1
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Lawson H, Holt-Martyn JP, Dembitz V, Kabayama Y, Wang LM, Bellani A, Atwal S, Saffoon N, Durko J, van de Lagemaat LN, De Pace AL, Tumber A, Corner T, Salah E, Arndt C, Brewitz L, Bowen M, Dubusse L, George D, Allen L, Guitart AV, Fung TK, So CWE, Schwaller J, Gallipoli P, O'Carroll D, Schofield CJ, Kranc KR. The selective prolyl hydroxylase inhibitor IOX5 stabilizes HIF-1α and compromises development and progression of acute myeloid leukemia. Nat Cancer 2024:10.1038/s43018-024-00761-w. [PMID: 38637657 DOI: 10.1038/s43018-024-00761-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 03/15/2024] [Indexed: 04/20/2024]
Abstract
Acute myeloid leukemia (AML) is a largely incurable disease, for which new treatments are urgently needed. While leukemogenesis occurs in the hypoxic bone marrow, the therapeutic tractability of the hypoxia-inducible factor (HIF) system remains undefined. Given that inactivation of HIF-1α/HIF-2α promotes AML, a possible clinical strategy is to target the HIF-prolyl hydroxylases (PHDs), which promote HIF-1α/HIF-2α degradation. Here, we reveal that genetic inactivation of Phd1/Phd2 hinders AML initiation and progression, without impacting normal hematopoiesis. We investigated clinically used PHD inhibitors and a new selective PHD inhibitor (IOX5), to stabilize HIF-α in AML cells. PHD inhibition compromises AML in a HIF-1α-dependent manner to disable pro-leukemogenic pathways, re-program metabolism and induce apoptosis, in part via upregulation of BNIP3. Notably, concurrent inhibition of BCL-2 by venetoclax potentiates the anti-leukemic effect of PHD inhibition. Thus, PHD inhibition, with consequent HIF-1α stabilization, is a promising nontoxic strategy for AML, including in combination with venetoclax.
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Affiliation(s)
- Hannah Lawson
- The Institute of Cancer Research, London, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - James P Holt-Martyn
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Vilma Dembitz
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Department of Physiology and Immunology and Croatian Institute for Brain Research, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Yuka Kabayama
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Lydia M Wang
- The Institute of Cancer Research, London, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Aarushi Bellani
- The Institute of Cancer Research, London, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Samanpreet Atwal
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Nadia Saffoon
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Jozef Durko
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Louie N van de Lagemaat
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Azzura L De Pace
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Thomas Corner
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Christine Arndt
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Matthew Bowen
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Louis Dubusse
- The Institute of Cancer Research, London, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Derek George
- The Institute of Cancer Research, London, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Lewis Allen
- The Institute of Cancer Research, London, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Amelie V Guitart
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
- Université de Bordeaux, Institut National de la Santé et de la Recherche Médicale INSERM U1035, Bordeaux, France
| | - Tsz Kan Fung
- Leukemia and Stem Cell Biology Group, Comprehensive Cancer Centre, King's College London, London, UK
- Department of Haematological Medicine, King's College Hospital, King's College London, London, UK
| | - Chi Wai Eric So
- Leukemia and Stem Cell Biology Group, Comprehensive Cancer Centre, King's College London, London, UK
- Department of Haematological Medicine, King's College Hospital, King's College London, London, UK
| | - Juerg Schwaller
- University Children's Hospital Basel (UKBB), Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Paolo Gallipoli
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Donal O'Carroll
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK.
| | - Kamil R Kranc
- The Institute of Cancer Research, London, UK.
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK.
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2
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Belle R, Saraç H, Salah E, Bhushan B, Szykowska A, Roper G, Tumber A, Kriaucionis S, Burgess-Brown N, Schofield CJ, Brown T, Kawamura A. Focused Screening Identifies Different Sensitivities of Human TET Oxygenases to the Oncometabolite 2-Hydroxyglutarate. J Med Chem 2024; 67:4525-4540. [PMID: 38294854 PMCID: PMC10983004 DOI: 10.1021/acs.jmedchem.3c01820] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 09/28/2023] [Revised: 12/10/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024]
Abstract
Ten-eleven translocation enzymes (TETs) are Fe(II)/2-oxoglutarate (2OG) oxygenases that catalyze the sequential oxidation of 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine in eukaryotic DNA. Despite their roles in epigenetic regulation, there is a lack of reported TET inhibitors. The extent to which 2OG oxygenase inhibitors, including clinically used inhibitors and oncometabolites, modulate DNA modifications via TETs has been unclear. Here, we report studies on human TET1-3 inhibition by a set of 2OG oxygenase-focused inhibitors, employing both enzyme-based and cellular assays. Most inhibitors manifested similar potencies for TET1-3 and caused increases in cellular 5hmC levels. (R)-2-Hydroxyglutarate, an oncometabolite elevated in isocitrate dehydrogenase mutant cancer cells, showed different degrees of inhibition, with TET1 being less potently inhibited than TET3 and TET2, potentially reflecting the proposed role of TET2 mutations in tumorigenesis. The results highlight the tractability of TETs as drug targets and provide starting points for selective inhibitor design.
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Affiliation(s)
- Roman Belle
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
| | - Hilal Saraç
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human
Genetics, Roosevelt Drive, OX3 7BN Oxford, United Kingdom
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Centre
for Medicines Discovery, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Bhaskar Bhushan
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human
Genetics, Roosevelt Drive, OX3 7BN Oxford, United Kingdom
| | - Aleksandra Szykowska
- Centre
for Medicines Discovery, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Grace Roper
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
| | - Anthony Tumber
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Skirmantas Kriaucionis
- Ludwig
Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Nicola Burgess-Brown
- Centre
for Medicines Discovery, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Tom Brown
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Akane Kawamura
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human
Genetics, Roosevelt Drive, OX3 7BN Oxford, United Kingdom
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3
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Šimelis K, Saraç H, Salah E, Nishio K, McAllister TE, Corner TP, Tumber A, Belle R, Schofield CJ, Suga H, Kawamura A. Selective targeting of human TET1 by cyclic peptide inhibitors: Insights from biochemical profiling. Bioorg Med Chem 2024; 99:117597. [PMID: 38262305 DOI: 10.1016/j.bmc.2024.117597] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/27/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/25/2024]
Abstract
Ten-Eleven Translocation (TET) enzymes are Fe(II)/2OG-dependent oxygenases that play important roles in epigenetic regulation, but selective inhibition of the TETs is an unmet challenge. We describe the profiling of previously identified TET1-binding macrocyclic peptides. TiP1 is established as a potent TET1 inhibitor (IC50 = 0.26 µM) with excellent selectivity over other TETs and 2OG oxygenases. TiP1 alanine scanning reveals the critical roles of Trp10 and Glu11 residues for inhibition of TET isoenzymes. The results highlight the utility of the RaPID method to identify potent enzyme inhibitors with selectivity over closely related paralogues. The structure-activity relationship data generated herein may find utility in the development of chemical probes for the TETs.
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Affiliation(s)
- Klemensas Šimelis
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Hilal Saraç
- Chemistry - School of Natural and Environmental Sciences, Newcastle University, Bedson Building, NE1 7RU Newcastle upon Tyne, United Kingdom
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Kosuke Nishio
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tom E McAllister
- Chemistry - School of Natural and Environmental Sciences, Newcastle University, Bedson Building, NE1 7RU Newcastle upon Tyne, United Kingdom
| | - Thomas P Corner
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Roman Belle
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom; Chemistry - School of Natural and Environmental Sciences, Newcastle University, Bedson Building, NE1 7RU Newcastle upon Tyne, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom; Chemistry - School of Natural and Environmental Sciences, Newcastle University, Bedson Building, NE1 7RU Newcastle upon Tyne, United Kingdom.
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4
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Corner TP, Teo RZR, Wu Y, Salah E, Nakashima Y, Fiorini G, Tumber A, Brasnett A, Holt-Martyn JP, Figg WD, Zhang X, Brewitz L, Schofield CJ. Structure-guided optimisation of N-hydroxythiazole-derived inhibitors of factor inhibiting hypoxia-inducible factor-α. Chem Sci 2023; 14:12098-12120. [PMID: 37969593 PMCID: PMC10631261 DOI: 10.1039/d3sc04253g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/12/2023] [Indexed: 11/17/2023] Open
Abstract
The human 2-oxoglutarate (2OG)- and Fe(ii)-dependent oxygenases factor inhibiting hypoxia-inducible factor-α (FIH) and HIF-α prolyl residue hydroxylases 1-3 (PHD1-3) regulate the response to hypoxia in humans via catalysing hydroxylation of the α-subunits of the hypoxia-inducible factors (HIFs). Small-molecule PHD inhibitors are used for anaemia treatment; by contrast, few selective inhibitors of FIH have been reported, despite their potential to regulate the hypoxic response, either alone or in combination with PHD inhibition. We report molecular, biophysical, and cellular evidence that the N-hydroxythiazole scaffold, reported to inhibit PHD2, is a useful broad spectrum 2OG oxygenase inhibitor scaffold, the inhibition potential of which can be tuned to achieve selective FIH inhibition. Structure-guided optimisation resulted in the discovery of N-hydroxythiazole derivatives that manifest substantially improved selectivity for FIH inhibition over PHD2 and other 2OG oxygenases, including Jumonji-C domain-containing protein 5 (∼25-fold), aspartate/asparagine-β-hydroxylase (>100-fold) and histone Nε-lysine demethylase 4A (>300-fold). The optimised N-hydroxythiazole-based FIH inhibitors modulate the expression of FIH-dependent HIF target genes and, consistent with reports that FIH regulates cellular metabolism, suppressed lipid accumulation in adipocytes. Crystallographic studies reveal that the N-hydroxythiazole derivatives compete with both 2OG and the substrate for binding to the FIH active site. Derivatisation of the N-hydroxythiazole scaffold has the potential to afford selective inhibitors for 2OG oxygenases other than FIH.
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Affiliation(s)
- Thomas P Corner
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Ryan Z R Teo
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Yue Wu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization and Department of Chemistry, China Pharmaceutical University Nanjing 211198 China
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Yu Nakashima
- Institute of Natural Medicine, University of Toyama 2630-Sugitani 930-0194 Toyama Japan
| | - Giorgia Fiorini
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Amelia Brasnett
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - James P Holt-Martyn
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - William D Figg
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Xiaojin Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization and Department of Chemistry, China Pharmaceutical University Nanjing 211198 China
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
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5
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Brewitz L, Nakashima Y, Piasecka SK, Salah E, Fletcher SC, Tumber A, Corner TP, Kennedy TJ, Fiorini G, Thalhammer A, Christensen KE, Coleman ML, Schofield CJ. 5-Substituted Pyridine-2,4-dicarboxylate Derivatives Have Potential for Selective Inhibition of Human Jumonji-C Domain-Containing Protein 5. J Med Chem 2023; 66:10849-10865. [PMID: 37527664 PMCID: PMC10424186 DOI: 10.1021/acs.jmedchem.3c01114] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 06/20/2023] [Indexed: 08/03/2023]
Abstract
Jumonji-C domain-containing protein 5 (JMJD5) is a 2-oxoglutarate (2OG)-dependent oxygenase that plays important roles in development, circadian rhythm, and cancer through unclear mechanisms. JMJD5 has been reported to have activity as a histone protease, as an Nε-methyl lysine demethylase, and as an arginine residue hydroxylase. Small-molecule JMJD5-selective inhibitors will be useful for investigating its (patho)physiological roles. Following the observation that the broad-spectrum 2OG oxygenase inhibitor pyridine-2,4-dicarboxylic acid (2,4-PDCA) is a 2OG-competing JMJD5 inhibitor, we report that 5-aminoalkyl-substituted 2,4-PDCA derivatives are potent JMJD5 inhibitors manifesting selectivity for JMJD5 over other human 2OG oxygenases. Crystallographic analyses with five inhibitors imply induced fit binding and reveal that the 2,4-PDCA C5 substituent orients into the JMJD5 substrate-binding pocket. Cellular studies indicate that the lead compounds display similar phenotypes as reported for clinically observed JMJD5 variants, which have a reduced catalytic activity compared to wild-type JMJD5.
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Affiliation(s)
- Lennart Brewitz
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.
| | - Yu Nakashima
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.
| | - Sonia K. Piasecka
- Institute
of Cancer and Genomic Sciences, University
of Birmingham, Edgbaston, B15 2TT Birmingham, U.K.
