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Rajapaksha P, Ojo I, Yang L, Pandeya A, Abeywansha T, Wei Y. Insight into the AcrAB-TolC Complex Assembly Process Learned from Competition Studies. Antibiotics (Basel) 2021; 10:antibiotics10070830. [PMID: 34356751 PMCID: PMC8300762 DOI: 10.3390/antibiotics10070830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/30/2021] [Accepted: 07/06/2021] [Indexed: 11/16/2022] Open
Abstract
The RND family efflux pump AcrAB-TolC in E. coli and its homologs in other Gram-negative bacteria are major players in conferring multidrug resistance to the cells. While the structure of the pump complex has been elucidated with ever-increasing resolution through crystallography and Cryo-EM efforts, the dynamic assembly process remains poorly understood. Here, we tested the effect of overexpressing functionally defective pump components in wild type E. coli cells to probe the pump assembly process. Incorporation of a defective component is expected to reduce the efflux efficiency of the complex, leading to the so called "dominant negative" effect. Being one of the most intensively studied bacterial multidrug efflux pumps, many AcrA and AcrB mutations have been reported that disrupt efflux through different mechanisms. We examined five groups of AcrB and AcrA mutants, defective in different aspects of assembly and substrate efflux. We found that none of them demonstrated the expected dominant negative effect, even when expressed at concentrations many folds higher than their genomic counterpart. The assembly of the AcrAB-TolC complex appears to have a proof-read mechanism that effectively eliminated the formation of futile pump complex.
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Zwama M, Nishino K. Ever-Adapting RND Efflux Pumps in Gram-Negative Multidrug-Resistant Pathogens: A Race against Time. Antibiotics (Basel) 2021; 10:774. [PMID: 34201908 PMCID: PMC8300642 DOI: 10.3390/antibiotics10070774] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 01/13/2023] Open
Abstract
The rise in multidrug resistance (MDR) is one of the greatest threats to human health worldwide. MDR in bacterial pathogens is a major challenge in healthcare, as bacterial infections are becoming untreatable by commercially available antibiotics. One of the main causes of MDR is the over-expression of intrinsic and acquired multidrug efflux pumps, belonging to the resistance-nodulation-division (RND) superfamily, which can efflux a wide range of structurally different antibiotics. Besides over-expression, however, recent amino acid substitutions within the pumps themselves-causing an increased drug efflux efficiency-are causing additional worry. In this review, we take a closer look at clinically, environmentally and laboratory-evolved Gram-negative bacterial strains and their decreased drug sensitivity as a result of mutations directly in the RND-type pumps themselves (from Escherichia coli, Salmonella enterica, Neisseria gonorrhoeae, Pseudomonas aeruginosa, Acinetobacter baumannii and Legionella pneumophila). We also focus on the evolution of the efflux pumps by comparing hundreds of efflux pumps to determine where conservation is concentrated and where differences in amino acids can shed light on the broad and even broadening drug recognition. Knowledge of conservation, as well as of novel gain-of-function efflux pump mutations, is essential for the development of novel antibiotics and efflux pump inhibitors.
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Affiliation(s)
- Martijn Zwama
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Kunihiko Nishino
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka 567-0047, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
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Antibiotic Substrate Selectivity of Pseudomonas aeruginosa MexY and MexB Efflux Systems Is Determined by a Goldilocks Affinity. Antimicrob Agents Chemother 2020; 64:AAC.00496-20. [PMID: 32457110 DOI: 10.1128/aac.00496-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/22/2020] [Indexed: 12/19/2022] Open
Abstract
Resistance-nodulation-division (RND) efflux pumps are important contributors to bacterial antibiotic resistance. In this study, we combined evolutionary sequence analyses, computational structural modeling, and ligand docking to develop a framework that can explain the known antibiotic substrate selectivity differences between two Pseudomonas aeruginosa RND transporters, MexY and MexB. For efficient efflux, antibiotic substrates must possess a "Goldilocks affinity": binding strong enough to allow interaction with transporter but not so tight as to impede movement through the pump.
