Pyridylpiperazine-based allosteric inhibitors of RND-type multidrug efflux pumps

Ple C.;Tam H. -K.;Vieira Da Cruz A.;Compagne N.;Jimenez-Castellanos J. -C.;Muller R. T.;Pradel E.;Foong W. E.;Malloci G.;Ballee A.;Kirchner M. A.;Moshfegh P.;Herledan A.;Herrmann A.;Deprez B.;Willand N.;Vargiu A. V.;Pos K. M.;Flipo M.;Hartkoorn R. C.

2022-01-01

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Abstract

Efflux transporters of the RND family confer resistance to multiple antibiotics in Gram-negative bacteria. Here, we identify and chemically optimize pyridylpiperazine-based compounds that potentiate antibiotic activity in E. coli through inhibition of its primary RND transporter, AcrAB-TolC. Characterisation of resistant E. coli mutants and structural biology analyses indicate that the compounds bind to a unique site on the transmembrane domain of the AcrB L protomer, lined by key catalytic residues involved in proton relay. Molecular dynamics simulations suggest that the inhibitors access this binding pocket from the cytoplasm via a channel exclusively present in the AcrB L protomer. Thus, our work unveils a class of allosteric efflux-pump inhibitors that likely act by preventing the functional catalytic cycle of the RND pump.