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Rathod S, Dey S, Pawar S, Dhavale R, Choudhari P, Rajakumara E, Mahuli D, Bhagwat D, Tamboli Y, Sankpal P, Mali S, More H. Identification of potential biogenic chalcones against antibiotic resistant efflux pump (AcrB) via computational study. J Biomol Struct Dyn 2024; 42:5178-5196. [PMID: 37340697 DOI: 10.1080/07391102.2023.2225099] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/09/2023] [Indexed: 06/22/2023]
Abstract
The cases of bacterial multidrug resistance are increasing every year and becoming a serious concern for human health. Multidrug efflux pumps are key players in the formation of antibiotic resistance, which transfer out a broad spectrum of drugs from the cell and convey resistance to the host. Efflux pumps have significantly reduced the efficacy of the previously available antibiotic armory, thereby increasing the frequency of therapeutic failures. In gram-negative bacteria, the AcrAB-TolC efflux pump is the principal transporter of the substrate and plays a major role in the formation of antibiotic resistance. In the current work, advanced computer-aided drug discovery approaches were utilized to find hit molecules from the library of biogenic chalcones against the bacterial AcrB efflux pump. The results of the performed computational studies via molecular docking, drug-likeness prediction, pharmacokinetic profiling, pharmacophore mapping, density functional theory, and molecular dynamics simulation study provided ZINC000004695648, ZINC000014762506, ZINC000014762510, ZINC000095099506, and ZINC000085510993 as stable hit molecules against the AcrB efflux pumps. Identified hits could successfully act against AcrB efflux pumps after optimization as lead molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Sreenath Dey
- Department of Biotechnology, Indian Institute of Technology, Hyderabad, Kandi, Sangareddy, Telangana, India
| | - Swaranjali Pawar
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Rakesh Dhavale
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Eerappa Rajakumara
- Department of Biotechnology, Indian Institute of Technology, Hyderabad, Kandi, Sangareddy, Telangana, India
| | - Deepak Mahuli
- Department of Pharmacology, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Durgacharan Bhagwat
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Yasinalli Tamboli
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Poournima Sankpal
- Department of Pharmaceutical Chemistry, Ashokrao Mane College of Pharmacy, Kolhapur, MS, India
| | - Sachin Mali
- Department of Pharmaceutics, Y. D. Mane College of Pharmacy, Kagal, MS, India Kolhapur
| | - Harinath More
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
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2
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Klenotic PA, Yu EW. Structural analysis of resistance-nodulation cell division transporters. Microbiol Mol Biol Rev 2024; 88:e0019823. [PMID: 38551344 DOI: 10.1128/mmbr.00198-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024] Open
Abstract
SUMMARYInfectious bacteria have both intrinsic and acquired mechanisms to combat harmful biocides that enter the cell. Through adaptive pressures, many of these pathogens have become resistant to many, if not all, of the current antibiotics used today to treat these often deadly infections. One prominent mechanism is the upregulation of efflux systems, especially the resistance-nodulation-cell division class of exporters. These tripartite systems consist of an inner membrane transporter coupled with a periplasmic adaptor protein and an outer membrane channel to efficiently transport a diverse array of substrates from inside the cell to the extracellular space. Detailed mechanistic insight into how these inner membrane transporters recognize and shuttle their substrates can ultimately inform both new antibiotic and efflux pump inhibitor design. This review examines the structural basis of substrate recognition of these pumps and the molecular mechanisms underlying multidrug extrusion, which in turn mediate antimicrobial resistance in bacterial pathogens.
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Affiliation(s)
- Philip A Klenotic
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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Tambat R, Kinthada RK, Saral Sariyer A, Leus IV, Sariyer E, D'Cunha N, Zhou H, Leask M, Walker JK, Zgurskaya HI. AdeIJK Pump-Specific Inhibitors Effective against Multidrug Resistant Acinetobacter baumannii. ACS Infect Dis 2024; 10:2239-2249. [PMID: 38787939 DOI: 10.1021/acsinfecdis.4c00190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Multidrug-resistant Acinetobacter baumannii is a serious threat pathogen rapidly spreading in clinics and causing a range of complicated human infections. The major contributor to A. baumannii antibiotic resistance is the overproduction of AdeIJK and AdeABC multidrug efflux pumps of the resistance-nodulation-division (RND) superfamily of proteins. The dominant role of efflux in antibiotic resistance and the relatively high permeability of the A. baumannii outer membrane to amphiphilic compounds make this pathogen a promising target for the discovery of clinically relevant efflux pump inhibitors. In this study, we identified 4,6-diaminoquoniline analogs with inhibitory activities against A. baumannii AdeIJK efflux pump and followed up on these compounds with a focused synthetic program to improve the target specificity and to reduce cytotoxicity. We identified several candidates that potentiate antibacterial activities of antibiotics erythromycin, tetracycline, and novobiocin not only in the laboratory antibiotic susceptible strain A. baumannii ATCC17978 but also in multidrug-resistant clinical isolates AB5075 and AYE. The best analogs potentiated the activities of antibiotics in low micromolar concentrations, did not have antibacterial activities on their own, inhibited AdeIJK-mediated efflux of its fluorescent substrate ethidium ion, and had low cytotoxicity in A549 human lung epithelial cells.
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Affiliation(s)
- Rushikesh Tambat
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Rama Kumar Kinthada
- School of Medicine, Saint Louis University, St. Louis, Missouri 63110, United States
| | - Aysegul Saral Sariyer
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Artvin Coruh University, 08000 Artvin, Turkey
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Emrah Sariyer
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Artvin Coruh University, 08000 Artvin, Turkey
- Vocational School of Health Services, Medical Laboratory Techniques, Artvin Coruh University, 08000 Artvin, Turkey
| | - Napoleon D'Cunha
- School of Medicine, Saint Louis University, St. Louis, Missouri 63110, United States
| | - Hinman Zhou
- School of Medicine, Saint Louis University, St. Louis, Missouri 63110, United States
| | - Makaila Leask
- School of Medicine, Saint Louis University, St. Louis, Missouri 63110, United States
| | - John K Walker
- School of Medicine, Saint Louis University, St. Louis, Missouri 63110, United States
- Department of Chemistry, Saint Louis University, St. Louis, Missouri 63110, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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Ding L, Wu Z, Zhang J, Zhao Q, Chen X, Jia Z, He D. Embedded monitoring system and teaching of artificial intelligence online drug component recognition. Open Life Sci 2024; 19:20220795. [PMID: 38867921 PMCID: PMC11167706 DOI: 10.1515/biol-2022-0795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/25/2023] [Accepted: 11/05/2023] [Indexed: 06/14/2024] Open
Abstract
Drug testing has many test elements. It aims to prevent unqualified drugs from entering the market and ensure drug safety. The existing artificial intelligence (AI) online monitoring system identifies active ingredients in the process of use. Owing to their openness, data are easy to be lost, failing to meet user needs and inducing a specific impact on the use of the monitoring system. With the continuous development of computer and measurement technologies, various biochemical data are increasing at an unprecedented speed, and numerous databases are emerging. Extracting patterns from considerable known data and experimental facts is an essential task for a wide range of biological and chemical workers. Pattern recognition is one of the essential technologies for data mining. It is widely used in industry, agriculture, national defense, biomedicine, meteorology, astronomy, and other fields. To improve the effect of the online drug ingredient recognition system, this study used AI to design an online drug ingredient recognition-embedded monitoring system and applied AI to the teaching field to improve teaching efficiency. First, this study constructed the framework of the AI online drug ingredient recognition-embedded monitoring system and introduced the process of online drug ingredient recognition. Then, it introduced the pattern recognition method, constructed the pattern recognition system, and presented the pattern recognition algorithm and the algorithm evaluation index. Afterward, it used pattern recognition to conduct a qualitative analysis of the infrared spectrum of drug components and introduced the overall process of the qualitative analysis. In addition, this study employed AI to implement changes to the embedded system instruction in colleges and universities, summarizing the current issues. The impact of drug component recognition and the educational impact of embedded systems were investigated in the experimental portion. The experimental findings demonstrated the excellent accuracy, sensitivity, specificity, and Matthew correlation coefficient of the online drug component recognition-integrated monitoring system in this work. Compared with that of other systems, its average drug component recognition accuracy was above 0.85. Students in five majors reported high levels of satisfaction with the embedded system teaching, which is better for delivering college instruction.
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Affiliation(s)
- Li Ding
- Materia Medica Development Group, Institute of Medicinal Chemistry, Lanzhou University School of Pharmacy, Lanzhou 730000, China
- The No. 2 People's Hospital of Lanzhou, Lanzhou 730000, China
| | - Zhengrong Wu
- Materia Medica Development Group, Institute of Medicinal Chemistry, Lanzhou University School of Pharmacy, Lanzhou 730000, China
| | - Junmin Zhang
- Materia Medica Development Group, Institute of Medicinal Chemistry, Lanzhou University School of Pharmacy, Lanzhou 730000, China
| | - Quanyi Zhao
- Materia Medica Development Group, Institute of Medicinal Chemistry, Lanzhou University School of Pharmacy, Lanzhou 730000, China
| | - Xiaoling Chen
- Materia Medica Development Group, Institute of Medicinal Chemistry, Lanzhou University School of Pharmacy, Lanzhou 730000, China
- The No. 2 People's Hospital of Lanzhou, Lanzhou 730000, China
| | - Zhong Jia
- Materia Medica Development Group, Institute of Medicinal Chemistry, Lanzhou University School of Pharmacy, Lanzhou 730000, China
- The No. 2 People's Hospital of Lanzhou, Lanzhou 730000, China
| | - Dian He
- Materia Medica Development Group, Institute of Medicinal Chemistry, Lanzhou University School of Pharmacy, Lanzhou 730000, China
- The No. 2 People's Hospital of Lanzhou, Lanzhou 730000, China
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5
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Lu W, Lu H, Huo X, Wang C, Zhang Z, Zong B, Wang G, Dong W, Li X, Li Y, Chen H, Tan C. EvfG is a multi-function protein located in the Type VI secretion system for ExPEC. Microbiol Res 2024; 283:127647. [PMID: 38452551 DOI: 10.1016/j.micres.2024.127647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/22/2024] [Accepted: 02/10/2024] [Indexed: 03/09/2024]
Abstract
The Type VI secretion system (T6SS) functions as a protein transport nanoweapon in several stages of bacterial life. Even though bacterial competition is the primary function of T6SS, different bacteria exhibit significant variations. Particularly in Extraintestinal pathogenic Escherichia coli (ExPEC), research into T6SS remains relatively limited. This study identified the uncharacterized gene evfG within the T6SS cluster of ExPEC RS218. Through our experiments, we showed that evfG is involved in T6SS expression in ExPEC RS218. We also found evfG can modulate T6SS activity by competitively binding to c-di-GMP, leading to a reduction in the inhibitory effect. Furthermore, we found that evfG can recruit sodA to alleviate oxidative stress. The research shown evfG controls an array of traits, both directly and indirectly, through transcriptome and additional tests. These traits include cell adhesion, invasion, motility, drug resistance, and pathogenicity of microorganisms. Overall, we contend that evfG serves as a multi-functional regulator for the T6SS and several crucial activities. This forms the basis for the advancement of T6SS function research, as well as new opportunities for vaccine and medication development.
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Affiliation(s)
- Wenjia Lu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; Hubei Hongshan Laboratory, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Hao Lu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Xinyu Huo
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Chenchen Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Zhaoran Zhang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Bingbing Zong
- School of animal science and nutrition engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Gaoyan Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Wenqi Dong
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Xiaodan Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Yuying Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; Hubei Hongshan Laboratory, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Chen Tan
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; Hubei Hongshan Laboratory, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China.
