Coarse-grained simulations of conformational changes in the multidrug efflux transporter AcrB

Jewel, Yead; Liu, Jin; Dutta, Prashanta

doi:10.1039/c7mb00276a

Cited by 14 publications

(14 citation statements)

References 54 publications

(86 reference statements)

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“…Thus, it is important to understand the molecular details of how Slp4-a triggers the pre-fusion for the exocytosis process. In this work, we conducted MD simulations using the hybrid PACE (protein in atomistic details coupled with a coarse-grained environment) force field [ [23] , [24] , [25] ] to examine the Ca 2+ -dependent response of Slp4-a. POPE is used as lipid membranes to study the interaction between Slp4-a and lipid membranes.…”

Section: Introductionmentioning

confidence: 99%

Effect of Calcium ion on synaptotagmin-like protein during pre-fusion of vesicle for exocytosis in blood-brain barrier

Dinh

Liu

Dutta

2020

Biochemistry and Biophysics Reports

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Section: Introductionmentioning

confidence: 99%

Effect of Calcium ion on synaptotagmin-like protein during pre-fusion of vesicle for exocytosis in blood-brain barrier

Dinh

Liu

Dutta

2020

Biochemistry and Biophysics Reports

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“…Mechanistic studies regarding the interaction between RND transporters and their substrates/inhibitors (see reference 8 for a recent review) have provided useful insights into the molecular determinants of polyspecificity (8,(40)(41)(42)(43)(44), the mechanisms of active transport of substrates (8,(45)(46)(47)(48)(49)(50), and the putative inhibition or modulation of transport routes (20,22,(51)(52)(53)(54). In particular, studies performed by the authors identified key structural determinants discriminating between substrates and inhibitors of AcrB in Escherichia coli (41), which were later confirmed by experimental findings (22).…”

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confidence: 99%

Chlorpromazine and Amitriptyline Are Substrates and Inhibitors of the AcrB Multidrug Efflux Pump

Grimsey

Fais

Marshall

et al. 2020

mBio

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Efflux is an important mechanism in Gram-negative bacteria conferring multidrug resistance. Inhibition of efflux is an encouraging strategy to restore the antibacterial activity of antibiotics. Chlorpromazine and amitriptyline have been shown to behave as efflux inhibitors. However, their mode of action is poorly understood. Exposure of Salmonella enterica serovar Typhimurium and Escherichia coli to chlorpromazine selected for mutations within genes encoding RamR and MarR, regulators of the multidrug tripartite efflux pump AcrAB-TolC. Further experiments with S. Typhimurium containing AcrB D408A (a nonfunctional efflux pump) and chlorpromazine or amitriptyline resulted in the reversion of the mutant acrB allele to the wild type. Together, this suggests these drugs are AcrB efflux substrates. Subsequent docking studies with AcrB from S. Typhimurium and E. coli, followed by molecular dynamics simulations and free energy calculations showed that chlorpromazine and amitriptyline bind at the hydrophobic trap, a preferred binding site for substrates and inhibitors within the distal binding pocket of AcrB. Based on these simulations, we suggest that chlorpromazine and amitriptyline inhibit AcrB-mediated efflux by interfering with substrate binding. Our findings provide evidence that these drugs are substrates and inhibitors of AcrB, yielding molecular details of their mechanism of action and informing drug discovery of new efflux inhibitors. IMPORTANCE Efflux pumps of the resistance nodulation-cell division (RND) superfamily are major contributors to multidrug resistance for most of the Gram-negative ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens. The development of inhibitors of these pumps would be highly desirable; however, several issues have thus far hindered all efforts at designing new efflux inhibitory compounds devoid of adverse effects. An alternative route to de novo design relies on the use of marketed drugs, for which side effects on human health have been already assessed. In this work, we provide experimental evidence that the antipsychotic drugs chlorpromazine and amitriptyline are inhibitors of the AcrB transporter, the engine of the major RND efflux pumps in Escherichia coli and Salmonella enterica serovar Typhimurium. Furthermore, in silico calculations have provided a molecular-level picture of the inhibition mechanism, allowing rationalization of experimental data and paving the way for similar studies with other classes of marketed compounds.

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“…It would be interesting to check whether drugs binding in state A could bind to state M‐A. If we presume that changes in the TM domain are due to the protonation, the value and fusion values of the clusters could suggest that either the kinetics of the protonation differ, or the number of protons differs (this number is still under debate even for AcrB) 14,39,40,54 …”

Section: Discussionmentioning

confidence: 99%

Studying dynamics without explicit dynamics: A structure‐based study of the export mechanism by AcrB

Simsir¹,

Broutin

Mus‐Veteau³

et al. 2020

Proteins

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RND family proteins are transmembrane proteins identified as large spectrum drug transporters involved in multi-drug resistance. A prototypical case in this superfamily, responsible for antibiotic resistance in selected gram negative bacteria, is AcrB. AcrB forms a trimer using the proton motive force to efflux drugs, implementing a functional rotation mechanism. Unfortunately, the size of the system (1049 amino-acid per monomer and membrane) has prevented a systematic dynamical exploration, so that the mild understanding of this coupled transport jeopardizes our ability to counter it. The large number of crystal structures of AcrB prompts studies to further our understanding of the mechanism. To this end, we present a novel strategy based on two key ingredients which are to study dynamics by exploiting information embodied in the numerous crystal structures obtained to date, and to systematically consider subdomains, their dynamics, and their interactions. Along the way, we identify the subdomains responsible for dynamic events, refine the states (A,B,E) of the functional rotation mechanism, and analyze the evolution of intramonomer and intermonomer interfaces along the functional cycle. Our analysis shows the relevance of AcrB's efflux mechanism as a template within the HAE1 family but not beyond. It also paves the way to targeted simulations exploiting the most relevant degrees of freedom at certain steps, and also to a targeting of specific interfaces to block the drug efflux. Our work shows that complex dynamics can be unveiled from static snapshots, a strategy that may be used on a variety of molecular machines of large size.

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Coarse-grained simulations of conformational changes in the multidrug efflux transporter AcrB

Cited by 14 publications

References 54 publications

Effect of Calcium ion on synaptotagmin-like protein during pre-fusion of vesicle for exocytosis in blood-brain barrier

Effect of Calcium ion on synaptotagmin-like protein during pre-fusion of vesicle for exocytosis in blood-brain barrier

Chlorpromazine and Amitriptyline Are Substrates and Inhibitors of the AcrB Multidrug Efflux Pump

Studying dynamics without explicit dynamics: A structure‐based study of the export mechanism by AcrB

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