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.
| | - Sally C. Fletcher
- Institute
of Cancer and Genomic Sciences, University
of Birmingham, Edgbaston, B15 2TT Birmingham, U.K.
| | - Anthony Tumber
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.
| | - Thomas P. Corner
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.
| | - Tristan J. Kennedy
- Institute
of Cancer and Genomic Sciences, University
of Birmingham, Edgbaston, B15 2TT Birmingham, U.K.
| | - Giorgia Fiorini
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.
| | - Armin Thalhammer
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.
| | - Kirsten E. Christensen
- Chemical
Crystallography, Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.
| | - Mathew L. Coleman
- Institute
of Cancer and Genomic Sciences, University
of Birmingham, Edgbaston, B15 2TT Birmingham, U.K.
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.
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6
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Tumber A, Salah E, Brewitz L, Corner TP, Schofield CJ. Kinetic and inhibition studies on human Jumonji-C (JmjC) domain-containing protein 5. RSC Chem Biol 2023; 4:399-413. [PMID: 37292060 PMCID: PMC10246557 DOI: 10.1039/d2cb00249c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/19/2023] [Indexed: 06/10/2023] Open
Abstract
Jumonji-C (JmjC) domain-containing protein 5 (JMJD5) is a human 2-oxoglutarate (2OG) and Fe(ii)-dependent oxygenase which catalyses the post-translational C3 hydroxylation of arginyl-residues and which is linked to the circadian rhythm and to cancer biology through as yet unidentified mechanisms. We report robust solid phase extraction coupled to mass spectrometry (SPE-MS)-based JMJD5 assays which enable kinetic and high-throughput inhibition studies. The kinetic studies reveal that some synthetic 2OG derivatives, notably including a 2OG derivative with a cyclic carbon backbone (i.e. (1R)-3-(carboxycarbonyl)cyclopentane-1-carboxylic acid), are efficient alternative cosubstrates of JMJD5 and of factor inhibiting hypoxia-inducible transcription factor HIF-α (FIH), but not of the Jumonji-C (JmjC) histone Nε-methyl lysine demethylase KDM4E, apparently reflecting the closer structural similarity of JMJD5 and FIH. The JMJD5 inhibition assays were validated by investigating the effect of reported 2OG oxygenase inhibitors on JMJD5 catalysis; the results reveal that broad-spectrum 2OG oxygenase inhibitors are also efficient JMJD5 inhibitors (e.g. N-oxalylglycine, pyridine-2,4-dicarboxylic acid, ebselen) whereas most 2OG oxygenase inhibitors that are in clinical use (e.g. roxadustat) do not inhibit JMJD5. The SPE-MS assays will help enable the development of efficient and selective JMJD5 inhibitors for investigating the biochemical functions of JMJD5 in cellular studies.
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Affiliation(s)
- Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Thomas P Corner
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
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7
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Miura T, Malla TR, Owen CD, Tumber A, Brewitz L, McDonough MA, Salah E, Terasaka N, Katoh T, Lukacik P, Strain-Damerell C, Mikolajek H, Walsh MA, Kawamura A, Schofield CJ, Suga H. In vitro selection of macrocyclic peptide inhibitors containing cyclic γ 2,4-amino acids targeting the SARS-CoV-2 main protease. Nat Chem 2023:10.1038/s41557-023-01205-1. [PMID: 37217786 DOI: 10.1038/s41557-023-01205-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/14/2023] [Indexed: 05/24/2023]
Abstract
γ-Amino acids can play important roles in the biological activities of natural products; however, the ribosomal incorporation of γ-amino acids into peptides is challenging. Here we report how a selection campaign employing a non-canonical peptide library containing cyclic γ2,4-amino acids resulted in the discovery of very potent inhibitors of the SARS-CoV-2 main protease (Mpro). Two kinds of cyclic γ2,4-amino acids, cis-3-aminocyclobutane carboxylic acid (γ1) and (1R,3S)-3-aminocyclopentane carboxylic acid (γ2), were ribosomally introduced into a library of thioether-macrocyclic peptides. One resultant potent Mpro inhibitor (half-maximal inhibitory concentration = 50 nM), GM4, comprising 13 residues with γ1 at the fourth position, manifests a 5.2 nM dissociation constant. An Mpro:GM4 complex crystal structure reveals the intact inhibitor spans the substrate binding cleft. The γ1 interacts with the S1' catalytic subsite and contributes to a 12-fold increase in proteolytic stability compared to its alanine-substituted variant. Knowledge of interactions between GM4 and Mpro enabled production of a variant with a 5-fold increase in potency.
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Affiliation(s)
- Takashi Miura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tika R Malla
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - C David Owen
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Anthony Tumber
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Lennart Brewitz
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Michael A McDonough
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Eidarus Salah
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Naohiro Terasaka
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Petra Lukacik
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Claire Strain-Damerell
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Halina Mikolajek
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Martin A Walsh
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Akane Kawamura
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
- Chemistry - School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher J Schofield
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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8
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Bonnici J, Oueini R, Salah E, Johansson C, Schofield CJ, Kawamura A. The catalytic domains of all human KDM5 JmjC demethylases catalyse N-methyl arginine demethylation. FEBS Lett 2023; 597:933-946. [PMID: 36700827 PMCID: PMC10952680 DOI: 10.1002/1873-3468.14586] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/13/2022] [Accepted: 12/28/2022] [Indexed: 01/27/2023]
Abstract
The demethylation of Nε -methyllysine residues on histones by Jumonji-C lysine demethylases (JmjC-KDMs) has been established. A subset of JmjC-KDMs has also been reported to have Nω -methylarginine residue demethylase (RDM) activity. Here, we describe biochemical screening studies, showing that the catalytic domains of all human KDM5s (KDM5A-KDM5D), KDM4E and, to a lesser extent, KDM4A/D, have both KDM and RDM activities with histone peptides. Ras GTPase-activating protein-binding protein 1 peptides were shown to be RDM substrates for KDM5C/D. No RDM activity was observed with KDM1A and the other JmjC-KDMs tested. The results highlight the potential of JmjC-KDMs to catalyse reactions other than Nε -methyllysine demethylation. Although our study is limited to peptide fragments, the results should help guide biological studies investigating JmjC functions.
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Affiliation(s)
- Joanna Bonnici
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
- Chemistry – School of Natural and Environmental SciencesNewcastle UniversityUK
| | - Razanne Oueini
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
| | - Catrine Johansson
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
- Botnar Research Centre, NIHR Oxford Biomedical Research UnitUniversity of OxfordUK
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
- Chemistry – School of Natural and Environmental SciencesNewcastle UniversityUK
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9
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Türkmen VA, Hintzen JCJ, Tumber A, Moesgaard L, Salah E, Kongsted J, Schofield CJ, Mecinović J. Substrate selectivity and inhibition of histidine JmjC hydroxylases MINA53 and NO66. RSC Chem Biol 2023; 4:235-243. [PMID: 36908702 PMCID: PMC9994133 DOI: 10.1039/d2cb00182a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/12/2023] [Indexed: 01/15/2023] Open
Abstract
Non-haem Fe(ii) and 2-oxoglutarate (2OG) dependent oxygenases catalyse oxidation of multiple proteins in organisms ranging from bacteria to humans. We describe studies on the substrate selectivity and inhibition of the human ribosomal oxygenases (ROX) MINA53 and NO66, members of the JmjC 2OG oxygenase subfamily, which catalyse C-3 hydroxylation of histidine residues in Rpl27a and Rpl8, respectively. Assays with natural and unnatural histidine analogues incorporated into Rpl peptides provide evidence that MINA53 and NO66 have narrow substrate selectivities compared to some other human JmjC hydroxylases, including factor inhibiting HIF and JMJD6. Notably, the results of inhibition assays with Rpl peptides containing histidine analogues with acyclic side chains, including Asn, Gln and homoGln, suggest the activities of MINA53/NO66, and by implication related 2OG dependent protein hydroxylases/demethylases, might be regulated in vivo by competition with non-oxidised proteins/peptides. The inhibition results also provide avenues for development of inhibitors selective for MINA53 and NO66.
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Affiliation(s)
- Vildan A Türkmen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
| | - Jordi C J Hintzen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
| | - Anthony Tumber
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road OX1 3TA Oxford UK
| | - Laust Moesgaard
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
| | - Eidarus Salah
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road OX1 3TA Oxford UK
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
| | - Christopher J Schofield
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road OX1 3TA Oxford UK
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
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10
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Brewitz L, Dumjahn L, Zhao Y, Owen CD, Laidlaw SM, Malla TR, Nguyen D, Lukacik P, Salah E, Crawshaw AD, Warren AJ, Trincao J, Strain-Damerell C, Carroll MW, Walsh MA, Schofield CJ. Alkyne Derivatives of SARS-CoV-2 Main Protease Inhibitors Including Nirmatrelvir Inhibit by Reacting Covalently with the Nucleophilic Cysteine. J Med Chem 2023; 66:2663-2680. [PMID: 36757959 PMCID: PMC9924091 DOI: 10.1021/acs.jmedchem.2c01627] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Indexed: 02/10/2023]
Abstract
Nirmatrelvir (PF-07321332) is a nitrile-bearing small-molecule inhibitor that, in combination with ritonavir, is used to treat infections by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Nirmatrelvir interrupts the viral life cycle by inhibiting the SARS-CoV-2 main protease (Mpro), which is essential for processing viral polyproteins into functional nonstructural proteins. We report studies which reveal that derivatives of nirmatrelvir and other Mpro inhibitors with a nonactivated terminal alkyne group positioned similarly to the electrophilic nitrile of nirmatrelvir can efficiently inhibit isolated Mpro and SARS-CoV-2 replication in cells. Mass spectrometric and crystallographic evidence shows that the alkyne derivatives inhibit Mpro by apparent irreversible covalent reactions with the active site cysteine (Cys145), while the analogous nitriles react reversibly. The results highlight the potential for irreversible covalent inhibition of Mpro and other nucleophilic cysteine proteases by alkynes, which, in contrast to nitriles, can be functionalized at their terminal position to optimize inhibition and selectivity, as well as pharmacodynamic and pharmacokinetic properties.
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Affiliation(s)
- Lennart Brewitz
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Leo Dumjahn
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Yilin Zhao
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - C. David Owen
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research
Complex at Harwell, Harwell Science and
Innovation Campus, Didcot OX11 0FA, United
Kingdom
| | - Stephen M. Laidlaw
- Wellcome
Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Tika R. Malla
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Dung Nguyen
- Wellcome
Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Petra Lukacik
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research
Complex at Harwell, Harwell Science and
Innovation Campus, Didcot OX11 0FA, United
Kingdom
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Adam D. Crawshaw
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Anna J. Warren
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Jose Trincao
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Claire Strain-Damerell
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research
Complex at Harwell, Harwell Science and
Innovation Campus, Didcot OX11 0FA, United
Kingdom
| | - Miles W. Carroll
- Wellcome
Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Martin A. Walsh
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research
Complex at Harwell, Harwell Science and
Innovation Campus, Didcot OX11 0FA, United
Kingdom
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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11
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John T, Pires E, Hester SS, Salah E, Hopkinson RJ, Schofield CJ. Formaldehyde reacts with N-terminal proline residues to give bicyclic aminals. Commun Chem 2023; 6:12. [PMID: 36698022 PMCID: PMC9839752 DOI: 10.1038/s42004-022-00801-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023] Open
Abstract
Formaldehyde (HCHO) is a potent electrophile that is toxic above threshold levels, but which is also produced in the nuclei of eukaryotic cells by demethylases. We report studies with the four canonical human histones revealing that histone H2B reacts with HCHO, including as generated by a histone demethylase, to give a stable product. NMR studies show that HCHO reacts with the N-terminal proline and associated amide of H2B to give a 5,5-bicyclic aminal that is relatively stable to competition with HCHO scavengers. While the roles of histone modification by this reaction require further investigation, we demonstrated the potential of N-terminal aminal formation to modulate protein function by conducting biochemical and cellular studies on the effects of HCHO on catalysis by 4-oxalocrotonate tautomerase, which employs a nucleophilic N-terminal proline. The results suggest that reactions of N-terminal residues with HCHO and other aldehydes have potential to alter protein function.
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Affiliation(s)
- Tobias John
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Elisabete Pires
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Svenja S Hester
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Eidarus Salah
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Richard J Hopkinson
- Leicester Institute for Structural and Chemical Biology and School of Chemistry, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7RH, UK.