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6
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Bailey ZM, Igler C, Wendling CC. Prophage maintenance is determined by environment-dependent selective sweeps rather than mutational availability. Curr Biol 2024; 34:1739-1749.e7. [PMID: 38599209 DOI: 10.1016/j.cub.2024.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 01/19/2024] [Accepted: 03/14/2024] [Indexed: 04/12/2024]
Abstract
Prophages, viral sequences integrated into bacterial genomes, can be beneficial and costly. Despite the risk of prophage activation and subsequent bacterial death, active prophages are present in most bacterial genomes. However, our understanding of the selective forces that maintain prophages in bacterial populations is limited. Combining experimental evolution with stochastic modeling, we show that prophage maintenance and loss are primarily determined by environmental conditions that alter the net fitness effect of a prophage on its bacterial host. When prophages are too costly, they are rapidly lost through environment-specific sequences of selective sweeps. Conflicting selection pressures that select against the prophage but for a prophage-encoded accessory gene can maintain prophages. The dynamics of prophage maintenance additionally depend on the sociality of this accessory gene. Prophage-encoded genes that exclusively benefit the lysogen maintain prophages at higher frequencies compared with genes that benefit the entire population. That is because the latter can protect phage-free "cheaters," reducing the benefit of maintaining the prophage. Our simulations suggest that environmental variation plays a larger role than mutation rates in determining prophage maintenance. These findings highlight the complexity of selection pressures that act on mobile genetic elements and challenge our understanding of the role of environmental factors relative to random chance events in shaping the evolutionary trajectory of bacterial populations. By shedding light on the key factors that shape microbial populations in the face of environmental changes, our study significantly advances our understanding of the complex dynamics of microbial evolution and diversification.
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Affiliation(s)
- Zachary M Bailey
- Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland.
| | - Claudia Igler
- Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland; Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK
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7
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Manrique PD, Leus IV, López CA, Mehla J, Malloci G, Gervasoni S, Vargiu AV, Kinthada RK, Herndon L, Hengartner NW, Walker JK, Rybenkov VV, Ruggerone P, Zgurskaya HI, Gnanakaran S. Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors. Commun Chem 2024; 7:84. [PMID: 38609430 PMCID: PMC11015012 DOI: 10.1038/s42004-024-01161-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
The ability Gram-negative pathogens have at adapting and protecting themselves against antibiotics has increasingly become a public health threat. Data-driven models identifying molecular properties that correlate with outer membrane (OM) permeation and growth inhibition while avoiding efflux could guide the discovery of novel classes of antibiotics. Here we evaluate 174 molecular descriptors in 1260 antimicrobial compounds and study their correlations with antibacterial activity in Gram-negative Pseudomonas aeruginosa. The descriptors are derived from traditional approaches quantifying the compounds' intrinsic physicochemical properties, together with, bacterium-specific from ensemble docking of compounds targeting specific MexB binding pockets, and all-atom molecular dynamics simulations in different subregions of the OM model. Using these descriptors and the measured inhibitory concentrations, we design a statistical protocol to identify predictors of OM permeation/inhibition. We find consistent rules across most of our data highlighting the role of the interaction between the compounds and the OM. An implementation of the rules uncovered in our study is shown, and it demonstrates the accuracy of our approach in a set of previously unseen compounds. Our analysis sheds new light on the key properties drug candidates need to effectively permeate/inhibit P. aeruginosa, and opens the gate to similar data-driven studies in other Gram-negative pathogens.
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Affiliation(s)
- Pedro D Manrique
- Physics Department, George Washington University, Washington, 20052, DC, USA.
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - César A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - Jitender Mehla
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Silvia Gervasoni
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Rama K Kinthada
- Department of Pharmacology and Physiology, Saint Louis University, St. Louis, 63103, MO, USA
| | - Liam Herndon
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - John K Walker
- Department of Pharmacology and Physiology, Saint Louis University, St. Louis, 63103, MO, USA
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA.
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8
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Shang Y, Zhang Y, Wang R, Peng Y, Ding B, Liu Y, Li C, Feng L, Liu H, Yang C, Tang Y. Deciphering the molecular and functional basis of TMexCD1: the plasmid-encoded efflux pump of resistance-nodulation-division superfamily. Antimicrob Agents Chemother 2024; 68:e0167823. [PMID: 38477539 PMCID: PMC10989000 DOI: 10.1128/aac.01678-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
Horizontal gene transfer has been demonstrated to be an important driver for the emergency of multidrug-resistant pathogens. Recently, a transferable gene cluster tmexCD1-toprJ1 of the resistance-nodulation-division (RND) superfamily was identified in the plasmids of animal-derived Klebsiella pneumoniae strains, with a higher efflux capacity for various drugs than the Escherichia coli AcrAB-TolC homolog system. In this study, we focused on the differences in the inner membrane pump of these two systems and identified some key residues that contribute to the robust efflux activity of the TMexCD1 system. With the aid of homologous modeling and molecular docking, eight residues from the proximal binding pocket (PBP) and nine from the distal binding pocket (DBP) were selected and subjected to site-directed mutagenesis. Several of them, such as S134, I139, D181, and A290, were shown to be important for substrate binding in the DBP region, and all residues in PBP and DBP showed certain substrate preferences. Apart from the conservative switch loop (L613-623TMexD1) previously identified in the E. coli AcrB (EcAcrB), a relatively unconservative loop (L665-675TMexD1) at the bottom of PBP was proposed as a critical element for the robust activity of TMexD1, due to variations at sites E669, G670, N673, and S674 compared to EcAcrAB, and the significantly altered efflux activity due to their mutations. The conservation and flexibility of these key factors can contribute to the evolution of the RND efflux pumps and thus serve as potential targets for developing inhibitors to block the widespread of the TMexCD1 system.
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Affiliation(s)
- Yan Shang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ye Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Ruimin Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yishu Peng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Bo Ding
- Shandong Institute for Food and Drug Control, Jinan, China
- School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Yuanxiang Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Chongzhou Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Luhua Feng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Honglei Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Chunyu Yang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yajie Tang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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9
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Gambino M, Sørensen MCH. Flagellotropic phages: common yet diverse host interaction strategies. Curr Opin Microbiol 2024; 78:102451. [PMID: 38452595 DOI: 10.1016/j.mib.2024.102451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/14/2024] [Accepted: 02/10/2024] [Indexed: 03/09/2024]
Abstract
Many bacteriophages (phages) interact with flagella and rely on bacterial motility for successful infection of their hosts. Yet, limited information is available on how phages have evolved to recognize and bind both flagella and subsequent surface receptors for phage DNA injection. Here, we present an update on the current knowledge of flagellotropic phages using a few well-studied phages as examples to unravel the molecular details of bacterial host recognition. We discuss the recent advances in the role of globular exposed flagellin domains and flagella glycosylation in phage binding to the flagella. In addition, we present diverse types of surface receptors and phage components responsible for the interaction with the host. Finally, we point to questions remaining to be answered and new approaches to study this unique group of phages.
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Affiliation(s)
- Michela Gambino
- Institute of Conservation, Royal Danish Academy, Copenhagen, Denmark
| | - Martine C H Sørensen
- Section of Food Safety and Zoonoses, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.
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10
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Wang W, Ma Y, Ma Y, Zheng X, Yu J, Li L, Liu X, Gao H, Xu H, Wang M. Significant Impact of AcrB Amino Acid Polymorphism at Residue 716 on Susceptibility to Tigecycline and Other Antibiotics in Klebsiella pneumoniae. ACS Infect Dis 2024; 10:541-552. [PMID: 38181222 DOI: 10.1021/acsinfecdis.3c00478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2024]
Abstract
AcrAB-TolC is a multidrug RND-type efflux pump that is widespread in Gram-negative bacteria. As the substrate-binding subunit, AcrB was shown to modulate antimicrobial resistance in Escherichia coli, but the influence of AcrB mutation on Klebsiella pneumoniae, a major clinical pathogen, has not been well-studied. The finding of an R716L mutation in AcrB in a clinical tigecycline-nonsusceptible K. pneumoniae S1 strain inspired us to probe the role of AcrB residue 716 in antimicrobial resistance. This residue was subsequently subjected to saturation mutagenesis, followed by antibiotic susceptibility tests, survival assays, and antibiotic accumulation assays, showing strong influences of AcrB mutation on antimicrobial resistance. In particular, resistance levels to azithromycin, tetracycline, tigecycline, and cefoxitin were significantly changed by AcrB mutation at residue 716. Mutations to charged residues, polar residues, and residues that disrupt secondary structures have particularly reduced the antimicrobial susceptibility of bacteria, except for azithromycin, and the impact is not due to the abolishment of the efflux function of the pump. Therefore, it is concluded that residue 716 is an important residue that significantly influences antimicrobial resistance in K. pneumoniae, adding to our understanding of antimicrobial resistance mechanisms in this key clinical pathogen.
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Affiliation(s)
- Wenjia Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong 266237, China
| | - Yanan Ma
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong 266237, China
| | - Yueyi Ma
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong 266237, China
| | - Xinrou Zheng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong 266237, China
| | - Jianghao Yu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong 266237, China
| | - Ling Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong 266237, China
| | - Xuedong Liu
- Qingdao Hospital, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, Shandong 266011, China
| | - Haidong Gao
- Oncology Laboratory, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, Shandong 266035, China
| | - Hai Xu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong 266237, China
| | - Mingyu Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong 266237, China
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11
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Wilhelm J, Pos KM. Molecular insights into the determinants of substrate specificity and efflux inhibition of the RND efflux pumps AcrB and AdeB. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001438. [PMID: 38358391 PMCID: PMC10924465 DOI: 10.1099/mic.0.001438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/30/2024] [Indexed: 02/16/2024]
Abstract
Gram-negative bacterial members of the Resistance Nodulation and cell Division (RND) superfamily form tripartite efflux pump systems that span the cell envelope. One of the intriguing features of the multiple drug efflux members of this superfamily is their ability to recognize different classes of antibiotics, dyes, solvents, bile salts, and detergents. This review provides an overview of the molecular mechanisms of multiple drug efflux catalysed by the tripartite RND efflux system AcrAB-TolC from Eschericha coli. The determinants for sequential or simultaneous multiple substrate binding and efflux pump inhibitor binding are discussed. A comparison is made with the determinants for substrate binding of AdeB from Acinetobacter baumannii, which acts within the AdeABC multidrug efflux system. There is an apparent general similarity between the structures of AcrB and AdeB and their substrate specificity. However, the presence of distinct conformational states and different drug efflux capacities as revealed by single-particle cryo-EM and mutational analysis suggest that the drug binding and transport features exhibited by AcrB may not be directly extrapolated to the homolog AdeB efflux pump.
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Affiliation(s)
- Julia Wilhelm
- Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Klaas Martinus Pos
- Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
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12
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Pos KM. RND multidrug efflux transporters: similar appearances, diverse actions. J Bacteriol 2024; 206:e0040323. [PMID: 38084964 PMCID: PMC10810212 DOI: 10.1128/jb.00403-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
In a recent study by Inga V. Leus, Sean R. Roberts, Anhthu Trinh, Edward W. Yu, and Helen I. Zgurskaya (J Bacteriol, 2023, https://doi.org/10.1128/jb.00217-23), it was found that the clinically relevant resistance-nodulation-cell division (RND)-type AdeABC antibiotic efflux pump from Acinetobacter baumannii exhibits close communication between its antibiotic binding sites. Alterations in one of them can have far-reaching impacts on the drug translocation pathway. These insights could reshape our understanding of RND-type efflux pump mechanisms.
