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Lee JH, Kim SG, Jang KM, Shin K, Jin H, Kim DW, Jeong BC, Lee SH. Elucidation of critical chemical moieties of metallo-β-lactamase inhibitors and prioritisation of target metallo-β-lactamases. J Enzyme Inhib Med Chem 2024; 39:2318830. [PMID: 38488135 PMCID: PMC10946278 DOI: 10.1080/14756366.2024.2318830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 02/07/2024] [Indexed: 03/19/2024] Open
Abstract
The urgent demand for effective countermeasures against metallo-β-lactamases (MBLs) necessitates development of novel metallo-β-lactamase inhibitors (MBLIs). This study is dedicated to identifying critical chemical moieties within previously developed MBLIs, and critical MBLs should serve as the target in MBLI evaluations. Using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), a systematic literature analysis was conducted, and the NCBI RefSeq genome database was exploited to access the abundance profile and taxonomic distribution of MBLs and their variant types. Through the implementation of two distinct systematic approaches, we elucidated critical chemical moieties of MBLIs, providing pivotal information for rational drug design. We also prioritised MBLs and their variant types, highlighting the imperative need for comprehensive testing to ensure the potency and efficacy of the newly developed MBLIs. This approach contributes valuable information to advance the field of antimicrobial drug discovery.
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Affiliation(s)
- Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Sang-Gyu Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju, Republic of Korea
| | - Kyung-Min Jang
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Kyoungmin Shin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Hyeonku Jin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Dae-Wi Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju, Republic of Korea
| | - Byeong Chul Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
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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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Thomas CA, Cheng Z, Bethel CR, Hujer AM, Sturgill AM, Onuoha K, Page RC, Bonomo RA, Crowder MW. The directed evolution of NDM-1. Antimicrob Agents Chemother 2023; 67:e0071423. [PMID: 37874296 PMCID: PMC10649027 DOI: 10.1128/aac.00714-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/10/2023] [Indexed: 10/25/2023] Open
Abstract
β-Lactam antibiotics are among the most frequently prescribed therapeutic agents. A common mechanism of resistance toward β-lactam antibiotics is the production of β-lactamases. These enzymes are capable of hydrolyzing the β-lactam bond, rendering the drug inactive. Among the four described classes, the metallo- β-lactamases (MBLs, class B) employ one or two zinc ions in the active site for catalysis. One of the three most clinically relevant MBLs is New Delhi Metallo- β-Lactamase (NDM-1). The current study sought to investigate the in vitro protein evolution of NDM-1 β-lactamase using error-prone polymerase chain reaction. Evaluation revealed that variants were not found to confer higher levels of resistance toward meropenem based on amino acid substitutions. Thus, we postulate that increases in transcription or changes in zinc transport may be clinically more relevant to meropenem resistance than amino acid substitutions.
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Affiliation(s)
- Caitlyn A. Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Christopher R. Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Andrea M. Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Aidan M. Sturgill
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Kelechi Onuoha
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Richard C. Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Clinician Scientist Investigator, Ohio, Cleveland, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
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4
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Legru A, Verdirosa F, Vo-Hoang Y, Tassone G, Vascon F, Thomas CA, Sannio F, Corsica G, Benvenuti M, Feller G, Coulon R, Marcoccia F, Devente SR, Bouajila E, Piveteau C, Leroux F, Deprez-Poulain R, Deprez B, Licznar-Fajardo P, Crowder MW, Cendron L, Pozzi C, Mangani S, Docquier JD, Hernandez JF, Gavara L. Optimization of 1,2,4-Triazole-3-thiones toward Broad-Spectrum Metallo-β-lactamase Inhibitors Showing Potent Synergistic Activity on VIM- and NDM-1-Producing Clinical Isolates. J Med Chem 2022; 65:16392-16419. [PMID: 36450011 DOI: 10.1021/acs.jmedchem.2c01257] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Metallo-β-lactamases (MBLs) contribute to the resistance of Gram-negative bacteria to carbapenems, last-resort antibiotics at hospital, and MBL inhibitors are urgently needed to preserve these important antibacterial drugs. Here, we describe a series of 1,2,4-triazole-3-thione-based inhibitors displaying an α-amino acid substituent, which amine was mono- or disubstituted by (hetero)aryl groups. Compounds disubstituted by certain nitrogen-containing heterocycles showed submicromolar activities against VIM-type enzymes and strong NDM-1 inhibition (Ki = 10-30 nM). Equilibrium dialysis, native mass spectrometry, isothermal calorimetry (ITC), and X-ray crystallography showed that the compounds inhibited both VIM-2 and NDM-1 at least partially by stripping the catalytic zinc ions. These inhibitors also displayed a very potent synergistic activity with meropenem (16- to 1000-fold minimum inhibitory concentration (MIC) reduction) against VIM-type- and NDM-1-producing ultraresistant clinical isolates, including Enterobacterales and Pseudomonas aeruginosa. Furthermore, selected compounds exhibited no or moderate toxicity toward HeLa cells, favorable absorption, distribution, metabolism, excretion (ADME) properties, and no or modest inhibition of several mammalian metalloenzymes.
