Phytochemical-based drug designing against efflux-pump of ESKAPE pathogen to combat multidrug-resistant: an <i>in silico</i> study

The <i>Enterococcus faecium</i>, <i>Staphylococcus aureus</i>, <i>Klebsiella pneumoniae</i>, <i>Acinetobacter baumannii</i>, <i>Pseudomonas aeruginosa</i> and <i>Enterobacter species</i> are ciphered as ESKAPE pathogens leading agents for multidrug resistance (MDR) related infections. The current research study used kanamycin nucleotidyltransferase (PDB ID: 1KNY), OXA-24 class D beta-lactamase (PDB ID: 3ZNT), efflux pump proteins as a target to identify potential inhibitor phytochemical for ameliorating antimicrobial resistance caused by ESKAPE pathogens. A total of 61 MDR genes of ESKAPE pathogens were scrutinized phylogenetically and protein-protein interaction (PPIs) analysis were performed. The target proteins for structure-based drug design were culled based on functional partners of efflux pump proteins obtained after PPIs analysis in all ESKAPE pathogens. We deployed a comprehensive sequential filtering approach including high throughput virtual screening of an in-house created bioactive phytochemicals library from the IMPPAT database. First, a molecular docking-based high throughput virtual screening process, followed by meticulous filtering of hits based on binding energy and detailed active-site interaction analysis was performed on each target protein separately. During this stage, native ligands of the target proteins were deployed as a control ligand and for docking protocol validation. These 50 top phytochemicals against both proteins were culled. Then filtration of hits was done based on pharmacokinetics, toxicity and bioactivity of phytochemicals. The retained phytochemicals against each protein were analyzed through density functional theory (DFT) to check potential reactivity. After, analyzing DFT-based energy calculations final lead phytochemicals were selected. The lead phytochemical stability within respective active-site and dynamic behavior was analyzed through molecular dynamic (MD) simulations and principal component analysis (PCA). In this way, diosgenin and paulownin phytochemicals were identified as a lead inhibitor ligand against 1KNY and 3ZNT target receptors, respectively. The 1KNY-diosgenin and 3ZNT-paulownin complexes exhibited binding energies of -8.1 kcal/mol and -9.0 kcal/mol, respectively, forming hydrogen bonds with specific key residues (1KNY-Arg22, Ser105, Thr186) and (3ZNT-Trp221, Tyr 112, Met114) displaying stable dynamic behavior during 100 ns MD simulation, with DFT-based energy gaps of -0.254 52 eV and -0.195 87 eV, respectively, suggesting greater stability compared to control ligands. The diosgenin and paulownin phytochemicals are promising starting natural candidates for drug development against multidrug-resistant infections cure.