Model for testing immunogenicity of peptides

Abstract

Assay methods for determining whether a peptide is likely to be immunogenic are based on a computer modeling of binding to a Class II MHC DR1 receptor. This is confirmed by competitive inhibition binding assays. The peptides are useful for eliciting an immune response for vaccination or the production of antibodies or T-cells.

1 . A method of preliminarily screening peptides for immunogenicity comprising the steps of: 
 1) creating a molecular model of receptor DR1 Class II MHC and minimizing the model of the DR1;    2) modeling a peptide to be tested and minimizing the model of the peptide; and    3) testing fit of model obtained in step 2 into the model obtained in step 1 to produce a composite receptor/peptide model.    
     
     
         2 . A computerized model comprising a model of the DR1 molecule having fitted in a cleft therein a model of a peptide.  
     
     
         3 . A method of  claim 1  wherein, additionally, the receptor/peptide model is subjected to computer-simulated heating.  
     
     
         4 . A method of  claim 1 , further comprising, assaying the peptide by competitive inhibition binding to a Class II MHC receptor DR1.  
     
     
         5 . A peptide capable of binding to a Class II MHC receptor DR1 and inhibiting the binding of HA (306-318).  
     
     
         6 . A synthetic peptide, wherein the amino acid sequence of the minimized peptide according to  claim 5  has been modified to have a superior binding affinity for a Class II MHC receptor DR1 to form at least a portion of the synthetic peptide.  
     
     
         7 . A synthetic peptide, wherein the amino acid sequences of the minimized peptide according to  claim 5 , has been modified to have greater inhibition of HA (306-318) binding to a Class II MHC receptor DR1 to form at least a portion of the synthetic peptide.  
     
     
         8 . A synthetic peptide according to  claim 6 , wherein an amino acid has been modified from a charged amino acid to an uncharged amino acid.  
     
     
         9 . A synthetic peptide according to  claim 7 , wherein an amino acid has been modified from a charged amino acid to an uncharged amino acid.  
     
     
         10 . A synthetic peptide according to  claim 8 , wherein said uncharged amino acid is alanine.  
     
     
         11 . A synthetic peptide according to  claim 9 , wherein said uncharged amino acid is alanine.  
     
     
         12 . A peptide according to  claim 5 , wherein the sequence is selected from the group consisting of PKYVKQNTLKLAT and AAYAAAAAAKAA, SEQ ID NO: 1, and SEQ ID NO: 2 respectively.  
     
     
         13 . A peptide according to  claim 5 , wherein the sequence is contained in a CFA.  
     
     
         14 . A peptide according to  claim 13 , wherein the sequence is selected from the group consisting of DEYGLGRLVNTAK, IIYQIVDEKGKKK, LNYTSGEKKISPG, WQYKSLDVNVNIE, QLYTVEMTIPAGV, TSYTFSAIYTGGE, GEYPNSGYSSGTY and GTYAGHLTVSFYS, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11 AND SEQ ID NO: 12 respectively.  
     
     
         15 - 20 . (canceled)  
     
     
         21 . An immunogenic composition comprising: a peptide, said peptide selected from the group of: 
 CS6α7 consisting of the amino acid sequence of IIYQIVDEKGKKK, Seq. ID No: 6,    CS6α6 consisting of the amino acid sequence of DEYGLGRLVNTAD, Seq. ID No: 5,    CS6β5 consisting of the amino acid sequence of GTYAGHLTVSFYS, Seq. ID No: 12,    CS6β4 consisting of the amino acid sequence of GEYPNSGYSSGTY, Seq. ID No: 11,    CS6β3 consisting of the amino acid sequence of TSYTFSAIYTGGE, Seq. ID No: 10, and    CS6β2 consisting of the amino acid sequence of QLYTVEMTIPAGV, Seq. ID No: 9.    
     
     
         22 . A method of eliciting an immune response in an animal comprising administering said animal with the immunogenic composition according to  claim 21 .  
     
     
         23 . The immunogenic composition of  claim 21 , wherein said composition is immunogenic against pathogenic microorganisms and neoplasms.  
     
     
         24 . The immunogenic composition of  claim 21 , wherein said composition is immunogenic against Enterotoxogenic  E. Coli.    
     
     
         25 . The immunogenic composition of  claim 21 , wherein said composition is combined with an immunologically acceptable carrier.  
     