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Affiliation(s)
- Alice Legru
- IBMM, CNRS, Univ Montpellier, ENSCM, 34000 Montpellier, France
| | - Federica Verdirosa
- Dipartimento di Biotecnologie Mediche, Università di Siena, 53100 Siena, Italy
| | - Yen Vo-Hoang
- IBMM, CNRS, Univ Montpellier, ENSCM, 34000 Montpellier, France
| | - Giusy Tassone
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, 53100 Siena, Italy
| | - Filippo Vascon
- Laboratory of Structural Biology, Department of Biology, University of Padua, 35121 Padova, Italy
| | - Caitlyn A Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Filomena Sannio
- Dipartimento di Biotecnologie Mediche, Università di Siena, 53100 Siena, Italy
| | - Giuseppina Corsica
- Dipartimento di Biotecnologie Mediche, Università di Siena, 53100 Siena, Italy
| | - Manuela Benvenuti
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, 53100 Siena, Italy
| | - Georges Feller
- Laboratoire de Biochimie, Centre d'Ingénierie des Protéines-InBioS, Université de Liège, Allée du 6 août B6, Sart-Tilman, B-4000 Liège, Belgium
| | - Rémi Coulon
- IBMM, CNRS, Univ Montpellier, ENSCM, 34000 Montpellier, France
| | - Francesca Marcoccia
- Dipartimento di Biotecnologie Mediche, Università di Siena, 53100 Siena, Italy
| | | | | | - Catherine Piveteau
- Drugs and Molecules for Living System, U1177, Inserm, Université de Lille, Faculté de Pharmacie, 59006 Lille, France
| | - Florence Leroux
- Drugs and Molecules for Living System, U1177, Inserm, Université de Lille, Faculté de Pharmacie, 59006 Lille, France
| | - Rebecca Deprez-Poulain
- Drugs and Molecules for Living System, U1177, Inserm, Université de Lille, Faculté de Pharmacie, 59006 Lille, France
| | - Benoît Deprez
- Drugs and Molecules for Living System, U1177, Inserm, Université de Lille, Faculté de Pharmacie, 59006 Lille, France
| | - Patricia Licznar-Fajardo
- HydroSciences Montpellier, UMR5151, Univ Montpellier, CNRS, IRD, CHU Montpellier, 34000 Montpellier, France
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Laura Cendron
- Laboratory of Structural Biology, Department of Biology, University of Padua, 35121 Padova, Italy
| | - Cecilia Pozzi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, 53100 Siena, Italy
| | - Stefano Mangani
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, 53100 Siena, Italy
| | - Jean-Denis Docquier
- Dipartimento di Biotecnologie Mediche, Università di Siena, 53100 Siena, Italy.,Centre d'Ingénierie des Protéines-InBioS, Université de Liège, B-4000 Liège, Belgium
| | | | - Laurent Gavara
- IBMM, CNRS, Univ Montpellier, ENSCM, 34000 Montpellier, France
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5
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Malysheva SF, Kuimov VA, Belogorlova NA, Beloveghets LA, Albanov AI, Usoltsev YK, Trofimov BA. Synthesis of Diorganylphosphine Oxides Bearing Hetarylalkyl Moieties and Study of Their Antimicrobial Activities. ChemistrySelect 2022. [DOI: 10.1002/slct.202202149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Svetlana F. Malysheva
- A. E. Favorsky Irkutsk Institute of Chemistry Siberian Branch of the Russian Academy of Sciences 1 Favorsky St. 664033 Irkutsk Russian Federation
| | - Vladimir A. Kuimov
