Methods and systems for generating and evaluating peptides

Abstract

A method has been developed to create databases of peptides having a desirable property, such as antimicrobial activity, based on analyzing a database of known peptides for a pattern statistically associated with an activity. One can determine a set of patterns that may be representative of a peptide having a desired characteristic or property, and evaluate a set of sequences against the set of patterns (grammars) to determine if the peptide sequence being evaluated has similar patterns to those of a peptide having the desired characteristic or property. The set of sequences being evaluated may include peptide sequences of a desired length comprising all or substantially all combinations of amino acids that conform to at least one of the set of patterns. Once the database is identified, the database may be processed in a pattern recognition procedure that identifies a set of patterns that could be understood as representative of a peptide having the characteristic of interest. A set of newly generated peptides sequences may then be processed to score these new sequences against the identified patterns to correlate the patterns to the sequences and determine a degree of association or a similarity between a respective one of the new sequences and the set of identified patterns. The method is used to provide a database of sequences that are expected to have one or more desired activities, specific sequences within the database proven to have the desired activity, and the patterns or grammars used to create the database of sequences. Although described with reference to antimicrobial peptides, a database of peptides may be identified that contains peptides that have antiviral properties, wound response properties, or some other property of interest.

1 - 24 . (canceled) 
     
     
         25 . A set of antimicrobial peptides obtained by the method
 comprising enumerating possible peptide sequences which are homologous to grammars from the database of antimicrobial peptides produced by   (a) providing a database of known antimicrobial peptides,   (b) defining a set of integer parameters comprising L, W and K,   wherein L is the minimum number of characters that may define a pattern,   wherein L/W is the minimum density of non-wild card characters over a window of W characters, and   wherein K is the minimum number of times a pattern occurs in the database,   (c) screening the database with an algorithm that discovers all grammars in the database of antimicrobial peptides by applying integer parameters L=6, W=6, and K=2,   (d) masking the resulting grammars from the input sequences,   (e) repeating the algorithm with L=7, W=15, and K=5 with the amino acid equivalency group [[AG], [DE], [FYW], [KR], [ILMV], [QN], [ST]],   (f) dividing all grammars to sliding windows of ten amino acids,   (g) filtering grammars for selectivity by eliminating grammars that are not 80% selective for antimicrobial peptides in a database of 750 known antimicrobial peptides from AMSdb and 200 known antimicrobial peptides from Swiss-Prot/TrEMBL in combination with the entire Swiss-ProtJTrEMBL library in 2002,   (h) enumerating all 20 amino acid sequences which are matched over every sliding window of 10 amino acids by at least one grammar,   (i) scoring the enumerated sequences against the grammars of step (g) and selecting relatively high scoring sequences for synthesizing and testing, and   (j) testing the synthesized sequences for antimicrobial activity.   
     
     
         26 . The set of  claim 25   not including the antimicrobial peptides in the database of 750 known antimicrobial peptides from AMSdb and 200 known antimicrobial peptides from Swiss-Prot/TrEMBL in combination with the entire Swiss-ProtJTrEMBL library in 2002.   
     
     
         27 . The set of  claim 25 , wherein the antimicrobial peptides are pharmaceutically acceptable. 
     
     
         28 . The set of  claim 25  wherein the grammar is selected from the group consisting of 
       
         
           
                 
               
                   (SEQ ID NO: 6) 
                 
                 
               
                   T[L/G][T/I/P]LL[T/I/S/P][A/T]LL[L/G] 
                 
                   and 
                 
                     
                 
                 
               
                   (SEQ ID NO: 7) 
                 
                 
               
                   [A/F/T]L[I/L]LA[I/V][S/F/A/T][V/A][G/A/D][P/G/S/Q] 
                 
             
                
               
            
             
                
                
                
               
            
             
                
               
            
             
                
               
            
           
         
       
     
     
         29 . The set of  claim 28  comprising: 
       
         
           
                 
                 
               
                     
                   ALFSLASKVVPSVFSMVTKK (SEQ ID NO: 9) 
                 
                     
                     
                 
                     
                   VVFRVASKVFPAVYCTVSKK (SEQ ID NO: 10) 
                 
                     
                     
                 
                     
                   FLFGLASKVFPAVYCKVTRK (SEQ ID NO: 13) 
                 
                     
                     
                 
                     
                   LSAVGKIASKVVPSVIGAFK (SEQ ID NO: 14) 
                 
                     
                     
                 
                     
                   PVIGKLASKVVPSVFSMIKR (SEQ ID NO: 15) 
                 
                     
                     
                 
                     
                   GLMSLVKDIAKLAAKQGAKQ (SEQ ID NO: 17) 
                 
                     
                     
                 
                     
                   SALGRVASKVFPAVYCSITK (SEQ ID NO: 23) 
                 
                     
                     
                 
                     
                   LGALFRVASKVFPAVISMVK (SEQ ID NO: 30) 
                 
                     
                     
                 
                     
                   ALGKLASKVFPAVYCTISRK (SEQ ID NO: 31) 
                 
                     
                     
                 
                     
                   GFIGKLASKVVPSVYCKVTG (SEQ ID NO: 32) 
                 
                     
                     
                 
                     
                   PVVFSVASKVVPSLISALKR (SEQ ID NO: 33) 
                 
                     
                     
                 
                     
                   FLGVVFKLASKVFPAVFGKV (SEQ ID NO: 36) 
                 
