Systems and methods for generating peptides

Abstract

Antimicrobial peptides are small proteins used by the innate immune system to combat bacterial infection in multicellular eukaryotes. There is mounting evidence that these peptides are less susceptible to bacterial resistance than traditional antibiotics and that they may form the basis for a novel class of therapeutics. Systems and methods may treat the amino acid sequences of these peptides as a formal language and build a set of right-linear grammars that describe this language. These grammars may allow for rationally designed novel antimicrobial peptides in silico. These peptides conform to the syntax of natural antimicrobial peptides lack significant homology to any natural sequences, thus populating a previously unexplored region of protein sequence space. Synthesis of these peptides, leads to de novo AmPs.

1 .- 20 . (canceled) 
     
     
         21 . An antimicrobial peptide produced by a method comprising the steps of
 determining a set of patterns of primary amino acid sequences being representative of a peptide having antimicrobial activity in a database of antimicrobial peptides selected from the group consisting of AMSDb and SWISS-PROT,   providing a set of randomly generated peptide sequences at least ten amino acids in length,   correlating the set of patterns with the randomly generated peptide sequences by calculating the S score,   selecting at least one of said randomly generated peptide sequences having a score S=16/21 or 0.73 or higher and mutating the selected peptide sequence,   repeating the step of correlating the set of patterns with the mutated peptide sequences to identify mutated peptide sequences having a score S=16/21 or 0.73 or higher scored peptide sequences,   selecting an identified peptide sequence, wherein the peptide sequence is not present in the database, and   synthesizing the peptide sequence.   
     
     
         22 . The antimicrobial peptide according to claim  1 , wherein the step of correlating the set of patterns with the randomly generated sequences includes processing a sequence to determine a score representative of a percentage of the sequence that matches to a pattern in the set of patterns, wherein the percentage is 90%. 
     
     
         23 . The antimicrobial peptide according to claim  1 , wherein the step of mutating a sequence includes a substitution process wherein substitution among similar entities is preferred. 
     
     
         24 . The antimicrobial peptide according to claim  1 , wherein the step of determining a set of patterns includes identifying a set of patterns in a data set of biological sequences having antimicrobial activity. 
     
     
         25 . The antimicrobial peptide according to  claim 24 , further comprising the step of identifying a database of biological sequence data wherein the biological sequence data is representative of naturally occurring antimicrobial peptides. 
     
     
         26 . The antimicrobial peptide according to  claim 24 , wherein the step of identifying a set of patterns includes identifying a substantially exhaustive set of patterns from the database of biological sequences. 
     
     
         27 . The antimicrobial peptide according to claim  1 , further comprising the step of determining a second set of patterns being representative of a peptide having a second characteristic of interest, and correlating the mutated peptide sequences with the second set of patterns to identify peptide sequences having the first characteristic and the second characteristic of interest. 
     
     
         28 . The antimicrobial peptide of  claim 27 , wherein the second characteristic of interest is selected from the group consisting of anti-viral, a selected topography, hydrophobic, hydrophilic, and thermally stable. 
     
     
         29 . The antimicrobial peptide of  claim 21 , further comprising the step of comparing the mutated peptide with a sequence representative of a naturally occurring peptide and determining a degree of homology. 
     
     
         30 . The antimicrobial peptide according to  claim 29 , further comprising the step of removing a mutated peptide having a degree of homology greater than a selected maximum. 
     
     
         31 . The antimicrobial peptide of claim  1 , further comprising the step of synthesizing a peptide having substantially the selected mutated peptide sequence. 
     
     
         32 . The antimicrobial peptide of  claim 31  further comprising the step of testing activity of a synthesized peptide for antimicrobial activity.