An integrated subtractive genomics and immunoinformatics approach for designing a universal multi-epitope vaccine against Brucella spp.
Introduction Brucella spp. are Gram-negative bacteria accountable for brucellosis in immunocompromised individuals and livestock. Due to the slow-growing latent phenotype, current antibiotics are insufficient to treat the infection. The lack of an approved vaccine for human use against this pathogen represents a significant public health concern and indicates the urgent need for novel prophylactic interventions. Methodology In this study, the reverse vaccinology method was combined with pan-genome analysis to identify potential vaccine targets. Proteins have been screened for antigenicity, solubility, immunogenicity, and subcellular localization. B cell and T cell epitopes exhibiting high immunogenicity and solubility have been identified. Multi-epitope vaccine constructs have been evaluated and further analyzed depending on their physicochemical properties. Molecular docking, conformational dynamics, in silico cloning, and immune simulations were conducted to identify the optimal vaccine candidate. Results Four proteins, trigger factor, outer membrane protein assembly factor BamA, urease subunit beta (UreB), and urease subunit alpha (UreC1) were considered for potential vaccine targets. A total of 26 B cell and 97 T cell epitopes with notable immunogenicity and solubility have been shortlisted. Twelve multi-epitope vaccine constructs were generated, among which Vc7 has been chosen based on structural and physicochemical properties. Molecular docking analysis revealed a good correlation with 2FSE and 2Z65, which were further analyzed to reveal that Vc7 exhibited stronger binding affinity (−135.24 kcal/mol) towards 2FSE, mediated by hydrophobic contacts, salt bridges, and intermolecular hydrogen bonds, making it the ideal vaccine complex and validated through a 150 ns molecular dynamics simulation. In silico cloning established construct compatibility, and immune simulation confirmed Vc7’s potential to elicit T cell, B cell, antibody, and cytokine-mediated responses. Conclusion Vc7 has been identified as a structurally stable and highly immunogenic construct, suggesting its potential as a universal multi-epitope vaccine candidate for the prevention of brucellosis.