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Balıkçı E, Marques ASMC, Bauer LG, Seupel R, Bennett J, Raux B, Buchan K, Simelis K, Singh U, Rogers C, Ward J, Cheng C, Szommer T, Schützenhofer K, Elkins JM, Sloman DL, Ahel I, Fedorov O, Brennan PE, Huber KVM. Unexpected Noncovalent Off-Target Activity of Clinical BTK Inhibitors Leads to Discovery of a Dual NUDT5/14 Antagonist. J Med Chem 2024. [PMID: 38635563 DOI: 10.1021/acs.jmedchem.4c00072] [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: 04/20/2024]
Abstract
Cofactor mimicry represents an attractive strategy for the development of enzyme inhibitors but can lead to off-target effects due to the evolutionary conservation of binding sites across the proteome. Here, we uncover the ADP-ribose (ADPr) hydrolase NUDT5 as an unexpected, noncovalent, off-target of clinical BTK inhibitors. Using a combination of biochemical, biophysical, and intact cell NanoBRET assays as well as X-ray crystallography, we confirm catalytic inhibition and cellular target engagement of NUDT5 and reveal an unusual binding mode that is independent of the reactive acrylamide warhead. Further investigation of the prototypical BTK inhibitor ibrutinib also revealed potent inhibition of the largely unstudied NUDIX hydrolase family member NUDT14. By exploring structure-activity relationships (SARs) around the core scaffold, we identify a potent, noncovalent, and cell-active dual NUDT5/14 inhibitor. Cocrystallization experiments yielded new insights into the NUDT14 hydrolase active site architecture and inhibitor binding, thus providing a basis for future chemical probe design.
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Affiliation(s)
- Esra Balıkçı
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Anne-Sophie M C Marques
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Ludwig G Bauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Raina Seupel
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - James Bennett
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Brigitt Raux
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Karly Buchan
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Klemensas Simelis
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Usha Singh
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Catherine Rogers
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Jennifer Ward
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Carol Cheng
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Tamas Szommer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Kira Schützenhofer
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, U.K
| | - Jonathan M Elkins
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - David L Sloman
- Departments of Discovery Chemistry, Merck & Co. Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, U.K
| | - Oleg Fedorov
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Paul E Brennan
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
- Alzheimer's Research UK Oxford Drug Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Kilian V M Huber
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
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Bradshaw WJ, Kennedy EC, Moreira T, Smith LA, Chalk R, Katis VL, Benesch JLP, Brennan PE, Murphy EJ, Gileadi O. Regulation of inositol 5-phosphatase activity by the C2 domain of SHIP1 and SHIP2. Structure 2024; 32:453-466.e6. [PMID: 38309262 PMCID: PMC10997489 DOI: 10.1016/j.str.2024.01.005] [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: 08/01/2023] [Revised: 12/12/2023] [Accepted: 01/08/2024] [Indexed: 02/05/2024]
Abstract
SHIP1, an inositol 5-phosphatase, plays a central role in cellular signaling. As such, it has been implicated in many conditions. Exploiting SHIP1 as a drug target will require structural knowledge and the design of selective small molecules. We have determined apo, and magnesium and phosphate-bound structures of the phosphatase and C2 domains of SHIP1. The C2 domains of SHIP1 and the related SHIP2 modulate the activity of the phosphatase domain. To understand the mechanism, we performed activity assays, hydrogen-deuterium exchange mass spectrometry, and molecular dynamics on SHIP1 and SHIP2. Our findings demonstrate that the influence of the C2 domain is more pronounced for SHIP2 than SHIP1. We determined 91 structures of SHIP1 with fragments bound, with some near the interface between the two domains. We performed a mass spectrometry screen and determined four structures with covalent fragments. These structures could act as starting points for the development of potent, selective probes.
