1
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Henderson SH, Sorrell FJ, Bennett JM, Fedorov O, Hanley MT, Godoi PH, Ruela de Sousa R, Robinson S, Navratilova IH, Elkins JM, Ward SE. Imidazo[1,2-b]pyridazines as inhibitors of DYRK kinases. Eur J Med Chem 2024; 269:116292. [PMID: 38479168 DOI: 10.1016/j.ejmech.2024.116292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 04/07/2024]
Abstract
Selective inhibitors of DYRK1A are of interest for the treatment of cancer, Type 2 diabetes and neurological disorders. Optimization of imidazo [1,2-b]pyridazine fragment 1 through structure-activity relationship exploration and in silico drug design efforts led to the discovery of compound 17 as a potent cellular inhibitor of DYRK1A with selectivity over much of the kinome. The binding mode of compound 17 was elucidated with X-ray crystallography, facilitating the rational design of compound 29, an imidazo [1,2-b]pyridazine with improved kinase selectivity with respect to closely related CLK kinases.
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Affiliation(s)
- Scott H Henderson
- Sussex Drug Discovery Centre, University of Sussex, Brighton, BN1 9RH, UK.
| | - Fiona J Sorrell
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - James M Bennett
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK
| | - Oleg Fedorov
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Marcus T Hanley
- Medicines Discovery Institute, Cardiff University, CF10 3AT, UK
| | - Paulo H Godoi
- Structural Genomics Consortium, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Av. Dr. André Tosello, 550, Barão Geraldo, Campinas, SP, 13083-886, Brazil
| | - Roberta Ruela de Sousa
- Structural Genomics Consortium, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Av. Dr. André Tosello, 550, Barão Geraldo, Campinas, SP, 13083-886, Brazil
| | - Sean Robinson
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Iva Hopkins Navratilova
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK; University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Jonathan M Elkins
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK; Structural Genomics Consortium, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Av. Dr. André Tosello, 550, Barão Geraldo, Campinas, SP, 13083-886, Brazil.
| | - Simon E Ward
- Medicines Discovery Institute, Cardiff University, CF10 3AT, UK.
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2
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Shepherd C, Robinson S, Berizzi A, Thompson LEJ, Bird L, Culurgioni S, Varzandeh S, Rawlins PB, Olsen RHJ, Navratilova IH. Surface Plasmon Resonance Screening to Identify Active and Selective Adenosine Receptor Binding Fragments. ACS Med Chem Lett 2022; 13:1172-1181. [DOI: 10.1021/acsmedchemlett.2c00099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Claire Shepherd
- University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
- Kinetic Discovery Ltd., The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Sean Robinson
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Alice Berizzi
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Laura E. J. Thompson
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Louise Bird
- Kinetic Discovery Ltd., The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Simone Culurgioni
- Kinetic Discovery Ltd., The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Simon Varzandeh
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Philip B. Rawlins
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Reid H. J. Olsen
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Iva Hopkins Navratilova
- University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
- Kinetic Discovery Ltd., The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
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3
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Brem J, Panduwawala T, Hansen JU, Hewitt J, Liepins E, Donets P, Espina L, Farley AJM, Shubin K, Campillos GG, Kiuru P, Shishodia S, Krahn D, Leśniak RK, Schmidt Adrian J, Calvopiña K, Turrientes MC, Kavanagh ME, Lubriks D, Hinchliffe P, Langley GW, Aboklaish AF, Eneroth A, Backlund M, Baran AG, Nielsen EI, Speake M, Kuka J, Robinson J, Grinberga S, Robinson L, McDonough MA, Rydzik AM, Leissing TM, Jimenez-Castellanos JC, Avison MB, Da Silva Pinto S, Pannifer AD, Martjuga M, Widlake E, Priede M, Hopkins Navratilova I, Gniadkowski M, Belfrage AK, Brandt P, Yli-Kauhaluoma J, Bacque E, Page MGP, Björkling F, Tyrrell JM, Spencer J, Lang PA, Baranczewski P, Cantón R, McElroy SP, Jones PS, Baquero F, Suna E, Morrison A, Walsh TR, Schofield CJ. Imitation of β-lactam binding enables broad-spectrum metallo-β-lactamase inhibitors. Nat Chem 2022; 14:15-24. [PMID: 34903857 DOI: 10.1038/s41557-021-00831-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 09/30/2021] [Indexed: 11/08/2022]
Abstract
