Design of a novel proteome-derived scaffold presenting epitopes of Pseudomonas aeruginosa in native conformation

Pseudomonas aeruginosa is a ubiquitous Gram-negative bacterium that poses a significant threat in nosocomial infections due to its intrinsic resistance to antibiotics and remarkable adaptability. The emergence of multidrug-resistant strains necessitates the development of prophylactic strategies, and vaccination is a promising approach. This study aimed to design a novel immunogenic scaffold derived from P. aeruginosa itself to present epitopes in their native conformation and elicit a robust protective immune response. A bioinformatics-driven strategy was used to analyze the P. aeruginosa proteome and identify a multimeric protein scaffold with suitable structural stability and epitope accommodation capacity. Conserved linear and conformational B-cell epitopes were predicted from surface-exposed immunogenic proteins and computationally HIV into the scaffold. The structural stability of the engineered construct was evaluated using molecular docking and molecular dynamics simulations, and its immunogenic profile was assessed through in silico immune simulations. Bioinformatic screening of the P. aeruginosa proteome identified MexA, a periplasmic homomeric protein, as an optimal scaffold based on its structural stability and capacity to accommodate epitopes. Proteome-wide analysis further revealed conserved, surface-exposed immunogenic antigens, from which linear and conformational B-cell epitopes were successfully predicted and prioritized. Computational integration of the selected epitopes into the MexA scaffold produced a structurally coherent multiepitope construct that preserved scaffold integrity. Molecular docking and molecular dynamics simulations confirmed the structural stability and favorable receptor interactions of the engineered construct, while in silico immune simulations demonstrated robust humoral and cellular immune responses, indicating its potential as an effective vaccine candidate. This study successfully designed a novel immunogenic scaffold derived from P. aeruginosa that displays bacterial epitopes in their native conformation through a comprehensive bioinformatics approach. The engineered construct warrants further exploration through in vitro and in vivo studies to evaluate its potential as a vaccine candidate against P. aeruginosa.