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Nahar L, Hagiya H, Gotoh K, Asaduzzaman M, Otsuka F. New Delhi Metallo-Beta-Lactamase Inhibitors: A Systematic Scoping Review. J Clin Med 2024; 13:4199. [PMID: 39064239 PMCID: PMC11277577 DOI: 10.3390/jcm13144199] [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: 06/05/2024] [Revised: 07/14/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Background/Objectives: Among various carbapenemases, New Delhi metallo-beta-lactamases (NDMs) are recognized as the most powerful type capable of hydrolyzing all beta-lactam antibiotics, often conferring multi-drug resistance to the microorganism. The objective of this review is to synthesize current scientific data on NDM inhibitors to facilitate the development of future therapeutics for challenging-to-treat pathogens. Methods: Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Extension for Scoping Reviews, we conducted a MEDLINE search for articles with relevant keywords from the beginning of 2009 to December 2022. We employed various generic terms to encompass all the literature ever published on potential NDM inhibitors. Results: Out of the 1760 articles identified through the database search, 91 met the eligibility criteria and were included in our analysis. The fractional inhibitory concentration index was assessed using the checkerboard assay for 47 compounds in 37 articles, which included 8 compounds already approved by the Food and Drug Administration (FDA) of the United States. Time-killing curve assays (14 studies, 25%), kinetic assays (15 studies, 40.5%), molecular investigations (25 studies, 67.6%), in vivo studies (14 studies, 37.8%), and toxicity assays (13 studies, 35.1%) were also conducted to strengthen the laboratory-level evidence of the potential inhibitors. None of them appeared to have been applied to human infections. Conclusions: Ongoing research efforts have identified several potential NDM inhibitors; however, there are currently no clinically applicable drugs. To address this, we must foster interdisciplinary and multifaceted collaborations by broadening our own horizons.
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Affiliation(s)
- Lutfun Nahar
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Hideharu Hagiya
- Department of Infectious Diseases, Okayama University Hospital, Okayama 700-8558, Japan
| | - Kazuyoshi Gotoh
- Department of Bacteriology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan (M.A.)
| | - Md Asaduzzaman
- Department of Bacteriology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan (M.A.)
| | - Fumio Otsuka
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
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2
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Bhat MF, Prats Luján A, Saifuddin M, Fodran P, Poelarends GJ. Multigram-scale chemoenzymatic synthesis of diverse aminopolycarboxylic acids as potential metallo-β-lactamase inhibitors. Org Biomol Chem 2024; 22:491-495. [PMID: 38126753 PMCID: PMC10792612 DOI: 10.1039/d3ob01405c] [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] [Received: 09/02/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023]
Abstract
Toxin A, a precursor to naturally occurring aspergillomarasmine A, aspergillomarasmine B, lycomarasmine and related aminopolycarboxylic acids, was synthesized as the desired (2S,2'S)-diastereomer on a multigram-scale (>99% conversion, 82% isolated yield, dr > 95 : 5) from commercially available starting materials using the enzyme ethylenediamine-N,N'-disuccinic acid lyase. A single-step protection route of this chiral synthon was developed to aid N-sulfonylation/-alkylation and reductive amination at the terminal primary amine for easy derivatization, followed by global deprotection to give the corresponding toxin A derivatives, including lycomarasmine, in moderate to good yields (23-66%) and with high stereopurity (dr > 95 : 5). Furthermore, a chemoenzymatic route was developed to introduce a click handle on toxin A (yield 72%, dr > 95 : 5) and its cyclized congener for further analogue design. Finally, a chemoenzymatic route towards the synthesis of photocaged aspergillomarasmine B (yield 8%, dr > 95 : 5) was established, prompting further steps into smart prodrug design and precision delivery. These new synthetic methodologies have the prospective of facilitating research into the finding of more selective and potent metallo-β-lactamase (MBL) inhibitors, which are urgently needed to combat MBL-based infections.
