Protac antibody conjugates and methods of use

Abstract

The subject matter described herein is directed to antibody-PROTAC conjugates (PACs), to pharmaceutical compositions containing them, and to their use in treating diseases and conditions where targeted protein degradation is beneficial.

What is claimed is: 
     
         1 . A conjugate having the chemical structure
   Ab-(L1-D) p ,   wherein,
 D is a PROTAC having the structure E3LB-L2-PB; 
 E3LB is an E3 ligase binding group covalently bound to L2; 
 L2 is a linker covalently bound to E3LB and PB; 
 PB is a protein binding group covalently bound to L2; 
 Ab is an antibody covalently bound to L1; 
 L1 is a linker, covalently bound to Ab and D; and 
 p has a value from about 1 to about 8. 
   
     
     
         2 . The conjugate of  claim 1 , wherein E3LB is a group that binds an E3 ligase, wherein said E3 ligase is listed in Tables 13-27. 
     
     
         3 . The conjugate of  claim 1 , wherein E3LB is a group that binds an E3 ligase, wherein said E3 ligase is selected from the group consisting of von Hippel-Lindau (VHL); cereblon; XIAP; E3A; MDM2; Anaphase-promoting complex (APC); UBR5 (EDD1); SOCS/BC-box/eloBC/CUL5/RING; LNXp80; CBX4; CBLL1; HACE1; HECTD1; HECTD2; HECTD3; HECW1; HECW2; HERC1; HERC2; HERC3; HERC4; HUWE1; ITCH; NEDD4; NEDD4L; PPIL2; PRPF19; PIAS1; PIAS2; PIAS3; PIAS4; RANBP2; RNF4; RBX1; SMURF1; SMURF2; STUB1; TOPORS; TRIP12; UBE3A; UBE3B; UBE3C; UBE4A; UBE4B; UBOX5; UBR5; WWP1; WWP2; Parkin; A20/TNFAIP3; AMFR/gp78; ARA54; beta-TrCP1/BTRC; BRCA1; CBL; CHIP/STUB1; E6; E6AP/UBE3A; F-box protein 15/FBXO15; FBXW7/Cdc4; GRAIL/RNF128; HOIP/RNF31; cIAP-1/HIAP-2; cIAP-2/HIAP-1; cIAP (pan); ITCH/AIP4; KAP1; MARCH8; Mind Bomb 1/MIB1; Mind Bomb 2/MIB2; MuRF1/TRIM63; NDFIP1; NEDD4; NleL; Parkin; RNF2; RNF4; RNF8; RNF168; RNF43; SART1; Skp2; SMURF2; TRAF-1; TRAF-2; TRAF-3; TRAF-4; TRAF-5; TRAF-6; TRIM5; TRIM21; TRIM32; UBR5; and ZNRF3. 
     
     
         4 . The conjugate of  claim 1 , wherein E3LB is a group that binds an E3 ligase selected from the group consisting of XIAP, VHL, cereblon and MDM2. 
     
     
         5 . The conjugate of  claim 1 , wherein E3LB is selected from the group consisting of a compound that binds VHL, a hydroxyproline compound that binds VHL, a compound that binds MDM2, a compound that binds cereblon, a tetrahydro-benzodiazepinone a nutlin, thalidomide, lenalidomide, and pomalidomide. 
     
     
         6 . The conjugate of  claim 1 , wherein E3LB is a XIAP inhibitor that is a tetrahydro-benzodiazepinone having the formula: 
       
         
           
           
               
               
           
         
         wherein, R1, R2, R3, R4 and R5 are as described in WO/2015/071393. 
       
