Peptides and other small molecules derived from regions of interacting proteins and uses thereof

Abstract

The present invention relates generally to the field of peptides and other small molecules (i.e. peptide mimetics) as pharmaceutical and/or therapeutic agents, and to methods for identification and design of peptides and peptide mimetics having desired functional activities. Specifically, peptides and other small molecules derived from regions of interacting intracellular signaling proteins are provided. More specifically, peptides and other small molecules derived from regions of the Gβ subunit of heterotrimeric GTP binding proteins are provided. Such molecules include specific agonists and antagonists of Gβ downstream effectors, including adenylyl cyclase and phospholipase C. Such molecules are targeted to predicted regions of interaction between intracellular signaling proteins and tested for activity in functional assays using methods of the invention. One major advantage of the invention is the incorporation of three-dimensional structural information in models used for predicting interaction surfaces between intracellular proteins. Another major advantage is the ability to distinguish, within a predicted interaction surface, a signal transfer region from a general binding domain. Resolution of such signal transfer regions from general binding domains is useful for prediction and validation of pharmacologic and therapeutic agonists and antagonists.

We claim:  
     
         1 . An isolated peptide or derivative thereof selected from the group consisting of SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9 and SEQ ID NO:10.  
     
     
         2 . The peptide or derivative of  claim 1 , which is capable of immunospecific binding to an anti-peptide antibody.  
     
     
         3 . A chimeric peptide comprising the peptide or derivative of  claim 1  fused by a covalent bond to a second peptide.  
     
     
         4 . The chimeric peptide of  claim 3 , wherein the peptide is capable of immunospecific binding to an anti-peptide antibody.  
     
     
         5 . A purified antibody or an antigen-binding derivative thereof capable of immunospecific binding to the peptide or derivative thereof of  claim 1  and not to a protein from which the peptide was derived.  
     
     
         6 . The antibody of  claim 5  which is polyclonal.  
     
     
         7 . The antibody of  claim 5  which is monoclonal.  
     
     
         8 . A method of producing a recombinant peptide comprising: 
 (a) growing a recombinant cell containing a nucleic acid comprising a nucleotide sequence encoding an amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9 and SEQ ID NO:10 such that the encoded peptide is expressed by the cell, and    (b) recovering the expressed recombinant peptide.    
     
     
         9 . A purified recombinant peptide produced by the method of  claim 8 .  
     
     
         10 . A pharmaceutical composition comprising: 
 (a) a peptide or derivative thereof selected from the group consisting of SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9 and SEQ ID NO:10; and    (b) a pharmaceutically acceptable carrier.    
     
     
         11 . A method of identifying a peptide or derivative thereof having a biological activity of interest comprising: 
 (a) providing a molecular model of an intracellular protein-protein interaction based on three dimensional structure information;    (b) predicting a candidate interaction surface of the intracellular protein-protein interaction from the molecular model provided; and    (c) measuring an activity in a functional assay of a peptide encoded by at least a portion of the candidate interaction surface predicted.    
     
     
         12 . The method of  claim 11 , wherein the functional assay is selected from the group consisting of an adenylyl cyclase assay, a phospholipase Cβ assay, a potassium channel assay and a calcium channel assay.  
     
     
         13 . A method of identifying one or more molecules that specifically bind to a peptide or derivative thereof selected from the group consisting of SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9 and SEQ ID NO:10 comprising: 
 (a) contacting the peptide or derivative thereof with a plurality of molecules under conditions conducive to binding between the peptide or derivative thereof and the plurality of molecules; and    (b) identifying any molecules from within the plurality of molecules contacted in step (a) that specifically bind to the peptide or fragment thereof.    
     
     
         14 . The method of  claim 13 , wherein the peptide or derivative thereof is labeled with a detectable label.  
     
     
         15 . A method for identification of a peptide mimetic comprising: 
 predicting an interaction surface between a first interacting protein and a second interacting protein;    identifying a portion of the interaction surface predicted which comprises a core signal transfer region or a general binding domain by measuring a functional activity of a peptide comprising at least three residues of the portion in a functional assay;    designing a molecule having a three dimensional conformation of the peptide as folded in the portion of the interaction surface identified; and    testing whether the molecule designed has the functional activity of the peptide in the functional assay,    wherein the molecule is identified as the peptide mimetic if the functional activity of the molecule is at least 0.1 times the functional activity of the peptide when tested at the same molar concentration.    
     
     
         16 . The method of  claim 15 , wherein the core signal transfer region is identified by presence of agonist activity.  
     
     
         17 . The method of  claim 15 , wherein the general binding domain is identified by absence of agonist activity and presence of antagonist activity.  
     
     
         18 . The method of  claim 15 , wherein the interaction surface between the first interacting protein and the second interacting protein is predicted using three-dimensional structure information.  
     
     
         19 . The method of  claim 15 , wherein the functional activity of the molecule is greater than 0.1 times the functional activity of the peptide in the functional assay.  
     
     
         20 . The method of  claim 15 , wherein the functional activity of the molecule is selected from the group consisting of from 0.1 to 10,000,000, from 0.1 to 100,000, from 0.1 to 1,000 and from 0.1 to 10 times the functional activity of the peptide in the functional assay.  
     
     
         21 . The method of  claim 15 , wherein the first interacting protein is a Gβ protein and the core signal transfer region of the Gβ protein comprises at least six contiguous residues of SEQ ID NO:5.  
     
     
         22 . The method of  claim 15 , wherein the first interacting protein is a Gβ protein and the general binding domain of the Gβ protein comprises at least six contiguous residues of SEQ ID NO:6.  
     
     
         23 . The method of  claim 15 , wherein the second interacting protein is selected from the group consisting of an adenylyl cyclase protein and a phospholipase C protein.  
     
     
         24 . A method for mapping a surface of an intracellular interacting protein comprising: 
 modeling a surface representation of the interacting protein with one or more other proteins;    predicting an interaction from the surface representation modeled; and    testing the interaction predicted in a functional assay by measuring a functional activity of a peptide comprising at least six amino acid residues of the surface representation.