       
         
           
           
               
               
           
         
         wherein PI comprises a CDK4/6 ligand and EL comprises a degradation/disruption tag. 
       
     
     
         9 . The bivalent compound of  claim 8 , wherein PI has the structure of Formula II, 
       
         
           
           
               
               
           
         
         wherein X 1 , X 2 , and X 3  are independently hydrogen, halogen, C1-C8 alkyl, C1-C8 alkoxy, C1-C8 alkoxyalkyl, NR 5 R 6 , CN, NO 2 , COR 5 , CO 2 R 5 , CONR 5 R 6 , or NR 5 COR 6 ; 
         R 1  and R 4  are independently hydrogen, halogen, C1-C8 alkyl, C1-C8 alkoxy, C1-C8 alkoxyalkyl, C1-C8 haloalkyl, C1-C8 hydroxyalkyl, C3-C7 cycloalkyl, C3-C7 heterocyclyl, C2-C8 alkenyl, C2-C8 alkynyl, OR 5 , SR 5 , NR 5 R 6 , CN, NO 2 , (CR 5 R 6 )mNR 7 R 8 , (CR 5 R 6 )mC(O)R 7 , COR 5 , CO 2 R 5 , CONR 5 R 6 , NR 5 COR 6 , NR 5 SOR 6 , NR 5 SO 2 R 6 , SOR 5 , SO 2 R 5 , SO 2 NR 5 R 6 , (CR 5 R 6 )m-aryl, or (CR 5 R 6 )m-heteroaryl, wherein m is 0-8; 
         R 2  is hydrogen, halogen, C1-C8 alkyl, C1-C8 alkoxy, C3-C7 cycloalkyl, or C3-C7 heterocyclyl; 
         R 3  is hydrogen, aryl, C1-C8 alkyl, C1-C8 alkoxy, C3-C7 cycloalkyl, or C3-C7 heterocyclyl; 
         R 5 , R 6 , R 7 , and R 8  are independently hydrogen, C1-C8 alkyl, C2-C8 alkenyl, C2-C8 alkynyl, arylalkyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, or heteroarylalkyl; 
         optionally, R 1  and R 2 , R 5  and R 6 , or R 7  and R 8  independently form 4-8 membered alkyl or heterocyclyl rings; and 
         X and Y are independently CR 5 R 6  or N; 
         the structure of Formula III, 
       
       
         
           
           
               
               
           
         
         wherein R 1  is hydrogen, C1-C8 alkyl, C1-C8 alkoxyalkyl, C1-C8 haloalkyl, C1-C8 hydroxyalkyl, C3-C7 cycloalkyl, C3-C7 heterocyclyl, C2-C8 alkenyl, or C2-C8 alkynyl; 
         R 2  is hydrogen, C1-C3 alkyl, or cyclopropyl; 
         R 3 , R 4 , and R 5  are independently hydrogen, halogen, C1-C8 alkyl, C1-C8 alkoxy, C3-C7 cycloalkyl, or C3-C7 heterocyclyl; 
         R 6  is hydrogen, halogen, C1-C8 alkyl, C1-C8 alkoxy, C1-C8 alkoxyalkyl, C1-C8 haloalkyl, C1-C8 hydroxyalkyl, C3-C7 cycloalkyl, C3-C7 heterocyclyl, C2-C8 alkenyl, C2-C8 alkynyl, OR 7 , SR 7 , NR 7 R 8 , CN, NO 2 , (CR 7 R 8 )mNR 9 R 10 , (CR 7 R 8 )mC(O)R 9 , COR 7 , CO 2 R 7 , CONR 7 R 8 , NR 7 COR 8 , NR 7 SOR 8 , NR 7 SO 2 R 8 , SORT, SO 2 R 7 , SO 2 NR 7 R 8 , (CR 7 R 8 )m-aryl, or (CR 7 R 8 )m-heteroaryl; wherein m is 0-8; 
         R 7 , R 8 , R 9 , and R 10  are independently hydrogen, C1-C8 alkyl, C2-C8 alkenyl, C2-C8 alkynyl, arylalkyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, or heteroarylalkyl; 
         optionally, R 7  and R 8  or R 9  and R 10  independently form 4-8 membered alkyl or heterocyclyl rings; and 
         X and Y are independently CR 7 R 8 , or N; 
         the structure of Formula IV, 
       
       
         
