51
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Salimraj R, Hinchliffe P, Kosmopoulou M, Tyrrell JM, Brem J, van Berkel SS, Verma A, Owens RJ, McDonough MA, Walsh TR, Schofield CJ, Spencer J. Crystal structures of VIM-1 complexes explain active site heterogeneity in VIM-class metallo-β-lactamases. FEBS J 2019; 286:169-183. [PMID: 30430727 PMCID: PMC6326847 DOI: 10.1111/febs.14695] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/06/2018] [Accepted: 11/02/2018] [Indexed: 12/12/2022]
Abstract
Metallo-β-Lactamases (MBLs) protect bacteria from almost all β-lactam antibiotics. Verona integron-encoded MBL (VIM) enzymes are among the most clinically important MBLs, with VIM-1 increasing in carbapenem-resistant Enterobacteriaceae (Escherichia coli, Klebsiella pneumoniae) that are among the hardest bacterial pathogens to treat. VIM enzymes display sequence variation at residues (224 and 228) that in related MBLs are conserved and participate in substrate binding. How they accommodate this variability, while retaining catalytic efficiency against a broad substrate range, has remained unclear. Here, we present crystal structures of VIM-1 and its complexes with a substrate-mimicking thioenolate inhibitor, ML302F, that restores meropenem activity against a range of VIM-1 producing clinical strains, and the hydrolysed product of the carbapenem meropenem. Comparison of these two structures identifies a water-mediated hydrogen bond, between the carboxylate group of substrate/inhibitor and the backbone carbonyl of the active site zinc ligand Cys221, that is common to both complexes. Structural comparisons show that the responsible Cys221-bound water is observed in all known VIM structures, participates in carboxylate binding with other inhibitor classes, and thus effectively replicates the role of the conserved Lys224 in analogous complexes with other MBLs. These results provide a mechanism for substrate binding that permits the variation at positions 224 and 228 that is a hallmark of VIM MBLs. ENZYMES: EC 3.5.2.6 DATABASES: Co-ordinates and structure factors for protein structures described in this manuscript have been deposited in the Protein Data Bank (www.rcsb.org/pdb) with accession codes 5N5G (VIM-1), 5N5H (VIM-1:ML302F complex) and 5N5I (VIM-1-hydrolysed meropenem complex).
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Affiliation(s)
- Ramya Salimraj
- School of Cellular and Molecular MedicineUniversity of BristolUK
| | | | | | | | - Jürgen Brem
- Department of ChemistryUniversity of OxfordUK
| | | | - Anil Verma
- Oxford Protein Production Facility UKRutherford Appleton LaboratoryOxfordshireUK
| | - Raymond J. Owens
- Oxford Protein Production Facility UKRutherford Appleton LaboratoryOxfordshireUK
| | | | | | | | - James Spencer
- School of Cellular and Molecular MedicineUniversity of BristolUK
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52
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Konaklieva MI. Addressing Antimicrobial Resistance through New Medicinal and Synthetic Chemistry Strategies. SLAS DISCOVERY 2018; 24:419-439. [PMID: 30523713 DOI: 10.1177/2472555218812657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the past century, a multitude of derivatives of structural scaffolds with established antimicrobial potential have been prepared and tested, and a variety of new scaffolds have emerged. The effectiveness of antibiotics, however, is in sharp decline because of the emergence of drug-resistant microorganisms. The prevalence of drug resistance, both in clinical and community settings, is a consequence of bacterial ingenuity in altering pathways and/or cell morphology, making it a persistent threat to human health. The fundamental ability of pathogens to survive in a multitude of habitats can be triggered by recognition of chemical signals that warn organisms of exposure to a potentially harmful environment. Host immune defenses, including reactive oxygen intermediates and antibacterial substances, are among the multitude of chemical signals that can subsequently trigger expression of phenotypes better adapted for survival in that hostile environment. Thus, resistance development appears to be unavoidable, which leads to the conclusion that developing an alternative perspective for treatment options is vital. This review will discuss emerging medicinal chemistry approaches for addressing the global multidrug resistance in the 21st century.
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53
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Vance NR, Witkin KR, Rooney PW, Li Y, Pope M, Spies MA. Elucidating the Catalytic Power of Glutamate Racemase by Investigating a Series of Covalent Inhibitors. ChemMedChem 2018; 13:2514-2521. [PMID: 30264520 DOI: 10.1002/cmdc.201800592] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Indexed: 12/29/2022]
Abstract
The application of covalent inhibitors has experienced a renaissance within drug discovery programs in the last decade. To leverage the superior potency and drug target residence time of covalent inhibitors, there have been extensive efforts to develop highly specific covalent modifications to decrease off-target liabilities. Herein, we present a series of covalent inhibitors of an antimicrobial drug target, glutamate racemase, discovered through structure-based virtual screening. A combination of enzyme kinetics, mass spectrometry, and surface-plasmon resonance experiments details a highly specific 1,4-conjugate addition of a small-molecule inhibitor with a catalytic cysteine of glutamate racemase. Molecular dynamics simulations and quantum mechanics-molecular mechanics geometry optimizations reveal the chemistry of the conjugate addition. Two compounds from this series of inhibitors display antimicrobial potency similar to β-lactam antibiotics, with significant activity against methicillin-resistant S. aureus strains. This study elucidates a detailed chemical rationale for covalent inhibition and provides a platform for the development of antimicrobials with a novel mechanism of action against a target in the cell wall biosynthesis pathway.
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Affiliation(s)
- Nicholas R Vance
- Division of Medicinal and Natural Products Chemistry, College of Pharmacy, University of Iowa, 115 S. Grand Ave., Iowa City, IA, 52242, USA
| | - Katie R Witkin
- Division of Medicinal and Natural Products Chemistry, College of Pharmacy, University of Iowa, 115 S. Grand Ave., Iowa City, IA, 52242, USA
| | - Patrick W Rooney
- Department of Biochemistry, Carver College of Medicine, University of Iowa, 51 Newton Road, 4-403 Bowen Science Building, Iowa City, IA, 52242, USA
| | - Yalan Li
- Proteomics Facility, Carver College of Medicine, University of Iowa, 355 EMRB, Iowa City, IA, 52242, USA
| | - Marshall Pope
- Proteomics Facility, Carver College of Medicine, University of Iowa, 355 EMRB, Iowa City, IA, 52242, USA
| | - M Ashley Spies
- Division of Medicinal and Natural Products Chemistry, College of Pharmacy, University of Iowa, 115 S. Grand Ave., Iowa City, IA, 52242, USA.,Department of Biochemistry, Carver College of Medicine, University of Iowa, 51 Newton Road, 4-403 Bowen Science Building, Iowa City, IA, 52242, USA
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54
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Tehrani KHME, Martin NI. β-lactam/β-lactamase inhibitor combinations: an update. MEDCHEMCOMM 2018; 9:1439-1456. [PMID: 30288219 PMCID: PMC6151480 DOI: 10.1039/c8md00342d] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 08/16/2018] [Indexed: 12/22/2022]
Abstract
Antibiotic resistance caused by β-lactamase production continues to present a growing challenge to the efficacy of β-lactams and their role as the most important class of clinically used antibiotics. In response to this threat however, only a handful of β-lactamase inhibitors have been introduced to the market over the past thirty years. The first-generation β-lactamase inhibitors (clavulanic acid, sulbactam and tazobactam) are all β-lactam derivatives and work primarily by inactivating class A and some class C serine β-lactamases. The newer generations of β-lactamase inhibitors including avibactam and vaborbactam are based on non-β-lactam structures and their spectrum of inhibition is extended to KPC as an important class A carbapenemase. Despite these advances several class D and virtually all important class B β-lactamases are resistant to existing inhibitors. The present review provides an overview of recent FDA-approved β-lactam/β-lactamase inhibitor combinations as well as an update on research efforts aimed at the discovery and development of novel β-lactamase inhibitors.
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Affiliation(s)
- Kamaleddin H M E Tehrani
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands
| | - Nathaniel I Martin
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands
- Biological Chemistry Group , Institute of Biology Leiden , Leiden University , Sylvius Laboratories, Sylviusweg 72 , 2333 BE Leiden , The Netherlands . ; Tel: +31 (0)6 1878 5274
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55
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Raczynska JE, Shabalin IG, Minor W, Wlodawer A, Jaskolski M. A close look onto structural models and primary ligands of metallo-β-lactamases. Drug Resist Updat 2018; 40:1-12. [PMID: 30466711 PMCID: PMC6260963 DOI: 10.1016/j.drup.2018.08.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/14/2018] [Accepted: 08/16/2018] [Indexed: 10/28/2022]
Abstract
β-Lactamases are hydrolytic enzymes capable of opening the β-lactam ring of antibiotics such as penicillin, thus endowing the bacteria that produce them with antibiotic resistance. Of particular medical concern are metallo-β-lactamases (MBLs), with an active site built around coordinated Zn cations. MBLs are pan-reactive enzymes that can break down almost all classes of β-lactams, including such last-resort antibiotics as carbapenems. They are not only broad-spectrum-reactive but are often plasmid-borne (e.g., the New Delhi enzyme, NDM), and can spread horizontally even among unrelated bacteria. Acquired MBLs are encoded by mobile genetic elements, which often include other resistance genes, making the microbiological situation particularly alarming. There is an urgent need to develop MBL inhibitors in order to rescue our antibiotic armory. A number of such efforts have been undertaken, most notably using the 3D structures of various MBLs as drug-design targets. Structure-guided drug discovery depends on the quality of the structures that are collected in the Protein Data Bank (PDB) and on the consistency of the information in dedicated β-lactamase databases. We conducted a careful review of the crystal structures of class B β-lactamases, concluding that the quality of these structures varies widely, especially in the regions where small molecules interact with the macromolecules. In a number of examples the interpretation of the bound ligands (e.g., inhibitors, substrate/product analogs) is doubtful or even incorrect, and it appears that in some cases the modeling of ligands was not supported by electron density. For ten MBL structures, alternative interpretations of the original diffraction data could be proposed and the new models have been deposited in the PDB. In four cases, these models, prepared jointly with the authors of the original depositions, superseded the previous deposits. This review emphasizes the importance of critical assessment of structural models describing key drug design targets at the level of the raw experimental data. Since the structures reviewed here are the basis for ongoing design of new MBL inhibitors, it is important to identify and correct the problems with ambiguous crystallographic interpretations, thus enhancing reproducibility in this highly medically relevant area.
