A framework for dissecting affinities of multidrug efflux transporter AcrB to fluoroquinolones

A competitive efflux assay combined with computational approaches reveal how different quinolones interact with the prototypical bacterial multidrug efflux transporter AcrB, providing insights which may help optimise antibiotics. Sufficient concentration of antibiotics close to their target is key for antimicrobial action. Among the tools exploited by bacteria to reduce the internal concentration of antibiotics, multidrug efflux pumps stand out for their ability to capture and expel many unrelated compounds out of the cell. Determining the specificities and efflux efficiency of these pumps towards their substrates would provide quantitative insights into the development of antibacterial strategies. In this light, we developed a competition efflux assay on whole cells, that allows measuring the efficacy of extrusion of clinically used quinolones in populations and individual bacteria. Experiments reveal the efficient competitive action of some quinolones that restore an active concentration of other fluoroquinolones. Computational methods show how quinolones interact with the multidrug efflux transporter AcrB. Combining experiments and computations unveils a key molecular mechanism acting in vivo to detoxify bacterial cells. The developed assay can be generalized to the study of other efflux pumps.

Automated summary

This study combines experimental and computational approaches to reveal the interaction and molecular mechanism between quinolone antibiotics and bacterial multidrug efflux pumps. The findings are important for optimizing antibiotics and can be extended to the study of other efflux pumps.