Immunoinformatics-driven design of a multi-epitope vaccine targeting non-typhoidal Salmonella's type IV secretion system VirB4, VirB5, and VirB6 proteins.

Non-typhoidal Salmonella (NTS) remains a major global health concern, aggravated by the emergence of multidrug-resistant strains. This study employed immunoinformatics and structural bioinformatics approaches to design a multi-epitope vaccine targeting the Type IV Secretion System (T4SS) proteins VirB4, VirB5, and VirB6 of Salmonella enterica. B-cell, CTL, and HTL epitopes were screened for antigenicity, non-allergenicity, non-toxicity, and cytokine-inducing capacity, and assembled using AAY and GPGPG linkers. The HbhA adjuvant from Mycobacterium tuberculosis was fused via an EAAAK linker to enhance immunogenicity. The final construct exhibited favorable physicochemical properties, high solubility, and structural stability. Molecular docking revealed strong binding affinities with TLR1, TLR2, and TLR4, with TLR2 showing the most favorable interaction profile. Molecular dynamics simulations over 100 ns confirmed the structural stability of all complexes, as evidenced by stable RMSD, radius of gyration, and compact interfaces. MM/PBSA binding free energy decomposition indicated that van der Waals and electrostatic interactions were the primary favorable contributions to complex stabilization, while polar solvation energies contributed unfavorably, particularly in the TLR2 and TLR4 systems, for which results were evaluated comparatively. Immune simulation predicted robust humoral and cellular responses, including elevated IgG and IgM titers, memory formation, and a Th1-biased cytokine pattern. In general, the designed construct represents a promising, stable, and immunogenic multi-epitope vaccine candidate against non-typhoidal Salmonella, warranting further experimental validation.