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Affiliation(s)
- William J Bradshaw
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK.
| | - Emma C Kennedy
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK
| | - Tiago Moreira
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK
| | - Luke A Smith
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Rod Chalk
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK
| | - Vittorio L Katis
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK
| | - Justin L P Benesch
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Paul E Brennan
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK
| | - Emma J Murphy
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK
| | - Opher Gileadi
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK.
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Bashore FM, Katis VL, Du Y, Sikdar A, Wang D, Bradshaw WJ, Rygiel KA, Leisner TM, Chalk R, Mishra S, Williams CA, Gileadi O, Brennan PE, Wiley JC, Gockley J, Cary GA, Carter GW, Young JE, Pearce KH, Fu H, Axtman AD. Characterization of covalent inhibitors that disrupt the interaction between the tandem SH2 domains of SYK and FCER1G phospho-ITAM. PLoS One 2024; 19:e0293548. [PMID: 38359047 PMCID: PMC10868801 DOI: 10.1371/journal.pone.0293548] [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: 08/02/2023] [Accepted: 10/15/2023] [Indexed: 02/17/2024] Open
Abstract
RNA sequencing and genetic data support spleen tyrosine kinase (SYK) and high affinity immunoglobulin epsilon receptor subunit gamma (FCER1G) as putative targets to be modulated for Alzheimer's disease (AD) therapy. FCER1G is a component of Fc receptor complexes that contain an immunoreceptor tyrosine-based activation motif (ITAM). SYK interacts with the Fc receptor by binding to doubly phosphorylated ITAM (p-ITAM) via its two tandem SH2 domains (SYK-tSH2). Interaction of the FCER1G p-ITAM with SYK-tSH2 enables SYK activation via phosphorylation. Since SYK activation is reported to exacerbate AD pathology, we hypothesized that disruption of this interaction would be beneficial for AD patients. Herein, we developed biochemical and biophysical assays to enable the discovery of small molecules that perturb the interaction between the FCER1G p-ITAM and SYK-tSH2. We identified two distinct chemotypes using a high-throughput screen (HTS) and orthogonally assessed their binding. Both chemotypes covalently modify SYK-tSH2 and inhibit its interaction with FCER1G p-ITAM, however, these compounds lack selectivity and this limits their utility as chemical tools.
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Affiliation(s)
- Frances M. Bashore
- Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Vittorio L. Katis
- Nuffield Department of Medicine, Centre for Medicines Discovery, ARUK Oxford Drug Discovery Institute, University of Oxford, Headington, Oxford, United Kingdom
| | - Yuhong Du
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, United States of America
- Emory Chemical Biology Discovery Center, School of Medicine, Emory University, Atlanta, GA, United States of America
| | - Arunima Sikdar
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Dongxue Wang
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, United States of America
- Emory Chemical Biology Discovery Center, School of Medicine, Emory University, Atlanta, GA, United States of America
| | - William J. Bradshaw
- Nuffield Department of Medicine, Centre for Medicines Discovery, ARUK Oxford Drug Discovery Institute, University of Oxford, Headington, Oxford, United Kingdom
| | - Karolina A. Rygiel
- Nuffield Department of Medicine, Centre for Medicines Discovery, ARUK Oxford Drug Discovery Institute, University of Oxford, Headington, Oxford, United Kingdom
| | - Tina M. Leisner
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Rod Chalk
- Nuffield Department of Medicine, Centre for Medicines Discovery, ARUK Oxford Drug Discovery Institute, University of Oxford, Headington, Oxford, United Kingdom
| | - Swati Mishra
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, United States of America
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States of America
| | - C. Andrew Williams
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, United States of America
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States of America
| | - Opher Gileadi
- Nuffield Department of Medicine, Centre for Medicines Discovery, ARUK Oxford Drug Discovery Institute, University of Oxford, Headington, Oxford, United Kingdom
| | - Paul E. Brennan
- Nuffield Department of Medicine, Centre for Medicines Discovery, ARUK Oxford Drug Discovery Institute, University of Oxford, Headington, Oxford, United Kingdom
| | | | - Jake Gockley
- Sage Bionetworks, Seattle, WA, United States of America
| | - Gregory A. Cary
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, United States of America
