Compounds that participate in cooperative binding and uses thereof

Abstract

The invention features compounds (e.g., macrocyclic compounds) capable of modulating biological processes, for example through binding to a presenter protein (e.g., a member of the FKBP family, a member of the cyclophilin family, or PIN1) and a target protein (e.g., a eukaryotic target protein such as a mammalian target protein or a fungal target protein or a prokaryotic target protein such as a bacterial target protein). These compounds bind endogenous intracellular presenter proteins, such as the FKBPs or cyclophilins, and the resulting binary complexes selectively bind and modulate the activity of intracellular target proteins. Formation of a tripartite complex among the presenter protein, the compound, and the target protein is driven by both protein-compound and protein-protein interactions, and both are required for modulation of the targeted protein's activity. In some embodiments, the compounds of the invention “re-program” the binding of the presenter proteins to protein targets that either do not normally bind to the presenter protein (e.g., do not show detectable binding in mammalian cells absent the compound). In some embodiments, provided compounds “re-program” presenter protein binding to greatly enhance interaction with a particular target with which it may have some interaction absent the compound. Interactions achieved through such reprogramming result in an ability to modulate the activity of these new targets.

1 . A macrocyclic compound, or a pharmaceutically acceptable salt thereof, comprising 14 to 40 ring atoms, said compound comprising:
 (a) a mammalian target protein interacting moiety; and   (b) a presenter protein binding moiety;   wherein said compound and a presenter protein form a complex that specifically binds to a target protein, and each of said compound and said presenter protein do not substantially bind to said target protein in the absence of forming said complex; or   said compound and a presenter protein form a complex that binds to a target protein with at least 5-fold greater affinity than the affinity of each of said compound and said presenter protein to said target protein in the absence of forming said complex.   
     
     
         2 . The compound of  claim 1 , or a pharmaceutically acceptable salt thereof, wherein said presenter protein binding moiety comprises the structure of Formula I: 
       
         
           
           
               
               
           
         
         wherein n is 0 or 1; 
         X 1  and X 3  are each independently O, S, CR 3 R 4 , or NR 5 ; 
         X 2  is O, S, or NR 5 ; 
         R 1 , R 2 , R 3 , and R 4  are each independently hydrogen, hydroxyl, optionally substituted amino, halogen, thiol, optionally substituted C 1 -C 6  alkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  heteroalkenyl, optionally substituted C 2 -C 6  heteroalkynyl, optionally substituted C 3 -C 10  carbocyclyl, optionally substituted C 6 -C 10  aryl, optionally substituted C 6 -C 10  aryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heteroaryl, optionally substituted C 2 -C 9  heteroaryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heterocyclyl, or optionally substituted C 2 -C 9  heterocyclyl C 1 -C 6  alkyl, or any two of R 1  R 2 , R 3 , or R 4  are taken together with the atom or atoms to which they are bound to form an optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl; 
         each R 5  is, independently, hydrogen, hydroxyl, optionally substituted C 1 -C 6  alkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  heteroalkenyl, optionally substituted C 2 -C 6  heteroalkynyl, optionally substituted C 3 -C 10  carbocyclyl, optionally substituted C 6 -C 10  aryl, optionally substituted C 6 -C 10  aryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heteroaryl, optionally substituted C 2 -C 9  heteroaryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heterocyclyl, or optionally substituted C 2 -C 9  heterocyclyl C 1 -C 6  alkyl, or R 5  and one of R 1 , R 2 , R 3 , or R 4  are taken together with the atom or atoms to which they are bound to form an optionally substituted heterocyclyl or optionally substituted heteroaryl. 
       