- A. E. Favorsky Irkutsk Institute of Chemistry Siberian Branch of the Russian Academy of Sciences 1 Favorsky St. 664033 Irkutsk Russian Federation
| | - Natalia A. Belogorlova
- A. E. Favorsky Irkutsk Institute of Chemistry Siberian Branch of the Russian Academy of Sciences 1 Favorsky St. 664033 Irkutsk Russian Federation
| | - Ludmila A. Beloveghets
- A. E. Favorsky Irkutsk Institute of Chemistry Siberian Branch of the Russian Academy of Sciences 1 Favorsky St. 664033 Irkutsk Russian Federation
| | - Alexander I. Albanov
- A. E. Favorsky Irkutsk Institute of Chemistry Siberian Branch of the Russian Academy of Sciences 1 Favorsky St. 664033 Irkutsk Russian Federation
| | - Yurii K. Usoltsev
- Hospital of the Irkutsk Scientific Center of the Siberian Branch of the Russian Academy of Sciences 283b Lermontova St. 664033 Irkutsk Russian Federation
| | - Boris A. Trofimov
- A. E. Favorsky Irkutsk Institute of Chemistry Siberian Branch of the Russian Academy of Sciences 1 Favorsky St. 664033 Irkutsk Russian Federation
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6
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Volkov PA, Khrapova KO, Telezhkin AA, Albanov AI, Apartsin KA, Trofimov BA. SNHAr Reaction of Pyridines with Bis(polyfluoroalkyl)phosphonates Assisted by Electron-Deficient Acetylenes. RUSS J GEN CHEM+ 2022. [DOI: 10.1134/s1070363222090134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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7
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van Groesen E, Innocenti P, Martin NI. Recent Advances in the Development of Semisynthetic Glycopeptide Antibiotics: 2014-2022. ACS Infect Dis 2022; 8:1381-1407. [PMID: 35895325 PMCID: PMC9379927 DOI: 10.1021/acsinfecdis.2c00253] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The accelerated appearance of drug-resistant bacteria poses an ever-growing threat to modern medicine's capacity to fight infectious diseases. Gram-positive species such as methicillin-resistant Staphylococcus aureus (MRSA) and Streptococcus pneumoniae continue to contribute significantly to the global burden of antimicrobial resistance. For decades, the treatment of serious Gram-positive infections relied upon the glycopeptide family of antibiotics, typified by vancomycin, as a last line of defense. With the emergence of vancomycin resistance, the semisynthetic glycopeptides telavancin, dalbavancin, and oritavancin were developed. The clinical use of these compounds is somewhat limited due to toxicity concerns and their unusual pharmacokinetics, highlighting the importance of developing next-generation semisynthetic glycopeptides with enhanced antibacterial activities and improved safety profiles. This Review provides an updated overview of recent advancements made in the development of novel semisynthetic glycopeptides, spanning the period from 2014 to today. A wide range of approaches are covered, encompassing innovative strategies that have delivered semisynthetic glycopeptides with potent activities against Gram-positive bacteria, including drug-resistant strains. We also address recent efforts aimed at developing targeted therapies and advances made in extending the activity of the glycopeptides toward Gram-negative organisms.
