Computer Simulations of Multidrug Efflux Pumps of the Resistance-Nodulation-Cell Division Superfamily.

Bacterial efflux pumps of the resistance-nodulation-cell division (RND) superfamily are major contributors to intrinsic and acquired multidrug resistance in Gram-negative bacteria. Structural and biochemical studies on AcrAB-TolC (E. coli) and MexAB-OprM (P. aeruginosa) pumps performed in the past decade have elucidated the molecular basis of allosteric transport by these complex machineries. Alongside these efforts, studies have also characterized the broad substrate specificity (polyspecificity) and molecular determinants that dictate the fate of substrates, inhibitors, and "avoiders" (molecules not actively transported) of RND transporters. Computational approaches have contributed to elucidating the structural and dynamic details of the functioning mechanisms of these transporters, including the interactions with substrates and inhibitors. In this chapter, we will discuss and illustrate several protocols developed in our lab on molecular docking, homology modeling, all-atom molecular dynamics simulations, and binding free energy estimation that have provided valuable insights into substrate recognition, extrusion mechanisms, optimization of efflux avoidance, and potential inhibition strategies.