Meropenem vs. Imipenem interacting with MexB: structural and dynamical determinants of the efflux action on two substrates

Collu F;VARGIU, ATTILIO VITTORIO;Cascella M;RUGGERONE, PAOLO

2011-01-01

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Abstract

Active extrusion of drugs through efflux pumps constitutes one of the main mechanisms of multidrug resistance in cells. In recent years, large efforts have been devoted to the biochemical and structural characterization of RND efflux pumps in Gram-negative bacteria, in particular the AcrB/ATolC system of E.Coli. Specific attention has been addressed to the active part of the efflux system, constituted by the AcrB unit. Despite the presence of several data, crucial questions concerning its functioning are still open. The understanding of the structure-dynamics-function relationship of MexB, the analogous transporter in P. Aeruginosa, encounters even more difficulties, because of the lack of structural data of the transporter in complex with substrates. To shade some light on the activity of MexB, we performed computational studies on MexB interacting with two compounds, meropenem and imipenem, the first known to be a good substrate, and the second a modest one. Several techniques were used in the present work, ranging from flexible docking [1] to standard and targeted molecular dynamics (MD) simulations. Starting from the published crystal structure [2] we identified the most probable poses of the two compounds in both the original experimental and in the MD-equilibrated structures. We used information from AcrB binding pocket in order to find relevant binding sites of the two compounds in the analogous binding pocket of MexB. Meropenem frequently lies with appropriate orientation in a pocket similar to the one identified for doxorubicin in AcrB [3], while the occurrence of imipenem poses in the same pocket is very scarce. Additionally, when present in the pocket, imipenem is located in a position that renders very unlikely its extrusion toward the OprM docking domain during the simulation of the functional peristalsis. The analysis of the trajectories has provided a complete inventory of the transporter and antibiotic hot spots, which is key information in terms of screening and design of antibiotics and inhibitors. [1] Zacharias M., Protein Sci 2003, 12, 1271-82. [2] Sennhauser G., et al., J Mol Biol 2009, 389, 134-145. [3] Murakami S., et al., Nature 2006, 443, 173-9.