In Silico Subtractive Proteome Analysis to Design Multi-Epitope-Based Subunit Vaccine against Eikenella corrodens

Eikenella corrodens is a gram-negative, facultatively anaerobic bacterium typically found in the oropharynx and respiratory tract of humans. It is responsible for various infections, including head-and-neck infections, pericarditis, and abscesses of the deltoid, perirenal tissue, brain, and liver. Increasing antibiotic resistance requires urgent identification of novel drug targets to fight this bacterium. In this study, subtractive proteomics and immunoinformatics approaches were used to identify the most suitable candidates for multi-epitope vaccine development. A non-homologous and pathogenic protein, penicillin-binding protein 1A (PBP1A), was identified after extracting the entire proteome sequence of E. corrodens NCTC 10596. PBP1A is antigenic and necessary for pathogen survival. Helper T-cell (HTL), cytotoxic T-cell (CTL), and B-cell lymphocyte-inducing epitopes were integrated through immunoinformatic methods and rigorous immunological screening processes. Various physicochemical, allergenic, and antigenic properties were also evaluated to ensure the safety and immunogenicity of the vaccine candidates. Dynamic modeling and molecular docking techniques were used to examine the molecular interactions, thermodynamic stability, and binding affinities. The vaccine demonstrated a robust and consistent interaction with Toll-like receptors (TLRs), and its potential to elicit an immunological response was evaluated in silico. For in silico cloning, the final vaccine candidates were back-translated and cloned into an E. coli host to achieve high expression of the predicted protein. Computational analyses suggested that the proposed vaccine candidate shows promise for combating bacterial infections and eliciting a robust immune response. However, experimental validation is crucial to authenticate the precise safety and immunogenicity profiles of this vaccine.