Molecular rationale for the specificities of Mex transporters of Pseudomonas aeruginosa

Efflux pumps of the RND (Resistance Nodulation-cell Division) superfamily such as MexB, MexD, MexF, and MexY of Pseudomonas aeruginosa play an essential role in multidrug resistance of Gram-negative bacteria. Structural studies performed on MexB and homologous transporters in other Gram-negative bacteria revealed the presence of two main substrate recognition sites, accessed by substrate molecules through up to four (to date) different entry channels. Efforts at understanding correlations between the physico-chemical properties of compounds and their behaviour as substrates, non-substrates, or inhibitors of RND transporters have mostly relied on data about the interaction of compounds with the two main recognition sites, namely the access pocket and the deep binding pocket. However, considering also their interaction with protein channels and possibly other undetected sites could provide precious hints regarding both specificity and susceptibility. Under these premises, we performed a systematic blind ensemble-docking study addressing the binding propensities of several classes of antibiotics to the whole surface of the Mex transporters of P. aeruginosa. Our findings were employed to rationalize experimental data about the specificities of the compounds towards the different Mex transporters.