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O'Brien DP, Jones HBL, Guenther F, Murphy EJ, England KS, Vendrell I, Anderson M, Brennan PE, Davis JB, Pinto-Fernández A, Turnbull AP, Kessler BM. Structural Premise of Selective Deubiquitinase USP30 Inhibition by Small-Molecule Benzosulfonamides. Mol Cell Proteomics 2023; 22:100609. [PMID: 37385347 PMCID: PMC10400906 DOI: 10.1016/j.mcpro.2023.100609] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 10/31/2022] [Revised: 06/07/2023] [Accepted: 06/25/2023] [Indexed: 07/01/2023] Open
Abstract
Dampening functional levels of the mitochondrial deubiquitylating enzyme Ubiquitin-specific protease 30 (USP30) has been suggested as an effective therapeutic strategy against neurodegenerative disorders such as Parkinson's Disease. USP30 inhibition may counteract the deleterious effects of impaired turnover of damaged mitochondria, which is inherent to both familial and sporadic forms of the disease. Small-molecule inhibitors targeting USP30 are currently in development, but little is known about their precise nature of binding to the protein. We have integrated biochemical and structural approaches to gain novel mechanistic insights into USP30 inhibition by a small-molecule benzosulfonamide-containing compound, USP30inh. Activity-based protein profiling mass spectrometry confirmed target engagement, high selectivity, and potency of USP30inh for USP30 against 49 other deubiquitylating enzymes in a neuroblastoma cell line. In vitro characterization of USP30inh enzyme kinetics inferred slow and tight binding behavior, which is comparable with features of covalent modification of USP30. Finally, we blended hydrogen-deuterium exchange mass spectrometry and computational docking to elucidate the molecular architecture and geometry of USP30 complex formation with USP30inh, identifying structural rearrangements at the cleft of the USP30 thumb and palm subdomains. These studies suggest that USP30inh binds to this thumb-palm cleft, which guides the ubiquitin C terminus into the active site, thereby preventing ubiquitin binding and isopeptide bond cleavage, and confirming its importance in the inhibitory process. Our data will pave the way for the design and development of next-generation inhibitors targeting USP30 and associated deubiquitinylases.
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Affiliation(s)
- Darragh P O'Brien
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK.
| | - Hannah B L Jones
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Franziska Guenther
- ARUK-Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Emma J Murphy
- ARUK-Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Katherine S England
- ARUK-Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Iolanda Vendrell
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | | | - Paul E Brennan
- ARUK-Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - John B Davis
- ARUK-Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Adán Pinto-Fernández
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK; Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | | | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK; Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK.
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2
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Le Bihan YV, Lanigan RM, Atrash B, McLaughlin MG, Velupillai S, Malcolm AG, England KS, Ruda GF, Mok NY, Tumber A, Tomlin K, Saville H, Shehu E, McAndrew C, Carmichael L, Bennett JM, Jeganathan F, Eve P, Donovan A, Hayes A, Wood F, Raynaud FI, Fedorov O, Brennan PE, Burke R, van Montfort RLM, Rossanese OW, Blagg J, Bavetsias V. C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur J Med Chem 2019; 177:316-337. [PMID: 31158747 PMCID: PMC6580095 DOI: 10.1016/j.ejmech.2019.05.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 01/04/2019] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 12/25/2022]
Abstract
Residues in the histone substrate binding sites that differ between the KDM4 and KDM5 subfamilies were identified. Subsequently, a C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one series was designed to rationally exploit these residue differences between the histone substrate binding sites in order to improve affinity for the KDM4-subfamily over KDM5-subfamily enzymes. In particular, residues E169 and V313 (KDM4A numbering) were targeted. Additionally, conformational restriction of the flexible pyridopyrimidinone C8-substituent was investigated. These approaches yielded potent and cell-penetrant dual KDM4/5-subfamily inhibitors including 19a (KDM4A and KDM5B Ki = 0.004 and 0.007 μM, respectively). Compound cellular profiling in two orthogonal target engagement assays revealed a significant reduction from biochemical to cell-based activity across multiple analogues; this decrease was shown to be consistent with 2OG competition, and suggests that sub-nanomolar biochemical potency will be required with C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one compounds to achieve sub-micromolar target inhibition in cells.
