Bioinformatics-Guided structural characterization and immunogenicity assessment of multi-epitope vaccine candidates against Zika virus

The Zika virus (ZIKV) causes a significant global health threat, necessitating the development of effective vaccines. In this study, using bioinformatics and software-based vaccinology approaches, firstly we evaluated the antigenicity of all proteins of ZIKV (EU545988.1), identifying Protein Pr, E, and NS1 as the most antigenic. Subsequent investigation into the antigenic profiles of these proteins across the top 10 infectious ZIKV strains unveiled Strain Zika (USA, KU312312), Rio-U1 (Brazil, KX601166), and Zika (Brazil, KU321639) as harboring the highest antigenicity for Protein Pr (0.7194555), E (0.6559635), and NS1 (0.6115945), respectively. Next, T cell and B cell epitopes were predicted for these proteins, and their antigenicity, allergenicity, and toxicity were evaluated. Binding affinity of T cell epitopes with MHC I and II molecules was determined. Population coverage and conservancy analysis were conducted. Three B cell epitopes (ATMSYECPMLDHVQI, TMSGKAISFATTLG, and KDAHAKRQTVYVCKR) and three T cell epitopes (DLGHTCDATMSYECP, ALGGVMIFLSTAVSA, and TSVWLKYHPDSPRRL) from Protein Pr, E, and NS1 were identified as optimal vaccine candidates. Among them, ALGGVMIFLSTAVSA and TSVWLKYHPDSPRRL showed 100% conservancy and 71.88% and 95.24% Population coverage (worldwide) where DLGHTCDATMSYECP showed 95.24% Conservancy and 94.77% Population coverage. Using them, the multi-epitope vaccine (MEV) was constructed with an appropriate adjuvant (P29459) and linkers, including a His-tag for ease of isolation during in vivo procedures. Secondary and tertiary structures of the MEV were predicted, and physiochemical properties and subcellular localization were analyzed. Furthermore, allergenicity, toxicity and immune simulation of the MEV were assessed. Molecular docking analysis confirmed binding affinity with human receptor proteins TLR3 (PDB: 7C76) and stability was evaluated through Molecular Dynamics Simulation analysis. Post-translational modifications analysis was conducted, and in silico cloning in E. coli was performed to assess cloning feasibility of the MEV. This integrative approach provides insights into the development of a potential ZIKV vaccine, laying the groundwork for further wet lab validation and preclinical and clinical investigations.