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12
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Belle R, Kamps JJAG, Poater J, Kumar K, Pieters BJGE, Salah E, Claridge TDW, Paton RS, Bickelhaupt FM, Kawamura A, Schofield CJ, Mecinović J. Reading and erasing of the phosphonium analogue of trimethyllysine by epigenetic proteins. Commun Chem 2022; 5:10.1038/s42004-022-00640-4. [PMID: 36071790 PMCID: PMC7613515 DOI: 10.1038/s42004-022-00640-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/03/2022] [Indexed: 01/27/2023] Open
Abstract
N ε-Methylation of lysine residues in histones plays an essential role in the regulation of eukaryotic transcription. The 'highest' methylation mark, N ε-trimethyllysine, is specifically recognised by N ε-trimethyllysine binding 'reader' domains, and undergoes demethylation, as catalysed by 2-oxoglutarate dependent JmjC oxygenases. We report studies on the recognition of the closest positively charged N ε-trimethyllysine analogue, i.e. its trimethylphosphonium derivative (KPme3), by N ε-trimethyllysine histone binding proteins and Nε-trimethyllysine demethylases. Calorimetric and computational studies with histone binding proteins reveal that H3KP4me3 binds more tightly than the natural H3K4me3 substrate, though the relative differences in binding affinity vary. Studies with JmjC demethylases show that some, but not all, of them can accept the phosphonium analogue of their natural substrates and that the methylation state selectivity can be changed by substitution of nitrogen for phosphorus. The combined results reveal that very subtle changes, e.g. substitution of nitrogen for phosphorus, can substantially affect interactions between ligand and reader domains / demethylases, knowledge that we hope will inspire the development of highly selective small molecules modulating their activity.
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Affiliation(s)
- Roman Belle
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA UK
- Chemistry—School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Jos J. A. G. Kamps
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA UK
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jordi Poater
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Kiran Kumar
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA UK
| | - Bas J. G. E. Pieters
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Eidarus Salah
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA UK
| | - Timothy D. W. Claridge
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA UK
| | - Robert S. Paton
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA UK
| | - F. Matthias Bickelhaupt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Akane Kawamura
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA UK
- Chemistry—School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Christopher J. Schofield
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA UK
| | - Jasmin Mecinović
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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13
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Hanke T, Mathea S, Woortman J, Salah E, Berger BT, Tumber A, Kashima R, Hata A, Kuster B, Müller S, Knapp S. Development and Characterization of Type I, Type II, and Type III LIM-Kinase Chemical Probes. J Med Chem 2022; 65:13264-13287. [PMID: 36136092 DOI: 10.1021/acs.jmedchem.2c01106] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
LIMKs are important regulators of actin and microtubule dynamics, and they play essential roles in many cellular processes. Deregulation of LIMKs has been linked to the development of diverse diseases, including cancers and cognitive disabilities, but well-characterized inhibitors known as chemical probes are still lacking. Here, we report the characterization of three highly selective LIMK1/2 inhibitors covering all canonical binding modes (type I/II/III) and the structure-based design of the type II/III inhibitors. Characterization of these chemical probes revealed a low nanomolar affinity for LIMK1/2, and all inhibitors 1 (LIMKi3; type I), 48 (TH470; type II), and 15 (TH257; type III) showed excellent selectivity in a comprehensive scanMAX kinase selectivity panel. Phosphoproteomics revealed remarkable differences between type I and type II inhibitors compared with the allosteric inhibitor 15. In phenotypic assays such as neurite outgrowth models of fragile X-chromosome, 15 showed promising activity, suggesting the potential application of allosteric LIMK inhibitors treating this orphan disease.
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Affiliation(s)
- Thomas Hanke
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Sebastian Mathea
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Julia Woortman
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Eidarus Salah
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Benedict-Tilman Berger
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Anthony Tumber
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Risa Kashima
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94143, United States
| | - Akiko Hata
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94143, United States
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), D-85354 Freising, Germany.,German Translational Cancer Network (DKTK), Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Susanne Müller
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany.,German Translational Cancer Network (DKTK), Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
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14
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Cockman ME, Sugimoto Y, Pegg HB, Masson N, Salah E, Tumber A, Flynn HR, Kirkpatrick JM, Schofield CJ, Ratcliffe PJ. Widespread hydroxylation of unstructured lysine-rich protein domains by JMJD6. Proc Natl Acad Sci U S A 2022; 119:e2201483119. [PMID: 35930668 PMCID: PMC9371714 DOI: 10.1073/pnas.2201483119] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/24/2022] [Indexed: 11/18/2022] Open
Abstract
The Jumonji domain-containing protein JMJD6 is a 2-oxoglutarate-dependent dioxygenase associated with a broad range of biological functions. Cellular studies have implicated the enzyme in chromatin biology, transcription, DNA repair, mRNA splicing, and cotranscriptional processing. Although not all studies agree, JMJD6 has been reported to catalyze both hydroxylation of lysine residues and demethylation of arginine residues. However, despite extensive study and indirect evidence for JMJD6 catalysis in many cellular processes, direct assignment of JMJD6 catalytic substrates has been limited. Examination of a reported site of proline hydroxylation within a lysine-rich region of the tandem bromodomain protein BRD4 led us to conclude that hydroxylation was in fact on lysine and catalyzed by JMJD6. This prompted a wider search for JMJD6-catalyzed protein modifications deploying mass spectrometric methods designed to improve the analysis of such lysine-rich regions. Using lysine derivatization with propionic anhydride to improve the analysis of tryptic peptides and nontryptic proteolysis, we report 150 sites of JMJD6-catalyzed lysine hydroxylation on 48 protein substrates, including 19 sites of hydroxylation on BRD4. Most hydroxylations were within lysine-rich regions that are predicted to be unstructured; in some, multiple modifications were observed on adjacent lysine residues. Almost all of the JMJD6 substrates defined in these studies have been associated with membraneless organelle formation. Given the reported roles of lysine-rich regions in subcellular partitioning by liquid-liquid phase separation, our findings raise the possibility that JMJD6 may play a role in regulating such processes in response to stresses, including hypoxia.
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Affiliation(s)
- Matthew E. Cockman
- Hypoxia Biology Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Yoichiro Sugimoto
- Hypoxia Biology Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Hamish B. Pegg
- Hypoxia Biology Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Norma Masson
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Helen R. Flynn
- Hypoxia Biology Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Joanna M. Kirkpatrick
- Hypoxia Biology Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Peter J. Ratcliffe
- Hypoxia Biology Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
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15
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Malla TR, Brewitz L, Muntean DG, Aslam H, Owen CD, Salah E, Tumber A, Lukacik P, Strain-Damerell C, Mikolajek H, Walsh MA, Schofield CJ. Penicillin Derivatives Inhibit the SARS-CoV-2 Main Protease by Reaction with Its Nucleophilic Cysteine. J Med Chem 2022; 65:7682-7696. [PMID: 35549342 PMCID: PMC9115881 DOI: 10.1021/acs.jmedchem.1c02214] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 12/26/2021] [Indexed: 12/05/2022]
Abstract
The SARS-CoV-2 main protease (Mpro) is a medicinal chemistry target for COVID-19 treatment. Given the clinical efficacy of β-lactams as inhibitors of bacterial nucleophilic enzymes, they are of interest as inhibitors of viral nucleophilic serine and cysteine proteases. We describe the synthesis of penicillin derivatives which are potent Mpro inhibitors and investigate their mechanism of inhibition using mass spectrometric and crystallographic analyses. The results suggest that β-lactams have considerable potential as Mpro inhibitors via a mechanism involving reaction with the nucleophilic cysteine to form a stable acyl-enzyme complex as shown by crystallographic analysis. The results highlight the potential for inhibition of viral proteases employing nucleophilic catalysis by β-lactams and related acylating agents.
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Affiliation(s)
- Tika R. Malla
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Lennart Brewitz
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Dorian-Gabriel Muntean
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Hiba Aslam
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - C. David Owen
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Anthony Tumber
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Petra Lukacik
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Claire Strain-Damerell
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Halina Mikolajek
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Martin A. Walsh
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
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16
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Thun‐Hohenstein STD, Suits TF, Malla TR, Tumber A, Brewitz L, Choudhry H, Salah E, Schofield CJ. Structure-Activity Studies Reveal Scope for Optimisation of Ebselen-Type Inhibition of SARS-CoV-2 Main Protease. ChemMedChem 2022; 17:e202100582. [PMID: 34850566 PMCID: PMC9015279 DOI: 10.1002/cmdc.202100582] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Indexed: 11/08/2022]
Abstract
The reactive organoselenium compound ebselen is being investigated for treatment of coronavirus disease 2019 (COVID-19) and other diseases. We report structure-activity studies on sulfur analogues of ebselen with the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro ), employing turnover and protein-observed mass spectrometry-based assays. The results reveal scope for optimisation of ebselen/ebselen derivative- mediated inhibition of Mpro , particularly with respect to improved selectivity.
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Affiliation(s)
- Siegfried T. D. Thun‐Hohenstein
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
| | - Timothy F. Suits
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
| | - Tika R. Malla
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
| | - Anthony Tumber
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
| | - Lennart Brewitz
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
| | - Hani Choudhry
- Department of BiochemistryCenter for Artificial Intelligence in Precision MedicinesKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Eidarus Salah
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
| | - Christopher J. Schofield
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
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17
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Nowak R, Tumber A, Hendrix E, Ansari MS, Sabatino M, Antonini L, Andrijes R, Salah E, Mautone N, Pellegrini FR, Simelis K, Kawamura A, Johansson C, Passeri D, Pellicciari R, Ciogli A, Del Bufalo D, Ragno R, Coleman ML, Trisciuoglio D, Mai A, Oppermann U, Schofield CJ, Rotili D. First-in-Class Inhibitors of the Ribosomal Oxygenase MINA53. J Med Chem 2021; 64:17031-17050. [PMID: 34843649 PMCID: PMC8667043 DOI: 10.1021/acs.jmedchem.1c00605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 04/01/2021] [Indexed: 01/05/2023]
Abstract
MINA53 is a JmjC domain 2-oxoglutarate-dependent oxygenase that catalyzes ribosomal hydroxylation and is a target of the oncogenic transcription factor c-MYC. Despite its anticancer target potential, no small-molecule MINA53 inhibitors are reported. Using ribosomal substrate fragments, we developed mass spectrometry assays for MINA53 and the related oxygenase NO66. These assays enabled the identification of 2-(aryl)alkylthio-3,4-dihydro-4-oxoypyrimidine-5-carboxylic acids as potent MINA53 inhibitors, with selectivity over NO66 and other JmjC oxygenases. Crystallographic studies with the JmjC demethylase KDM5B revealed active site binding but without direct metal chelation; however, molecular modeling investigations indicated that the inhibitors bind to MINA53 by directly interacting with the iron cofactor. The MINA53 inhibitors manifest evidence for target engagement and selectivity for MINA53 over KDM4-6. The MINA53 inhibitors show antiproliferative activity with solid cancer lines and sensitize cancer cells to conventional chemotherapy, suggesting that further work investigating their potential in combination therapies is warranted.
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Affiliation(s)
- Radosław
P. Nowak
- Botnar
Research Centre, Nuffield Orthopaedic Centre, University of Oxford, Headington OX3 7LD, U.K.
| | - Anthony Tumber
- Botnar
Research Centre, Nuffield Orthopaedic Centre, University of Oxford, Headington OX3 7LD, U.K.
