Selection and Enhancement of Porcine T Helper Cell Epitopes for Peptide Vaccine Development

The presentation of antigenic peptides by major histocompatibility complex (MHC) class II to T helper (Th) cell may assist adaptive immune responses to induce higher antibody titers against infections. Our aims were applied to selection and optimization of porcine Th cell epitopes enhancement in vaccine developing applications. First, determined ninety-six sequences by ProPred program prediction for promiscuous epitopes binding to more than six different human leukocyte antigen-group DR (HLA-DR) alleles among 196 confirmed sequences retrieved from IEDB database. Determine five candidate Th cell epitope binding cores based on the criterion of greater than 0.3 hydrophobic moments for amphipathic segments by helical wheels evaluation from 18 binding cores which appeared more than twice in different validated sequences. Furthermore, three optimization strategies for epitope enhancements including 1) incorporated the two most favored amino acids at corresponding positions 1 and 6 to fit the diverse sizes of binding pockets in 14 modeling SLA-DR structures, 2) substitution of Arginine residue at position 2 in epitope binding core sequences for providing additional binding affinity to MHC molecules and 3) extensions of 4 and 2 amino acids appeared favorable for binding at N- and C- terminus, respectively. In concluded, there are five leader sequences selected and optimized interactions between polymorphic MHC class II alleles for rational adjuvant component designs in the application of synthetic epitope-based vaccines against foot-and-mouth disease.