Carbapenems are vital antibiotics, but their efficacy is increasingly compromised by metallo-β-lactamases (MBLs). Here we report the discovery and optimization of potent broad-spectrum MBL inhibitors. A high-throughput screen for NDM-1 inhibitors identified indole-2-carboxylates (InCs) as potential β-lactamase stable β-lactam mimics. Subsequent structure-activity relationship studies revealed InCs as a new class of potent MBL inhibitor, active against all MBL classes of major clinical relevance. Crystallographic studies revealed a binding mode of the InCs to MBLs that, in some regards, mimics that predicted for intact carbapenems, including with respect to maintenance of the Zn(II)-bound hydroxyl, and in other regards mimics binding observed in MBL-carbapenem product complexes. InCs restore carbapenem activity against multiple drug-resistant Gram-negative bacteria and have a low frequency of resistance. InCs also have a good in vivo safety profile, and when combined with meropenem show a strong in vivo efficacy in peritonitis and thigh mouse infection models.
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Affiliation(s)
- Jürgen Brem
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK.
| | - Tharindi Panduwawala
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | | | - Joanne Hewitt
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
| | | | - Pawel Donets
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Laura Espina
- Department of Medical Microbiology, Institute of infection & Immunity, Cardiff University, Cardiff, UK
| | - Alistair J M Farley
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Kirill Shubin
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Gonzalo Gomez Campillos
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Paula Kiuru
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Shifali Shishodia
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Daniel Krahn
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Robert K Leśniak
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Juliane Schmidt Adrian
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Karina Calvopiña
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - María-Carmen Turrientes
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Madeline E Kavanagh
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Gareth W Langley
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
- Charles River Laboratories, Saffron Walden, UK
| | - Ali F Aboklaish
- Department of Medical Microbiology, Institute of infection & Immunity, Cardiff University, Cardiff, UK
| | - Anders Eneroth
- Department of Pharmacy, Uppsala Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Uppsala University, Uppsala, Sweden
| | - Maria Backlund
- Department of Pharmacy, Uppsala Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Uppsala University, Uppsala, Sweden
| | | | | | - Michael Speake
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
- BioAscent Discovery Ltd, Newhouse, UK
| | - Janis Kuka
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - John Robinson
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
- BioAscent Discovery Ltd, Newhouse, UK
| | | | - Lindsay Robinson
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
- BioAscent Discovery Ltd, Newhouse, UK
| | - Michael A McDonough
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Anna M Rydzik
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
- Research and Early Development, Respiratory & Immunology, AstraZeneca, Mölndal, Sweden
| | - Thomas M Leissing
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Juan Carlos Jimenez-Castellanos
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- Chemical Biology of Antibiotics, Centre for Infection & Immunity (CIIL), Pasteur Institute, INSERM U1019 - CNRS UMR 9017, Lille, France
| | - Matthew B Avison
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Solange Da Silva Pinto
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Andrew D Pannifer
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
| | | | - Emma Widlake
- Department of Medical Microbiology, Institute of infection & Immunity, Cardiff University, Cardiff, UK
| | | | | | - Marek Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - Anna Karin Belfrage
- Department of Medicinal Chemistry, Drug Design and Discovery, Uppsala University, Uppsala, Sweden
| | - Peter Brandt
- Department of Medicinal Chemistry, Drug Design and Discovery, Uppsala University, Uppsala, Sweden
- Beactica Therapeutics AB, Uppsala, Sweden
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Eric Bacque
- Evotec Infectious Diseases Lyon, Marcy l'Etoile, France
| | | | - Fredrik Björkling
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan M Tyrrell
- Department of Medical Microbiology, Institute of infection & Immunity, Cardiff University, Cardiff, UK
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Pauline A Lang
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Pawel Baranczewski
- Department of Pharmacy, SciLifeLab Drug Discovery and Development Platform, ADME of Therapeutics Facility, Uppsala University, Uppsala, Sweden
| | - Rafael Cantón
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Stuart P McElroy
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
- BioAscent Discovery Ltd, Newhouse, UK
| | - Philip S Jones
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
- BioAscent Discovery Ltd, Newhouse, UK
| | - Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Edgars Suna
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Angus Morrison
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
- BioAscent Discovery Ltd, Newhouse, UK
| | - Timothy R Walsh
- Department of Medical Microbiology, Institute of infection & Immunity, Cardiff University, Cardiff, UK
| | - Christopher J Schofield
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK.
