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Lee JH, Kim SG, Jang KM, Shin K, Jin H, Kim DW, Jeong BC, Lee SH. Elucidation of critical chemical moieties of metallo-β-lactamase inhibitors and prioritisation of target metallo-β-lactamases. J Enzyme Inhib Med Chem 2024; 39:2318830. [PMID: 38488135 PMCID: PMC10946278 DOI: 10.1080/14756366.2024.2318830] [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: 12/30/2023] [Accepted: 02/07/2024] [Indexed: 03/19/2024] Open
Abstract
The urgent demand for effective countermeasures against metallo-β-lactamases (MBLs) necessitates development of novel metallo-β-lactamase inhibitors (MBLIs). This study is dedicated to identifying critical chemical moieties within previously developed MBLIs, and critical MBLs should serve as the target in MBLI evaluations. Using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), a systematic literature analysis was conducted, and the NCBI RefSeq genome database was exploited to access the abundance profile and taxonomic distribution of MBLs and their variant types. Through the implementation of two distinct systematic approaches, we elucidated critical chemical moieties of MBLIs, providing pivotal information for rational drug design. We also prioritised MBLs and their variant types, highlighting the imperative need for comprehensive testing to ensure the potency and efficacy of the newly developed MBLIs. This approach contributes valuable information to advance the field of antimicrobial drug discovery.
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Affiliation(s)
- Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Sang-Gyu Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju, Republic of Korea
| | - Kyung-Min Jang
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Kyoungmin Shin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Hyeonku Jin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Dae-Wi Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju, Republic of Korea
| | - Byeong Chul Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
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Kar B, Kundu CN, Singh MK, Dehury B, Pati S, Bhattacharya D. Identification of potential inhibitor against CTX-M-3 and CTX-M-15 proteins: an in silico and in vitro study. J Biomol Struct Dyn 2024; 42:177-193. [PMID: 36995090 DOI: 10.1080/07391102.2023.2192811] [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: 01/19/2023] [Accepted: 03/10/2023] [Indexed: 03/31/2023]
Abstract
Extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae infection is a serious global threat. ESBLs target 3rd generation cephalosporin antibiotics, the most commonly prescribed medicine for gram-negative bacterial infections. As bacteria are prone to develop resistance against market-available ESBL inhibitors, finding a novel and effective inhibitor has become mandatory. Among ESBL, the worldwide reported two enzymes, CTX-M-15 and CTX-M-3, are selected for the present study. CTX-M-3 protein was modeled, and two thousand phyto-compounds were virtually screened against both proteins. After filtering through docking and pharmacokinetic properties, four phyto-compounds (catechin gallate, silibinin, luteolin, uvaol) were further selected for intermolecular contact analysis and molecular dynamics (MD) simulation. MD trajectory analysis results were compared, revealing that both catechin gallate and silibinin had a stabilizing effect against both proteins. Silibinin having the lowest docking score, also displayed the lowest MIC (128 µg/mL) against the bacterial strains. Silibinin was also reported to have synergistic activity with cefotaxime and proved to have bactericidal effect. Nitrocefin assay confirmed that silibinin could inhibit beta-lactamase enzyme only in living cells, unlike clavulanic acid. Thus the present study validated the CTX-M inhibitory activity of silibinin both in silico and in vitro and suggested its promotion for further studies as a potential lead. The present study adopted a protocol through the culmination of bioinformatics and microbiological analyses, which will help future researchers identify more potential leads and design new effective drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bipasa Kar
- Department of Health Research, Ministry of Health & Family Welfare, Govt. of India, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, India
| | - Chanakya Nath Kundu
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, India
| | - Mahender Kumar Singh
- Data Science Laboratory, National Brain Research Centre, Gurgaon, Haryana, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Sanghamitra Pati
- Department of Health Research, Ministry of Health & Family Welfare, Govt. of India, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Debdutta Bhattacharya
- Department of Health Research, Ministry of Health & Family Welfare, Govt. of India, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
