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Jamshidi S, Sutton JM, Rahman KM. Computational Study Reveals the Molecular Mechanism of the Interaction between the Efflux Inhibitor PAβN and the AdeB Transporter from Acinetobacter baumannii. ACS OMEGA 2017; 2:3002-3016. [PMID: 30023681 PMCID: PMC6044690 DOI: 10.1021/acsomega.7b00131] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/07/2017] [Indexed: 06/08/2023]
Abstract
Phenylalanine-arginine β-naphthylamide (PAβN) is a broad-spectrum efflux pump inhibitor that has shown to potentiate the activity of antibiotics in Gram-negative bacteria. AdeB is a part of the AdeABC tripartite pump that plays a pivotal role in conferring efflux-mediated resistance in Acinetobacter baumannii. To understand the molecular mechanism of efflux pump inhibition by PAβN, we investigated the interaction of PAβN with AdeB using different computational methods. We observed that PAβN does not have specific binding interactions with the proximal binding site and interacts strongly with the distal binding pocket. The Phe loop located between the proximal and distal binding pockets plays a key role in the PAβN-mediated inhibition and acts as a gate between the binding pockets. Molecular dynamics simulations suggested that PAβN behaved like a climber as we observed switching of the interaction energies between the ligand and the key Phe residues of the binding site during the course of the simulation. PAβN uses the hydrophobic microenvironment formed by Phe residues in the distal binding pocket to keep the binding monomer in the binding conformation. The simulation data suggests that this binding event should result in the inhibition of the peristaltic mechanism and prevent the exporter from extruding any other substrates leading to the inhibition of the tripartite pump.
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Affiliation(s)
- Shirin Jamshidi
- Institute
of Pharmaceutical Science, King’s
College London, London SE1 1DB, U.K.
| | - J. Mark Sutton
- National
Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire SP4 0JG, U.K.
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Yılmaz Ç, Özcengiz G. Antibiotics: Pharmacokinetics, toxicity, resistance and multidrug efflux pumps. Biochem Pharmacol 2017; 133:43-62. [DOI: 10.1016/j.bcp.2016.10.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/14/2016] [Indexed: 02/03/2023]
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Mikalayeva V, Sakalauskaitė S, Daugelavičius R. Interaction of ethidium and tetraphenylphosphonium cations with Salmonella enterica cells. MEDICINA-LITHUANIA 2017; 53:122-130. [PMID: 28462872 DOI: 10.1016/j.medici.2017.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/01/2017] [Accepted: 04/04/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND AND OBJECTIVE One of the main causes of bacterial resistance to antimicrobials is multidrug resistance induced by the increased efficiency of the efflux pumps. In this study we analyzed how the conditions of assay affect the efflux of indicator substrates ethidium (Et+) and tetraphenylphosphonium (TPP+) in Salmonella enterica ser. Typhimurium cells. Impact of the outer membrane permeability barrier, composition and temperature of the medium on accumulation of the indicator compounds also was analyzed. MATERIALS AND METHODS The fluorescence of Et+ and Nile Red was measured using 96-well plates and a plate reader. In parallel to traditional studies of fluorescence we applied a constructed selective electrode to follow the accumulation of Et+ in S. enterica cells. Simultaneously with monitoring of Et+ concentration in the cell incubation medium, electrochemical measurements of TPP+ accumulation were performed. Furthermore, Et+ and TPP+ were used within the same sample as agents competing for the interaction with the efflux pumps. An inhibitor phenylalanyl-arginyl-β-naphtylamide (PAβN) was applied to evaluate the input of RND-family pumps in the total efflux of these indicator compounds. RESULTS S. enterica cells with the intact outer membrane (OM) bound very low amounts of Et+ or TPP+. Cells with the permeabilized OM accumulate considerably higher amounts of the indicator compounds at pH 8.0, but only Et+ was considerably accumulated at pH 6.5. At conditions of electrochemical monitoring accumulation of Et+ by the permeabilized cells at 37°C was considerably faster than at 23°C, but at the higher temperature most of the cell-accumulated Et+ was extruded back to the medium. The fluorescence of Et+ in suspension of cells incubated in 400mmol/L Tris buffer was about twice higher compared to 100mmol/L one. The inhibitory action of TPP+ on Et+ efflux was evident only in 400mmol/L Tris although PAβN effectively increased Et+ fluorescence at both buffer concentrations. CONCLUSIONS Results of our experiments indicate that ionic strength of the incubation medium influence the selectivity, the medium temperature and the assay conditions impact the kinetics of efflux. The lower accumulated amount and the weaker fluorescence of Et+ registered in slightly acidic medium indicate that ΔΨ plays a role in the accumulation of this indicator cation. The bound amount of Et+ to the de-energized or permeabilized cells considerably varies depending on the conditions and methods of de-energization or permeabilization of cells. Tris/EDTA permeabilization of the cells does not inhibit the efflux.
