Molecular docking, dynamics, and DFT-based discovery of novel CTX-M β-lactamase inhibitors in Klebsiella pneumoniae

The increasing prevalence of CTX-M β-lactamase-producing Klebsiella pneumoniae has become a critical public health concern due to its ability to hydrolyse broad-spectrum β-lactam antibiotics, thereby undermining clinical treatment. This study applied a multistage computational analysis to identify and characterise potential inhibitors of CTX-M β-lactamase. Virtual screening of the ZINC database compounds using RASPD+ yielded 21,246 candidates, which were refined through physicochemical, pharmacokinetic, and medicinal chemistry filters. Twenty compounds met drug-likeness and ADMET criteria and were subjected to molecular docking using AutoDock 4.2. The top hits, ZINC12152876 (−9.54 kcal/mol) and ZINC15305595 (-9.65 kcal/mol), exhibited stronger binding affinities than Avibactam (-6.20 kcal/mol) through hydrogen bonding with Ser73, Ser240, and Asn135 and hydrophobic stabilisation within the Ω-loop. Three-hundred-nanosecond molecular dynamics simulations in Amber22 confirmed the high structural stability of both complexes, with ZINC12152876 displaying superior compactness, low RMSD, and stable hydrogen-bond networks. MM-GBSA analysis revealed total binding energies of -44.4 and -43.5 kcal/mol for ZINC12152876 and ZINC15305595, respectively, dominated by van der Waals and electrostatic interactions. DFT-based HOMO-LUMO and molecular electrostatic potential analyses showed that ZINC12152876 possessed higher electronic softness and stronger polar character, supporting its strong interaction profile. The combined results highlight ZINC12152876 as a promising lead compound for the rational design of potent non-covalent CTX-M β-lactamase inhibitors against multidrug-resistant K. pneumoniae.