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Affiliation(s)
- Klaas Martinus Pos
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt, Germany
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13
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Leus IV, Roberts SR, Trinh A, W. Yu E, Zgurskaya HI. Nonadditive functional interactions between ligand-binding sites of the multidrug efflux pump AdeB from Acinetobacter baumannii. J Bacteriol 2024; 206:e0021723. [PMID: 37850798 PMCID: PMC10809976 DOI: 10.1128/jb.00217-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/12/2023] [Indexed: 10/19/2023] Open
Abstract
Multidrug efflux is one of the major mechanisms of antibiotic resistance identified in clinical isolates of the human pathogen Acinetobacter baumannii. The multiple antibiotic resistance in this species is often enabled by the overproduction of the tripartite efflux pump AdeABC. In this pump, AdeB is the inner membrane transporter from the resistance-nodulation-division (RND) superfamily of proteins, which is responsible for the recognition and efflux of multiple structurally unrelated compounds. Like other RND transporters, AdeB is a trimeric protein with ligand-binding sites located in the large periplasmic domains. Previous structural studies, however, highlighted the uniqueness of AdeB interactions with ligands. Up to three ligand molecules were bound to one protomer of AdeB, mapping its substrate translocation path. In this study, we introduced single and double substitutions in the identified ligand-binding sites of AdeB. Our results show that the mechanism of substrate translocation by AdeB is different from that of other characterized RND transporters and that the functional interactions between the sites are nonadditive. We identified AdeB mutants with both the loss and the gain of antibiotic susceptibility phenotypes, as well as AdeB mutations making A. baumannii cells overproducing such pump variants even more susceptible to multiple antibiotics than efflux-deficient cells. IMPORTANCE Multidrug efflux pumps of the resistance-nodulation-division superfamily of proteins are important contributors to various aspects of bacterial physiology and antibiotic resistance. Studies of the best-characterized model transporter AcrB from Escherichia coli suggested that these transporters operate by a functional rotation mechanism in which various substrates bind to at least two different binding sites. This study suggests that the mechanism of AdeB is distinct and that the binding sites in this transporter are functionally linked.
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Affiliation(s)
- Inga V. Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Sean R. Roberts
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Anhthu Trinh
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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14
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Roy RK, Patra N. Probing the pH Sensitivity of OprM: Insights into Metastable States and Semi-Open Conformation. J Phys Chem B 2024; 128:622-634. [PMID: 38047375 DOI: 10.1021/acs.jpcb.3c05384] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Efflux pumps are specialized transport proteins that play a key role in the bacterial defense against a wide spectrum of antibiotics. Hence, understanding the biophysical mechanism associated with this complex system of drug expulsion becomes crucial. This work deals with some vital aspects of the outer membrane factor (OMF) of MexAB-OprM. After being passed through MexB and MexA, efflux substrates have to go through OprM for their final judgment. Thus, it is very important to understand the periplasmic pore opening mechanism and the associated biophysical changes during this process. Our study captures a detailed analysis of the pore opening mechanism involving OprM. With powerful molecular dynamics (MD) techniques such as well-tempered metadynamics, the presence of metastable states in between open and closed states was confirmed. Also, upon mutating R376, the energy barrier for the conversion of the close to open conformation decreases, indicating an important role played by the residue. Further, constant pH MD was performed to capture the effect of pH in both conformations. OprM exhibits distinct conformational states at pH values greater than 5.5 and lower than 5.5, suggesting its pH-responsive characteristics. Overall, our study elucidates a crucial undertaking toward discovering potential inhibitors for MexAB-OprM efflux pumps.
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Affiliation(s)
- Rakesh Kumar Roy
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| | - Niladri Patra
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
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15
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Rathod S, Dey S, Choudhari P, Mahuli D, Rochlani S, Dhavale R, Chaudhari S, Tamboli Y, Kilbile J, Rajakumara E. High-throughput computational screening for identification of potential hits against bacterial Acriflavine resistance protein B (AcrB) efflux pump. J Biomol Struct Dyn 2024:1-17. [PMID: 38264919 DOI: 10.1080/07391102.2024.2302936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
Antibiotic resistance is a pressing global health challenge, driven in part by the remarkable efflux capabilities of efflux pump in AcrB (Acriflavine Resistance Protein B) protein in Gram-negative bacteria. In this study, a multi-approached computational screening strategy encompassing molecular docking, In silico absorption, distribution, metabolism, excretion and toxicity (ADMET) analysis, druglikeness assessment, molecular dynamics simulations and density functional theory studies was employed to identify novel hits capable of acting against AcrB-mediated antibiotic resistance. Ligand library was acquired from the COCONUT database. Performed computational analyses unveiled four promising hit molecules (CNP0298667, CNP0399927, CNP0321542 and CNP0269513). Notably, CNP0298667 exhibited the highest negative binding affinity of -11.5 kcal/mol, indicating a possibility of strong potential to disrupt AcrB function. Importantly, all four hits met stringent druglikeness criteria and demonstrated favorable in silico ADMET profiles, underscoring their potential for further development. MD simulations over 100 ns revealed that the CNP0321542-4DX5 and CNP0269513-4DX5 complexes formed robust and stable interactions with the AcrB efflux pump. The identified hits represent a promising starting point for the design and optimization of novel therapeutics aimed at combating AcrB-mediated antibiotic resistance in Gram-negative bacteria.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Sreenath Dey
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology, Hyderabad, Sangareddy, India
| | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Deepak Mahuli
- Department of Pharmacology, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Sneha Rochlani
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Rakesh Dhavale
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Somdatta Chaudhari
- Department of Pharmaceutical Chemistry, Progressive Education Society's Modern College of Pharmacy, Nigdi, India
| | - Yasinalli Tamboli
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Jaydeo Kilbile
- University Department of Basic and Applied Sciences (Chemistry), MGM University, Aurangabad, India
| | - Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology, Hyderabad, Sangareddy, India
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16
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Geng X, Yang YJ, Li Z, Ge WB, Xu X, Liu XW, Li JY. Fingolimod Inhibits Exopolysaccharide Production and Regulates Relevant Genes to Eliminate the Biofilm of K. pneumoniae. Int J Mol Sci 2024; 25:1397. [PMID: 38338675 PMCID: PMC10855953 DOI: 10.3390/ijms25031397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Klebsiella pneumoniae (K. pneumoniae) exhibits the ability to form biofilms as a means of adapting to its adverse surroundings. K. pneumoniae in this biofilm state demonstrates remarkable resistance, evades immune system attacks, and poses challenges for complete eradication, thereby complicating clinical anti-infection efforts. Moreover, the precise mechanisms governing biofilm formation and disruption remain elusive. Recent studies have discovered that fingolimod (FLD) exhibits biofilm properties against Gram-positive bacteria. Therefore, the antibiofilm properties of FLD were evaluated against multidrug-resistant (MDR) K. pneumoniae in this study. The antibiofilm activity of FLD against K. pneumoniae was assessed utilizing the Alamar Blue assay along with confocal laser scanning microscopy (CLSM), scanning electron microscopy (SEM), and crystal violet (CV) staining. The results showed that FLD effectively reduced biofilm formation, exopolysaccharide (EPS), motility, and bacterial abundance within K. pneumoniae biofilms without impeding its growth and metabolic activity. Furthermore, the inhibitory impact of FLD on the production of autoinducer-2 (AI-2) signaling molecules was identified, thereby demonstrating its notable anti-quorum sensing (QS) properties. The results of qRT-PCR analysis demonstrated that FLD significantly decreased the expression of genes associated with the efflux pump gene (AcrB, kexD, ketM, kdeA, and kpnE), outer membrane (OM) porin proteins (OmpK35, OmpK36), the quorum-sensing (QS) system (luxS), lipopolysaccharide (LPS) production (wzm), and EPS production (pgaA). Simultaneously, FLD exhibited evident antibacterial synergism, leading to an increased survival rate of G. mellonella infected with MDR K. pneumoniae. These findings suggested that FLD has substantial antibiofilm properties and synergistic antibacterial potential for colistin in treating K. pneumoniae infections.
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Affiliation(s)
| | | | | | | | | | - Xi-Wang Liu
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.G.); (Y.-J.Y.); (Z.L.); (W.-B.G.); (X.X.)
| | - Jian-Yong Li
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.G.); (Y.-J.Y.); (Z.L.); (W.-B.G.); (X.X.)
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17
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Dai JS, Xu J, Shen HJ, Chen NP, Zhu BQ, Xue ZJ, Chen HH, Ding ZS, Ding R, Qian CD. The induced and intrinsic resistance of Escherichia coli to sanguinarine is mediated by AcrB efflux pump. Microbiol Spectr 2024; 12:e0323723. [PMID: 38038452 PMCID: PMC10783092 DOI: 10.1128/spectrum.03237-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE The use of plant extracts is increasing as an alternative to synthetic compounds, especially antibiotics. However, there is no sufficient knowledge on the mechanisms and potential risks of antibiotic resistance induced by these phytochemicals. In the present study, we found that stable drug resistant mutants of E. coli emerged after repetitive exposure to sanguinarine and demonstrated that the AcrB efflux pump contributed to the emerging of induced and intrinsic resistance of E. coli to this phytochemical. Our results offered some insights into comprehending and preventing the onset of drug-resistant strains when utilizing products containing sanguinarine.
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Affiliation(s)
- Jian-Sheng Dai
- College of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jian Xu
- College of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Hao-Jie Shen
- College of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Ni-Pi Chen
- College of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Bing-Qi Zhu
- College of Medical Technology, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zheng-Jie Xue
- College of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Hao-Han Chen
- College of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhi-Shan Ding
- College of Medical Technology, Zhejiang Chinese Medical University, Hangzhou, China
| | - Rui Ding
- School of Life Sciences, Anhui Medical University, Hefei, China
| | - Chao-Dong Qian
- College of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
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18
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Xu Y, Wang W, Su W, Wang M, Xu H, Zhang X, Li L. A widespread single amino acid mutation in AcrA reduces tigecycline susceptibility in Klebsiella pneumoniae. Microbiol Spectr 2024; 12:e0203023. [PMID: 38032193 PMCID: PMC10782974 DOI: 10.1128/spectrum.02030-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Tigecycline, a glycecycline antibiotic with broad-spectrum activity against almost all Gram-positive and Gram-negative bacteria, is a highly concerned "last-resort" antibiotic. In addition to plasmid-hosted mobile tet(X) conferring high-level resistance to tigecycline, there are many reports suggesting increased expression of AcrAB-TolC efflux pump leads to tigecycline non-susceptibility. However, the role of mutations in AcrAB-TolC on tigecycline resistance has not been identified. This study reports a novel T188A mutation of the AcrA subunit of AcrAB-TolC complex in a clinical tigecycline-resistant Klebsiella pneumoniae strain and reveals the role of AcrA mutation on tigecycline resistance in K. pneumoniae. High prevalence of A188 type AcrA in hypervirulent multidrug-resistant K. pneumoniae indicates that mutations of the AcrAB-TolC complex may play a larger role in determining bacterial pathogenesis and antibiotic susceptibility than previously expected.