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Zhang JW, Guo C, Xuan CG, Gu JW, Cui ZN, Zhang J, Zhang L, Jiang W, Zhang LQ. High-Throughput, Quantitative Screening of Quorum-Sensing Inhibitors Based on a Bacterial Biosensor. ACS Chem Biol 2023; 18:2544-2554. [PMID: 37983266 DOI: 10.1021/acschembio.3c00537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Quorum sensing (QS) is a cell-cell communication mechanism by which bacteria synchronize social behaviors such as biofilm formation and virulence factor secretion by producing and sensing small molecular signals. Quorum quenching (QQ) by degrading signals or blocking signal transmissions has become a promising strategy for disrupting QS and preventing bacterial infection and biofilm formation. However, studies of high-throughput screening and identification approaches for quorum-sensing inhibitors (QSIs) are still inadequate. In this work, we developed a sensitive, high-throughput approach for screening QSIs based on the bacterial biosensor strain Agrobacterium tumefaciens N5 (pBA7P), which contains a traG gene promoter induced by QS signals fused with a promoterless β-lactamase gene reporter. Using this approach, we identified 31 QQ bacteria from ∼2000 soil bacterial isolates, some belonging to the genera Bosea, Cupriavidus, and Flavobacterium that have not been reported previously as QQ bacteria. We also identified four QS inhibitory compounds and one QS signal analogue from ∼5000 small-molecule compounds, which profoundly affected the expression of QS-regulated genes and phenotypes of the pathogenic bacteria. This high-throughput screening system is effective and sensitive for screening of both QQ microbes and small molecules, enabling the discovery of a wide variety of biocompatible compounds.
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Affiliation(s)
- Jun-Wei Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Cong Guo
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Chen-Guang Xuan
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jing-Wen Gu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China
| | - Zi-Ning Cui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
| | - Jing Zhang
- Institute of Functional Molecules, Shenyang University of Chemical Technology, Shenyang, Liaoning 110142, China
| | - Lixin Zhang
- Institute of Functional Molecules, Shenyang University of Chemical Technology, Shenyang, Liaoning 110142, China
| | - Wenjun Jiang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Li-Qun Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
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Ayipo YO, Ahmad I, Alananzeh W, Lawal A, Patel H, Mordi MN. Computational modelling of potential Zn-sensitive non-β-lactam inhibitors of imipenemase-1 (IMP-1). J Biomol Struct Dyn 2023; 41:10096-10116. [PMID: 36476097 DOI: 10.1080/07391102.2022.2153168] [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: 07/01/2022] [Accepted: 11/24/2022] [Indexed: 12/13/2022]
Abstract
Antibiotic resistance (AR) remains one of the leading global health challenges, mostly implicated in disease-related deaths. The Enterobacteriaceae-producing metallo-β-lactamases (MBLs) are critically involved in AR pathogenesis through Zn-dependent catalytic destruction of β-lactam antibiotics, yet with limited successful clinical inhibitors. The efficacy of relevant broad-spectrum β-lactams including imipenem and meropenem are seriously challenged by their susceptibility to the Zn-dependent carbapenemase hydrolysis, as such, searching for alternatives remains imperative. In this study, computational molecular modelling and virtual screening methods were extensively applied to identify new putative Zn-sensitive broad-spectrum inhibitors of MBLs, specifically imipenemase-1 (IMP-1) from the IBScreen database. Three ligands, STOCK3S-30154, STOCK3S-30418 and STOCK3S-30514 selectively displayed stronger binding interactions with the enzymes compared to reference inhibitors, imipenem and meropenem. For instance, the ligands showed molecular docking scores of -9.450, -8.005 and -10.159 kcal/mol, and MM-GBSA values of -40.404, -31.902 and -33.680 kcal/mol respectively against the IMP-1. Whereas, imipenem and meropenem showed docking scores of -9.038 and -10.875 kcal/mol, and MM-GBSA of -31.184 and -32.330 kcal/mol respectively against the enzyme. The ligands demonstrated good thermodynamic stability and compactness in complexes with IMP-1 throughout the 100 ns molecular dynamics (MD) trajectories. Interestingly, their binding affinities and stabilities were significantly affected in contacts with the remodelled Zn-deficient IMP-1, indicating sensitivity to the carbapenemase active Zn site, however, with non-β-lactam scaffolds, tenable to resist catalytic hydrolysis. They displayed ideal drug-like ADMET properties, thus, representing putative Zn-sensitive non-β-lactam inhibitors of IMP-1 amenable for further experimental studies.