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Affiliation(s)
- Valeryia Mikalayeva
- Department of Biochemistry, Faculty of Natural Sciences, Vytautas Magnus University, Kaunas, Lithuania; Institute of Cardiology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Sandra Sakalauskaitė
- Department of Biochemistry, Faculty of Natural Sciences, Vytautas Magnus University, Kaunas, Lithuania
| | - Rimantas Daugelavičius
- Department of Biochemistry, Faculty of Natural Sciences, Vytautas Magnus University, Kaunas, Lithuania.
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Spengler G, Kincses A, Gajdács M, Amaral L. New Roads Leading to Old Destinations: Efflux Pumps as Targets to Reverse Multidrug Resistance in Bacteria. Molecules 2017; 22:molecules22030468. [PMID: 28294992 PMCID: PMC6155429 DOI: 10.3390/molecules22030468] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/09/2017] [Accepted: 03/10/2017] [Indexed: 01/05/2023] Open
Abstract
Multidrug resistance (MDR) has appeared in response to selective pressures resulting from the incorrect use of antibiotics and other antimicrobials. This inappropriate application and mismanagement of antibiotics have led to serious problems in the therapy of infectious diseases. Bacteria can develop resistance by various mechanisms and one of the most important factors resulting in MDR is efflux pump-mediated resistance. Because of the importance of the efflux-related multidrug resistance the development of new therapeutic approaches aiming to inhibit bacterial efflux pumps is a promising way to combat bacteria having over-expressed MDR efflux systems. The definition of an efflux pump inhibitor (EPI) includes the ability to render the bacterium increasingly more sensitive to a given antibiotic or even reverse the multidrug resistant phenotype. In the recent years numerous EPIs have been developed, although so far their clinical application has not yet been achieved due to their in vivo toxicity and side effects. In this review, we aim to give a short overview of efflux mediated resistance in bacteria, EPI compounds of plant and synthetic origin, and the possible methods to investigate and screen EPI compounds in bacterial systems.
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Affiliation(s)
- Gabriella Spengler
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary.
| | - Annamária Kincses
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary.
| | - Márió Gajdács
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary.
| | - Leonard Amaral
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary.
- Travel Medicine, Institute of Hygiene and Tropical Medicine, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal.
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55
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Computational modelling of efflux pumps and their inhibitors. Essays Biochem 2017; 61:141-156. [PMID: 28258237 DOI: 10.1042/ebc20160065] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 12/13/2016] [Accepted: 12/19/2016] [Indexed: 11/17/2022]
Abstract
Antimicrobial resistance is based on the multifarious strategies that bacteria adopt to face antibiotic therapies, making it a key public health concern of our era. Among these strategies, efflux pumps (EPs) contribute significantly to increase the levels and profiles of resistance by expelling a broad range of unrelated compounds - buying time for the organisms to develop specific resistance. In Gram-negative bacteria, many of these chromosomally encoded transporters form multicomponent 'pumps' that span both inner and outer membranes and are driven energetically by a primary or secondary transporter component.One of the strategies to reinvigorate the efficacy of antimicrobials is by joint administration with EP inhibitors (EPI), which either block the substrate binding and/or hinder any of the transport-dependent steps of the pump. In this review, we provide an overview of multidrug-resistance EPs, their inhibition strategies and the relevant findings from the various computational simulation studies reported to date with respect to deciphering the mechanism of action of inhibitors with the purpose of improving their rational design.