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Affiliation(s)
- Yingchao Xu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Wenjia Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Wenya Su
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Mingyu Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Hai Xu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Xuhua Zhang
- Laboratory Medicine Center, The Second Hospital of Shandong University, Jinan, China
| | - Ling Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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19
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Sahoo M, Behera DU, Gaur M, Subudhi E. Molecular docking, molecular dynamics simulation, and MM/PBSA analysis of ginger phytocompounds as a potential inhibitor of AcrB for treating multidrug-resistant Klebsiella pneumoniae infections. J Biomol Struct Dyn 2024:1-17. [PMID: 38165647 DOI: 10.1080/07391102.2023.2299741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/20/2023] [Indexed: 01/04/2024]
Abstract
The emergence of Multidrug resistance (MDR) in human pathogens has defected the existing antibiotics and compelled us to understand more about the basic science behind alternate anti-infective drug discovery. Soon, proteome analysis identified AcrB efflux pump protein as a promising drug target using plant-driven phytocompounds used in traditional medicine systems with lesser side effects. Thus, the present study aims to explore the novel, less toxic, and natural inhibitors of Klebsiella pneumoniae AcrB pump protein from 69 Zingiber officinale phyto-molecules available in the SpiceRx database through computational-biology approaches. AcrB protein's homology-modelling was carried out to get a 3D structure. The multistep-docking (HTVS, SP, and XP) were employed to eliminate less-suitable compounds in each step based on the docking score. The chosen hit-compounds underwent induced-fit docking (IFD). Based on the XP GScore, the top three compounds, epicatechin (-10.78), 6-gingerol (-9.71), and quercetin (-9.09) kcal/mol, were selected for further calculation of binding free energy (MM/GBSA). Furthermore, the short-listed compounds were assessed for their drug-like properties based on in silico ADMET properties and Pa, Pi values. In addition, the molecular dynamics simulation (MDS) studies for 250 ns elucidated the binding mechanism of epicatechin, 6-gingerol, and quercetin to AcrB. From the dynamic binding free energy calculations using MM/PBSA, 6-gingerol exhibited a strong binding affinity towards AcrB. Further, the 6-gingerol complex's energy fluctuation was observed from the free energy landscape. In conclusion, 6-gingerol has a promising inhibiting potential against the AcrB efflux pump and thus necessitates further validation through in vitro and in vivo experiments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maheswata Sahoo
- Centre for Biotechnology, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | | | - Mahendra Gaur
- Drug Development, and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, India
- Department of Biotechnology, Punjabi University, Patiala, India
| | - Enketeswara Subudhi
- Centre for Biotechnology, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
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20
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Chubiz LM. The Mar, Sox, and Rob Systems. EcoSal Plus 2023; 11:eesp00102022. [PMID: 37220096 PMCID: PMC10729928 DOI: 10.1128/ecosalplus.esp-0010-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/03/2023] [Indexed: 01/28/2024]
Abstract
Environments inhabited by Enterobacteriaceae are diverse and often stressful. This is particularly true for Escherichia coli and Salmonella during host association in the gastrointestinal systems of animals. There, E. coli and Salmonella must survive exposure to various antimicrobial compounds produced or ingested by their host. A myriad of changes to cellular physiology and metabolism are required to achieve this feat. A central regulatory network responsible for sensing and responding to intracellular chemical stressors like antibiotics are the Mar, Sox, and Rob systems found throughout the Enterobacteriaceae. Each of these distinct regulatory networks controls expression of an overlapping set of downstream genes whose collective effects result in increased resistance to a wide array of antimicrobial compounds. This collection of genes is known as the mar-sox-rob regulon. This review will provide an overview of the mar-sox-rob regulon and molecular architecture of the Mar, Sox, and Rob systems.
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Affiliation(s)
- Lon M. Chubiz
- Department of Biology, University of Missouri–St. Louis, St. Louis, Missouri, USA
- Biochemistry and Biotechnology Program, University of Missouri–St. Louis, St. Louis, Missouri, USA
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21
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Pisoni LA, Semple SJ, Liu S, Sykes MJ, Venter H. Combined Structure- and Ligand-Based Approach for the Identification of Inhibitors of AcrAB-TolC in Escherichia coli. ACS Infect Dis 2023; 9:2504-2522. [PMID: 37888944 DOI: 10.1021/acsinfecdis.3c00350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The inhibition of efflux pumps is a promising approach to combating multidrug-resistant bacteria. We have developed a combined structure- and ligand-based model, using OpenEye software, for the identification of inhibitors of AcrB, the inner membrane protein component of the AcrAB-TolC efflux pump in Escherichia coli. From a database of 1391 FDA-approved drugs, 23 compounds were selected to test for efflux inhibition in E. coli. Seven compounds, including ivacaftor (25), butenafine (19), naftifine (27), pimozide (30), thioridazine (35), trifluoperazine (37), and meloxicam (26), enhanced the activity of at least one antimicrobial substrate and inhibited the efflux pump-mediated removal of the substrate Nile Red from cells. Ivacaftor (25) inhibited efflux dose dependently, had no effect on an E. coli strain with genomic deletion of the gene encoding AcrB, and did not damage the bacterial outer membrane. In the presence of a sub-minimum inhibitory concentration (MIC) of the outer membrane permeabilizer colistin, ivacaftor at 1 μg/mL reduced the MICs of erythromycin and minocycline by 4- to 8-fold. The identification of seven potential AcrB inhibitors shows the merits of a combined structure- and ligand-based approach to virtual screening.
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Affiliation(s)
- Lily A Pisoni
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
- Quality Use of Medicines and Pharmacy Research Centre, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Susan J Semple
- Quality Use of Medicines and Pharmacy Research Centre, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Sida Liu
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Matthew J Sykes
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Henrietta Venter
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
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22
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Li M, Liu Y, Gong Y, Yan X, Wang L, Zheng W, Ai H, Zhao Y. Recent advances in nanoantibiotics against multidrug-resistant bacteria. NANOSCALE ADVANCES 2023; 5:6278-6317. [PMID: 38024316 PMCID: PMC10662204 DOI: 10.1039/d3na00530e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023]
Abstract
Multidrug-resistant (MDR) bacteria-caused infections have been a major threat to human health. The abuse of conventional antibiotics accelerates the generation of MDR bacteria and makes the situation worse. The emergence of nanomaterials holds great promise for solving this tricky problem due to their multiple antibacterial mechanisms, tunable antibacterial spectra, and low probabilities of inducing drug resistance. In this review, we summarize the mechanism of the generation of drug resistance, and introduce the recently developed nanomaterials for dealing with MDR bacteria via various antibacterial mechanisms. Considering that biosafety and mass production are the major bottlenecks hurdling the commercialization of nanoantibiotics, we introduce the related development in these two aspects. We discuss urgent challenges in this field and future perspectives to promote the development and translation of nanoantibiotics as alternatives against MDR pathogens to traditional antibiotics-based approaches.
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Affiliation(s)
- Mulan Li
- Cancer Research Center, Jiangxi University of Chinese Medicine No. 1688 Meiling Avenue, Xinjian District Nanchang Jiangxi 330004 P. R. China
| | - Ying Liu
- Key Laboratory of Follicular Development and Reproductive Health in Liaoning Province, Third Affiliated Hospital of Jinzhou Medical University No. 2, Section 5, Heping Road Jin Zhou Liaoning 121000 P. R. China
| | - Youhuan Gong
- Cancer Research Center, Jiangxi University of Chinese Medicine No. 1688 Meiling Avenue, Xinjian District Nanchang Jiangxi 330004 P. R. China
| | - Xiaojie Yan
- Cancer Research Center, Jiangxi University of Chinese Medicine No. 1688 Meiling Avenue, Xinjian District Nanchang Jiangxi 330004 P. R. China
| | - Le Wang
- Cancer Research Center, Jiangxi University of Chinese Medicine No. 1688 Meiling Avenue, Xinjian District Nanchang Jiangxi 330004 P. R. China
| | - Wenfu Zheng
- CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology No. 11 Zhongguancun Beiyitiao, Haidian District Beijing 100190 P. R. China
- The University of Chinese Academy of Sciences 19A Yuquan Road, Shijingshan District Beijing 100049 P. R. China
- Cannano Tefei Technology, Co. LTD Room 1013, Building D, No. 136 Kaiyuan Avenue, Huangpu District Guangzhou Guangdong Province 510535 P. R. China
| | - Hao Ai
- Key Laboratory of Follicular Development and Reproductive Health in Liaoning Province, Third Affiliated Hospital of Jinzhou Medical University No. 2, Section 5, Heping Road Jin Zhou Liaoning 121000 P. R. China
| | - Yuliang Zhao
- CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology No. 11 Zhongguancun Beiyitiao, Haidian District Beijing 100190 P. R. China
- The University of Chinese Academy of Sciences 19A Yuquan Road, Shijingshan District Beijing 100049 P. R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences 19B Yuquan Road, Shijingshan District Beijing 100049 P. R. China
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23
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Hu Y, Zhang K, Li N, Wang S. Composition, antibiotic resistance, and virulence analysis of microbiota in dormitory drain pipes. Front Microbiol 2023; 14:1272605. [PMID: 38029096 PMCID: PMC10679431 DOI: 10.3389/fmicb.2023.1272605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Dormitory washbasins can breed microorganisms that produce odorous gases, polluting the indoor environment. Methods We utilized metagenome sequencing to analyze the microbiota of 40 samples from the drain pipes of dormitory washbasins. Our study aimed to investigate the microbial community structure, antibiotic resistance genes, and virulence factors, and to identify potential influencing factors such as gender, hometown, frequency of hand sanitizer usage, and number of dormitory residents. Results The analysis revealed 12 phyla and 147 genera, with Proteobacteria and Actinobacteria being the dominant phyla, and Mycobacterium and Nakamurella being the dominant genera. We found that the factors influencing the microbial community structure of the dormitory washbasin drain pipe are complex. The investigated factors have a slight influence on the drain pipe microbial community, with gender exerting a discernible influence. The annotation results revealed the presence of various virulence factors, pathogenic toxins and antibiotic resistance genes, including 246 different toxin types and 30 different types of antibiotic resistance genes. In contrast to the observed differences in microbial composition among samples, the distribution of resistance genes shows relatively small changes among samples. Antibiotics should be a contributing factor in the overall increase of antibiotic resistance genes in drain pipes. Discussion Overall, our study provides important insights into the community structure and function of microorganisms in dormitory drainage systems, and can guide efforts to prevent and control microbial pollution.
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Affiliation(s)
- Yan Hu
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Wenzhou University, Wenzhou, China
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, China
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Kunyuan Zhang
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Wenzhou University, Wenzhou, China
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, China
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Nan Li
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Wenzhou University, Wenzhou, China
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Shengqin Wang
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Wenzhou University, Wenzhou, China
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, China
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
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24
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Compagne N, Jiménez-Castellanos JC, Meurillon V, Pradel E, Vieira Da Cruz A, Piveteau C, Biela A, Eveque M, Leroux F, Deprez B, Willand N, Hartkoorn RC, Flipo M. Optimization of pyridylpiperazine-based inhibitors of the Escherichia coli AcrAB-TolC efflux pump. Eur J Med Chem 2023; 259:115630. [PMID: 37459793 DOI: 10.1016/j.ejmech.2023.115630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/15/2023] [Accepted: 07/06/2023] [Indexed: 08/22/2023]
Abstract
Multidrug-resistant Escherichia coli is a continuously growing worldwide public health problem, in which the well-known AcrAB-TolC tripartite RND efflux pump is a critical driver. We have previously described pyridylpiperazines as a novel class of allosteric inhibitors of E. coli AcrB which bind to a unique site in the protein transmembrane domain, allowing for the potentiation of antibiotic activity. Here, we show a rational optimization of pyridylpiperazines by modifying three specific derivatization points of the pyridine core to improve the potency and the pharmacokinetic properties of this chemical series. In particular, this work found that the introduction of a primary amine to the pyridine through ester (29, BDM91270) or oxadiazole (44, BDM91514) based linkers allowed for analogues with improved antibiotic boosting potency through AcrB inhibition. In vitro studies, using genetically engineered mutants, showed that this improvement in potency is mediated through novel interactions with distal acidic residues of the AcrB binding pocket. Of the two leads, compound 44 was found to have favorable physico-chemical properties and suitable plasma and microsomal stability. Together, this work expands the current structure-activity relationship data on pyridylpiperazine efflux pump inhibitors, and provides a promising step towards future in vivo proof of concept of pyridylpiperazines as antibiotic potentiators.
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Affiliation(s)
- Nina Compagne
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Juan-Carlos Jiménez-Castellanos
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Virginie Meurillon
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Elizabeth Pradel
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Anais Vieira Da Cruz
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Alexandre Biela
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Maxime Eveque
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, US 41-UAR 2014-PLBS, F-59000, Lille, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Ruben C Hartkoorn
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France.
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France.
