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Catte A, K. Ramaswamy V, Vargiu AV, Malloci G, Bosin A, Ruggerone P. Common recognition topology of mex transporters of Pseudomonas aeruginosa revealed by molecular modelling. Front Pharmacol 2022; 13:1021916. [PMID: 36438787 PMCID: PMC9691783 DOI: 10.3389/fphar.2022.1021916] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/24/2022] [Indexed: 11/13/2022] Open
Abstract
The secondary transporters of the resistance-nodulation-cell division (RND) superfamily mediate multidrug resistance in Gram-negative bacteria like Pseudomonas aeruginosa. Among these RND transporters, MexB, MexF, and MexY, with partly overlapping specificities, have been implicated in pathogenicity. Only the structure of the former has been resolved experimentally, which together with the lack of data about the functional dynamics of the full set of transporters, limited a systematic investigation of the molecular determinants defining their peculiar and shared features. In a previous work (Ramaswamy et al., Front. Microbiol., 2018, 9, 1144), we compared at an atomistic level the two main putative recognition sites (named access and deep binding pockets) of MexB and MexY. In this work, we expand the comparison by performing extended molecular dynamics (MD) simulations of these transporters and the pathologically relevant transporter MexF. We employed a more realistic model of the inner phospholipid membrane of P. aeruginosa and more accurate force-fields. To elucidate structure/dynamics-activity relationships we performed physico-chemical analyses and mapped the binding propensities of several organic probes on all transporters. Our data revealed the presence, also in MexF, of a few multifunctional sites at locations equivalent to the access and deep binding pockets detected in MexB. Furthermore, we report for the first time about the multidrug binding abilities of two out of five gates of the channels deputed to peripheral (early) recognition of substrates. Overall, our findings help to define a common “recognition topology” characterizing Mex transporters, which can be exploited to optimize transport and inhibition propensities of antimicrobial compounds.
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Bharatham N, Bhowmik P, Aoki M, Okada U, Sharma S, Yamashita E, Shanbhag AP, Rajagopal S, Thomas T, Sarma M, Narjari R, Nagaraj S, Ramachandran V, Katagihallimath N, Datta S, Murakami S. Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae. Nat Commun 2021; 12:5400. [PMID: 34518546 PMCID: PMC8437966 DOI: 10.1038/s41467-021-25679-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 08/20/2021] [Indexed: 02/08/2023] Open
Abstract
OqxB is an RND (Resistance-Nodulation-Division) efflux pump that has emerged as a factor contributing to the antibiotic resistance in Klebsiella pneumoniae. OqxB underwent horizontal gene transfer and is now seen in other Gram-negative bacterial pathogens including Escherichia coli, Enterobacter cloacae and Salmonella spp., further disseminating multi-drug resistance. In this study, we describe crystal structure of OqxB with n-dodecyl-β-D-maltoside (DDM) molecules bound in its substrate-binding pocket, at 1.85 Å resolution. We utilize this structure in computational studies to predict the key amino acids contributing to the efflux of fluoroquinolones by OqxB, distinct from analogous residues in related transporters AcrB and MexB. Finally, our complementation assays with mutated OqxB and minimum inhibitory concentration (MIC) experiments with clinical isolates of E. coli provide further evidence that the predicted structural features are indeed involved in ciprofloxacin efflux.