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, 12, Mansfield Road, University of Oxford, Oxford OX1 3TA, U.K.
| | - Eline Hendrix
- Institute
of Cancer and Genomic Sciences, University
of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Mohammad Salik
Zeya Ansari
- Institute
of Molecular Biology and Pathology (IMBP), National Research Council
(CNR) c/o Department of Biology and Biotechnology “Charles
Darwin” Sapienza University of Rome, Via degli Apuli 4, Rome 00185, Italy
| | - Manuela Sabatino
- Rome
Center for Molecular Design, Department of Chemistry and Technology
of Drugs, ″Sapienza″ University
of Rome, Piazzale Aldo
Moro 5, Rome 00185, Italy
| | - Lorenzo Antonini
- Rome
Center for Molecular Design, Department of Chemistry and Technology
of Drugs, ″Sapienza″ University
of Rome, Piazzale Aldo
Moro 5, Rome 00185, Italy
| | - Regina Andrijes
- Institute
of Cancer and Genomic Sciences, University
of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, 12, Mansfield Road, University of Oxford, Oxford OX1 3TA, U.K.
| | - Nicola Mautone
- Department
of Chemistry and Technology of Drugs, ″Sapienza″
University of Rome, Piazzale
Aldo Moro 5, Rome 00185, Italy
| | - Francesca Romana Pellegrini
- Institute
of Molecular Biology and Pathology (IMBP), National Research Council
(CNR) c/o Department of Biology and Biotechnology “Charles
Darwin” Sapienza University of Rome, Via degli Apuli 4, Rome 00185, Italy
| | - Klemensas Simelis
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, 12, Mansfield Road, University of Oxford, Oxford OX1 3TA, U.K.
| | - Akane Kawamura
- Chemistry
- School of Natural and Environmental Sciences, Newcastle University, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Catrine Johansson
- Botnar
Research Centre, Nuffield Orthopaedic Centre, University of Oxford, Headington OX3 7LD, U.K.
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, 12, Mansfield Road, University of Oxford, Oxford OX1 3TA, U.K.
| | - Daniela Passeri
- TES
Pharma S.r.l. Via P. Togliatti 20, Corciano, Perugia 06073, Italy
| | | | - Alessia Ciogli
- Department
of Chemistry and Technology of Drugs, ″Sapienza″
University of Rome, Piazzale
Aldo Moro 5, Rome 00185, Italy
| | - Donatella Del Bufalo
- Preclinical
Models and New Therapeutic Agents Unit, IRCCS-Regina Elena National Cancer Institute, Via Elio Chianesi 53, Rome 00144, Italy
| | - Rino Ragno
- Rome
Center for Molecular Design, Department of Chemistry and Technology
of Drugs, ″Sapienza″ University
of Rome, Piazzale Aldo
Moro 5, Rome 00185, Italy
| | - Mathew L. Coleman
- Institute
of Cancer and Genomic Sciences, University
of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Daniela Trisciuoglio
- Institute
of Molecular Biology and Pathology (IMBP), National Research Council
(CNR) c/o Department of Biology and Biotechnology “Charles
Darwin” Sapienza University of Rome, Via degli Apuli 4, Rome 00185, Italy
| | - Antonello Mai
- Department
of Chemistry and Technology of Drugs, ″Sapienza″
University of Rome, Piazzale
Aldo Moro 5, Rome 00185, Italy
| | - Udo Oppermann
- Botnar
Research Centre, Nuffield Orthopaedic Centre, University of Oxford, Headington OX3 7LD, U.K.
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, 12, Mansfield Road, University of Oxford, Oxford OX1 3TA, U.K.
| | - Dante Rotili
- Department
of Chemistry and Technology of Drugs, ″Sapienza″
University of Rome, Piazzale
Aldo Moro 5, Rome 00185, Italy
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18
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Shishodia S, Demetriades M, Zhang D, Tam NY, Maheswaran P, Clunie-O’Connor C, Tumber A, Leung IKH, Ng YM, Leissing TM, El-Sagheer AH, Salah E, Brown T, Aik WS, McDonough MA, Schofield CJ. Structure-Based Design of Selective Fat Mass and Obesity Associated Protein (FTO) Inhibitors. J Med Chem 2021; 64:16609-16625. [PMID: 34762429 PMCID: PMC8631710 DOI: 10.1021/acs.jmedchem.1c01204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 07/06/2021] [Indexed: 01/09/2023]
Abstract
FTO catalyzes the Fe(II) and 2-oxoglutarate (2OG)-dependent modification of nucleic acids, including the demethylation of N6-methyladenosine (m6A) in mRNA. FTO is a proposed target for anti-cancer therapy. Using information from crystal structures of FTO in complex with 2OG and substrate mimics, we designed and synthesized two series of FTO inhibitors, which were characterized by turnover and binding assays, and by X-ray crystallography with FTO and the related bacterial enzyme AlkB. A potent inhibitor employing binding interactions spanning the FTO 2OG and substrate binding sites was identified. Selectivity over other clinically targeted 2OG oxygenases was demonstrated, including with respect to the hypoxia-inducible factor prolyl and asparaginyl hydroxylases (PHD2 and FIH) and selected JmjC histone demethylases (KDMs). The results illustrate how structure-based design can enable the identification of potent and selective 2OG oxygenase inhibitors and will be useful for the development of FTO inhibitors for use in vivo.
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Affiliation(s)
- Shifali Shishodia
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Marina Demetriades
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Dong Zhang
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Nok Yin Tam
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong
SAR 999077, China
| | - Pratheesh Maheswaran
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Caitlin Clunie-O’Connor
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Anthony Tumber
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Ivanhoe K. H. Leung
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Yi Min Ng
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong
SAR 999077, China
| | - Thomas M. Leissing
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Afaf H. El-Sagheer
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
- Chemistry
Branch Department of Science and Mathematics, Suez University, Suez 43721, Egypt
| | - Eidarus Salah
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Tom Brown
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Wei Shen Aik
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong
SAR 999077, China
| | - Michael A. McDonough
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Christopher J. Schofield
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
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19
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Nakashima Y, Brewitz L, Tumber A, Salah E, Schofield CJ. 2-Oxoglutarate derivatives can selectively enhance or inhibit the activity of human oxygenases. Nat Commun 2021; 12:6478. [PMID: 34759269 PMCID: PMC8580996 DOI: 10.1038/s41467-021-26673-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/12/2021] [Indexed: 01/18/2023] Open
Abstract
2-Oxoglutarate (2OG) oxygenases are validated agrochemical and human drug targets. The potential for modulating their activity with 2OG derivatives has not been explored, possibly due to concerns regarding selectivity. We report proof-of-principle studies demonstrating selective enhancement or inhibition of 2OG oxygenase activity by 2-oxo acids. The human 2OG oxygenases studied, factor inhibiting hypoxia-inducible transcription factor HIF-α (FIH) and aspartate/asparagine-β-hydroxylase (AspH), catalyze C3 hydroxylations of Asp/Asn-residues. Of 35 tested 2OG derivatives, 10 enhance and 17 inhibit FIH activity. Comparison with results for AspH reveals that 2OG derivatives selectively enhance or inhibit FIH or AspH. Comparison of FIH structures complexed with 2OG derivatives to those for AspH provides insight into the basis of the observed selectivity. 2-Oxo acid derivatives have potential as drugs, for use in biomimetic catalysis, and in functional studies. The results suggest that the in vivo activity of 2OG oxygenases may be regulated by natural 2-oxo acids other than 2OG.
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Affiliation(s)
- Yu Nakashima
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
- Institute of Natural Medicine, University of Toyama, 2630-Sugitani, 930-0194, Toyama, Japan
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK.
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20
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Chan HTH, Moesser MA, Walters RK, Malla TR, Twidale RM, John T, Deeks HM, Johnston-Wood T, Mikhailov V, Sessions RB, Dawson W, Salah E, Lukacik P, Strain-Damerell C, Owen CD, Nakajima T, Świderek K, Lodola A, Moliner V, Glowacki DR, Spencer J, Walsh MA, Schofield CJ, Genovese L, Shoemark DK, Mulholland AJ, Duarte F, Morris GM. Discovery of SARS-CoV-2 M pro peptide inhibitors from modelling substrate and ligand binding. Chem Sci 2021; 12:13686-13703. [PMID: 34760153 PMCID: PMC8549791 DOI: 10.1039/d1sc03628a] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/05/2021] [Indexed: 12/22/2022] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is central to viral maturation and is a promising drug target, but little is known about structural aspects of how it binds to its 11 natural cleavage sites. We used biophysical and crystallographic data and an array of biomolecular simulation techniques, including automated docking, molecular dynamics (MD) and interactive MD in virtual reality, QM/MM, and linear-scaling DFT, to investigate the molecular features underlying recognition of the natural Mpro substrates. We extensively analysed the subsite interactions of modelled 11-residue cleavage site peptides, crystallographic ligands, and docked COVID Moonshot-designed covalent inhibitors. Our modelling studies reveal remarkable consistency in the hydrogen bonding patterns of the natural Mpro substrates, particularly on the N-terminal side of the scissile bond. They highlight the critical role of interactions beyond the immediate active site in recognition and catalysis, in particular plasticity at the S2 site. Building on our initial Mpro-substrate models, we used predictive saturation variation scanning (PreSaVS) to design peptides with improved affinity. Non-denaturing mass spectrometry and other biophysical analyses confirm these new and effective 'peptibitors' inhibit Mpro competitively. Our combined results provide new insights and highlight opportunities for the development of Mpro inhibitors as anti-COVID-19 drugs.
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Affiliation(s)
- H T Henry Chan
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Marc A Moesser
- Department of Statistics, University of Oxford 24-29 St Giles' Oxford OX1 3LB UK
| | - Rebecca K Walters
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tika R Malla
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Rebecca M Twidale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tobias John
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Helen M Deeks
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tristan Johnston-Wood
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Victor Mikhailov
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building University Walk Bristol BS8 1TD UK
| | - William Dawson
- RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe Hyogo 650-0047 Japan
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Petra Lukacik
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Claire Strain-Damerell
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - C David Owen
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Takahito Nakajima
- RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe Hyogo 650-0047 Japan
| | - Katarzyna Świderek
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castello Spain
| | - Alessio Lodola
- Food and Drug Department, University of Parma Parco Area delle Scienze, 27/A 43124 Parma Italy
| | - Vicent Moliner
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castello Spain
| | - David R Glowacki
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - James Spencer
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Martin A Walsh
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Luigi Genovese
- Univ. Grenoble Alpes, CEA, IRIG-MEM-L_Sim 38000 Grenoble France
| | - Deborah K Shoemark
- School of Biochemistry, University of Bristol, Medical Sciences Building University Walk Bristol BS8 1TD UK
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Garrett M Morris
- Department of Statistics, University of Oxford 24-29 St Giles' Oxford OX1 3LB UK
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21
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Brewitz L, Nakashima Y, Tumber A, Salah E, Schofield CJ. Fluorinated derivatives of pyridine-2,4-dicarboxylate are potent inhibitors of human 2-oxoglutarate dependent oxygenases. J Fluor Chem 2021; 247:109804. [PMID: 34219804 PMCID: PMC8223498 DOI: 10.1016/j.jfluchem.2021.109804] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/30/2021] [Accepted: 05/01/2021] [Indexed: 01/21/2023]
Abstract
2-Oxoglutarate (2OG) oxygenases have important roles in human biology and are validated medicinal chemistry targets. Improving the selectivity profile of broad-spectrum 2OG oxygenase inhibitors may help enable the identification of selective inhibitors for use in functional assignment work. We report the synthesis of F- and CF3-substituted derivatives of the broad-spectrum 2OG oxygenase inhibitor pyridine-2,4-dicarboxylate (2,4-PDCA). Their inhibition selectivity profile against selected functionally distinct human 2OG oxygenases was determined using mass spectrometry-based assays. F-substituted 2,4-PDCA derivatives efficiently inhibit the 2OG oxygenases aspartate/asparagine-β-hydroxylase (AspH) and the JmjC lysine-specific N ε-demethylase 4E (KDM4E); The F- and CF3-substituted 2,4-PDCA derivatives were all less efficient inhibitors of the tested 2OG oxygenases than 2,4-PDCA itself, except for the C5 F-substituted 2,4-PDCA derivative which inhibited AspH with a similar efficiency as 2,4-PDCA. Notably, the introduction of a F- or CF3-substituent at the C5 position of 2,4-PDCA results in a substantial increase in selectivity for AspH over KDM4E compared to 2,4-PDCA. Crystallographic studies inform on the structural basis of our observations, which exemplifies how a small change on a 2OG analogue can make a substantial difference in the potency of 2OG oxygenase inhibition.
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Affiliation(s)
- Lennart Brewitz
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom
| | - Yu Nakashima
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom
- Present address: Institute of Natural Medicine, University of Toyama, 2630-Sugitani, 930-0194, Toyama, Japan
| | - Anthony Tumber
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom
| | - Eidarus Salah
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom
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22
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Malla TR, Tumber A, John T, Brewitz L, Strain-Damerell C, Owen CD, Lukacik P, Chan HTH, Maheswaran P, Salah E, Duarte F, Yang H, Rao Z, Walsh MA, Schofield CJ. Mass spectrometry reveals potential of β-lactams as SARS-CoV-2 M pro inhibitors. Chem Commun (Camb) 2021; 57:1430-1433. [PMID: 33462575 PMCID: PMC8006714 DOI: 10.1039/d0cc06870e] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The main viral protease (Mpro) of SARS-CoV-2 is a nucleophilic cysteine hydrolase and a current target for anti-viral chemotherapy. We describe a high-throughput solid phase extraction coupled to mass spectrometry Mpro assay. The results reveal some β-lactams, including penicillin esters, are active site reacting Mpro inhibitors, thus highlighting the potential of acylating agents for Mpro inhibition.