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Affiliation(s)
- Yusuf Oloruntoyin Ayipo
- Centre for Drug Research, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia
- Department of Chemistry and Industrial Chemistry, Kwara State University, Ilorin, Nigeria
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Waleed Alananzeh
- Centre for Drug Research, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia
| | - Amudat Lawal
- Department of Chemistry, University of Ilorin, Ilorin, Nigeria
| | - Harun Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Mohd Nizam Mordi
- Centre for Drug Research, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia
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Bibi Z, Asghar I, Ashraf NM, Zeb I, Rashid U, Hamid A, Ali MK, Hatamleh AA, Al-Dosary MA, Ahmad R, Ali M. Prediction of Phytochemicals for Their Potential to Inhibit New Delhi Metallo β-Lactamase (NDM-1). Pharmaceuticals (Basel) 2023; 16:1404. [PMID: 37895875 PMCID: PMC10610165 DOI: 10.3390/ph16101404] [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: 08/09/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
The effectiveness of all antibiotics in the β-lactam group to cure bacterial infections has been impaired by the introduction of the New Delhi Metallo-β-lactamase (NDM-1) enzyme. Attempts have been made to discover a potent chemical as an inhibitor to this enzyme in order to restore the efficacy of antibiotics. However, it has been a challenging task to develop broad-spectrum inhibitors of metallo-β-lactamases. Lack of sequence homology across metallo-β-lactamases (MBLs), the rapidly evolving active site of the enzyme, and structural similarities between human enzymes and metallo-β-lactamases, are the primary causes for the difficulty in the development of these inhibitors. Therefore, it is imperative to concentrate on the discovery of an effective NDM-1 inhibitor. This study used various in silico approaches, including molecular docking and molecular dynamics simulations, to investigate the potential of phytochemicals to inhibit the NDM-1 enzyme. For this purpose, a library of about 59,000 phytochemicals was created from the literature and other databases, including FoodB, IMPPAT, and Phenol-Explorer. A physiochemical and pharmacokinetics analysis was performed to determine possible toxicity and mutagenicity of the ligands. Following the virtual screening, phytochemicals were assessed for their binding with NDM-1using docking scores, RMSD values, and other critical parameters. The docking score was determined by selecting the best conformation of the protein-ligand complex. Three phytochemicals, i.e., butein (polyphenol), monodemethylcurcumin (polyphenol), and rosmarinic acid (polyphenol) were identified as result of pharmacokinetics and molecular docking studies. Furthermore, molecular dynamics simulations were performed to determine structural stabilities of the protein-ligand complexes. Monodemethylcurcumin, butein, and rosmarinic acid were identified as potential inhibitors of NDM-1 based on their low RMSD, RMSF, hydrogen bond count, average Coulomb-Schrödinger interaction energy, and Lennard-Jones-Schrödinger interaction energy. The present investigation suggested that these phytochemicals might be promising candidates for future NDM-1 medication development to respond to antibiotic resistance.
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Affiliation(s)
- Zainab Bibi
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
| | - Irfa Asghar
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
| | - Naeem Mahmood Ashraf
- School of Biochemistry and Biotechnology, University of Punjab, Lahore P.O. Box 54590, Pakistan;
| | - Iftikhar Zeb
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
| | - Umer Rashid
- Department of Chemistry, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan;
| | - Arslan Hamid
- LIMES Institute, University of Bonn, D-53113 Bonn, Germany;
| | - Maria Kanwal Ali
- Institute of Nuclear Medicine, Oncology and Radiotherapy (INOR), Abbottabad 22060, Pakistan;
| | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.A.H.); (M.A.A.-D.)
| | - Munirah Abdullah Al-Dosary
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.A.H.); (M.A.A.-D.)