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Affiliation(s)
- Mohammad Faizan Bhat
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Alejandro Prats Luján
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Mohammad Saifuddin
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Peter Fodran
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Gerrit J Poelarends
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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3
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Jia Y, Schroeder B, Pfeifer Y, Fröhlich C, Deng L, Arkona C, Kuropka B, Sticht J, Ataka K, Bergemann S, Wolber G, Nitsche C, Mielke M, Leiros HKS, Werner G, Rademann J. Kinetics, Thermodynamics, and Structural Effects of Quinoline-2-Carboxylates, Zinc-Binding Inhibitors of New Delhi Metallo-β-lactamase-1 Re-sensitizing Multidrug-Resistant Bacteria for Carbapenems. J Med Chem 2023; 66:11761-11791. [PMID: 37585683 DOI: 10.1021/acs.jmedchem.3c00171] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Carbapenem resistance mediated by metallo-β-lactamases (MBL) such as New Delhi metallo-β-lactamase-1 (NDM-1) has become a major factor threatening the efficacy of essential β-lactam antibiotics. Starting from hit fragment dipicolinic acid (DPA), 8-hydroxy- and 8-sulfonamido-quinoline-2-carboxylic acids were developed as inhibitors of NDM-1 with highly improved inhibitory activity and binding affinity. The most active compounds formed reversibly inactive ternary protein-inhibitor complexes with two zinc ions as proven by native protein mass spectrometry and bio-layer interferometry. Modification of the NDM-1 structure with remarkable entropic gain was shown by isothermal titration calorimetry and NMR spectroscopy of isotopically labeled protein. The best compounds were potent inhibitors of NDM-1 and other representative MBL with no or little inhibition of human zinc-binding enzymes. These inhibitors significantly reduced the minimum inhibitory concentrations (MIC) of meropenem for multidrug-resistant bacteria recombinantly expressing blaNDM-1 as well as for several multidrug-resistant clinical strains at concentrations non-toxic to human cells.
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Affiliation(s)
- Yuwen Jia
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Barbara Schroeder
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Yvonne Pfeifer
- FG13 Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Burgstraße 37, Wernigerode 38855, Germany
| | - Christopher Fröhlich
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - Lihua Deng
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Christoph Arkona
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Benno Kuropka
- Core Facility BioSupraMol, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Jana Sticht
- Core Facility BioSupraMol, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Kenichi Ataka
- Department of Physics, Freie Universität Berlin, Arnimallee 14, Berlin 14195, Germany
| | - Silke Bergemann
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Gerhard Wolber
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Martin Mielke
- Department of Infectious Diseases, Robert Koch Institute, Nordufer 20, Berlin 13353, Germany
| | - Hanna-Kirsti S Leiros
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - Guido Werner
- FG13 Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Burgstraße 37, Wernigerode 38855, Germany
| | - Jörg Rademann
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
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4
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Buijs N, Vlaming HC, van Haren MJ, Martin NI. Synthetic Studies with Bacitracin A and Preparation of Analogues Containing Alternative Zinc Binding Groups. Chembiochem 2022; 23:e202200547. [PMID: 36287040 PMCID: PMC10099996 DOI: 10.1002/cbic.202200547] [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: 09/18/2022] [Revised: 10/26/2022] [Indexed: 01/25/2023]
Abstract
The growing threat of drug-resistant bacteria is a global concern, highlighting the urgent need for new antibiotics and antibacterial strategies. In this light, practical synthetic access to natural product antibiotics can provide important structure-activity insights while also opening avenues for the development of novel analogues with improved properties. To this end, we report an optimised synthetic route for the preparation of the clinically used macrocyclic peptide antibiotic bacitracin. Our combined solid- and solution-phase approach addresses the problematic, and previously unreported, formation of undesired epimers associated with the stereochemically fragile N-terminal thiazoline moiety. A number of bacitracin analogues were also prepared wherein the thiazoline motif was replaced by other known zinc-binding moieties and their antibacterial activities evaluated.