     
     
         7 . The conjugate of  claim 1 , wherein PB is a group that binds FoxOl, HDAC, DP-1, E2F, ABL, AMPK, BRK, BRSK I, BRSK2, BTK, CAMKK1, CAMKK alpha, CAMKK beta, Rb, Suv39HI, SCF, p19INK4D, GSK-3, pi 8 INK4, myc, cyclin E, CDK2, CDK9, CDG4/6, Cycline D, p16 INK4A, cdc25A, BMI1, SCF, Akt, CHK1/2, C 1 delta, CK1 gamma, C 2, CLK2, CSK, DDR2, DYRKIA/2/3, EF2K, EPH-A2/A4/B1/B2/B3/B4, EIF2A 3, Smad2, Smad3, Smad4, Smad7, p53, p21 Cipl, PAX, Fyn, CAS, C3G, SOS, Tal, Raptor, RACK-1, CRK, Rapl, Rac, KRas, NRas, HRas, GRB2, FAK, PI3K, spred, Spry, mTOR, MPK, LKB1, PAK 1/2/4/5/6, PDGFRA, PYK2, Src, SRPK1, PLC, PKC, PKA, PKB alpha/beta, PKC alpha/gamma/zeta, PKD, PLK1, PRAK, PRK2, RIPK2, WAVE-2, TSC2, DAPK1, BAD, IMP, C-TAK1, TAK1, TAO1, TBK1, TESK1, TGFBR1, TIE2, TLK1, TrkA, TSSK1, TTBK1/2, TTK, Tpl2/cotl, MEK1, MEK2, PLDL Erk1, Erk2, Erk5, Erk8, p90RSK, PEA-15, SRF, p27 KIP1, TIF 1a, HMGN1, ER81, MKP-3, c-Fos, FGF-R 1 , GCK, GSK3 beta, HER4, HIPK1/2/3, IGF-1R, cdc25, UBF, LAMTOR2, Statl, StaO, CREB, JAK, Src, PTEN, NF-kappaB, HECTH9, Bax, HSP70, HSP90, Apaf-1, Cyto c, BCL-2, Bcl-xL, Smac, XIAP, Caspase-9, Caspase-3, Caspase-6, Caspase-7, CDC37, TAB, IKK, TRADD, TRAF2, R1P1, FLIP, TAK1, JNK1/2/3, Lck, A-Raf, B-Raf, C-Raf, MOS, MLK1/3, MN 1/2, MSK1, MST2/3/4, MPSK1, MEKK1, ME K4, MEL, ASK1, MINK1, MKK 1/2/3/4/6/7, NE 2a/6/7, NUAK1, OSR1, SAP, STK33, Syk, Lyn, PDK1, PHK, PIM 1/2/3, Ataxin-1, mTORC1, MDM2, p21 Wafl, Cyclin D1, Lamin A, Tpl2, Myc, catenin, Wnt, IKK-beta, IKK-gamma, IKK-alpha, IKK-epsilon, ELK, p65RelA, IRAKI, IRA 2, IRAK4, IRR, FADD, TRAF6, TRAF3, MKK3, MKK6, ROCK2, RSK1/2, SGK 1, SmMLCK, SIK2/3, ULK1/2, VEGFR1, WNK 1, YES1, ZAP70, MAP4K3, MAP4K5, MAPK1b, MAPKAP-K2 K3, p38 alpha/beta/delta/gamma MAPK, Aurora A, Aurora B, Aurora C, MCAK, Clip, MAPKAPK, FAK, MARK 1/2/3/4, Mucl, SHC, CXCR4, Gap-1, Myc, beta-catenin/TCF, Cbl, BRM, Mcl1, BRD2, BRD3, BRD4, AR, RAS, ErbB3, EGFR, IRE1, HPK1, RIPK2, and ERα, including all variants, mutations, splice variants, indels and fusions thereof. 
     
     
         8 . The conjugate of  claim 1 , wherein PB is selected from the group consisting of Heat Shock Protein 90 (HSP90) inhibitors, Kinase and Phosphatase inhibitors, MDM2 inhibitors, HDAC inhibitors, Human Lysine Methyltransferase Inhibitors, Angiogenesis inhibitors, Immunosuppressive compounds, and compounds that target: Human BET Bromodomain-containing proteins, the aryl hydrocarbon receptor (AHR), REF receptor kinase, FKBP, Androgen Receptor (AR), Estrogen receptor (ER), Thyroid Hormone Receptor, HIV Protease, HIV Integrase, HCV Protease, and Acyl-protein Thioesterase-1 and -2 (APT1 and APT2). 
     