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Affiliation(s)
- Emma van Groesen
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University 2333 BE Leiden, The Netherlands
| | - Paolo Innocenti
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University 2333 BE Leiden, The Netherlands
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University 2333 BE Leiden, The Netherlands
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8
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The development of New Delhi metallo-β-lactamase-1 inhibitors since 2018. Microbiol Res 2022; 261:127079. [DOI: 10.1016/j.micres.2022.127079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/22/2022] [Accepted: 05/23/2022] [Indexed: 11/21/2022]
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9
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Ayipo YO, Osunniran WA, Babamale HF, Ayinde MO, Mordi MN. Metalloenzyme mimicry and modulation strategies to conquer antimicrobial resistance: Metal-ligand coordination perspectives. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214317] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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10
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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11
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Zhang H, Yang K, Cheng Z, Thomas C, Steinbrunner A, Pryor C, Vulcan M, Kemp C, Orea D, Paththamperuma C, Chen AY, Cohen SM, Page RC, Tierney DL, Crowder MW. Spectroscopic and biochemical characterization of metallo-β-lactamase IMP-1 with dicarboxylic, sulfonyl, and thiol inhibitors. Bioorg Med Chem 2021; 40:116183. [PMID: 33965839 PMCID: PMC8170513 DOI: 10.1016/j.bmc.2021.116183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/20/2021] [Accepted: 04/26/2021] [Indexed: 02/02/2023]
Abstract
In an effort to probe the biophysical mechanisms of inhibition for ten previously-reported inhibitors of metallo-β-lactamases (MBL) with MBL IMP-1, equilibrium dialysis, metal analyses coupled with atomic absorption spectroscopy (AAS), native state mass spectrometry (native MS), and ultraviolet-visible spectrophotometry (UV-VIS) were used. 6-(1H-tetrazol-5-yl) picolinic acid (1T5PA), ANT431, D/l-captopril, thiorphan, and tiopronin were shown to form IMP-1/Zn(II)/inhibitor ternary complexes, while dipicolinic acid (DPA) and 4-(3-aminophenyl)pyridine-2,6-dicarboxylic acid (3AP-DPA) stripped some metal from the active site of IMP but also formed ternary complexes. DPA and 3AP-DPA stripped less metal from IMP-1 than from VIM-2 but stripped more metal from IMP-1 than from NDM-1. In contrast to a previous report, pterostilbene does not appear to bind to IMP-1 under our conditions. These results, along with previous studies, demonstrate similar mechanisms of inhibition toward different MBLs for different MBL inhibitors.
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Affiliation(s)
- Huan Zhang
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Kundi Yang
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Caitlyn Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Abbie Steinbrunner
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Cecily Pryor
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Maya Vulcan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Claire Kemp
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Diego Orea
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | | | - Allie Y Chen
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Richard C Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - David L Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.
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12
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Mehta R, Rivera DD, Reilley DJ, Tan D, Thomas PW, Hinojosa A, Stewart AC, Cheng Z, Thomas CA, Crowder MW, Alexandrova AN, Fast W, Que EL. Visualizing the Dynamic Metalation State of New Delhi Metallo-β-lactamase-1 in Bacteria Using a Reversible Fluorescent Probe. J Am Chem Soc 2021; 143:8314-8323. [PMID: 34038127 DOI: 10.1021/jacs.1c00290] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
New Delhi metallo-β-lactamase (NDM) grants resistance to a broad spectrum of β-lactam antibiotics, including last-resort carbapenems, and is emerging as a global antibiotic resistance threat. Limited zinc availability adversely impacts the ability of NDM-1 to provide resistance, but a number of clinical variants have emerged that are more resistant to zinc scarcity (e.g., NDM-15). To provide a novel tool to better study metal ion sequestration in host-pathogen interactions, we describe the development of a fluorescent probe that reports on the dynamic metalation state of NDM within Escherichia coli. The thiol-containing probe selectively coordinates the dizinc metal cluster of NDM and results in a 17-fold increase in fluorescence intensity. Reversible binding enables competition and time-dependent studies that reveal fluorescence changes used to detect enzyme localization, substrate and inhibitor engagement, and changes to metalation state through the imaging of live E. coli using confocal microscopy. NDM-1 is shown to be susceptible to demetalation by intracellular and extracellular metal chelators in a live-cell model of zinc dyshomeostasis, whereas the NDM-15 metalation state is shown to be more resistant to zinc flux. The development of this reversible turn-on fluorescent probe for the metalation state of NDM provides a new tool for monitoring the impact of metal ion sequestration by host defense mechanisms and for detecting inhibitor-target engagement during the development of therapeutics to counter this resistance determinant.