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Affiliation(s)
- Joanna E Raczynska
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases, Charlottesville, VA 22908, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases, Charlottesville, VA 22908, USA
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.
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56
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Kang JS, Zhang AL, Faheem M, Zhang CJ, Ai N, Buynak JD, Welsh WJ, Oelschlaeger P. Virtual Screening and Experimental Testing of B1 Metallo-β-lactamase Inhibitors. J Chem Inf Model 2018; 58:1902-1914. [PMID: 30107123 DOI: 10.1021/acs.jcim.8b00133] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The global rise of metallo-β-lactamases (MBLs) is problematic due to their ability to inactivate most β-lactam antibiotics. MBL inhibitors that could be coadministered with and restore the efficacy of β-lactams are highly sought after. In this study, we employ virtual screening of candidate MBL inhibitors without thiols or carboxylates to avoid off-target effects using the Avalanche software package, followed by experimental validation of the selected compounds. As target enzymes, we chose the clinically relevant B1 MBLs NDM-1, IMP-1, and VIM-2. Among 32 compounds selected from an approximately 1.5 million compound library, 6 exhibited IC50 values less than 40 μM against NDM-1 and/or IMP-1. The most potent inhibitors of NDM-1, IMP-1, and VIM-2 had IC50 values of 19 ± 2, 14 ± 1, and 50 ± 20 μM, respectively. While chemically diverse, the most potent inhibitors all contain combinations of hydroxyl, ketone, ester, amide, or sulfonyl groups. Docking studies suggest that these electron-dense moieties are involved in Zn(II) coordination and interaction with protein residues. These novel scaffolds could serve as the basis for further development of MBL inhibitors. A procedure for renaming NDM-1 residues to conform to the class B β-lactamase (BBL) numbering scheme is also included.
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Affiliation(s)
- Joon S Kang
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States.,Department of Biological Sciences , California State Polytechnic University , Pomona , California 91768-2557 , United States
| | - Antonia L Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
| | - Mohammad Faheem
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
| | - Charles J Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
| | - Ni Ai
- Pharmaceutical Informatics Institute, School of Pharmaceutical Sciences , Zhejiang University , Zhejiang 31005 , People's Republic of China
| | - John D Buynak
- Department of Chemistry , Southern Methodist University , Dallas , Texas 75275-0314 , United States
| | - William J Welsh
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, and Division of Chem Informatics, Biomedical Informatics Shared Resource, Rutgers-Cancer Institute of New Jersey , The State University of New Jersey , Piscataway , New Jersey 08854-8021 , United States
| | - Peter Oelschlaeger
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
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57
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Protein‐protein interactions as antibiotic targets: A medicinal chemistry perspective. Med Res Rev 2018; 40:469-494. [DOI: 10.1002/med.21519] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 05/28/2018] [Accepted: 06/03/2018] [Indexed: 12/27/2022]
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58
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Yarlagadda V, Sarkar P, Samaddar S, Manjunath GB, Mitra SD, Paramanandham K, Shome BR, Haldar J. Vancomycin Analogue Restores Meropenem Activity against NDM-1 Gram-Negative Pathogens. ACS Infect Dis 2018; 4:1093-1101. [PMID: 29726673 DOI: 10.1021/acsinfecdis.8b00011] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1) is the major contributor to the emergence of carbapenem resistance in Gram-negative pathogens (GNPs) and has caused many clinically available β-lactam antibiotics to become obsolete. A clinically approved inhibitor of metallo-β-lactamase (MBL) that could restore the activity of carbapenems against resistant GNPs has not yet been found, making NDM-1 a serious threat to human health. Here, we have rationally developed an inhibitor for the NDM-1 enzyme, which has the ability to penetrate the outer membrane of GNPs and inactivate the enzyme by depleting the metal ion (Zn2+) from the active site. The inhibitor reinstated the activity of meropenem against NDM-1 producing clinical isolates of GNPs like Klebsiella pneumoniae and Escherichia coli. Further, the inhibitor efficiently restored meropenem activity against NDM-1 producing K. pneumoniae in a murine sepsis infection model. These findings demonstrate that a combination of the present inhibitor and meropenem has high potential to be translated clinically to combat carbapenem-resistant GNPs.
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Affiliation(s)
- Venkateswarlu Yarlagadda
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka 560064, India
| | - Paramita Sarkar
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka 560064, India
| | - Sandip Samaddar
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka 560064, India
| | - Goutham Belagula Manjunath
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka 560064, India
| | - Susweta Das Mitra
- National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka 560064, India
| | - Krishnamoorthy Paramanandham
- National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka 560064, India
| | - Bibek Ranjan Shome
- National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka 560064, India
| | - Jayanta Haldar
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka 560064, India
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59
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Discovery of a Novel Metallo-β-Lactamase Inhibitor That Potentiates Meropenem Activity against Carbapenem-Resistant Enterobacteriaceae. Antimicrob Agents Chemother 2018. [PMID: 29530861 DOI: 10.1128/aac.00074-18] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Infections caused by carbapenem-resistant Enterobacteriaceae (CRE) are increasingly prevalent and have become a major worldwide threat to human health. Carbapenem resistance is driven primarily by the acquisition of β-lactamase enzymes, which are able to degrade carbapenem antibiotics (hence termed carbapenemases) and result in high levels of resistance and treatment failure. Clinically relevant carbapenemases include both serine β-lactamases (SBLs; e.g., KPC-2 and OXA-48) and metallo-β-lactamases (MBLs), such as NDM-1. MBL-producing strains are endemic within the community in many Asian countries, have successfully spread worldwide, and account for many significant CRE outbreaks. Recently approved combinations of β-lactam antibiotics with β-lactamase inhibitors are active only against SBL-producing pathogens. Therefore, new drugs that specifically target MBLs and which restore carbapenem efficacy against MBL-producing CRE pathogens are urgently needed. Here we report the discovery of a novel MBL inhibitor, ANT431, that can potentiate the activity of meropenem (MEM) against a broad range of MBL-producing CRE and restore its efficacy against an Escherichia coli NDM-1-producing strain in a murine thigh infection model. This is a strong starting point for a chemistry lead optimization program that could deliver a first-in-class MBL inhibitor-carbapenem combination. This would complement the existing weaponry against CRE and address an important and growing unmet medical need.
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60
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Xiang Y, Chen C, Wang WM, Xu LW, Yang KW, Oelschlaeger P, He Y. Rhodanine as a Potent Scaffold for the Development of Broad-Spectrum Metallo-β-lactamase Inhibitors. ACS Med Chem Lett 2018; 9:359-364. [PMID: 29670701 DOI: 10.1021/acsmedchemlett.7b00548] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 03/22/2018] [Indexed: 11/28/2022] Open
Abstract
A series of rhodanines was constructed, their Z-configuration was confirmed by small molecule X-ray crystal structures, and their activity against metallo-β-lactamases (MβLs) was measured. The obtained 26 molecules and a thioenolate specifically inhibited the MβL L1 with an IC50 range of 0.02-1.7 μM, and compounds 2h-m exhibited broad-spectrum inhibition of the MβLs NDM-1, VIM-2, ImiS, and L1 with IC50 values <16 μM. All inhibitors increased the antimicrobial effect of cefazolin against E. coli cells expressing L1, resulting in a 2-8-fold reduction in MIC. Docking studies suggested that the nitro (NDM-1, CphA, and L1) or carboxyl group (VIM-2) of 2l coordinates one or two Zn(II) ions, while the N-phenyl group of the inhibitor enhances its hydrophobic interaction with MβLs. These studies demonstrate that the diaryl-substituted rhodanines are good scaffolds for the design of future broad-spectrum inhibitors of MβLs.
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Affiliation(s)
- Yang Xiang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Wen-Ming Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Li-Wei Xu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Peter Oelschlaeger
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, 309 East Second Street, Pomona, California 91766, United States
| | - Yuan He
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
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61
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Li GB, Brem J, Lesniak R, Abboud MI, Lohans CT, Clifton IJ, Yang SY, Jiménez-Castellanos JC, Avison MB, Spencer J, McDonough MA, Schofield CJ. Crystallographic analyses of isoquinoline complexes reveal a new mode of metallo-β-lactamase inhibition. Chem Commun (Camb) 2018; 53:5806-5809. [PMID: 28470248 DOI: 10.1039/c7cc02394d] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Crystallographic analyses of the VIM-5 metallo-β-lactamase (MBL) with isoquinoline inhibitors reveal non zinc ion binding modes. Comparison with other MBL-inhibitor structures directed addition of a zinc-binding thiol enabling identification of potent B1 MBL inhibitors. The inhibitors potentiate meropenem activity against clinical isolates harboring MBLs.
