Discovery of multidrug efflux pump inhibitors with a novel chemical scaffold

Biochim Biophys Acta Gen Subj. 2020 Jun;1864(6):129546. doi: 10.1016/j.bbagen.2020.129546. Epub 2020 Feb 4.


Multidrug efflux is a major contributor to antibiotic resistance in Gram-negative bacterial pathogens. Inhibition of multidrug efflux pumps is a promising approach for reviving the efficacy of existing antibiotics. Previously, inhibitors targeting both the efflux transporter AcrB and the membrane fusion protein AcrA in the Escherichia coli AcrAB-TolC efflux pump were identified. Here we use existing physicochemical property guidelines to generate a filtered library of compounds for computational docking. We then experimentally test the top candidate coumpounds using in vitro binding assays and in vivo potentiation assays in bacterial strains with controllable permeability barriers. We thus identify a new class of inhibitors of E. coli AcrAB-TolC. Six molecules with a shared scaffold were found to potentiate the antimicrobial activity of erythromycin and novobiocin in hyperporinated E. coli cells. Importantly, these six molecules were also active in wild-type strains of both Acinetobacter baumannii and Klebsiella pneumoniae, potentiating the activity of erythromycin and novobiocin up to 8-fold.

Keywords: Docking; Gram-negative; Minimum inhibitory concentration; Permeability; Resistance nodulation division; Substrate.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Acinetobacter baumannii / drug effects
  • Acinetobacter baumannii / pathogenicity
  • Anti-Bacterial Agents / adverse effects
  • Anti-Bacterial Agents / pharmacology
  • Anti-Infective Agents / chemistry
  • Anti-Infective Agents / pharmacology*
  • Carrier Proteins / antagonists & inhibitors
  • Carrier Proteins / chemistry*
  • Computational Biology / methods
  • Drug Resistance, Bacterial / drug effects
  • Drug Resistance, Bacterial / genetics
  • Drug Synergism
  • Erythromycin / chemistry
  • Erythromycin / pharmacology
  • Escherichia coli Proteins / antagonists & inhibitors
  • Escherichia coli Proteins / chemistry*
  • Gram-Negative Bacteria / drug effects
  • Gram-Negative Bacteria / pathogenicity
  • Gram-Negative Bacterial Infections / drug therapy*
  • Gram-Negative Bacterial Infections / microbiology
  • Gram-Negative Bacterial Infections / pathology
  • Humans
  • Klebsiella pneumoniae
  • Lipoproteins / antagonists & inhibitors
  • Lipoproteins / chemistry*
  • Membrane Transport Proteins / chemistry*
  • Molecular Docking Simulation
  • Multidrug Resistance-Associated Proteins / antagonists & inhibitors
  • Multidrug Resistance-Associated Proteins / chemistry*
  • Novobiocin / chemistry
  • Novobiocin / pharmacology


  • AcrA protein, E coli
  • AcrAB-TolC protein, E coli
  • AcrB protein, E coli
  • Anti-Bacterial Agents
  • Anti-Infective Agents
  • Carrier Proteins
  • Escherichia coli Proteins
  • Lipoproteins
  • Membrane Transport Proteins
  • Multidrug Resistance-Associated Proteins
  • Novobiocin
  • Erythromycin