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25
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Zheng M, Lupoli TJ. Counteracting antibiotic resistance enzymes and efflux pumps. Curr Opin Microbiol 2023; 75:102334. [PMID: 37329679 DOI: 10.1016/j.mib.2023.102334] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/02/2023] [Accepted: 05/17/2023] [Indexed: 06/19/2023]
Abstract
Bacterial pathogens are constantly evolving new resistance mechanisms against antibiotics; hence, strategies to potentiate existing antibiotics or combat mechanisms of resistance using adjuvants are always in demand. Recently, inhibitors have been identified that counteract enzymatic modification of the drugs isoniazid and rifampin, which have implications in the study of multi-drug-resistant mycobacteria. A wealth of structural studies on efflux pumps from diverse bacteria has also fueled the design of new small-molecule and peptide-based agents to prevent the active transport of antibiotics. We envision that these findings will inspire microbiologists to apply existing adjuvants to clinically relevant resistant strains, or to use described platforms to discover novel antibiotic adjuvant scaffolds.
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Affiliation(s)
- Meng Zheng
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Tania J Lupoli
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA.
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26
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Hadchity L, Houard J, Lanois A, Payelleville A, Nassar F, Gualtieri M, Givaudan A, Abi Khattar Z. The AcrAB efflux pump confers self-resistance to stilbenes in Photorhabdus laumondii. Res Microbiol 2023; 174:104081. [PMID: 37196776 DOI: 10.1016/j.resmic.2023.104081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
The Resistance-nodulation-division (RND)-type AcrAB-TolC efflux pump contributes to multidrug resistance in Gram-negative bacteria. Recently, the bacterium Photorhabdus laumondii TT01 has emerged as a goldmine for novel anti-infective drug discovery. Outside plants, Photorhabdus is the only Gram-negative known to produce stilbene-derivatives including 3,5-dihydroxy-4-ethyl-trans-stilbene and 3,5-dihydroxy-4-isopropyl-trans-stilbene (IPS). IPS is a bioactive polyketide which received considerable attention, mainly because of its antimicrobial properties, and is currently in late-stage clinical development as a topical treatment for psoriasis and dermatitis. To date, little is known about how Photorhabdus survives in the presence of stilbenes. We combined genetic and biochemical approaches to assess whether AcrAB efflux pump exports stilbenes in P. laumondii. We demonstrated that the wild-type (WT) exerts an antagonistic activity against its derivative ΔacrA mutant, and that is able to outcompete it in a dual-strain co-culture assay. The ΔacrA mutant also showed high sensitivity to 3,5-dihydroxy-4-ethyl-trans-stilbene and IPS as well as decreased IPS concentrations in its supernatant comparing to the WT. We report here a mechanism of self-resistance against stilbene derivatives of P. laumondii TT01, which enables these bacteria to survive under high concentrations of stilbenes by extruding them out via the AcrAB efflux pump.
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Affiliation(s)
- Linda Hadchity
- Laboratory of Georesources, Geosciences and Environment (L2GE), Microbiology/Tox-Ecotoxicology Team, Faculty of Sciences 2, Lebanese University, P.O.Box 90656, Jdeidet El-Metn, Lebanon; DGIMI, Université Montpellier, INRAE, Montpellier, France.
| | | | - Anne Lanois
- DGIMI, Université Montpellier, INRAE, Montpellier, France.
| | - Amaury Payelleville
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Gosselies, Belgium.
| | - Fida Nassar
- Laboratory of Georesources, Geosciences and Environment (L2GE), Microbiology/Tox-Ecotoxicology Team, Faculty of Sciences 2, Lebanese University, P.O.Box 90656, Jdeidet El-Metn, Lebanon.
| | | | - Alain Givaudan
- DGIMI, Université Montpellier, INRAE, Montpellier, France.
| | - Ziad Abi Khattar
- Laboratory of Georesources, Geosciences and Environment (L2GE), Microbiology/Tox-Ecotoxicology Team, Faculty of Sciences 2, Lebanese University, P.O.Box 90656, Jdeidet El-Metn, Lebanon.
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27
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Gervasoni S, Mehla J, Bergen CR, Leus IV, Margiotta E, Malloci G, Bosin A, Vargiu AV, Lomovskaya O, Rybenkov VV, Ruggerone P, Zgurskaya HI. Molecular determinants of avoidance and inhibition of Pseudomonas aeruginosa MexB efflux pump. mBio 2023; 14:e0140323. [PMID: 37493633 PMCID: PMC10470492 DOI: 10.1128/mbio.01403-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 07/27/2023] Open
Abstract
Transporters of the resistance-nodulation-cell division (RND) superfamily of proteins are the dominant multidrug efflux power of Gram-negative bacteria. The major RND efflux pump of Pseudomonas aeruginosa is MexAB-OprM, in which the inner membrane transporter MexB is responsible for the recognition and binding of compounds. The high importance of this pump in clinical antibiotic resistance made it a subject of intense investigations and a promising target for the discovery of efflux pump inhibitors. This study is focused on a series of peptidomimetic compounds developed as effective inhibitors of MexAB-OprM. We performed multi-copy molecular dynamics simulations, machine-learning (ML) analyses, and site-directed mutagenesis of MexB to investigate interactions of MexB with representatives of efflux avoiders, substrates, and inhibitors. The analysis of both direct and water-mediated protein-ligand interactions revealed characteristic patterns for each class, highlighting significant differences between them. We found that efflux avoiders poorly interact with the access binding site of MexB, and inhibition engages amino acid residues that are not directly involved in binding and transport of substrates. In agreement, machine-learning models selected different residues predictive of MexB substrates and inhibitors. The differences in interactions were further validated by site-directed mutagenesis. We conclude that the substrate translocation and inhibition pathways of MexB split at the interface (between the main putative binding sites) and at the deep binding pocket and that interactions outside of the hydrophobic patch contribute to the inhibition of MexB. This molecular-level information could help in the rational design of new inhibitors and antibiotics less susceptible to the efflux mechanism. IMPORTANCE Multidrug transporters recognize and expel from cells a broad range of ligands including their own inhibitors. The difference between the substrate translocation and inhibition routes remains unclear. In this study, machine learning and computational and experimental approaches were used to understand dynamics of MexB interactions with its ligands. Our results show that some ligands engage a certain combination of polar and charged residues in MexB binding sites to be effectively expelled into the exit funnel, whereas others engage aromatic and hydrophobic residues that slow down or hinder the next step in the transporter cycle. These findings suggest that all MexB ligands fit into this substrate-inhibitor spectrum depending on their physico-chemical structures and properties.
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Affiliation(s)
- Silvia Gervasoni
- Department of Physics, University of Cagliari, Monserrato, Italy
| | - Jitender Mehla
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Charles R. Bergen
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Inga V. Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Enrico Margiotta
- Department of Physics, University of Cagliari, Monserrato, Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Monserrato, Italy
| | - Andrea Bosin
- Department of Physics, University of Cagliari, Monserrato, Italy
| | | | | | - Valentin V. Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Monserrato, Italy
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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28
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Avakh A, Grant GD, Cheesman MJ, Kalkundri T, Hall S. The Art of War with Pseudomonas aeruginosa: Targeting Mex Efflux Pumps Directly to Strategically Enhance Antipseudomonal Drug Efficacy. Antibiotics (Basel) 2023; 12:1304. [PMID: 37627724 PMCID: PMC10451789 DOI: 10.3390/antibiotics12081304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) poses a grave clinical challenge due to its multidrug resistance (MDR) phenotype, leading to severe and life-threatening infections. This bacterium exhibits both intrinsic resistance to various antipseudomonal agents and acquired resistance against nearly all available antibiotics, contributing to its MDR phenotype. Multiple mechanisms, including enzyme production, loss of outer membrane proteins, target mutations, and multidrug efflux systems, contribute to its antimicrobial resistance. The clinical importance of addressing MDR in P. aeruginosa is paramount, and one pivotal determinant is the resistance-nodulation-division (RND) family of drug/proton antiporters, notably the Mex efflux pumps. These pumps function as crucial defenders, reinforcing the emergence of extensively drug-resistant (XDR) and pandrug-resistant (PDR) strains, which underscores the urgency of the situation. Overcoming this challenge necessitates the exploration and development of potent efflux pump inhibitors (EPIs) to restore the efficacy of existing antipseudomonal drugs. By effectively countering or bypassing efflux activities, EPIs hold tremendous potential for restoring the antibacterial activity against P. aeruginosa and other Gram-negative pathogens. This review focuses on concurrent MDR, highlighting the clinical significance of efflux pumps, particularly the Mex efflux pumps, in driving MDR. It explores promising EPIs and delves into the structural characteristics of the MexB subunit and its substrate binding sites.
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Affiliation(s)
| | | | | | | | - Susan Hall
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, QLD 4222, Australia; (A.A.); (G.D.G.); (M.J.C.); (T.K.)
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29
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Kato T, Okada U, Hung LW, Yamashita E, Kim HB, Kim CY, Terwilliger TC, Schweizer HP, Murakami S. Crystal structures of multidrug efflux transporters from Burkholderia pseudomallei suggest details of transport mechanism. Proc Natl Acad Sci U S A 2023; 120:e2215072120. [PMID: 37428905 PMCID: PMC10629574 DOI: 10.1073/pnas.2215072120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/24/2023] [Indexed: 07/12/2023] Open
Abstract
BpeB and BpeF are multidrug efflux transporters from Burkholderia pseudomallei that enable multidrug resistance. Here, we report the crystal structures of BpeB and BpeF at 2.94 Å and 3.0 Å resolution, respectively. BpeB was found as an asymmetric trimer, consistent with the widely-accepted functional rotation mechanism for this type of transporter. One of the monomers has a distinct structure that we interpret as an intermediate along this functional cycle. Additionally, a detergent molecule bound in a previously undescribed binding site provides insights into substrate translocation through the pathway. BpeF shares structural similarities with the crystal structure of OqxB from Klebsiella pneumoniae, where both are symmetric trimers composed of three "binding"-state monomers. The structures of BpeB and BpeF further our understanding of the functional mechanisms of transporters belonging to the HAE1-RND superfamily.
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Affiliation(s)
- Takaaki Kato
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama226-8501, Japan
| | - Ui Okada
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama226-8501, Japan
| | - Li-Wei Hung
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM87545
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University, Osaka565-0871, Japan
| | - Heung-Bok Kim
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM87545
| | - Chang-Yub Kim
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM87545
| | - Thomas C. Terwilliger
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM87545
- New Mexico Consortium, Los Alamos, NM87544
| | - Herbert P. Schweizer
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ86011
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ86011
| | - Satoshi Murakami
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama226-8501, Japan
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30
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Yamasaki S, Zwama M, Yoneda T, Hayashi-Nishino M, Nishino K. Drug resistance and physiological roles of RND multidrug efflux pumps in Salmonella enterica, Escherichia coli and Pseudomonas aeruginosa. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001322. [PMID: 37319001 PMCID: PMC10333786 DOI: 10.1099/mic.0.001322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/18/2023] [Indexed: 06/17/2023]
Abstract
Drug efflux pumps transport antimicrobial agents out of bacteria, thereby reducing the intracellular antimicrobial concentration, which is associated with intrinsic and acquired bacterial resistance to these antimicrobials. As genome analysis has advanced, many drug efflux pump genes have been detected in the genomes of bacterial species. In addition to drug resistance, these pumps are involved in various essential physiological functions, such as bacterial adaptation to hostile environments, toxin and metabolite efflux, biofilm formation and quorum sensing. In Gram-negative bacteria, efflux pumps in the resistance–nodulation–division (RND) superfamily play a clinically important role. In this review, we focus on Gram-negative bacteria, including Salmonella enterica , Escherichia coli and Pseudomonas aeruginosa , and discuss the role of RND efflux pumps in drug resistance and physiological functions.
