Molecular assessment of the HIV pol gene and use of computational vaccine design targeting Pakistani isolates

Human immunodeficiency virus (HIV) is considered a major threat to human health. The global prevalence of individuals infected with HIV-1 continues to rise. Consequently, the development of an effective immune-stimulatory vaccine has recently garnered significant attention in the field of HIV-1 vaccine formulation. This study conducted a molecular assessment of the Pol region, identifying conserved sequences across our 14 HIV isolates. Utilizing multiple servers and filtering methods, highly effective B-cell epitopes, along with helper T lymphocyte (HTL) and cytotoxic T lymphocyte (CTL) epitopes, were identified. Specifically, five B-cell epitopes, eight CTL epitopes, and twelve HTL epitopes were selected for vaccine development. The resulting vaccine construct comprises 557 amino acids, has a theoretical isoelectric point of 8.98, and a GRAVY score of - 0.785. Codon optimization and in-silico cloning into prokaryotic vectors were performed to enhance expression Escherichia coli hosts. Molecular dynamics simulations confirmed the most stable interaction of the vaccine components with Toll-like receptor 3 (TLR3), while also demonstrating stable interactions with TLR5, TLR7, TLR8, and TLR9, eliciting a robust immunogenic response. The vaccine model effectively activates both humoral and cellular immune responses; however, experimental validation is required to confirm these in silico findings.