Immunoinformatics-driven design of a multi-epitope vaccine against Clostridium perfringens in yaks

Clostridium perfringens is the primary causative agent of enterotoxemia in yaks, resulting in substantial economic losses on the Qinghai-Tibet Plateau. Conventional vaccines exhibit limited protective breadth and suboptimal efficacy, highlighting the need for innovative strategies. Here, we aimed to construct a novel vaccine candidate incorporating epitopes from multiple prevalent toxinotypes (A, C, E) of C. perfringens affecting yaks, using immunoinformatics approach.

A hierarchical immunoinformatics pipeline was implemented, encompassing subtractive genomics to identify core virulence factors, prediction and filtering of immunogenic T-cell and B-cell epitopes, rational multi-epitope vaccine design incorporating adjuvant and linkers, three-dimensional structure modeling and validation, molecular docking to evaluate interactions with TLR4, molecular dynamics simulations to confirm complex stability, and codon optimization to facilitate heterologous expression.

Five core virulence proteins (Iap, CpsE, NanH, Plc, Pfo) were identified from genomic data, leading to the prediction and selection of ten cytotoxic T lymphocyte (CTL) epitopes, five helper T lymphocyte (HTL) epitopes, and five B-cell epitopes. The final 352-amino-acid multi-epitope vaccine (MEV) construct was assembled using the adjuvant human β-defensin-3 and specific linkers (AAY, GPGPG, KK). Computational evaluations confirmed the vaccine's high antigenicity (VaxiJen score: 0.9092), non-allergenic nature, and structural stability. Molecular docking revealed strong binding affinity with TLR2 (-1024.6 kcal/mol) and TLR4 (-1104.4 kcal/mol). Molecular dynamics simulations over 100 ns confirmed stable TLR4 complex with an average RMSD of 0.1971 ± 0.0377 nm, while the TLR2 complex showed an average RMSD of 0.2692 ± 0.0420 nm. Immune simulation profiles predicted the induction of robust humoral and cellular immune responses, including elevated antibody titers, T-cell activation, and cytokine production. In silico cloning verified the potential for efficient expression in E. coli.

This study designed a novel multi-epitope vaccine against C. perfringens in yaks using an immunoinformatics approach. The vaccine showed high antigenicity, stability, and broad allelic coverage in silico, providing a promising candidate that requires rigorous in vitro and in vivo experimental validation to confirm these computational predictions. This work offers a foundation for the development of effective vaccines against yak C. perfringens infections on the Qinghai-Tibet Plateau.