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Affiliation(s)
- Seiji Yamasaki
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
- Institute for Advanced Co-Creation Studies, Osaka University, 1-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Martijn Zwama
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Tomohiro Yoneda
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mitsuko Hayashi-Nishino
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kunihiko Nishino
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
- Center for Infectious Disease Education and Research, 2-8 Yamadaoka, Osaka University, Suita, Osaka 565-0871, Japan
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31
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Jang S. AcrAB-TolC, a major efflux pump in Gram negative bacteria: toward understanding its operation mechanism. BMB Rep 2023; 56:326-334. [PMID: 37254571 PMCID: PMC10315565 DOI: 10.5483/bmbrep.2023-0070] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/18/2023] [Accepted: 05/30/2023] [Indexed: 08/27/2023] Open
Abstract
Antibiotic resistance (AR) is a silent pandemic that kills millions worldwide. Although the development of new therapeutic agents against antibiotic resistance is in urgent demand, this has presented a great challenge, especially for Gram-negative bacteria that have inherent drug-resistance mediated by impermeable outer membranes and multidrug efflux pumps that actively extrude various drugs from the bacteria. For the last two decades, multidrug efflux pumps, including AcrAB-TolC, the most clinically important efflux pump in Gram-negative bacteria, have drawn great attention as strategic targets for re-sensitizing bacteria to the existing antibiotics. This article aims to provide a concise overview of the AcrAB-TolC operational mechanism, reviewing its architecture and substrate specificity, as well as the recent development of AcrAB-TolC inhibitors. [BMB Reports 2023; 56(6): 326-334].
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Affiliation(s)
- Soojin Jang
- Department of Discovery Biology, Antibacterial Resistance Laboratory, Institut Pasteur Korea, Seongnam 13488, Korea
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32
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Al-Marzooq F, Ghazawi A, Daoud L, Tariq S. Boosting the Antibacterial Activity of Azithromycin on Multidrug-Resistant Escherichia coli by Efflux Pump Inhibition Coupled with Outer Membrane Permeabilization Induced by Phenylalanine-Arginine β-Naphthylamide. Int J Mol Sci 2023; 24:ijms24108662. [PMID: 37240007 DOI: 10.3390/ijms24108662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
The global spread of multidrug-resistant (MDR) bacteria increases the demand for the discovery of new antibiotics and adjuvants. Phenylalanine-arginine β-naphthylamide (PAβN) is an inhibitor of efflux pumps in Gram-negative bacteria, such as the AcrAB-TolC complex in Escherichia coli. We aimed to explore the synergistic effect and mechanism of action of PAβN combined with azithromycin (AZT) on a group of MDR E. coli strains. Antibiotic susceptibility was tested for 56 strains, which were screened for macrolide resistance genes. Then, 29 strains were tested for synergy using the checkerboard assay. PAβN significantly enhanced AZT activity in a dose-dependent manner in strains expressing the mphA gene and encoding macrolide phosphotransferase, but not in strains carrying the ermB gene and encoding macrolide methylase. Early bacterial killing (6 h) was observed in a colistin-resistant strain with the mcr-1 gene, leading to lipid remodeling, which caused outer membrane (OM) permeability defects. Clear OM damage was revealed by transmission electron microscopy in bacteria exposed to high doses of PAβN. Increased OM permeability was also proven by fluorometric assays, confirming the action of PAβN on OM. PAβN maintained its activity as an efflux pump inhibitor at low doses without permeabilizing OM. A non-significant increase in acrA, acrB, and tolC expression in response to prolonged exposure to PAβN was noted in cells treated with PAβN alone or with AZT, as a reflection of bacterial attempts to counteract pump inhibition. Thus, PAβN was found to be effective in potentiating the antibacterial activity of AZT on E. coli through dose-dependent action. This warrants further investigations of its effect combined with other antibiotics on multiple Gram-negative bacterial species. Synergetic combinations will help in the battle against MDR pathogens, adding new tools to the arsenal of existing medications.
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Affiliation(s)
- Farah Al-Marzooq
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Lana Daoud
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Saeed Tariq
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
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Trampari E, Prischi F, Vargiu AV, Abi-Assaf J, Bavro VN, Webber MA. Functionally distinct mutations within AcrB underpin antibiotic resistance in different lifestyles. NPJ ANTIMICROBIALS AND RESISTANCE 2023; 1:2. [PMID: 38686215 PMCID: PMC11057200 DOI: 10.1038/s44259-023-00001-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/27/2023] [Indexed: 05/02/2024]
Abstract
Antibiotic resistance is a pressing healthcare challenge and is mediated by various mechanisms, including the active export of drugs via multidrug efflux systems, which prevent drug accumulation within the cell. Here, we studied how Salmonella evolved resistance to two key antibiotics, cefotaxime and azithromycin, when grown planktonically or as a biofilm. Resistance to both drugs emerged in both conditions and was associated with different substitutions within the efflux-associated transporter, AcrB. Azithromycin exposure selected for an R717L substitution, while cefotaxime for Q176K. Additional mutations in ramR or envZ accumulated concurrently with the R717L or Q176K substitutions respectively, resulting in clinical resistance to the selective antibiotics and cross-resistance to other drugs. Structural, genetic, and phenotypic analysis showed the two AcrB substitutions confer their benefits in profoundly different ways. R717L reduces steric barriers associated with transit through the substrate channel 2 of AcrB. Q176K increases binding energy for cefotaxime, improving recognition in the distal binding pocket, resulting in increased efflux efficiency. Finally, we show the R717 substitution is present in isolates recovered around the world.
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Affiliation(s)
- Eleftheria Trampari
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ UK
| | - Filippo Prischi
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ UK
| | - Attilio V. Vargiu
- Department of Physics, University of Cagliari, S. P. 8, km. 0.700, 09042 Monserrato, Italy
| | - Justin Abi-Assaf
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ UK
| | - Vassiliy N. Bavro
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ UK
| | - Mark A. Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ UK
- Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7UA UK
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Darby EM, Trampari E, Siasat P, Gaya MS, Alav I, Webber MA, Blair JMA. Molecular mechanisms of antibiotic resistance revisited. Nat Rev Microbiol 2023; 21:280-295. [PMID: 36411397 DOI: 10.1038/s41579-022-00820-y] [Citation(s) in RCA: 195] [Impact Index Per Article: 195.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2022] [Indexed: 11/22/2022]
Abstract
Antibiotic resistance is a global health emergency, with resistance detected to all antibiotics currently in clinical use and only a few novel drugs in the pipeline. Understanding the molecular mechanisms that bacteria use to resist the action of antimicrobials is critical to recognize global patterns of resistance and to improve the use of current drugs, as well as for the design of new drugs less susceptible to resistance development and novel strategies to combat resistance. In this Review, we explore recent advances in understanding how resistance genes contribute to the biology of the host, new structural details of relevant molecular events underpinning resistance, the identification of new resistance gene families and the interactions between different resistance mechanisms. Finally, we discuss how we can use this information to develop the next generation of antimicrobial therapies.
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Affiliation(s)
- Elizabeth M Darby
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Pauline Siasat
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Ilyas Alav
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
- Medical School, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Jessica M A Blair
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
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Akshay SD, Nayak S, Deekshit VK, Rohit A, Maiti B. Differential expression of outer membrane proteins and quinolone resistance determining region mutations can lead to ciprofloxacin resistance in Salmonella Typhi. Arch Microbiol 2023; 205:136. [PMID: 36961627 DOI: 10.1007/s00203-023-03485-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/17/2023] [Accepted: 03/13/2023] [Indexed: 03/25/2023]
Abstract
Multi-drug resistance in Salmonella Typhi remains a public health concern globally. This study aimed to investigate the function of quinolone resistance determining region (QRDR) of gyrA and parC in ciprofloxacin (CIP) resistant isolates and examine the differential expression of outer membrane proteins (OMPs) on exposure to sub-lethal concentrations of CIP in S. Typhi. The CIP-resistant isolates were screened for mutations in the QRDR and analyzed for bacterial growth. Furthermore, major OMPs encoding genes such as ompF, lamB, yaeT, tolC, ompS1, and phoE were examined for differential expression under the sub-lethal concentrations of CIP by real-time PCR and SDS-PAGE. Notably, our study has shown a single-point mutation in gyrA at codon 83 (Ser83-tyrosine and Ser83-phenylalanine), also the rare amino acid substitution in parC gene at codon 80 (Glu80-glycine) in CIP-resistant isolates. Additionally, CIP-resistant isolates showed moderate growth compared to susceptible isolates. Although most of the OMP-encoding genes (tolC, ompS1, and phoE) showed some degree of upregulation, a significant level of upregulation (p < 0.05) was observed only for yaeT. However, ompF and lamB genes were down-regulated compared to CIP-susceptible isolates. Whereas OMPs profiling using SDS-PAGE did not show any changes in the banding pattern. These results provide valuable information on the QRDR mutation, and the difference in the growth, and expression of OMP-encoding genes in resistant and susceptible isolates of S. Typhi. This further provides insight into the involvement of QRDR mutation and OMPs associated with CIP resistance in S. Typhi.
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Affiliation(s)
- Sadanand Dangari Akshay
- Division of Infectious Diseases, Nitte (Deemed to Be University), Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India
| | - Srajana Nayak
- Division of Infectious Diseases, Nitte (Deemed to Be University), Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India
| | - Vijaya Kumar Deekshit
- Division of Infectious Diseases, Nitte (Deemed to Be University), Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India
| | - Anusha Rohit
- Division of Infectious Diseases, Nitte (Deemed to Be University), Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India
- Department of Microbiology, The Madras Medical Mission, 4-A, Dr, Mogappair, Chennai, Tamil Nadu, 600037, India
| | - Biswajit Maiti
- Division of Infectious Diseases, Nitte (Deemed to Be University), Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India.
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Guo T, Chen Y, Chen W, Semple SJ, Gu X, Polyak SW, Sun G, Venter H, Ma S. Design and synthesis of benzochromene derivatives as AcrB inhibitors for the reversal of bacterial multidrug resistance. Eur J Med Chem 2023; 249:115148. [PMID: 36709649 DOI: 10.1016/j.ejmech.2023.115148] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/17/2023] [Accepted: 01/22/2023] [Indexed: 01/26/2023]
Abstract
A series of novel benzo[h]chromene compounds were designed, synthesized and evaluated for their biological activity as AcrB inhibitors. The compounds were assessed for their ability to potentiate the effect of antibiotics. Compounds with antibiotic-potentiating effects were then evaluated for inhibition of Nile Red efflux, and for off-target effects including activity on the outer and inner bacterial membranes and toxicity. Six compounds were identified to reduce the MIC values of at least one of the tested antibiotics by at least 4-fold, and further reduced the MICs in the presence of a membrane permeabilizer. The identified compounds were also able to inhibit Nile Red efflux at concentrations between 50 μM and 200 μM. The compounds did not disrupt the bacterial outer membrane nor display toxicity in a nematode model (Caenorhabditis elegans). The 4-methoxyphenoxy)propoxy derivative compound G6 possessed the most potent antibacterial potentiation with erythromycin by 8-fold even without the presence of a membrane permeabilizer. Furthermore, H6, G6, G10 and G11 completely abolished the Nile Red efflux at a concentration of 50 μM. The 3,4-dihydro-2H-benzo[h]chromen-5-yl)(morpholino)methanone core appears to be a promising chemical skeleton to be further studied in the discovery of more putative AcrB inhibitors.
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Affiliation(s)
- Ting Guo
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Yang Chen
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Weijin Chen
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Susan J Semple
- Quality Use of Medicines and Pharmacy Research Centre, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Xiaotong Gu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Steven W Polyak
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Guanglin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Henrietta Venter
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia.
| | - Shutao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China.