| | - Gregory W. Carter
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, United States of America
| | - Jessica E. Young
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, United States of America
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States of America
| | - Kenneth H. Pearce
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Haian Fu
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, United States of America
- Emory Chemical Biology Discovery Center, School of Medicine, Emory University, Atlanta, GA, United States of America
| | | | - Alison D. Axtman
- Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
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Du Y, Bradshaw WJ, Leisner TM, Annor-Gyamfi JK, Qian K, Bashore FM, Sikdar A, Nwogbo FO, Ivanov AA, Frye SV, Gileadi O, Brennan PE, Levey AI, Axtman AD, Pearce KH, Fu H, Katis VL. Discovery of FERM domain protein-protein interaction inhibitors for MSN and CD44 as a potential therapeutic approach for Alzheimer's disease. J Biol Chem 2023; 299:105382. [PMID: 37866628 PMCID: PMC10692723 DOI: 10.1016/j.jbc.2023.105382] [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: 05/22/2023] [Revised: 09/11/2023] [Accepted: 09/27/2023] [Indexed: 10/24/2023] Open
Abstract
Proteomic studies have identified moesin (MSN), a protein containing a four-point-one, ezrin, radixin, moesin (FERM) domain, and the receptor CD44 as hub proteins found within a coexpression module strongly linked to Alzheimer's disease (AD) traits and microglia. These proteins are more abundant in Alzheimer's patient brains, and their levels are positively correlated with cognitive decline, amyloid plaque deposition, and neurofibrillary tangle burden. The MSN FERM domain interacts with the phospholipid phosphatidylinositol 4,5-bisphosphate (PIP2) and the cytoplasmic tail of CD44. Inhibiting the MSN-CD44 interaction may help limit AD-associated neuronal damage. Here, we investigated the feasibility of developing inhibitors that target this protein-protein interaction. We have employed structural, mutational, and phage-display studies to examine how CD44 binds to the FERM domain of MSN. Interestingly, we have identified an allosteric site located close to the PIP2 binding pocket that influences CD44 binding. These findings suggest a mechanism in which PIP2 binding to the FERM domain stimulates CD44 binding through an allosteric effect, leading to the formation of a neighboring pocket capable of accommodating a receptor tail. Furthermore, high-throughput screening of a chemical library identified two compounds that disrupt the MSN-CD44 interaction. One compound series was further optimized for biochemical activity, specificity, and solubility. Our results suggest that the FERM domain holds potential as a drug development target. Small molecule preliminary leads generated from this study could serve as a foundation for additional medicinal chemistry efforts with the goal of controlling microglial activity in AD by modifying the MSN-CD44 interaction.
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Affiliation(s)
- Yuhong Du
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - William J Bradshaw
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, University of Oxford, Oxford, UK
| | - Tina M Leisner
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, North Carolina, USA
| | - Joel K Annor-Gyamfi
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Structural Genomics Consortium, Chapel Hill, North Carolina, USA
| | - Kun Qian
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Frances M Bashore
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Structural Genomics Consortium, Chapel Hill, North Carolina, USA
| | - Arunima Sikdar
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, North Carolina, USA
| | - Felix O Nwogbo
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, North Carolina, USA
| | - Andrey A Ivanov
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Stephen V Frye
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, North Carolina, USA
| | - Opher Gileadi
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, University of Oxford, Oxford, UK
| | - Paul E Brennan
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, University of Oxford, Oxford, UK
| | - Allan I Levey
- Department of Neurology, Emory Goizueta Alzheimer's Disease Research Center, Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Alison D Axtman
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Structural Genomics Consortium, Chapel Hill, North Carolina, USA.
| | - Kenneth H Pearce
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, North Carolina, USA.
| | - Haian Fu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, Georgia, USA.
| | - Vittorio L Katis
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, University of Oxford, Oxford, UK.
