In silico targeting of AmpC beta-lactamases in Enterobacter cloacae: unveiling Piperenol B as a potent antimicrobial lead

Antimicrobial Resistance poses a major threat to human health worldwide. Microorganisms develop multi-drug resistance due to intrinsic factors, evolutionary chromosomal alterations, and horizontal gene transfer. Enterobacter cloacae, a common nosocomial bacterium, can cause various infections and is classified as multidrug-resistant. This species produces AmpC enzymes, serine beta-lactamases that hydrolyze beta-lactam antibiotics by cleaving their beta-lactam ring, contributing to its resistance. Traditionally, many phytoconstituents have been used for their antibacterial properties against microorganisms. This study explores phytocompounds to mitigate the effects of beta-lactamase enzymes. In this study, we selected 12592 phytoconstituents with antibacterial properties from Dr. Duke's Ethnobotanical and Phytochemical Database for the virtual screening process. Initial hits were selected based on highest docking scores and then filtered using the ADMET property. Among these, a promising compound Piperenol B showed the highest docking score of -9.1 kcal/mol. A 240 ns molecular dynamics simulation showed that Piperenol B maintained stable conformation and showed consistent results in multiple runs with AmpC protein. Piperenol B complex had a binding free energy score of -61.75 ± 8.0 kJ/mol, whereas the known AmpC inhibitor Clavulanic acid showed -46.64 ± 3.2 kJ/mol. Non-covalent contacts in protein-ligand interactions and specific subunit interfaces were examined using the Protein Contacts Atlas. The STRING database was used to construct the Protein-Protein interaction for AmpC and its interacting proteins. The findings of this study suggested that Piperenol B could be an effective inhibitor of the targeted AmpC protein in Enterobacter cloacae which requires validation in in vitro studies.