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Marshall RL, Bavro VN. Mutations in the TolC Periplasmic Domain Affect Substrate Specificity of the AcrAB-TolC Pump. Front Mol Biosci 2020; 7:166. [PMID: 32850959 PMCID: PMC7396618 DOI: 10.3389/fmolb.2020.00166] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/01/2020] [Indexed: 01/08/2023] Open
Abstract
TolC and the other members of the outer membrane factor (OMF) family are outer membrane proteins forming trimeric channels that serve as a conduit for most actively effluxed substrates in Gram-negative bacteria by providing a key component in a multitude of tripartite efflux-pumps. Current models of tripartite pump assembly ascribe substrate selection to the inner-membrane transporter and periplasmic-adapter protein (PAP) assembly, suggesting that TolC is a passive, non-selective channel. While the membrane-embedded portion of the protein adopts a porin-like fold, the periplasmic domain of TolC presents a unique "alpha-barrel" architecture. This alpha-barrel consists of pseudo-continuous α-helices forming curved coiled-coils, whose tips form α-helical hairpins, relaxation of which results in a transition of TolC from a closed to an open-aperture state allowing effective efflux of substrates through its channel. Here, we analyzed the effects of site-directed mutations targeting the alpha-barrel of TolC, of the principal tripartite efflux-pump Escherichia coli AcrAB-TolC, on the activity and specificity of efflux. Live-cell functional assays with these TolC mutants revealed that positions both at the periplasmic tip of, and partway up the TolC coiled-coil alpha-barrel domain are involved in determining the functionality of the complex. We report that mutations affecting the electrostatic properties of the channel, particularly the D371V mutation, significantly impact growth even in the absence of antibiotics, causing hyper-susceptibility to all tested efflux-substrates. These results suggest that inhibition of TolC functionality is less well-tolerated than deletion of tolC, and such inhibition may have an antibacterial effect. Significantly and unexpectedly, we identified antibiotic-specific phenotypes associated with novel TolC mutations, suggesting that substrate specificity may not be determined solely by the transporter protein or the PAP, but may reside at least partially with the TolC-channel. Furthermore, some of the effects of mutations are difficult to reconcile with the currently prevalent tip-to-tip model of PAP-TolC interaction due to their location higher-up on the TolC alpha-barrel relative to the proposed PAP-docking sites. Taken together our results suggest a possible new role for TolC in vetting of efflux substrates, alongside its established role in tripartite complex assembly.
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Affiliation(s)
- Robert L. Marshall
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Vassiliy N. Bavro
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- School of Life Sciences, University of Essex, Colchester, United Kingdom
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5
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Johnson RM, Fais C, Parmar M, Cheruvara H, Marshall RL, Hesketh SJ, Feasey MC, Ruggerone P, Vargiu AV, Postis VLG, Muench SP, Bavro VN. Cryo-EM Structure and Molecular Dynamics Analysis of the Fluoroquinolone Resistant Mutant of the AcrB Transporter from Salmonella. Microorganisms 2020; 8:E943. [PMID: 32585951 PMCID: PMC7355581 DOI: 10.3390/microorganisms8060943] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/09/2020] [Accepted: 06/20/2020] [Indexed: 12/31/2022] Open
Abstract
Salmonella is an important genus of Gram-negative pathogens, treatment of which has become problematic due to increases in antimicrobial resistance. This is partly attributable to the overexpression of tripartite efflux pumps, particularly the constitutively expressed AcrAB-TolC. Despite its clinical importance, the structure of the Salmonella AcrB transporter remained unknown to-date, with much of our structural understanding coming from the Escherichia coli orthologue. Here, by taking advantage of the styrene maleic acid (SMA) technology to isolate membrane proteins with closely associated lipids, we report the very first experimental structure of Salmonella AcrB transporter. Furthermore, this novel structure provides additional insight into mechanisms of drug efflux as it bears the mutation (G288D), originating from a clinical isolate of Salmonella Typhimurium presenting an increased resistance to fluoroquinolones. Experimental data are complemented by state-of-the-art molecular dynamics (MD) simulations on both the wild type and G288D variant of Salmonella AcrB. Together, these reveal several important differences with respect to the E. coli protein, providing insights into the role of the G288D mutation in increasing drug efflux and extending our understanding of the mechanisms underlying antibiotic resistance.
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Affiliation(s)
- Rachel M. Johnson
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (R.M.J.); (S.J.H.); (M.C.F.)
| | - Chiara Fais
- Department of Physics, University of Cagliari, s.p. 8, Cittadella Universitaria, 09042 Monserrato, Italy; (C.F.); (P.R.); (A.V.V.)
| | - Mayuriben Parmar
- Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, Leeds LS1 3HE, UK; (M.P.); (V.L.G.P.)
| | - Harish Cheruvara
- Diamond Light Source, Membrane Protein Laboratory (MPL), Diamond House, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK;
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Robert L. Marshall
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK;
| | - Sophie J. Hesketh
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (R.M.J.); (S.J.H.); (M.C.F.)
| | - Matthew C. Feasey
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (R.M.J.); (S.J.H.); (M.C.F.)
