1
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Ghomashi S, Ghomashi R, Damavandi MS, Fakhar Z, Mousavi SY, Salari-Jazi A, Gharaghani S, Massah AR. Evaluation of antibacterial, cytotoxicity, and apoptosis activity of novel chromene-sulfonamide hybrids synthesized under solvent-free conditions and 3D-QSAR modeling studies. Sci Rep 2024; 14:12878. [PMID: 38834651 DOI: 10.1038/s41598-024-63535-5] [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: 03/07/2024] [Accepted: 05/29/2024] [Indexed: 06/06/2024] Open
Abstract
In this study, eleven novel chromene sulfonamide hybrids were synthesized by a convenient method in accordance with green chemistry. At first, chromene derivatives (1-9a) were prepared through the multi-component reaction between aryl aldehydes, malononitrile, and 3-aminophenol. Then, synthesized chromenes were reacted with appropriate sulfonyl chlorides by grinding method to give the corresponding chromene sulfonamide hybrids (1-11b). Synthesized hybrids were obtained in good to high yield and characterized by IR, 1HNMR, 13CNMR, CHN and melting point techniques. In addition, the broth microdilution assay was used to determine the minimal inhibitory concentration of newly synthesized chromene-sulfonamide hybrids. The MTT test was used to determine the cytotoxicity and apoptotic activity of the newly synthesized compounds against fibroblast L929 cells. The 3D‑QSAR analysis confirmed the experimental assays, demonstrating that our predictive model is useful for developing new antibacterial inhibitors. Consequently, molecular docking studies were performed to validate the findings of the 3D-QSAR analysis, confirming the potential binding interactions of the synthesized chromene-sulfonamide hybrids with the target enzymes. Molecular docking studies were employed to support the 3D-QSAR predictions, providing insights into the binding interactions between the newly synthesized chromene-sulfonamide hybrids and their target bacterial enzymes, thereby reinforcing the potential efficacy of these compounds as antibacterial agents. Also, some of the experimental outcomes supported or conflicted with the pharmacokinetic prediction (especially about compound carcinogenicity). The performance of ADMET predictor results was assessed. The work presented here proposes a computationally driven strategy for designing and discovering a new sulfonamide scaffold for bacterial inhibition.
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Affiliation(s)
- Shakila Ghomashi
- Department of Medicinal Chemistry, Shahreza Branch, Islamic Azad University, P.O. Box 311-86145, Shahreza, Isfahan, Iran
| | - Reihane Ghomashi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Sadegh Damavandi
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zeynab Fakhar
- Laboratory of Bioinformatics and Drug Design (LBD), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Seyedeh Yasaman Mousavi
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Azhar Salari-Jazi
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
- Department of Drug Development and Innovation, Behban Pharmed Lotus, Tehran, Iran.
| | - Sajjad Gharaghani
- Laboratory of Bioinformatics and Drug Design (LBD), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | - Ahmad Reza Massah
- Department of Chemistry, Shahreza Branch, Islamic Azad University, P.O. Box 311-86145, Shahreza, Isfahan, Iran.
- Department of Chemistry, Brock University, St. Catharines, ON, Canada.
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2
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Cheng Z, Aitha M, Thomas CA, Sturgill A, Fairweather M, Hu A, Bethel CR, Rivera DD, Dranchak P, Thomas PW, Li H, Feng Q, Tao K, Song M, Sun N, Wang S, Silwal SB, Page RC, Fast W, Bonomo RA, Weese M, Martinez W, Inglese J, Crowder MW. Machine Learning Models Identify Inhibitors of New Delhi Metallo-β-lactamase. J Chem Inf Model 2024; 64:3977-3991. [PMID: 38727192 PMCID: PMC11129921 DOI: 10.1021/acs.jcim.3c02015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024]
Abstract
The worldwide spread of the metallo-β-lactamases (MBL), especially New Delhi metallo-β-lactamase-1 (NDM-1), is threatening the efficacy of β-lactams, which are the most potent and prescribed class of antibiotics in the clinic. Currently, FDA-approved MBL inhibitors are lacking in the clinic even though many strategies have been used in inhibitor development, including quantitative high-throughput screening (qHTS), fragment-based drug discovery (FBDD), and molecular docking. Herein, a machine learning-based prediction tool is described, which was generated using results from HTS of a large chemical library and previously published inhibition data. The prediction tool was then used for virtual screening of the NIH Genesis library, which was subsequently screened using qHTS. A novel MBL inhibitor was identified and shown to lower minimum inhibitory concentrations (MICs) of Meropenem for a panel of E. coli and K. pneumoniae clinical isolates expressing NDM-1. The mechanism of inhibition of this novel scaffold was probed utilizing equilibrium dialyses with metal analyses, native state electrospray ionization mass spectrometry, UV-vis spectrophotometry, and molecular docking. The uncovered inhibitor, compound 72922413, was shown to be 9-hydroxy-3-[(5-hydroxy-1-oxa-9-azaspiro[5.5]undec-9-yl)carbonyl]-4H-pyrido[1,2-a]pyrimidin-4-one.
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Affiliation(s)
- Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Mahesh Aitha
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Caitlyn A. Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Aidan Sturgill
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Mitch Fairweather
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Amy Hu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Christopher R. Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
| | - Dann D. Rivera
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA
| | - Patricia Dranchak
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Pei W. Thomas
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA
| | - Han Li
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Qi Feng
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Kaicheng Tao
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Minshuai Song
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Na Sun
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Shuo Wang
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | | | - Richard C. Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Walt Fast
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
- Departments of Medicine, Biochemistry, Molecular Biology and Microbiology, Pharmacology, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Clinician Scientist Investigator, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH 44106, USA
| | - Maria Weese
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Waldyn Martinez
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - James Inglese
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
- Metabolic Medicine Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20817, USA
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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3
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Moussa AY. Endophytes: a uniquely tailored source of potential antibiotic adjuvants. Arch Microbiol 2024; 206:207. [PMID: 38581477 PMCID: PMC10998792 DOI: 10.1007/s00203-024-03891-y] [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: 12/25/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 04/08/2024]
Abstract
Multidrug microbial resistance is risking an annual loss of more than 10 million people' lives by 2050. Solutions include the rational use of antibiotics and the use of drugs that reduce resistance or completely obliterate them. Here endophytes come to play due to their high-yield production and inherent nature to produce antimicrobial molecules. Around 40%, 45% and 17% of antibacterial agents were obtained from fungi, actinomycetes, and bacteria, respectively, whose secondary metabolites revealed effectiveness against resistant microbes such as MRSA, MRSE, and Shigella flexneri. Endophyte's role was not confined to bactericidal effect but extended to other mechanisms against MDR microbes, among which was the adjuvant role or the "magic bullets". Scarce focus was given to antibiotic adjuvants, and many laboratories today just screen for the antimicrobial activity without considering combinations with traditional antibiotics, which means real loss of promising resistance combating molecules. While some examples of synthetic adjuvants were introduced in the last decade, the number is still far from covering the disused antibiotics and restoring them back to clinical use. The data compiled in this article demonstrated the significance of quorum sensing as a foreseen mechanism for adjuvants from endophytes secondary metabolites, which call for urgent in-depth studies of their molecular mechanisms. This review, comprehensively and for the first time, sheds light on the significance of endophytes secondary metabolites in solving AMR problem as AB adjuvants.
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Affiliation(s)
- Ashaimaa Y Moussa
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, African Union Organization Street, Abbassia, Cairo, 11566, Egypt.