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4
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Henderson SH, Sorrell F, Bennett J, Fedorov O, Hanley MT, Godoi PH, Ruela de Sousa R, Robinson S, Ashall-Kelly A, Hopkins Navratilova I, Walter DS, Elkins JM, Ward SE. Discovery and Characterization of Selective and Ligand-Efficient DYRK Inhibitors. J Med Chem 2021; 64:11709-11728. [PMID: 34342227 PMCID: PMC8482766 DOI: 10.1021/acs.jmedchem.1c01115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Indexed: 11/29/2022]
Abstract
Dual-specificity tyrosine-regulated kinase 1A (DYRK1A) regulates the proliferation and differentiation of neuronal progenitor cells during brain development. Consequently, DYRK1A has attracted interest as a target for the treatment of neurodegenerative diseases, including Alzheimer's disease (AD) and Down's syndrome. Recently, the inhibition of DYRK1A has been investigated as a potential treatment for diabetes, while DYRK1A's role as a mediator in the cell cycle has garnered interest in oncologic indications. Structure-activity relationship (SAR) analysis in combination with high-resolution X-ray crystallography leads to a series of pyrazolo[1,5-b]pyridazine inhibitors with excellent ligand efficiencies, good physicochemical properties, and a high degree of selectivity over the kinome. Compound 11 exhibited good permeability and cellular activity without P-glycoprotein liability, extending the utility of 11 in an in vivo setting. These pyrazolo[1,5-b]pyridazines are a viable lead series in the discovery of new therapies for the treatment of diseases linked to DYRK1A function.
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Affiliation(s)
- Scott H. Henderson
- Sussex
Drug Discovery Centre, University of Sussex, Brighton BN1 9RH, U.K.
| | - Fiona Sorrell
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, U.K.
| | - James Bennett
- Target
Discovery Institute, University of Oxford, Oxford OX3 7FZ, U.K.
| | - Oleg Fedorov
- Target
Discovery Institute, University of Oxford, Oxford OX3 7FZ, U.K.
| | - Marcus T. Hanley
- Medicines
Discovery Institute, Cardiff University, Cardiff CF10 3AT, U.K.
| | - Paulo H. Godoi
- Structural
Genomics Consortium, Universidade Estadual
de Campinas, Cidade Universitária
Zeferino Vaz, Av. Dr. André Tosello, 550, Barão Geraldo, Campinas, SP 13083-886, Brazil
| | - Roberta Ruela de Sousa
- Structural
Genomics Consortium, Universidade Estadual
de Campinas, Cidade Universitária
Zeferino Vaz, Av. Dr. André Tosello, 550, Barão Geraldo, Campinas, SP 13083-886, Brazil
| | - Sean Robinson
- Exscientia, The Schrödinger Building,
Oxford Science Park, Oxford OX4 4GE, U.K.
| | | | - Iva Hopkins Navratilova
- Exscientia, The Schrödinger Building,
Oxford Science Park, Oxford OX4 4GE, U.K.
- University
of Dundee, Dow Street, Dundee DD1
5EH, U.K
| | - Daryl S. Walter
- Evotec (UK)
Ltd., 112-114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K.
| | - Jonathan M. Elkins
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, U.K.
- Structural
Genomics Consortium, Universidade Estadual
de Campinas, Cidade Universitária
Zeferino Vaz, Av. Dr. André Tosello, 550, Barão Geraldo, Campinas, SP 13083-886, Brazil
| | - Simon E. Ward
- Medicines
Discovery Institute, Cardiff University, Cardiff CF10 3AT, U.K.