     
         9 . The conjugate of  claim 1 , wherein PB is a group that targets Estrogen Receptor alpha (ERa). 
     
     
         10 . The conjugate of  claim 1 , wherein said Ab is a cysteine engineered antibody or variant thereof. 
     
     
         11 . The conjugate of  claim 1 , wherein Ab binds to one or more of polypeptides selected from the group consisting of DLL3, EDAR, CLL1; BMPR1B; E16; STEAP1; 0772P; MPF; NaPi2b; Sema 5b; PSCA hlg; ETBR; MSG783; STEAP2; TrpM4; CRIPTO; CD21; CD79b; FcRH2; B7-H4; HER2; NCA; MDP; IL20Rα; Brevican; EphB2R; ASLG659; PSCA; GEDA; BAFF-R; CD22; CD79a; CXCR5; HLA-DOB; P2X5; CD72; LY64; FcRH1; IRTA2; TENB2; PMEL17; TMEFF1; GDNF-Ra1; Ly6E; TMEM46; Ly6G6D; LGR5; RET; LY6K; GPR19; GPR54; ASPHD1; Tyrosinase; TMEM118; GPR172A; MUC16 and CD33. 
     
     
         12 . The conjugate of  claim 10 , wherein Ab binds to one or more of polypeptides selected from the group consisting of CLL1, STEAP1, NaPi2b, STEAP2, TrpM4, CRIPTO, CD21, CD79b, FcRH2, B7-H4, HER2, CD22, CD79a, CD72, LY64, Ly6E, MUC16, and CD33. 
     
     
         13 . The conjugate of  claim 12 , wherein Ab is an antibody that binds to one or more polypeptides selected from the group consisting of B7-H4, HER2, CLL1, CD33, CD22 and NaPi2b. 
     
     
         14 . The conjugate of  claim 12 , wherein the antibody binds to HER2 or B7-H4. 
     
     
         15 . The conjugate of  claim 14 , wherein the antibody binds to HER2. 
     
     
         16 . The conjugate of  claim 1 , wherein L1 is a peptidomimetic linker. 
     
     
         17 . The conjugate of  claim 16 , wherein L1 is a peptidomimetic linker represented by the following formula:
   -Str-(PM)-Sp-   wherein,   Str is a stretcher unit covalently attached to Ab;   Ab is an antibody;   Sp is a bond or spacer unit covalently attached to a PROTAC moiety;   PM is a non-peptide chemical moiety selected from the group consisting of:   
       
         
           
           
               
               
           
         
         W is —NH-heterocycloalkyl- or heterocycloalkyl; 
         Y is heteroaryl, aryl, —C(O)C 1 -C 6 alkylene, C 1 -C 6 alkylene-NH 2 , C 1 -C 6 alkylene-NH—CH 3 , C 1 -C 6 alkylene-N—(CH 3 ) 2 , C 1 -C 6 alkenyl or C 1 -C 6 alkylenyl; 
         each R 1  is independently C 1 -C 10 alkyl, C 1 -C 10 alkenyl, (C 1 -C 6 alkyl)NHC(NH)NH 2 , (C 1 -C 6 alkyl)NHC(O)NH 2 , (C 1 -C 10 alkyl)NHC(NH)NH 2  or (C 1 -C 10 alkyl)NHC(O)NH 2 ; 
         R 3  and R 2  are each independently H, C 1 -C 10 alkyl, C 1 -C 10 alkenyl, arylalkyl or heteroarylalkyl, or R 3  and R 2  together may form a C 3 -C 7 cycloalkyl; and 
         R 4  and R 5  are each independently C 1 -C 10 alkyl, C 1 -C 10 alkenyl, arylalkyl, heteroarylalkyl, (C 1 -C 10 alkyl)OCH 2 —, or R 4  and R 5  together may form a C 3 -C 7 cycloalkyl ring. 
       
     
     
         18 . The conjugate of  claim 17 , wherein Y is heteroaryl; R 4  and R 5  together form a cyclobutyl ring. 
     