| | - Raza Ahmad
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
| | - Muhammad Ali
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
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Xie P, Gao Y, Wu C, Li X, Yang Y. The inhibitory mechanism of echinacoside against Staphylococcus aureus Ser/Thr phosphatase Stp1 by virtual screening and molecular modeling. J Mol Model 2023; 29:320. [PMID: 37725157 DOI: 10.1007/s00894-023-05723-0] [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: 06/26/2023] [Accepted: 09/09/2023] [Indexed: 09/21/2023]
Abstract
CONTEXT Stp1 is a new potential target closely related to the pathogenicity of Staphylococcus aureus (S. aureus). In this study, effective Stp1 inhibitors were screened via virtual screening and enzyme activity experiments, and the inhibition mechanism was analyzed using molecular dynamics simulation. METHODS AutoDock Vina 4.0 software was used for virtual screening. The molecular structures of Stp1 and ligands were obtained from the RCSB Protein Data Bank and Zinc database, respectively. The molecular dynamics simulation used the Gromacs 4.5.5 software package with the Amberff99sb force field and TIP3P water model. AutoDock Tools was used to add polar hydrogen atoms to Stp1 and distribute part of the charge generated by Kollman's combined atoms. The binding free energies were calculated using the Amber 10 package. RESULTS The theoretical calculation results are consistent with the experimental results. We found that echinacoside (ECH) substantially inhibits the hydrolytic activity of Stp1. ECH competes with the substrate by binding to the active center of Stp1, resulting in a decrease in Stp1 activity. In addition, Met39, Gly41, Asp120, Asn162, and Ile163 were identified to play key roles in the binding of Stp1 to ECH. The benzene ring of ECH also plays an important role in complex binding. These findings provide a robust foundation for the development of innovative anti-infection drugs.
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Affiliation(s)
- Peng Xie
- Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China
| | - Yue Gao
- Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China
| | - Chenqi Wu
- Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China
| | - Xuenan Li
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Yanan Yang
- Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China.
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Gao Y, Wang H, Li X, Niu X. Molecular mechanism of green tea polyphenol epicatechin gallate attenuating Staphylococcus aureus pathogenicity by targeting Ser/Thr phosphatase Stp1. Food Funct 2023; 14:4792-4806. [PMID: 37128867 DOI: 10.1039/d3fo00170a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In this study, through virtual screening and in vitro bioactivity assays, we discovered that (-)-epicatechin gallate (ECG), a polyphenol compound extracted from green tea, demonstrated marked anti-Ser/Thr phosphatase (Stp1) activity towards Staphylococcus aureus (S. aureus) with an IC50 value of 8.35 μM. By targeting S. aureus Stp1, ECG prevented the up-regulation of virulence gene and the formation of antibody membrane and protected the mice from S. aureus infection. Through MD simulation, the allosteric inhibitory mechanism of ECG on Stp1 was determined. The Stp1-ECG complex model underwent a significant change in conformation; its flap subdomain changed from opening to closing, whereas Stp1 activity was lost when bound to ECG. In addition, the MD simulation results of Stp1 and several tea polyphenol compounds showed that gallate groups and fewer adjacent phenolic hydroxyl groups contributed to the binding of Stp1 and inhibitors. As an inhibitor targeting S. aureus Stp1, ECG reduced the pathogenicity of S. aureus without inhibiting S. aureus, which largely reduced the possibility of drug resistance. Our findings demonstrated a novel molecular mechanism of green tea as the usual drink against S. aureus infection and elucidated the future design of allosteric inhibitors targeting Stp1.
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Affiliation(s)
- Yawen Gao
- College of Food Science and Engineering, Jilin University, Changchun 130062, P.R. China.
| | - Hongsu Wang
- College of Food Science and Engineering, Jilin University, Changchun 130062, P.R. China.
| | - Xuening Li
- College of Food Science and Engineering, Jilin University, Changchun 130062, P.R. China.
| | - Xiaodi Niu
- College of Food Science and Engineering, Jilin University, Changchun 130062, P.R. China.
