Method and system for optimizing minigenes and peptides encoded thereby
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 method for designing an optimized multi-epitope polypeptide comprising:
(i) selecting ten or more epitopes that contain human leukocyte antigen (HLA) allele-specific motifs or supermotifs, wherein said epitopes are HLA class I cytotoxic T lymphocyte (CTL) epitopes;
(ii) sorting said ten or more epitopes to minimize the number of junctional epitopes, and
(iii) incorporating said ten or more CTL epitopes into a multi-epitope polypeptide, wherein, during the incorporation step (iii):
at least one flanking or spacer amino acid residue is introduced at the C-terminus of one or more of said ten or more CTL epitopes; wherein said flanking or spacer amino acid residue is selected from the group consisting of lysine (K), arginine (R), asparagine (N), glutamine (Q), glycine (G), alanine (A), serine (S), cysteine (C), and threonine (T); and
wherein said flanking or spacer amino acid residue prevents the occurrence of a CTL junctional epitope.
2. The method of claim 1 , wherein said flanking or spacer amino acid residues comprise 1, 2, 3, 4, 5, 6, 7, or 8 amino acid residues selected from the group consisting of alanine (A) and glycine (G).
3. The method of claim 1 , wherein said flanking or spacer amino acid residues are selected from the group consisting of lysine (K), arginine (R), asparagine (N), glycine (G) and alanine (A).
4. The method of claim 1 , further comprising substituting an N-terminal residue of an HLA epitope that is adjacent to a C-terminus of an HLA epitope comprised by the multi-epitope polypeptide with a residue selected from the group consisting of lysine (K), arginine (R), asparagine (N), glycine (G) and alanine (A).
5. The method of claim 1 , wherein said multi-epitope polypeptide contains 20 or more CTL epitopes.
6. The method of claim 5 , wherein said multi-epitope polypeptide contains 30 or more CTL epitopes.
7. The method of claim 6 , wherein said multi-epitope polypeptide contains 40 or more CTL epitopes.
8. A method for designing an optimized multi-epitope polypeptide comprising:
(i) selecting five or more epitopes that contain human leukocyte antigen (HLA) allele-specific motifs or supermotifs, wherein said epitopes are HLA class II helper T lymphocyte (HTL) epitopes;
(ii) sorting said five or more epitopes to minimize the number of junctional epitopes, and
(iii) incorporating said five or more HTL epitopes into a multi-epitope polypeptide, wherein, during the incorporation step (iii):
at least one flanking or spacer amino acid residue is introduced at the C-terminus of one or more of said five or more HTL epitopes; wherein said flanking or spacer amino acid residue is selected from the group consisting of glycine (G), proline (P), asparagine (N) or alanine (A); and
wherein said flanking or spacer amino acid residue prevents the occurrence of an HTL junctional epitope.
9. The method of claim 8 , wherein said flanking or spacer amino acid residues are independently selected from residues that are not known human leukocyte antigen (HLA) Class II primary anchor residues.
10. The method of claim 8 , wherein said flanking or spacer amino acid residues comprise at least 5 amino acid residues independently selected from the group consisting of glycine (G), proline (P) and asparagine (N).
11. The method of claim 10 , wherein said flanking or spacer amino acid residues are glycine-proline-glycine-proline-glycine (GPGPG) (SEQ ID NO: 369).
12. The method of claim 8 , wherein said multi-epitope polypeptide contains 10 or more HTL epitopes.
13. The method of claim 12 , wherein said multi-epitope polypeptide contains 20 or more HTL epitopes.
14. The method of claim 13 , wherein said multi-epitope polypeptide contains 30 or more HTL epitopes.
15. The method of claim 14 , wherein said multi-epitope polypeptide contains 40 or more HTL epitopes.
16. A method for designing a polynucleotide encoding an optimized multi-epitope polypeptide comprising:
(i) selecting five or more nucleic acid sequences which encode epitopes that contain human leukocyte antigen (HLA) allele-specific motifs or supermotifs, wherein said epitopes are HLA class I cytotoxic T lymphocyte (CTL) epitopes;
(ii) sorting said five or more nucleic acid sequences to minimize the number of encoded junctional epitopes, and
(iii) incorporating said five or more CTL epitope-encoding nucleic acid sequences into a multi-epitope polynucleotide, wherein, during the incorporation step (iii):
a polynucleotide encoding at least one flanking or spacer amino acid residue is introduced at the C-terminus of one or more of said five or more CTL epitope-encoding nucleic acid sequences; wherein said flanking or spacer amino acid residue is selected from the group consisting of lysine (K), arginine (R), asparagine (N), glutamine (Q), glycine (G), alanine (A), seine (S), cysteine (C) and threonine (T); and
wherein said flanking or spacer amino acid residue prevents the occurrence of a CTL junctional epitope.
17. The method of claim 16 , wherein said flanking or spacer amino acid residues are selected from the group consisting of lysine (K), arginine (R), asparagine (N), glycine (G) and alanine (A).
18. A method for designing a polynucleotide encoding an optimized multi-epitope polypeptide comprising:
(i) selecting five or more nucleic acid sequences which encode epitopes that contain human leukocyte antigen (HLA) allele-specific motifs or supermotifs, wherein said epitopes are HLA class II helper T lymphocyte (HTL) epitopes;
(ii) sorting said five or more nucleic acid sequences to minimize the number of encoded junctional epitopes, and
(iii) incorporating said five or more HTL epitope-encoding nucleic acid sequences into a multi-epitope polynucleotide, wherein, during the incorporation step (iii):
polynucleotide encoding at least one flanking or spacer amino acid residue is introduced at the C-terminus of one or more of said five or more HTL epitope-encoding nucleic acid sequences; wherein said flanking or spacer amino acid residue is selected from the group consisting of glycine (G), proline (P), asparagine (N) or alanine (A); and
wherein said flanking or spacer amino acid residue prevents the occurrence of a HTL junctional epitope.
19. The method of claim 18 , wherein said flanking or spacer amino acid residues comprise at least 5 amino acid residues independently selected from the group consisting of glycine (G), proline (P) and asparagine (N).
20. The method of claim 18 , wherein said flanking or spacer amino acid residues are glycine-proline-glycine-proline-glycine (GPGPG) (SEQ ID NO: 369).