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Affiliation(s)
- Guo-Bo Li
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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62
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Yu ZJ, Liu S, Zhou S, Li H, Yang F, Yang LL, Wu Y, Guo L, Li GB. Virtual target screening reveals rosmarinic acid and salvianolic acid A inhibiting metallo- and serine-β-lactamases. Bioorg Med Chem Lett 2018; 28:1037-1042. [PMID: 29477271 DOI: 10.1016/j.bmcl.2018.02.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 01/31/2018] [Accepted: 02/13/2018] [Indexed: 01/08/2023]
Abstract
Rosmarinic acid (RA), a polyphenolic phytochemical, has broad-spectrum biological and pharmacological activity. A virtual target screening method termed IFPTarget combined with enzyme inhibition assays led to the identification of the clinically relevant metallo-β-lactamase (MBL) VIM-2 as one of unexploited targets of RA. The enzyme kinetic studies indicated that RA is a fully reversible, substrate-competitive VIM-2 inhibitor. The isothermal titration calorimetry (ITC) analyses revealed that the initial binding of RA to VIM-2 is mainly due to enthalpy contribution. Further inhibition assays with RA related compounds revealed that salvianolic acid A, a derivative of RA, manifests potent inhibition to VIM-2, more interestingly, which shows inhibitory activity against the NDM-1, another clinically relevant MBL subtype, and the serine-β-lactamase TEM-1 that is structurally and mechanistically distinct from the VIM-2 and NDM-1.
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Affiliation(s)
- Zhu-Jun Yu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Sha Liu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Shu Zhou
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Hui Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Fan Yang
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Ling-Ling Yang
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Yong Wu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Li Guo
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Guo-Bo Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China.
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63
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Hinchliffe P, Tanner CA, Krismanich AP, Labbé G, Goodfellow VJ, Marrone L, Desoky AY, Calvopiña K, Whittle EE, Zeng F, Avison MB, Bols NC, Siemann S, Spencer J, Dmitrienko GI. Structural and Kinetic Studies of the Potent Inhibition of Metallo-β-lactamases by 6-Phosphonomethylpyridine-2-carboxylates. Biochemistry 2018; 57:1880-1892. [PMID: 29485857 PMCID: PMC6007964 DOI: 10.1021/acs.biochem.7b01299] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 02/15/2018] [Indexed: 01/05/2023]
Abstract
There are currently no clinically available inhibitors of metallo-β-lactamases (MBLs), enzymes that hydrolyze β-lactam antibiotics and confer resistance to Gram-negative bacteria. Here we present 6-phosphonomethylpyridine-2-carboxylates (PMPCs) as potent inhibitors of subclass B1 (IMP-1, VIM-2, and NDM-1) and B3 (L1) MBLs. Inhibition followed a competitive, slow-binding model without an isomerization step (IC50 values of 0.3-7.2 μM; Ki values of 0.03-1.5 μM). Minimum inhibitory concentration assays demonstrated potentiation of β-lactam (Meropenem) activity against MBL-producing bacteria, including clinical isolates, at concentrations at which eukaryotic cells remain viable. Crystal structures revealed unprecedented modes of binding of inhibitor to B1 (IMP-1) and B3 (L1) MBLs. In IMP-1, binding does not replace the nucleophilic hydroxide, and the PMPC carboxylate and pyridine nitrogen interact closely (2.3 and 2.7 Å, respectively) with the Zn2 ion of the binuclear metal site. The phosphonate group makes limited interactions but is 2.6 Å from the nucleophilic hydroxide. Furthermore, the presence of a water molecule interacting with the PMPC phosphonate and pyridine N-C2 π-bond, as well as the nucleophilic hydroxide, suggests that the PMPC binds to the MBL active site as its hydrate. Binding is markedly different in L1, with the phosphonate displacing both Zn2, forming a monozinc enzyme, and the nucleophilic hydroxide, while also making multiple interactions with the protein main chain and Zn1. The carboxylate and pyridine nitrogen interact with Ser221 and -223, respectively (3 Å distance). The potency, low toxicity, cellular activity, and amenability to further modification of PMPCs indicate these and similar phosphonate compounds can be further considered for future MBL inhibitor development.
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Affiliation(s)
- Philip Hinchliffe
- School
of Cellular & Molecular Medicine, University
of Bristol, Bristol BS8 1TD, U.K.
| | - Carol A. Tanner
- Department
of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | | | - Geneviève Labbé
- Department
of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | | | - Laura Marrone
- Department
of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Ahmed Y. Desoky
- Department
of Chemistry, College of Science, University
of Hail, Saudi Arabia
| | - Karina Calvopiña
- School
of Cellular & Molecular Medicine, University
of Bristol, Bristol BS8 1TD, U.K.
| | - Emily E. Whittle
- School
of Cellular & Molecular Medicine, University
of Bristol, Bristol BS8 1TD, U.K.
| | - Fanxing Zeng
- Department
of Biology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Matthew B. Avison
- School
of Cellular & Molecular Medicine, University
of Bristol, Bristol BS8 1TD, U.K.
| | - Niels C. Bols
- Department
of Biology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Stefan Siemann
- Department
of Chemistry and Biochemistry, Laurentian
University, Sudbury, Ontario, Canada P3E 2C6
| | - James Spencer
- School
of Cellular & Molecular Medicine, University
of Bristol, Bristol BS8 1TD, U.K.
| | - Gary I. Dmitrienko
- Department
of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
- School
of Pharmacy, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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64
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Structure activity relationship studies on rhodanines and derived enethiol inhibitors of metallo-β-lactamases. Bioorg Med Chem 2018; 26:2928-2936. [PMID: 29655609 PMCID: PMC6008492 DOI: 10.1016/j.bmc.2018.02.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 02/20/2018] [Accepted: 02/22/2018] [Indexed: 12/14/2022]
Abstract
Metallo-β-lactamases (MBLs) enable bacterial resistance to almost all classes of β-lactam antibiotics. We report studies on enethiol containing MBL inhibitors, which were prepared by rhodanine hydrolysis. The enethiols inhibit MBLs from different subclasses. Crystallographic analyses reveal that the enethiol sulphur displaces the di-Zn(II) ion bridging ‘hydrolytic’ water. In some, but not all, cases biophysical analyses provide evidence that rhodanine/enethiol inhibition involves formation of a ternary MBL enethiol rhodanine complex. The results demonstrate how low molecular weight active site Zn(II) chelating compounds can inhibit a range of clinically relevant MBLs and provide additional evidence for the potential of rhodanines to be hydrolysed to potent inhibitors of MBL protein fold and, maybe, other metallo-enzymes, perhaps contributing to the complex biological effects of rhodanines. The results imply that any medicinal chemistry studies employing rhodanines (and related scaffolds) as inhibitors should as a matter of course include testing of their hydrolysis products.
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65
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Liu S, Jing L, Yu ZJ, Wu C, Zheng Y, Zhang E, Chen Q, Yu Y, Guo L, Wu Y, Li GB. (( S )-3-Mercapto-2-methylpropanamido)acetic acid derivatives as metallo-β-lactamase inhibitors: Synthesis, kinetic and crystallographic studies. Eur J Med Chem 2018; 145:649-660. [DOI: 10.1016/j.ejmech.2018.01.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 10/18/2022]
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66
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Wang R, Lai TP, Gao P, Zhang H, Ho PL, Woo PCY, Ma G, Kao RYT, Li H, Sun H. Bismuth antimicrobial drugs serve as broad-spectrum metallo-β-lactamase inhibitors. Nat Commun 2018; 9:439. [PMID: 29382822 PMCID: PMC5789847 DOI: 10.1038/s41467-018-02828-6] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/03/2018] [Indexed: 11/09/2022] Open
Abstract
Drug-resistant superbugs pose a huge threat to human health. Infections by Enterobacteriaceae producing metallo-β-lactamases (MBLs), e.g., New Delhi metallo-β-lactamase 1 (NDM-1) are very difficult to treat. Development of effective MBL inhibitors to revive the efficacy of existing antibiotics is highly desirable. However, such inhibitors are not clinically available till now. Here we show that an anti-Helicobacter pylori drug, colloidal bismuth subcitrate (CBS), and related Bi(III) compounds irreversibly inhibit different types of MBLs via the mechanism, with one Bi(III) displacing two Zn(II) ions as revealed by X-ray crystallography, leading to the release of Zn(II) cofactors. CBS restores meropenem (MER) efficacy against MBL-positive bacteria in vitro, and in mice infection model, importantly, also slows down the development of higher-level resistance in NDM-1-positive bacteria. This study demonstrates a high potential of Bi(III) compounds as the first broad-spectrum B1 MBL inhibitors to treat MBL-positive bacterial infection in conjunction with existing carbapenems.
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Affiliation(s)
- Runming Wang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Pok Fu Lam, Hong Kong
- Department of Microbiology, The University of Hong Kong, Sassoon Road, Pok Fu Lam, Hong Kong
| | - Tsz-Pui Lai
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Pok Fu Lam, Hong Kong
| | - Peng Gao
- Department of Microbiology, The University of Hong Kong, Sassoon Road, Pok Fu Lam, Hong Kong
- The Research Centre of Infection and Immunology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Hongmin Zhang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Pok Fu Lam, Hong Kong
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Pak-Leung Ho
- Department of Microbiology, The University of Hong Kong, Sassoon Road, Pok Fu Lam, Hong Kong
- The Research Centre of Infection and Immunology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Sassoon Road, Pok Fu Lam, Hong Kong
| | - Patrick Chiu-Yat Woo
- Department of Microbiology, The University of Hong Kong, Sassoon Road, Pok Fu Lam, Hong Kong
- The Research Centre of Infection and Immunology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Sassoon Road, Pok Fu Lam, Hong Kong
| | - Guixing Ma
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Richard Yi-Tsun Kao
- Department of Microbiology, The University of Hong Kong, Sassoon Road, Pok Fu Lam, Hong Kong
- The Research Centre of Infection and Immunology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Sassoon Road, Pok Fu Lam, Hong Kong
| | - Hongyan Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Pok Fu Lam, Hong Kong
| | - Hongzhe Sun
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Pok Fu Lam, Hong Kong.