     
         19 . The conjugate of  claim 17 , wherein Y is a moiety selected from the group consisting of 
       
         
           
           
               
               
           
         
       
     
     
         20 . The conjugate of  claim 17 , wherein
 Str is a chemical moiety represented by the following formula:   
       
         
           
           
               
               
           
         
         wherein R 6  is selected from the group consisting of C 1 -C 10 alkylene, C 1 -C 10 alkenyl, C 3 -C 8 cycloalkyl, (C 1 -C 8 alkylene)O—, and C 1 -C 10 alkylene-C(O)N(R a )—C 2 -C 6 alkylene, where each alkylene may be substituted by one to five substituents selected from the group consisting of halo, trifluoromethyl, difluoromethyl, amino, alkylamino, cyano, sulfonyl, sulfonamide, sulfoxide, hydroxy, alkoxy, ester, carboxylic acid, alkylthio, C 3 -C 5 cycloalkyl, C 4 -C 7 heterocycloalkyl, heteroarylalkyl, aryl arylalkyl, heteroarylalkyl and heteroaryl each R a  is independently H or C 1 -C 6 alkyl; and 
         Sp is —C 1 -C 6 alkylene-C(O)NH— or —Ar—R b —, wherein Ar is aryl or heteroaryl, and R b  is (C 1 -C 10 alkylene)O—. 
       
     
     
         21 . The conjugate of  claim 17 , wherein Str has the formula: 
       
         
           
           
               
               
           
         
         wherein R 7  is selected from C 1 -C 10 alkylene, C 1 -C 10 alkenyl, (C 1 -C 10 alkylene)O—, N(R c )—(C 2 -C 6  alkylene)-N(R c ) and N(R c )—(C 2 -C 6 alkylene); where each R c  is independently H or C 1 -C 6  alkyl; and 
         Sp is —C 1 -C 6 alkylene-C(O)NH— or —Ar—R b —, wherein Ar is aryl or heteroaryl, and R b  is (C 1 -C 10 alkylene)O—. 
       
     
     
         22 . The conjugate of  claim 17 , wherein L1 has the following formula 
       
         
           
           
               
               
           
         
         R 1  is C 1 -C 6 alkyl, C 1 -C 6 alkenyl, (C 1 -C 6 alkyl)NHC(NH)NH 2  or (C 1 -C 6 alkyl)NHC(O)NH 2 ; 
         R 3  and R 2  are each independently H, C 1 -C 10 alkyl. 
       
     
     
         23 . The conjugate of  claim 17 , wherein L1 has the following formula: 
       
         
           
           
               
               
           
         
         R 1  is C 1 -C 6 alkyl, (C 1 -C 6 alkyl)NHC(NH)NH 2  or (C 1 -C 6 alkyl)NHC(O)NH 2 ; 
         R 4  and R 5  together form a C 3 -C 7 cycloalkyl ring. 
       
     
     
         24 . The conjugate of  claim 17 , wherein L1 has the following formula: 
       
         
           
           
               
               
           
         
         R 1  is C 1 -C 6 alkyl, (C 1 -C 6 alkyl)NHC(NH)NH 2  or (C 1 -C 6 alkyl)NHC(O)NH 2 . 
       
     
     
         25 . The conjugate compound of  claim 1 , having the formula: 
       
         
           
           
               
               
           
         
         wherein 
         Sp is a bond or spacer unit covalently attached to PROTAC moiety D; 
         Y is heteroaryl, aryl, —C(O)C 1 -C 6 alkylene, C 1 -C 6 alkylene-NH 2 , C 1 -C 6 alkylene-NH—CH 3 , C 1 -C 6 alkylene-N—(CH 3 ) 2 , C 1 -C 6 alkenyl or C 1 -C 6 alkylenyl; 
         R 1  is independently C 1 -C 10 alkyl, C 1 -C 10 alkenyl, (C 1 -C 6 alkyl)NHC(NH)NH 2 , (C 1 -C 6 alkyl)NHC(O)NH 2 , (C 1 -C 10 alkyl)NHC(NH)NH 2  or (C 1 -C 10 alkyl)NHC(O)NH 2 ; 
         R 3  and R 2  are each independently H, C 1 -C 10 alkyl, C 1 -C 10 alkenyl, arylalkyl or heteroarylalkyl, or R 3  and R 2  together may form a C 3 -C 7 cycloalkyl; and 
         Str is a chemical moiety represented by the following formula: 
       