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Affiliation(s)
- Tika R Malla
- Chemistry Research Laboratory, Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Tobias John
- Chemistry Research Laboratory, Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Claire Strain-Damerell
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK and Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0FA, UK
| | - C David Owen
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK and Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0FA, UK
| | - Petra Lukacik
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK and Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0FA, UK
| | - H T Henry Chan
- Chemistry Research Laboratory, Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Pratheesh Maheswaran
- Chemistry Research Laboratory, Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Martin A Walsh
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK and Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0FA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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23
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Van Hout MC, Stöver H, Benamara K, Bauer P, Salah E. 90-90-90: catalysing the response to HIV by enhancing prison visibility in the Joint United Nations Programme on HIV and AIDS (UNAIDS) strategy beyond 2021. Public Health 2020; 190:e5-e6. [PMID: 33250154 DOI: 10.1016/j.puhe.2020.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 11/29/2022]
Affiliation(s)
- M C Van Hout
- Public Health Institute, Liverpool John Moores University, United Kingdom.
| | - H Stöver
- Faculty of Health and Social Work, Frankfurt University of Applied Sciences, Germany.
| | - K Benamara
- HIV/AIDS Section, United Nations Office on Drugs and Crime (UNODC), Austria.
| | - P Bauer
- HIV/AIDS Section, United Nations Office on Drugs and Crime (UNODC), Austria.
| | - E Salah
- HIV/AIDS Section, United Nations Office on Drugs and Crime (UNODC), Austria.
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24
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Salah E. Women’s health in prisons in Africa: prevalence and challenges to address HIV among women in prison in Africa. Eur J Public Health 2020. [DOI: 10.1093/eurpub/ckaa165.1367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
In Africa around 3.2% of the prison population is represented by women. People in prison are 5 times more likely to be living with HIV than adults in the general population. Moreover, women in prison have a higher HIV prevalence than men. The factors that lead to women becoming incarcerated are often also those that lead to their increased risk of acquiring HIV infection.
Their situation in prison is exacerbated by stigma and discrimination, gender-based violence and inequality. Women have limited access to health care in prison settings and are less likely to receive treatment than men. This is even more the case in Africa, where the precarious and sometimes inhuman prison conditions, render the health-related interventions addressing women health particularly challenging. Their specific health care needs, such as sexual and reproductive health care, treatment of infectious diseases including STIs, as well as nutrition and hygiene requirements, are often neglected. The limited access for women (and their children) to ante- and postnatal care, labour and delivery services and antiretroviral therapy also leads to infants born in prisons being at high risk of contracting HIV. Women in prison should be able to access gender-responsive health care services which are equivalent and of the same quality as those available in the community.
The presentation will present the latest available data on health status and HIV in particular among women in prison in Africa and will present the international standards in health interventions of women in prison.
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Affiliation(s)
- E Salah
- HIV/AIDS Section, United Nations Office on Drugs and Crime, Vienna, Austria
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25
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Brewitz L, Tumber A, Thalhammer A, Salah E, Christensen KE, Schofield CJ. Synthesis of Novel Pyridine-Carboxylates as Small-Molecule Inhibitors of Human Aspartate/Asparagine-β-Hydroxylase. ChemMedChem 2020; 15:1139-1149. [PMID: 32330361 PMCID: PMC7383925 DOI: 10.1002/cmdc.202000147] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Indexed: 12/19/2022]
Abstract
The human 2‐oxoglutarate (2OG)‐dependent oxygenase aspartate/asparagine‐β‐hydroxylase (AspH) is a potential medicinal chemistry target for anticancer therapy. AspH is present on the cell surface of invasive cancer cells and accepts epidermal growth factor‐like domain (EGFD) substrates with a noncanonical (i. e., Cys 1–2, 3–4, 5–6) disulfide pattern. We report a concise synthesis of C‐3‐substituted derivatives of pyridine‐2,4‐dicarboxylic acid (2,4‐PDCA) as 2OG competitors for use in SAR studies on AspH inhibition. AspH inhibition was assayed by using a mass spectrometry‐based assay with a stable thioether analogue of a natural EGFD AspH substrate. Certain C‐3‐substituted 2,4‐PDCA derivatives were potent AspH inhibitors, manifesting selectivity over some, but not all, other tested human 2OG oxygenases. The results raise questions about the use of pyridine‐carboxylate‐related 2OG analogues as selective functional probes for specific 2OG oxygenases, and should aid in the development of AspH inhibitors suitable for in vivo use.
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Affiliation(s)
- Lennart Brewitz
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Anthony Tumber
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Armin Thalhammer
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Eidarus Salah
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Kirsten E Christensen
- Chemical Crystallography Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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26
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Pinto-Fernández A, Davis S, Schofield AB, Scott HC, Zhang P, Salah E, Mathea S, Charles PD, Damianou A, Bond G, Fischer R, Kessler BM. Comprehensive Landscape of Active Deubiquitinating Enzymes Profiled by Advanced Chemoproteomics. Front Chem 2019; 7:592. [PMID: 31555637 PMCID: PMC6727631 DOI: 10.3389/fchem.2019.00592] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 08/09/2019] [Indexed: 12/11/2022] Open
Abstract
Enzymes that bind and process ubiquitin, a small 76-amino-acid protein, have been recognized as pharmacological targets in oncology, immunological disorders, and neurodegeneration. Mass spectrometry technology has now reached the capacity to cover the proteome with enough depth to interrogate entire biochemical pathways including those that contain DUBs and E3 ligase substrates. We have recently characterized the breast cancer cell (MCF7) deep proteome by detecting and quantifying ~10,000 proteins, and within this data set, we can detect endogenous expression of 65 deubiquitylating enzymes (DUBs), whereas matching transcriptomics detected 78 DUB mRNAs. Since enzyme activity provides another meaningful layer of information in addition to the expression levels, we have combined advanced mass spectrometry technology, pre-fractionation, and more potent/selective ubiquitin active-site probes with propargylic-based electrophiles to profile 74 DUBs including distinguishable isoforms for 5 DUBs in MCF7 crude extract material. Competition experiments with cysteine alkylating agents and pan-DUB inhibitors combined with probe labeling revealed the proportion of active cellular DUBs directly engaged with probes by label-free quantitative (LFQ) mass spectrometry. This demonstrated that USP13, 39, and 40 are non-reactive to probe, indicating restricted enzymatic activity under these cellular conditions. Our extended chemoproteomics workflow increases depth of covering the active DUBome, including isoform-specific resolution, and provides the framework for more comprehensive cell-based small-molecule DUB selectivity profiling.
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Affiliation(s)
- Adán Pinto-Fernández
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Simon Davis
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Abigail B Schofield
- University of Oxford, Oxford, United Kingdom.,Christ Church, University of Oxford, Oxford, United Kingdom
| | - Hannah C Scott
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ping Zhang
- University of Oxford, Oxford, United Kingdom.,Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Eidarus Salah
- University of Oxford, Oxford, United Kingdom.,Department of Chemistry, University of Oxford, Oxford, United Kingdom.,Structural Genomics Consortium (United Kingdom), Oxford, United Kingdom
| | - Sebastian Mathea
- Structural Genomics Consortium (United Kingdom), Oxford, United Kingdom.,Institute of Pharmaceutical Chemistry, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Philip D Charles
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andreas Damianou
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gareth Bond
- University of Oxford, Oxford, United Kingdom.,Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Roman Fischer
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt M Kessler
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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27
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Abstract
Protein kinases are major targets for the development of new medicines and play key roles in cellular signaling. The flexible nature of these proteins, posttranslational modifications, and the large size of some protein kinases pose a particular challenge obtaining homogeneous, active recombinant protein kinases suitable for functional or structural studies. Here we describe our expertise expressing protein kinases in two frequently used host systems: E. coli and insect cells using the baculovirus expression vector system. In particular, we will discuss and provide detailed methods on construct design, high-throughput cloning, parallel expression testing and scale up as well as purification and co-expression strategies leading to stable and homogeneous recombinant protein samples.
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Affiliation(s)
- Sebastian Mathea
- Target Discovery Institute and Structural Genomics Consortium, Oxford University, Oxford, UK
- Goethe-University Frankfurt, Institute of Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
- German Cancer Network (DKTK), Frankfurt am Main, Germany
- German Cancer Centre (DKFZ), Heidelberg, Germany
| | - Eidarus Salah
- Target Discovery Institute and Structural Genomics Consortium, Oxford University, Oxford, UK
| | - Stefan Knapp
- Target Discovery Institute and Structural Genomics Consortium, Oxford University, Oxford, UK.
- Goethe-University Frankfurt, Institute of Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Network (DKTK), Frankfurt am Main, Germany.
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28
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Suh JL, Watts B, Stuckey JI, Norris-Drouin JL, Cholensky SH, Dickson BM, An Y, Mathea S, Salah E, Knapp S, Khan A, Adams AT, Strahl BD, Sagum CA, Bedford MT, James LI, Kireev DB, Frye SV. Correction to “Quantitative Characterization of Bivalent Probes for a Dual Bromodomain Protein, Transcription Initiation Factor TFIID subunit 1”. Biochemistry 2018; 57:6806. [DOI: 10.1021/acs.biochem.8b01187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Hopkinson RJ, Langley GW, Belle R, Walport LJ, Dunne K, Münzel M, Salah E, Kawamura A, Claridge TDW, Schofield CJ. Human histone demethylase KDM6B can catalyse sequential oxidations. Chem Commun (Camb) 2018; 54:7975-7978. [PMID: 29961803 PMCID: PMC6044289 DOI: 10.1039/c8cc04057e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 06/06/2018] [Indexed: 12/12/2022]
Abstract
Jumonji domain-containing demethylases (JmjC-KDMs) catalyse demethylation of Nε-methylated lysines on histones and play important roles in gene regulation. We report selectivity studies on KDM6B (JMJD3), a disease-relevant JmjC-KDM, using synthetic lysine analogues. The results unexpectedly reveal that KDM6B accepts multiple Nε-alkylated lysine analogues, forming alcohol, aldehyde and carboxylic acid products.
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Affiliation(s)
- Richard J. Hopkinson
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
- Leicester Institute of Structural and Chemical Biology and Department of Chemistry
, University of Leicester
,
Lancaster Road
, Leicester
, LE1 7RH
, UK
.
| | - Gareth W. Langley
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
| | - Roman Belle
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
| | - Louise J. Walport
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
| | - Kate Dunne
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
- Radcliffe Department of Medicine
, Division of Cardiovascular Medicine
, BHF Centre of Research Excellence
, Wellcome Trust Centre for Human Genetics
,
Roosevelt Drive
, Oxford
, OX3 7BN
, UK
| | - Martin Münzel
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
| | - Eidarus Salah
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
| | - Akane Kawamura
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
- Radcliffe Department of Medicine
, Division of Cardiovascular Medicine
, BHF Centre of Research Excellence
, Wellcome Trust Centre for Human Genetics
,
Roosevelt Drive
, Oxford
, OX3 7BN
, UK
| | - Timothy D. W. Claridge
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
| | - Christopher J. Schofield
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
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30
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Suh JL, Watts B, Stuckey JI, Norris-Drouin JL, Cholensky SH, Dickson BM, An Y, Mathea S, Salah E, Knapp S, Khan A, Adams AT, Strahl BD, Sagum CA, Bedford MT, James LI, Kireev DB, Frye SV. Quantitative Characterization of Bivalent Probes for a Dual Bromodomain Protein, Transcription Initiation Factor TFIID Subunit 1. Biochemistry 2018; 57:2140-2149. [PMID: 29558110 DOI: 10.1021/acs.biochem.8b00150] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multivalent binding is an efficient means to enhance the affinity and specificity of chemical probes targeting multidomain proteins in order to study their function and role in disease. While the theory of multivalent binding is straightforward, physical and structural characterization of bivalent binding encounters multiple technical difficulties. We present a case study where a combination of experimental techniques and computational simulations was used to comprehensively characterize the binding and structure-affinity relationships for a series of Bromosporine-based bivalent bromodomain ligands with a bivalent protein, Transcription Initiation Factor TFIID subunit 1 (TAF1). Experimental techniques-Isothermal Titration Calorimetry, X-ray Crystallography, Circular Dichroism, Size Exclusion Chromatography-Multi-Angle Light Scattering, and Surface Plasmon Resonance-were used to determine structures, binding affinities, and kinetics of monovalent ligands and bivalent ligands with varying linker lengths. The experimental data for monomeric ligands were fed into explicit computational simulations, in which both ligand and protein species were present in a broad range of concentrations, and in up to a 100 s time regime, to match experimental conditions. These simulations provided accurate estimates for apparent affinities (in good agreement with experimental data), individual dissociation microconstants and other microscopic details for each type of protein-ligand complex. We conclude that the expected efficiency of bivalent ligands in a cellular context is difficult to estimate by a single technique in vitro, due to higher order associations favored at the concentrations used, and other complicating processes. Rather, a combination of structural, biophysical, and computational approaches should be utilized to estimate and characterize multivalent interactions.