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5
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Henderson SH, Sorrell F, Bennett J, Hanley MT, Robinson S, Hopkins Navratilova I, Elkins JM, Ward SE. Mining Public Domain Data to Develop Selective DYRK1A Inhibitors. ACS Med Chem Lett 2020; 11:1620-1626. [PMID: 32832032 DOI: 10.1021/acsmedchemlett.0c00279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/30/2020] [Indexed: 01/08/2023] Open
Abstract
Kinases represent one of the most intensively pursued groups of targets in modern-day drug discovery. Often it is desirable to achieve selective inhibition of the kinase of interest over the remaining ∼500 kinases in the human kinome. This is especially true when inhibitors are intended to be used to study the biology of the target of interest. We present a pipeline of open-source software that analyzes public domain data to repurpose compounds that have been used in previous kinase inhibitor development projects. We define the dual-specificity tyrosine-regulated kinase 1A (DYRK1A) as the kinase of interest, and by addition of a single methyl group to the chosen starting point we remove glycogen synthase kinase β (GSK3β) and cyclin-dependent kinase (CDK) inhibition. Thus, in an efficient manner we repurpose a GSK3β/CDK chemotype to deliver 8b, a highly selective DYRK1A inhibitor.
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Affiliation(s)
- Scott H. Henderson
- Sussex Drug Discovery Centre, University of Sussex, Brighton BN1 9RH, U.K
| | - Fiona Sorrell
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, U.K
| | - James Bennett
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, U.K
| | - Marcus T. Hanley
- Medicines Discovery Institute, Cardiff University, Cardiff CF10 3AT, U.K
| | - Sean Robinson
- Exscientia, The Schrödinger Building, Oxford Science
Park, Oxford OX4 4GE, U.K
| | - Iva Hopkins Navratilova
- Exscientia, The Schrödinger Building, Oxford Science
Park, Oxford OX4 4GE, U.K
- University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Jonathan M. Elkins
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, U.K
- Structural Genomics Consortium, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Av. Dr. André Tosello, 550, Barão Geraldo, Campinas, SP 13083-886, Brazil
| | - Simon E. Ward
- Medicines Discovery Institute, Cardiff University, Cardiff CF10 3AT, U.K
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6
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Cahill ST, Tyrrell JM, Navratilova IH, Calvopiña K, Robinson SW, Lohans CT, McDonough MA, Cain R, Fishwick CWG, Avison MB, Walsh TR, Schofield CJ, Brem J. Studies on the inhibition of AmpC and other β-lactamases by cyclic boronates. Biochim Biophys Acta Gen Subj 2019; 1863:742-748. [PMID: 30738906 DOI: 10.1016/j.bbagen.2019.02.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/23/2019] [Accepted: 02/04/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND The β-lactam antibiotics represent the most successful drug class for treatment of bacterial infections. Resistance to them, importantly via production of β-lactamases, which collectively are able to hydrolyse all classes of β-lactams, threatens their continued widespread use. Bicyclic boronates show potential as broad spectrum inhibitors of the mechanistically distinct serine- (SBL) and metallo- (MBL) β-lactamase families. METHODS Using biophysical methods, including crystallographic analysis, we have investigated the binding mode of bicyclic boronates to clinically important β-lactamases. Induction experiments and agar-based MIC screening against MDR-Enterobacteriaceae (n = 132) were used to evaluate induction properties and the in vitro efficacy of a bicyclic boronate in combination with meropenem. RESULTS Crystallographic analysis of a bicyclic boronate in complex with AmpC from Pseudomonas aeruginosa reveals it binds to form a tetrahedral boronate species. Microbiological studies on the clinical coverage (in combination with meropenem) and induction of β-lactamases by bicyclic boronates further support the promise of such compounds as broad spectrum β-lactamase inhibitors. CONCLUSIONS Together with reported studies on the structural basis of their inhibition of class A, B and D β-lactamases, biophysical studies, including crystallographic analysis, support the proposal that bicyclic boronates mimic tetrahedral intermediates common to SBL and MBL catalysis. GENERAL SIGNIFICANCE Bicyclic boronates are a new generation of broad spectrum inhibitors of both SBLs and MBLs.