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Heithoff DM, Mahan SP, Barnes V L, Leyn SA, George CX, Zlamal JE, Limwongyut J, Bazan GC, Fried JC, Fitzgibbons LN, House JK, Samuel CE, Osterman AL, Low DA, Mahan MJ. A broad-spectrum synthetic antibiotic that does not evoke bacterial resistance. EBioMedicine 2023; 89:104461. [PMID: 36801104 PMCID: PMC10025758 DOI: 10.1016/j.ebiom.2023.104461] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) poses a critical threat to public health and disproportionately affects the health and well-being of persons in low-income and middle-income countries. Our aim was to identify synthetic antimicrobials termed conjugated oligoelectrolytes (COEs) that effectively treated AMR infections and whose structures could be readily modified to address current and anticipated patient needs. METHODS Fifteen chemical variants were synthesized that contain specific alterations to the COE modular structure, and each variant was evaluated for broad-spectrum antibacterial activity and for in vitro cytotoxicity in cultured mammalian cells. Antibiotic efficacy was analyzed in murine models of sepsis; in vivo toxicity was evaluated via a blinded study of mouse clinical signs as an outcome of drug treatment. FINDINGS We identified a compound, COE2-2hexyl, that displayed broad-spectrum antibacterial activity. This compound cured mice infected with clinical bacterial isolates derived from patients with refractory bacteremia and did not evoke bacterial resistance. COE2-2hexyl has specific effects on multiple membrane-associated functions (e.g., septation, motility, ATP synthesis, respiration, membrane permeability to small molecules) that may act together to negate bacterial cell viability and the evolution of drug-resistance. Disruption of these bacterial properties may occur through alteration of critical protein-protein or protein-lipid membrane interfaces-a mechanism of action distinct from many membrane disrupting antimicrobials or detergents that destabilize membranes to induce bacterial cell lysis. INTERPRETATION The ease of molecular design, synthesis and modular nature of COEs offer many advantages over conventional antimicrobials, making synthesis simple, scalable and affordable. These COE features enable the construction of a spectrum of compounds with the potential for development as a new versatile therapy for an imminent global health crisis. FUNDING U.S. Army Research Office, National Institute of Allergy and Infectious Diseases, and National Heart, Lung, and Blood Institute.
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Affiliation(s)
- Douglas M Heithoff
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA
| | - Scott P Mahan
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA; Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA
| | - Lucien Barnes V
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA
| | - Semen A Leyn
- Infectious and Inflammatory Diseases Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Cyril X George
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA
| | - Jaime E Zlamal
- Infectious and Inflammatory Diseases Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Jakkarin Limwongyut
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA; Center for Polymers and Organic Solids, Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - Guillermo C Bazan
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA; Center for Polymers and Organic Solids, Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA; Department of Chemistry, National University of Singapore, 117543, Singapore
| | - Jeffrey C Fried
- Department of Medical Education, Santa Barbara Cottage Hospital, Santa Barbara, CA, 93105, USA; Department of Pulmonary and Critical Care Medicine, Santa Barbara Cottage Hospital, Santa Barbara, CA, 93105, USA
| | - Lynn N Fitzgibbons
- Department of Medical Education, Santa Barbara Cottage Hospital, Santa Barbara, CA, 93105, USA; Division of Infectious Diseases, Santa Barbara Cottage Hospital, Santa Barbara, CA, 93105, USA
| | - John K House
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camden, New South Wales, 2570, Australia
| | - Charles E Samuel
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Diseases Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - David A Low
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA.
| | - Michael J Mahan
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA.
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Athar M, Gervasoni S, Catte A, Basciu A, Malloci G, Ruggerone P, Vargiu AV. Tripartite efflux pumps of the RND superfamily: what did we learn from computational studies? MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36972322 DOI: 10.1099/mic.0.001307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Bacterial resistance to antibiotics has been long recognized as a priority to address for human health. Among all micro-organisms, the so-called multi-drug resistant (MDR) bacteria, which are resistant to most, if not all drugs in our current arsenal, are particularly worrisome. The World Health Organization has prioritized the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species) pathogens, which include four Gram-negative bacterial species. In these bacteria, active extrusion of antimicrobial compounds out of the cell by means of 'molecular guns' known as efflux pumps is a main determinant of MDR phenotypes. The resistance-nodulation-cell division (RND) superfamily of efflux pumps connecting the inner and outer membrane in Gram-negative bacteria is crucial to the onset of MDR and virulence, as well as biofilm formation. Thus, understanding the molecular basis of the interaction of antibiotics and inhibitors with these pumps is key to the design of more effective therapeutics. With the aim to contribute to this challenge, and complement and inspire experimental research, in silico studies on RND efflux pumps have flourished in recent decades. Here, we review a selection of such investigations addressing the main determinants behind the polyspecificity of these pumps, the mechanisms of substrate recognition, transport and inhibition, as well as the relevance of their assembly for proper functioning, and the role of protein-lipid interactions. The journey will end with a perspective on the role of computer simulations in addressing the challenges posed by these beautifully complex machineries and in supporting the fight against the spread of MDR bacteria.
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Affiliation(s)
- Mohd Athar
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Silvia Gervasoni
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Andrea Catte
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Andrea Basciu
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Giuliano Malloci
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Paolo Ruggerone
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Attilio Vittorio Vargiu
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
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Oyedara OO, Fadare OA, Franco-Frías E, Heredia N, García S. Computational assessment of phytochemicals of medicinal plants from Mexico as potential inhibitors of Salmonella enterica efflux pump AcrB protein. J Biomol Struct Dyn 2023; 41:1776-1789. [PMID: 34996337 DOI: 10.1080/07391102.2021.2024261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The AcrAB-TolC efflux pump (EP) confers multidrug resistance to Salmonella enterica, a major etiological agent of foodborne infections. Phytochemicals that inhibit the functions of AcrAB-TolC EP present ideal candidates for reversal of antibiotic resistance. Progressive technological advancements, have facilitated the development of computational methods that offer a rapid low-cost approach to screen and identify phytochemicals with inhibitory potential against EP. In this study, 71 phytochemicals derived from plants used for medicinal purposes in Mexico were screened for their potential as inhibitors of Salmonella AcrB protein using in silico approaches including molecular docking and molecular dynamics (MD) simulation. Consequently, naringenin, 5-methoxypsoralen, and licarin A were identified as candidate inhibitors of AcrB protein. The three phytochemicals bound distal/deep pocket (DP) and hydrophobic trap (HPT) residues of AcrB protein critical for interactions with inhibitors, with estimated binding free energies of -95.5 kJ/mol, -97.4 kJ/mol, and -143.8 kJ/mol for naringenin, 5-methoxypsoralen, and licarin A, respectively. Data from the 50 ns MD simulation study revealed stability of the protein-ligand complex and alterations in the AcrB protein DP conformation upon binding of phytochemicals to the DP and HPT regions. Based on the estimated binding free energy and interactions with three out of five residues lining the hydrophobic trap, licarin A demonstrated the highest inhibitory potential, supporting its further application as a candidate for overcoming drug resistance in pathogens. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Omotayo O Oyedara
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México.,Department of Microbiology, Faculty of Basic and Applied Sciences, Osun State University, Osogbo, Nigeria
| | | | - Eduardo Franco-Frías
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Norma Heredia
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Santos García
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
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40
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Preston A. Microbial Musings: Winter 2023. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37171861 DOI: 10.1099/mic.0.001331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Affiliation(s)
- Andrew Preston
- Department of Life Sciences, University of Bath, Bath, UK
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41
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Update on the Discovery of Efflux Pump Inhibitors against Critical Priority Gram-Negative Bacteria. Antibiotics (Basel) 2023; 12:antibiotics12010180. [PMID: 36671381 PMCID: PMC9854755 DOI: 10.3390/antibiotics12010180] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Antimicrobial resistance (AMR) has become a major problem in public health leading to an estimated 4.95 million deaths in 2019. The selective pressure caused by the massive and repeated use of antibiotics has led to bacterial strains that are partially or even entirely resistant to known antibiotics. AMR is caused by several mechanisms, among which the (over)expression of multidrug efflux pumps plays a central role. Multidrug efflux pumps are transmembrane transporters, naturally expressed by Gram-negative bacteria, able to extrude and confer resistance to several classes of antibiotics. Targeting them would be an effective way to revive various options for treatment. Many efflux pump inhibitors (EPIs) have been described in the literature; however, none of them have entered clinical trials to date. This review presents eight families of EPIs active against Escherichia coli or Pseudomonas aeruginosa. Structure-activity relationships, chemical synthesis, in vitro and in vivo activities, and pharmacological properties are reported. Their binding sites and their mechanisms of action are also analyzed comparatively.
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Radi MS, Munro LJ, Salcedo-Sora JE, Kim SH, Feist AM, Kell DB. Understanding Functional Redundancy and Promiscuity of Multidrug Transporters in E. coli under Lipophilic Cation Stress. MEMBRANES 2022; 12:1264. [PMID: 36557171 PMCID: PMC9783932 DOI: 10.3390/membranes12121264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/27/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Multidrug transporters (MDTs) are major contributors to microbial drug resistance and are further utilized for improving host phenotypes in biotechnological applications. Therefore, the identification of these MDTs and the understanding of their mechanisms of action in vivo are of great importance. However, their promiscuity and functional redundancy represent a major challenge towards their identification. Here, a multistep tolerance adaptive laboratory evolution (TALE) approach was leveraged to achieve this goal. Specifically, a wild-type E. coli K-12-MG1655 and its cognate knockout individual mutants ΔemrE, ΔtolC, and ΔacrB were evolved separately under increasing concentrations of two lipophilic cations, tetraphenylphosphonium (TPP+), and methyltriphenylphosphonium (MTPP+). The evolved strains showed a significant increase in MIC values of both cations and an apparent cross-cation resistance. Sequencing of all evolved mutants highlighted diverse mutational mechanisms that affect the activity of nine MDTs including acrB, mdtK, mdfA, acrE, emrD, tolC, acrA, mdtL, and mdtP. Besides regulatory mutations, several structural mutations were recognized in the proximal binding domain of acrB and the permeation pathways of both mdtK and mdfA. These details can aid in the rational design of MDT inhibitors to efficiently combat efflux-based drug resistance. Additionally, the TALE approach can be scaled to different microbes and molecules of medical and biotechnological relevance.
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Affiliation(s)
- Mohammad S. Radi
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Lachlan J. Munro
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Jesus E. Salcedo-Sora
- GeneMill, Shared Research Facilities, Faculty of Health and Life Sciences, University of Liverpool, Crown St., Liverpool L69 7ZB, UK
| | - Se Hyeuk Kim
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Adam M. Feist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kongens Lyngby, Denmark
- Department of Bioengineering, University of California, 9500 Gilman Drive, La Jolla, San Diego, CA 92093, USA
| | - Douglas B. Kell
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kongens Lyngby, Denmark
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St., Liverpool L69 7ZB, UK
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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: 0] [Impact Index Per Article: 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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44
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Goetz JA, Kuehfuss NM, Botschner AJ, Zhu S, Thompson LK, Cox G. Exploring functional interplay amongst Escherichia coli efflux pumps. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36318669 DOI: 10.1099/mic.0.001261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Bacterial efflux pumps exhibit functional interplay that can translate to additive or multiplicative effects on resistance to antimicrobial compounds. In diderm bacteria, two different efflux pump structural types - single-component inner membrane efflux pumps and cell envelope-spanning multicomponent systems - cooperatively export antimicrobials with cytoplasmic targets from the cell. Harnessing our recently developed efflux platform, which is built upon an extensively efflux-deficient strain of Escherichia coli, here we explore interplay amongst a panel of diverse E. coli efflux pumps. Specifically, we assessed the effect of simultaneously expressing two efflux pump-encoding genes on drug resistance, including single-component inner membrane efflux pumps (MdfA, MdtK and EmrE), tripartite complexes (AcrAB, AcrAD, MdtEF and AcrEF), and the acquired TetA(C) tetracycline resistance pump. Overall, the expression of two efflux pump-encoding genes from the same structural type did not enhance resistance levels regardless of the antimicrobial compound or efflux pump under investigation. In contrast, a combination of the tripartite efflux systems with single-component pumps sharing common substrates provided multiplicative increases to antimicrobial resistance levels. In some instances, resistance was increased beyond the product of resistance provided by the two pumps individually. In summary, the developed efflux platform enables the isolation of efflux pump function, facilitating the identification of interactions between efflux pumps.