     
     
         3 . The compound of  claim 2 , or a pharmaceutically acceptable salt thereof, wherein said presenter protein binding moiety comprises the structure of any one of Formulae II-IV: 
       
         
           
           
               
               
           
         
         wherein o, and p are independently 0, 1, or 2; 
         q is an integer between 0 and 7; 
         r is an integer between 0 and 4; 
         X 4  and X 5  are each, independently, absent, CH 2 , O, S, SO, SO 2 , or NR 11 ; 
         each R 6  and R 7  are independently hydrogen, hydroxyl, optionally substituted amino, halogen, thiol, optionally substituted C 1 -C 6  alkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  heteroalkenyl, optionally substituted C 2 -C 6  heteroalkynyl, optionally substituted C 3 -C 10  carbocyclyl, optionally substituted C 6 -C 10  aryl, optionally substituted C 6 -C 10  aryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heteroaryl, optionally substituted C 2 -C 9  heteroaryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heterocyclyl, optionally substituted C 2 -C 9  heterocyclyl C 1 -C 6  alkyl, or R 6  and R 7  combine with the carbon atom to which they are bound to form C═O; 
         each R 8  is, independently, hydroxyl, optionally substituted amino, halogen, thiol, optionally substituted C 1 -C 6  alkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  heteroalkenyl, optionally substituted C 2 -C 6  heteroalkynyl, optionally substituted C 3 -C 10  carbocyclyl, optionally substituted C 6 -C 10  aryl, optionally substituted C 6 -C 10  aryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heteroaryl, optionally substituted C 2 -C 9  heteroaryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heterocyclyl, or optionally substituted C 2 -C 9  heterocyclyl C 1 -C 6  alkyl, or two R 8  combine to form an optionally substituted C 3 -C 10  carbocyclyl, optionally substituted C 6 -C 10  aryl, or optionally substituted C 2 -C 9  heteroaryl; 
         R 9  is optionally substituted C 1 -C 6  alkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  heteroalkenyl, optionally substituted C 2 -C 6  heteroalkynyl, optionally substituted C 3 -C 10  carbocyclyl, optionally substituted C 6 -C 10  aryl, optionally substituted C 6 -C 10  aryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heteroaryl, optionally substituted C 2 -C 9  heteroaryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heterocyclyl, or optionally substituted C 2 -C 9  heterocyclyl C 1 -C 6  alkyl; 
         R 10  is optionally substituted C 1 -C 6  alkyl; 
         each R 11  is, independently, hydroxyl, cyano, optionally substituted amino, halogen, thiol, optionally substituted C 1 -C 6  alkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  heteroalkenyl, optionally substituted C 2 -C 6  heteroalkynyl, optionally substituted C 3 -C 10  carbocyclyl, optionally substituted C 6 -C 10  aryl, optionally substituted C 6 -C 10  aryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heteroaryl, optionally substituted C 2 -C 9  heteroaryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heterocyclyl, or optionally substituted C 2 -C 9  heterocyclyl C 1 -C 6  alkyl; and 
         R 12  and R 13  are each, independently, hydrogen, optionally substituted C 1 -C 6  alkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted aryl, C 3 -C 7  carbocyclyl, optionally substituted C 6 -C 10  aryl C 1 -C 6  alkyl, and optionally substituted C 3 -C 7  carbocyclyl C 1 -C 6  alkyl. 
       
     
     
         4 . The compound of  claim 3 , or a pharmaceutically acceptable salt thereof, wherein said presenter protein binding moiety comprises the structure of Formula V: 
       
         
           
           
               
               
           
         
         wherein R 14  is hydrogen, hydroxyl, optionally substituted C 1 -C 6  alkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  heteroalkenyl, optionally substituted C 2 -C 6  heteroalkynyl, optionally substituted C 3 -C 10  carbocyclyl, optionally substituted C 6 -C 10  aryl, optionally substituted C 6 -C 10  aryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heteroaryl, optionally substituted C 2 -C 9  heteroaryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heterocyclyl, optionally substituted C 2 -C 9  heterocyclyl C 1 -C 6  alkyl. 
       