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4
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Kulshreshtha A, Bhatnagar S. Structural effect of the H992D/H418D mutation of angiotensin-converting enzyme in the Indian population: implications for health and disease. J Biomol Struct Dyn 2024:1-18. [PMID: 38411559 DOI: 10.1080/07391102.2024.2321246] [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: 08/11/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024]
Abstract
The Non synonymous SNPs (nsSNPs) of the renin-angiotensin-system (RAS) pathway, unique to the Indian population were investigated in view of its importance as an endocrine system. nsSNPs of the RAS pathway genes were mined from the IndiGenome database. Damaging nsSNPs were predicted using SIFT, PredictSNP, SNP and GO, Snap2 and Protein Variation Effect Analyzer. Loss of function was predicted based on protein stability change using I mutant, PremPS and CONSURF. The structural impact of the nsSNPs was predicted using HOPE and Missense3d followed by modeling, refinement, and energy minimization. Molecular Dynamics studies were carried out using Gromacsv2021.1. 23 Indian nsSNPs of the RAS pathway genes were selected for structural analysis and 8 were predicted to be damaging. Further sequence analysis showed that HEMGH zinc binding motif changes to HEMGD in somatic ACE-C domain (sACE-C) H992D and Testis ACE (tACE) H418D resulted in loss of zinc coordination, which is essential for enzymatic activity in this metalloprotease. There was a loss of internal interactions around the zinc coordination residues in the protein structural network. This was also confirmed by Principal Component Analysis, Free Energy Landscape and residue contact maps. Both mutations lead to broadening of the AngI binding cavity. The H992D mutation in sACE-C is likely to be favorable for cardiovascular health, but may lead to renal abnormalities with secondary impact on the heart. H418D in tACE is potentially associated with male infertility.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akanksha Kulshreshtha
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
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5
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Azman AA, Leow ATC, Noor NDM, Noor SAM, Latip W, Ali MSM. Worldwide trend discovery of structural and functional relationship of metallo-β-lactamase for structure-based drug design: A bibliometric evaluation and patent analysis. Int J Biol Macromol 2024; 256:128230. [PMID: 38013072 DOI: 10.1016/j.ijbiomac.2023.128230] [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: 05/25/2023] [Revised: 10/11/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
Metallo-β-lactamase (MBL) is an enzyme produced by clinically important bacteria that can inactivate many commonly used antibiotics, making them a significant concern in treating bacterial infections and the risk of having high antibiotic resistance issues among the community. This review presents a bibliometric and patent analysis of MBL worldwide research trend based on the Scopus and World Intellectual Property Organization databases in 2013-2022. Based on the keywords related to MBL in the article title, abstract, and keywords, 592 research articles were retrieved for further analysis using various tools such as Microsoft Excel to determine the frequency analysis, VOSviewer for bibliometric networks visualization, and Harzing's Publish or Perish for citation metrics analysis. Standard bibliometric parameters were analysed to evaluate the field's research trend, such as the growth of publications, topographical distribution, top subject area, most relevant journal, top cited documents, most relevant authors, and keyword trend analysis. Within 10 years, MBL discovery has shown a steady and continuous growth of interest among the community of researchers. United States of America, China, and the United Kingdom are the top 3 countries contribute high productivity to the field. The patent analysis also shows several impactful filed patents, indicating the significance of development research on the structural and functional relationship of MBL for an effective structure-based drug design (SBDD). Developing new MBL inhibitors using SBDD could help address the research gap and provide new successful therapeutic options for treating MBL-producing bacterial infections.
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Affiliation(s)
- Ameera Aisyah Azman
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Siti Aminah Mohd Noor
- Center for Defence Foundation Studies, National Defence University of Malaysia, Kem Perdana Sungai Besi, Kuala Lumpur 57000, Malaysia
| | - Wahhida Latip
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia.
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6
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Diaz A, G S, Balaji S, Ramakrishnan J, Thamotharan S, Ramakrishnan V. Comprehensive screening of marine metabolites against class B1 metallo-β-lactamases of Klebsiella pneumoniae using two-pronged in silico approach. J Biomol Struct Dyn 2023; 41:10930-10943. [PMID: 36541935 DOI: 10.1080/07391102.2022.2159532] [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: 08/01/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
The emergence of antibiotic resistance is one of the major global threats in healthcare. Metallo-β-Lactamases (MBL) are a class of enzymes in bacteria that cleave β-lactam antibiotics and confer resistance. MBLs are further divided into subclasses B1, B2 and B3. Of these, subclasses B1-MBLs (including NDM-1, VIM-2 and IMP-1) constitute the clinically prevalent lactamases conferring resistance. To date, no effective drugs are available clinically against MBLs. In this work, we aim to identify potent inhibitors for the B1 subclass of MBL from available marine metabolites in Comprehensive Marine Natural Product database through integrated in silico approaches. We have used two methods, namely, the high-throughput strategy and the pharmacophore-based strategy to identify potential inhibitors from marine metabolites. High-throughput virtual screening identified N-methyl mycosporine-Ser, which had the highest binding affinity to NDM-1. The pharmacophore-based approach based on co-crystallized ligands identified makaluvic acid and didymellamide with higher binding affinity across B1-MBLs. Taking into account of the advantage of a pharmacophore model-based approach with higher binding affinity, we conclude that both makaluvic acid and didymellamide show potential broad-spectrum effects by binding to all three B1-MBL receptors. The study also indicates the need to take multiple in silico approaches to screen and identify novel inhibitors. Together, our study reveals promising inhibitors that can be identified from marine systems.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aathithya Diaz
- School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
- Bioinformatics Center, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Shripushkar G
- School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Shruti Balaji
- School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | | | - Subbiah Thamotharan
- School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
- Bioinformatics Center, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Vigneshwar Ramakrishnan
- School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
- Bioinformatics Center, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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7
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S S, N H, Fasim A, More SS, Das Mitra S. Identification of a potential inhibitor for New Delhi metallo-β-lactamase 1 (NDM-1) from FDA approved chemical library- a drug repurposing approach to combat carbapenem resistance. J Biomol Struct Dyn 2023; 41:7700-7711. [PMID: 36165602 DOI: 10.1080/07391102.2022.2123402] [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: 03/21/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022]
Abstract
Superbugs producing New Delhi metallo-β-lactamase 1 (NDM-1) enzyme is a growing crisis, that is adversely affecting the global health care system. NDM-1 empowers the bacteria to inactivate entire arsenal of β-lactam antibiotics including carbapenem (the last resort antibiotic) and remains ineffective to all the available β lactamase inhibitors used in the clinics. Limited therapeutic option available for rapidly disseminating NDM-1 producing bacteria makes it imperative to identify a potential inhibitor for NDM-1 enzyme. With drug repurposing approach, in this study, we used virtual screening of available Food and Drug Administration (FDA) approved chemical library (ZINC12 database) and captured 'adapalene' (FDA drug) as a potent inhibitor candidate for NDM-1 enzyme. Active site docking with NDM-1, showed adapalene with binding energy -9.21 kcal/mol and interacting with key amino acid residues (Asp124, His122, His189, His250, Cys208) in the active site of NDM-1. Further, molecular dynamic simulation of NDM-1 docked with the adapalene at 100 ns displayed a stable conformation dynamic, with relative RMSD and RMSF in the acceptable range. Subsequently, in vitro enzyme assays using recombinant NDM-1 protein demonstrated inhibition of NDM-1 by adapalene. Further, the combination of adapalene plus meropenem (carbapenem antibiotic) showed synergistic effect against the NDM-1 producing carbapenem (meropenem) resistant clinical isolates (Escherichia coli and Klebsiella pneumoniae). Overall, our data indicated that adapalene can be a potential inhibitor candidate for NDM-1 enzyme that can contribute to the development of a suitable adjuvant to save the activity of carbapenem antibiotic against infections caused by NDM-1 positive gram-negative bacteria. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shailaja S
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, Karnataka, India
| | - Harshitha N
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, Karnataka, India
| | - Aneesa Fasim
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, Karnataka, India
| | - Sunil S More
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, Karnataka, India
| | - Susweta Das Mitra
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, Karnataka, India
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8
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Cheepurupalli L, Diaz A, Gopal AC, Rathore SS, Ramakrishnan V, Ramakrishnan J. In vitro and in silico screening of Klebsiella pneumoniae new Delhi metallo-β-lactamase-1 inhibitors from endophytic Streptomyces spp. J Biomol Struct Dyn 2022; 40:13593-13605. [PMID: 34657563 DOI: 10.1080/07391102.2021.1990132] [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: 12/29/2022]
Abstract