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Affiliation(s)
- Samuel T Cahill
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jonathan M Tyrrell
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Iva Hopkins Navratilova
- University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom; Research Complex at Harwell, Rutherford Appleton Lab, Harwell, Oxford OX11 0FA, United Kingdom
| | - Karina Calvopiña
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, United Kingdom
| | - Sean W Robinson
- Kinetic Discovery Ltd, Rutherford Appleton Laboratory, Oxford, Didcot OX11 0FA, United Kingdom
| | - Christopher T Lohans
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael A McDonough
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Ricky Cain
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
| | | | - Matthew B Avison
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, United Kingdom
| | - Timothy R Walsh
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Christopher J Schofield
- 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.
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7
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Urbaniak MD, Collie IT, Fang W, Aristotelous T, Eskilsson S, Raimi OG, Harrison J, Navratilova IH, Frearson JA, van Aalten DMF, Ferguson MAJ. A novel allosteric inhibitor of the uridine diphosphate N-acetylglucosamine pyrophosphorylase from Trypanosoma brucei. ACS Chem Biol 2013; 8:1981-7. [PMID: 23834437 PMCID: PMC3780468 DOI: 10.1021/cb400411x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
![]()
Uridine
diphosphate N-acetylglucosamine pyrophosphorylase
(UAP) catalyzes the final reaction in the biosynthesis of UDP-GlcNAc,
an essential metabolite in many organisms including Trypanosoma
brucei, the etiological agent of Human African Trypanosomiasis.
High-throughput screening of recombinant T. brucei UAP identified a UTP-competitive inhibitor with selectivity over
the human counterpart despite the high level of conservation of active
site residues. Biophysical characterization of the UAP enzyme kinetics
revealed that the human and trypanosome enzymes both display a strictly
ordered bi–bi mechanism, but with the order of substrate binding reversed.
Structural characterization of the T. brucei UAP–inhibitor
complex revealed that the inhibitor binds at an allosteric site absent
in the human homologue that prevents the conformational rearrangement
required to bind UTP. The identification of a selective inhibitory
allosteric binding site in the parasite enzyme has therapeutic potential.
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Affiliation(s)
- Michael D. Urbaniak
- Division
of Biological Chemistry and Drug Discovery, ‡Division of Molecular Microbiology, and §MRC Protein Phosphorylation
and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Iain T. Collie
- Division
of Biological Chemistry and Drug Discovery, ‡Division of Molecular Microbiology, and §MRC Protein Phosphorylation
and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Wenxia Fang
- Division
of Biological Chemistry and Drug Discovery, ‡Division of Molecular Microbiology, and §MRC Protein Phosphorylation
and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Tonia Aristotelous
- Division
of Biological Chemistry and Drug Discovery, ‡Division of Molecular Microbiology, and §MRC Protein Phosphorylation
and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Susanne Eskilsson
- Division
of Biological Chemistry and Drug Discovery, ‡Division of Molecular Microbiology, and §MRC Protein Phosphorylation
and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Olawale G. Raimi
- Division
of Biological Chemistry and Drug Discovery, ‡Division of Molecular Microbiology, and §MRC Protein Phosphorylation
and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Justin Harrison
- Division
of Biological Chemistry and Drug Discovery, ‡Division of Molecular Microbiology, and §MRC Protein Phosphorylation
and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Iva Hopkins Navratilova
- Division
of Biological Chemistry and Drug Discovery, ‡Division of Molecular Microbiology, and §MRC Protein Phosphorylation
and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Julie A. Frearson
- Division
of Biological Chemistry and Drug Discovery, ‡Division of Molecular Microbiology, and §MRC Protein Phosphorylation
and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Daan M. F. van Aalten
- Division
of Biological Chemistry and Drug Discovery, ‡Division of Molecular Microbiology, and §MRC Protein Phosphorylation
and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Michael A. J. Ferguson
- Division
of Biological Chemistry and Drug Discovery, ‡Division of Molecular Microbiology, and §MRC Protein Phosphorylation
and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
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