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Fazazi MR, Ruda GF, Brennan PE, Rangachari M. The X-linked histone demethylases KDM5C and KDM6A as regulators of T cell-driven autoimmunity in the central nervous system. Brain Res Bull 2023; 202:110748. [PMID: 37657612 DOI: 10.1016/j.brainresbull.2023.110748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/19/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/03/2023]
Abstract
T cell-driven autoimmune responses are subject to striking sex-dependent effects. While the contributions of sex hormones are well-understood, those of sex chromosomes are meeting with increased appreciation. Here, we outline what is known about the contribution of sex chromosome-linked factors to experimental autoimmune encephalomyelitis (EAE), a mouse model that recapitulates many of the T cell-driven mechanisms of multiple sclerosis (MS) pathology. Particular attention is paid to the KDM family of histone demethylases, several of which - KDM5C, KDM5D and KDM6A - are sex chromosome encoded. Finally, we provide evidence that functional inhibition of KDM5 molecules can suppress interferon (IFN)γ production from murine male effector T cells, and that an increased ratio of inflammatory Kdm6a to immunomodulatory Kdm5c transcript is observed in T helper 17 (Th17) cells from women with the autoimmune disorder ankylosing spondylitis (AS). Histone lysine demethlyases thus represent intriguing targets for the treatment of T cell-driven autoimmune disorders.
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Affiliation(s)
- Mohamed Reda Fazazi
- axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Gian Filippo Ruda
- Centre for Medicines Discovery and NIHR, Oxford Biomedical Research Centre, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Paul E Brennan
- Centre for Medicines Discovery and NIHR, Oxford Biomedical Research Centre, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Alzheimer's Research UK, Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Manu Rangachari
- axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada; Département de médecine moléculaire, Faculté de médecine, Université Laval, Québec, QC, Canada.
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6
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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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Bashore FM, Katis VL, Du Y, Sikdar A, Wang D, Bradshaw WJ, Rygiel KA, Leisner TM, Chalk R, Mishra S, Williams AC, Gileadi O, Brennan PE, Wiley JC, Gockley J, Cary GA, Carter GW, Young JE, Pearce KH, Fu H, Axtman AD. Characterization of covalent inhibitors that disrupt the interaction between the tandem SH2 domains of SYK and FCER1G phospho-ITAM. bioRxiv 2023:2023.07.28.551026. [PMID: 37547005 PMCID: PMC10402180 DOI: 10.1101/2023.07.28.551026] [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] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
RNA sequencing and genetic data support spleen tyrosine kinase (SYK) and high affinity immunoglobulin epsilon receptor subunit gamma (FCER1G) as putative targets to be modulated for Alzheimer's disease (AD) therapy. FCER1G is a component of Fc receptor complexes that contain an immunoreceptor tyrosine-based activation motif (ITAM). SYK interacts with the Fc receptor by binding to doubly phosphorylated ITAM (p-ITAM) via its two tandem SH2 domains (SYK-tSH2). Interaction of the FCER1G p-ITAM with SYK-tSH2 enables SYK activation via phosphorylation. Since SYK activation is reported to exacerbate AD pathology, we hypothesized that disruption of this interaction would be beneficial for AD patients. Herein, we developed biochemical and biophysical assays to enable the discovery of small molecules that perturb the interaction between the FCER1G p-ITAM and SYK-tSH2. We identified two distinct chemotypes using a high-throughput screen (HTS) and orthogonally assessed their binding. Both chemotypes covalently modify SYK-tSH2 and inhibit its interaction with FCER1G p-ITAM.
