Recognition of Imipenem and Meropenem by the RND-Transporter MexB Studied by Computer Simulations

Abstract

Basic understanding of the means by which multidrug efflux systems can efficiently recognize and transport drugs constitutes a fundamental step toward development of compounds able to tackle the continuous outbreak of new bacterial strains resistant to traditional antibiotics. We applied a series of computational techniques, from molecular docking to molecular dynamics simulations and free energy estimate methods, to determine the differences in the binding properties of imipenem and meropenem, two potent antibiotics of the carbapenem family, to MexB, the RND transporter of the major efflux system of Pseudomonas aeruginosa. We identified and characterized two affinity sites in the periplasmic domain of the transporter, sharing strong similarities with the distal and proximal binding pockets identified in AcrB, the homologue of MexB in Escherichia coli. According to our results, meropenem has a higher affinity to the distal binding pocket than imipenem while both compounds are weakly bound to the proximal pocket. This different behavior is mainly due to the hydration properties of the nonpharmacophore part of the two compounds, being that of imipenem less bulky and hydrophobic. Our data provide for the first time a rationale at molecular level for the experimental evidence indicating meropenem as a compound strongly affected by MexB contrary to imipenem, which is apparently poorly transported by the same pump.

Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps

“…Several studies evaluating compounds’ MICs indicated that MexAB-OprM affects the activity of MER, while that of IMI is essentially insensitive to over-expression of the pump [96–99]. To identify the molecular basis of the underlying carbapenem–efflux-pump interactions Collu and co-workers performed docking and 8 standard 50ns-long MD simulations using a truncated model of MexB [92]. Configurations assumed by the compounds during the simulations are reported in Figure 4.…”

“…Arrows denote the orientation of the compounds in panels a, b, and c. In panel d we report the shift of IMI. Adapted from [92], modified.…”

Current Advances in Developing Inhibitors of Bacterial Multidrug Efflux Pumps

“…Their experiments produced an insight into the mechanism that MDR efflux pumps adopt in order to differentiate between their substrates from their inhibitors or modulating agents [119]. The transporter’s periplasmic domain identified two affinity binding sites that appeared to share multiple resemblances with the proximal and distal binding regions found in that of AcrB of E. coli , a close homologue of MexB.…”

“…Applying MDS, along with free energy estimation methods and molecular docking produced results in good agreement with the experimental evidence of the carbapenems. It also highlights the important role played by the surrounding solvent in antibiotic transport as both imipenem and meropenem showed a high degree of solvation in both binding pockets [119]. …”

Extracting Conformational Ensembles of Small Molecules from Molecular Dynamics Simulations: Ampicillin as a Test Case

“…Our database, freely accessible online, is to our knowledge the first extensive one including dynamical properties for a large set of compounds. Besides the specific application to the translocation of antibiotics through bacterial porins [28,29] and to their extrusion by efflux pumps [30,31], this piece of information can be useful for protein-ligand molecular docking [32], whose success rate is known to be strongly dependent on the generation of accurate input geometries and on the description of the flexibility of both partners involved in the binding process [33]. While receptor flexibility is nowadays routinely considered using different techniques [34][35][36], in the vast majority of docking campaigns, ligand flexibility is generally taken into account by considering the rotatable bonds of one given input structure, sometimes generating the 3D structure from 2D drawings or directly from SMILES strings [33].…”