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Affiliation(s)
- Ned Buijs
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Halana C Vlaming
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - 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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5
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Wu D, Lei X. Enzymatic cascade reactions for the efficient synthesis of natural products. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133099] [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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6
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Bhat MF, Luján AP, Saifuddin M, Poelarends GJ. Chemoenzymatic Asymmetric Synthesis of Complex Heterocycles: Dihydrobenzoxazinones and Dihydroquinoxalinones. ACS Catal 2022; 12:11421-11427. [PMID: 36158903 PMCID: PMC9486952 DOI: 10.1021/acscatal.2c03008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/25/2022] [Indexed: 01/08/2023]
Affiliation(s)
- Mohammad Faizan Bhat
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Alejandro Prats Luján
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Mohammad Saifuddin
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Gerrit J. Poelarends
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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7
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Amara AAAF. The Role of Divalent Cations in Antibiotic Sensitivity. BIOMOLECULES FROM NATURAL SOURCES 2022:252-277. [DOI: 10.1002/9781119769620.ch8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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8
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Sychantha D, Rotondo CM, Tehrani KHME, Martin NI, Wright GD. Aspergillomarasmine A inhibits metallo-β-lactamases by selectively sequestering Zn 2. J Biol Chem 2021; 297:100918. [PMID: 34181945 PMCID: PMC8319579 DOI: 10.1016/j.jbc.2021.100918] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/14/2021] [Accepted: 06/23/2021] [Indexed: 11/05/2022] Open
Abstract
Class B metallo-β-lactamases (MBLs) are Zn2+-dependent enzymes that catalyze the hydrolysis of β-lactam antibiotics to confer resistance in bacteria. Several problematic groups of MBLs belong to subclass B1, including the binuclear New Delhi MBL (NDM), Verona integrin-encoded MBL, and imipenemase-type enzymes, which are responsible for widespread antibiotic resistance. Aspergillomarasmine A (AMA) is a natural aminopolycarboxylic acid that functions as an effective inhibitor of class B1 MBLs. The precise mechanism of action of AMA is not thoroughly understood, but it is known to inactivate MBLs by removing one catalytic Zn2+ cofactor. We investigated the kinetics of MBL inactivation in detail and report that AMA is a selective Zn2+ scavenger that indirectly inactivates NDM-1 by encouraging the dissociation of a metal cofactor. To further investigate the mechanism in living bacteria, we used an active site probe and showed that AMA causes the loss of a Zn2+ ion from a low-affinity binding site of NDM-1. Zn2+-depleted NDM-1 is rapidly degraded, contributing to the efficacy of AMA as a β-lactam potentiator. However, MBLs with higher metal affinity and stability such as NDM-6 and imipenemase-7 exhibit greater tolerance to AMA. These results indicate that the mechanism of AMA is broadly applicable to diverse Zn2+ chelators and highlight that leveraging Zn2+ availability can influence the survival of MBL-producing bacteria when they are exposed to β-lactam antibiotics.
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Affiliation(s)
- David Sychantha
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada; M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Caitlyn M Rotondo
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada; M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Kamaleddin H M E Tehrani
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Gerard D Wright
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada; M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
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9
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Abidin MZ, Saravanan T, Bothof L, Tepper PG, Thunnissen AMWH, Poelarends GJ. Biocatalytic enantioselective hydroaminations enabling synthesis of N-arylalkyl-substituted L-aspartic acids. Org Biomol Chem 2021; 19:6407-6411. [PMID: 34235532 PMCID: PMC8317194 DOI: 10.1039/d1ob00748c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 06/30/2021] [Indexed: 01/26/2023]
Abstract
N-Substituted l-aspartic acids are important chiral building blocks for pharmaceuticals and food additives. Here we report the asymmetric synthesis of various N-arylalkyl-substituted l-aspartic acids using ethylenediamine-N,N'-disuccinic acid lyase (EDDS lyase) as a biocatalyst. This C-N lyase shows a broad non-natural amine substrate scope and outstanding enantioselectivity, allowing the efficient addition of structurally diverse arylalkylamines to fumarate to afford the corresponding N-arylalkyl-substituted l-aspartic acids in good isolated yield (up to 79%) and with excellent enantiopurity (>99% ee). These results further demonstrate that C-N lyases working in reverse constitute an extremely powerful synthetic tool to prepare difficult noncanonical amino acids.
