Immunoinformatics and molecular docking reveal potential multi-epitope vaccine against Pseudomonas aeruginosa

Pseudomonas aeruginosa is a common opportunistic pathogen and a leading cause of hospital-acquired pneumonia, yet there is currently no approved vaccine to prevent its infections. This study utilizes immunoinformatics to identify cytotoxic T-lymphocyte (CTL) epitopes derived from conserved regions of 6 key virulence factors: Pili, FliD, AlgF, PelG, Exoenzyme T, and XcpQ.

Conserved peptide fragments were identified using the Protein Variability Server. The CTL epitopes were evaluated for immunogenicity, antigenicity, post-translational modifications, allergenicity, cross-reactivity, toxicity, and population coverage analysis. Molecular docking between human leukocyte antigens (HLAs) and the corresponding CTL epitopes, along with binding affinity analysis, was also conducted. A multi-epitope vaccine (PaMEV) construct was designed using selected epitopes, and its secondary and tertiary structures were predicted, refined, and validated.

All selected epitopes were highly conserved (Shannon index ≤0.1) and showed strong HLA binding (half maximal inhibitory concentration ≤500 nM). They were predicted to be non-allergenic, non-toxic, and non-cross-reactive. Molecular docking revealed stable HLA-epitope complexes with 8-14 hydrogen bonds and high binding affinity (values of the binding free energy <0 and dissociation constant <100 nM). A PaMEV was designed using the 6 CTL epitopes, and structure analysis confirmed its stability and effective epitope presentation.

The selected epitopes showed strong potential for inclusion in a peptide-based PaMEV, with favorable immunogenicity and docking results supporting its design. The final construct exhibited structural stability and strong HLA interactions, suggesting it as a promising vaccine candidate against P. aeruginosa. Experimental validation through in vitro and in vivo studies is recommended.