Method and System for Optimizing Minigenes and Peptides Encoded Thereby

Abstract

The invention relates to the field of biology. In particular, the invention relates to a method and system for designing optimized multi-epitope vaccines having selected combinations of amino acid insertions at the junctions of the multi-epitope constructs so as to minimize the number of junctional epitopes and provide vaccines with increased immunogenicity.

1 . A computerized method for designing a multi-epitope construct having multiple epitope nucleic acids, the method comprising the steps of:
 storing a plurality of input parameters in a memory of a computer system, said input parameters comprising a plurality of epitopes, at least one motif for identifying junctional epitopes, a plurality of amino acid insertions and at least one enhancement weight value for each insertion;   generating a list of epitope pairs from said plurality of epitopes;   determining for each of said epitope pairs at least one optimum combination of amino acid insertions based on said at least one motif, said plurality of insertions and said at least one enhancement weight value for each insertion; and   identifying at least one optimum arrangement of said plurality of epitopes, wherein a respective one of said at least one optimum combination of amino acid insertions is inserted at a respective junction of two epitopes, so as to provide an optimized multi-epitope construct.   
     
     
         2 . The method of  claim 1  wherein said step of identifying at least one optimum arrangement comprises performing an exhaustive search wherein all permutations of arrangements of said plurality of epitopes are evaluated. 
     
     
         3 . The method of  claim 1  wherein said step of identifying at least one optimum arrangement comprises performing a stochastic search wherein only a subset of all permutations of arrangements of said plurality of epitopes are evaluated. 
     
     
         4 . The method of  claim 1  wherein said step of identifying at least one optimum arrangement comprises:
 performing an exhaustive search of all permutations of arrangements of said plurality of epitopes when the number of epitopes to be included in said multi-epitope construct is less than a specified value X; and   performing a stochastic search, wherein only a subset of all permutations of arrangements of said plurality of epitopes are evaluated, when the number of epitopes to be included in said multi-epitope construct is greater than or equal to X.   
     
     
         5 . The method of  claim 1  wherein said plurality of input parameters further includes a maximum number of insertions (MaxInsertions) value, and said step of determining for each epitope pair at least one optimum combination of amino acid insertions comprises calculating a function value (F) for each possible combination of insertions for each epitope pair, wherein the number of insertions in a combination is in the range of 0 to MaxInsertions, said function value being calculated in accordance with the equation F=(C+N)/J, when J>0, and F=2(C+N), when J=0, wherein C equals the enhancement weight value of a C+1 flanking amino acid, N equals the enhancement weight value of an N−1 flanking amino acid, and J equals the number of junctional epitopes detected for each respective combination of insertions in an epitope pair based on said at least one motif. 
     
     
         6 . A computerized method for designing a multi-epitope construct having multiple epitopes, the method comprising the steps of:
 storing a plurality of input parameters in a memory of a computer system, said input parameters comprising a plurality of epitopes, at least one motif for identifying junctional epitopes, a plurality of amino acid insertions, a C+1 enhancement weight value for each insertion, a N−1 enhancement weight value for each insertion, and a maximum number of insertions (MaxInsertions);   generating a list of epitope pairs from said plurality of epitopes;   for each combination of insertions for each epitope pair, wherein the number of insertions is in the range of 0 to MaxInsertions, calculating a function value (F) using the equation F=(C+N)/J, when J>0, and F=2(C+N), when J=0, wherein C equals a C+1 enhancement weight value of a respective flanking amino acid insertion, N equals a N−1 enhancement weight value of a respective N−1 flanking amino acid insertion, and J equals the number of junctional epitopes detected for each respective combination of insertions in an epitope pair based on said at least one motif;   determining for each epitope pair at least one optimal combination of insertions yielding a maximum function value F;   generating a list of optimal combinations of insertions; and   based on said list of optimal combinations of insertions, identifying at least one optimum permutation of said multi-epitope construct comprising said plurality of epitopes arranged in an order that yields a maximum sum of function values, wherein a respective one of said optimal combinations of insertions are inserted at a respective junction of two epitopes of said multi-epitope construct.   
     
     
         7 . The method of  claim 6  wherein said step of identifying at least one optimum permutation comprises performing an exhaustive search wherein all permutations of arrangements of said plurality of epitopes are evaluated. 
     
     
         8 . The method of  claim 6  wherein said step of identifying at least one optimum permutation comprises performing a stochastic search wherein only a subset of all permutations of arrangements of said plurality of epitopes are evaluated. 
     
     
         9 . The method of  claim 8  wherein said plurality of input parameters further comprises a maximum search time (MaxSearchTime) value and said stochastic search is performed for a period of time approximately equal to said MaxSearchTime value, wherein said at least one optimum permutation comprises at least one permutation evaluated as having a maximum sum of function values. 
     