The increase in drug resistance over the last two decades is a big threat in health care settings. More importantly, the dissemination of carbapenem-resistant Enterobacteriaceae is the major threat to public health with an increase in morbidity and mortality. β-lactamase is known to confer enteric bacteria with nearly complete resistance to all β-lactam antibiotics including the late-generation carbapenems. The commercially available β-lactamase inhibitors, clavulanic acid, sulbactam, and tazobactam are being met with an increasing number of resistant phenotypes and are ineffective against pathogens harbouring New Delhi metallo-β-lactamase (NDM-1). Inhibition of New Delhi metallo-β-lactamase-1 activity is one potential way to treat metallo β-lactamase (MBL) producing multi drug resistant (MDR) pathogen. The present study focused on screening of Klebsiella pneumoniae New Delhi metallo-β-lactamase-1 (BLIs) from endophytic Streptomyces spp. using in vitro and in silico methods. The study identified three potential inhibitors of New Delhi metallo-β-lactamase-1, namely dodecanoic acid, dl-alanyl-l-leucine and phenyl propanedioic acid. These molecules were found to bind to other MBLs namely, IMP-1 and VIM-2. To the best of our knowledge, this is the first kind of study reporting the binding mode of these molecules with New Delhi metallo-β-lactamase-1.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lalitha Cheepurupalli
- Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, Tamil Nadu, India
| | - Aathithya Diaz
- Computational Molecular Biophysics Laboratory (CMBL), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, Tamil Nadu, India
| | - Adithya Conjeevaram Gopal
- Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, Tamil Nadu, India
| | - Sudarshan Singh Rathore
- Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, Tamil Nadu, India
| | - Vigneshwar Ramakrishnan
- School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, Tamil Nadu, India
| | - Jayapradha Ramakrishnan
- Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, Tamil Nadu, India
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9
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Moreira JS, Galvão DS, Xavier CFC, Cunha S, Pita SSDR, Reis JN, Freitas HFD. Phenotypic and in silico studies for a series of synthetic thiosemicarbazones as New Delhi metallo-beta-lactamase carbapenemase inhibitors. J Biomol Struct Dyn 2022; 40:14223-14235. [PMID: 34766882 DOI: 10.1080/07391102.2021.2001379] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The past two decades have been marked by a global spread of bacterial resistance to β-lactam drugs and carbapenems derivatives are the ultimate treatment against multidrug-resistant bacteria. β-lactamase expression is related to resistance which demands the development of bacterial resistance blockers. Drug inhibitor combinations of serine-β-lactamase and β-lactam were successful employed in therapy despite their inactivity against New Delhi metallo-beta-lactamase (NDM). Until now, few compounds are active against NDM-producing bacteria and no specific inhibitors are available yet. The rational strategy for NDM inhibitors development starts with in vitro assays aiming to seek compounds that could act synergistically with β-lactam antibiotics. Thus, eight thiosemicarbazone derivatives were synthesized and investigated for their ability to reverse the resistant phenotype in NDM in Enterobacter cloacae. Phenotypic screening indicated that four isatin-beta-thiosemicarbazones showed Fractional Inhibitory Concentration (FIC) ≤ 250 µM in the presence of meropenem (4 µg/mL). The most promising compound (FIC= 31.25 µM) also presented synergistic effect (FICI = 0.34). Docking and molecular dynamics studies on NDM-thiosemicarbazone complex suggested that 2,3-dihydro-1H-indol-2-one subunit interacts with catalytic zinc and interacted through hydrogen bonds with Asp124 acting like a carboxylic acid bioisostere. Additionally, thiosemicarbazone tautomer with oxidized sulfur (thione) seems to act as a spacer rather than zinc chelator, and the aromatic moieties are stabilized by pi-pi and cation-pi interactions with His189 and Lys221 residues. Our results addressed some thiosemicarbazone structural changes to increase its biological activity against NDM and highlight its scaffold as promising alternatives to treat bacterial resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jonatham Souza Moreira
- Post-Graduation Program in Pharmacy, Pharmacy College, Federal University of Bahia, Salvador, Bahia, Brazil
| | | | | | - Silvio Cunha
- Chemistry Institute, Federal University of Bahia, Ondina, Salvador, Bahia, Brazil
| | - Samuel Silva da Rocha Pita
- Pharmacy College, Federal University of Bahia, Salvador, Bahia, Brazil.,Bioinformatics and Molecular Modeling Laboratory (LaBiMM), Federal University of Bahia, Salvador, Bahia, Brazil
| | - Joice Neves Reis
- Post-Graduation Program in Pharmacy, Pharmacy College, Federal University of Bahia, Salvador, Bahia, Brazil.,Pharmacy College, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Humberto Fonseca de Freitas
- Post-Graduation Program in Pharmacy, Pharmacy College, Federal University of Bahia, Salvador, Bahia, Brazil.,Pharmacy College, Federal University of Bahia, Salvador, Bahia, Brazil.,Bioinformatics and Molecular Modeling Laboratory (LaBiMM), Federal University of Bahia, Salvador, Bahia, Brazil
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10
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Li X, Zhao J, Zhang B, Duan X, Jiao J, Wu W, Zhou Y, Wang H. Drug development concerning metallo-β-lactamases in gram-negative bacteria. Front Microbiol 2022; 13:959107. [PMID: 36187949 PMCID: PMC9520474 DOI: 10.3389/fmicb.2022.959107] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
β-Lactams have been a clinical focus since their emergence and indeed act as a powerful tool to combat severe bacterial infections, but their effectiveness is threatened by drug resistance in bacteria, primarily by the production of serine- and metallo-β-lactamases. Although once of less clinical relevance, metallo-β-lactamases are now increasingly threatening. The rapid dissemination of resistance mediated by metallo-β-lactamases poses an increasing challenge to public health worldwide and comprises most existing antibacterial chemotherapies. Regrettably, there have been no clinically available inhibitors of metallo-β-lactamases until now. To cope with this unique challenge, researchers are exploring multidimensional strategies to combat metallo-β-lactamases. Several studies have been conducted to develop new drug candidates or calibrate already available drugs against metallo-β-lactamases. To provide an overview of this field and inspire more researchers to explore it further, we outline some promising candidates targeting metallo-β-lactamase producers, with a focus on Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. Promising candidates in this review are composed of new antibacterial drugs, non-antibacterial drugs, antimicrobial peptides, natural products, and zinc chelators, as well as their combinations with existing antibiotics. This review may provide ideas and insight for others to explore candidate metallo-β-lactamases as well as promote the improvement of existing data to obtain further convincing evidence.
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Affiliation(s)
- Xiuyun Li
- Maternal and Child Health Development Research Center, Shandong Provincial Maternal and Child Health Care Hospital, Jinan, China
| | - Jing Zhao
- Pharmaceutical Department, Shandong Provincial Taishan Hospital, Taian, China
| | - Bin Zhang
- Department of Ophthalmology, Shandong Provincial Maternal and Child Health Care Hospital, Jinan, China
| | - Xuexia Duan
- Physical Examination Center, Shandong Provincial Maternal and Child Health Care Hospital, Jinan, China
| | - Jin Jiao
- Department of Clinical Laboratory, Shandong Provincial Maternal and Child Health Care Hospital, Jinan, China
| | - Weiwei Wu
- Department of Clinical Laboratory, Shandong Provincial Maternal and Child Health Care Hospital, Jinan, China
| | - Yuxia Zhou
- Department of Clinical Laboratory, Shandong Provincial Maternal and Child Health Care Hospital, Jinan, China
- *Correspondence: Yuxia Zhou
| | - Hefeng Wang
- Department of Pediatric Surgery, Shandong Provincial Maternal and Child Health Care Hospital, Jinan, China
- Hefeng Wang
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11
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Broad-Spectrum Inhibitors against Class A, B, and C Type β-Lactamases to Block the Hydrolysis against Antibiotics: Kinetics and Structural Characterization. Microbiol Spectr 2022; 10:e0045022. [PMID: 36069578 PMCID: PMC9603770 DOI: 10.1128/spectrum.00450-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The emergence of antibiotic resistance has led to a global crisis for the physician to handle infection control issues. All antibiotics, including colistin, have lost efficiency against emerging drug-resistant bacterial strains due to the production of metallo-β-lactamases (MBLs) and serine-β-lactamases (SBLs). Therefore, it is of the utmost importance to design inhibitors against these enzymes to block the hydrolytic action against antibiotics being used. Although various novel β-lactamase inhibitors are being authorized or are under clinical studies, the coverage of their activity spectrum does not include MDR organisms expressing multiple classes of β-lactamases at a single time. This study reports three novel broad-spectrum inhibitors effective against both SBLs and MBLs. Virtual screening, molecular docking, molecular dynamics simulations, and an in silico pharmacokinetic study were performed to identify the lead molecules with broad-spectrum ability to inhibit the hydrolysis of β-lactam. The selected compounds were further assessed by in vitro cell assays (MIC, 50% inhibitory concentration [IC50], kinetics, and fluorescence against class A, B, and C type β-lactamases) to confirm their efficacies. A 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay was performed to check the toxicity of screened lead molecules. All three selected inhibitors were found to reduce MIC and showed good affinity against all the SBLs and MBLs produced by class A, B, and C type β-lactamases. These nontoxic novel non-β-lactam broad-spectrum inhibitors bind to the active site residues of selected β-lactamases, which are crucial for β-lactam antibiotic hydrolysis. These inhibitors may be proposed as a future drug candidate in combination with antibiotics as a single formulation to control infection caused by resistant strains. Hence, this study plays a significant role in the cure of infections caused by antibiotic-resistant bacteria. IMPORTANCE Several inhibitors for usage in conjunction with antibiotics have been developed. However, to date, there is no commercially available broad-spectrum β-lactamase inhibitor that targets both MBLs and SBLs. Here, we showed three novel broad-spectrum inhibitors with promising results through computational techniques and in vitro studies. These inhibitors are effective against both SBLs and MBLs and hence could be used as future drug candidates to treat infections caused by multidrug-resistant bacteria producing both types of enzymes (SBLs and MBLs).
