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

  • Nat Commun. 2022 Jan 10;13(1):115. doi: 10.1038/s41467-021-27726-2.
Coline Plé  #  1 ,  Heng-Keat Tam  #  2  3 ,  Anais Vieira Da Cruz  4 ,  Nina Compagne  4 ,  Juan-Carlos Jiménez-Castellanos  1 ,  Reinke T Müller  2 ,  Elizabeth Pradel  1 ,  Wuen Ee Foong  2 ,  Giuliano Malloci  5 ,  Alexia Ballée  4 ,  Moritz A Kirchner  2 ,  Parisa Moshfegh  4 ,  Adrien Herledan  4 ,  Andrea Herrmann  2 ,  Benoit Deprez  4 ,  Nicolas Willand  4 ,  Attilio Vittorio Vargiu  5 ,  Klaas M Pos  6 ,  Marion Flipo  7 ,  Ruben C Hartkoorn  8
Affiliations
  • 1. Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, F-59000, Lille, France.
  • 2. Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438, Frankfurt am Main, Germany.
  • 3. Hengyang Medical School, University of South China, 421002, Hengyang, Hunan Province, China.
  • 4. Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France.
  • 5. Department of Physics, University of Cagliari, 09042, Monserrato (Cagliari), Italy.
  • 6. Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438, Frankfurt am Main, Germany. [email protected].
  • 7. Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France. [email protected].
  • 8. Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, F-59000, Lille, France. [email protected].
  • # Contributed equally.
PMID: 35013254 DOI: 10.1038/s41467-021-27726-2
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.

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