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Affiliation(s)
- Yann-Vaï Le Bihan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Rachel M Lanigan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Butrus Atrash
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Mark G McLaughlin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Srikannathasan Velupillai
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Andrew G Malcolm
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Katherine S England
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Gian Filippo Ruda
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - N Yi Mok
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Anthony Tumber
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Kathy Tomlin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Harry Saville
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Erald Shehu
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Craig McAndrew
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - LeAnne Carmichael
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - James M Bennett
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Fiona Jeganathan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Paul Eve
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Adam Donovan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Angela Hayes
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Francesca Wood
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Florence I Raynaud
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Oleg Fedorov
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Paul E Brennan
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Rosemary Burke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Rob L M van Montfort
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Olivia W Rossanese
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.
| | - Vassilios Bavetsias
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.
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3
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Tumber A, Nuzzi A, Hookway ES, Hatch SB, Velupillai S, Johansson C, Kawamura A, Savitsky P, Yapp C, Szykowska A, Wu N, Bountra C, Strain-Damerell C, Burgess-Brown NA, Ruda GF, Fedorov O, Munro S, England KS, Nowak RP, Schofield CJ, La Thangue NB, Pawlyn C, Davies F, Morgan G, Athanasou N, Müller S, Oppermann U, Brennan PE. Potent and Selective KDM5 Inhibitor Stops Cellular Demethylation of H3K4me3 at Transcription Start Sites and Proliferation of MM1S Myeloma Cells. Cell Chem Biol 2017; 24:371-380. [PMID: 28262558 PMCID: PMC5361737 DOI: 10.1016/j.chembiol.2017.02.006] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [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: 04/02/2016] [Revised: 10/31/2016] [Accepted: 02/01/2017] [Indexed: 12/16/2022]
Abstract
Methylation of lysine residues on histone tail is a dynamic epigenetic modification that plays a key role in chromatin structure and gene regulation. Members of the KDM5 (also known as JARID1) sub-family are 2-oxoglutarate (2-OG) and Fe2+-dependent oxygenases acting as histone 3 lysine 4 trimethyl (H3K4me3) demethylases, regulating proliferation, stem cell self-renewal, and differentiation. Here we present the characterization of KDOAM-25, an inhibitor of KDM5 enzymes. KDOAM-25 shows biochemical half maximal inhibitory concentration values of <100 nM for KDM5A-D in vitro, high selectivity toward other 2-OG oxygenases sub-families, and no off-target activity on a panel of 55 receptors and enzymes. In human cell assay systems, KDOAM-25 has a half maximal effective concentration of ∼50 μM and good selectivity toward other demethylases. KDM5B is overexpressed in multiple myeloma and negatively correlated with the overall survival. Multiple myeloma MM1S cells treated with KDOAM-25 show increased global H3K4 methylation at transcriptional start sites and impaired proliferation.
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Affiliation(s)
- Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Andrea Nuzzi
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Edward S Hookway
- NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Stephanie B Hatch
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Srikannathasan Velupillai
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Catrine Johansson
- NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK; 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; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Pavel Savitsky
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - Clarence Yapp
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | | | - Na Wu
- NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Chas Bountra
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | | | | | - Gian Filippo Ruda
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Oleg Fedorov
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Shonagh Munro
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Katherine S England
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Radoslaw P Nowak
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | | | | | - Charlotte Pawlyn
- Division of Cancer Therapeutics, Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Faith Davies
- Division of Cancer Therapeutics, Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK; University of Arkansas for Medical Sciences, Myeloma Institute, 4301 W. Markham #816, Little Rock, AR 72205, USA
| | - Gareth Morgan
- Division of Cancer Therapeutics, Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK; University of Arkansas for Medical Sciences, Myeloma Institute, 4301 W. Markham #816, Little Rock, AR 72205, USA
| | - Nick Athanasou
- NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Susanne Müller
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK.
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK.
| | - Paul E Brennan
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK.
