Targeted Molecular Dynamics Simulations Suggest Direct Ligand Competition as a Plausible Efflux Inhibition Mechanism in the Multidrug Resistance Pump AcrB

We report computer simulation results using the Targeted Molecular Dynamics technique to explore possible transport mechanisms in the multidrug efflux pump AcrB for two substrates, ethidium bromide and a tetrahydropyridine derivative. These studies revealed structural elements, including specific α-helices, β-strands and flexible loops that define a physically plausible pathway for substrates to the extracellular environment. These calculation results can be used to plan future biophysical experiments and may suggest interesting drug design possibilities to address drug resistance due to AcrB function.ImportanceAddressing the issue of antimicrobial resistance mediated by efflux, this study presents possible binding sites and structures in the AcrB MDR pump that could be molecular targets for drugs. Targeted molecular dynamics simulations suggested that these sites and structures seem vital for a successful efflux. The AcrB is proposed to be divided into three distinct zones, with loops, sheets and helices mediating the passage of molecules from one zone to another. We also described possible capture sites on the outer part of the protein and access ways to its interior. Finally, we proposed that ligand competition for same pathways could be thought as an efflux inhibitory mechanism, thus assisting to conceive new ways of designing efflux pump inhibitors.