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12
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Farhat N, Ali A, Waheed M, Gupta D, Khan AU. Chemically synthesised flavone and coumarin based isoxazole derivatives as broad spectrum inhibitors of serine β-lactamases and metallo-β-lactamases: a computational, biophysical and biochemical study. J Biomol Struct Dyn 2022:1-11. [PMID: 35848348 DOI: 10.1080/07391102.2022.2099977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The β-lactam antibiotics are the most effective medicines for treating bacterial infections. Resistance to them, particularly through the production of β-lactamases, which can hydrolyse all kinds of β-lactams, poses a threat to their continued use. The synthesised flavone and coumarin based isoxazole derivatives have the potential to be used as broad-spectrum inhibitors of the mechanistically different serine-(SBL) and metallo-β-lactamases (MBL). The synthesised compounds were discovered as potent β-lactamase inhibitors using molecular docking and in silico pharmacokinetic analysis. We studied the binding of chemically synthesised inhibitors to clinically significant β-lactamases of class A, B, and C using biophysical and biochemical approaches, and computational analyses. These molecules follow Lipinski's rule of five and have acceptable solubility, permeability, and oral bioavailability. These molecules were found to be non-toxic and non-carcinogenic. MIC results suggest that these molecules restore the antibiotic efficacy against class A, B, and C β-lactamases. Kinetics data showed that these molecules reduce the catalytic efficiency of clinically relevant class A, B, and C β-lactamases. Fluorescence study showed significant interaction between these flavone-/coumarin-based isoxazole derivatives and class A/B/ C β-lactamases. This study showed promising effect of these new generation compounds as broad spectrum β-lactamase inhibitors of both SBLs and MBLs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nabeela Farhat
- Medical Microbiology and Molecular Biology Lab., Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Abid Ali
- Medical Microbiology and Molecular Biology Lab., Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Mohd Waheed
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttrakhand, India
| | - Divya Gupta
- Medical Microbiology and Molecular Biology Lab., Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Lab., Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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13
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Fan P, Ma Z, Partow AJ, Kim M, Shoemaker GM, Tan R, Tong Z, Nelson CD, Jang Y, Jeong KC. A novel combination therapy for multidrug resistant pathogens using chitosan nanoparticles loaded with β-lactam antibiotics and β-lactamase inhibitors. Int J Biol Macromol 2022; 195:506-514. [PMID: 34920071 DOI: 10.1016/j.ijbiomac.2021.12.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/24/2021] [Accepted: 12/05/2021] [Indexed: 12/20/2022]
Abstract
Antimicrobial resistance is one of the greatest global threats. Particularly, multidrug resistant extended-spectrum β-lactamase (ESBL)-producing pathogens confer resistance to many commonly used medically important antibiotics, especially beta-lactam antibiotics. Here, we developed an innovative combination approach to therapy for multidrug resistant pathogens by encapsulating cephalosporin antibiotics and β-lactamase inhibitors with chitosan nanoparticles (CNAIs). The four combinations of CNAIs including two cephalosporin antibiotics (cefotaxime and ceftiofur) with two β-lactamase inhibitors (tazobactam and clavulanate) were engineered as water-oil-water emulsions. Four combinations of CNAIs showed efficient antimicrobial activity against multidrug resistant ESBL-producing Enterobacteriaceae. The CNAIs showed enhanced antimicrobial activity compared to naïve chitosan nanoparticles and to the combination of cephalosporin antibiotics and β-lactamase inhibitors. Furthermore, CNAIs attached on the bacterial surface changed the permeability to the outer membrane, resulting in cell damage that leads to cell death. Taken together, CNAIs have provided promising potential for treatment of diseases caused by critically important ESBL-producing multidrug resistant pathogens.
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Affiliation(s)
- Peixin Fan
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA; Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Zhengxin Ma
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA; Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Arianna J Partow
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Miju Kim
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA; Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Grace M Shoemaker
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Ruwen Tan
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Zhaohui Tong
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Corwin D Nelson
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Yeongseon Jang
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Kwangcheol C Jeong
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA; Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA.
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14
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Wang F, Wang L, Chen H, Li N, Wang Y, Li Y, Liang W. Rapid Detection of blaKPC, blaNDM, blaOXA-48-like and blaIMP Carbapenemases in Enterobacterales Using Recombinase Polymerase Amplification Combined With Lateral Flow Strip. Front Cell Infect Microbiol 2021; 11:772966. [PMID: 34926319 PMCID: PMC8674914 DOI: 10.3389/fcimb.2021.772966] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/15/2021] [Indexed: 12/31/2022] Open
Abstract
The emergence of carbapenemase-producing Enterobacterales (CPE) infections is a major global public health threat. Rapid and accurate detection of pathogenic bacteria is essential to optimize treatment and timely avoid further transmission of these bacteria. Here, we aimed to develop a rapid on site visualization detection method for CPE using improved recombinase polymerase amplification (RPA) combined with lateral flow strip (LFS) method, based on four most popular carbapenemase genes: blaKPC, blaNDM, blaOXA-48-like, and blaIMP. All available allelic variants of the above carbapenemases were downloaded from the β-lactamase database, and the conserved regions were used as targets for RPA assay. Five primer sets were designed targeting to each carbapenemase gene and the RPA amplification products were analyzed by agarose gel electrophoresis. FITC-labeled specific probes were selected, combined with the best performance primer set (Biotin-labeled on the reverse primer), and detected by RPA-LFS. Mismatches were made to exclude the false positive signals interference. This assay was evaluated in 207 clinically validated carbapenem-resistant Enterobacterales (CRE) isolates and made a comparison with conventional PCR. Results showed that the established RPA-LFS assay for CPE could be realized within 30 min at a constant temperature of 37°C and visually detected amplification products without the need for special equipment. This assay could specifically differentiate the four classes of carbapenemases without cross-reactivity and shared a minimum detection limit of 100 fg/reaction (for blaKPC, blaNDM, and blaOXA-48-like) or 1000 fg/reaction (for blaIMP), which is ten times more sensitive than PCR. Furthermore, the detection of 207 pre-validated clinically CRE strains using the RPA-LFS method resulted in 134 blaKPC, 69 blaNDM, 3 blaOXA-48-like, and 1 blaIMP. The results of the RPA-LFS assay were in consistent with PCR, indicating that this method shared high sensitivity and specificity. Therefore, the RPA-LFS method for CPE may be a simple, specific, and sensitive method for the rapid diagnosis of carbapenemase Enterobacterales.