     
     
         5 . The compound of  claim 4 , or a pharmaceutically acceptable salt thereof, wherein said presenter protein binding moiety comprises the structure of Formula VI or VII: 
       
         
           
           
               
               
           
         
         wherein s and t are each, independently, an integer from 0 to 7; 
         X 6  and X 7  are each, independently, O, S, SO, SO 2 , or NR 19 ; 
         R 15  and R 17  are each, independently, hydrogen hydroxyl, or optionally substituted C 1 -C 6  alkyl; 
         R 16  and R 18  are each, independently, hydroxyl, optionally substituted amino, halogen, thiol, optionally substituted C 1 -C 6  alkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted C 1 -C 6  heteroalkyl, optionally substituted C 2 -C 6  heteroalkenyl, optionally substituted C 2 -C 6  heteroalkynyl, optionally substituted C 3 -C 10  carbocyclyl, optionally substituted C 6 -C 10  aryl, optionally substituted C 6 -C 10  aryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heteroaryl, optionally substituted C 2 -C 9  heteroaryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heterocyclyl, or optionally substituted C 2 -C 9  heterocyclyl C 1 -C 6  alkyl; 
         R 19  is hydrogen, optionally substituted C 1 -C 6  alkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted C 6 -C 10  aryl, C 3 -C 7  carbocyclyl, optionally substituted C 6 -C 10  aryl C 1 -C 6  alkyl, and optionally substituted C 3 -C 7  carbocyclyl C 1 -C 6  alkyl; and 
         Ar is optionally substituted C 6 -C 10  aryl or optionally substituted C 2 -C 9  heteroaryl. 
       
     
     
         6 . The compound of  claim 1 , or a pharmaceutically acceptable salt thereof, wherein said target interacting moiety comprises the structure of Formula IX: 
       
         
           
           
               
               
           
         
         wherein u is an integer from 1 to 20; and 
         each Y is, independently, any amino acid, O, NR, S, S(O) SO 2 , or has the structure of any one of Formulae X-XIII: 
       
       
         
           
           
               
               
           
         
         wherein each R 20  is, independently, hydrogen, optionally substituted C 1 -C 6  alkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted aryl, C 3 -C 7  carbocyclyl, optionally substituted C 6 -C 10  aryl C 1 -C 6  alkyl, and optionally substituted C 3 -C 7  carbocyclyl C 1 -C 6  alkyl or R 19  combines with any R 20 , R 21 , R 22 , R 23 , R 24 , R 25 , R 26 , R 27 , R 28 , R 29 , or R 30  to form an optionally substituted C 3 -C 10  carbocyclyl, optionally substituted C 6 -C 10  aryl, or optionally substituted C 2 -C 9  heteroaryl; 
         each R 21  and R 22  is, independently, hydrogen, halogen, optionally substituted hydroxyl, optionally substituted amino, or R 20  and R 21  combine to form ═O, optionally substituted C 1 -C 6  alkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted C 3 -C 10  carbocyclyl, optionally substituted C 6 -C 10  aryl, optionally substituted C 6 -C 10  aryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heteroaryl, optionally substituted C 2 -C 9  heteroaryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heterocyclyl, or optionally substituted C 2 -C 9  heterocyclyl C 1 -C 6  alkyl, or R 21  or R 22  combines with any R 20 , R 21 , R 22 , R 23 , R 24 , R 25 , R 26 , R 27 , R 28 , R 29 , or R 30  to form an optionally substituted C 3 -C 10  carbocyclyl, optionally substituted C 6 -C 10  aryl, or optionally substituted C 2 -C 9  heteroaryl; 
         each R 23  R 24 , R 25  and R 26  is, independently, hydrogen, hydroxyl, or R 22  and R 23  combine to form ═O, or R 23  R 24  R 25  or R 26  combines with any R 20 , R 21 , R 22 , R 23 , R 24 , R 25 , R 26 , R 27 , R 28 , R 29 , or R 30  to form an optionally substituted C 3 -C 10  carbocyclyl, optionally substituted C 6 -C 10  aryl, or optionally substituted C 2 -C 9  heteroaryl; and 
         each R 27 , R 28 , R 29 , and R 30  is, independently, hydrogen, halogen, optionally substituted hydroxyl, optionally substituted amino, optionally substituted C 1 -C 6  alkyl, optionally substituted C 2 -C 6  alkenyl, optionally substituted C 2 -C 6  alkynyl, optionally substituted C 3 -C 10  carbocyclyl, optionally substituted C 6 -C 10  aryl, optionally substituted C 6 -C 10  aryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heteroaryl, optionally substituted C 2 -C 9  heteroaryl C 1 -C 6  alkyl, optionally substituted C 2 -C 9  heterocyclyl, or optionally substituted C 2 -C 9  heterocyclyl C 1 -C 6  alkyl, or R 27 , R 28 , R 29 , or R 30  combines with any R 20 , R 21 , R 22 , R 23 , R 24 , R 25 , R 26 , R 27 , R 28 , R 29 , or R 30  to form an optionally substituted C 3 -C 10  carbocyclyl, optionally substituted C 6 -C 10  aryl, or optionally substituted C 2 -C 9  heteroaryl. 
       