     
         10 . The method of  claim 6  wherein said step of identifying at least one optimum permutation comprises:
 performing an exhaustive search of all permutations of arrangements of said plurality of epitopes when the number of epitopes to be included in said multi-epitope construct is less than a specified value X; and   performing a stochastic search, wherein only a subset of all permutations of arrangements of said plurality of epitopes are evaluated, when the number of epitopes to be included in said multi-epitope construct is greater than or equal to X.   
     
     
         11 . A computer system for designing a multi-epitope construct having multiple epitopes, the system comprising:
 a memory for storing a plurality of input parameters, said input parameters comprising a plurality of epitopes, at least one motif for identifying junctional epitopes, a plurality of amino acid insertions and at least one enhancement weight value for each insertion;   a processor for retrieving said input parameters from said memory and generating a list of epitope pairs from said plurality of epitopes;   said processor further determining for each of said epitope pairs at least one optimum combination of amino acid insertions, based on said at least one motif, said plurality of insertions and said at least one enhancement weight value for each insertion;   said processor further identifying at least one optimum arrangement of said plurality of epitopes, wherein a respective one of said optimum combinations of amino acid insertions are inserted at a respective junction of two epitopes, so as to provide an optimized multi-epitope construct; and   a display monitor, coupled to said processor, for displaying said at least one optimum arrangement of said plurality of epitopes to a user.   
     
     
         12 . The system of  claim 11  wherein said processor, when identifying at least one optimum arrangement of said plurality of epitopes, performs an exhaustive search wherein all permutations of arrangements of said plurality of epitopes are evaluated to identify at least one optimized multi-epitope construct. 
     
     
         13 . The system of  claim 11  wherein said processor, when identifying at least one optimum arrangement of said plurality of epitopes, performs a stochastic search wherein only a subset of all permutations of arrangements of said plurality of epitopes are evaluated to identify at least one optimized multi-epitope construct. 
     
     
         14 . The system of  claim 11  wherein said processor, when identifying at least one optimum arrangement of said plurality of epitopes, performs an exhaustive search of all permutations of arrangements of said plurality of epitopes when the number of epitopes to be included in said multi-epitope construct is less than a specified value X, and performs a stochastic search, wherein only a subset of all permutations of arrangements of said plurality of epitopes are evaluated, when the number of epitopes to be included in said multi-epitope construct is greater than or equal to X. 
     
     
         15 . The system of  claim 11  wherein said plurality of input parameters further includes a maximum number of insertions (MaxInsertions) value and said processor, when determining for each epitope pair at least one optimum combination of amino acid insertions, calculates a function value (F) for each possible combination of insertions for each epitope pair, wherein the number of insertions in a combination is in the range of 0 to MaxInsertions, said function value being calculated in accordance with the equation F=(C+N)/J, when J>0, and F=2(C+N), when J=0, wherein C equals the enhancement weight value of a C+1 flanking amino acid, N equals the enhancement weight value of an N−1 flanking amino acid, and J equals the number of junctional epitopes detected for each respective combination of insertions in an epitope pair based on said at least one motif. 
     
     
         16 . A computer system for designing an optimized multi-epitope construct having multiple epitopes, the system comprising:
 an input device for inputting a plurality of input parameters specified by a user;   a memory, coupled to the input device, for storing said plurality of input parameters, said input parameters comprising a plurality of epitopes, at least one motif for identifying junctional epitopes, a plurality of amino acid insertions, a C+1 enhancement weight value for each insertion, a N−1 enhancement weight value for each insertion, and a maximum number of insertions (MaxInsertions);   a processor for retrieving said input parameters from said memory and generating a list of epitope pairs from said plurality of epitopes;   wherein said processor, for each combination of insertions for each epitope pair, wherein the number of insertions is in the range of 0 to MaxInsertions, calculates a function value (F) using the equation F=(C+N)/J, when J>0, and F=2(C+N), when J=0, wherein C equals a C+1 enhancement weight value of a respective flanking amino acid insertion, N equals a N−1 enhancement weight value of a respective N−1 flanking amino acid insertion, and J equals the number of junctional epitopes detected for each respective combination of insertions in an epitope pair based on said at least one motif; and   wherein said processor further determines for each epitope pair at least one optimal combination of insertions yielding a maximum function value F, generates a list of optimal combinations of insertions, and, based on said list of optimal combinations of insertions, identifies at least one optimum permutation of said multi-epitope construct comprising said plurality of epitopes arranged in an order that yields a maximum sum of function values, wherein a respective one of said optimal combinations of insertions are inserted at a respective junction of two epitopes of said optimized multi-epitope construct.   
     