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Affiliation(s)
- Fang Wang
- Department of Central Laboratory, The Second People’s Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Lei Wang
- Department of Central Laboratory, The Second People’s Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China,School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Huimin Chen
- Department of Central Laboratory, The Second People’s Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Na Li
- Department of Central Laboratory, The Second People’s Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Yan Wang
- Department of Central Laboratory, The Second People’s Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China,*Correspondence: Yan Wang, ; Yan Li, ; Wei Liang,
| | - Yan Li
- Department of Central Laboratory, The Second People’s Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China,*Correspondence: Yan Wang, ; Yan Li, ; Wei Liang,
| | - Wei Liang
- Department of Central Laboratory, The Second People’s Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China,*Correspondence: Yan Wang, ; Yan Li, ; Wei Liang,
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15
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Boucherit H, Chikhi A, Bensegueni A, Merzoug A, Bolla JM. The Research of New Inhibitors of Bacterial Methionine Aminopeptidase by Structure Based Virtual Screening Approach of ZINC DATABASE and In Vitro Validation. Curr Comput Aided Drug Des 2021; 16:389-401. [PMID: 31244429 DOI: 10.2174/1573409915666190617165643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/26/2019] [Accepted: 05/06/2019] [Indexed: 01/13/2023]
Abstract
BACKGROUND The great emergence of multi-resistant bacterial strains and the low renewal of antibiotics molecules are leading human and veterinary medicine to certain therapeutic impasses. Therefore, there is an urgent need to find new therapeutic alternatives including new molecules in the current treatments of infectious diseases. Methionine aminopeptidase (MetAP) is a promising target for developing new antibiotics because it is essential for bacterial survival. OBJECTIVE To screen for potential MetAP inhibitors by in silico virtual screening of the ZINC database and evaluate the best potential lead molecules by in vitro studies. METHODS We have considered 200,000 compounds from the ZINC database for virtual screening with FlexX software to identify potential inhibitors against bacterial MetAP. Nine chemical compounds of the top hits predicted were purchased and evaluated in vitro. The antimicrobial activity of each inhibitor of MetAP was tested by the disc-diffusion assay against one Gram-positive (Staphylococcus aureus) and two Gram-negative (Escherichia coli & Pseudomonas aeruginosa) bacteria. Among the studied compounds, compounds ZINC04785369 and ZINC03307916 showed promising antibacterial activity. To further characterize their efficacy, the minimum inhibitory concentration was determined for each compound by the microdilution method which showed significant results. RESULTS These results suggest compounds ZINC04785369 and ZINC03307916 as promising molecules for developing MetAP inhibitors. CONCLUSION Furthermore, they could therefore serve as lead molecules for further chemical modifications to obtain clinically useful antibacterial agents.
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Affiliation(s)
- Hanane Boucherit
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, Mentouri Brothers University, Constantine 1, Algeria
| | - Abdelouahab Chikhi
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, Mentouri Brothers University, Constantine 1, Algeria
| | - Abderrahmane Bensegueni
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, Mentouri Brothers University, Constantine 1, Algeria
| | - Amina Merzoug
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, Mentouri Brothers University, Constantine 1, Algeria
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16
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Kumari M, Subbarao N. Identification of novel multitarget antitubercular inhibitors against mycobacterial peptidoglycan biosynthetic Mur enzymes by structure-based virtual screening. J Biomol Struct Dyn 2021; 40:8185-8196. [PMID: 33826470 DOI: 10.1080/07391102.2021.1908913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Current therapeutic strategies for several diseases, including Mycobacterium tuberculosis infection, have evolved from an initial single-target treatment to a multitarget one. A multitarget antitubercular drugs targeting different mycobacterial proteins are more effective at suppressing bacterial growth. In this study, a high throughput virtual screening was performed to identify hits to the potential antitubercular multitarget: murA, murB, murC, murD, murE, murF, murG and murI from M. tuberculosis that is involved in peptidoglycan biosynthesis. In the virtual screening, we were docked 56,400 compounds of the ChEMBL antimycobacterial library and re-scored and identified the top 10 ranked compounds as antitubercular drug candidates. Further, the best common docked complex CHEMBL446262 was subjected to molecular dynamics simulation to understand the molecule's stability in the presence of an active site environment. After that, we have calculated binding free energy the top-ranked docked complexes using the MM/PBSA method. These ligands exhibited the highest binding affinity; find out novel drug-likeness might show the M. tuberculosis effect's inhibitor by interacting with multitarget Mur enzymes. New antitubercular therapies that include multitarget drugs may have higher efficacy than single-target medicines and provide a more straightforward antitubercular therapy regimen.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Madhulata Kumari
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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17
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Li QQ, Kang OH, Kwon DY. Study on Demethoxycurcumin as a Promising Approach to Reverse Methicillin-Resistance of Staphylococcus aureus. Int J Mol Sci 2021; 22:ijms22073778. [PMID: 33917423 PMCID: PMC8038695 DOI: 10.3390/ijms22073778] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/31/2021] [Accepted: 04/03/2021] [Indexed: 12/19/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has always been a threatening pathogen. Research on phytochemical components that can replace antibiotics with limited efficacy may be an innovative method to solve intractable MRSA infections. The present study was devoted to investigate the antibacterial activity of the natural compound demethoxycurcumin (DMC) against MRSA and explore its possible mechanism for eliminating MRSA. The minimum inhibitory concentrations (MICs) of DMC against MRSA strains was determined by the broth microdilution method, and the results showed that the MIC of DMC was 62.5 μg/mL. The synergistic effects of DMC and antibiotics were investigated by the checkerboard method and the time–kill assay. The ATP synthase inhibitors were employed to block the metabolic ability of bacteria to explore their synergistic effect on the antibacterial ability of DMC. In addition, western blot analysis and qRT-PCR were performed to detect the proteins and genes related to drug resistance and S. aureus exotoxins. As results, DMC hindered the translation of penicillin-binding protein 2a (PBP2a) and staphylococcal enterotoxin and reduced the transcription of related genes. This study provides experimental evidences that DMC has the potential to be a candidate substance for the treatment of MRSA infections.
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Affiliation(s)
| | - Ok-Hwa Kang
- Correspondence: (O.-H.K.); (D.-Y.K.); Tel.: +82-63-850-6802 (O.-H.K. & D.-Y.K.)
| | - Dong-Yeul Kwon
- Correspondence: (O.-H.K.); (D.-Y.K.); Tel.: +82-63-850-6802 (O.-H.K. & D.-Y.K.)
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18
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Understanding the molecular interactions of inhibitors against Bla1 beta-lactamase towards unraveling the mechanism of antimicrobial resistance. Int J Biol Macromol 2021; 177:337-350. [PMID: 33582216 DOI: 10.1016/j.ijbiomac.2021.02.069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/07/2021] [Accepted: 02/08/2021] [Indexed: 11/24/2022]
Abstract
This study evaluated the inhibitory potential of various beta-lactamase inhibitors such as mechanism-based inhibitors (MBIs), carbapenems, monobactam, and non-beta-lactam inhibitors against Bla1, a class-A beta-lactamase encoded by Bacillus anthracis. The binding potential of different inhibitors was estimated using competitive kinetic assay, isothermal titration calorimetry, and Biolayer interferometry. We observed that tazobactam has better inhibition among other MBIs with a characteristics inhibition dissociation constant of 0.51 ± 0.13 μM. Avibactam was also identified as good inhibitor with an inhibition efficiency of 0.6 ± 0.04 μM. All the MBIs (KD = 1.90E-04 M, 2.05E-05 M, 3.55E-04 M for clavulanate, sulbactam and tazobactam) showed significantly better binding potential than carbapenems (KD = 1.02E-03 M, 2.74E-03 M, 1.24E-03 M for ertapenem, imipenem and biapenem respectively). Molecular dynamics simulations were carried out using Bla1-inhibitor complexes to understand the dynamics and stability. The minimum inhibitory concentration (MIC) was carried out by taking various substrates and inhibitors, and later it was followed by cell viability assay. Together, our study helps develop a proper understanding of Bla1 beta-lactamase and its interaction with inhibitory molecules. This study would facilitate comprehending the catalytic divergence of beta-lactamases and the newly emergent resistant strains, focusing on the new generation of therapeutics being less prone to antimicrobial resistance.
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Satapathy P, Prakash JK, More SS, Chandramohan V, Zameer F. Structural modulation of dual oxidase (Duox) in Drosophila melanogaster by phyto-elicitors: A free energy study with molecular dynamics approach. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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20
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Jin WB, Xu C, Qi XL, Zeng P, Gao W, Lai KH, Chiou J, Chan EWC, Leung YC, Chan TH, Wong KY, Chen S, Chan KF. Synthesis of 1,3,4-trisubstituted pyrrolidines as meropenem adjuvants targeting New Delhi metallo-β-lactamase. NEW J CHEM 2021. [DOI: 10.1039/d0nj06090a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A promising NDM-1 inhibitor was discovered by the construction of pyrrolidine library via boric acid-catalyzed 1,3-dipolar cycloaddition and cell-based screens.