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Affiliation(s)
- Mohammad Z Abidin
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands. g.j.poelarends.rug.nl and Department of Animal Product Technology, Faculty of Animal Science, Gadjah Mada University, Bulaksumur, Yogyakarta, 55281, Indonesia
| | - Thangavelu Saravanan
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands. g.j.poelarends.rug.nl and School of Chemistry, University of Hyderabad, P.O. Central University, Hyderabad-500046, India.
| | - Laura Bothof
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands. g.j.poelarends.rug.nl
| | - Pieter G Tepper
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands. g.j.poelarends.rug.nl
| | - Andy-Mark W H Thunnissen
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Gerrit J Poelarends
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands. g.j.poelarends.rug.nl
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10
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Wade N, Tehrani KHME, Brüchle NC, van Haren MJ, Mashayekhi V, Martin NI. Mechanistic Investigations of Metallo-β-lactamase Inhibitors: Strong Zinc Binding Is Not Required for Potent Enzyme Inhibition*. ChemMedChem 2021; 16:1651-1659. [PMID: 33534956 PMCID: PMC8248298 DOI: 10.1002/cmdc.202100042] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/03/2021] [Indexed: 12/21/2022]
Abstract
Metallo-β-lactamases (MBLs) are zinc-dependent bacterial enzymes that inactivate essentially all classes of β-lactam antibiotics including last-resort carbapenems. At present there are no clinically approved MBL inhibitors, and in order to develop such agents it is essential to understand their inhibitory mechanisms. Herein, we describe a comprehensive mechanistic study of a panel of structurally distinct MBL inhibitors reported in both the scientific and patent literature. Specifically, we determined the half-maximal inhibitory concentration (IC50 ) for each inhibitor against MBLs belonging to the NDM and IMP families. In addition, the binding affinities of the inhibitors for Zn2+ , Ca2+ and Mg2+ were assessed by using isothermal titration calorimetry (ITC). We also compared the ability of the different inhibitors to resensitize a highly resistant MBL-expressing Escherichia coli strain to meropenem. These investigations reveal clear differences between the MBL inhibitors studied in terms of their IC50 value, metal binding ability, and capacity to synergize with meropenem. Notably, our studies demonstrate that potent MBL inhibition and synergy with meropenem are not explicitly dependent on the capacity of an inhibitor to strongly chelate zinc.
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Affiliation(s)
- Nicola Wade
- Biological Chemistry GroupInstitute of Biology LeidenLeiden UniversitySylviusweg 722333 BELeiden (TheNetherlands
| | - Kamaleddin H. M. E. Tehrani
- Biological Chemistry GroupInstitute of Biology LeidenLeiden UniversitySylviusweg 722333 BELeiden (TheNetherlands
| | - Nora C. Brüchle
- Biological Chemistry GroupInstitute of Biology LeidenLeiden UniversitySylviusweg 722333 BELeiden (TheNetherlands
| | - Matthijs J. van Haren
- Biological Chemistry GroupInstitute of Biology LeidenLeiden UniversitySylviusweg 722333 BELeiden (TheNetherlands
| | - Vida Mashayekhi
- Department of BiologyUtrecht UniversityPadualaan 83584 CHUtrecht (TheNetherlands
| | - Nathaniel I. Martin
- Biological Chemistry GroupInstitute of Biology LeidenLeiden UniversitySylviusweg 722333 BELeiden (TheNetherlands
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11
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Mendoza JA, Pineda RY, Nguyen M, Tellez M, Awad AM. Molecular docking studies, in-silico ADMET predictions and synthesis of novel PEGA-nucleosides as antimicrobial agents targeting class B1 metallo-β-lactamases. In Silico Pharmacol 2021; 9:33. [PMID: 33936929 DOI: 10.1007/s40203-021-00092-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/12/2021] [Indexed: 11/29/2022] Open
Abstract
Class B1 metallo-β-lactamases (MBLs) are metalloenzymes found in drug resistant bacteria. The enzyme requires zinc ions, along with conserved amino acid coordination for nucleophilic attack of the lactam ring to induce hydrolysis and inactivation of β-lactam and some carbapenem antibiotics. To this date there are no clinically relevant class B1 MBL inhibitors, however L-captopril has shown significant results against NDM-1, the most difficult MBL to inhibit. Herein, we report the synthesis and evaluation of novel nucleoside analogues modified with polyethylene glycolamino (PEGA) as potential inhibitors for class B1 MBLs. Molecular dynamics simulations, using internal coordinate mechanics (ICM) algorithm, were performed on subclass B1 enzyme complex models screened with twenty-one possible PEGA-nucleosides. Analogue A, 3'-deoxy-3'-(2-(2-hydroxyethoxy)ethanamino)-β-D-xylofuranosyluracil showed superior binding, with high specificity to the conserved zinc ions in the class B1 MBL active site by utilizing key β-lactam mimic points in the uridine nucleobase. The PEGA moiety showed chelating activity with zinc and disrupted the metal-binding amino acid geometry. In all subclass B1 proteins tested, analogue A had the most effective inhibition when compared to penicillin or L-captopril. Chemical synthesis was performed by condensation of the corresponding keto ribonucleoside with PEGA, followed by enantioselective reduction of the formed imine to produce the amino derivative with desired configuration. Pharmacokinetic and pharmacodynamic screenings revealed that PEGA-pyrimidine nucleosides are not toxic, nor violate Lipinski's rules. These results suggested that analogue A can be proposed as a potential metalloenzyme inhibitor against the widespread antibiotic resistant bacteria and is worth further in vitro and in vivo investigations.