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Affiliation(s)
- Junghyun L Suh
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Brian Watts
- Duke Human Vaccine Institute, Duke University School of Medicine , Duke University , Durham , North Carolina 27710 , United States
| | - Jacob I Stuckey
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States.,Constellation Pharmaceuticals , 215 First Street, Suite 200 , Cambridge , Massachusetts 02141 , United States
| | - Jacqueline L Norris-Drouin
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Stephanie H Cholensky
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Bradley M Dickson
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States.,Center for Epigenetics , Van Andel Research Institute , Grand Rapids , Michigan 49503 , United States
| | - Yi An
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Sebastian Mathea
- Nuffield Department of Medicine, Structural Genomics Consortium , Old Road Campus Research Building, Oxford University , Oxford , OX3 7DQ , United Kingdom.,German Cancer Centre (DKFZ), DKTK Consortium , 60438 Frankfurt am Main , Germany
| | - Eidarus Salah
- Nuffield Department of Medicine, Structural Genomics Consortium , Old Road Campus Research Building, Oxford University , Oxford , OX3 7DQ , United Kingdom
| | - Stefan Knapp
- Nuffield Department of Medicine, Structural Genomics Consortium , Old Road Campus Research Building, Oxford University , Oxford , OX3 7DQ , United Kingdom.,Institute of Pharmaceutical Chemistry and Buchmann Institute for Life Sciences (BMLS), Structure Genomics Consortium , Goethe-University Frankfurt , Max von Lauestrasse 9 , 60438 Frankfurt am Main , Germany
| | - Abid Khan
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center , University of North Carolina School of Medicine , Chapel Hill , North Carolina 27599 , United States
| | - Alexander T Adams
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center , University of North Carolina School of Medicine , Chapel Hill , North Carolina 27599 , United States
| | - Brian D Strahl
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center , University of North Carolina School of Medicine , Chapel Hill , North Carolina 27599 , United States
| | - Cari A Sagum
- Department of Epigenetics and Molecular Carcinogenesis , University of Texas MD Anderson Cancer Center , Smithville , Texas 78957 , United States
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis , University of Texas MD Anderson Cancer Center , Smithville , Texas 78957 , United States
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Dmitri B Kireev
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Stephen V Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
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31
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Essam-Eldin S, Salah E, Ahmed H, Elhalawani H, Abdel-Rahman O. Hematological toxicities following treatment of cancer patients with PARP inhibitors. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx668.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Affiliation(s)
- E. Salah
- Lecturer of Dermatology, Venereology & Andrology; Faculty of Medicine; Zagazig University; Zagazig Egypt
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33
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Borghetti P, Bonù M, Roca E, Salah E, Baiguini A, Pedretti S, Maddalo M, Buglione M, Magrini S. EP-1219: Concomitant radiotherapy and TKI in EGFR mutant or ALK positive stage IV non-small cell lung cancer. Radiother Oncol 2017. [DOI: 10.1016/s0167-8140(17)31654-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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34
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Miranda F, Mannion D, Liu S, Zheng Y, Mangala LS, Redondo C, Herrero-Gonzalez S, Xu R, Taylor C, Chedom DF, Carrami EM, Albukhari A, Jiang D, Pradeep S, Rodriguez-Aguayo C, Lopez-Berestein G, Salah E, Abdul Azeez KR, Elkins JM, Campo L, Myers KA, Klotz D, Bivona S, Dhar S, Bast RC, Saya H, Choi HG, Gray NS, Fischer R, Kessler BM, Yau C, Sood AK, Motohara T, Knapp S, Ahmed AA. Salt-Inducible Kinase 2 Couples Ovarian Cancer Cell Metabolism with Survival at the Adipocyte-Rich Metastatic Niche. Cancer Cell 2016; 30:273-289. [PMID: 27478041 DOI: 10.1016/j.ccell.2016.06.020] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 12/24/2015] [Accepted: 06/23/2016] [Indexed: 02/08/2023]
Abstract
The adipocyte-rich microenvironment forms a niche for ovarian cancer metastasis, but the mechanisms driving this process are incompletely understood. Here we show that salt-inducible kinase 2 (SIK2) is overexpressed in adipocyte-rich metastatic deposits compared with ovarian primary lesions. Overexpression of SIK2 in ovarian cancer cells promotes abdominal metastasis while SIK2 depletion prevents metastasis in vivo. Importantly, adipocytes induce calcium-dependent activation and autophosphorylation of SIK2. Activated SIK2 plays a dual role in augmenting AMPK-induced phosphorylation of acetyl-CoA carboxylase and in activating the PI3K/AKT pathway through p85α-S154 phosphorylation. These findings identify SIK2 at the apex of the adipocyte-induced signaling cascades in cancer cells and make a compelling case for targeting SIK2 for therapy in ovarian cancer.
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Affiliation(s)
- Fabrizio Miranda
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - David Mannion
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Shujuan Liu
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Yiyan Zheng
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Lingegowda S Mangala
- Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Center for RNAi and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Clara Redondo
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK; Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Sandra Herrero-Gonzalez
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Ruoyan Xu
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Charlotte Taylor
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Donatien Fotso Chedom
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Eli M Carrami
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Ashwag Albukhari
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK; Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21551, Saudi Arabia
| | - Dahai Jiang
- Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Center for RNAi and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Sunila Pradeep
- Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Cristian Rodriguez-Aguayo
- Center for RNAi and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Gabriel Lopez-Berestein
- Center for RNAi and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Eidarus Salah
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Kamal R Abdul Azeez
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Jonathan M Elkins
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Leticia Campo
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Kevin A Myers
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Daniel Klotz
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Serena Bivona
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Sunanda Dhar
- Department of Histopathology, Oxford University Hospitals, Oxford OX3 9DU, UK
| | - Robert C Bast
- Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Hideyuki Saya
- Division of Gene Regulation, Institute for Advanced Medical Research, School of Medicine, Keio University, Tokyo 160-8582, Japan
| | - Hwan Geun Choi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Nathanael S Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Benedikt M Kessler
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Christopher Yau
- Wellcome Trust Centre for Human Genetics, NIHR Biomedical Research Centre, Roosevelt Drive, Oxford OX3 7BN, UK; Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Anil K Sood
- Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Center for RNAi and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Takeshi Motohara
- Department of Obstetrics and Gynecology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Stefan Knapp
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK; Goethe-University Frankfurt, Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, Riedberg Campus, 60438 Frankfurt am Main, Germany
| | - Ahmed Ashour Ahmed
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK.
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35
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Mathea S, Abdul Azeez KR, Salah E, Tallant C, Wolfreys F, Konietzny R, Fischer R, Lou HJ, Brennan PE, Schnapp G, Pautsch A, Kessler BM, Turk BE, Knapp S. Structure of the Human Protein Kinase ZAK in Complex with Vemurafenib. ACS Chem Biol 2016; 11:1595-602. [PMID: 26999302 DOI: 10.1021/acschembio.6b00043] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The mixed lineage kinase ZAK is a key regulator of the MAPK pathway mediating cell survival and inflammatory response. ZAK is targeted by several clinically approved kinase inhibitors, and inhibition of ZAK has been reported to protect from doxorubicin-induced cardiomyopathy. On the other hand, unintended targeting of ZAK has been linked to severe adverse effects such as the development of cutaneous squamous cell carcinoma. Therefore, both specific inhibitors of ZAK, as well as anticancer drugs lacking off-target activity against ZAK, may provide therapeutic benefit. Here, we report the first crystal structure of ZAK in complex with the B-RAF inhibitor vemurafenib. The cocrystal structure displayed a number of ZAK-specific features including a highly distorted P loop conformation enabling rational inhibitor design. Positional scanning peptide library analysis revealed a unique substrate specificity of the ZAK kinase including unprecedented preferences for histidine residues at positions -1 and +2 relative to the phosphoacceptor site. In addition, we screened a library of clinical kinase inhibitors identifying several inhibitors that potently inhibit ZAK, demonstrating that this kinase is commonly mistargeted by currently used anticancer drugs.
