Therapeutic peptidomimetic macrocycles

Abstract

The present invention provides biologically active peptidomimetic macrocycles for the treatment of cell proliferative disorders such as cancer and immunoproliferative disease.

1 .- 87 . (canceled) 
     
     
         88 . A peptidomimetic macrocycle capable of binding MCL-1, wherein the peptidomimetic macrocycle comprises a polypeptide and a crosslinker connecting two amino acid residues of the polypeptide and has Formula (I): 
       
         
           
           
               
               
           
         
         wherein: 
         each A, C, D, and E, is independently a natural or non-natural amino acid; 
         each B is independently a natural or non-natural amino acid, an amino acid analog, 
       
       
         
           
           
               
               
           
         
         [—NH-L 3 -CO-], [—NH-L 3 -SO 2 -], or [—NH-L 3 -]; 
         each R 1  and R 2  is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, cycloalkylalkyl, heteroalkyl, or heterocycloalkyl, each of which except —H is unsubstituted or substituted with halo-; 
         each R 3  is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, cycloalkylalkyl, aryl, or heteroaryl, each of which except —H is optionally substituted with R 5 ; 
         each L is independently a macrocycle-forming linker of the formula -L 1 -L 2 - or the formula -L 1 -L 2 -L 3 -; 
         each L 1  and L 2  and L 3  is independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, arylene, heteroarylene, or [—R 4 —K—R 4 -] n , each being optionally substituted with R 5 ;
 each R 4  is independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, arylene, or heteroarylene; 
 each K is independently O, S, SO, SO 2 , CO, CO 2 , or CONR 3 ; 
 
         each R 5  is independently halogen, alkyl, —OR 6 , —N(R 6 ) 2 , —SR 6 , —SOR E , —SO 2 R 6 , —CO 2 R 6 , a fluorescent moiety, a radioisotope, or a therapeutic agent;
 each R 6  is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heterocycloalkyl, a fluorescent moiety, a radioisotope, or a therapeutic agent; 
 
         each R 7  is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, aryl, or heteroaryl, each of which except —H is optionally substituted with R 5 , or part of a cyclic structure with a D residue; 
         each R 8  is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, aryl, or heteroaryl, each of which except —H is optionally substituted with R 5 , or part of a cyclic structure with an E residue; 
         each v and w is independently an integer from 1-1000; 
         each x, y, and z is independently an integer from 0-10; 
         u is an integer from 1-10; 
         each n is independently an integer from 1-5; and 
         wherein the peptidomimetic macrocycle possesses an affinity (K D ) of 1 μM or less for MCL-1. 
       
     
     
         89 . The peptidomimetic macrocycle of  claim 88 , wherein the peptidomimetic macrocycle possesses an affinity (K D ) of about 100 nM or less for MCL-1. 
     
     
         90 . The peptidomimetic macrocycle of  claim 88 , wherein the peptidomimetic macrocycle antagonizes the interaction between MCL-1 and a pro-apoptotic protein. 
     
     
         91 . The peptidomimetic macrocycle of  claim 88 , wherein the peptidomimetic macrocycle comprises a BH3 domain. 
     
     
         92 . The peptidomimetic macrocycle of  claim 88 , wherein the peptidomimetic macrocycle is at least about 60% identical to an amino acid sequence IWIAQELR*IGD*FNAYYARR (SEQ ID NO:1) wherein each * is independently a non-natural amino acid. 
     
     
         93 . The peptidomimetic macrocycle of  claim 88 , wherein the peptidomimetic macrocycle is at least about 80% identical to an amino acid sequence IWIAQELR*IGD*FNAYYARR (SEQ ID NO:1) wherein each * is independently a non-natural amino acid. 
     
     
         94 . The peptidomimetic macrocycle of  claim 88 , wherein the peptidomimetic macrocycle comprises an α-helix. 
     
     
         95 . The peptidomimetic macrocycle of  claim 88 , wherein an α-carbon atom in the peptidomimetic macrocycle is additionally substituted with independent substituents of formula R—, wherein R— is alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heteroalkyl, or heterocycloalkyl, unsubstituted or substituted with halo-. 
     
     
         96 . The peptidomimetic macrocycle of  claim 88 , wherein L is the formula -L 1 -L 2 -, and each L 1  and L 2  is independently C 3 -C 6  alkylene or C 3 -C 6  alkenylene. 
     
