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

Zbigniew M. Darzynkiewicz; Adam T. Green; Narges Abdali; Anthony Hazel; Ronnie L. Fulton; Joseph Kimball; Zygmunt Gryczynski; James C. Gumbart; Jerry M. Parks; Jeremy C. Smith; Helen I. Zgurskaya

doi:10.1016/j.bpj.2019.01.010

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

Zbigniew M. Darzynkiewicz, Adam T. Green, Narges Abdali, Anthony Hazel, Ronnie L. Fulton, Joseph Kimball, Zygmunt Gryczynski, James C. Gumbart, Jerry M. Parks, Jeremy C. Smith, Helen I. Zgurskaya

Research output: Contribution to journal › Article › peer-review

7 Scopus citations

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 β-barrel domains of AcrA.

Original language	English
Pages (from-to)	648-658
Number of pages	11
Journal	Biophysical Journal
Volume	116
Issue number	4
DOIs	https://doi.org/10.1016/j.bpj.2019.01.010
State	Published - 19 Feb 2019

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Darzynkiewicz, Zbigniew M. ; Green, Adam T. ; Abdali, Narges ; Hazel, Anthony ; Fulton, Ronnie L. ; Kimball, Joseph ; Gryczynski, Zygmunt ; Gumbart, James C. ; Parks, Jerry M. ; Smith, Jeremy C. ; Zgurskaya, Helen I. / Identification of Binding Sites for Efflux Pump Inhibitors of the AcrAB-TolC Component AcrA. In: Biophysical Journal. 2019 ; Vol. 116, No. 4. pp. 648-658.

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title = "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 β-barrel domains of AcrA.",

author = "Darzynkiewicz, {Zbigniew M.} and Green, {Adam T.} and Narges Abdali and Anthony Hazel and Fulton, {Ronnie L.} and Joseph Kimball and Zygmunt Gryczynski and Gumbart, {James C.} and Parks, {Jerry M.} and Smith, {Jeremy C.} and Zgurskaya, {Helen I.}",

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Identification of Binding Sites for Efflux Pump Inhibitors of the AcrAB-TolC Component AcrA. / Darzynkiewicz, Zbigniew M.; Green, Adam T.; Abdali, Narges; Hazel, Anthony; Fulton, Ronnie L.; Kimball, Joseph; Gryczynski, Zygmunt; Gumbart, James C.; Parks, Jerry M.; Smith, Jeremy C.; Zgurskaya, Helen I.

In: Biophysical Journal, Vol. 116, No. 4, 19.02.2019, p. 648-658.

Research output: Contribution to journal › Article › peer-review

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AU - Darzynkiewicz, Zbigniew M.

AU - Green, Adam T.

AU - Abdali, Narges

AU - Hazel, Anthony

AU - Fulton, Ronnie L.

AU - Kimball, Joseph

AU - Gryczynski, Zygmunt

AU - Gumbart, James C.

AU - Parks, Jerry M.

AU - Smith, Jeremy C.

AU - Zgurskaya, Helen I.

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AB - 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 β-barrel domains of AcrA.

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