           
           
               
               
           
         
         wherein R 1  is hydrogen, C1-C8 alkyl, C1-C8 alkoxyalkyl, C1-C8 haloalkyl, C1-C8 hydroxyalkyl, C3-C7 cycloalkyl, C3-C7 heterocyclyl, C2-C8 alkenyl, or C2-C8 alkynyl; 
         R 2  is hydrogen, C1-C8 alkyl, C1-C8 alkoxyalkyl, C1-C8 haloalkyl, C1-C8 hydroxyalkyl, C3-C7 cycloalkyl, C3-C7 heterocyclyl, C2-C8 alkenyl, or C2-C8 alkynyl, CN, COR 4 , CO 2 R 4 , or CONR 4 R 5 ; 
         R 3  is hydrogen, halogen, C1-C8 alkyl, C1-C8 alkoxy, C1-C8 alkoxyalkyl, C1-C8 haloalkyl, C1-C8 hydroxyalkyl, C3-C7 cycloalkyl, C3-C7 heterocyclyl, C2-C8 alkenyl, C2-C8 alkynyl, OR 4 , SR 4 , NR 4 R 5 , CN, NO 2 , (CR 4 R 5 )mNR 6 R 7 , (CR 4 R 5 )mC(O)R 6 , COR 4 , CO 2 R 4 , CONR 4 R 5 , NR 4 COR 5 , NR 4 SOR 5 , NR 4 SO 2 R 5 , SOR 4 , SO 2 R 4 , SO 2 NR 4 R 5 , (CR 4 R 5 )m-aryl, or (CR 4 R 5 )m-heteroaryl, wherein m is 0-8; 
         R 4 , R 5 , R 6 , and R 7  are independently hydrogen, C1-C8 alkyl, C2-C8 alkenyl, C2-C8 alkynyl, arylalkyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, or heteroarylalkyl; 
         optionally, R 1  and R 2 , R 4  and R 5 , or R 6  and R 7  independently form 4-8 membered alkyl or heterocyclyl rings; and 
         V, W, X, Y, and Z are independently CR 4 R 5  or N; 
         or the structure of Formula VI, 
       
       
         
           
           
               
               
           
         
         wherein R 1  and R 2  are independently hydrogen, C1-C8 alkyl, C1-C8 alkoxyalkyl, C1-C8 haloalkyl, C1-C8 hydroxyalkyl, C3-C7 cycloalkyl, C3-C7 heterocyclyl, C2-C8 alkenyl, or C2-C8 alkynyl; 
         R 3  is hydrogen, C1-C6 alkyl, C1-C6 alkoxyalkyl, C1-C6 haloalkyl, C1-C6 hydroxyalkyl, C3-C6 cycloalkyl, C3-C6 heterocyclyl, C2-C6 alkenyl, or C2-C6 alkynyl; 
         R 4  is hydrogen, halogen, C1-C8 alkyl, C1-C8 alkoxy, C1-C8 alkoxyalkyl, C1-C8 haloalkyl, C1-C8 hydroxyalkyl, C3-C7 cycloalkyl, C3-C7 heterocyclyl, C2-C8 alkenyl, C2-C8 alkynyl, OR 5 , SR 5 , NR 5 R 6 , CN, NO 2 , (CR 5 R 6 )mNR 7 R 8 , (CR 5 R 6 )mC(O)R 7 , COR 5 , CO 2 R 5 , CONR 5 R 6 , NR 5 COR 6 , NR 5 SOR 6 , NR 5 SO 2 R 6 , SOR 5 , SO 2 R 5 , SO 2 NR 5 R 6 , (CR 5 R 6 )m-aryl, or (CR 5 R 6 )m-heteroaryl, wherein m is 0-8; 
         n is 0-4; 
         optionally, R 1  and R 2 , R 5  and R 6 , or Rand R 8  independently form 4-8 membered alkyl or heterocyclyl rings; and 
         V, W, X, Y, and Z are independently CR 5 R 6  or N. 
       
     
     
         10 . The bivalent compound of  claim 8  or  9 , wherein the CDK4/6 ligand is selected from the group consisting of abemaciclib, palbociclib, ribociclib, trilaciclib (G1T28), G1T38, SHR6390, and analogs thereof. 
     