     
         26 . The immunogenic composition of  claim 25  wherein said immunologically acceptable carrier comprises encapsulating microspheres.  
     
     
         27 . The immunogenic composition of  claim 26 , wherein said encapsulating microspheres comprise biodegradable bio-compatible poly (DL-lactide-co-glycolide) as a bulk matrix.  
     
     
         28 . The immunogenic composition of  claim 21  wherein said peptide is a synthetic peptide.  
     
     
         29 . The immunogenic composition of  claim 21 , wherein when said peptide is minimized, the minimized peptide binds to a Class II MHC receptor DR1 inhibiting the binding of HA residues 306-318.  
     
     
         30 . An immunogenic composition comprising: 
 CS6α7 peptide consisting of the amino acid sequence of IIYQIVDEKGKKK, Seq. ID No: 6,    CS6α6 peptide consisting of the amino acid sequence of DEYGLGRLVNTAD, Seq. ID No: 5,    CS6β5 peptide consisting of the amino acid sequence of GTYAGHLTVSFYS, Seq. ID No: 12,    CS6β4 peptide consisting of the amino acid sequence of GEYPNSGYSSGTY, Seq. ID No: 11,    CS6β3 peptide consisting of the amino acid sequence of TSYTFSAIYTGGE, Seq. ID No: 10, or    CS6β2 peptide consisting of the amino acid sequence of QLYTVEMTIPAGV, Seq. ID No: 9, or combinations thereof, wherein said peptide is not a whole protein.    
     
     
         31 . The immunogenic composition of  claim 30 , wherein when said peptide is minimized, the minimized peptide binds to a Class II MHC receptor DR1 inhibiting the binding of HA residues 306-318.  
     
     
         32 . (New) An immunogenic composition comprising: a synthetic CS6α6 peptide, a synthetic CS6β5 peptide, synthetic CS6β4 peptide, synthetic CS6β3peptide, or synthetic CS6β2 peptide that has been modified from its natural peptide sequence to bind to a Class II MHC receptor DR1.  
     
     
         33 . An immunogenic composition comprising a CS6α6 peptide fragment, CS6β5 peptide fragment, CS6β4 peptide fragment, CS6β3peptide fragment, or CS6β2 peptide fragment that binds to a Class II MHC receptor DR1.  
     
     
         34 . A synthetic peptide fragment comprising a CS6α6 peptide fragment, CS6β5 peptide fragment, CS6β4 peptide fragment, CS6β3peptide fragment, or CS6β2 peptide fragment that binds to a Class II MHC receptor DR1.  
     
     
         35 . A peptide that is immunogenic against Enterotoxogenic  E. Coli , wherein when said peptide is minimized, the minimized peptide is capable of binding to a Class II MHC receptor DR1 and inhibiting the binding of HA residues 306-318.  
     
     
         36 . The peptide of  claim 35 , wherein an amino acid sequence of said peptide has been modified to form a synthetic peptide, wherein when said synthetic peptide is minimized, the minimized synthetic peptide has superior binding affinity for a Class II MHC receptor DR1.  
     
     
         37 . The peptide of  claim 35 , wherein an amino acid sequence of said peptide has been modified to form a synthetic peptide, wherein when said synthetic peptide is minimized, the minimized synthetic peptide has greater inhibition of HA residues 306-318 binding to a Class II MHC receptor DR1.  
     
     
         38 . The peptide of  claim 35 , wherein said peptide comprises CS6α7 having the amino acid sequence of IIYQIVDEKGKKK, Seq. ID No: 6.  
     
     
         39 . The vaccine of  claim 35 , wherein said peptide comprises CS6α6 having the amino acid sequence of DEYGLGRLVNTAD, Seq. ID No: 5.  
     
     
         40 . The vaccine of  claim 35 , wherein said peptide comprises CS6β5 having the amino acid sequence of GTYAGHLTVSFYS, Seq. ID No: 12.  
     
     
         41 . The vaccine of  claim 35 , wherein said peptide comprises CS6β4 having the amino acid sequence of GEYPNSGYSSGTY, Seq. ID No: 11.  
     
     
         42 . The vaccine of  claim 35 , wherein said peptide comprises CS6β3 having the amino acid sequence of TSYTFSAIYTGGE, Seq. ID No: 10.  
     
     
         43 . The vaccine of  claim 35 , wherein said peptide comprises CS6β2 having the amino acid sequence of QLYTVEMTIPAGV, Seq. ID No: 9