       
         
           
           
               
               
           
         
         R 6  is selected from the group consisting of C 1 -C 10 alkylene, and C 1 -C 10 alkylene-C(O)N(R a )—C 2 -C 6 alkylene, where each alkylene may be substituted by one to five substituents selected from the group consisting of halo, trifluoromethyl, difluoromethyl, amino, alkylamino, cyano, sulfonyl, sulfonamide, sulfoxide, hydroxy, alkoxy, ester, carboxylic acid, alkylthio, C 3 -C 5 cycloalkyl, C 4 -C 7 heterocycloalkyl, heteroarylalkyl, aryl, arylalkyl, heteroarylalkyl and heteroaryl each R a  is independently H or C 1 -C 6 alkyl; 
         p is 1, 2, 3 or 4. 
       
     
     
         26 . The conjugate of  claim 1 , having the formula: 
       
         
           
           
               
               
           
         
         wherein 
         Sp is a bond or spacer unit covalently attached to PROTAC moiety D; 
         R 4  and R 5  are each independently C 1 -C 10 alkyl, C 1 -C 10 alkenyl, arylalkyl, heteroarylalkyl, (C 1 -C 10 alkyl)OCH 2 —, or R 4  and R 5  together may form a C 3 -C 7 cycloalkyl ring 
         R 1  is independently C 1 -C 10 alkyl, C 1 -C 10 alkenyl, (C 1 -C 6 alkyl)NHC(NH)NH 2 , (C 1 -C 6 alkyl)NHC(O)NH 2 , (C 1 -C 10 alkyl)NHC(NH)NH 2  or (C 1 -C 10 alkyl)NHC(O)NH 2 ; 
         Str is a chemical moiety represented by the following formula: 
       
       
         
           
           
               
               
           
         
         R 6  is selected from the group consisting of C 1 -C 10 alkylene, and C 1 -C 10 alkylene-C(O)N(R a )—C 2 -C 6 alkylene, where each alkylene may be substituted by one to five substituents selected from the group consisting of halo, trifluoromethyl, difluoromethyl, amino, alkylamino, cyano, sulfonyl, sulfonamide, sulfoxide, hydroxy, alkoxy, ester, carboxylic acid, alkylthio, C 3 -C 5 cycloalkyl, C 4 -C 7 heterocycloalkyl, aryl, arylalkyl, heteroarylalkyl and heteroaryl each R is independently H or C 1 -C 6 alkyl; 
         p is 1, 2, 3 or 4. 
       
     
     
         27 . The conjugate of  claim 25 , wherein Y is heteroaryl, aryl or alkenyl; R 6  is C 1 -C 10 alkylene. 
     
     
         28 . The conjugate of  claim 25 , wherein Y is 
       
         
           
           
               
               
           
         
       
     
     
         29 . The conjugate of  claim 25 , wherein Y is 
       
         
           
           
               
               
           
         
       
     
     
         30 . The conjugate of  claim 25 , wherein Y is 
       
         
           
           
               
               
           
         
       
     
     
         31 . The conjugate of  claim 25 , wherein
 Str is a chemical moiety represented b the following formula:   
       
         
           
           
               
               
           
         
         R 6  is C 1 -C 6 alkylene; 
         Sp is —C 1 -C 6 alkylene-C(O)NH— or —Ar—R b —, where Ar is aryl, R b  is (C 1 -C 3 alkylene)O—. 
       