     
         17 . A data storage device storing a computer program for designing a multiepitope construct having multiple epitopes, the computer program, when executed by a computer system, performing a process comprising the steps of:
 retrieving a plurality of input parameters from a memory of a computer system, said input parameters comprising a plurality of epitopes, at least one motif for identifying junctional epitopes, a plurality of amino acid insertions and at least one enhancement weight value for each insertion;   generating a list of epitope pairs from said plurality of epitopes;   determining for each of said epitope pairs at least one optimum combination of amino acid insertions based on said at least one motif, said plurality of insertions and said at least one enhancement weight value for each insertion; and   identifying at least one optimum arrangement of said plurality of epitopes, wherein a respective one of said at least one optimum combination of amino acid insertions is inserted at a respective junction of two epitopes, so as to provide an optimized multi-epitope construct.   
     
     
         18 . The data storage device of  claim 17  wherein said computer program, when executed, performs an exhaustive search wherein all permutations of arrangements of said plurality of epitopes are evaluated so as to identify said at least one optimum arrangement of said plurality of epitopes. 
     
     
         19 . The data storage device of  claim 17  wherein said computer program, when executed, performs a stochastic search wherein only a subset of all permutations of arrangements of said plurality of epitopes are evaluated so as to identify said at least one optimum arrangement of said plurality of epitopes. 
     
     
         20 . The data storage device of  claim 17  wherein said computer program, when executed, performs an exhaustive search wherein all permutations of arrangements of said plurality of epitopes are evaluated, when the number of epitopes to be included in said multiepitope construct is less than a specified value X, and performs a stochastic search, wherein only a subset of all permutations are evaluated, when the number of epitopes to be included in said multi-epitope construct is greater than or equal to X, so as to identify said at least one optimum arrangement of said plurality of epitopes. 
     
     
         21 . The data storage device of  claim 17  wherein said computer program, when executed, further retrieves a maximum number of insertions (MaxInsertions) value from said memory of said computer system, and further performs said step of determining for each
 epitope pair at least one optimum combination of amino acid insertions comprises by calculating a function value (F) for each possible combination of insertions for each epitope pair, wherein the number of insertions in a combination is in the range of 0 to MaxInsertions, said function value being calculated in accordance with the equation F=(C+N)/J, when J>0, and F=2(C+N), when J=0, wherein C equals the enhancement weight value of a C+1 flanking amino acid, N equals the enhancement weight value of an N−1 flanking amino acid, and J equals the number of junctional epitopes detected for each respective combination of insertions in an epitope pair based on said at least one motif.   
     
     
         22 . An apparatus for designing a multi-epitope construct having multiple epitopes, comprising:
 means for storing a plurality of input parameters in a memory of a computer system, said input parameters comprising a plurality of epitopes, at least one motif for identifying junctional epitopes, a plurality of amino acid insertions and at least one enhancement weight value for each insertion;   means for generating a list of epitope pairs from said plurality of epitopes;   means for determining for each of said epitope pairs at least one optimum combination of amino acid insertions based on said at least one motif, said plurality of insertions and said at least one enhancement weight value for each insertion; and   means for identifying at least one optimum arrangement of said plurality of epitopes, wherein a respective one of said at least one optimum combination of amino acid insertions is inserted at a respective junction of two epitopes, so as to provide an optimized multi-epitope construct.   
     
     
         23 . The apparatus of  claim 22  wherein said means for identifying at least one optimum arrangement comprises means for performing an exhaustive search wherein all permutations of arrangements of said plurality of epitopes are evaluated. 
     
     
         24 . The apparatus of  claim 22  wherein said means for identifying at least one optimum arrangement comprises means performing a stochastic search wherein only a subset of all permutations of arrangements of said plurality of epitopes are evaluated. 
     
     
         25 . The apparatus of  claim 22  wherein said means for identifying at least one optimum arrangement comprises:
 means for performing an exhaustive search of all permutations of arrangements of said plurality of epitopes when the number of epitopes to be included in said multi-epitope construct is less than a specified value X; and   means for performing a stochastic search, wherein only a subset of all permutations of arrangements of said plurality of epitopes are evaluated, when the number of epitopes to be included in said multi-epitope construct is greater than or equal to X.   
     
     
         26 . The apparatus of  claim 22  wherein said plurality of input parameters further includes a maximum number of insertions (MaxInsertions) value, and said means for determining for each epitope pair at least one optimum combination of amino acid insertions comprises means for calculating a function value (F) for each possible combination of insertions for each epitope pair, wherein the number of insertions in a combination is in the range of 0 to MaxInsertions, said function value being calculated in accordance with the equation F=(C+N)/J, when J>0, and F=2(C+N), when J=0, wherein C equals the enhancement weight value of a C+1 flanking amino acid, N equals the enhancement weight value of an N−1 flanking amino acid, and J equals the number of junctional epitopes detected for each respective combination of insertions in an epitope pair based on said at least one motif.