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Affiliation(s)
- Sebastian Mathea
- Structural
Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX37DQ, United Kingdom
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Kamal R. Abdul Azeez
- Structural
Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX37DQ, United Kingdom
| | - Eidarus Salah
- Structural
Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX37DQ, United Kingdom
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Cynthia Tallant
- Structural
Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX37DQ, United Kingdom
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Finn Wolfreys
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Rebecca Konietzny
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Roman Fischer
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Hua Jane Lou
- Department
of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Paul E. Brennan
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Gisela Schnapp
- Lead Discovery and Optimisation Support, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, 88400, Germany
| | - Alexander Pautsch
- Lead Discovery and Optimisation Support, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, 88400, Germany
| | - Benedikt M. Kessler
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Benjamin E. Turk
- Department
of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Stefan Knapp
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
- Institute
for Pharmaceutical Chemistry and Buchmann Institute for Molecular
Life Sciences (BMLS), Johann Wolfgang Goethe University, Frankfurt am Main, 60438, Germany
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36
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Coutandin D, Osterburg C, Srivastav RK, Sumyk M, Kehrloesser S, Gebel J, Tuppi M, Hannewald J, Schäfer B, Salah E, Mathea S, Müller-Kuller U, Doutch J, Grez M, Knapp S, Dötsch V. Quality control in oocytes by p63 is based on a spring-loaded activation mechanism on the molecular and cellular level. eLife 2016; 5. [PMID: 27021569 PMCID: PMC4876613 DOI: 10.7554/elife.13909] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/28/2016] [Indexed: 01/07/2023] Open
Abstract
Mammalian oocytes are arrested in the dictyate stage of meiotic prophase I for long
periods of time, during which the high concentration of the p53 family member TAp63α
sensitizes them to DNA damage-induced apoptosis. TAp63α is kept in an inactive and
exclusively dimeric state but undergoes rapid phosphorylation-induced tetramerization
and concomitant activation upon detection of DNA damage. Here we show that the TAp63α
dimer is a kinetically trapped state. Activation follows a spring-loaded mechanism
not requiring further translation of other cellular factors in oocytes and is
associated with unfolding of the inhibitory structure that blocks the tetramerization
interface. Using a combination of biophysical methods as well as cell and ovary
culture experiments we explain how TAp63α is kept inactive in the absence of DNA
damage but causes rapid oocyte elimination in response to a few DNA double strand
breaks thereby acting as the key quality control factor in maternal reproduction. DOI:http://dx.doi.org/10.7554/eLife.13909.001 The irradiation and chemotherapy drugs that are used to destroy cancer cells also
damage healthy cells. Germ cells – from which egg cells and sperm cells develop – are
particularly vulnerable as they contain sensitive quality control mechanisms that
kill any cell that contain damaged DNA. Consequently, after surviving cancer many
patients are confronted with infertility. A protein called p63, which is closely related to another protein that suppresses the
formation of tumors, plays an essential role in detecting and responding to DNA
damage. In immature egg cells (also known as oocytes), p63 mostly exists in an
inactive form. The protein then switches to an active form when DNA damage is
detected to trigger the process of cell self-destruction. Now, Coutandin, Osterburg et al. have performed a range of biochemical, biophysical
and cell culture experiments to study how p63 is kept in its inactive form in the
oocytes of mice. The experiments showed that in the inactive form, the two ends of
the protein form a sheet that closes a key site on the protein and prevents it from
changing into its active form. However, this closed form can be thought of as being
like a spring-loaded trap – it doesn’t take much energy to spring the trap and open
the protein into its active form. Once this change has occurred, it is
irreversible. Coutandin, Osterburg et al. also found that the oocytes of mice already contain all
the proteins necessary to activate p63. This means that once the switch to the active
form is triggered there is no delay waiting for other proteins to be made, which
makes oocytes extremely sensitive to DNA damage. Further work is now needed to
investigate the exact molecular mechanisms behind the activation of p63. DOI:http://dx.doi.org/10.7554/eLife.13909.002
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Affiliation(s)
- Daniel Coutandin
- Institute of Biophysical Chemistry, Goethe University, Frankfurt, Germany.,Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany.,Cluster of Excellence Macromolecular Complexes, Goethe University, Frankfurt, Germany
| | - Christian Osterburg
- Institute of Biophysical Chemistry, Goethe University, Frankfurt, Germany.,Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany.,Cluster of Excellence Macromolecular Complexes, Goethe University, Frankfurt, Germany
| | - Ratnesh Kumar Srivastav
- Institute of Biophysical Chemistry, Goethe University, Frankfurt, Germany.,Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany.,Cluster of Excellence Macromolecular Complexes, Goethe University, Frankfurt, Germany
| | - Manuela Sumyk
- Institute of Biophysical Chemistry, Goethe University, Frankfurt, Germany.,Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany.,Cluster of Excellence Macromolecular Complexes, Goethe University, Frankfurt, Germany
| | - Sebastian Kehrloesser
- Institute of Biophysical Chemistry, Goethe University, Frankfurt, Germany.,Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany.,Cluster of Excellence Macromolecular Complexes, Goethe University, Frankfurt, Germany
| | - Jakob Gebel
- Institute of Biophysical Chemistry, Goethe University, Frankfurt, Germany.,Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany.,Cluster of Excellence Macromolecular Complexes, Goethe University, Frankfurt, Germany
| | - Marcel Tuppi
- Institute of Biophysical Chemistry, Goethe University, Frankfurt, Germany.,Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany.,Cluster of Excellence Macromolecular Complexes, Goethe University, Frankfurt, Germany
| | - Jens Hannewald
- MS-DTB-C Protein Purification, Merck KGaA, Darmstadt, Germany
| | - Birgit Schäfer
- Institute of Biophysical Chemistry, Goethe University, Frankfurt, Germany.,Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany.,Cluster of Excellence Macromolecular Complexes, Goethe University, Frankfurt, Germany
| | - Eidarus Salah
- Nuffield Department of Medicine, Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom
| | - Sebastian Mathea
- Nuffield Department of Medicine, Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom
| | | | - James Doutch
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Didcot, United Kingdom
| | | | - Stefan Knapp
- Nuffield Department of Medicine, Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom.,Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany.,Buchmann Institute for Molecular Life Science, Goethe University, Frankfurt, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Goethe University, Frankfurt, Germany.,Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany.,Cluster of Excellence Macromolecular Complexes, Goethe University, Frankfurt, Germany
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37
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Elkins JM, Fedele V, Szklarz M, Abdul Azeez KR, Salah E, Mikolajczyk J, Romanov S, Sepetov N, Huang XP, Roth BL, Al Haj Zen A, Fourches D, Muratov E, Tropsha A, Morris J, Teicher BA, Kunkel M, Polley E, Lackey KE, Atkinson FL, Overington JP, Bamborough P, Müller S, Price DJ, Willson TM, Drewry DH, Knapp S, Zuercher WJ. Comprehensive characterization of the Published Kinase Inhibitor Set. Nat Biotechnol 2015; 34:95-103. [PMID: 26501955 DOI: 10.1038/nbt.3374] [Citation(s) in RCA: 220] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 08/31/2015] [Indexed: 12/21/2022]
Abstract
Despite the success of protein kinase inhibitors as approved therapeutics, drug discovery has focused on a small subset of kinase targets. Here we provide a thorough characterization of the Published Kinase Inhibitor Set (PKIS), a set of 367 small-molecule ATP-competitive kinase inhibitors that was recently made freely available with the aim of expanding research in this field and as an experiment in open-source target validation. We screen the set in activity assays with 224 recombinant kinases and 24 G protein-coupled receptors and in cellular assays of cancer cell proliferation and angiogenesis. We identify chemical starting points for designing new chemical probes of orphan kinases and illustrate the utility of these leads by developing a selective inhibitor for the previously untargeted kinases LOK and SLK. Our cellular screens reveal compounds that modulate cancer cell growth and angiogenesis in vitro. These reagents and associated data illustrate an efficient way forward to increasing understanding of the historically untargeted kinome.
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Affiliation(s)
- Jonathan M Elkins
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford, UK
| | - Vita Fedele
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford, UK
| | - Marta Szklarz
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford, UK
| | - Kamal R Abdul Azeez
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford, UK
| | - Eidarus Salah
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford, UK
| | | | | | | | - Xi-Ping Huang
- The National Institute of Mental Health Psychoactive Active Drug Screening Program, (NIMH PDSP), Department of Pharmacology and Division of Chemical Biology and Medicinal Chemistry, The University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Bryan L Roth
- The National Institute of Mental Health Psychoactive Active Drug Screening Program, (NIMH PDSP), Department of Pharmacology and Division of Chemical Biology and Medicinal Chemistry, The University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Ayman Al Haj Zen
- British Heart Foundation Centre of Research Excellence, Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Denis Fourches
- Laboratory for Molecular Modeling Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Eugene Muratov
- Laboratory for Molecular Modeling Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alex Tropsha
- Laboratory for Molecular Modeling Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joel Morris
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland, USA
| | - Beverly A Teicher
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland, USA
| | - Mark Kunkel
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland, USA
| | - Eric Polley
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland, USA
| | - Karen E Lackey
- Medical University of South Carolina, Charleston, South Carolina, USA
| | - Francis L Atkinson
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - John P Overington
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Susanne Müller
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford, UK
| | - Daniel J Price
- Chemical Sciences, GlaxoSmithKline, Research Triangle Park, North Carolina, USA
| | - Timothy M Willson
- Chemical Sciences, GlaxoSmithKline, Research Triangle Park, North Carolina, USA
| | - David H Drewry
- Chemical Sciences, GlaxoSmithKline, Research Triangle Park, North Carolina, USA
| | - Stefan Knapp
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford, UK.,Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany
| | - William J Zuercher
- Chemical Sciences, GlaxoSmithKline, Research Triangle Park, North Carolina, USA
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38
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Huber KVM, Salah E, Radic B, Gridling M, Elkins JM, Stukalov A, Jemth AS, Gokturk C, Sanjiv K, Strömberg K, Pham T, Berglund UW, Colinge J, Bennett KL, Loizou J, Helleday T, Knapp S, Superti-Furga G. Stereospecific targeting of MTH1 by (S)-crizotinib as an anticancer strategy. Nature 2014; 508:222-7. [PMID: 24695225 PMCID: PMC4150021 DOI: 10.1038/nature13194] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 03/04/2014] [Indexed: 12/21/2022]
Abstract
Activated RAS GTPase signalling is a critical driver of oncogenic transformation and malignant disease. Cellular models of RAS-dependent cancers have been used to identify experimental small molecules, such as SCH51344, but their molecular mechanism of action remains generally unknown. Here, using a chemical proteomic approach, we identify the target of SCH51344 as the human mutT homologue MTH1 (also known as NUDT1), a nucleotide pool sanitizing enzyme. Loss-of-function of MTH1 impaired growth of KRAS tumour cells, whereas MTH1 overexpression mitigated sensitivity towards SCH51344. Searching for more drug-like inhibitors, we identified the kinase inhibitor crizotinib as a nanomolar suppressor of MTH1 activity. Surprisingly, the clinically used (R)-enantiomer of the drug was inactive, whereas the (S)-enantiomer selectively inhibited MTH1 catalytic activity. Enzymatic assays, chemical proteomic profiling, kinome-wide activity surveys and MTH1 co-crystal structures of both enantiomers provide a rationale for this remarkable stereospecificity. Disruption of nucleotide pool homeostasis via MTH1 inhibition by (S)-crizotinib induced an increase in DNA single-strand breaks, activated DNA repair in human colon carcinoma cells, and effectively suppressed tumour growth in animal models. Our results propose (S)-crizotinib as an attractive chemical entity for further pre-clinical evaluation, and small-molecule inhibitors of MTH1 in general as a promising novel class of anticancer agents.
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Affiliation(s)
- Kilian V. M. Huber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Eidarus Salah
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Branka Radic
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Manuela Gridling
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jonathan M. Elkins
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Alexey Stukalov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Camilla Gokturk
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kumar Sanjiv
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kia Strömberg
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Therese Pham
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ulrika Warpman Berglund
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jacques Colinge
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Joanna Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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39
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Chira I, Ambert V, Braticevici B, Jinga V, Salah E, Gutuie S, Pisoschi M, Tata E. UP-03.074 Stone and Patient Related Factors in Connection with Short Term Complications Following E.S.W.L. Stone Management. Urology 2011. [DOI: 10.1016/j.urology.2011.07.1164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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40
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Salah E, Ugochukwu E, Barr AJ, von Delft F, Knapp S, Elkins JM. Crystal structures of ABL-related gene (ABL2) in complex with imatinib, tozasertib (VX-680), and a type I inhibitor of the triazole carbothioamide class. J Med Chem 2011; 54:2359-67. [PMID: 21417343 PMCID: PMC3075623 DOI: 10.1021/jm101506n] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [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: 12/02/2022]
Abstract
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ABL2 (also known as ARG (ABL related gene)) is closely related to the well-studied Abelson kinase cABL. ABL2 is involved in human neoplastic diseases and is deregulated in solid tumors. Oncogenic gene translocations occur in acute leukemia. So far no structural information for ABL2 has been reported. To elucidate structural determinants for inhibitor interaction, we determined the cocrystal structure of ABL2 with the oncology drug imatinib. Interestingly, imatinib not only interacted with the ATP binding site of the inactive kinase but was also bound to the regulatory myristate binding site. This structure may therefore serve as a tool for the development of allosteric ABL inhibitors. In addition, we determined the structures of ABL2 in complex with VX-680 and with an ATP-mimetic type I inhibitor, which revealed an interesting position of the DFG motif intermediate between active and inactive conformations, that may also serve as a template for future inhibitor design.
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Affiliation(s)
- Eidarus Salah
- Structural Genomics Consortium, Oxford University, Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7DQ, UK
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Rellos P, Pike ACW, Niesen FH, Salah E, Lee WH, von Delft F, Knapp S. Structure of the CaMKIIdelta/calmodulin complex reveals the molecular mechanism of CaMKII kinase activation. PLoS Biol 2010; 8:e1000426. [PMID: 20668654 PMCID: PMC2910593 DOI: 10.1371/journal.pbio.1000426] [Citation(s) in RCA: 189] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 06/08/2010] [Indexed: 11/25/2022] Open
Abstract
Structural and biophysical studies reveal how CaMKII kinases, which are important for cellular learning and memory, are switched on by binding of Ca2+/calmodulin. Long-term potentiation (LTP), a long-lasting enhancement in communication between neurons, is considered to be the major cellular mechanism underlying learning and memory. LTP triggers high-frequency calcium pulses that result in the activation of Calcium/Calmodulin (CaM)-dependent kinase II (CaMKII). CaMKII acts as a molecular switch because it remains active for a long time after the return to basal calcium levels, which is a unique property required for CaMKII function. Here we describe the crystal structure of the human CaMKIIδ/Ca2+/CaM complex, structures of all four human CaMKII catalytic domains in their autoinhibited states, as well as structures of human CaMKII oligomerization domains in their tetradecameric and physiological dodecameric states. All four autoinhibited human CaMKIIs were monomeric in the determined crystal structures but associated weakly in solution. In the CaMKIIδ/Ca2+/CaM complex, the inhibitory region adopted an extended conformation and interacted with an adjacent catalytic domain positioning T287 into the active site of the interacting protomer. Comparisons with autoinhibited CaMKII structures showed that binding of calmodulin leads to the rearrangement of residues in the active site to a conformation suitable for ATP binding and to the closure of the binding groove for the autoinhibitory helix by helix αD. The structural data, together with biophysical interaction studies, reveals the mechanism of CaMKII activation by calmodulin and explains many of the unique regulatory properties of these two essential signaling molecules. Enhanced version This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3-D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the Web plugin are available in Text S1. CaMKII enzymes transmit calcium ion (Ca2+) signals released inside the cell by regulating signal transduction pathways through phosphorylation: Ca2+ first binds to the small regulatory protein CaM; this Ca2+/CaM complex then binds to and activates the kinase, which phosphorylates other proteins in the cell. Since CaMKs remain active long after rapid Ca2+ pulses have dropped they function as molecular switches that turn on or off crucial cell functions in response to Ca2+ levels. The multifunctional CaMKII forms of this enzyme – of which there are four in human – are important in many processes including signaling in neurons and controlling of the heart rate. They are particularly abundant in the brain where they probably play a role in memory. CaMKII forms an exceptionally large, dodecameric complex. Here, we describe the crystal structure of this complex for each of the four human CaMKII catalytic domains in their autoinhibited states, a complex of CaMKII with Ca2+/CaM, as well as the structure of the oligomerization domain (the part of the protein that mediates complex formation) in its physiological dodecameric state and in a tetradecameric state. Detailed comparison of this large body of structural data together with biophysical studies has allowed us to better understand the structural mechanisms of CaMKII activation by CaM and to explain many of the complex regulatory features of these essential enzymes.
