Immunoinformatics-based design of a next generation multi-epitope vaccine candidate against Shigella boydii using a hierarchical subtractive proteomics approach

Shigella boydii (strain CDC 3083-94 / BS512) is a Gram-negative facultative anaerobic bacterium that plays a significant role as a pathogen causing bacillary dysentery, especially in developing areas where hygiene is poor. Although less frequently reported compared to other Shigella species, S. boydii still contributes substantially to global shigellosis cases, particularly in low-income endemic regions. Despite its clinical relevance, there has been limited research dedicated on identifying strain-specific antigenic targets for vaccine development. The current study utilized the subtractive proteomics approach established on reverse vaccinology to develop a multi-epitope subunit vaccine (MEV) against S. boydii (strain CDC 3083-94 / BS512). From the proteome analysis, two key virulent and antigenic proteins were identified as possible vaccine candidates: the LPS-assembly protein LptD (B2U262) and the cell division protein FtsZ (B2U2A0). The B-cell and T-cell epitopes of these proteins were computationally predicted and sensibly evaluated based on a number of immunological standards, including as antigenicity, toxicity, allergenicity, solubility, and MHC binding affinity. To produce a multi-epitope vaccination, these designated epitopes were successively conjugated with an adjuvant and appropriate linkers. The vaccine construct underwent structural refinement, and the outcomes presented that an excellent structural model was constructed, with 89.4% of residues lying in promising Ramachandran plot areas. The vaccine construct and human Toll-like receptor 4 (TLR4) have shown considerable contact, according to molecular docking experiments, with a binding energy of - 1391.4 kcal/mol. With 50% GC content and a score of 0.9 from in silico cloning on Codon Adaptation Index, it is expressed to the maximum potential in an Escherichia coli host system. The outcomes highlight the multi-epitope vaccine's potential as a preventative measure against S. boydii-caused ailments.