     
         97 . The peptidomimetic macrocycle of  claim 88 , wherein L is the formula -L 1 -L 2 -L 3 -, and each L 1  and L 3  is independently C 3 -C 6  alkylene, and L 2  is heteroarylene. 
     
     
         98 . The peptidomimetic macrocycle of  claim 88 , wherein R 1  and R 2  are methyl. 
     
     
         99 . The peptidomimetic macrocycle of  claim 88 , wherein R 1  and R 2  are H. 
     
     
         100 . The peptidomimetic macrocycle of  claim 88 , wherein x+y+z is 6. 
     
     
         101 . The peptidomimetic macrocycle of  claim 88 , wherein x+y+z is 3. 
     
     
         102 . The peptidomimetic macrocycle of  claim 88 , wherein [A] x -[B] y —[C] z  is IGD. 
     
     
         103 . The peptidomimetic macrocycle of  claim 88 , wherein w is 3. 
     
     
         104 . The peptidomimetic macrocycle of  claim 88 , wherein w is 8. 
     
     
         105 . The peptidomimetic macrocycle of  claim 88 , wherein v is 8. 
     
     
         106 . A method of treating a disorder in a human patient in need thereof comprising administering to the patient a peptidomimetic macrocycle capable of binding MCL-1, wherein the peptidomimetic macrocycle comprises a polypeptide and a crosslinker connecting two amino acid residues of the polypeptide and has Formula (I): 
       
         
           
           
               
               
           
         
         wherein: 
         each A, C, D, and E, is independently a natural or non-natural amino acid; 
         each B is independently a natural or non-natural amino acid, an amino acid analog, 
       
       
         
           
           
               
               
           
         
         [—NH-L 3 -CO-], [—NH-L 3 -SO 2 -], or [—NH-L 3 -]; 
         each R 1  and R 2  is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, cycloalkylalkyl, heteroalkyl, or heterocycloalkyl, each of which except —H is unsubstituted or substituted with halo-; 
         each R 3  is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, cycloalkylalkyl, aryl, or heteroaryl, each of which except —H is optionally substituted with R 5 ; 
         each L is independently a macrocycle-forming linker of the formula -L 1 -L 2 - or the formula -L 1 -L 2 -L 3 -; 
         each L 1  and L 2  and L 3  is independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, arylene, heteroarylene, or [—R 4 —K—R 4 -] n , each being optionally substituted with R 5 ;
 each R 4  is independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, arylene, or heteroarylene; 
 each K is independently O, S, SO, SO 2 , CO, CO 2 , or CONR 3 ; 
 
         each R 5  is independently halogen, alkyl, —OR 6 , —N(R 6 ) 2 , —SR 6 , —SOR E , —SO 2 R 6 , —CO 2 R 6 , a fluorescent moiety, a radioisotope, or a therapeutic agent;
 each R 6  is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heterocycloalkyl, a fluorescent moiety, a radioisotope, or a therapeutic agent; 
 
         each R 7  is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, aryl, or heteroaryl, each of which except —H is optionally substituted with R 5 , or part of a cyclic structure with a D residue; 
         each R 8  is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, aryl, or heteroaryl, each of which except —H is optionally substituted with R 5 , or part of a cyclic structure with an E residue; 
         each v and w is independently an integer from 1-1000; 
         each x, y, and z is independently an integer from 0-10; 
         u is an integer from 1-10; 
         each n is independently an integer from 1-5; and 
         wherein the peptidomimetic macrocycle possesses an affinity (K D ) of 1 μM or less for MCL-1. 
       
     
     
         107 . The method of  claim 106 , wherein the disorder is cancer. 
     
     
         108 . The method of  claim 107 , wherein the cancer is selected from the group consisting of ovarian cancer, skin cancer, prostate cancer, renal cancer, breast cancer, pancreatic cancer, small-cell lung cancer, colon cancer, liver cancer, Multiple myeloma, Burkitt's lymphoma, acute lymphocytic leukemia (ALL) of T cell lineage or B cell lineage or mixed lineage, Chronic lymphocytic leukemia (CLL), Ph+ acute lymphocytic leukemia, Cutaneous T cell lymphoma (CTCL), Acute myelocytic leukemia (AML), Chronic Myelocytic leukemia, and follicular lymphoma. 
     