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4
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Jones P, Storer RI, Sabnis YA, Wakenhut FM, Whitlock GA, England KS, Mukaiyama T, Dehnhardt CM, Coe JW, Kortum SW, Chrencik JE, Brown DG, Jones RM, Murphy JR, Yeoh T, Morgan P, Kilty I. Design and Synthesis of a Pan-Janus Kinase Inhibitor Clinical Candidate (PF-06263276) Suitable for Inhaled and Topical Delivery for the Treatment of Inflammatory Diseases of the Lungs and Skin. J Med Chem 2017; 60:767-786. [DOI: 10.1021/acs.jmedchem.6b01634] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Peter Jones
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - R. Ian Storer
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Yogesh A. Sabnis
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Florian M. Wakenhut
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Gavin A. Whitlock
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Katherine S. England
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Takasuke Mukaiyama
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Christoph M. Dehnhardt
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Jotham W. Coe
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Steve W. Kortum
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Jill E. Chrencik
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - David G. Brown
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Rhys M. Jones
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - John R. Murphy
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Thean Yeoh
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Paul Morgan
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Iain Kilty
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
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5
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Abstract
There is increasing interest in targeting histone N-methyl-lysine demethylases (KDMs) with small molecules both for the generation of probes for target exploration and for therapeutic purposes. Here we update on previous reviews on the inhibition of the lysine-specific demethylases (LSDs or KDM1s) and JmjC families of N-methyl-lysine demethylases (JmjC KDMs, KDM2-7), focusing on the academic and patent literature from 2014 to date. We also highlight recent biochemical, biological, and structural studies which are relevant to KDM inhibitor development.
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Affiliation(s)
- Tom E McAllister
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford, OX1 3TA, U.K
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford , Old Road Campus, Roosevelt Drive, Headington, OX3 7BN, U.K
| | - Katherine S England
- Structural Genomics Consortium, University of Oxford , Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Headington, OX3 7FZ, U.K
| | - Richard J Hopkinson
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford, OX1 3TA, U.K
| | - Paul E Brennan
- Structural Genomics Consortium, University of Oxford , Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Headington, OX3 7FZ, U.K
| | - Akane Kawamura
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford, OX1 3TA, U.K
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford , Old Road Campus, Roosevelt Drive, Headington, OX3 7BN, U.K
| | - Christopher J Schofield
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford, OX1 3TA, U.K
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6
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Thinnes CC, England KS, Kawamura A, Chowdhury R, Schofield CJ, Hopkinson RJ. Targeting histone lysine demethylases - progress, challenges, and the future. Biochim Biophys Acta 2014; 1839:1416-32. [PMID: 24859458 PMCID: PMC4316176 DOI: 10.1016/j.bbagrm.2014.05.009] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 05/06/2014] [Accepted: 05/13/2014] [Indexed: 12/20/2022]
Abstract
N-Methylation of lysine and arginine residues has emerged as a major mechanism of transcriptional regulation in eukaryotes. In humans, N(ε)-methyllysine residue demethylation is catalysed by two distinct subfamilies of demethylases (KDMs), the flavin-dependent KDM1 subfamily and the 2-oxoglutarate- (2OG) dependent JmjC subfamily, which both employ oxidative mechanisms. Modulation of histone methylation status is proposed to be important in epigenetic regulation and has substantial medicinal potential for the treatment of diseases including cancer and genetic disorders. This article provides an introduction to the enzymology of the KDMs and the therapeutic possibilities and challenges associated with targeting them, followed by a review of reported KDM inhibitors and their mechanisms of action from kinetic and structural perspectives.
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Affiliation(s)
- Cyrille C Thinnes
- The Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | | | - Akane Kawamura
- The Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
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England KS, Tumber A, Krojer T, Scozzafava G, Ng SS, Daniel M, Szykowska A, Che K, von Delft F, Burgess-Brown NA, Kawamura A, Schofield CJ, Brennan PE. Optimisation of a triazolopyridine based histone demethylase inhibitor yields a potent and selective KDM2A (FBXL11) inhibitor. Medchemcomm 2014; 5:1879-1886. [PMID: 26682034 PMCID: PMC4678576 DOI: 10.1039/c4md00291a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A potent inhibitor of the JmjC histone lysine demethylase KDM2A (compound 35, pIC50 7.2) with excellent selectivity over representatives from other KDM subfamilies has been developed; the discovery that a triazolopyridine compound binds to the active site of JmjC KDMs was followed by optimisation of the triazole substituent for KDM2A inhibition and selectivity.
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Affiliation(s)
- Katherine S. England
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - Giuseppe Scozzafava
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Stanley S. Ng
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - Michelle Daniel
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - Aleksandra Szykowska
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - KaHing Che
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Nicola A. Burgess-Brown
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | | | - Paul E. Brennan
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, UK
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