     
         11 . The bivalent compound of  claim 8  or  9 , wherein the CDK4/6 ligand is selected from the group consisting of: 
       
         
           
           
               
               
           
         
       
     
     
         12 . The bivalent compound of any one of  claims 8 - 11 , wherein the CDK4/6 ligand is bound to CDK4/6. 
     
     
         13 . The bivalent compound of any one of  claims 8 - 12 , wherein EL is selected from: 
       
         
           
           
               
               
           
         
         wherein V, W, and X are independently CR 2  or N; 
         Y is CO or CH 2 ; 
         Z is CH 2 , NH, or O; 
         R 1  is hydrogen, methyl, or fluoro; and 
         R 2  is hydrogen, halogen, or C1-C5 alkyl; 
       
       
         
           
           
               
               
           
         
         wherein R 1  and R 2  are independently hydrogen, C1-C8 alkyl, C1-C8 alkoxyalkyl, C1-C8 haloalkyl, C1-C8 hydroxyalkyl, C3-C7 cycloalkyl, C3-C7 heterocyclyl, C2-C8 alkenyl, or C2-C8 alkynyl; 
         or 
       
       
         
           
           
               
               
           
         
         wherein R 1 , R 2 , R 3  and R 4  are independently hydrogen, C1-C8 alkyl, C1-C8 alkoxyalkyl, C1-C8 haloalkyl, C1-C8 hydroxyalkyl, C3-C7 cycloalkyl, C3-C7 heterocyclyl, C2-C8 alkenyl, or C2-C8 alkynyl; and 
         V, W, X, and Z are independently CR 4  or N. 
       
     
     
         14 . The bivalent compound of any one of  claims 1 - 13 , wherein the degradation/disruption tag is selected from the group consisting of pomalidomide, thalidomide, lenalidomide, VHL-1, adamantane, 1-((4,4,5,5,5-pentafluoropentyl) sulfinyl)nonane, nutlin-3a, RG7112, RG7338, AMG 232, AA-115, bestatin, MV-1, LCL161, and analogs thereof. 
     
     
         15 . The bivalent compound of any one of  claims 1 - 13 , wherein the degradation/disruption tag is selected from the group consisting of: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
         
           
           
               
               
           
         
       
     
     
         16 . The bivalent compound of any one of  claims 1 - 15 , wherein the degradation/disruption tag is bound to a ubiquitin ligase. 
     
     
         17 . The bivalent compound of any one of  claims 1 - 16 , wherein the degradation/disruption tag functions as a hydrophobic group that leads to CDK4 or CDK6 protein misfolding. 
     
     
         18 . The bivalent compound of any one of  claims 8 - 17 , wherein the linker comprises acyclic or cyclic saturated or unsaturated carbon, ethylene glycol, amide, amino, ether, urea, carbamate, aromatic, heteroaromatic, heterocyclic or carbonyl containing groups with different lengths. 
     
     
         19 . The bivalent compound of any one of  claims 8 - 17 , wherein the linker is selected from the group consisting of: 
       
         
           
           
               
               
           
         
         wherein X is C═O or CH 2 ; 
         Y is C═O or CH 2 ; and 
         n is 0-15; 
       
       
         
           
           
               
               
           
         
         wherein X is C═O or CH 2 ; 
         Y is C═O or CH 2 ; 
         m is 0-15; 
         n is 0-6; and 
         o is 0-15; or 
       
       
         
           
           
               
               
           
         
         wherein X is C═O or CH 2 ; 
         Y is C═O or CH 2 ; 
         R is —CH 2 —, —CF 2 —, —CH(C 1-3  alkyl)-, —C(C 1-3  alkyl)(C 1-3  alkyl)-, —CH═CH—, —C(C 1-3  alkyl)═C(C 1-3  alkyl)-, —C═C—, —O—, —NH—, —N(C 1-3  alkyl)-, —C(O)NH—, —C(O)N(C 1-3  alkyl)-, a 3-13 membered ring, a 3-13 membered fused ring, a 3-13 membered bridged ring, or a 3-13 membered spiro ring; 
         m is 0-15; and 
         n is 0-15. 
       
     
     
         20 . The bivalent compound of  claim 19 , wherein the linker is Formula C and R is selected from the group consisting of 3-13 membered rings, 3-13 membered fused rings, 3-13 membered bridged rings, and 3-13 membered spiro rings,
 wherein R contains one or more heteroatoms.   
     
