Identification of Binding Sites for Efflux Pump Inhibitors of the AcrAB-TolC Component AcrA

Abstract

The overexpression of multidrug efflux pumps is an important mechanism of clinical resistance in Gram-negative bacteria. Recently, four small molecules were discovered that inhibit efflux in Escherichia coli and interact with the AcrAB-TolC efflux pump component AcrA. However, the binding site(s) for these molecules was not determined. Here, we combine ensemble docking and molecular dynamics simulations with tryptophan fluorescence spectroscopy, site-directed mutagenesis, and antibiotic susceptibility assays to probe binding sites and effects of binding of these molecules. We conclude that clorobiocin and SLU-258 likely bind at a site located between the lipoyl and b-barrel domains of AcrA.

Repurposing Therapeutics for COVID-19: Supercomputer-Based Docking to the SARS-CoV-2 Viral Spike Protein and Viral Spike Protein-Human ACE2 Interface

“…By accounting for the conformational diversity of the receptor, ensemble docking enhances the likelihood of identifying predicted hits (enrichment), which may be lost when screening against a single conformation of the target 13 . We have previously applied this technique to derive experimentally-verified hits for many protein targets involved in the treatment of diseases ranging from bacterial infections to osteoporosis [15][16][17][18][19][20][21][22][23] . For this work, three phases of calculations were performed: structural modeling, molecular simulations (ensemble building), and small-molecule docking (in silico ligand screening)…”

Repurposing Therapeutics for COVID-19: Supercomputer-Based Docking to the SARS-CoV-2 Viral Spike Protein and Viral Spike Protein-Human ACE2 Interface

“…By accounting for the conformational diversity of the receptor ensemble docking enhances the likelihood of identifying predicted hits (enrichment), which may be lost when screening against a single conformation of the target 12 . We have previously applied this technique to derive experimentally-verified hits for several protein targets to treat diseases ranging from bacterial infections to osteoporosis [14][15][16][17][18][19][20][21][22] . For this work three phases of calculations were performed: structural modeling, molecular simulations (ensemble building), and small-molecule docking (in silico ligand screening)…”

Repurposing Therapeutics for the Wuhan Coronavirus nCov-2019: Supercomputer-Based Docking to the Viral S Protein and Human ACE2 Interface

“…By accounting for the conformational diversity of the receptor ensemble docking enhances the likelihood of identifying predicted hits (enrichment), which may be lost when screening against a single configuration 9 . We have previously applied this technique to derive experimentallyverified hits for several protein targets [11][12][13][14][15][16][17][18][19] . Briefly, the work reported here was performed in three phases: structural modeling, molecular simulations (ensemble building), and smallmolecule docking (in silico ligand screening)…”