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Kar B, Kundu CN, Pati S, Bhattacharya D. Discovery of phyto-compounds as novel inhibitors against NDM-1 and VIM-1 protein through virtual screening and molecular modelling. J Biomol Struct Dyn 2023; 41:1267-1280. [PMID: 34961397 DOI: 10.1080/07391102.2021.2019125] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Amid the rise of multi-drug resistance among bacterial pathogens, the drying of the development pipeline of new antibiotics is worrisome. In search of new effective alternatives, phytocompounds can be considered a good one because of their immense antimicrobial property, low toxicity and huge structural diversity. In the present study, 200 phytocompounds were targeted against two Metallo β-lactamase (MBL) enzymes (NDM-1 and VIM-1) through molecular docking and meropenem was used as a reference drug. The phytocompounds with docking score ≤-8.0 kcal/mol were screened for their pharmacokinetic properties. The three best selected phytocompounds are Coriandrinonediol, Oleanderolide and Uzarigenin. Molecular docking helps to understand binding affinity. The selected phytocompounds showed better result than meropenem. Molecular interaction study reveals their competitive mechanism of inhibition against the target proteins. Coriandrinonediol has docking score -8.3 kcal/mol (NDM-1) and -8.9 kcal/mol (VIM-1), and oleanderolide has docking score -8.2 kcal/mol (NDM-1) and -9.3 kcal/mol (VIM-1). Uzarigenin has the highest binding affinity (-10.4 kcal/mol) among the three against VIM-1 and the lowest binding affinity (-8.1 kcal/mol) against NDM-1. Molecular dynamic (MD) simulation study also supports the stability and flexibility of the above phytocompounds during the MD run. Among the abovementioned three phytocompounds, oleanderolide has given the best result against both target proteins. These phytocompounds are first time reported as MBL inhibitors and their promising in silico results encourage to promote them for further investigation for in vitro and in vivo clinical trials.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bipasa Kar
- ICMR-Regional Medical Research Centre (Dept. of Health Research, Ministry of Health & Family Welfare, Govt. of India), Chandrasekharpur, Odisha, India.,KIIT School of Biotechnology, Patia, Bhubaneswar, Odisha, India
| | | | - Sanghamitra Pati
- ICMR-Regional Medical Research Centre (Dept. of Health Research, Ministry of Health & Family Welfare, Govt. of India), Chandrasekharpur, Odisha, India
| | - Debdutta Bhattacharya
- ICMR-Regional Medical Research Centre (Dept. of Health Research, Ministry of Health & Family Welfare, Govt. of India), Chandrasekharpur, Odisha, India
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Awada B, Chahine DA, Derbaj G, Khalek PA, Awad MK, Fayad AA. Antimicrobial Natural Products Derived from Microorganisms Inhabiting the MENA Region. Nat Prod Commun 2023. [DOI: 10.1177/1934578x231154989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Objective/Background Natural products (NPs) derived from microorganisms are the basis of a plethora of clinically utilized medications, namely, antimicrobial remedies. Although these secondary metabolites have been extensively explored all over the planet, they remain understudied in the Middle East and North Africa (MENA) region. Methods A literature search was conducted to first find NPs that were isolated from environmental fungi and bacteria that inhabit the soils and seawater of the MENA region. Then, purified molecules with biological activity against pathogenic bacteria, biofilms, fungi, and parasites were described in terms of structure, function, and location. Moreover, the methods that could be used to ameliorate the discovery of novel NPs from this region were investigated. Results A multitude of antimicrobial molecules from various chemical classes were found to be derived from the environmental microbes of MENA. Although many were rediscovered, some represented novel structural scaffolds for novel families of antimicrobial agents. Additionally, the geographical distribution showed a high number of these NPs were unraveled in a restricted area leaving much of MENA untapped. Furthermore, as relatively traditional and low-efficiency methods were typically used in the discovery process, advanced high-throughput techniques were suggested to enhance this practice at the regional level. Conclusion MENA represents a fairly unexploited region where antimicrobial drug discovery could be performed comprehensively through the concomitant exploration of untouched geographical locations and advanced molecular techniques.