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, s.p. 8, Cittadella Universitaria, 09042 Monserrato, Italy; (C.F.); (P.R.); (A.V.V.)
| | - Attilio V. Vargiu
- Department of Physics, University of Cagliari, s.p. 8, Cittadella Universitaria, 09042 Monserrato, Italy; (C.F.); (P.R.); (A.V.V.)
| | - Vincent L. G. Postis
- Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, Leeds LS1 3HE, UK; (M.P.); (V.L.G.P.)
| | - Stephen P. Muench
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (R.M.J.); (S.J.H.); (M.C.F.)
| | - Vassiliy N. Bavro
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
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Shaheen A, Afridi WA, Mahboob S, Sana M, Zeeshan N, Ismat F, Mirza O, Iqbal M, Rahman M. Reserpine Is the New Addition into the Repertoire of AcrB Efflux Pump Inhibitors. Mol Biol 2019. [DOI: 10.1134/s0026893319040113] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ding Y, Wang H, Zheng H, Wang L, Zhang G, Yang J, Lu X, Bai Y, Zhang H, Li J, Gao W, Chen F, Hu S, Wu J, Xu L. Evaluation of drug efficacy based on the spatial position comparison of drug–target interaction centers. Brief Bioinform 2019; 21:762-776. [DOI: 10.1093/bib/bbz024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/28/2019] [Accepted: 02/09/2019] [Indexed: 02/06/2023] Open
Abstract
Abstract
The spatial position and interaction of drugs and their targets is the most important characteristics for understanding a drug’s pharmacological effect, and it could help both in finding new and more precise treatment targets for diseases and in exploring the targeting effects of the new drugs. In this work, we develop a computational pipeline to confirm the spatial interaction relationship of the drugs and their targets and compare the drugs’ efficacies based on the interaction centers. First, we produce a 100-sample set to reconstruct a stable docking model of the confirmed drug–target pairs. Second, we set 5.5 Å as the maximum distance threshold for the drug–amino acid residue atom interaction and construct 3-dimensional interaction surface models. Third, by calculating the spatial position of the 3-dimensional interaction surface center, we develop a comparison strategy for estimating the efficacy of different drug–target pairs. For the 1199 drug–target interactions of the 649 drugs and 355 targets, the drugs that have similar interaction center positions tend to have similar efficacies in disease treatment, especially in the analysis of the 37 targeted relationships between the 15 known anti-cancer drugs and 10 target molecules. Furthermore, the analysis of the unpaired anti-cancer drug and target molecules suggests that there is a potential application for discovering new drug actions using the sampling molecular docking and analyzing method. The comparison of the drug–target interaction center spatial position method better reflect the drug–target interaction situations and could support the discovery of new efficacies among the known anti-cancer drugs.
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Affiliation(s)
- Yu Ding
- Harbin Medical University, Harbin, P. R. China
- Wenzhou Medical University, Wenzhou
| | - Hong Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, P. R. China
| | - Hewei Zheng
- Harbin Medical University, Harbin, P. R. China
- Wenzhou Medical University, Wenzhou
| | - Lianzong Wang
- Harbin Medical University, Harbin, P. R. China
- Wenzhou Medical University, Wenzhou
| | - Guosi Zhang
- Harbin Medical University, Harbin, P. R. China
- Wenzhou Medical University, Wenzhou
| | - Jiaxin Yang
- Harbin Medical University, Harbin, P. R. China
- Wenzhou Medical University, Wenzhou
| | - Xiaoyan Lu
- Harbin Medical University, Harbin, P. R. China
- Wenzhou Medical University, Wenzhou
| | - Yu Bai
- Harbin Medical University, Harbin, P. R. China
- Wenzhou Medical University, Wenzhou
| | - Haotian Zhang
- Harbin Medical University, Harbin, P. R. China
- Wenzhou Medical University, Wenzhou
| | - Jing Li
- Harbin Medical University, Harbin, P. R. China
- Wenzhou Medical University, Wenzhou
| | - Wenyan Gao
- Harbin Medical University, Harbin, P. R. China
- Wenzhou Medical University, Wenzhou
| | - Fukun Chen
- Harbin Medical University, Harbin, P. R. China
- Wenzhou Medical University, Wenzhou
| | - Shui Hu
- Harbin Medical University, Harbin, P. R. China
- Wenzhou Medical University, Wenzhou
| | - Jingqi Wu
- Harbin Medical University, Harbin, P. R. China
- Wenzhou Medical University, Wenzhou
| | - Liangde Xu
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou
- Training Center for Students Innovation and Entrepreneurship Education, Harbin Medical University, Harbin
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Jin J, Hsieh YH, Cui J, Damera K, Dai C, Chaudhary AS, Zhang H, Yang H, Cao N, Jiang C, Vaara M, Wang B, Tai PC. Using Chemical Probes to Assess the Feasibility of Targeting SecA for Developing Antimicrobial Agents against Gram-Negative Bacteria. ChemMedChem 2016; 11:2511-2521. [PMID: 27753464 PMCID: PMC5189635 DOI: 10.1002/cmdc.201600421] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/25/2016] [Indexed: 11/07/2022]
Abstract