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21
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Satapathy P, Prakash JK, Gowda VC, More SS, K M, Chandramohan V, Zameer F. Targeting Imd pathway receptor in Drosophila melanogaster and repurposing of phyto-inhibitors: structural modulation and molecular dynamics. J Biomol Struct Dyn 2020; 40:1659-1670. [PMID: 33050786 DOI: 10.1080/07391102.2020.1831611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Dysbiosis is a major cause of disease in an individual, generally initiated in the gastrointestinal tract. The gut, also known as the second brain, constitutes a major role in immune signaling. To study the immunity cascade, the Drosophila model was considered targeting the Imd pathway receptor (2F2L) located in the midgut. This receptor further initiates the immune signaling mechanism influenced by bacteria. To inhibit the Imd pathway, the crystal structure of Imd with PDB: 2F2L was considered for the screening of suitable ligand/inhibitor. In light of our previous studies, repurposing of anti-diabetic ligands from the banana plant namely lupeol (LUP), stigmasterol (STI), β-sitosterol (BST) and umbelliferone (UMB) were screened. This study identifies the potential inhibitor along with the tracheal toxin (TCT), a major peptidoglycan constituent of microbes. The molecular docking and molecular dynamics simulation of complexes 2F2L-MLD, 2F2L- CAP, 2F2L-LUP, 2F2L-BST, 2F2L-STI and 2F2L-UMB elucidates the intermolecular interaction into the inhibitory property of ligands. The results of this study infer LUP and UMB as better ligands with high stability and functionality among the screened candidates. This study provides insights into the dysbiosis and its amelioration by plant-derived molecules. The identified drugs (LUP & UMB) will probably act as an inhibitor against microbial dysbiosis and other related pathogenesis (diabetes and diabetic neuropathy). Further, this study will widen avenues in fly biology research and which could be used as a therapeutic model in the rapid, reliable and reproducible screening of phytobiologics in complementary and alternative medicine for various lifestyle associated complications.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pankaj Satapathy
- School of Basic and Applied Sciences, Department of Biological Sciences, Dayananda Sagar University, Bengaluru, Karnataka, India
| | - Jeevan Kallur Prakash
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, Karnataka, India
| | - V Chirag Gowda
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, Karnataka, India
| | - Sunil S More
- School of Basic and Applied Sciences, Department of Biological Sciences, Dayananda Sagar University, Bengaluru, Karnataka, India
| | - Muthuchelian K
- School of Basic and Applied Sciences, Department of Biological Sciences, Dayananda Sagar University, Bengaluru, Karnataka, India
| | - Vivek Chandramohan
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, Karnataka, India
| | - Farhan Zameer
- School of Basic and Applied Sciences, Department of Biological Sciences, Dayananda Sagar University, Bengaluru, Karnataka, India
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22
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Yang Y, Guo Y, Zhou Y, Gao Y, Wang X, Wang J, Niu X. Discovery of a Novel Natural Allosteric Inhibitor That Targets NDM-1 Against Escherichia coli. Front Pharmacol 2020; 11:581001. [PMID: 33123013 PMCID: PMC7566295 DOI: 10.3389/fphar.2020.581001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/07/2020] [Indexed: 11/25/2022] Open
Abstract
At present, the resistance of New Delhi metallo-β-lactamase-1 (NDM-1) to carbapenems and cephalosporins, one of the mechanisms of bacterial resistance against β-lactam antibiotics, poses a threat to human health. In this work, based on the virtual ligand screen method, we found that carnosic acid1 (CA), a natural compound, exhibited a significant inhibitory effect against NDM-1 (IC50 = 27.07 μM). Although carnosic acid did not display direct antibacterial activity, the combination of carnosic acid and meropenem still showed bactericidal activity after the loss of bactericidal effect of meropenem. The experimental results showed that carnosic acid can enhance the antibacterial activity of meropenem against Escherichia coli ZC-YN3. To explore the inhibitory mechanism of carnosic acid against NDM-1, we performed the molecular dynamics simulation and binding energy calculation for the NDM-1-CA complex system. Notably, the 3D structure of the complex obtained from molecular modeling indicates that the binding region of carnosic acid with NDM-1 was not situated in the active region of protein. Due to binding to the allosteric pocket of carnosic acid, the active region conformation of NDM-1 was observed to have been altered. The distance from the active center of the NDM-1-CA complex was larger than that of the free protein, leading to loss of activity. Then, the mutation experiments showed that carnosic acid had lower inhibitory activity against mutated protein than wild-type proteins. Fluorescence experiments verified the results reported above. Thus, our data indicate that carnosic acid is a potential NDM-1 inhibitor and is a promising drug for the treatment of NDM-1 producing pathogens.
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Affiliation(s)
- Yanan Yang
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Yan Guo
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, China
| | - Yonglin Zhou
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, China
| | - Yawen Gao
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Xiyan Wang
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Jianfeng Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, China
| | - Xiaodi Niu
- College of Food Science and Engineering, Jilin University, Changchun, China
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23
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Ali A, Kumar R, Khan A, Khan AU. Interaction of LysM BON family protein domain with carbapenems: A putative mechanism of carbapenem resistance. Int J Biol Macromol 2020; 160:212-223. [PMID: 32464197 DOI: 10.1016/j.ijbiomac.2020.05.172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 10/24/2022]
Abstract
Carbapenem resistance in Gram-negative pathogens has become a global concern for health workers worldwide. In one of our earlier studies, a Klebsiella pneumoniae-carbapenemase-2 producing strain was induced with meropenem to explore differentially expressed proteins under induced and uninduced conditions. There is, LysM domain BON family protein, was found over 12-fold expressed under the induced state. A hypothesis was proposed that LysM domain protein might have an affinity towards carbapenem antibiotics making them unavailable to bind with their target. Hence, we initiated a study to understand the binding mode of carbapenem with LysM domain protein. MICs of imipenem and meropenem against LysM clone were increased by several folds as compared to NP-6 clinical strain as well as DH5 α (PET-28a KPC-2) clone. This study further revealed a strong binding of both antibiotics to LysM domain protein. Molecular simulation studies of LysM domain protein with meropenem and imipenem for 80 ns has also showed stable structure. We concluded that overexpressed LysM domain under induced condition interacted with carbapenems, leading to enhanced resistance as proved by high MIC values. Hence, the study proved the proposed hypothesis that the LysM domain plays a significant role in the putative mechanism of antibiotics resistance.
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Affiliation(s)
- Abid Ali
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP, India
| | - Rakesh Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Arbab Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP, India
| | - Asad U Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP, India; Faculty of Science and Marine Environment, University Malysia Terengganu, Kuala Terengganu, Malaysia.
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24
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Rivière G, Oueslati S, Gayral M, Créchet JB, Nhiri N, Jacquet E, Cintrat JC, Giraud F, van Heijenoort C, Lescop E, Pethe S, Iorga BI, Naas T, Guittet E, Morellet N. NMR Characterization of the Influence of Zinc(II) Ions on the Structural and Dynamic Behavior of the New Delhi Metallo-β-Lactamase-1 and on the Binding with Flavonols as Inhibitors. ACS OMEGA 2020; 5:10466-10480. [PMID: 32426604 PMCID: PMC7226869 DOI: 10.1021/acsomega.0c00590] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/15/2020] [Indexed: 05/22/2023]
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1) has recently emerged as a global threat because of its ability to confer resistance to all common β-lactam antibiotics. Understanding the molecular basis of β-lactam hydrolysis by NDM is crucial for designing NDM inhibitors or β-lactams resistant to their hydrolysis. In this study, for the first time, NMR was used to study the influence of Zn(II) ions on the dynamic behavior of NDM-1. Our results highlighted that the binding of Zn(II) in the NDM-1 active site induced several structural and dynamic changes on active site loop 2 (ASL2) and L9 loops and on helix α2. We subsequently studied the interaction of several flavonols: morin, quercetin, and myricetin were identified as natural and specific inhibitors of NDM-1. Quercetin conjugates were also synthesized in an attempt to increase the solubility and bioavailability. Our NMR investigations on NDM-1/flavonol interactions highlighted that both Zn(II) ions and the residues of the NDM-1 ASL1, ASL2, and ASL4 loops are involved in the binding of flavonols. This is the first NMR interaction study of NDM-1/inhibitors, and the models generated using HADDOCK will be useful for the rational design of more active inhibitors, directed against NDM-1.