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Affiliation(s)
- Radhika Mehta
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Dann D Rivera
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - David J Reilley
- Department of Chemistry and Biochemistry, University of California-Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Dominique Tan
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Pei W Thomas
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Abigail Hinojosa
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Alesha C Stewart
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Caitlyn A Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California-Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Walter Fast
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Emily L Que
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
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13
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Adamek RN, Ludford P, Duggan SM, Tor Y, Cohen SM. Identification of Adenosine Deaminase Inhibitors by Metal-binding Pharmacophore Screening. ChemMedChem 2020; 15:2151-2156. [PMID: 32729197 DOI: 10.1002/cmdc.202000271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/25/2020] [Indexed: 12/20/2022]
Abstract
Adenosine deaminase (ADA) is a human mononuclear Zn2+ metalloenzyme that converts adenosine to inosine. ADA is a validated drug target for cancer, but there has been little recent work on the development of new therapeutics against this enzyme. The lack of new advancements can be partially attributed to an absence of suitable assays for high-throughput screening (HTS) against ADA. To facilitate more rapid drug discovery efforts for this target, an in vitro assay was developed that utilizes the enzymatic conversion of a visibly emitting adenosine analogue to the corresponding fluorescent inosine analogue by ADA, which can be monitored via fluorescence intensity changes. Utilizing this assay, a library of ∼350 small molecules containing metal-binding pharmacophores (MBPs) was screened in an HTS format to identify new inhibitor scaffolds against ADA. This approach yielded a new metal-binding scaffold with a Ki value of 26±1 μM.
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Affiliation(s)
- Rebecca N Adamek
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
| | - Paul Ludford
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
| | - Stephanie M Duggan
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
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14
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Chen AY, Thomas CA, Thomas PW, Yang K, Cheng Z, Fast W, Crowder MW, Cohen SM. Iminodiacetic Acid as a Novel Metal-Binding Pharmacophore for New Delhi Metallo-β-lactamase Inhibitor Development. ChemMedChem 2020; 15:1272-1282. [PMID: 32315115 PMCID: PMC7434514 DOI: 10.1002/cmdc.202000123] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/20/2020] [Indexed: 12/12/2022]
Abstract
The fungal natural product aspergillomarasmine A (AMA) has been identified as a noncompetitive inhibitor of New Delhi metallo-β-lactamase-1 (NDM-1) that inhibits by removing ZnII from the active-site. The nonselective metal-chelating properties and difficult synthesis and derivatization of AMA have hindered the development of this scaffold into a potent and selective inhibitor of NDM-1. Iminodiacetic acid (IDA) has been identified as the metal-binding pharmacophore (MBP) core of AMA that can be leveraged for inhibitor development. Herein, we report the use of IDA for fragment-based drug discovery (FBDD) of NDM-1 inhibitors. IDA (IC50 =120 μM) was developed into inhibitor 23 f (IC50 =8.6 μM, Ki =2.6 μM), which formed a ternary complex with NDM-1, as evidenced by protein thermal-shift and native-state electrospray ionization mass spectrometry (ESI-MS) experiments. Combining mechanistic analysis with inhibitor derivatization, the use of IDA as an alternative AMA scaffold for NDM-1 inhibitor development is detailed.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Caitlyn A Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Pei W Thomas