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67
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Gilberg E, Gütschow M, Bajorath J. X-ray Structures of Target–Ligand Complexes Containing Compounds with Assay Interference Potential. J Med Chem 2018; 61:1276-1284. [DOI: 10.1021/acs.jmedchem.7b01780] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Erik Gilberg
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
- Pharmaceutical
Institute, Rheinische Friedrich-Wilhelms-Universität, An der Immenburg 4, D-53121 Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical
Institute, Rheinische Friedrich-Wilhelms-Universität, An der Immenburg 4, D-53121 Bonn, Germany
| | - Jürgen Bajorath
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
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68
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Cain R, Brem J, Zollman D, McDonough MA, Johnson RM, Spencer J, Makena A, Abboud MI, Cahill S, Lee SY, McHugh PJ, Schofield CJ, Fishwick CWG. In Silico Fragment-Based Design Identifies Subfamily B1 Metallo-β-lactamase Inhibitors. J Med Chem 2018; 61:1255-1260. [PMID: 29271657 DOI: 10.1021/acs.jmedchem.7b01728] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Zinc ion-dependent β-lactamases (MBLs) catalyze the hydrolysis of almost all β-lactam antibiotics and resist the action of clinically available β-lactamase inhibitors. We report how application of in silico fragment-based molecular design employing thiol-mediated metal anchorage leads to potent MBL inhibitors. The new inhibitors manifest potent inhibition of clinically important B1 subfamily MBLs, including the widespread NDM-1, IMP-1, and VIM-2 enzymes; with lower potency, some of them also inhibit clinically relevant Class A and D serine-β-lactamases. The inhibitors show selectivity for bacterial MBL enzymes compared to that for human MBL fold nucleases. Cocrystallization of one inhibitor, which shows potentiation of Meropenem activity against MBL-expressing Enterobacteriaceae, with VIM-2 reveals an unexpected binding mode, involving interactions with residues from conserved active site bordering loops.
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Affiliation(s)
- Ricky Cain
- School of Chemistry, University of Leeds , Leeds LS2 9JT, United Kingdom
| | - Jürgen Brem
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - David Zollman
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael A McDonough
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Rachel M Johnson
- School of Chemistry, University of Leeds , Leeds LS2 9JT, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol , Biomedical Sciences Building, Bristol BS8 1TD, United Kingdom
| | - Anne Makena
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Martine I Abboud
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Samuel Cahill
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sook Y Lee
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.,Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford , John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Peter J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford , John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Colin W G Fishwick
- School of Chemistry, University of Leeds , Leeds LS2 9JT, United Kingdom
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69
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Zhang C, Pu YC, Yu ZJ, Wu CY, Brem J, McDonough MA, Schofield CJ, Li GB, Wu Y. Rh(iii)-Catalyzed directed C–H carbenoid coupling reveals aromatic bisphosphonates inhibiting metallo- and Serine-β-lactamases. Org Chem Front 2018. [DOI: 10.1039/c8qo00009c] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The C–H coupling of arenes with diazo-methylene-diphosphonates enables efficient synthesis of new diphosphonates, which exhibit dual MBL and SBL inhibition.
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Affiliation(s)
- Chen Zhang
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy
- Sichuan University Sichuan 610041
- China
| | - Yan-chi Pu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy
- Sichuan University Sichuan 610041
- China
| | - Zhu-Jun Yu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy
- Sichuan University Sichuan 610041
- China
| | - Cheng-yong Wu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy
- Sichuan University Sichuan 610041
- China
| | - Jürgen Brem
- Department of Chemistry
- University of Oxford
- Oxford
- UK
| | | | | | - Guo-Bo Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy
- Sichuan University Sichuan 610041
- China
| | - Yong Wu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy
- Sichuan University Sichuan 610041
- China
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70
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Docquier JD, Mangani S. An update on β-lactamase inhibitor discovery and development. Drug Resist Updat 2017; 36:13-29. [PMID: 29499835 DOI: 10.1016/j.drup.2017.11.002] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 11/01/2017] [Accepted: 11/03/2017] [Indexed: 11/27/2022]
Abstract
Antibiotic resistance, and the emergence of pan-resistant clinical isolates, seriously threatens our capability to treat bacterial diseases, including potentially deadly hospital-acquired infections. This growing issue certainly requires multiple adequate responses, including the improvement of both diagnosis methods and use of antibacterial agents, and obviously the development of novel antibacterial drugs, especially active against Gram-negative pathogens, which represent an urgent medical need. Considering the clinical relevance of both β-lactam antibiotics and β-lactamase-mediated resistance, the discovery and development of combinations including a β-lactamase inhibitor seems to be particularly attractive, despite being extremely challenging due to the enormous diversity, both structurally and mechanistically, of the potential β-lactamase targets. This review will cover the evolution of currently available β-lactamase inhibitors along with the most recent research leading to new β-lactamase inhibitors of potential clinical interest or already in the stage of clinical development.
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Affiliation(s)
- Jean-Denis Docquier
- Department of Medical Biotechnology, University of Siena, Viale Bracci 16, 53100 Siena, Italy.
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
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71
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Xiang Y, Chang YN, Ge Y, Kang JS, Zhang YL, Liu XL, Oelschlaeger P, Yang KW. Azolylthioacetamides as a potent scaffold for the development of metallo-β-lactamase inhibitors. Bioorg Med Chem Lett 2017; 27:5225-5229. [PMID: 29122480 DOI: 10.1016/j.bmcl.2017.10.038] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/18/2017] [Accepted: 10/19/2017] [Indexed: 11/29/2022]
Abstract
In an effort to develop new inhibitors of metallo-β-lactamases (MβLs), twenty-eight azolylthioacetamides were synthesized and assayed against MβLs. The obtained benzimidazolyl and benzioxazolyl substituted 1-19 specifically inhibited the enzyme ImiS, and 10 was found to be the most potent inhibitor of ImiS with an IC50 value of 15 nM. The nitrobenzimidazolyl substituted 20-28 specifically inhibited NDM-1, with 27 being the most potent inhibitor with an IC50 value of 170 nM. Further studies with 10, 11, and 27 revealed a mixed inhibition mode with competitive and uncompetitive inhibition constants in a similar range as the IC50 values. These inhibitors resulted in a 2-4-fold decrease in imipenem MIC values using E. coli cells producing ImiS or NDM-1. While the source of uncompetitive (possibly allosteric) inhibition remains unclear, docking studies indicate that 10 and 11 may interact orthosterically with Zn2 in the active site of CphA, while 27 could bridge the two Zn(II) ions in the active site of NDM-1 via its nitro group.
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Affiliation(s)
- Yang Xiang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Innovation Laboratory of Chemical Biology, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Ya-Nan Chang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Innovation Laboratory of Chemical Biology, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Ying Ge
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Innovation Laboratory of Chemical Biology, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Joon S Kang
- Department of Biological Sciences, California State Polytechnic University, 3801 West Temple Avenue, Pomona, CA 91768, USA
| | - Yi-Lin Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Innovation Laboratory of Chemical Biology, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Xiao-Long Liu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Innovation Laboratory of Chemical Biology, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Peter Oelschlaeger
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, 309 East Second Street, Pomona, CA 91766, USA
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Innovation Laboratory of Chemical Biology, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China.
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72
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Tehrani KHME, Martin NI. Thiol-Containing Metallo-β-Lactamase Inhibitors Resensitize Resistant Gram-Negative Bacteria to Meropenem. ACS Infect Dis 2017; 3:711-717. [PMID: 28820574 PMCID: PMC5644712 DOI: 10.1021/acsinfecdis.7b00094] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The prevalence of infections caused by metallo-β-lactamase (MBL) expressing Gram-negative bacteria has grown at an alarming rate in recent years. Despite the fact that MBLs can deactivate virtually all β-lactam antibiotics, there are as of yet no approved drugs available that inhibit their activity. We here examine the ability of previously reported thiol-based MBL inhibitors to synergize with meropenem and cefoperazone against a panel of Gram-negative carbapenem-resistant isolates expressing different β-lactamases. Among the compounds tested, thiomandelic acid 3 and 2-mercapto-3-phenylpropionic acid 4 were found to efficiently potentiate the activity of meropenem, especially against an imipenemase (IMP) producing strain of K. pneumoniae. In light of the zinc-dependent hydrolytic mechanism employed by MBLs, biophysical studies using isothermal titration calorimetry were also performed, revealing a correlation between the synergistic activity of thiols 3 and 4 and their zinc-binding ability with measured Kd values of 9.8 and 20.0 μM, respectively.