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Affiliation(s)
- Gwladys Rivière
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Saoussen Oueslati
- EA7361
“Structure, Dynamic, Function and Expression of Broad Spectrum
β-Lactamases”, Faculty of Medicine, Université Paris-Sud, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France
| | - Maud Gayral
- Institut
de Chimie Moléculaire et des Matériaux d’Orsay
(ICMMO), CNRS, Université Paris Sud, Université Paris-Saclay, 15 rue Georges Clemenceau, 91405 Orsay Cedex, France
| | | | - Naïma Nhiri
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Eric Jacquet
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Jean-Christophe Cintrat
- Service
de Chimie Bio-organique et Marquage (SCBM), CEA, Université Paris-Saclay, LabEx LERMIT, 91191 Gif/Yvette, France
| | - François Giraud
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Carine van Heijenoort
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Ewen Lescop
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Stéphanie Pethe
- EA7361
“Structure, Dynamic, Function and Expression of Broad Spectrum
β-Lactamases”, Faculty of Medicine, Université Paris-Sud, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France
| | - Bogdan I. Iorga
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Thierry Naas
- EA7361
“Structure, Dynamic, Function and Expression of Broad Spectrum
β-Lactamases”, Faculty of Medicine, Université Paris-Sud, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France
- . Phone:(33)145212019 or (33)145213030. Fax: (33)145216340
| | - Eric Guittet
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Nelly Morellet
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
- . Phone:(33)169823762. Fax: (33)169823784
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25
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Guo H, Cheng K, Gao Y, Bai W, Wu C, He W, Li C, Li Z. A novel potent metal-binding NDM-1 inhibitor was identified by fragment virtual, SPR and NMR screening. Bioorg Med Chem 2020; 28:115437. [DOI: 10.1016/j.bmc.2020.115437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/05/2020] [Accepted: 03/10/2020] [Indexed: 01/25/2023]
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26
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Liu Y, Yang K, Jia Y, Wang Z. Repurposing Peptidomimetic as Potential Inhibitor of New Delhi Metallo-β-lactamases in Gram-Negative Bacteria. ACS Infect Dis 2019; 5:2061-2066. [PMID: 31637907 DOI: 10.1021/acsinfecdis.9b00364] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The emergence, prevalence, and rapid spread of New Delhi metallo-β-lactamases (NDMs) in Gram-negative pathogens threaten our traditional regimen to treat bacterial infectious diseases. Discovery of novel NDMs inhibitors offers an alternative approach to restore the carbapenems activity. However, thus far, no clinical inhibitor of NDMs has been approved. In this study, the potential of peptides and analogues as carbapenems adjuvant in NDMs-positive pathogens was investigated. Herein, we successfully found that peptidomimetic 4 (PEP4) is a potential inhibitor of NDM enzymes. PEP4 displayed significant synergistic activity with Meropenem against NDM-expression Gram-negative bacteria in vitro. Moreover, PEP4 effectively restored Meropenem efficacy in mice infection models infected with NDM-5-positive E. coli. These data demonstrated the high potential of PEP4 as carbapenems adjuvant to address NDMs-positive Gram-negative pathogens.
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Affiliation(s)
- Yuan Liu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China
| | | | | | - Zhiqiang Wang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China
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27
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Gangadharappa BS, Sharath R, Revanasiddappa PD, Chandramohan V, Balasubramaniam M, Vardhineni TP. Structural insights of metallo-beta-lactamase revealed an effective way of inhibition of enzyme by natural inhibitors. J Biomol Struct Dyn 2019; 38:3757-3771. [DOI: 10.1080/07391102.2019.1667265] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Bhavya Somalapura Gangadharappa
- Department of Biotechnology, M.S Ramaiah Institute of Technology, Bengaluru, Karnataka, India
- Visvesvaraya Technological University, Belagavi, Karnataka, India
| | | | | | - Vivek Chandramohan
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, Karnataka, India
| | | | - Teja Priya Vardhineni
- Biotecthology Skill Enhancement Program, Siddaganga Institute of Technology, Tumakuru, Karnataka, India
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28
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The assemblage of covalent and metal binding dual functional scaffold for cross-class metallo-β-lactamases inhibition. Future Med Chem 2019; 11:2381-2394. [PMID: 31544522 DOI: 10.4155/fmc-2019-0008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aim: The discovery and development of novel broad-spectrum MβLs inhibitors are urgent to overcome antibiotic resistance mediated by MβLs. Methods & results: Herein, the synthesized 21 compounds exhibited potent inhibition to the clinically important MβLs (NDM-1, IMP-1 and ImiS) and effectively restored the antibacterial efficacy of cefazolin and imipenem against Escherichia coli harboring MβLs. 5b was first identified to be dual functional broad-spectrum MβLs inhibitor through assemblage of covalent and metal binding scaffold, which irreversibly inhibited B1, B2 MβLs via forming a Se–S covalent bond, and competitively inhibited B3 MβLs by coordinating the metals at active site. Conclusion: The designed compounds can serve as potent broad-spectrum MβLs inhibitors and combat MβLs-producing ‘superbug’ in combination with β-lactams.
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29
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Ma B, Fang C, Lu L, Wang M, Xue X, Zhou Y, Li M, Hu Y, Luo X, Hou Z. The antimicrobial peptide thanatin disrupts the bacterial outer membrane and inactivates the NDM-1 metallo-β-lactamase. Nat Commun 2019; 10:3517. [PMID: 31388008 PMCID: PMC6684654 DOI: 10.1038/s41467-019-11503-3] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 07/16/2019] [Indexed: 12/28/2022] Open
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1) is the most prevalent type of metallo-β-lactamase and hydrolyzes almost all clinically used β-lactam antibiotics. Here we show that the antimicrobial peptide thanatin disrupts the outer membrane of NDM-1-producing bacteria by competitively displacing divalent cations on the outer membrane and inducing the release of lipopolysaccharides. In addition, thanatin inhibits the enzymatic activity of NDM-1 by displacing zinc ions from the active site, and reverses carbapenem resistance in NDM-1-producing bacteria in vitro and in vivo. Thus, thanatin’s dual mechanism of action may be useful for combating infections caused by NDM-1-producing pathogens. The NDM-1 metallo-β-lactamase confers resistance to β-lactam antibiotics. Here, the authors show that the antimicrobial peptide thanatin is active against NDM-1-producing bacteria through a dual mechanism of action consisting of disruption of outer membrane integrity and inhibition of the NDM-1 enzymatic activity.
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Affiliation(s)
- Bo Ma
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, 710032, China
| | - Chao Fang
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, 710032, China
| | - Linshan Lu
- Department of Obstetrics and Gynecology, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710038, China
| | - Mingzhi Wang
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, 710032, China
| | - Xiaoyan Xue
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, 710032, China
| | - Ying Zhou
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, 710032, China
| | - Mingkai Li
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, 710032, China
| | - Yue Hu
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, 710032, China
| | - Xiaoxing Luo
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, 710032, China.
| | - Zheng Hou
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, 710032, China.
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30
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Linciano P, Cendron L, Gianquinto E, Spyrakis F, Tondi D. Ten Years with New Delhi Metallo-β-lactamase-1 (NDM-1): From Structural Insights to Inhibitor Design. ACS Infect Dis 2019; 5:9-34. [PMID: 30421910 DOI: 10.1021/acsinfecdis.8b00247] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The worldwide emergence of New Delhi metallo-β-lactamase-1 (NDM-1) as a carbapenemase able to hydrolyze nearly all available β-lactam antibiotics has characterized the past decade, endangering efficacious antibacterial treatments. No inhibitors for NDM-1 are available in therapy, nor are promising compounds in the pipeline for future NDM-1 inhibitors. We report the studies dedicated to the design and development of effective NDM-1 inhibitors. The discussion for each agent moves from the employed design strategy to the ability of the identified inhibitor to synergize β-lactam antibiotics. A structural analysis of NDM-1 mechanism of action based on selected X-ray complexes is also reported: the intrinsic flexibility of the binding site and the comparison between penicillin/cephalosporin and carbapenem mechanisms of hydrolysis are evaluated. Despite the valuable progress in terms of structural and mechanistic information, the design of a potent NDM-1 inhibitor to be introduced in therapy remains challenging. Certainly, only the deep knowledge of NDM-1 architecture and of the variable mechanism of action that NDM-1 employs against different classes of substrates could orient a successful drug discovery campaign.
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Affiliation(s)
- Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy
| | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
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31
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Ali A, Kumar R, Iquebal MA, Jaiswal S, Kumar D, Khan AU. The role of conserved residues in the catalytic activity of NDM-1: an approach involving site directed mutagenesis and molecular dynamics. Phys Chem Chem Phys 2019; 21:17821-17835. [DOI: 10.1039/c9cp02734c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Drug degraded by enzyme and hence not targeted on to the cell leading to cell survival. After mutation leading to conformational changes and loss of function hence drug was not degraded and remained available for the target to lyse the cell.