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Austin, TX 78712, USA
| | - Kundi Yang
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Walter Fast
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Austin, TX 78712, USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
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15
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Probing the mechanisms of inhibition for various inhibitors of metallo-β-lactamases VIM-2 and NDM-1. J Inorg Biochem 2020; 210:111123. [PMID: 32622213 DOI: 10.1016/j.jinorgbio.2020.111123] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/15/2022]
Abstract
To probe the mechanism of inhibition of several previously-published metallo-β-lactamase (MBL) inhibitors for the clinically-important MBL Verona integron-encoded metallo-β-lactamase 2 (VIM-2), equilibrium dialyses with metal analyses, native state electrospray ionization mass spectrometry (ESI-MS), and UV-Vis spectrophotometry were utilized. The mechanisms of inhibition were analyzed for ethylenediaminetetraacetic acid (EDTA); dipicolinic acid (DPA) and DPA analogs 6-(1H-tetrazol-5-yl)picolinic acid (1T5PA) and 4-(3-aminophenyl)pyridine-2,6-dicarboxylic acid (3AP-DPA); thiol-containing compounds, 2,3-dimercaprol, thiorphan, captopril, and tiopronin; and 5-(pyridine-3-sulfonamido)-1,3-thiazole-4-carboxylic acid (ANT-431). UV-Vis spectroscopy and native-state ESI-MS results showed the formation of ternary complexes between VIM-2 and 1T5PA, ANT-431, thiorphan, captopril, and tiopronin, while a metal stripping mechanism was shown with VIM-2 and EDTA and DPA. The same approaches were used to show the formation of a ternary complex between New Delhi Metallo-β-lactamase (NDM-1) and ANT-431. The studies presented herein show that most of the inhibitors utilize a similar mechanism of inhibition as previously reported for NDM-1. These studies also demonstrate that native mass spectrometry can be used to probe the mechanism of inhibition at lower enzyme/inhibitor concentrations than has previously been achieved.
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16
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Tehrani KHME, Brüchle NC, Wade N, Mashayekhi V, Pesce D, van Haren MJ, Martin NI. Small Molecule Carboxylates Inhibit Metallo-β-lactamases and Resensitize Carbapenem-Resistant Bacteria to Meropenem. ACS Infect Dis 2020; 6:1366-1371. [PMID: 32227874 PMCID: PMC7296533 DOI: 10.1021/acsinfecdis.9b00459] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the search for new inhibitors of bacterial metallo-β-lactamases (MBLs), a series of commonly used small molecule carboxylic acid derivatives were evaluated for their ability to inhibit New Delhi metallo-β-lactamase (NDM)-, Verona integron-encoded metallo-β-lactamase (VIM)-, and imipenemase (IMP)-type enzymes. Nitrilotriacetic acid (3) and N-(phosphonomethyl)iminodiacetic acid (5) showed promising activity especially against NDM-1 and VIM-2 with IC50 values in the low-to-sub μM range. Binding assays using isothermal titration calorimetry reveal that 3 and 5 bind zinc with high affinity with dissociation constant (Kd) values of 121 and 56 nM, respectively. The in vitro biological activity of 3 and 5 against E. coli expressing NDM-1 was evaluated in checkerboard format, demonstrating a strong synergistic relationship for both compounds when combined with Meropenem. Compounds 3 and 5 were then tested against 35 pathogenic strains expressing MBLs of the NDM, VIM, or IMP classes. Notably, when combined with Meropenem, compounds 3 and 5 were found to lower the minimum inhibitory concentration (MIC) of Meropenem up to 128-fold against strains producing NDM- and VIM-type enzymes.