     
         109 . The method of  claim 107 , wherein the cancer is resistant to a compound that possesses an affinity greater than 10 μM for MCL-1. 
     
     
         110 . The method of  claim 107 , wherein the cancer is resistant to ABT-737 or an analog thereof. 
     
     
         111 . The method of  claim 107 , wherein, the peptidomimetic macrocycle is a BIM polypeptide and the cancer is at least 2-fold less sensitive to treatment using a corresponding uncrosslinked polypeptide or a corresponding crosslinked BID polypeptide as measured in an in vitro cell viability assay. 
     
     
         112 . The method of  claim 107 , wherein the peptidomimetic macrocycle shows an EC 50  lower than 5 μM when tested in an in vitro cell viability assay against a cell line derived from the cancer. 
     
     
         113 . The method of  claim 106 , wherein the disorder is a metabolic disorder or an immunoproliferative disorder. 
     
     
         114 . The method of  claim 106 , wherein the peptidomimetic macrocycle is administered in conjunction with a standard method of care selected from the group consisting of chemotherapy, radiation therapy, and surgery. 
     
     
         115 . The method of  claim 106 , wherein the method further comprises performing an assay to detect a level of MCL-1 in the patient and administering to the patient the peptidomimetic macrocycle if the detected level of MCL-1 is aberrant or irregular. 
     
     
         116 . The method of  claim 106 , wherein the peptidomimetic macrocycle has a reduced immune response in an in vivo assay as compared to a corresponding uncrosslinked polypeptide. 
     
     
         117 . A method of preparing a therapeutic peptidomimetic macrocycle capable of binding MCL-1 comprising:
 (a) preparing a peptidomimetic macrocycle by forming a crosslinking two amino acid residues of a polypeptide to stabilize a secondary structure of the peptidomimetic macrocycle;   (b) testing the peptidomimetic macrocycle for a reduced antibody response in an in vivo assay as compared to a corresponding uncrosslinked polypeptide; and   (c) selecting the tested peptidomimetic macrocycle as the therapeutic peptidomimetic macrocycle if the tested peptidomimetic macrocycle has a reduced immune response relative to the corresponding uncrosslinked polypeptide; and   wherein the peptidomimetic macrocycle comprises a polypeptide and a crosslinker connecting two amino acid residues of the polypeptide and has Formula (I):   
       
         
           
           
               
               
           
         
         wherein: 
         each A, C, D, and E, is independently a natural or non-natural amino acid; 
         each B is independently a natural or non-natural amino acid, an amino acid analog, 
       
       
         
           
           
               
               
           
         
         [—NH-L 3 -CO-], [—NH-L 3 -SO 2 -], or [—NH-L 3 -]; 
         each R 1  and R 2  is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, cycloalkylalkyl, heteroalkyl, or heterocycloalkyl, each of which except —H is unsubstituted or substituted with halo-; 
         each R 3  is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, cycloalkylalkyl, aryl, or heteroaryl, each of which except —H is optionally substituted with R 5 ; 
         each L is independently a macrocycle-forming linker of the formula -L 1 -L 2 - or the formula -L 1 -L2-L 3 -; 
         each L 1  and L 2  and L 3  is independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, arylene, heteroarylene, or [—R 4 —K—R 4 -] n , each being optionally substituted with R 5 ;
 each R 4  is independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, arylene, or heteroarylene; 
 each K is independently O, S, SO, SO 2 , CO, CO 2 , or CONR 3 ; 
 
         each R 5  is independently halogen, alkyl, —OR 6 , —N(R 6 ) 2 , —SR 6 , —SOR E , —SO 2 R 6 , —CO 2 R 6 , a fluorescent moiety, a radioisotope, or a therapeutic agent;
 each R 6  is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heterocycloalkyl, a fluorescent moiety, a radioisotope, or a therapeutic agent; 
 
         each R 7  is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, aryl, or heteroaryl, each of which except —H is optionally substituted with R 5 , or part of a cyclic structure with a D residue; 
         each R 8  is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, aryl, or heteroaryl, each of which except —H is optionally substituted with R 5 , or part of a cyclic structure with an E residue; 
         each v and w is independently an integer from 1-1000; 
         each x, y, and z is independently an integer from 0-10; 
         u is an integer from 1-10; 
         each n is independently an integer from 1-5; and 
         wherein the peptidomimetic macrocycle possesses an affinity (K D ) of 1 μM or less for MCL-1.