Insight into the PmrB structures of colistin-resistant Gram-negative bacteria through the multi-template ligand-guided homology modeling and <i>in silico</i> mutagenesis

The increasing prevalence of colistin-resistant Gram-negative bacteria necessitates the development of novel therapeutic strategies. PmrB, a histidine kinase involved in colistin resistance, represents a promising drug target. However, the absence of experimentally resolved PmrB structures limits structure-based drug design efforts. This study employed a multi-template, ligand-guided homology modeling approach to construct full-length PmrB models for four pathogens: <i>Acinetobacter baumannii</i>, <i>Escherichia coli</i>, <i>Klebsiella pneumoniae</i>, and <i>Pseudomonas aeruginosa</i>. The resulting models demonstrated high structural integrity, with over 95% of residues located in favored regions and QMEANDisCo global scores ranging from 0.55 to 0.57. Molecular docking simulations guided the selection of representative ligand-bound states for adenosine triphosphate (ATP)-binding site prediction and yielded superior docking scores compared to models generated by AlphaFold, I-TASSER, and SWISS-MODEL. Molecular dynamics (MD) simulations and Molecular Mechanics Generalized Born Surface Area (MM/GBSA) analysis confirmed the stability and binding affinity of the PmrB-ATP complexes, with ΔG values ranging from -27.72 to -47.71 kcal/mol. <i>In silico</i> mutagenesis revealed that the T246A and L344P mutations in <i>K. pneumoniae</i> enhanced ATP binding affinity and protein stability, potentially contributing to colistin resistance. Analysis of the PmrB-ATP complexes identified both conserved and species-specific interactions. This research provides valuable structural models and mechanistic insights into PmrB, supporting future structure-based drug design and the development of novel interventions against colistin-resistant infections.