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Affiliation(s)
- Bassel Awada
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
| | - Dany Abi Chahine
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
- Laboratory of Biodiversity and Functional Genomics, UR EGP, Faculty of Science, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
| | - Ghada Derbaj
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
| | - Pascal Abdel Khalek
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
| | - Mireille Kallassy Awad
- Laboratory of Biodiversity and Functional Genomics, UR EGP, Faculty of Science, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
| | - Antoine Abou Fayad
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
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Xu L, Zhou Y, Niu S, Liu Z, Zou Y, Yang Y, Feng H, Liu D, Niu X, Deng X, Wang Y, Wang J. A novel inhibitor of monooxygenase reversed the activity of tetracyclines against tet(X3)/tet(X4)-positive bacteria. EBioMedicine 2022; 78:103943. [PMID: 35306337 PMCID: PMC8933826 DOI: 10.1016/j.ebiom.2022.103943] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 02/26/2022] [Accepted: 02/28/2022] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Tigecycline is one of the few last-resort antibiotics for the treatment of carbapenem-resistant Enterobacteriaceae infection, the incidence of which has been rapidly increasing. However, the emergence and spread of tigecycline resistance genes tet(X) (including tet(X3) and tet(X4)) has largely compromised the efficient usage of tetracyclines in the clinical settings. METHODS The synergistic effect was determined by a checkerboard minimum inhibitory concentration (MIC) assay, a time-killing assay and scanning electron microscopy (SEM) analysis. In-depth mechanisms were defined using an enzyme inhibition assay, western blotting, RT-PCR analysis, molecular dynamics (MD) simulations, biolayer interferometry (BLI) assay and metabolomics analysis. FINDINGS Herein, our work identified a natural compound, plumbagin, as an effective broad-spectrum inhibitor of Tet(X) (also known as monooxygenase) by simultaneously inhibiting the activity and the production of Tet(X3)/Tet(X4). Plumbagin in combination with tetracyclines showed a synergistic bactericidal effect against Tet(X3)/Tet(X4)-producing bacteria. Mechanistic studies revealed that direct engagement of plumbagin with the catalytic pocket of Tet(X3)/Tet(X4) induced an alternation in its secondary structure to inhibit the activity of these monooxygenases. As a consequence, monotherapy or combination therapy with plumbagin increases the oxidative stress and metabolism in bacteria. Moreover, in a mouse systemic infection model of tet(X4)-positive E. coli, the combination of plumbagin and methacycline exhibited remarkable treatment benefits, as shown by a reduced bacterial load and the alleviation of pathological injury. INTERPRETATION Plumbagin, as an inhibitor of Tet(X3)/Tet(X4), represents a promising lead drug, as well as an adjunct with tetracyclines to treat bacterial infections, especially for extensively drug-resistant bacteria harbouring Tet(X3)/Tet(X4). FUNDING The National Natural Science Foundation of China.
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Affiliation(s)
- Lei Xu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yonglin Zhou
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Sen Niu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhiying Liu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yinuo Zou
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yanan Yang
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Haihua Feng
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Dejun Liu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaodi Niu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xuming Deng
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China.
| | - Jianfeng Wang
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.
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11
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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12
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Jackson AC, Pinter TBJ, Talley DC, Baker-Agha A, Patel D, Smith PJ, Franz KJ. Benzimidazole and Benzoxazole Zinc Chelators as Inhibitors of Metallo-β-Lactamase NDM-1. ChemMedChem 2021; 16:654-661. [PMID: 33211374 PMCID: PMC8114186 DOI: 10.1002/cmdc.202000607] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Indexed: 12/11/2022]
Abstract
Bacterial expression of β-lactamases, which hydrolyze β-lactam antibiotics, contributes to the growing threat of antibacterial drug resistance. Metallo-β-lactamases, such as NDM-1, use catalytic zinc ions in their active sites and hydrolyze nearly all clinically available β-lactam antibiotics. Inhibitors of metallo-β-lactamases are urgently needed to overcome this resistance mechanism. Zinc-binding compounds are promising leads for inhibitor development, as many NDM-1 inhibitors contain zinc-binding pharmacophores. Here, we evaluated 13 chelating agents containing benzimidazole and benzoxazole scaffolds as NDM-1 inhibitors. Six of the compounds showed potent inhibitory activity with IC50 values as low as 0.38 μM, and several compounds restored the meropenem susceptibility of NDM-1-expressing E. coli. Spectroscopic and docking studies suggest ternary complex formation as the mechanism of inhibition, making these compounds promising for development as NDM-1 inhibitors.
