VOLUME 18 NUMBER 1 (January to June 2025)

In silico approach for designing a pan-proteomic and pan-genotypic hepatitis C virus multi-epitope subunit vaccine

Hepatitis C Virus (HCV) is the most infectious hepatitis virus and the leading cause of liver-related mortality. The lack of a vaccine, combined with HCV’s hypervariability, contributes to this global health concern; thus, there is an urgent need for a potent, cross-protective vaccine. With the aid of computational vaccinology, we aimed to design and evaluate multi-epitope vaccines based on highly conserved epitopes from multiple proteins across 8 recognized HCV genotypes and 47 subtypes. The designed HCV vaccine constructs (VC) are composed of antigenic, non-allergenic, non-toxic, non-human homologues, and conserved epitopes within the structural and non-structural HCV proteins, linked with proper adjuvants and linkers. The final HCV VC had an instability index of 33.69. Tertiary structure validation of the modelled HCV VC revealed a high-quality protein. Molecular docking, molecular dynamic simulations, and Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA) and General Born Surface Area (MM/GBSA) calculations demonstrated a strong and stable binding interaction between the HCV VC and immune receptors (TLR2, 3, and 4). The final HCV VC-TLR3 is the best docking complex (-226.61 kcal/mol) with a highly stable binding affinity in the entire 200 ns molecular dynamics simulation. Notably, immune simulation revealed that HCV VC elicited a high antibody level and stronger IFN-ɣ and IL-2 levels compared to reference studies. This study designed a novel multi-epitope HCV VC that could provide a stronger immune response and cross-protection against hypervariable HCV that requires further in vitro validation.