     
         21 . The bivalent compound of  claim 19 , wherein the linker is Formula C and R is selected from the group consisting of: 
       
         
           
           
               
               
           
         
       
     
     
         22 . The bivalent compound of  claim 1 , wherein the CDK4/6 ligand is selected from the group consisting of: 
       
         
           
           
               
               
           
         
       
     
     
         23 . The bivalent compound of any one of  claims 6 - 22 , wherein the ubiquitin ligase is an E3 ligase. 
     
     
         24 . The bivalent compound of  claim 23 , wherein the E3 ligase is selected from the group consisting of cereblon E3 ligase, VHL E3 ligase, MDM2 ligase, TRIM24 ligase, TRIM21 ligase, and TAP ligase. 
     
     
         25 . The bivalent compound of any one of  claims 1 - 8 , wherein the bivalent compound is selected from the group consisting of XY028-082, XY028-003, XY028-004, XY028-005, XY019-098, XY028-006, XY028-007, XY028-008, XY028-009, XY028-085, XY028-084, XY028-083, XY028-132, XY028-133, XY019-106, XY028-162, XY028-163, XY028-002, XY028-114, XY028-097, XY019-108, XY028-105, XY028-106, XY028-140, XY028-141, XY028-142, XY028-143, XY028-144, XY028-145, YX26-56, YX26-66, YX26-58, YX30-108, YX30-107, YX30-85, YX30-86, YX30-117, YX30-118, YX30-126, YX30-125, XY028-186, YX33-29, YX33-31, YX33-74, YX33-94, YX33-108, YX33-96, YX33-97, YX33-109, YX33-110, YX33-112, YX33-123, YX35-48, YX39-47, YX39-48, YX39-56, YX39-65, YX39-74, YX39-123, YX39-124, YX39-147, YX44-18, YX44-19, YX44-22, YX44-46, YX44-48, YX44-78, YS36-95, YS36-60, YS36-61, YS36-62, YS36-63, YS36-64, YS36-65, YS36-66, YS36-67, YS36-68, YS36-69, YS36-70, YS36-71, compound examples 80-135, and analogs thereof. 
     
     
         26 . A bivalent compound selected from the group consisting of XY028-082, XY028-003, XY028-004, XY028-005, XY019-098, XY028-006, XY028-007, XY028-008, XY028-009, XY028-085, XY028-084, XY028-083, XY028-132, XY028-133, XY019-106, XY028-162, XY028-163, XY028-002, XY028-114, XY028-097, XY019-108, XY028-105, XY028-106, XY028-140, XY028-141, XY028-142, XY028-143, XY028-144, XY028-145, YX26-56, YX26-66, YX26-58, YX30-108, YX30-107, YX30-85, YX30-86, YX30-117, YX30-118, YX30-126, YX30-125, XY028-186, YX33-29, YX33-31, YX33-74, YX33-94, YX33-108, YX33-96, YX33-97, YX33-109, YX33-110, YX33-112, YX33-123, YX35-48, YX39-47, YX39-48, YX39-56, YX39-65, YX39-74, YX39-123, YX39-124, YX39-147, YX44-18, YX44-19, YX44-22, YX44-46, YX44-48, YX44-78, YS36-95, YS36-60, YS36-61, YS36-62, YS36-63, YS36-64, YS36-65, YS36-66, YS36-67, YS36-68, YS36-69, YS36-70, YS36-71, compound examples 80-135, and analogs thereof. 
     
     
         27 . A method of treating a cyclin-dependent kinase 4/6 (CDK4/6)-mediated cancer, which comprises administering to a subject in need thereof with a CDK4/6-mediated cancer a bivalent compound comprising a CDK4/6 ligand conjugated to a degradation/disruption tag. 
     
     
         28 . The method of  claim 27 , wherein the CDK4/6-mediated cancer overexpresses cyclin-dependent kinase 4 (CDK4) or cyclin-dependent kinase 6 (CDK6) relative to a wild-type tissue of the same species and tissue type. 
     
     
         29 . The method of  claim 27 , wherein the CDK4/6-mediated cancer comprises higher CDK4 or CDK6 enzymatic activity relative to a wild-type tissue of the same species and tissue type. 
     
