Pharmacophore-guided identification and dynamic characterization of potential binders of the sporulation histidine kinase KinA in Bacillus subtilis

Abstract

Bacterial histidine kinases represent attractive yet underexplored targets for antibacterial drug discovery owing to their central roles in environmental sensing and adaptive signaling. Among these, the sporulation histidine kinase KinA regulates entry into the phosphorelay controlling sporulation initiation in Bacillus species. In this study, a pharmacophore-guided virtual screening strategy based on the structural features of the histidine kinase inhibitor waldiomycin was employed to identify structurally diverse candidate KinA-binding compounds. A library of 2500 compounds was screened and prioritized through hierarchical molecular docking, pre-molecular dynamics MM/GBSA analysis, molecular dynamics simulations, post-molecular dynamics MM/GBSA analysis, and in silico ADMET profiling. Five compounds exhibiting favorable predicted interaction profiles within the KinA DHp–CA region were prioritized. Comparative trajectory analysis demonstrated that energetic estimates did not necessarily correspond to dynamic behavior, with Compound 3 exhibiting the most favorable post-molecular dynamics MM/GBSA estimate (ΔGbind = − 53.89 kcal mol − 1), whereas Compound 5 showed comparatively favorable dynamic stability and persistent multi-residue interactions. Analysis of the enantiomeric pair represented by Compounds 4 and 5 further suggested that stereochemistry may influence ligand accommodation and interaction patterns within the predicted KinA binding region. Several screened compounds also showed favorable predicted absorption and toxicity characteristics relative to waldiomycin. Overall, the findings prioritize structurally distinct compounds for further investigation and provide a computational framework for identifying potential KinA-binding candidates. Experimental biochemical and sporulation-based studies will be required to determine whether these compounds modulate KinA activity or affect sporulations.