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Affiliation(s)
- Jesica A Mendoza
- Department of Chemistry, California State University Channel Islands, Camarillo, CA 93012 USA
| | - Richard Y Pineda
- Department of Chemistry, California State University Channel Islands, Camarillo, CA 93012 USA
| | - Michelle Nguyen
- Department of Chemistry, California State University Channel Islands, Camarillo, CA 93012 USA
| | - Marisol Tellez
- Department of Chemistry, California State University Channel Islands, Camarillo, CA 93012 USA
| | - Ahmed M Awad
- Department of Chemistry, California State University Channel Islands, Camarillo, CA 93012 USA
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12
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Li JQ, Gao H, Zhai L, Sun LY, Chen C, Chigan JZ, Ding HH, Yang KW. Dipyridyl-substituted thiosemicarbazone as a potent broad-spectrum inhibitor of metallo-β-lactamases. Bioorg Med Chem 2021; 38:116128. [PMID: 33862468 DOI: 10.1016/j.bmc.2021.116128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 11/17/2022]
Abstract
To combat the superbug infection caused by metallo-β-lactamases (MβLs), a dipyridyl-substituted thiosemicarbazone (DpC), was identified to be the broad-spectrum inhibitor of MβLs (NDM-1, VIM-2, IMP-1, ImiS, L1), with an IC50 value in the range of 0.021-1.08 µM. It reversibly and competitively inhibited NDM-1 with a Ki value of 10.2 nM. DpC showed broad-spectrum antibacterial effect on clinical isolate K. pneumonia, CRE, VRE, CRPA and MRSA, with MIC value ranged from 16 to 32 µg/mL, and exhibited synergistic antibacterial effect with meropenem on MβLs-producing bacteria, resulting in a 2-16-, 2-8-, and 8-fold reduction in MIC of meropenem against EC-MβLs, EC01-EC24, K. pneumonia, respectively. Moreover, mice experiments showed that DpC also had synergistic antibacterial action with meropenem. In this work, DpC was identified to be a potent scaffold for the development of broad-spectrum inhibitors of MβLs.
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Affiliation(s)
- Jia-Qi Li
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Han Gao
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Le Zhai
- Shaanxi Key Laboratory of Phytochemistry, College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji 72101, Shaanxi Province, PR China
| | - Le-Yun Sun
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jia-Zhu Chigan
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Huan-Huan Ding
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China.
