Virtual screening and conformational equilibrium assessment of phenolic-based MexAB-OprM inhibitors

The multidrug resistance of Pseudomonas aeruginosa is predominantly caused by the MexAB-OprM efflux pump (EP) system, a Resistance-Nodulation-Cell Division (RND) transporter that expels toxins throughout the cell membrane. The development of thermodynamically favorable inhibitors that promote the rigidification of the MexB subunit is a promising strategy to revert this resistance. Therefore, this work aimed to screen phenolic compounds that function as efflux pump inhibitors (EPIs) via molecular simulations. Using the Phenol-Explorer as a database, the study subjected 484 molecules to drug-likeness filters, such as Lipinski, Veber, Ghose, and Muegge, followed by molecular docking using AutoDock Vina and a 100 ns Molecular Dynamics (MD) simulations using GROMACS. Statistical analyses were applied to determine the selection in each phase. Regarding the results, from the initial library, 100 compounds met the drug-likeness criteria. These qualifying candidates were clustered based on docking free energy most favorable mean affinity (-7.194 ± 0.222 kcal/mol) and structural stability (1.886 ± 0.378 Å), yielding 23 molecules for MD simulations. In this final stage, five compounds - conidendrin, avenanthramide 2p, eriodictyol, galangin, and syringaresinol - exhibited superior thermodynamic behavior. Collectively, these top candidates displayed backbone RMSD values between 0.4 and 0.5 nm and ligand RMSD ranging from 0.2 to 0.5 nm, confirming global structural integrity. Dynamic analysis revealed distinct binding mechanisms, while conidendrin and avenanthramide 2p showed rapid stabilization, eriodictyol, syringaresinol, and galangin presented an induced fit behavior. Furthermore, RMSF analysis indicated that these ligands induced a net reduction in residue fluctuation compared to the apoprotein. These findings suggest that the selected compounds effectively reduce the conformational entropy required for the pump's peristaltic function.