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

Abstract

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: Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. 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 1G values ranging from –27.72 to –47.71 kcal/mol. In silico mutagenesis revealed that the T246A and L344P mutations in K. pneumoniae enhanced ATP binding affinity and protein stability, potentially contributing to colistin resistance. Analysis of the PmrB_ATP complexes identified both conserved and speciesspecific 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. Subjects Biochemistry, Bioinformatics, Computational Biology, Microbiology, Infectious Diseases