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Affiliation(s)
- Kamaleddin Haj Mohammad Ebrahim Tehrani
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Nathaniel I. Martin
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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73
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Kaminskyy D, Kryshchyshyn A, Lesyk R. Recent developments with rhodanine as a scaffold for drug discovery. Expert Opin Drug Discov 2017; 12:1233-1252. [PMID: 29019278 DOI: 10.1080/17460441.2017.1388370] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Rhodanines, as one of the 4-thiazolidinones subtypes, are recognized as privileged heterocycles in medicinal chemistry. The main achievements include the development of drug-like molecules with numerous biological activities as well as approved drugs. Among rhodanines, 5-ene-rhodanines are of special interest, and are often claimed as pan assay interference compounds due to Michael acceptor functionality. Areas covered: Herein, the synthetic protocols for rhodanines and their transformation are reviewed. Biological activity is briefly discussed as well as biotargets, mode of actions and optimization directions. Furthermore, the utilization of 5-ene-rhodanines in Michael additions are discussed while both pro and contra arguments have been outlined within medicinal chemistry application. Expert opinion: Rhodanines remain privileged heterocycles in drug discovery. They are accessible building blocks for optimization and transformation into related heterocycles, simplified analogues and fused heterocycles with a thiazolidine framework. Michael acceptor functionality, as well as the thesis about low selectivity towards biotargets of rhodanines, must be confirmed experimentally and it cannot be based on just the presence of conjugated α,β-unsaturated carbonyl. Moreover, the positive aspects of Michael acceptors must be considered as well as their multitarget properties. New criteria for target affinity must be found. In conclusion, rhodanines are generally not problematic per se.
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Affiliation(s)
- Danylo Kaminskyy
- a Department of Pharmaceutical, Organic and Bioorganic Chemistry , Danylo Halytsky Lviv National Medical University , Lviv-10 , Ukraine
| | - Anna Kryshchyshyn
- a Department of Pharmaceutical, Organic and Bioorganic Chemistry , Danylo Halytsky Lviv National Medical University , Lviv-10 , Ukraine
| | - Roman Lesyk
- a Department of Pharmaceutical, Organic and Bioorganic Chemistry , Danylo Halytsky Lviv National Medical University , Lviv-10 , Ukraine
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74
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Inhibitors of metallo-β-lactamases. Curr Opin Microbiol 2017; 39:96-105. [DOI: 10.1016/j.mib.2017.10.026] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/09/2017] [Accepted: 10/28/2017] [Indexed: 11/19/2022]
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75
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McNeill LA, Brown TJN, Sami M, Clifton IJ, Burzlaff NI, Claridge TDW, Adlington RM, Baldwin JE, Rutledge PJ, Schofield CJ. Terminally Truncated Isopenicillin N Synthase Generates a Dithioester Product: Evidence for a Thioaldehyde Intermediate during Catalysis and a New Mode of Reaction for Non-Heme Iron Oxidases. Chemistry 2017; 23:12815-12824. [PMID: 28703303 PMCID: PMC5637899 DOI: 10.1002/chem.201701592] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Indexed: 11/25/2022]
Abstract
Isopenicillin N synthase (IPNS) catalyses the four-electron oxidation of a tripeptide, l-δ-(α-aminoadipoyl)-l-cysteinyl-d-valine (ACV), to give isopenicillin N (IPN), the first-formed β-lactam in penicillin and cephalosporin biosynthesis. IPNS catalysis is dependent upon an iron(II) cofactor and oxygen as a co-substrate. In the absence of substrate, the carbonyl oxygen of the side-chain amide of the penultimate residue, Gln330, co-ordinates to the active-site metal iron. Substrate binding ablates the interaction between Gln330 and the metal, triggering rearrangement of seven C-terminal residues, which move to take up a conformation that extends the final α-helix and encloses ACV in the active site. Mutagenesis studies are reported, which probe the role of the C-terminal and other aspects of the substrate binding pocket in IPNS. The hydrophobic nature of amino acid side-chains around the ACV binding pocket is important in catalysis. Deletion of seven C-terminal residues exposes the active site and leads to formation of a new type of thiol oxidation product. The isolated product is shown by LC-MS and NMR analyses to be the ene-thiol tautomer of a dithioester, made up from two molecules of ACV linked between the thiol sulfur of one tripeptide and the oxidised cysteinyl β-carbon of the other. A mechanism for its formation is proposed, supported by an X-ray crystal structure, which shows the substrate ACV bound at the active site, its cysteinyl β-carbon exposed to attack by a second molecule of substrate, adjacent. Formation of this product constitutes a new mode of reaction for IPNS and non-heme iron oxidases in general.
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Affiliation(s)
- Luke A. McNeill
- Oxford Centre for Molecular Sciences and the Department of ChemistryChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
- Present Address: Oxford Nanopore Technologies, Oxford Science ParkOX4 4GAUK
| | - Toby J. N. Brown
- Oxford Centre for Molecular Sciences and the Department of ChemistryChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
- Present Address: The Brattle GroupLevel 15 5 Martin PlaceSydney, NSW2000Australia
| | - Malkit Sami
- Oxford Centre for Molecular Sciences and the Department of ChemistryChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
- Present Address: Immunocore Limited101 Park Drive, Milton ParkAbingdonOX14 4RYUK
| | - Ian J. Clifton
- Oxford Centre for Molecular Sciences and the Department of ChemistryChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
| | - Nicolai I. Burzlaff
- Department of Chemistry and PharmacyUniversity of Erlangen-NurembergEgerlandstraße 191058ErlangenGermany
| | - Timothy D. W. Claridge
- Oxford Centre for Molecular Sciences and the Department of ChemistryChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
| | - Robert M. Adlington
- Oxford Centre for Molecular Sciences and the Department of ChemistryChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
| | - Jack E. Baldwin
- Oxford Centre for Molecular Sciences and the Department of ChemistryChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
| | | | - Christopher J. Schofield
- Oxford Centre for Molecular Sciences and the Department of ChemistryChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
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76
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Ye L, Song Q, Lo BTW, Zheng J, Kong D, Murray CA, Tang CC, Tsang SCE. Decarboxylation of Lactones over Zn/ZSM-5: Elucidation of the Structure of the Active Site and Molecular Interactions. Angew Chem Int Ed Engl 2017; 56:10711-10716. [PMID: 28618178 DOI: 10.1002/anie.201704347] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/05/2017] [Indexed: 11/08/2022]
Abstract
Herein, we report the catalytic decarboxylation of γ-valerolactone (GVL) over Zn/ZSM-5 to butene, followed by aromatization at high yield with co-feeding of water. An evaluation of the catalytic performance after prolonged periods of time showed that a water molecule is essential to maintain the decarboxylation and aromatization activities and avoid rapid catalyst deactivation. Synchrotron X-ray powder diffraction and Rietveld refinement were then used to elucidate the structures of adsorbed GVL and immobilized Zn species in combination with EXAFS and NMR spectroscopy. A new route for the cooperative hydrolysis of GVL by framework Zn-OH and Brønsted acidic sites to butene and then to aromatic compounds has thus been demonstrated. The structures and fundamental pathways for the nucleophilic attack of terminal Zn-OH sites are comparable to those of Zn-containing enzymes in biological systems.
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Affiliation(s)
- Lin Ye
- Department of Chemistry, University of Oxford, Oxford, OX1 3QR, UK
| | - Qi Song
- Shanghai Research Institute of Petrochemical Technology SRIPT, SINOPEC, Shanghai, 201208, China
| | - Benedict T W Lo
- Department of Chemistry, University of Oxford, Oxford, OX1 3QR, UK
| | - Junlin Zheng
- Shanghai Research Institute of Petrochemical Technology SRIPT, SINOPEC, Shanghai, 201208, China
| | - Dejing Kong
- Shanghai Research Institute of Petrochemical Technology SRIPT, SINOPEC, Shanghai, 201208, China
| | - Claire A Murray
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Chiu C Tang
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - S C Edman Tsang
- Department of Chemistry, University of Oxford, Oxford, OX1 3QR, UK
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77
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Ye L, Song Q, Lo BTW, Zheng J, Kong D, Murray CA, Tang CC, Tsang SCE. Decarboxylation of Lactones over Zn/ZSM-5: Elucidation of the Structure of the Active Site and Molecular Interactions. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704347] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lin Ye
- Department of Chemistry; University of Oxford; Oxford OX1 3QR UK
| | - Qi Song
- Shanghai Research Institute of Petrochemical Technology SRIPT, SINOPEC; Shanghai 201208 China
| | | | - Junlin Zheng
- Shanghai Research Institute of Petrochemical Technology SRIPT, SINOPEC; Shanghai 201208 China
| | - Dejing Kong
- Shanghai Research Institute of Petrochemical Technology SRIPT, SINOPEC; Shanghai 201208 China
| | - Claire A. Murray
- Diamond Light Source Ltd, Harwell Science and Innovation Campus; Didcot Oxfordshire OX11 0DE UK
| | - Chiu C. Tang
- Diamond Light Source Ltd, Harwell Science and Innovation Campus; Didcot Oxfordshire OX11 0DE UK
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78
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Brønsted acid-catalyzed aza-Mannich reaction of N-Boc aminals: access to multifunctional rhodanine/hydantoin derivatives. RESEARCH ON CHEMICAL INTERMEDIATES 2017. [DOI: 10.1007/s11164-017-2892-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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79
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Wang WJ, Wang Q, Zhang Y, Lu R, Zhang YL, Yang KW, Lei JE, He Y. Characterization of β-lactamase activity using isothermal titration calorimetry. Biochim Biophys Acta Gen Subj 2017; 1861:2031-2038. [DOI: 10.1016/j.bbagen.2017.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/12/2017] [Accepted: 04/24/2017] [Indexed: 10/19/2022]
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80
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Li GB, Yu ZJ, Liu S, Huang LY, Yang LL, Lohans CT, Yang SY. IFPTarget: A Customized Virtual Target Identification Method Based on Protein–Ligand Interaction Fingerprinting Analyses. J Chem Inf Model 2017; 57:1640-1651. [PMID: 28661143 DOI: 10.1021/acs.jcim.7b00225] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Guo-Bo Li
- Key
Laboratory of Drug Targeting and Drug Delivery System of Ministry
of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Zhu-Jun Yu
- Key
Laboratory of Drug Targeting and Drug Delivery System of Ministry
of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Sha Liu
- Key
Laboratory of Drug Targeting and Drug Delivery System of Ministry
of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Lu-Yi Huang
- Laboratory
of Biotherapy and Cancer Center, West China Hospital, West China Medical
School, Sichuan University, Sichuan 610041, China
| | - Ling-Ling Yang
- College
of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Christopher T. Lohans
- Department
of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Sheng-Yong Yang
- Laboratory
of Biotherapy and Cancer Center, West China Hospital, West China Medical
School, Sichuan University, Sichuan 610041, China
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81
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Metallo-β-lactamase inhibitors by bioisosteric replacement: Preparation, activity and binding. Eur J Med Chem 2017; 135:159-173. [DOI: 10.1016/j.ejmech.2017.04.035] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/24/2017] [Accepted: 04/11/2017] [Indexed: 01/28/2023]
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82
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Abstract
The global overuse of antibiotics has led to the emergence of drug-resistant pathogenic bacteria. Bacteria can combat β-lactams by expressing β-lactamases. Inhibitors of one class of β-lactamase, the serine-β-lactamases, are used clinically to prevent degradation of β-lactam antibiotics. However, a second class of β-lactamase, the metallo-β-lactamases (MBLs), function by a different mechanism to serine-β-lactamases and no inhibitors of MBLs have progressed to be used in the clinic. Bacteria that express MBLs are an increasingly important threat to human health. This review outlines various approaches taken to discover MBL inhibitors, with an emphasis on the different chemical classes of inhibitors. Recent progress, particularly new screening methods and the rational design of potent MBL inhibitors are discussed.
