Structural vaccinology considerations for in silico designing of a multi-epitope vaccine.

Multi-epitope peptide vaccines, as a kind of fusion proteins, usually possess a string-of-beads structure, consisting of several peptidic epitopes, probably adjuvants and linkers. Very numerous options are possible in selecting the order of different segments and linkers. Such factors can affect the vaccine efficacy through impacting physicochemical characteristics and protein tertiary structure. To investigate such relations, eleven different constructs were designed and studied as a multi-epitope prophylaxis vaccine for human papilloma virus (HPV). The vaccine contained two epitopes from the minor protein of virus capsid (L2) of HPV16, two TLR agonists as adjuvants (flagellin and RS09, as TLR5 and TLR4 agonists, respectively), and two universal T-helper epitopes. Since the used TLR4 agonist was inserted in the middle of the construct, its appropriate interaction with the bulky TLR4 was a serious concern. Thus, beyond evaluating the physicochemical properties, secondary and tertiary structures, and conformational B-cell epitopes of the designed constructs, TLR4 agonist exposability was also studied. Besides, the interaction between TLR4 and its agonist was investigated through docking and MD studies. Consequently, one structure ("D") with proper physicochemical features, a high frequency of conformational B-cell epitopes, and appropriate interactions with TLR4 and TLR5 in docking and MD studies, was selected as a proper candidate. Accordingly, for in silico designing of multi-epitope vaccines, structural concerns should be considered, and the linkers and arrangement of epitopes and adjuvants should be optimized. Considering the diversity of the possible structures, devising computational tools for such investigations would be very valuable.