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van Haren MJ, Tehrani KHME, Kotsogianni I, Wade N, Brüchle NC, Mashayekhi V, Martin NI. Cephalosporin Prodrug Inhibitors Overcome Metallo-β-Lactamase Driven Antibiotic Resistance. Chemistry 2021; 27:3806-3811. [PMID: 33237604 PMCID: PMC7986777 DOI: 10.1002/chem.202004694] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/24/2020] [Indexed: 12/21/2022]
Abstract
The increasing prevalence of metallo-β-lactamase (MBL)-expressing bacteria presents a worrying trend in antibiotic resistance. MBLs rely on active site zinc ions for their hydrolytic activity and the pursuit of MBL-inhibitors has therefore involved the investigation of zinc chelators. To ensure that such chelators specifically target MBLs, a series of cephalosporin prodrugs of two potent zinc-binders: dipicolinic acid (DPA) and 8-thioquinoline (8-TQ) was prepared. Although both DPA and 8-TQ bind free zinc very tightly (Kd values in the low nm range), the corresponding cephalosporin conjugates do not. The cephalosporin conjugates are efficiently hydrolyzed by MBLs to release DPA or 8-TQ, as confirmed by using both NMR and LC-MS studies. Notably, the cephalosporin prodrugs of DPA and 8-TQ show potent inhibitory activity against NDM, VIM, and IMP classes of MBLs and display potent synergy with meropenem against MBL-expressing clinical isolates of K. pneumoniae and E. coli.
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Affiliation(s)
- Matthijs J. van Haren
- Biological Chemistry GroupInstitute of Biology LeidenLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
| | - Kamaleddin H. M. E. Tehrani
- Biological Chemistry GroupInstitute of Biology LeidenLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
| | - Ioli Kotsogianni
- Biological Chemistry GroupInstitute of Biology LeidenLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
| | - Nicola Wade
- Biological Chemistry GroupInstitute of Biology LeidenLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
| | - Nora C. Brüchle
- Biological Chemistry GroupInstitute of Biology LeidenLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
| | - Vida Mashayekhi
- Department of BiologyUtrecht UniversityUniversiteitsweg 993584 CGUtrechtThe Netherlands
| | - Nathaniel I. Martin
- Biological Chemistry GroupInstitute of Biology LeidenLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
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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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Zhang J, Abidin MZ, Saravanan T, Poelarends GJ. Recent Applications of Carbon-Nitrogen Lyases in Asymmetric Synthesis of Noncanonical Amino Acids and Heterocyclic Compounds. Chembiochem 2020; 21:2733-2742. [PMID: 32315503 PMCID: PMC7586795 DOI: 10.1002/cbic.202000214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/21/2020] [Indexed: 12/04/2022]
Abstract
Carbon-nitrogen (C-N) lyases are enzymes that normally catalyze the cleavage of C-N bonds. Reversing this reaction towards carbon-nitrogen bond formation can be a powerful approach to prepare valuable compounds that could find applications in everyday life. This review focuses on recent (last five years) applications of native and engineered C-N lyases, either as stand-alone biocatalysts or as part of multienzymatic and chemoenzymatic cascades, in enantioselective synthesis of noncanonical amino acids and dinitrogen-fused heterocycles, which are useful tools for neurobiological research and important synthetic precursors to pharmaceuticals and food additives.
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Affiliation(s)
- Jielin Zhang
- Department of Chemical and Pharmaceutical Biology Groningen Research Institute of PharmacyUniversity of GroningenAntonius Deusinglaan 19713 AVGroningenThe Netherlands
- State Key Laboratory of Natural Medicines and Laboratory of Chemical BiologyChina Pharmaceutical University639 Longmian AvenueNanjing211198P. R. China
| | - Mohammad Z. Abidin
- Department of Chemical and Pharmaceutical Biology Groningen Research Institute of PharmacyUniversity of GroningenAntonius Deusinglaan 19713 AVGroningenThe Netherlands
- Department of Animal Product Technology, Faculty of Animal ScienceGadjah Mada University BulaksumurYogyakarta55281Indonesia
| | - Thangavelu Saravanan
- Department of Chemical and Pharmaceutical Biology Groningen Research Institute of PharmacyUniversity of GroningenAntonius Deusinglaan 19713 AVGroningenThe Netherlands
- School of ChemistryUniversity of Hyderabad GachibowliHyderabad500046 TelanganaIndia
| | - Gerrit J. Poelarends
- Department of Chemical and Pharmaceutical Biology Groningen Research Institute of PharmacyUniversity of GroningenAntonius Deusinglaan 19713 AVGroningenThe Netherlands
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16
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New Delhi metallo-β-lactamase-1 inhibitors for combating antibiotic drug resistance: recent developments. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02580-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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