Cyclic peptides as protein targeting agents

Abstract

Peptides having activity as protein binding agents are disclosed. The peptides have the following structure (I):including stereoisomers, pharmaceutically acceptable salts and prodrugs thereof, wherein R, R1, L1, L2, G, M, Y1 Y2 and SEQ are as defined herein. Methods associated with preparation and use of such peptides, as well as pharmaceutical compositions comprising such peptides, are also disclosed.

1 - 67 . (canceled) 
     
     
         68 . A library comprising a plurality of cyclic peptides, wherein each cyclic peptide of the library has a structure (Ic): 
       
         
           
           
               
               
           
         
         or a salt, tautomer, prodrug or stereoisomer thereof, 
         wherein:
 L 1  and L 2  are each linker moieties; 
 G is a carbon-carbon double bond or an amide; 
 R is H, -L 3 -A or —C(═O)-L 3 -A, where L 3  is a linker moiety and A is an alkyne, azide; and 
 SEQ is an amino acid sequence comprising from 2 to 20 amino acids selected from natural and non-natural amino acids, wherein SEQ of each of the plurality of the cyclic peptides in the library are different. 
 
       
     
     
         69 . The cyclic peptide of  claim 68 , wherein G is a carbon-carbon double bond. 
     
     
         70 . The cyclic peptide of  claim 68 , wherein G is an amide. 
     
     
         71 . The cyclic peptide of  claim 68 , wherein L 1 , L 2 , or both, comprise one or more substituents selected from alkyl and aminocarbonyl. 
     
     
         72 . The cyclic peptide of  claim 68 , wherein L 1 , L 2 , or both, comprise a linkage selected from a linkage to a solid support, a linkage to a reporter moiety and a linkage to a peptide ligand. 
     
     
         73 . The cyclic peptide of  claim 68 , wherein L 1  and L 2  are alkylene. 
     
     
         74 . The cyclic peptide of  claim 68 , wherein SEQ comprises from 2 to 9 amino acids. 
     
     
         75 . The cyclic peptide of  claim 74 , wherein SEQ comprises from 5 to 7 amino acids. 
     
     
         76 . The cyclic peptide of  claim 68 , wherein the amino acids are selected from D and L stereoisomers of Ala, Gly, Leu, Ile, Val, Phe, Trp, Arg, His, Lys, Asp, Glu, Asn, Gln, Ser, Thr, Tyr and Pro. 
     
     
         77 . The cyclic peptide of  claim 68 , wherein A is an azide. 
     
     
         78 . The cyclic peptide of  claim 68 , wherein A is an alkyne. 
     
     
         79 . The cyclic peptide of  claim 77 , wherein A is a bond to a peptide ligand. 
     
     
         80 . A method for identifying a target binding compound, the method comprising:
 (a) contacting a first peptide library with a target protein or peptide, wherein the first peptide library comprises the library of  claim 68 , wherein the plurality of cyclic peptides in the first peptide library constitutes a plurality of first peptide library members, wherein the first peptide library members comprise an alkyne or azide, wherein the target protein or peptide comprises a first binding site and an alkyne or azide; and   (b) identifying a first peptide library member with affinity for the first binding site, wherein the first peptide library member with affinity for the first binding site is identified by identifying first peptide library members that form a triazole linkage with the target protein or peptide;   
       and optionally:
 (c) contacting a second peptide library with a composition comprising the target protein or peptide and the first peptide library member of step (b), wherein the second peptide library comprises a second instance of the first peptide library, wherein the plurality of cyclic peptides in the second peptide library constitutes a plurality of second peptide library members, wherein the second peptide library members comprise an azide or alkyne or both, wherein; and 
 (d) forming a triazole-linked conjugate between the first peptide library member of step (b) and a second peptide library member, wherein the second peptide library member has affinity for a second binding site on the target protein or peptide. 
 
     
     
         81 . The method of  claim 80 , wherein the linker region comprises a α-amino carbonyl group bound to the amino terminus of the peptide sequence. 
     