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Affiliation(s)
- Nagakumar Bharatham
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Purnendu Bhowmik
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Maho Aoki
- grid.32197.3e0000 0001 2179 2105Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ui Okada
- grid.32197.3e0000 0001 2179 2105Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Sreevalli Sharma
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Eiki Yamashita
- grid.136593.b0000 0004 0373 3971Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Anirudh P. Shanbhag
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | - Sreenath Rajagopal
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | - Teby Thomas
- grid.418280.70000 0004 1794 3160St. John’s Research Institute, Bengaluru, Karnataka India
| | - Maitrayee Sarma
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | - Riya Narjari
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | | | - Vasanthi Ramachandran
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Nainesh Katagihallimath
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Santanu Datta
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | - Satoshi Murakami
- grid.32197.3e0000 0001 2179 2105Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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Emergence of two AcrB substitutions conferring multidrug resistance to Salmonella spp. Antimicrob Agents Chemother 2021; 65:AAC.01589-20. [PMID: 33685897 PMCID: PMC8092907 DOI: 10.1128/aac.01589-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
AcrAB-TolC is a major tripartite multidrug efflux pump conferring resistance to a wide variety of compounds in Gram-negative pathogens. Many AcrB mutants have been constructed through site-directed mutagenesis to probe the mechanism of AcrB function in antibiotic resistance. However, much less is known about the actual drug resistance related mutants that naturally occur in clinically isolated pathogens. Here, we report two novel AcrB substitutions, M78I and P319L, in clinically isolated Salmonella strains with high-level ciprofloxacin resistance. Plasmids expressing the detected acrB mutations were constructed and introduced into SL1344△acrB Antimicrobial susceptibility assay showed that all AcrB M78I, AcrB P319L and AcrB M78I/319L conferred reduced susceptibilities to multiple substrates, including fluoroquinolones, erythromycin, tetracyclines, bile salts and dyes. Site-directed mutagenesis and MIC results revealed that increased hydrophobicity of M78I was one of the reasons why AcrB M78I had lower susceptibility to fluoroquinolones. Fluorescence labeling experiments suggested that the AcrB M78I substitution enhanced the binding of substrates to certain amino acid sites in the efflux pathway (e.g., site Q89, E673 and F617) and weakened the binding to other amino acids (e.g., S134 and N274). Structural modeling disclosed the increased flexibility of Leu was favorable for the functional rotation of AcrB compared to the original Pro. AcrA 319L makes the functional rotation of AcrB more flexible, this enables substrate efflux more efficiently. In order to understand the mechanism of AcrAB-TolC drug efflux well, interaction between AcrA and AcrB in the role of substrate efflux of AcrAB-TolC should be further investigated.
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Jesin JA, Stone TA, Mitchell CJ, Reading E, Deber CM. Peptide-Based Approach to Inhibition of the Multidrug Resistance Efflux Pump AcrB. Biochemistry 2020; 59:3973-3981. [PMID: 33026802 DOI: 10.1021/acs.biochem.0c00417] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Clinically relevant multidrug-resistant bacteria often arise due to overproduction of membrane-embedded efflux proteins that are capable of pumping antibiotics out of the bacterial cell before the drugs can exert their intended toxic effect. The Escherichia coli membrane protein AcrB is the archetypal protein utilized for bacterial efflux study because it can extrude a diverse range of antibiotic substrates and has close homologues in many Gram-negative pathogens. Three AcrB subunits, each of which contains 12 transmembrane (TM) helices, are known to trimerize to form the minimal functional unit, stabilized noncovalently by helix-helix interactions between TM1 and TM8. To inhibit the efflux activity of AcrB, we have rationally designed synthetic peptides aimed at destabilizing the AcrB trimerization interface by outcompeting the subunit interaction sites within the membrane. Here we report that peptides mimicking TM1 or TM8, with flanking N-terminal peptoid tags, and C-terminal lysine tags that aid in directing the peptides to their membrane-embedded target, decrease the AcrB-mediated efflux of the fluorescent substrate Nile red and potentiate the effect of the antimicrobials chloramphenicol and ethidium bromide. To further characterize the motif encompassing the interaction between TM1 and TM8, we used Förster resonance energy transfer to demonstrate dimerization. Using the TM1 and TM8 peptides, in conjunction with several selected mutant peptides, we highlight residues that may increase the potency and specificity of the peptide drug candidates. In targeting membrane-embedded protein-protein interactions, this work represents a novel approach to AcrB inhibition and, more broadly, a potential route to a new category of efflux pump inhibitors.
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Affiliation(s)
- Joshua A Jesin
- Division of Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto M5G 0A4, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Tracy A Stone
- Division of Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto M5G 0A4, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Chloe J Mitchell
- Division of Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto M5G 0A4, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Eamonn Reading
- Department of Chemistry, Britannia House, King's College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Charles M Deber
- Division of Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto M5G 0A4, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Ontario, Canada
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