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83
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Abboud MI, Hinchliffe P, Brem J, Macsics R, Pfeffer I, Makena A, Umland KD, Rydzik AM, Li GB, Spencer J, Claridge TDW, Schofield CJ. 19
F-NMR Reveals the Role of Mobile Loops in Product and Inhibitor Binding by the São Paulo Metallo-β-Lactamase. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Martine I. Abboud
- Department of Chemistry; University of Oxford; 12 Mansfield Road OX1 3TA Oxford UK
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine; University of Bristol; Bristol UK
| | - Jürgen Brem
- Department of Chemistry; University of Oxford; 12 Mansfield Road OX1 3TA Oxford UK
| | - Robert Macsics
- Department of Chemistry; University of Oxford; 12 Mansfield Road OX1 3TA Oxford UK
| | - Inga Pfeffer
- Department of Chemistry; University of Oxford; 12 Mansfield Road OX1 3TA Oxford UK
| | - Anne Makena
- Department of Chemistry; University of Oxford; 12 Mansfield Road OX1 3TA Oxford UK
| | - Klaus-Daniel Umland
- Department of Chemistry; University of Oxford; 12 Mansfield Road OX1 3TA Oxford UK
| | - Anna M. Rydzik
- Department of Chemistry; University of Oxford; 12 Mansfield Road OX1 3TA Oxford UK
| | - Guo-Bo Li
- Department of Chemistry; University of Oxford; 12 Mansfield Road OX1 3TA Oxford UK
| | - James Spencer
- School of Cellular and Molecular Medicine; University of Bristol; Bristol UK
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84
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Abboud MI, Hinchliffe P, Brem J, Macsics R, Pfeffer I, Makena A, Umland KD, Rydzik AM, Li GB, Spencer J, Claridge TDW, Schofield CJ. 19 F-NMR Reveals the Role of Mobile Loops in Product and Inhibitor Binding by the São Paulo Metallo-β-Lactamase. Angew Chem Int Ed Engl 2017; 56:3862-3866. [PMID: 28252254 PMCID: PMC5396265 DOI: 10.1002/anie.201612185] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/16/2016] [Indexed: 01/19/2023]
Abstract
Resistance to β‐lactam antibiotics mediated by metallo‐β‐lactamases (MBLs) is a growing problem. We describe the use of protein‐observe 19F‐NMR (PrOF NMR) to study the dynamics of the São Paulo MBL (SPM‐1) from β‐lactam‐resistant Pseudomonas aeruginosa. Cysteinyl variants on the α3 and L3 regions, which flank the di‐ZnII active site, were selectively 19F‐labeled using 3‐bromo‐1,1,1‐trifluoroacetone. The PrOF NMR results reveal roles for the mobile α3 and L3 regions in the binding of both inhibitors and hydrolyzed β‐lactam products to SPM‐1. These results have implications for the mechanisms and inhibition of MBLs by β‐lactams and non‐β‐lactams and illustrate the utility of PrOF NMR for efficiently analyzing metal chelation, identifying new binding modes, and studying protein binding from a mixture of equilibrating isomers.
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Affiliation(s)
- Martine I Abboud
- Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Robert Macsics
- Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Inga Pfeffer
- Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Anne Makena
- Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Klaus-Daniel Umland
- Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Anna M Rydzik
- Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Guo-Bo Li
- Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Timothy D W Claridge
- Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
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85
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Bataille CJR, Brennan MB, Byrne S, Davies SG, Durbin M, Fedorov O, Huber KVM, Jones AM, Knapp S, Liu G, Nadali A, Quevedo CE, Russell AJ, Walker RG, Westwood R, Wynne GM. Thiazolidine derivatives as potent and selective inhibitors of the PIM kinase family. Bioorg Med Chem 2017; 25:2657-2665. [PMID: 28341403 DOI: 10.1016/j.bmc.2017.02.056] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/23/2017] [Accepted: 02/25/2017] [Indexed: 12/31/2022]
Abstract
The PIM family of serine/threonine kinases have become an attractive target for anti-cancer drug development, particularly for certain hematological malignancies. Here, we describe the discovery of a series of inhibitors of the PIM kinase family using a high throughput screening strategy. Through a combination of molecular modeling and optimization studies, the intrinsic potencies and molecular properties of this series of compounds was significantly improved. An excellent pan-PIM isoform inhibition profile was observed across the series, while optimized examples show good selectivity over other kinases. Two PIM-expressing leukemic cancer cell lines, MV4-11 and K562, were employed to evaluate the in vitro anti-proliferative effects of selected inhibitors. Encouraging activities were observed for many examples, with the best example (44) giving an IC50 of 0.75μM against the K562 cell line. These data provide a promising starting point for further development of this series as a new cancer therapy through PIM kinase inhibition.
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Affiliation(s)
- Carole J R Bataille
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Méabh B Brennan
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Simon Byrne
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Stephen G Davies
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK.
| | - Matthew Durbin
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Oleg Fedorov
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, UK
| | - Kilian V M Huber
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Alan M Jones
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Stefan Knapp
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, UK
| | - Gu Liu
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Anna Nadali
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Camilo E Quevedo
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Angela J Russell
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK; Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK.
| | - Roderick G Walker
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Robert Westwood
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Graham M Wynne
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
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86
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Gilberg E, Stumpfe D, Bajorath J. Activity profiles of analog series containing pan assay interference compounds. RSC Adv 2017. [DOI: 10.1039/c7ra06736d] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Shown is the distribution of activity profiles (color-coded bars) of analog series containing PAINS substructures in a heatmap.
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Affiliation(s)
- Erik Gilberg
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
| | - Dagmar Stumpfe
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
| | - Jürgen Bajorath
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
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87
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Li GB, Abboud MI, Brem J, Someya H, Lohans CT, Yang SY, Spencer J, Wareham DW, McDonough MA, Schofield CJ. NMR-filtered virtual screening leads to non-metal chelating metallo-β-lactamase inhibitors. Chem Sci 2016; 8:928-937. [PMID: 28451231 PMCID: PMC5369532 DOI: 10.1039/c6sc04524c] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/13/2016] [Indexed: 02/05/2023] Open
Abstract
There are no clinically useful inhibitors of metallo-β-lactamases (MBLs), which are a growing problem because they hydrolyse almost all β-lactam antibacterials. Inhibition by most reported MBL inhibitors involves zinc ion chelation. A structure-based virtual screening approach combined with NMR filtering led to the identification of inhibitors of the clinically relevant Verona Integron-encoded MBL (VIM)-2. Crystallographic analyses reveal a new mode of MBL inhibition involving binding adjacent to the active site zinc ions, but which does not involve metal chelation. The results will aid efforts to develop new types of clinically useful inhibitors targeting MBLs/MBL-fold metallo-enzymes involved in antibacterial and anticancer drug resistance.
