Pyridylpiperazine-based allosteric inhibitors of RND-type multidrug efflux pumps
Coline Plé, Heng-Keat Tam, Anaïs Vieira Da Cruz, Nina Compagne, Juan-Carlos Jiménez-Castellanos, Reinke T. Müller, Elizabeth Pradel, Wuen Ee Foong, Giuliano Malloci, Alexia Ballée, Moritz A Kirchner, Parisa Moshfegh, Adrien Herlédan, Andrea Herrmann, Benoît Déprez, Nicolas Willand, Attilio V. Vargiu, Klaas M. Pos, Marion Flipo, Ruben C. Hartkoorn
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.