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Affiliation(s)
- Kamaleddin H. M. E. Tehrani
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Nora C. Brüchle
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Nicola Wade
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Vida Mashayekhi
- Division of Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Diego Pesce
- Laboratory of Genetics, Wageningen University and Research, 6700 AA Wageningen, The Netherlands
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Matthijs J. van Haren
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Nathaniel I. Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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17
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Jackson AC, Zaengle-Barone JM, Puccio EA, Franz KJ. A Cephalosporin Prochelator Inhibits New Delhi Metallo-β-lactamase 1 without Removing Zinc. ACS Infect Dis 2020; 6:1264-1272. [PMID: 32298084 DOI: 10.1021/acsinfecdis.0c00083] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Antibacterial drug resistance is a rapidly growing clinical threat, partially due to expression of β-lactamase enzymes, which confer resistance to bacteria by hydrolyzing and inactivating β-lactam antibiotics. The increasing prevalence of metallo-β-lactamases poses a unique challenge, as currently available β-lactamase inhibitors target the active site of serine β-lactamases but are ineffective against the zinc-containing active sites of metallo-β-lactamases. There is an urgent need for metallo-β-lactamase inhibitors and antibiotics that circumvent resistance mediated by metallo-β-lactamases in order to extend the utility of existing β-lactam antibiotics for treating infection. Here we investigated the antibacterial chelator-releasing prodrug PcephPT (2-((((6R,7R)-2-carboxy-8-oxo-7-(2-phenylacetamido)-5-thia-1-azabicyclo[4.2.0]oct-2-en-3-yl)methyl)thio) pyridine 1-oxide) as an inhibitor of New Delhi metallo-β-lactamase 1 (NDM-1). PcephPT is an experimental compound that we have previously shown inhibits growth of β-lactamase-expressing E. coli using a mechanism that is dependent on both copper availability and β-lactamase expression. Here, we found that PcephPT, in addition to being a copper-dependent antibacterial compound, inhibits hydrolysis activity of purified NDM-1with an IC50 of 7.6 μM without removing zinc from the active site and restores activity of the carbapenem antibiotic meropenem against NDM-1-producing E. coli. This work demonstrates that targeting a metal-binding pharmacophore to β-lactamase-producing bacteria is a promising strategy for inhibition of both bacterial growth and metallo-β-lactamases.
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Affiliation(s)
- Abigail C. Jackson
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | | | - Elena A. Puccio
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Katherine J. Franz
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
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18
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Jin WB, Xu C, Cheung Q, Gao W, Zeng P, Liu J, Chan EWC, Leung YC, Chan TH, Wong KY, Chen S, Chan KF. Bioisosteric investigation of ebselen: Synthesis and in vitro characterization of 1,2-benzisothiazol-3(2H)-one derivatives as potent New Delhi metallo-β-lactamase inhibitors. Bioorg Chem 2020; 100:103873. [PMID: 32361294 DOI: 10.1016/j.bioorg.2020.103873] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 04/07/2020] [Accepted: 04/21/2020] [Indexed: 01/10/2023]
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) producing New Delhi metallo-β-lactamase (NDM-1) cause untreatable bacterial infections, posing a significant threat to human health. In the present study, by employing the concept of bioisosteric replacement of the selenium moiety of ebselen, we have designed, synthesized and characterized a small compound library of 2-substituted 1,2-benzisothiazol-3(2H)-one derivatives and related compounds for evaluating their cytotoxicity and synergistic activity in combination with meropenem against the E. coli Tg1 (NDM-1) strain. The most promising compound 3a demonstrated potent synergistic activity against a panel of clinically isolated NDM-1 positive CRE strains with FICI as low as 0.09. Moreover, its IC50 value and inhibition mechanism were also confirmed by using the enzyme inhibition assay and the ESI-MS analysis respectively. Importantly, compound 3a has acceptable toxicity and is not a PAINS. Because of its structural simplicity and potent synergistic activity in combination with meropenem, we propose that compound 3a may be a promising meropenem adjuvant and a new series of such compounds may worth further investigations.
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Affiliation(s)
- Wen Bin Jin
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region; Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Chen Xu
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region; Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, The Hong Kong PolyU Shenzhen Research Institute, Shenzhen, China
| | - Qipeng Cheung
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region; Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, The Hong Kong PolyU Shenzhen Research Institute, Shenzhen, China
| | - Wei Gao
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region
| | - Ping Zeng
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region
| | - Jun Liu
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region
| | - Edward W C Chan
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region
| | - Yun-Chung Leung
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region
| | - Tak Hang Chan
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region; Department of Chemistry, McGill University, Montreal, Quebec H3A 2K6, Canada
| | - Kwok-Yin Wong
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region.
| | - Kin-Fai Chan
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region.