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56
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Mechanisms of envelope permeability and antibiotic influx and efflux in Gram-negative bacteria. Nat Microbiol 2017; 2:17001. [PMID: 28224989 DOI: 10.1038/nmicrobiol.2017.1] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/23/2016] [Indexed: 01/26/2023]
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Evaluation of a series of 2-napthamide derivatives as inhibitors of the drug efflux pump AcrB for the reversal of antimicrobial resistance. Bioorg Med Chem Lett 2017; 27:733-739. [DOI: 10.1016/j.bmcl.2017.01.042] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 01/13/2017] [Indexed: 11/18/2022]
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Abdali N, Parks JM, Haynes KM, Chaney JL, Green AT, Wolloscheck D, Walker JK, Rybenkov VV, Baudry J, Smith JC, Zgurskaya HI. Reviving Antibiotics: Efflux Pump Inhibitors That Interact with AcrA, a Membrane Fusion Protein of the AcrAB-TolC Multidrug Efflux Pump. ACS Infect Dis 2017; 3:89-98. [PMID: 27768847 DOI: 10.1021/acsinfecdis.6b00167] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Antibiotic resistance is a major threat to human welfare. Inhibitors of multidrug efflux pumps (EPIs) are promising alternative therapeutics that could revive activities of antibiotics and reduce bacterial virulence. Identification of new druggable sites for inhibition is critical for the development of effective EPIs, especially in light of constantly emerging resistance. Here, we describe EPIs that interact with periplasmic membrane fusion proteins, critical components of efflux pumps that are responsible for the activation of the transporter and the recruitment of the outer-membrane channel. The discovered EPIs bind to AcrA, a component of the prototypical AcrAB-TolC pump, change its structure in vivo, inhibit efflux of fluorescent probes, and potentiate the activities of antibiotics in Escherichia coli and other Gram-negative bacteria. Our findings expand the chemical and mechanistic diversity of EPIs, suggest the mechanism for regulation of the efflux pump assembly and activity, and provide a promising path for reviving the activities of antibiotics in resistant bacteria.
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Affiliation(s)
- Narges Abdali
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Jerry M. Parks
- UT/ORNL Center
for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry and Cellular
and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Keith M. Haynes
- Department of Pharmacological & Physiological Science, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States
| | - Julie L. Chaney
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Adam T. Green
- UT/ORNL Center
for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - David Wolloscheck
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - John K. Walker
- Department of Pharmacological & Physiological Science, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States
| | - Valentin V. Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Jerome Baudry
- UT/ORNL Center
for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry and Cellular
and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jeremy C. Smith
- UT/ORNL Center
for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry and Cellular
and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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Kinana AD, Vargiu AV, Nikaido H. Effect of site-directed mutations in multidrug efflux pump AcrB examined by quantitative efflux assays. Biochem Biophys Res Commun 2016; 480:552-557. [PMID: 27789287 DOI: 10.1016/j.bbrc.2016.10.083] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 10/23/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND The Resistance-Nodulation-Division (RND) family transporter AcrB plays a major role in the intrinsic and increased resistance of Escherichia coli to a large number of antibiotics. The distal binding pocket within this multidrug efflux transporter is very large, but the effort to define the roles of various residues facing this pocket through site-directed mutagenesis so far involved only the determination of minimal inhibitory concentrations of drugs in mutants. METHODS We measured in intact E. coli cells the kinetics of efflux of two substrates, nitrocefin (a cephalosporin) that is predicted mainly to bind to the upper, "groove" domain of the pocket, and L-alanyl-β-naphthylamide (Ala-Naph) that is likely to bind to the lower, "cave" domain, in a number of site-directed mutants of AcrB, where a hydrophobic or aromatic residue was changed into alanine. RESULTS The efflux of nitrocefin became attenuated by some mutations in the groove domain, such as I278A and F178A, but in some experiments a mutation in the cave domain, F628A produced a similar result. In some cases an increased value of KM was detected. The efflux of Ala-Naph was increased by mutations in the cave domain, such as F136A and I626A, but also by those in the groove domain (I277A, I278A, F178A). In most cases the increased Vmax values appeared to be responsible. F610A mutation had a profound effect on the efflux of both substrates, as reported earlier. CONCLUSIONS Our data show for the first time effects of various substrate-binding pocket mutations on the kinetics of efflux of two substrates by the AcrB pump. They also confirm interactions between substrates and drugs predicted by MD simulation studies, and also reveal areas that need future research.