     
         30 . The method of any one of  claims 27 - 29 , wherein at least one bivalent compound is selected from the group consisting of XY028-082, XY028-003, XY028-004, XY028-005, XY019-098, XY028-006, XY028-007, XY028-008, XY028-009, XY028-085, XY028-084, XY028-083, XY028-132, XY028-133, XY019-106, XY028-162, XY028-163, XY028-002, XY028-114, XY028-097, XY019-108, XY028-105, XY028-106, XY028-140, XY028-141, XY028-142, XY028-143, XY028-144, XY028-145, YX26-56, YX26-66, YX26-58, YX30-108, YX30-107, YX30-85, YX30-86, YX30-117, YX30-118, YX30-126, YX30-125, XY028-186, YX33-29, YX33-31, YX33-74, YX33-94, YX33-108, YX33-96, YX33-97, YX33-109, YX33-110, YX33-112, YX33-123, YX35-48, YX39-47, YX39-48, YX39-56, YX39-65, YX39-74, YX39-123, YX39-124, YX39-147, YX44-18, YX44-19, YX44-22, YX44-46, YX44-48, YX44-78, YS36-95, YS36-60, YS36-61, YS36-62, YS36-63, YS36-64, YS36-65, YS36-66, YS36-67, YS36-68, YS36-69, YS36-70, YS36-71, compound examples 80-135, and analogs thereof. 
     
     
         31 . The method of any one of  claims 27 - 30 , wherein at least one bivalent compound is administered orally, parenterally, intradermally, subcutaneously, topically, or rectally. 
     
     
         32 . The method of any one of  claims 28 - 31 , further comprising treating the subject with one or more additional therapeutic regimens for treating cancer. 
     
     
         33 . The method of  claim 32 , wherein the one or more additional therapeutic regimens are selected from the group consisting of surgery, chemotherapy, radiation therapy, hormone therapy, and immunotherapy. 
     
     
         34 . The method of any of  claims 27 - 33 , wherein the CDK4/6-mediated cancer is selected from the group consisting of mesothelioma, hepatocellular cancer, central nervous system neoplasm, lung cancer, bone cancer, pancreatic cancer, skin cancer, head and neck cancer, melanoma, ovarian cancer, colon cancer, rectal cancer, anal cancer, stomach cancer, gastrointestinal cancer, breast cancer, uterine cancer, fallopian tube cancer, endometrial cancer, cervical cancer, vaginal cancer, vulvar cancer, esophageal cancer, gastrointestinal cancer, endocrine cancer, thyroid cancer, parathyroid cancer, adrenal cancer, soft tissue sarcoma, urethral cancer, penile cancer, prostate cancer, testicular cancer, leukemia, lymphoma, bladder cancer, renal cell cancer, brain stem glioma, pituitary cancer, adrenocortical cancer, gallbladder cancer, multiple myeloma, cholangiocarcinoma, fibrosarcoma, neuroblastoma, and retinoblastoma. 
     
     
         35 . The method of  claim 34 , wherein the breast cancer is estrogen receptor positive (ER+). 
     
     
         36 . The method of any of  claims 27 - 35 , wherein the CDK4/6-mediated cancer is a relapsed cancer. 
     
     
         37 . The method of any of  claims 27 - 36 , wherein the CDK4/6-mediated cancer was refractory to one or more previous treatments. 
     
     
         38 . A method for identifying a bivalent compound which mediates degradation/disruption of CDK4 or CDK6, the method comprising:
 providing a heterobifunctional test compound comprising a CDK4/6 ligand conjugated to a degradation/disruption tag;   contacting the heterobifunctional test compound with a cell comprising a ubiquitin ligase and at least one of CDK4 and CDK6;   determining whether CDK4 or CDK6 levels decrease in the cell; and   (i) identifying the heterobifunctional test compound as a bivalent compound which mediates degradation/reduction of CDK4 if CDK4 levels decrease in the cell and CDK6 levels do not decrease in the cell,   (ii) identifying the heterobifunctional test compound as a bivalent compound which mediates degradation/reduction of CDK6 if CDK6 levels decrease in the cell and CDK4 levels do not decrease in the cell, or   (iii) identifying the heterobifunctional test compound as a bivalent compound which mediates degradation/reduction of CDK4 and CDK6 if both CDK4 and CDK6 levels decrease in the cell.   
     
     
         39 . The method of  claim 38 , wherein the cell is a cancer cell. 
     
     
         40 . The method of  claim 39 , wherein the cancer cell is a CDK4/6-mediated cancer cell.