In silico design of a multi-epitope vaccine targeting DENV-1 and DENV-3

Abstract The co-infection of DENV-1 and DENV-3 during endemic outbreaks can be potentially fatal and complicate the diagnostic process. In our study, we have focused on the development of a multiepitope vaccine against DENV-1 and DENV-3 co-infection, utilizing non-structural protein 1 (NS1) and envelope protein (E) as key antigens. B cell and T cell epitopes were predicted for their immunogenicity, antigenicity, and ability to elicit an IFN-γ response. The final construct showed predicted stability (Instability Index: 30.63), antigenicity (0.5509), non-allergenicity, and hydrophilic character (GRAVY: −0.226) based on computational assessments. Tertiary structural validation revealed 90.1% of residues in a favoured region. Molecular docking revealed a stronger binding of the DENV-TLR3 complex. The receptor and vaccine have stable interactions, according to molecular dynamics simulations and free energy estimations (-90 kJ/mol). Strong B and T cell memory responses were demonstrated by immune simulations, accompanied by increased levels of IgG, IFN-γ, and TGF-β. The codon-optimized sequence was successfully cloned into the pcDNA™3.1/V5-His-TOPO ® expression vector for potential experimental validation. As a result of this in silico approach, a targeted vaccine for DENV-1 and DENV-3 co-infections is possible, which merits further experimental evaluation.