With the widespread emergence of drug resistance, there is an urgent need to search for new antimicrobials, especially those against Gram-negative bacteria. Along this line, the identification of viable targets is a critical first step. The protein translocase SecA is commonly believed to be an excellent target for the development of broad-spectrum antimicrobials. In recent years, we developed three structural classes of SecA inhibitors that have proven to be very effective against Gram-positive bacteria. However, we have not achieved the same level of success against Gram-negative bacteria, despite the potent inhibition of SecA in enzyme assays by the same inhibitors. In this study, we use representative inhibitors as chemical probes to gain an understanding as to why these inhibitors were not effective against Gram-negative bacteria. The results validate our initial postulation that the major difference in effectiveness against Gram-positive and Gram-negative bacteria is in the additional permeability barrier posed by the outer membrane of Gram-negative bacteria. We also found that the expression of efflux pumps, which are responsible for multidrug resistance (MDR), have no effect on the effectiveness of these SecA inhibitors. Identification of an inhibitor-resistant mutant and complementation tests of the plasmids containing secA in a secAts mutant showed that a single secA-azi-9 mutation increased the resistance, providing genetic evidence that SecA is indeed the target of these inhibitors in bacteria. Such results strongly suggest SecA as an excellent target for developing effective antimicrobials against Gram-negative bacteria with the intrinsic ability to overcome MDR. A key future research direction should be the optimization of membrane permeability.
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Affiliation(s)
- Jinshan Jin
- Department of Biology, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Ying-Hsin Hsieh
- Department of Biology, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Jianmei Cui
- Department of Chemistry, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Krishna Damera
- Department of Chemistry, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Chaofeng Dai
- Department of Chemistry, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Arpana S. Chaudhary
- Department of Chemistry, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Hao Zhang
- Department of Biology, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Hsiuchin Yang
- Department of Biology, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Nannan Cao
- Department of Biology, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Chun Jiang
- Department of Biology, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Martti Vaara
- Division of Clinical Microbiology, Helsinki University Hospital, FI-00029 HUSLAB, Helsinki, Finland, and Northern Antibiotics Ltd, FI-00720, Helsinki, Finland
| | - Binghe Wang
- Department of Chemistry, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Phang C. Tai
- Department of Biology, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
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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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Aminoacyl β-naphthylamides as substrates and modulators of AcrB multidrug efflux pump. Proc Natl Acad Sci U S A 2016; 113:1405-10. [PMID: 26787896 DOI: 10.1073/pnas.1525143113] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Efflux pumps of the resistance-nodulation division superfamily, such as AcrB, make a major contribution to multidrug resistance in Gram-negative bacteria. Inhibitors of such pumps would improve the efficacy of antibiotics, and ameliorate the crisis in health care caused by the prevalence of multidrug resistant Gram-negative pathogens. Phenylalanyl-arginine β-naphthylamide (PAβN), is a well-known inhibitor of AcrB and its homologs. However, its mechanism of inhibition is not clear. Because the hydrolysis of PAβN in Escherichia coli was nearly entirely dependent on an aminopeptidase, PepN, expression of PepN in periplasm allowed us to carry out a quantitative determination of PAβN efflux kinetics through the determination of its periplasmic concentrations by quantitation of the first hydrolysis product, phenylalanine, after a short period of treatment. We found that PAβN is efficiently pumped out by AcrB, with a sigmoidal kinetics. We also examined the behavior of PAβN homologs, Ala β-naphthylamide, Arg β-naphthylamide, and Phe β-naphthylamide, as substrates of AcrB and as modulators of nitrocefin efflux through AcrB. Furthermore, molecular dynamics simulations indicated that the mode of binding of these compounds to AcrB affects the modulatory activity on the efflux of other substrates. These results, and the finding that PAβN changes the nitrocefin kinetics into a sigmoidal one, suggested that PAβN inhibited the efflux of other drugs by binding to the bottom of the distal binding pocket, the so-called hydrophobic trap, and also by interfering with the binding of other drug substrates to the upper part of the binding pocket.
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