Structure-guided in silico design of a methionine aminopeptidase–derived multi-epitope vaccine candidate against Neisseria gonorrhoeae

Escalating antimicrobial resistance in <i>Neisseria gonorrhoeae</i> underscores the need for vaccine strategies that avoid the pathogen's highly variable outer-membrane antigens. This study pursued an epitope-focused approach targeting methionine aminopeptidase (MAP), an essential, evolutionarily constrained metalloenzyme. An AlphaFold2 model with high confidence (mean pLDDT 90) guided mapping of solvent-exposed, non-catalytic loops, excluding residues within 15 Å of the catalytic H82/D110/H173/D206/E237 cluster. Linear and conformational B-cell epitopes (BepiPred-3.0, ABCpred, DiscoTope-3.0) and CD8⁺/CD4⁺ T-cell epitopes (NetMHCpan 4.1b; NetMHCIIpan 4.1) were prioritized by predicted affinity, surface accessibility, and cross-isolate conservation across 48 clinical genomes (2007-2022). Host-homology screening (BLASTp) and manufacturability filters (VaxiJen, SOLpro) were applied. A lead HLA-DRB1∗07:01 complex was validated by Rosetta docking and 100 ns AMBER MD<i>.</i> All shortlisted epitopes were invariant across isolates. A top CD8⁺ epitope, SMSDCAVAV (HLA-A∗02:01; %Rank_EL 0.16), showed strong IFN-γ induction (SVM 0.82). A CD4⁺ epitope, YTAVRQTAAHCLDAG (HLA-DRB1∗07:01; %Rank 1.4; IC₅₀ = 640 nM), overlapped a predicted B-cell patch (res. 66-75; VaxiJen 0.67). MAP exhibited favourable solubility (SOLpro 0.947). The HLA-DRB1∗07:01 complex maintained a stable binding register over 100 ns (protein Cα RMSD 2.1 Å), with restrained peptide-anchor fluctuations. Structural conservation, epitope invariance, and stable peptide-MHC interactions support MAP as a rational antigen for multi-epitope vaccine development with potential breadth across strains and HLA backgrounds. Experimental validation-immunogenicity, functional inhibition, and benchmarking versus OMP-based candidates-remains essential.