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Affiliation(s)
| | | | - Daniel C Talley
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Adnan Baker-Agha
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Dhruvil Patel
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Paul J Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
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13
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Inhibitory Potential of Polyclonal Camel Antibodies against New Delhi Metallo-β-lactamase-1 (NDM-1). Molecules 2020; 25:molecules25194453. [PMID: 32998307 PMCID: PMC7584030 DOI: 10.3390/molecules25194453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 11/16/2022] Open
Abstract
New Delhi Metallo-β-lactamase-1 (NDM-1) is the most prevalent type of metallo-β-lactamase, able to hydrolyze almost all antibiotics of the β-lactam group, leading to multidrug-resistant bacteria. To date, there are no clinically relevant inhibitors to fight NDM-1. The use of dromedary polyclonal antibody inhibitors against NDM-1 represents a promising new class of molecules with inhibitory activity. In the current study, immunoreactivities of dromedary Immunoglobulin G (IgG) isotypes containing heavy-chain and conventional antibodies were tested after successful immunization of dromedary using increasing amounts of the recombinant NDM-1 enzyme. Inhibition kinetic assays, performed using a spectrophotometric method with nitrocefin as a reporter substrate, demonstrated that IgG1, IgG2, and IgG3 were able to inhibit not only the hydrolytic activity of NDM-1 but also Verona integron-encoded metallo-β-lactamase (VIM-1) (subclass B1) and L1 metallo-β-lactamase (L1) (subclass B3) with inhibitory concentration (IC50) values ranging from 100 to 0.04 μM. Investigations on the ability of IgG subclasses to reduce the growth of recombinant Escherichia coli BL21(DE3)/codon plus cells containing the recombinant plasmid expressing NDM-1, L1, or VIM-1 showed that the addition of IgGs (4 and 8 mg/L) to the cell culture was unable to restore the susceptibility of carbapenems. Interestingly, IgGs were able to interact with NDM-1, L1, and VIM-1 when tested on the periplasm extract of each cultured strain. The inhibitory concentration was in the micromolar range for all β-lactams tested. A visualization of the 3D structural basis using the three enzyme Protein Data Bank (PDB) files supports preliminarily the recorded inhibition of the three MBLs.
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Virtual screening of approved drugs as potential SARS-CoV-2 main protease inhibitors. Comput Biol Chem 2020; 88:107325. [PMID: 32623357 PMCID: PMC7316061 DOI: 10.1016/j.compbiolchem.2020.107325] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/30/2020] [Accepted: 06/25/2020] [Indexed: 12/28/2022]
Abstract
The main protease of SARS-CoV-2 has a highly flexible active site. Drug repurposing is a treatment opportunity in the current COVID-19 pandemic. Nine drugs merit testing as inhibitors of the SARS-CoV-2 main protease.
The global emergency caused by COVID-19 makes the discovery of drugs capable of inhibiting SARS-CoV-2 a priority, to reduce the mortality and morbidity of this disease. Repurposing approved drugs can provide therapeutic alternatives that promise rapid and ample coverage because they have a documented safety record, as well as infrastructure for large-scale production. The main protease of SARS-CoV-2 (Mpro) is an excellent therapeutic target because it is critical for viral replication; however, Mpro has a highly flexible active site that must be considered when performing computer-assisted drug discovery. In this work, potential inhibitors of the main protease (Mpro) of SARS-Cov-2 were identified through a docking-assisted virtual screening procedure. A total of 4384 drugs, all approved for human use, were screened against three conformers of Mpro. The ligands were further studied through molecular dynamics simulations and binding free energy analysis. A total of nine currently approved molecules are proposed as potential inhibitors of SARS-CoV-2. These molecules can be further tested to speed the development of therapeutics against COVID-19.
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