     
         82 . The method of  claim 81 , further comprising determining the peptide sequence of one or more of the cyclic peptides by Edman degradation. 
     
     
         83 . The method of  claim 80 , wherein the first peptide library is contacted with a target peptide. 
     
     
         84 . The method of  claim 80 , further comprising modifying the triazole linked conjugate to contain a triazole or alkyne and contacting the modified conjugate with the target protein or peptide and a third peptide library, the third peptide library comprising a third instance of the first peptide library, wherein the plurality of cyclic peptides in the third peptide library constitutes a plurality of third peptide library members, each third peptide library member comprising an azide or alkyne. 
     
     
         85 . The method of  claim 84 , further comprising forming a triazole linkage between the modified conjugate and a member of the third peptide library, the third peptide library member having affinity for a third binding site on the target protein or peptide. 
     
     
         86 . The method of  claim 80 , wherein the first binding site is an epitope. 
     
     
         87 . The method of  claim 80 , wherein the second binding site is an epitope. 
     
     
         88 . The method of  claim 80 , wherein the third binding site is an epitope. 
     
     
         89 . The method of  claim 80 , wherein the linker region comprises a carbon-carbon double bond or a triazole. 
     
     
         90 . The method of  claim 80 , wherein the protein is an enzyme or cell surface protein. 
     
     
         91 . The method of  claim 80 , wherein the target protein is AkT2, pfLDH, pvLDH or HIV-1 p24 antigen. 
     
     
         92 . A library comprising a plurality of cyclic peptides, wherein each cyclic peptide of the library has a structure (Id): 
       
         
           
           
               
               
           
         
         or a salt, tautomer, prodrug or stereoisomer thereof, 
         wherein:
 R 3  is a linkage to a peptide ligand or to a solid support, wherein y is an integer from 1 to 8; 
 L 2  is a linker moiety; 
 G is a carbon-carbon double bond or an amide; 
 R is -L 3 -A or —C(═O)-L 3 -A, where L 3  is a linker moiety and A is an alkyne or azide; and 
 SEQ is an amino acid sequence comprising from 2 to 20 amino acids selected from natural and non-natural amino acids, wherein SEQ of each of the plurality of the cyclic peptides in the library are different. 
 
       
     
     
         93 . The cyclic peptide of  claim 92 , wherein A is an azide. 
     
     
         94 . The cyclic peptide of  claim 92 , wherein A is an alkyne. 
     
     
         95 . The cyclic peptide of  claim 92 , wherein R 3  is a linkage to a peptide ligand. 
     
     
         96 . The cyclic peptide of  claim 92 , wherein R 3  is a linkage to a solid support. 
     
     
         97 . A method for identifying a target binding compound, the method comprising:
 (a) contacting a first peptide library with a target protein or peptide, wherein the first peptide library comprises the library of  claim 92 , wherein the plurality of cyclic peptides in the first peptide library constitutes a plurality of first peptide library members, wherein the first peptide library members comprise an alkyne or azide, wherein the target protein or peptide comprising a first binding site and an alkyne or azide; and   (b) identifying a first peptide library member with affinity for the first binding site, wherein the first peptide library member with affinity for the first binding site is identified by identifying first peptide library members that form a triazole linkage with the target protein or peptide;   
       and optionally:
 (c) contacting a second peptide library with a composition comprising the target protein or peptide and the first peptide library member of step (b), wherein the second peptide library comprises a second instance of the first peptide library, wherein the plurality of cyclic peptides in the second peptide library constitutes a plurality of second peptide library members, wherein the second peptide library members comprise an azide or alkyne or both, wherein; and 
 (d) forming a triazole-linked conjugate between the first peptide library member of step (b) and a second peptide library member, wherein the second peptide library member has affinity for a second binding site on the target protein or peptide. 
 
