Multi-protein HIV-1 vaccine design: in silico prediction, structural assessment, and immunoinformatic validation

Abstract

HIV-1 remains a global health concern since there is no effective vaccine to date. In silico multi-protein vaccine design offers a promising strategy to induce widespread and durable immunity. Using linker and adjuvant sequences, including the PADRE universal helper T-cell epitope, conserved epitopes from several HIV-1 proteins were combined into a single construct. The design incorporated HTL (CD4⁺ helper T lymphocyte) epitopes to enhance cytokine secretion and B-cell help, CTL (CD8⁺ cytotoxic T lymphocyte) epitopes to promote targeted killing of infected cells, and B-cell epitopes to induce neutralizing antibody responses. Physicochemical properties, antigenicity, toxicity, and allergenicity were evaluated through immunoinformatics pipelines. The coverage was analysed using IEDB Population Coverage Calculation. The 3D structure was modeled and validated using MolProbity, Ramachandran analysis. Molecular docking with TLR-3 was performed to assess receptor interaction, and immune simulations were conducted to predict immune responses. The construct showed stability, antigenicity, and non-allergenicity, with >90% residues in favored Ramachandran regions. Docking confirmed stability of TLR-3 binding, while immune simulation predicted strong IgM and IgG responses and robust T-cell activation.