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Affiliation(s)
- James A Goetz
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Noah M Kuehfuss
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Alexander J Botschner
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Shawna Zhu
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Laura K Thompson
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Georgina Cox
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
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45
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Moniruzzaman M, Cooper CJ, Uddin MR, Walker JK, Parks JM, Zgurskaya HI. Analysis of Orthogonal Efflux and Permeation Properties of Compounds Leads to the Discovery of New Efflux Pump Inhibitors. ACS Infect Dis 2022; 8:2149-2160. [PMID: 36070489 PMCID: PMC9942517 DOI: 10.1021/acsinfecdis.2c00263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Optimization of compound permeation into Gram-negative bacteria is one of the most challenging tasks in the development of antibacterial agents. Two permeability barriers─the passive diffusion barrier of the outer membrane (OM) and active drug efflux─act synergistically to protect cells from the antibacterial action of compounds. In Escherichia coli (E. coli) and relatives, these two barriers sieve compounds based on different physicochemical properties that are defined by their interactions with OM porins and efflux pumps, respectively. In this study, we critically tested the hypothesis that the best substrates and inhibitors of efflux pumps are compounds that can effectively permeate the OM and are available at relatively high concentrations in the periplasm. For this purpose, we filtered a large subset of the ZINC15 database of commercially available compounds for compounds containing a primary amine, a chemical feature known to facilitate the uptake through E. coli general porins. The assembled library was screened by ensemble docking to AcrA, the periplasmic component of the AcrAB-TolC efflux pump, followed by experimental testing of the top predicted binders for antibacterial activities, efflux recognition, and inhibition. We found that the filtered primary amine library is a rich source of compounds with efflux-inhibiting activities and identified efflux pump inhibitors with novel chemical scaffolds effective against E. coli AcrAB-TolC and efflux pumps of multidrug-resistant clinical isolates of Acinetobacter baumannii. However, primary amines are not required for the recognition of compounds by efflux pumps and their efflux-inhibitory activities.
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Affiliation(s)
- Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - Connor J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Muhammad R Uddin
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - John K Walker
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri 63110, United States
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
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Vergalli J, Chauvet H, Oliva F, Pajović J, Malloci G, Vargiu AV, Réfrégiers M, Ruggerone P, Pagès JM. A framework for dissecting affinities of multidrug efflux transporter AcrB to fluoroquinolones. Commun Biol 2022; 5:1062. [PMID: 36203030 PMCID: PMC9537517 DOI: 10.1038/s42003-022-04024-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 09/22/2022] [Indexed: 11/10/2022] Open
Abstract
Sufficient concentration of antibiotics close to their target is key for antimicrobial action. Among the tools exploited by bacteria to reduce the internal concentration of antibiotics, multidrug efflux pumps stand out for their ability to capture and expel many unrelated compounds out of the cell. Determining the specificities and efflux efficiency of these pumps towards their substrates would provide quantitative insights into the development of antibacterial strategies. In this light, we developed a competition efflux assay on whole cells, that allows measuring the efficacy of extrusion of clinically used quinolones in populations and individual bacteria. Experiments reveal the efficient competitive action of some quinolones that restore an active concentration of other fluoroquinolones. Computational methods show how quinolones interact with the multidrug efflux transporter AcrB. Combining experiments and computations unveils a key molecular mechanism acting in vivo to detoxify bacterial cells. The developed assay can be generalized to the study of other efflux pumps. A competitive efflux assay combined with computational approaches reveal how different quinolones interact with the prototypical bacterial multidrug efflux transporter AcrB, providing insights which may help optimise antibiotics.
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Affiliation(s)
- Julia Vergalli
- UMR_MD1, U-1261, Aix-Marseille Univ, INSERM, IRBA, MCT, Marseille, France
| | - Hugo Chauvet
- DISCO beamline, Synchrotron Soleil, Saint-Aubin, France
| | - Francesco Oliva
- Department of Physics, University of Cagliari, 09042, Monserrato, (CA), Italy
| | - Jelena Pajović
- DISCO beamline, Synchrotron Soleil, Saint-Aubin, France.,University of Belgrade, Faculty of Physics, 11001, Belgrade, Serbia
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, 09042, Monserrato, (CA), Italy
| | | | - Matthieu Réfrégiers
- DISCO beamline, Synchrotron Soleil, Saint-Aubin, France.,Centre de Biophysique Moléculaire, CNRS UPR4301, Rue Charles Sadron, Orléans, France
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, 09042, Monserrato, (CA), Italy
| | - Jean-Marie Pagès
- UMR_MD1, U-1261, Aix-Marseille Univ, INSERM, IRBA, MCT, Marseille, France.
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47
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Bacterial diet modulates tamoxifen-induced death via host fatty acid metabolism. Nat Commun 2022; 13:5595. [PMID: 36151093 PMCID: PMC9508336 DOI: 10.1038/s41467-022-33299-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 09/06/2022] [Indexed: 11/18/2022] Open
Abstract
Tamoxifen is a selective estrogen receptor (ER) modulator that is used to treat ER-positive breast cancer, but that at high doses kills both ER-positive and ER-negative breast cancer cells. We recapitulate this off-target effect in Caenorhabditis elegans, which does not have an ER ortholog. We find that different bacteria dramatically modulate tamoxifen toxicity in C. elegans, with a three-order of magnitude difference between animals fed Escherichia coli, Comamonas aquatica, and Bacillus subtilis. Remarkably, host fatty acid (FA) biosynthesis mitigates tamoxifen toxicity, and different bacteria provide the animal with different FAs, resulting in distinct FA profiles. Surprisingly these bacteria modulate tamoxifen toxicity by different death mechanisms, some of which are modulated by FA supplementation and others by antioxidants. Together, this work reveals a complex interplay between microbiota, FA metabolism and tamoxifen toxicity that may provide a blueprint for similar studies in more complex mammals. Here, Diot et al. use the nematode Caenorhabditis elegans as a model to identify off-target toxicity mechanisms for tamoxifen, and find that these include fatty acid metabolism and cell death, which can be modulated by different bacterial species.
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48
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Jubair N, R. M, Fatima A, Mahdi YK, Abdullah NH. Evaluation of Catechin Synergistic and Antibacterial Efficacy on Biofilm Formation and acrA Gene Expression of Uropathogenic E. coli Clinical Isolates. Antibiotics (Basel) 2022; 11:antibiotics11091223. [PMID: 36140002 PMCID: PMC9495025 DOI: 10.3390/antibiotics11091223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Uropathogenic Escherichia coli has a propensity to build biofilms to resist host defense and antimicrobials. Recurrent urinary tract infection (UTI) caused by multidrug-resistant, biofilm-forming E. coli is a significant public health problem. Consequently, searching for alternative medications has become essential. This study was undertaken to investigate the antibacterial, synergistic, and antibiofilm activities of catechin isolated from Canarium patentinervium Miq. against three E. coli ATCC reference strains (ATCC 25922, ATCC 8739, and ATCC 43895) and fifteen clinical isolates collected from UTI patients in Baghdad, Iraq. In addition, the expression of the biofilm-related gene, acrA, was evaluated with and without catechin treatment. Molecular docking was performed to evaluate the binding mode between catechin and the target protein using Autodock Vina 1.2.0 software. Catechin demonstrated significant bactericidal activity with a minimum inhibitory concentration (MIC) range of 1–2 mg/mL and a minimum bactericidal concentration (MBC) range of 2–4 mg/mL and strong synergy when combined with tetracycline at the MBC value. In addition, catechin substantially reduced E. coli biofilm by downregulating the acrA gene with a reduction percent ≥ 60%. In silico analysis revealed that catechin bound with high affinity (∆G = −8.2 kcal/mol) to AcrB protein (PDB-ID: 5ENT), one of the key AcrAB-TolC efflux pump proteins suggesting that catechin might inhibit the acrA gene indirectly by docking at the active site of AcrB protein.
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Affiliation(s)
- Najwan Jubair
- Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur 56000, Malaysia
- Correspondence: (N.J.); (M.R.)
| | - Mogana R.
- Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur 56000, Malaysia
- Correspondence: (N.J.); (M.R.)
| | - Ayesha Fatima
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, 34820 Istanbul, Turkey
| | - Yasir K. Mahdi
- Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur 56000, Malaysia
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49
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Martin CS, Jubelin G, Darsonval M, Leroy S, Leneveu-Jenvrin C, Hmidene G, Omhover L, Stahl V, Guillier L, Briandet R, Desvaux M, Dubois-Brissonnet F. Genetic, physiological, and cellular heterogeneities of bacterial pathogens in food matrices: Consequences for food safety. Compr Rev Food Sci Food Saf 2022; 21:4294-4326. [PMID: 36018457 DOI: 10.1111/1541-4337.13020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 01/28/2023]
Abstract
In complex food systems, bacteria live in heterogeneous microstructures, and the population displays phenotypic heterogeneities at the single-cell level. This review provides an overview of spatiotemporal drivers of phenotypic heterogeneity of bacterial pathogens in food matrices at three levels. The first level is the genotypic heterogeneity due to the possibility for various strains of a given species to contaminate food, each of them having specific genetic features. Then, physiological heterogeneities are induced within the same strain, due to specific microenvironments and heterogeneous adaptative responses to the food microstructure. The third level of phenotypic heterogeneity is related to cellular heterogeneity of the same strain in a specific microenvironment. Finally, we consider how these phenotypic heterogeneities at the single-cell level could be implemented in mathematical models to predict bacterial behavior and help ensure microbiological food safety.
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Affiliation(s)
- Cédric Saint Martin
- MICALIS Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France.,Université Clermont Auvergne, INRAE, UMR454 MEDIS, Clermont-Ferrand, France
| | - Grégory Jubelin
- Université Clermont Auvergne, INRAE, UMR454 MEDIS, Clermont-Ferrand, France
| | - Maud Darsonval
- MICALIS Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Sabine Leroy
- Université Clermont Auvergne, INRAE, UMR454 MEDIS, Clermont-Ferrand, France
| | - Charlène Leneveu-Jenvrin
- MICALIS Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France.,Association pour le Développement de l'Industrie de la Viande (ADIV), Clermont-Ferrand, France
| | - Ghaya Hmidene
- Risk Assessment Department, ANSES, Maisons-Alfort, France
| | - Lysiane Omhover
- Aerial, Technical Institute of Agro-Industry, Illkirch, France
| | - Valérie Stahl
- Aerial, Technical Institute of Agro-Industry, Illkirch, France
| | | | - Romain Briandet
- MICALIS Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Mickaël Desvaux
- Université Clermont Auvergne, INRAE, UMR454 MEDIS, Clermont-Ferrand, France
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50
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Munro LJ, Kell DB. Analysis of a Library of Escherichia coli Transporter Knockout Strains to Identify Transport Pathways of Antibiotics. Antibiotics (Basel) 2022; 11:antibiotics11081129. [PMID: 36009997 PMCID: PMC9405208 DOI: 10.3390/antibiotics11081129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/15/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Antibiotic resistance is a major global healthcare issue. Antibiotic compounds cross the bacterial cell membrane via membrane transporters, and a major mechanism of antibiotic resistance is through modification of the membrane transporters to increase the efflux or reduce the influx of antibiotics. Targeting these transporters is a potential avenue to combat antibiotic resistance. In this study, we used an automated screening pipeline to evaluate the growth of a library of 447 Escherichia coli transporter knockout strains exposed to sub-inhibitory concentrations of 18 diverse antimicrobials. We found numerous knockout strains that showed more resistant or sensitive phenotypes to specific antimicrobials, suggestive of transport pathways. We highlight several specific drug-transporter interactions that we identified and provide the full dataset, which will be a useful resource in further research on antimicrobial transport pathways. Overall, we determined that transporters are involved in modulating the efficacy of almost all the antimicrobial compounds tested and can, thus, play a major role in the development of antimicrobial resistance.
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Affiliation(s)
- Lachlan Jake Munro
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Douglas B. Kell
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
- Correspondence: or
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