     
     
         98 . A library comprising a plurality of cyclic peptides, wherein each cyclic peptide of the library has a structure (Id): 
       
         
           
           
               
               
           
         
         or a salt, tautomer, prodrug or stereoisomer thereof, 
         wherein:
 R 3  is a linkage to an alkyne or azide, wherein y is an integer from 1 to 8; 
 L 2  is a linker moiety; 
 G is a carbon-carbon double bond or an amide; 
 R is H; and 
 SEQ is an amino acid sequence comprising from 2 to 20 amino acids selected from natural and non-natural amino acids, wherein SEQ of each of the plurality of the cyclic peptides in the library are different. 
 
       
     
     
         99 . The cyclic peptide of  claim 98 , wherein R 3  is a linkage to an azide. 
     
     
         100 . The cyclic peptide of  claim 98 , wherein R 3  is a linkage to an alkyne. 
     
     
         101 . A method for identifying a target binding compound, the method comprising:
 (a) contacting a first peptide library with a target protein or peptide, wherein the first peptide library comprises the library of  claim 98 , wherein the plurality of cyclic peptides in the first peptide library constitutes a plurality of first peptide library members, wherein the first peptide library members comprise an alkyne or azide, wherein the target protein or peptide comprising a first binding site and an alkyne or azide; and   (b) identifying a first peptide library member with affinity for the first binding site, wherein the first peptide library member with affinity for the first binding site is identified by identifying first peptide library members that form a triazole linkage with the target protein or peptide;   
       and optionally:
 (c) contacting a second peptide library with a composition comprising the target protein or peptide and the first peptide library member of step (b), wherein the second peptide library comprises a second instance of the first peptide library, wherein the plurality of cyclic peptides in the second peptide library constitutes a plurality of second peptide library members, wherein the second peptide library members comprise an azide or alkyne or both, wherein; and 
 (d) forming a triazole-linked conjugate between the first peptide library member of step (b) and a second peptide library member, wherein the second peptide library member has affinity for a second binding site on the target protein or peptide. 
 
     
     
         102 . A library comprising a plurality of cyclic peptides, wherein each cyclic peptide of the library has a structure (Id): 
       
         
           
           
               
               
           
         
         or a salt, tautomer, prodrug or stereoisomer thereof, 
         wherein:
 R 3  is a linkage to an alkyne or azide, wherein y is an integer from 1 to 8; 
 L 2  is a linker moiety; 
 G is a carbon-carbon double bond or an amide; 
 R is -L 3 -A or —C(═O)-L 3 -A, where L 3  is a linker moiety and A is a peptide ligand or a solid support; and 
 SEQ is an amino acid sequence comprising from 2 to 20 amino acids selected from natural and non-natural amino acids, wherein SEQ of each of the plurality of the cyclic peptides in the library are different. 
 
       
     
     
         103 . The cyclic peptide of  claim 102 , wherein A is a peptide ligand. 
     
     
         104 . The cyclic peptide of  claim 102 , wherein A is a solid support. 
     
     
         105 . The cyclic peptide of  claim 102 , wherein R 3  is a linkage to an azide. 
     
     
         106 . The cyclic peptide of  claim 102 , wherein R 3  is a linkage to an alkyne. 
     
     
         107 . A method for identifying a target binding compound, the method comprising:
 (a) contacting a first peptide library with a target protein or peptide, wherein the first peptide library comprises the library of  claim 102 , wherein the plurality of cyclic peptides in the first peptide library constitutes a plurality of first peptide library members, wherein the first peptide library members comprise an alkyne or azide, wherein the target protein or peptide comprising a first binding site and an alkyne or azide; and   (b) identifying a first peptide library member with affinity for the first binding site, wherein the first peptide library member with affinity for the first binding site is identified by identifying first peptide library members that form a triazole linkage with the target protein or peptide;   
       and optionally:
 (c) contacting a second peptide library with a composition comprising the target protein or peptide and the first peptide library member of step (b), wherein the second peptide library comprises a second instance of the first peptide library, wherein the plurality of cyclic peptides in the second peptide library constitutes a plurality of second peptide library members, wherein the second peptide library members comprise an azide or alkyne or both, wherein; and 
 (d) forming a triazole-linked conjugate between the first peptide library member of step (b) and a second peptide library member, wherein the second peptide library member has affinity for a second binding site on the target protein or peptide.