                     
                     
                 
                     
                   PAVFKIASKVVPSVYCKVSR (SEQ ID NO: 37) 
                 
                     
                     
                 
                     
                   GALFGLASKVFPAVFGAFKK (SEQ ID NO: 38) 
                 
                     
                     
                 
                     
                   SAVGKLASKVFPAVFSMVTK (SEQ ID NO: 39) 
                 
                     
                     
                 
                     
                   VKDLAKFIAKTVAKQGGCYL (SEQ ID NO: 41) 
                 
                     
                     
                 
                     
                   GVVGKLASKVVPSVFGSFTK (SEQ ID NO: 42) 
                 
                     
                     
                 
                     
                   LPVVFRVASKVFPALISKLT (SEQ ID NO: 43) 
                 
                     
                     
                 
                     
                   SAVGSVASKVVPSLISKVTK (SEQ ID NO: 44) 
                 
                     
                     
                 
                     
                   MKSIAKFIAKTVAKQGAKQG (SEQ ID NO: 47) 
                 
                     
                     
                 
                     
                   LPAVFKLASKVVPSVFGLVK (SEQ ID NO: 50) 
                 
                     
                     
                 
                     
                   SFVFKLASKVVPSVFSALTR (SEQ ID NO: 51) 
                 
                     
                     
                 
                     
                   SVIGKIASKVVPSVYCAISK (SEQ ID NO: 52) 
                 
                     
                     
                 
                     
                   PVVGRVASKVFPAVIGLVKK (SEQ ID NO: 53) 
                 
                     
                     
                 
                     
                   FLFRVASKVFPALIGKFKKK (SEQ ID NO: 59) 
                 
                     
                     
                 
                     
                   LSFVGRVASKVVPSLISMIK (SEQ ID NO: 63) 
                 
                     
                     
                 
                     
                   SALGRLASKVVPAVIGKVTT (SEQ ID NO: 64) 
                 
                     
                     
                 
                     
                   LGVVGSLASKVVPAVISKVK (SEQ ID NO: 65) 
                 
                     
                     
                 
                     
                   LPAVFKLASKVFPAVYCKAS (SEQ ID NO: 70) 
                 
                     
                     
                 
                     
                   LPVLFKLASKVFPAVFSSLK (SEQ ID NO: 71) 
                 
                     
                     
                 
                     
                   VVGRVASKVVPSLIGLFTTK (SEQ ID NO: 73) 
                 
                     
                     
                 
                     
                   SVVFGVASKVVPSVIGKVKT (SEQ ID NO: 77) 
                 
                     
                     
                 
                     
                   FLPFVGRIASKVVPSVIGKV (SEQ ID NO: 83) 
                 
                     
                     
                 
                     
                   GKKLAKTIAKEVAKQGAKFA (SEQ ID NO: 85) 
                 
                     
                     
                 
                     
                   PFVGRVASKVVPSVYCAITR (SEQ ID NO: 89) 
                 
                     
                     
                 
                     
                   FVGSLASKVVPSVFGAIKTK (SEQ ID NO: 90) 
                 
                     
                     
                 
                     
                   LPVVFKIASKVVPSVISKIT (SEQ ID NO: 91) 
                 
                     
                     
                 
                     
                   GAVFGVASKVVPSVFSAIKK (SEQ ID NO: 92) 
                 
                     
                     
                 
                     
                   FVGGVASKVVPSVYCKVSKK (SEQ ID NO: 93) 
                 
                     
                     
                 
                     
                   VVFKLASKVVPSVYCTITKK (SEQ ID NO: 96) 
                 
                     
                     
                 
                     
                   GALFSLASKVVPAVIGLIKK (SEQ ID NO: 104) 
                 
             
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
       
     
     
         30 . The set of  claim 29  comprising: 
       
         
           
                 
                 
                 
               
                     
                   FLGVVFKLASKVPPAVFGKV 
                   (SEQ ID NO: 36) 
                 
                     
                   And 
                 
                     
                     
                 
                     
                   FLFRVASKVFPALTGKFKKK 
                   (SEQ ID NO: 59) 
                 
             
                
                
                
                
               
            
           
         
       
     
     
         31 . The set of  claim 25  wherein the peptides are non-naturally occurring. 
     
     
         32 . (canceled) 
     
     
         32 . (canceled) 
     
     
         33 . An isolated, non-naturally occurring, antimicrobial peptide in a set of peptides of  claim 25 . 
     
     
         34 . The peptide of  claim 33  formulated as a pharmaceutical composition or incorporated onto or into a medical device. 
     
     
         35 . The peptide of  claim 33  formulated as an aerosol, inhalable or industrial additive. 
     
     
         36 . The peptide of  claim 33  immobilized on or incorporated into a polymer. 
     
     
         37 . The peptide of  claim 33  conjugated to a protein, peptide, lipid, or non-peptide chemical entity. 
     
     
         38 . The set of  claim 25 , wherein the database of known antimicrobial peptides includes the set of 526 AmP sequences from University of Nebraska Medical Center Antimicrobial Peptide Database APD. 
     
     
         39 . The set of  claim 25 , wherein the database of known antimicrobial peptides includes the set of 526 AmP sequences from University of Nebraska Medical Center Antimicrobial Peptide Database APD, AMSdb, supplemented with an additional 200 antimicrobial peptides from Swiss-ProtJTrEMBL, that were not included in AMSdb, for use with the selectivity filter.