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Affiliation(s)
- Abid Ali
- Medical Microbiology and Molecular Biology Lab
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University
- Aligarh 202002
- India
| | - Rakesh Kumar
- ICAR-Indian Agricultural Statistics Research Institute (IASRI)
- Library Avenue
- PUSA
- New Delhi –110012
- India
| | - Mir Asif Iquebal
- ICAR-Indian Agricultural Statistics Research Institute (IASRI)
- Library Avenue
- PUSA
- New Delhi –110012
- India
| | - Sarika Jaiswal
- ICAR-Indian Agricultural Statistics Research Institute (IASRI)
- Library Avenue
- PUSA
- New Delhi –110012
- India
| | - Dinesh Kumar
- ICAR-Indian Agricultural Statistics Research Institute (IASRI)
- Library Avenue
- PUSA
- New Delhi –110012
- India
| | - Asad U. Khan
- Medical Microbiology and Molecular Biology Lab
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University
- Aligarh 202002
- India
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32
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Ali A, Gupta D, Srivastava G, Sharma A, Khan AU. Molecular and computational approaches to understand resistance of New Delhi metallo β-lactamase variants (NDM-1, NDM-4, NDM-5, NDM-6, NDM-7)-producing strains against carbapenems. J Biomol Struct Dyn 2018; 37:2061-2071. [PMID: 29749296 DOI: 10.1080/07391102.2018.1475261] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The discovery of NDM-1 and its variants has caused the emergence of antibiotic resistance in the community and hospital setting, causing major concern for health care across the globe. New Delhi Metallo-β-lactamase is known to hydrolyse almost all β-lactam antibiotics. Studies have shown the hydrolytic activates of NDM-1 and some of its variants, however a comparative study of these NDM variants has not been explored in detail. Hence, we proposed to check their catalytic activity by performing a comparative study between NDM-1 and its variants. The study was initiated to clone NDM variants (NDM-1, NDM-4, NDM-5, NDM-6 and NDM-7) followed by overexpression of the recombinant proteins to check their hydrolytic properties against β-lactam antibiotics. The minimum inhibitory concentration of carbapenems antibiotics for blaNDM-5 clone was found four fold increased, whereas no change was observed in the clones having other variants. The hydrolytic activity of carbapenem with NDM-5 variant was found to be augmented as per the kinetics parameter where Km was decreased and kcat, kcat/Km values increased as compared to the NDM-1. Molecular docking studies were employed to identify the variations in the binding ability among all NDM variants with imipenem or meropenem. Simulation studies at 100 ns showed a good stability of NDM-5 with imipenem and meropenem as compared to NDM-1. CD spectroscopy data revealed significant changes in the secondary structure of NDM variants. We conclude that NDM-5 showed higher hydrolytic activity as compared to other variants. This study provides a comparative analysis of the severity of NDM producing strains.
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Affiliation(s)
- Abid Ali
- a Medical Microbiology and Molecular Biology Lab., Interdisciplinary Biotechnology Unit , Aligarh Muslim University , Aligarh , Uttar Pradhesh 202002 , India
| | - Divya Gupta
- a Medical Microbiology and Molecular Biology Lab., Interdisciplinary Biotechnology Unit , Aligarh Muslim University , Aligarh , Uttar Pradhesh 202002 , India.,b Department of Life sciences , Uttarakhand Technical University , Dehradun , Uttarakhand 248007 , India
| | - Gaurava Srivastava
- c Biotechnology Division, CSIR-CIMAP , Lucknow , Uttar Pradhesh 226015 , India
| | - Ashok Sharma
- c Biotechnology Division, CSIR-CIMAP , Lucknow , Uttar Pradhesh 226015 , India
| | - Asad U Khan
- a Medical Microbiology and Molecular Biology Lab., Interdisciplinary Biotechnology Unit , Aligarh Muslim University , Aligarh , Uttar Pradhesh 202002 , India
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33
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Chen C, Xiang Y, Liu Y, Hu X, Yang KW. Mercaptoacetate thioesters and their hydrolysate mercaptoacetic acids jointly inhibit metallo-β-lactamase L1. MEDCHEMCOMM 2018; 9:1172-1177. [PMID: 30109005 DOI: 10.1039/c8md00091c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/04/2018] [Indexed: 11/21/2022]
Abstract
The 'superbug' infection caused by metallo-β-lactamases (MβLs) including L1 has grown into an emerging threat. To probe whether mercaptoacetate thioesters inhibiting L1 is a contribution of the thioester itself or its hydrolysate, ten mercaptoacetate thioesters 1-10 were synthesized, which specifically inhibited L1, exhibiting IC50 values ranging from 0.17 to 1.2 μM, and 8 was found to be the best inhibitor (IC50 = 0.17 μM). These thioesters restored the antimicrobial activity of cefazolin against E. coli expressing L1 by 2-4-fold. UV-vis monitoring showed that 1, 8 and 9 were unhydrolyzed in Tris buffer (pH 6.0-8.5), but hydrolyzed by L1; further HPLC monitoring indicated that 1/3 of the thioester 9 was converted to mercaptoacetic acid. STD-NMR monitoring suggested that both the thioester and its hydrolysate mercaptoacetic acid jointly inhibited L1.
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Affiliation(s)
- Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , Innovation Laboratory of Chemical Biology , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Yang Xiang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , Innovation Laboratory of Chemical Biology , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Ya Liu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , Innovation Laboratory of Chemical Biology , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Xiangdong Hu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , Innovation Laboratory of Chemical Biology , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , Innovation Laboratory of Chemical Biology , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
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Duan J, Hu C, Guo J, Guo L, Sun J, Zhao Z. A molecular dynamics study of the complete binding process of meropenem to New Delhi metallo-β-lactamase 1. Phys Chem Chem Phys 2018; 20:6409-6420. [PMID: 29442101 DOI: 10.1039/c7cp07459j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mechanism of substrate hydrolysis of New Delhi metallo-β-lactamase 1 (NDM-1) has been reported, but the process in which NDM-1 captures and transports the substrate into its active center remains unknown. In this study, we investigated the process of the substrate entry into the NDM-1 activity center through long unguided molecular dynamics simulations using meropenem as the substrate. A total of 550 individual simulations were performed, each of which for 200 ns, and 110 of them showed enzyme-substrate binding events. The results reveal three categories of relatively persistent and noteworthy enzyme-substrate binding configurations, which we call configurations A, B, and C. We performed binding free energy calculations of the enzyme-substrate complexes of different configurations using the molecular mechanics Poisson-Boltzmann surface area method. The role of each residue of the active site in binding the substrate was investigated using energy decomposition analysis. The simulated trajectories provide a continuous atomic-level view of the entire binding process, revealing potentially valuable regions where the enzyme and the substrate interact persistently and five possible pathways of the substrate entering into the active center, which were validated using well-tempered metadynamics. These findings provide important insights into the binding mechanism of meropenem to NDM-1, which may provide new prospects for the design of novel metallo-β-lactamase inhibitors and enzyme-resistant antibiotics.
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Affiliation(s)
- Juan Duan
- Department of Microbiology and Immunology of Guangdong Medical University, No. 2 West Wenming Road, Zhanjiang City, Guangdong Province 524023, China.
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Saravanan M, Ramachandran B, Barabadi H. The prevalence and drug resistance pattern of extended spectrum β–lactamases (ESBLs) producing Enterobacteriaceae in Africa. Microb Pathog 2018; 114:180-192. [DOI: 10.1016/j.micpath.2017.11.061] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 10/18/2022]
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Structural and functional insight of New Delhi Metallo β-lactamase-1 variants. Future Med Chem 2018; 10:221-229. [DOI: 10.4155/fmc-2017-0143] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
New Delhi Metallo β-lactamase-1 (NDM-1) is a member of the Metallo-β-lactamase family, capable of catalyzing the hydrolysis of all β-lactam antibiotics. The rapid dissemination of NDM producers, ‘superbugs’, has become a worldwide concern to health workers. Seventeen different variants of NDM have been reported so far, across the world. These variants varied in their sequences either by single or multiple amino acid substitutions. This review summarizes the crystal structure of NDM and provides a comparative analysis of all variants. Moreover, we have for the first time highlighted the role of α-helix, β-sheet and loop structures of NDM enzyme, having different mutations occurred in these regions. The effect of these substitutions on its structure and functional aspect has to be thoroughly understood to design effective inhibitors in future.
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