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Affiliation(s)
- Alfred D Kinana
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, 09042, Monserrato, Italy
| | - Hiroshi Nikaido
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA.
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Li Y, Cao S, Zhang L, Lau GW, Wen Y, Wu R, Zhao Q, Huang X, Yan Q, Huang Y, Wen X. A TolC-Like Protein of Actinobacillus pleuropneumoniae Is Involved in Antibiotic Resistance and Biofilm Formation. Front Microbiol 2016; 7:1618. [PMID: 27822201 PMCID: PMC5075564 DOI: 10.3389/fmicb.2016.01618] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/28/2016] [Indexed: 11/13/2022] Open
Abstract
Actinobacillus pleuropneumoniae is the etiologic agent of porcine contagious pleuropneumonia, a significant disease that causes serious economic losses to the swine industry worldwide. Persistent infections caused by bacterial biofilms are recalcitrant to treat because of the particular drug resistance of biofilm-dwelling cells. TolC, a key component of multidrug efflux pumps, are responsible for multidrug resistance (MDR) in many Gram-negative bacteria. In this study, we identified two TolC-like proteins, TolC1 and TolC2, in A. pleuropneumoniae. Deletion of tolC1, but not tolC2, caused a significant reduction in biofilm formation, as well as increased drug sensitivity of both planktonic and biofilm cells. The genetic-complementation of the tolC1 mutation restored the competent biofilm and drug resistance. Besides, biofilm formation was inhibited and drug sensitivity was increased by the addition of phenylalanine-arginine beta-naphthylamide (PAβN), a well-known efflux pump inhibitor (EPI), suggesting a role for EPI in antibacterial strategies toward drug tolerance of A. pleuropneumoniae. Taken together, TolC1 is required for biofilm formation and is a part of the MDR machinery of both planktonic and biofilm cells, which could supplement therapeutic strategies for resistant bacteria and biofilm-related infections of A. pleuropneumoniae clinical isolate SC1516.
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Affiliation(s)
- Ying Li
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University Chengdu, China
| | - Sanjie Cao
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University Chengdu, China
| | - Luhua Zhang
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China; Department of Pathobiology, University of Illinois at Urbana-ChampaignUrbana, IL, USA
| | - Gee W Lau
- Department of Pathobiology, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - Yiping Wen
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University Chengdu, China
| | - Rui Wu
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University Chengdu, China
| | - Qin Zhao
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University Chengdu, China
| | - Xiaobo Huang
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University Chengdu, China
| | - Qigui Yan
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University Chengdu, China
| | - Yong Huang
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University Chengdu, China
| | - Xintian Wen
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University Chengdu, China
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The analysis of the antibiotic resistome offers new opportunities for therapeutic intervention. Future Med Chem 2016; 8:1133-51. [DOI: 10.4155/fmc-2016-0027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Most efforts in the development of antimicrobials have focused on the screening of lethal targets. Nevertheless, the constant expansion of antimicrobial resistance makes the antibiotic resistance determinants themselves suitable targets for finding inhibitors to be used in combination with antibiotics. Among them, inhibitors of antibiotic inactivating enzymes and of multidrug efflux pumps are suitable candidates for improving the efficacy of antibiotics. In addition, the application of systems biology tools is helping to understand the changes in bacterial physiology associated to the acquisition of resistance, including the increased susceptibility to other antibiotics displayed by some antibiotic-resistant mutants. This information is useful for implementing novel strategies based in metabolic interventions or combination of antibiotics for improving the efficacy of antibacterial therapy.
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