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Affiliation(s)
- Guo-Bo Li
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ; .,Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education , West China School of Pharmacy , Sichuan University , Chengdu , 610041 , China
| | - Martine I Abboud
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
| | - Jürgen Brem
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
| | - Hidenori Someya
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ; .,Medicinal Chemistry Research Laboratories , New Drug Research Division , Otsuka Pharmaceutical Co., Ltd. , 463-10 Kagasuno, Kawauchi-cho , Tokushima 771-0192 , Japan
| | - Christopher T Lohans
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
| | - Sheng-Yong Yang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy , West China Hospital , West China Medical School , Sichuan University , Sichuan 610041 , China
| | - James Spencer
- School of Cellular and Molecular Medicine , Biomedical Sciences Building , University of Bristol , Bristol BS8 1TD , UK
| | - David W Wareham
- Antimicrobial Research Group , Barts & The London School of Medicine and Dentistry , Queen Mary University of London , London , E1 2AT , UK
| | - Michael A McDonough
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
| | - Christopher J Schofield
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
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88
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Christopeit T, Yang KW, Yang SK, Leiros HKS. The structure of the metallo-β-lactamase VIM-2 in complex with a triazolylthioacetamide inhibitor. Acta Crystallogr F Struct Biol Commun 2016; 72:813-819. [PMID: 27834790 PMCID: PMC5101582 DOI: 10.1107/s2053230x16016113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/11/2016] [Indexed: 11/10/2022] Open
Abstract
The increasing number of pathogens expressing metallo-β-lactamases (MBLs), and in this way achieving resistance to β-lactam antibiotics, is a significant threat to global public health. A promising strategy to treat such resistant pathogens is the co-administration of MBL inhibitors together with β-lactam antibiotics. However, an MBL inhibitor suitable for clinical use has not yet been identified. Verona integron-encoded metallo-β-lactamase 2 (VIM-2) is a widespread MBL with a broad substrate spectrum and hence is an interesting drug target for the treatment of β-lactam-resistant infections. In this study, three triazolylthioacetamides were tested as inhibitors of VIM-2. One of the tested compounds showed clear inhibition of VIM-2, with an IC50 of 20 µM. The crystal structure of the inhibitor in complex with VIM-2 was obtained by DMSO-free co-crystallization and was solved at a resolution of 1.50 Å. To our knowledge, this is the first structure of a triazolylthioacetamide inhibitor in complex with an MBL. Analysis of the structure shows that the inhibitor binds to the two zinc ions in the active site of VIM-2 and revealed detailed information on the interactions involved. Furthermore, the crystal structure showed that binding of the inhibitor induced a conformational change of the conserved residue Trp87.
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Affiliation(s)
- Tony Christopeit
- The Norwegian Structural Biology Centre (Norstruct), Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, People’s Republic of China
| | - Shao-Kang Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, People’s Republic of China
| | - Hanna-Kirsti S. Leiros
- The Norwegian Structural Biology Centre (Norstruct), Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
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89
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Cahill ST, Tarhonskaya H, Rydzik AM, Flashman E, McDonough MA, Schofield CJ, Brem J. Use of ferrous iron by metallo-β-lactamases. J Inorg Biochem 2016; 163:185-193. [PMID: 27498591 PMCID: PMC5108564 DOI: 10.1016/j.jinorgbio.2016.07.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 07/12/2016] [Accepted: 07/25/2016] [Indexed: 01/01/2023]
Abstract
Metallo-β-lactamases (MBLs) catalyse the hydrolysis of almost all β-lactam antibacterials including the latest generation carbapenems and are a growing worldwide clinical problem. It is proposed that MBLs employ one or two zinc ion cofactors in vivo. Isolated MBLs are reported to use transition metal ions other than zinc, including copper, cadmium and manganese, with iron ions being a notable exception. We report kinetic and biophysical studies with the di-iron(II)-substituted metallo-β-lactamase II from Bacillus cereus (di-Fe(II) BcII) and the clinically relevant B1 subclass Verona integron-encoded metallo-β-lactamase 2 (di-Fe(II) VIM-2). The results reveal that MBLs can employ ferrous iron in catalysis, but with altered kinetic and inhibition profiles compared to the zinc enzymes. A crystal structure of di-Fe(II) BcII reveals only small overall changes in the active site compared to the di-Zn(II) enzyme including retention of the di-metal bridging water; however, the positions of the metal ions are altered in the di-Fe(II) compared to the di-Zn(II) structure. Stopped-flow analyses reveal that the mechanism of nitrocefin hydrolysis by both di-Fe(II) BcII and di-Fe(II) VIM-2 is altered compared to the di-Zn(II) enzymes. Notably, given that the MBLs are the subject of current medicinal chemistry efforts, the results raise the possibility the Fe(II)-substituted MBLs may be of clinical relevance under conditions of low zinc availability, and reveal potential variation in inhibitor activity against the differently metallated MBLs.
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Affiliation(s)
| | | | - Anna M Rydzik
- Chemistry Research Laboratory, Oxford, United Kingdom
| | | | | | | | - Jürgen Brem
- Chemistry Research Laboratory, Oxford, United Kingdom.
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90
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Brem J, Cain R, Cahill S, McDonough MA, Clifton IJ, Jiménez-Castellanos JC, Avison MB, Spencer J, Fishwick CWG, Schofield CJ. Structural basis of metallo-β-lactamase, serine-β-lactamase and penicillin-binding protein inhibition by cyclic boronates. Nat Commun 2016; 7:12406. [PMID: 27499424 PMCID: PMC4979060 DOI: 10.1038/ncomms12406] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/29/2016] [Indexed: 12/24/2022] Open
Abstract
β-Lactamases enable resistance to almost all β-lactam antibiotics. Pioneering work revealed that acyclic boronic acids can act as 'transition state analogue' inhibitors of nucleophilic serine enzymes, including serine-β-lactamases. Here we report biochemical and biophysical analyses revealing that cyclic boronates potently inhibit both nucleophilic serine and zinc-dependent β-lactamases by a mechanism involving mimicking of the common tetrahedral intermediate. Cyclic boronates also potently inhibit the non-essential penicillin-binding protein PBP 5 by the same mechanism of action. The results open the way for development of dual action inhibitors effective against both serine- and metallo-β-lactamases, and which could also have antimicrobial activity through inhibition of PBPs.
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Affiliation(s)
- Jürgen Brem
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Ricky Cain
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Samuel Cahill
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Michael A. McDonough
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Ian J. Clifton
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | | | - Matthew B. Avison
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, UK
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, UK
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91
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Cross-class metallo-β-lactamase inhibition by bisthiazolidines reveals multiple binding modes. Proc Natl Acad Sci U S A 2016; 113:E3745-54. [PMID: 27303030 DOI: 10.1073/pnas.1601368113] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Metallo-β-lactamases (MBLs) hydrolyze almost all β-lactam antibiotics and are unaffected by clinically available β-lactamase inhibitors (βLIs). Active-site architecture divides MBLs into three classes (B1, B2, and B3), complicating development of βLIs effective against all enzymes. Bisthiazolidines (BTZs) are carboxylate-containing, bicyclic compounds, considered as penicillin analogs with an additional free thiol. Here, we show both l- and d-BTZ enantiomers are micromolar competitive βLIs of all MBL classes in vitro, with Kis of 6-15 µM or 36-84 µM for subclass B1 MBLs (IMP-1 and BcII, respectively), and 10-12 µM for the B3 enzyme L1. Against the B2 MBL Sfh-I, the l-BTZ enantiomers exhibit 100-fold lower Kis (0.26-0.36 µM) than d-BTZs (26-29 µM). Importantly, cell-based time-kill assays show BTZs restore β-lactam susceptibility of Escherichia coli-producing MBLs (IMP-1, Sfh-1, BcII, and GOB-18) and, significantly, an extensively drug-resistant Stenotrophomonas maltophilia clinical isolate expressing L1. BTZs therefore inhibit the full range of MBLs and potentiate β-lactam activity against producer pathogens. X-ray crystal structures reveal insights into diverse BTZ binding modes, varying with orientation of the carboxylate and thiol moieties. BTZs bind the di-zinc centers of B1 (IMP-1; BcII) and B3 (L1) MBLs via the free thiol, but orient differently depending upon stereochemistry. In contrast, the l-BTZ carboxylate dominates interactions with the monozinc B2 MBL Sfh-I, with the thiol uninvolved. d-BTZ complexes most closely resemble β-lactam binding to B1 MBLs, but feature an unprecedented disruption of the D120-zinc interaction. Cross-class MBL inhibition therefore arises from the unexpected versatility of BTZ binding.
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92
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Lee SY, Brem J, Pettinati I, Claridge TDW, Gileadi O, Schofield CJ, McHugh PJ. Cephalosporins inhibit human metallo β-lactamase fold DNA repair nucleases SNM1A and SNM1B/apollo. Chem Commun (Camb) 2016; 52:6727-30. [PMID: 27121860 PMCID: PMC5063058 DOI: 10.1039/c6cc00529b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/18/2016] [Indexed: 12/19/2022]
Abstract
Bacterial metallo-β-lactamases (MBLs) are involved in resistance to β-lactam antibiotics including cephalosporins. Human SNM1A and SNM1B are MBL superfamily exonucleases that play a key role in the repair of DNA interstrand cross-links, which are induced by antitumour chemotherapeutics, and are therefore targets for cancer chemosensitization. We report that cephalosporins are competitive inhibitors of SNM1A and SNM1B exonuclease activity; both the intact β-lactam and their hydrolysed products are active. This discovery provides a lead for the development of potent and selective SNM1A and SNM1B inhibitors.
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Affiliation(s)
- Sook Y Lee
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK. and Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Ilaria Pettinati
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Timothy D W Claridge
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Opher Gileadi
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, OX3 7DQ, UK
| | | | - Peter J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
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93
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Evdokimov NM, Magedov IV, McBrayer D, Kornienko A. Isatin derivatives with activity against apoptosis-resistant cancer cells. Bioorg Med Chem Lett 2016; 26:1558-1560. [PMID: 26883150 PMCID: PMC4775416 DOI: 10.1016/j.bmcl.2016.02.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/04/2016] [Accepted: 02/06/2016] [Indexed: 12/19/2022]
Abstract
In a search of small molecules active against apoptosis-resistant cancer cells, a series of isatin-based heterocyclic compounds were synthesized and found to inhibit proliferation of cancer cell lines resistant to apoptosis. The synthesis of these compounds involved a condensation of commercially available, active methylene heterocycles with isatin proceeding in moderate to excellent yields. The heterocyclic scaffolds prepared in the current investigation appear to be a useful starting point for the development of agents to fight cancers with apoptosis resistance, and thus, associated with dismal prognoses.