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Affiliation(s)
- Peter Rellos
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford, United Kingdom
| | - Ashley C. W. Pike
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford, United Kingdom
| | - Frank H. Niesen
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford, United Kingdom
| | - Eidarus Salah
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford, United Kingdom
| | - Wen Hwa Lee
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford, United Kingdom
| | - Frank von Delft
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford, United Kingdom
| | - Stefan Knapp
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford, United Kingdom
- * E-mail:
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Hellwig S, Zhang J, Filippakopoulos P, Salah E, Knapp S, Gray NS, Smithgall TE. Abstract 3683: Small molecule inhibitors of the Fes non-receptor tyrosine kinase. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-3683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The c-fes/fps proto-oncogene encodes a unique 93 kDa protein-tyrosine kinase (Fes) expressed in myeloid, vascular endothelial, neuronal and epithelial cell types. Basal Fes catalytic activity is tightly regulated in vivo, with Fes adopting an inactive conformation in the absence of activating signals. The role of Fes in cancer is paradoxical, with some observations pointing to a tumor-suppressor role. For example, while Fes is strongly expressed in normal colonic epithelium, promoter methylation represses Fes expression in primary tumor tissue and many colorectal cancer cell lines. Restoration of Fes expression from a viral vector suppresses anchorage-independent growth of colorectal cancer cells. In a mouse model of breast cancer, disruption of the c-fes/fps locus correlates with more rapid tumor onset, and this effect can be rescued with a c-fes/fps transgene. In contrast to these observations, other lines of evidence support a pro-oncogenic role for Fes. Constitutively active mutants of Fes are capable of transforming rodent fibroblasts. In the mouse, expression of a gain-of-function human c-fes/fps allele results in hypervascularization and hemangioma formation. Fes has been identified as a phosphorylation target for a Kit mutant (D816V) implicated in mastocytosis, hematologic neoplasms, germ-cell tumors and melanomas. Targeting of Fes by siRNA knockdown inhibited proliferation of cells carrying the KITD816V mutation, identifying Fes as a potential therapeutic target in this cellular context. Another study demonstrated that siRNA knockdown of Fes reduces proliferation of two human renal carcinoma cell lines. One caveat of siRNA-mediated knockdown of Fes is that the resulting growth-inhibitory effect can not be attributed to loss of Fes activity as opposed to loss of the Fes protein. Delineation of kinase-dependent vs. kinase-independent cellular functions of Fes calls for Fes-specific kinase inhibitors, which have not been reported to date. In this study we aimed to identify inhibitors of the Fes tyrosine kinase. Using the recombinant Fes SH2-kinase region and an in vitro kinase assay (Z’-Lyte; Invitrogen), we screened a kinase-biased library of 586 compounds for inhibition of Tyr2 peptide phosphorylation by Fes. Lead compounds identified in vitro were then tested for their ability to inhibit full-length Fes autophosphorylation and microtubule association in transfected COS-7 cells and for their effect on rodent fibroblast transformation driven by constitutively active Fes mutants. A subset of active compounds was further evaluated for inhibition of tubulin phosphorylation by wild-type and active Fes in vitro. We will present a panel of type I and type II small molecule kinase inhibitors from various chemical classes with activity against Fes that are also non-toxic at inhibitory concentrations in cell lines. Our findings represent the first step towards developing a potent and selective inhibitor of Fes.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3683.
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Affiliation(s)
- Sabine Hellwig
- 1University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Jianming Zhang
- 2Dana Farber Cancer Institute/Harvard Medical School, Boston, MA
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Filippakopoulos P, Kofler M, Hantschel O, Gish GD, Grebien F, Salah E, Neudecker P, Kay LE, Turk BE, Superti-Furga G, Pawson T, Knapp S. Structural coupling of SH2-kinase domains links Fes and Abl substrate recognition and kinase activation. Cell 2008; 134:793-803. [PMID: 18775312 PMCID: PMC2572732 DOI: 10.1016/j.cell.2008.07.047] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 06/23/2008] [Accepted: 07/29/2008] [Indexed: 11/05/2022]
Abstract
The SH2 domain of cytoplasmic tyrosine kinases can enhance catalytic activity and substrate recognition, but the molecular mechanisms by which this is achieved are poorly understood. We have solved the structure of the prototypic SH2-kinase unit of the human Fes tyrosine kinase, which appears specialized for positive signaling. In its active conformation, the SH2 domain tightly interacts with the kinase N-terminal lobe and positions the kinase αC helix in an active configuration through essential packing and electrostatic interactions. This interaction is stabilized by ligand binding to the SH2 domain. Our data indicate that Fes kinase activation is closely coupled to substrate recognition through cooperative SH2-kinase-substrate interactions. Similarly, we find that the SH2 domain of the active Abl kinase stimulates catalytic activity and substrate phosphorylation through a distinct SH2-kinase interface. Thus, the SH2 and catalytic domains of active Fes and Abl pro-oncogenic kinases form integrated structures essential for effective tyrosine kinase signaling.
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Affiliation(s)
- Panagis Filippakopoulos
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
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Filippakopoulos P, Kofler M, Gish G, Salah E, Neudecker P, Kay L, Turk B, Pawson T, Knapp S. Fes kinase structure reveals cooperative interactions between SH2-kinase domains and substrate. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308089630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Gileadi O, Burgess-Brown NA, Colebrook SM, Berridge G, Savitsky P, Smee CEA, Loppnau P, Johansson C, Salah E, Pantic NH. High throughput production of recombinant human proteins for crystallography. Methods Mol Biol 2008; 426:221-246. [PMID: 18542867 DOI: 10.1007/978-1-60327-058-8_14] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This chapter presents in detail the process used in high throughput bacterial production of recombinant human proteins for crystal structure determination. The core principles are: (1) Generating at least 10 truncated constructs from each target gene. (2) Ligation-independent cloning (LIC) into a bacterial expression vector. All proteins are expressed with an N-terminal, TEV protease cleavable fusion peptide. (3) Small-scale test expression to identify constructs producing soluble protein. (4) Liter-scale production in shaker flasks. (5) Purification by Ni-affinity chromatography and gel filtration. (6) Protein characterization and preparation for crystallography. The chapter also briefly presents alternative procedures, to be applied based on specific knowledge of protein families or when the core protocol is unsatisfactory. This scheme has been applied to more than 550 human proteins (>10,000 constructs) and has resulted in the deposition of 112 unique structures. The methods presented do not depend on specialized equipment or robotics; hence, they provide an effective approach for handling individual proteins in a regular research lab.
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Affiliation(s)
- Opher Gileadi
- The Structural Genomics Consortium, Botnar Research Centre, University of Oxford, Oxford, UK
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Bunkoczi G, Salah E, Filippakopoulos P, Fedorov O, Müller S, Sobott F, Parker SA, Zhang H, Min W, Turk BE, Knapp S. Structural and functional characterization of the human protein kinase ASK1. Structure 2007; 15:1215-26. [PMID: 17937911 PMCID: PMC2100151 DOI: 10.1016/j.str.2007.08.011] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Revised: 08/17/2007] [Accepted: 08/21/2007] [Indexed: 11/30/2022]
Abstract
Apoptosis signal-regulating kinase 1 (ASK1) plays an essential role in stress and immune response and has been linked to the development of several diseases. Here, we present the structure of the human ASK1 catalytic domain in complex with staurosporine. Analytical ultracentrifugation (AUC) and crystallographic analysis showed that ASK1 forms a tight dimer (K(d) approximately 0.2 microM) interacting in a head-to-tail fashion. We found that the ASK1 phosphorylation motifs differ from known ASK1 phosphorylation sites but correspond well to autophosphorylation sites identified by mass spectrometry. Reporter gene assays showed that all three identified in vitro autophosphorylation sites (Thr813, Thr838, Thr842) regulate ASK1 signaling, but site-directed mutants showed catalytic activities similar to wild-type ASK1, suggesting a regulatory mechanism independent of ASK1 kinase activity. The determined high-resolution structure of ASK1 and identified ATP mimetic inhibitors will provide a first starting point for the further development of selective inhibitors.
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Affiliation(s)
- Gabor Bunkoczi
- University of Oxford, Structural Genomics Consortium, Botnar Research Centre, Oxford OX3 7LD, United Kingdom
| | - Eidarus Salah
- University of Oxford, Structural Genomics Consortium, Botnar Research Centre, Oxford OX3 7LD, United Kingdom
| | - Panagis Filippakopoulos
- University of Oxford, Structural Genomics Consortium, Botnar Research Centre, Oxford OX3 7LD, United Kingdom
| | - Oleg Fedorov
- University of Oxford, Structural Genomics Consortium, Botnar Research Centre, Oxford OX3 7LD, United Kingdom
| | - Susanne Müller
- University of Oxford, Structural Genomics Consortium, Botnar Research Centre, Oxford OX3 7LD, United Kingdom
| | - Frank Sobott
- University of Oxford, Structural Genomics Consortium, Botnar Research Centre, Oxford OX3 7LD, United Kingdom
| | - Sirlester A. Parker
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Haifeng Zhang
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Wang Min
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Benjamin E. Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Stefan Knapp
- University of Oxford, Structural Genomics Consortium, Botnar Research Centre, Oxford OX3 7LD, United Kingdom
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Belal A, Salah E, Hajjar W, El-Foudeh M, Memon M, Ezzat A, Al-Kattan K. Pulmonary metastatectomy for soft tissue sarcomas: is it valuable? J Cardiovasc Surg (Torino) 2001; 42:835-40. [PMID: 11698958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
BACKGROUND A retrospective study and analysis was performed to determine the value and benefit of pulmonary metastatectomy for soft tissue sarcomas, and which factors predict prognosis following resection. METHODS Twenty-three patients underwent resections for pulmonary metastases from a soft tissue sarcoma (STS) at King Faisal Specialist Hospital and Research Center (KFSH&RC), between January 1985 and December 1998. There were 11 male and 12 female patients. Thirteen of 23 patients (57%) had one to three metastases, and 10 (43%) had four or more metastases. A total of 41 thoracic explorations was performed for the 23 evaluable patients. Median sternotomy was used only for three patients and lateral thoracotomy was used for 20 patients as an initial surgical approach. Pulmonary resections performed included one or more wedge resections (n=16), segmentectomy (n=5), and lobectomy (n=2). No one in this series underwent pneumonectomy. The number of resected metastatic nodules ranged from one-six with average three. Eight patients (35%) received various kinds of postoperative adjuvant chemotherapy. RESULTS The overall and disease-free survival rate post-metastatectomy at five years was 24% and 21%, respectively. Various prognostic indicators were examined to evaluate their association with improved survival. Age, sex localization of the primary site and histologic type, tumor grade, size of the resected nodules, laterality (unilateral or bilateral), types of resection, adjuvant chemotherapy, and local recurrence did not significantly affect survival. However, patient with disease free interval >6 months, and those with three or fewer metastases showed a trend toward a higher five-year overall survival (p=0.06, 0.07, respectively). CONCLUSIONS Surgical excision of lung metastases from soft tissue sarcomas is well accepted and should be considered as a first line of treatment if preoperative evaluation indicated that complete resection of the metastases is possible. Further investigation is needed before chemotherapy can be recommended as additional therapy.
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Affiliation(s)
- A Belal
- Department of Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
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