Molecular Insights into Compound-Transporter Interactions: The Case of Inhibitors of Gram-Negative Bacteria Efflux Pumps

The Escherichia coli AcrAB-TolC efflux pump is the archetype of the Resistance-Nodulation-cell Division (RND) exporters from Gram-negative bacteria. Overexpression of RND-type efflux pumps is a major factor in multidrug resistance (MDR), which makes these polyspecific pumps important antibacterial drug discovery targets. However, the development of potent efflux pump inhibitors has been hindered by the lack of structural information for rational drug design. Here, we describe the molecular basis for pyranopyridine-based inhibition of AcrB, which is responsible for the recognition and the initial extrusion of substrates, using a combination of cellular, X-ray crystallographic, and molecular dynamics simulations studies.