     
     
         7 . The compound of  claim 1 , or a pharmaceutically acceptable salt thereof, wherein said complex binds to said target protein with at least 5-fold greater affinity than said complex binds to each of mTOR and/or calcineurin. 
     
     
         8 . The compound of  claim 1 , or a pharmaceutically acceptable salt thereof, wherein said complex binds to said target protein with at least 5-fold greater affinity than the affinity of said compound to said target when said compound is not bound in a complex with said presenter protein. 
     
     
         9 . The compound of  claim 1 , or a pharmaceutically acceptable salt thereof, wherein said complex inhibits the naturally occurring interaction between said target protein and a ligand that specifically binds said target protein. 
     
     
         10 . The compound of  claim 1 , or a pharmaceutically acceptable salt thereof, wherein said presenter protein is a prolyl isomerase. 
     
     
         11 . The compound of  claim 1 , or a pharmaceutically acceptable salt thereof, wherein said presenter protein is a member of the FKBP family, a member of the cyclophilin family, or PIN1. 
     
     
         12 . The compound of  claim 1 , or a pharmaceutically acceptable salt thereof, wherein said mammalian target protein is a GTPase, GTPase activating protein, Guanine nucleotide-exchange factor, a heat shock protein, an ion channel, a coiled-coil protein, a kinase, a phosphatase, a ubiquitin ligase, a transcription factor, a chromatin modifier/remodeler, or a protein with classical protein-protein interaction domains and motifs. 
     
     
         13 . A presenter protein/compound complex comprising a compound of  claim 1 , or a pharmaceutically acceptable salt thereof, and a presenter protein. 
     
     
         14 . A pharmaceutical composition comprising a compound of  claim 1 , or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient. 
     
     
         15 . A method of modulating a target protein, said method comprising contacting said target protein with a modulating amount of a compound of  claim 1  or a pharmaceutically acceptable salt thereof. 
     
     
         16 . A method of modulating a target protein, said method comprising forming a presenter protein/compound complex comprising a compound of  claim 1 , or a pharmaceutically acceptable salt thereof, and a presenter protein in a cell by contacting said cell with an effective amount of the compound or a pharmaceutically acceptable salt thereof. 
     
     
         17 . A method of modulating a target protein, said method comprising contacting said target protein with a presenter protein/compound complex comprising a compound of  claim 1 , or a pharmaceutically acceptable salt thereof, and a presenter protein. 
     
     
         18 . A method of inhibiting prolyl isomerase activity, said method comprising contacting a cell expressing said prolyl isomerase with a compound of  claim 1 , or a pharmaceutically acceptable salt thereof, under conditions that permit the formation of a complex between said compound and said prolyl isomerase, thereby inhibiting prolyl isomerase activity. 
     
     
         19 . A method of forming a presenter protein/compound complex comprising a compound of  claim 1 , or a pharmaceutically acceptable salt thereof, and a presenter protein in a cell, said method comprising contacting a cell expressing said presenter protein with the compound, or a pharmaceutically acceptable salt thereof, under conditions that permit the formation of a complex between said compound and said presenter protein. 
     
     
         20 . A tripartite complex comprising (i) a mammalian target protein and (ii) a presenter protein/compound complex, said presenter protein/compound complex comprising a presenter protein and a macrocyclic compound of  claim 1 , or a pharmaceutically acceptable salt thereof.