     
     
         32 . The conjugate of  claim 1 , having the formula: 
       
         
           
           
               
               
           
         
         wherein 
         Y is heteroaryl, aryl, —C(O)C 1 -C 6 alkylene, C 1 -C 6 alkylene-NH 2 , C 1 -C 6 alkylene-NH—CH 3 , C 1 -C 6 alkylene-N—(CH 3 ) 2 , C 1 -C 6 alkenyl or C 1 -C 6 alkylenyl; 
         R 1  is C 1 -C 6 alkyl-NH 2 , (C 1 -C 6 alkyl)NHC(NH)NH 2  or (C 1 -C 6 alkyl)NHC(O)NH 2 ; 
         R 3  and R 2  are each independently H, C 1 -C 10 alkyl, C 1 -C 10 alkenyl, arylalkyl or heteroarylalkyl, or R 3  and R 2  together may form a C 3 -C 7 cycloalkyl; and 
         p is 1, 2, 3 or 4. 
       
     
     
         33 . The conjugate of  claim 1 , having the formula: 
       
         
           
           
               
               
           
         
         wherein 
         p is 1, 2, 3 or 4; 
         R 1  is C 1 -C 6 alkyl-NH 2 , (C 1 -C 6 alkyl)NHC(NH)NH 2  or (C 1 -C 6 alkyl)NHC(O)NH 2 ; 
         R 4  and R 5  are each independently C 1 -C 6 alkyl, wherein said alkyl are unsubstituted, or R 4  and R 5  may form a C 3 -C 7 cycloalkyl ring. 
       
     
     
         34 . The conjugate of  claim 1 , wherein L1 has the following formula: 
       
         
           
           
               
               
           
         
         wherein, R 1  and R 2  are independently selected from H and C 1 -C 6  alkyl, or R 1  and R 2  form a 3, 4, 5, or 6-membered cycloalkyl or heterocyclyl group. 
       
     
     
         35 . The conjugate of  claim 1  selected from the group consisting of PAC1, PAC2, PAC3, PAC4 and PAC5. 
     
     
         36 . The conjugate of  claim 1 , wherein p is from about 1.0 to about 3. 
     
     
         37 . The conjugate of  claim 1 , wherein p is about 2. 
     
     
         38 . A pharmaceutical composition comprising a conjugate of  claim 1  and one or more pharmaceutically acceptable excipients. 
     
     
         39 . A method of treating a disease in a human in need thereof, comprising administering to said human an effective amount of a conjugate of  claim 1  or a composition of  claim 38 . 
     
     
         40 . The method of  claim 39 , wherein said disease is cancer. 
     
     
         41 . The method of  claim 40 , wherein said cancer is selected from the group consisting of a carcinoma, lymphoma, blastoma, sarcoma, leukemia, lymphoid malignancies, squamous cell cancer, lung cancer including small-cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung and squamous carcinoma of the lung, cancer of the peritoneum, hepatocellular cancer, gastric or stomach cancer including gastrointestinal cancer, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer, colon cancer, rectal cancer, colorectal cancer, endometrial or uterine carcinoma, salivary gland carcinoma, kidney or renal cancer, prostate cancer, vulval cancer, thyroid cancer, hepatic carcinoma, anal carcinoma, penile carcinoma, and head and neck cancer. 
     
     
         42 . The method of  claim 41 , wherein the cancer is a HER2-positive cancer. 
     
     
         43 . The method of  claim 42 , wherein the HER2-positive cancer is breast cancer or gastric cancer. 
     
     
         44 . A method of  claim 39 , wherein said disease is an autoimmune disease. 
     
     
         45 . The method of  claim 44 , wherein the autoimmune disease is selected from the group consisting of rheumatologic disorders, osteoarthritis, autoimmune gastrointestinal and liver disorders, vasculitis, autoimmune neurological disorders, renal disorders, autoimmune dermatologic disorders, hematologic disorders, atherosclerosis, uveitis, autoimmune hearing diseases, Behcet's disease, Raynaud's syndrome, organ transplant, autoimmune endocrine disorders, Addison's disease, and autoimmune thyroid disease. 
     
     
         46 . The method of  claim 45 , wherein the autoimmune disease is selected from the group consisting of rheumatoid arthritis, ulcerative colitis, ANCA-associated vasculitis, lupus, multiple sclerosis, Sjögren's syndrome, Graves' disease, IDDM, pernicious anemia, thyroiditis, and glomerulonephritis.