Rational computational design and development of an immunogenic multiepitope vaccine incorporating transmembrane proteins of Fusobacterium necrophorum

Fusobacterium necrophorum is a Gram-negative, anaerobic pathogen responsible for Lemierre's syndrome, bovine foot rot, and other necrotizing infections. The rise in antimicrobial resistance and the absence of effective vaccines underscore the need for alternative therapeutic strategies. This study employs computational biology to design a multi-epitope vaccine targeting transmembrane proteins of F. necrophorum to elicit strong immune responses. The selected proteins were evaluated for toxicity, allergenicity, and antigenicity, followed by epitope prediction and screening. B and T cell epitopes were linked using immunogenic linkers, forming a vaccine construct with a VaxiJen score of 0.7293 and a solubility score of 8.30 in E. coli. Structural validation using TrRosetta and Ramachandran plots confirmed 97.4% of residues in favored regions, indicating high stability. Population coverage analysis indicated over 99% global applicability, further enhancing its potential impact. Docking studies revealed strong interactions with immune receptors TLR7 and TLR8. TLR7 formed 12 hydrogen bonds, while TLR8(A) formed 9, and TLR8(B) exhibited the highest interaction, forming 13 hydrogen bonds with the vaccine construct. Molecular dynamics simulations confirmed structural stability and receptor engagement. The RMSD stabilized around 4-5 Å, indicating structural stability of the Vaccine-TLR8(B) complex. The Radius of Gyration remained around 36 Å, showing slight compaction over time, while RMSF peaked at 8-9 Å in flexible regions, with lower fluctuations (1.5-2.5 Å) in stable core regions. Principal component analysis (PCA) identified elastic regions critical for biological activity, and the stable energy levels (-5000 kJ/mol) further confirmed the reliability of the binding. Moreover, the vaccine exhibited high expression levels in E. coli, as demonstrated using SnapGene software with the pET-29a( +) vector. The vaccine demonstrated strong binding affinities with immune receptors and predicted activation of both humoral and cellular immune responses, including increased IgM, IgG, and cytokine levels. However, experimental validation is necessary to confirm safety and efficacy, and challenges in vaccine manufacturing and variable immune responses across populations must also be addressed.