Revealing potential dual inhibitors from <i>Trigonella foenumgraecum</i> components against AcrAB-TolC drug efflux pump and lipopolysac-charide in <i>E. coli</i> : <i>In silico</i> and molecular dynamics exploration

Gram-negative bacterial infections render serious public health problems worldwide. Drug efflux pumps in bacterial pathogens are one of the main mechanisms of resistance due to their ability to expel antimicrobials from the cell. The resistance-nodulation-division (RND) drug efflux pump superfamily has an important role in multidrug resistance (MDR) due to its role in conferring MDR to many bacterial species. The multidrug efflux pump AcrAB-TolC, which belongs to E. coli , a member of RND, and is considered one of the best models that could be targeted for studying to understand MDR, due to the availability of its functional and chemical structures and the similarity of these structures in many negative bacterial species. Furthermore, Gram-negative bacteria have an outer membrane, containing lipopolysaccharide (LPS), which plays a major role in innate resistance by preventing many antimicrobials from entering the bacteria. In this research, based on findings from our previous work, we employed in silico methods to identify and evaluate nine Fenugreek ( Trigonella foenum-graecum L.) compounds for their ability to target the AcrAB-TolC and LPS outer membrane (OM) assembly pathways in E. coli , including LptD and BamD. Subsequently, we used computer simulations to predict the compound’s behavior at the molecular level, drug-likeness properties, and ADMET properties. Among all compounds identified in Fenugreeks, gamma-tocopherol was the most promising candidate. It exhibited favorable binding interactions with both the AcrAB-TolC pump and LptD protein, weakening the bacterial cell wall and increasing its permeability to antibiotics. Furthermore, gamma-tocopherol exhibited a good level of flexibility and minimal movement within the protein in hinge regions. Using web-based predictive tools, the notable Fenugreek compounds exhibited promising drug-like properties, low hepatotoxicity, and cytotoxicity. While further investigation is needed, this study highlights the potential of Fenugreek-derived compounds as efflux pump inhibitors (EPIs) for developing novel therapeutics against MDR E. coli infections, particularly gamma-tocopherol, warranting further exploration of their therapeutic potential.