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Affiliation(s)
- Nikolai M Evdokimov
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, United States; Department of Chemistry, New Mexico Institute of Mining and Technology, Socorro, NM 87801, United States.
| | - Igor V Magedov
- Department of Chemistry, New Mexico Institute of Mining and Technology, Socorro, NM 87801, United States
| | - Dominic McBrayer
- Department of Chemistry, New Mexico Institute of Mining and Technology, Socorro, NM 87801, United States
| | - Alexander Kornienko
- Department of Chemistry, New Mexico Institute of Mining and Technology, Socorro, NM 87801, United States; Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, United States.
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94
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King DT, Sobhanifar S, Strynadka NCJ. One ring to rule them all: Current trends in combating bacterial resistance to the β-lactams. Protein Sci 2016; 25:787-803. [PMID: 26813250 DOI: 10.1002/pro.2889] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 01/27/2023]
Abstract
From humble beginnings of a contaminated petri dish, β-lactam antibiotics have distinguished themselves among some of the most powerful drugs in human history. The devastating effects of antibiotic resistance have nevertheless led to an "arms race" with disquieting prospects. The emergence of multidrug resistant bacteria threatens an ever-dwindling antibiotic arsenal, calling for new discovery, rediscovery, and innovation in β-lactam research. Here the current state of β-lactam antibiotics from a structural perspective was reviewed.
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Affiliation(s)
- Dustin T King
- Department of Biochemistry and Molecular Biology and Center for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Solmaz Sobhanifar
- Department of Biochemistry and Molecular Biology and Center for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Center for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
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95
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Betts JW, Phee LM, Abdul Momin MHF, Umland KD, Brem J, Schofield CJ, Wareham DW. In vitro and in vivo activity of ML302F: a thioenolate inhibitor of VIM-subfamily metallo β-lactamases. MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00380f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The thioenol ML302F, recently identified as an inhibitor of class B metallo-β-lactamases (MBLs), restores antibiotic susceptibility to meropenem resistant strains in cells and the Galleria mellonella invertebrate model.
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Affiliation(s)
- Jonathan W. Betts
- Antimicrobial Research Group
- Barts & The London School of Medicine and Dentistry
- Queen Mary University of London
- London
- UK
| | - Lynette M. Phee
- Antimicrobial Research Group
- Barts & The London School of Medicine and Dentistry
- Queen Mary University of London
- London
- UK
| | - Muhd H. F. Abdul Momin
- Antimicrobial Research Group
- Barts & The London School of Medicine and Dentistry
- Queen Mary University of London
- London
- UK
| | | | - Jurgen Brem
- Department of Chemistry
- University of Oxford
- Oxford
- UK
| | | | - David W. Wareham
- Antimicrobial Research Group
- Barts & The London School of Medicine and Dentistry
- Queen Mary University of London
- London
- UK
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96
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González MM, Vila AJ. An Elusive Task: A Clinically Useful Inhibitor of Metallo-β-Lactamases. TOPICS IN MEDICINAL CHEMISTRY 2016. [DOI: 10.1007/7355_2016_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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97
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Comparison of Verona Integron-Borne Metallo-β-Lactamase (VIM) Variants Reveals Differences in Stability and Inhibition Profiles. Antimicrob Agents Chemother 2015; 60:1377-84. [PMID: 26666919 PMCID: PMC4775916 DOI: 10.1128/aac.01768-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 12/05/2015] [Indexed: 01/28/2023] Open
Abstract
Metallo-β-lactamases (MBLs) are of increasing clinical significance; the development of clinically useful MBL inhibitors is challenged by the rapid evolution of variant MBLs. The Verona integron-borne metallo-β-lactamase (VIM) enzymes are among the most widely distributed MBLs, with >40 VIM variants having been reported. We report on the crystallographic analysis of VIM-5 and comparison of biochemical and biophysical properties of VIM-1, VIM-2, VIM-4, VIM-5, and VIM-38. Recombinant VIM variants were produced and purified, and their secondary structure and thermal stabilities were investigated by circular dichroism analyses. Steady-state kinetic analyses with a representative panel of β-lactam substrates were carried out to compare the catalytic efficiencies of the VIM variants. Furthermore, a set of metalloenzyme inhibitors were screened to compare their effects on the different VIM variants. The results reveal only small variations in the kinetic parameters of the VIM variants but substantial differences in their thermal stabilities and inhibition profiles. Overall, these results support the proposal that protein stability may be a factor in MBL evolution and highlight the importance of screening MBL variants during inhibitor development programs.
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98
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González MM, Kosmopoulou M, Mojica MF, Castillo V, Hinchliffe P, Pettinati I, Brem J, Schofield CJ, Mahler G, Bonomo RA, Llarrull LI, Spencer J, Vila AJ. Bisthiazolidines: A Substrate-Mimicking Scaffold as an Inhibitor of the NDM-1 Carbapenemase. ACS Infect Dis 2015; 1:544-54. [PMID: 27623409 DOI: 10.1021/acsinfecdis.5b00046] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Pathogenic Gram-negative bacteria resistant to almost all β-lactam antibiotics are a major public health threat. Zn(II)-dependent or metallo-β-lactamases (MBLs) produced by these bacteria inactivate most β-lactam antibiotics, including the carbapenems, which are "last line therapies" for life-threatening Gram-negative infections. NDM-1 is a carbapenemase belonging to the MBL family that is rapidly spreading worldwide. Regrettably, inhibitors of MBLs are not yet developed. Here we present the bisthiazolidine (BTZ) scaffold as a structure with some features of β-lactam substrates, which can be modified with metal-binding groups to target the MBL active site. Inspired by known interactions of MBLs with β-lactams, we designed four BTZs that behave as in vitro NDM-1 inhibitors with Ki values in the low micromolar range (from 7 ± 1 to 19 ± 3 μM). NMR spectroscopy demonstrated that they inhibit hydrolysis of imipenem in NDM-1-producing Escherichia coli. In vitro time kill cell-based assays against a variety of bacterial strains harboring blaNDM-1 including Acinetobacter baumannii show that the compounds restore the antibacterial activity of imipenem. A crystal structure of the most potent heterocycle (L-CS319) in complex with NDM-1 at 1.9 Å resolution identified both structural determinants for inhibitor binding and opportunities for further improvements in potency.
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Affiliation(s)
- Mariano M. González
- Instituto de Biologı́a Molecular y Celular
de Rosario (IBR-CONICET), Facultad de Ciencias Bioquı́micas
y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo
y Esmeralda, 2000 Rosario, Argentina
| | - Magda Kosmopoulou
- School of Cellular
and Molecular Medicine, Medical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
| | - Maria F. Mojica
- Research
Service, Louis Stokes Cleveland Department of Veterans Affairs Medical
Center, and Departments of Pharmacology, Biochemistry, Microbiology,
and Molecular Biology, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Valerie Castillo
- Laboratorio de Quı́mica Farmacéutica,
Facultad de Quı́mica, Universidad de la República (UdelaR), Montevideo 11800, Uruguay
| | - Philip Hinchliffe
- School of Cellular
and Molecular Medicine, Medical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
| | - Ilaria Pettinati
- Department
of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jürgen Brem
- Department
of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J. Schofield
- Department
of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Graciela Mahler
- Laboratorio de Quı́mica Farmacéutica,
Facultad de Quı́mica, Universidad de la República (UdelaR), Montevideo 11800, Uruguay
| | - Robert A. Bonomo
- Research
Service, Louis Stokes Cleveland Department of Veterans Affairs Medical
Center, and Departments of Pharmacology, Biochemistry, Microbiology,
and Molecular Biology, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Leticia I. Llarrull
- Instituto de Biologı́a Molecular y Celular
de Rosario (IBR-CONICET), Facultad de Ciencias Bioquı́micas
y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo
y Esmeralda, 2000 Rosario, Argentina
| | - James Spencer
- School of Cellular
and Molecular Medicine, Medical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
| | - Alejandro J. Vila
- Instituto de Biologı́a Molecular y Celular
de Rosario (IBR-CONICET), Facultad de Ciencias Bioquı́micas
y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo
y Esmeralda, 2000 Rosario, Argentina
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99
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Structural Basis of Metallo-β-Lactamase Inhibition by Captopril Stereoisomers. Antimicrob Agents Chemother 2015; 60:142-50. [PMID: 26482303 PMCID: PMC4704194 DOI: 10.1128/aac.01335-15] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 10/03/2015] [Indexed: 11/20/2022] Open
Abstract
β-Lactams are the most successful antibacterials, but their effectiveness is threatened by resistance, most importantly by production of serine- and metallo-β-lactamases (MBLs). MBLs are of increasing concern because they catalyze the hydrolysis of almost all β-lactam antibiotics, including recent-generation carbapenems. Clinically useful serine-β-lactamase inhibitors have been developed, but such inhibitors are not available for MBLs. l-Captopril, which is used to treat hypertension via angiotensin-converting enzyme inhibition, has been reported to inhibit MBLs by chelating the active site zinc ions via its thiol(ate). We report systematic studies on B1 MBL inhibition by all four captopril stereoisomers. High-resolution crystal structures of three MBLs (IMP-1, BcII, and VIM-2) in complex with either the l- or d-captopril stereoisomer reveal correlations between the binding mode and inhibition potency. The results will be useful in the design of MBL inhibitors with the breadth of selectivity required for clinical application against carbapenem-resistant Enterobacteriaceae and other organisms causing MBL-mediated resistant infections.
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100
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The importance of triaging in determining the quality of output from high-throughput screening. Future Med Chem 2015; 7:1847-52. [PMID: 26419190 DOI: 10.4155/fmc.15.121] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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