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19
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MBLinhibitors.com, a Website Resource Offering Information and Expertise for the Continued Development of Metallo--Lactamase Inhibitors. Biomolecules 2020; 10:biom10030459. [PMID: 32188106 PMCID: PMC7175331 DOI: 10.3390/biom10030459] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 12/29/2022] Open
Abstract
In an effort to facilitate the discovery of new, improved inhibitors of the metallo-β-lactamases (MBLs), a new, interactive website called MBLinhibitors.com was developed. Despite considerable efforts from the science community, there are no clinical inhibitors of the MBLs, which are now produced by human pathogens. The website, MBLinhibitors.com, contains a searchable database of known MBL inhibitors, and inhibitors can be searched by chemical name, chemical formula, chemical structure, Simplified Molecular-Input Line-Entry System (SMILES) format, and by the MBL on which studies were conducted. The site will also highlight a “MBL Inhibitor of the Month”, and researchers are invited to submit compounds for this feature. Importantly, MBLinhibitors.com was designed to encourage collaboration, and researchers are invited to submit their new compounds, using the “Submit” function on the site, as well as their expertise using the “Collaboration” function. The intention is for this site to be interactive, and the site will be improved in the future as researchers use the site and suggest improvements. It is hoped that MBLinhibitors.com will serve as the one-stop site for any important information on MBL inhibitors and will aid in the discovery of a clinically useful MBL inhibitor.
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20
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Yan Y, Li G, Li G. Principles and current strategies targeting metallo‐β‐lactamase mediated antibacterial resistance. Med Res Rev 2020; 40:1558-1592. [PMID: 32100311 DOI: 10.1002/med.21665] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/18/2019] [Accepted: 02/11/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Yu‐Hang Yan
- Key Laboratory of Drug‐Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant‐Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of PharmacySichuan UniversityChengdu Sichuan China
| | - Gen Li
- Key Laboratory of Drug‐Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant‐Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of PharmacySichuan UniversityChengdu Sichuan China
| | - Guo‐Bo Li
- Key Laboratory of Drug‐Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant‐Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of PharmacySichuan UniversityChengdu Sichuan China
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21
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Morrison CN, Prosser KE, Stokes RW, Cordes A, Metzler-Nolte N, Cohen SM. Expanding medicinal chemistry into 3D space: metallofragments as 3D scaffolds for fragment-based drug discovery. Chem Sci 2019; 11:1216-1225. [PMID: 34123246 PMCID: PMC8148059 DOI: 10.1039/c9sc05586j] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/12/2019] [Indexed: 01/02/2023] Open
Abstract
Fragment-based drug discovery (FBDD) is a powerful strategy for the identification of new bioactive molecules. FBDD relies on fragment libraries, generally of modest size, but of high chemical diversity. Although good chemical diversity in FBDD libraries has been achieved in many respects, achieving shape diversity - particularly fragments with three-dimensional (3D) structures - has remained challenging. A recent analysis revealed that >75% of all conventional, organic fragments are predominantly 1D or 2D in shape. However, 3D fragments are desired because molecular shape is one of the most important factors in molecular recognition by a biomolecule. To address this challenge, the use of inert metal complexes, so-called 'metallofragments' (mFs), to construct a 3D fragment library is introduced. A modest library of 71 compounds has been prepared with rich shape diversity as gauged by normalized principle moment of inertia (PMI) analysis. PMI analysis shows that these metallofragments occupy an area of fragment space that is unique and highly underrepresented when compared to conventional organic fragment libraries that are comprised of orders of magnitude more molecules. The potential value of this metallofragment library is demonstrated by screening against several different types of proteins, including an antiviral, an antibacterial, and an anticancer target. The suitability of the metallofragments for future hit-to-lead development was validated through the determination of IC50 and thermal shift values for select fragments against several proteins. These findings demonstrate the utility of metallofragment libraries as a means of accessing underutilized 3D fragment space for FBDD against a variety of protein targets.
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Affiliation(s)
- Christine N Morrison
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
| | - Kathleen E Prosser
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
| | - Ryjul W Stokes
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
| | - Anna Cordes
- Lehrstuhl für Anorganische Chemie 1, Bioanorganische Chemie, Ruhr-Universität Bochum Universitätsstraße 150 44801 Bochum Germany
| | - Nils Metzler-Nolte
- Lehrstuhl für Anorganische Chemie 1, Bioanorganische Chemie, Ruhr-Universität Bochum Universitätsstraße 150 44801 Bochum Germany
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
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