2. Academic Validation
  3. Molecular mechanism of transition-state inhibitors of bacterial antibiotic efflux pumps

Molecular mechanism of transition-state inhibitors of bacterial antibiotic efflux pumps

  • NPJ Antimicrob Resist. 2026 May 4;4(1):35. doi: 10.1038/s44259-026-00207-6.
Clara Börnsen # 1 2,  Reinke T Müller # 3 4,  Anais Vieira Da Cruz 5,  Juan-Carlos Jiménez-Castellanos 6,  Virginie Meurillon 5,  Lorenz Brandstätter 2 7,  Eszter V Lodinsky 2 7,  Mohd Athar 8,  Attilio V Vargiu 8,  Ruben C Hartkoorn 9,  Marion Flipo 10,  Achilleas S Frangakis 11 12,  Klaas M Pos 13 14
Affiliations

Affiliations

  • 1 Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany.
  • 2 Cluster of Excellence SubCellular Architecture of Life (SCALE), Goethe University, Frankfurt, Frankfurt am Main, Germany.
  • 3 Cluster of Excellence SubCellular Architecture of Life (SCALE), Goethe University, Frankfurt, Frankfurt am Main, Germany. [email protected].
  • 4 Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany. [email protected].
  • 5 Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France.
  • 6 Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France.
  • 7 Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany.
  • 8 Department of Physics, University of Cagliari, Cagliari, Italy.
  • 9 Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France. [email protected].
  • 10 Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France. [email protected].
  • 11 Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany. [email protected].
  • 12 Cluster of Excellence SubCellular Architecture of Life (SCALE), Goethe University, Frankfurt, Frankfurt am Main, Germany. [email protected].
  • 13 Cluster of Excellence SubCellular Architecture of Life (SCALE), Goethe University, Frankfurt, Frankfurt am Main, Germany. [email protected].
  • 14 Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany. [email protected].
  • # Contributed equally.
PMID: 42082832 DOI: 10.1038/s44259-026-00207-6
Abstract

In many Gram-negative bacteria such as Escherichia coli and Klebsiella pneumoniae, the AcrAB-TolC efflux pump is central to multidrug resistance. We report the development of BDM91531, a nanomolar pyridylpiperazine inhibitor that potentiates the activity of several Antibiotics. Structural analyses by X-ray crystallography and cryo-EM revealed that the divalent cationic BDM91531 binds AcrB through electrostatic interactions with a central role for residues D408 and E947, trapping protomers in an O to L transitional state and blocking the conformational cycling of the trimer. Differential scanning fluorimetry and susceptibility tests confirmed this inhibitory mechanism. Negative charges at the cytoplasmic rim are essential for inhibitor uptake as electrostatic attraction from rim carboxylates, including E947 and D951, facilitates entry. Loss of D951 abolished inhibitor sensitivity, whereas introducing alternative negative charges restored activity. These findings establish BDM91531 as a potent AcrB efflux pump inhibitor and highlight structural determinants for inhibitor access and binding.

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