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Affiliation(s)
- Frances M. Bashore
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Structural Genomics Consortium, University of North Carolina, Chapel Hill, NC, USA
| | - Vittorio L. Katis
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Headington, Oxford, OX3 7FZ, UK
| | - Yuhong Du
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Emory Chemical Biology Discovery Center, School of Medicine, Emory University, Atlanta, GA, USA
| | - Arunima Sikdar
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC, USA
| | - Dongxue Wang
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Emory Chemical Biology Discovery Center, School of Medicine, Emory University, Atlanta, GA, USA
| | - William J. Bradshaw
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Headington, Oxford, OX3 7FZ, UK
| | - Karolina A. Rygiel
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Headington, Oxford, OX3 7FZ, UK
| | - Tina M. Leisner
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC, USA
| | - Rod Chalk
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Headington, Oxford, OX3 7FZ, UK
| | | | | | - Opher Gileadi
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Headington, Oxford, OX3 7FZ, UK
- Current address: Structural Genomics Consortium, Department of Medicine, Karolinska Hospital and Karolinska Institute, 171 76 Stockholm, Sweden
| | - Paul E. Brennan
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Headington, Oxford, OX3 7FZ, UK
| | | | | | | | | | | | - Kenneth H. Pearce
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC, USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Emory Chemical Biology Discovery Center, School of Medicine, Emory University, Atlanta, GA, USA
| | | | - Alison D. Axtman
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Structural Genomics Consortium, University of North Carolina, Chapel Hill, NC, USA
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8
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Du Y, Bradshaw WJ, Leisner TM, Annor-Gyamfi JK, Qian K, Bashore FM, Sikdar A, Nwogbo FO, Ivanov AA, Frye SV, Gileadi O, Brennan PE, Levey AI, Axtman AD, Pearce KH, Fu H, Katis VL. Development of FERM domain protein-protein interaction inhibitors for MSN and CD44 as a potential therapeutic strategy for Alzheimer's disease. bioRxiv 2023:2023.05.22.541727. [PMID: 37292860 PMCID: PMC10245921 DOI: 10.1101/2023.05.22.541727] [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] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recent genome-wide association studies have revealed genetic risk factors for Alzheimer's disease (AD) that are exclusively expressed in microglia within the brain. A proteomics approach identified moesin (MSN), a FERM (four-point-one ezrin radixin moesin) domain protein, and the receptor CD44 as hub proteins found within a co-expression module strongly linked to AD clinical and pathological traits as well as microglia. The FERM domain of MSN interacts with the phospholipid PIP2 and the cytoplasmic tails of receptors such as CD44. This study explored the feasibility of developing protein-protein interaction inhibitors that target the MSN-CD44 interaction. Structural and mutational analyses revealed that the FERM domain of MSN binds to CD44 by incorporating a beta strand within the F3 lobe. Phage-display studies identified an allosteric site located close to the PIP2 binding site in the FERM domain that affects CD44 binding within the F3 lobe. These findings support a model in which PIP2 binding to the FERM domain stimulates receptor tail binding through an allosteric mechanism that causes the F3 lobe to adopt an open conformation permissive for binding. High-throughput screening of a chemical library identified two compounds that disrupt the MSN-CD44 interaction, and one compound series was further optimized for biochemical activity, specificity, and solubility. The results suggest that the FERM domain holds potential as a drug development target. The small molecule preliminary leads generated from the study could serve as a foundation for additional medicinal chemistry effort with the goal of controlling microglial activity in AD by modifying the MSN-CD44 interaction.
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Affiliation(s)
- Yuhong Du
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - William J. Bradshaw
- Alzheimer’s Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford, OX3 7FZ, UK
| | - Tina M. Leisner
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, NC 27599, USA
| | - Joel K. Annor-Gyamfi
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Structural Genomics Consortium, Chapel Hill, NC 27599, USA
| | - Kun Qian
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Current address: Chemical Biology Consortium Sweden, Division of Chemical Biology and Genome Engineering, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Solna, Sweden
| | - Frances M. Bashore
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Structural Genomics Consortium, Chapel Hill, NC 27599, USA
| | - Arunima Sikdar
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, NC 27599, USA
| | - Felix O. Nwogbo
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, NC 27599, USA
| | - Andrey A. Ivanov
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stephen V. Frye
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, NC 27599, USA
| | - Opher Gileadi
- Alzheimer’s Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford, OX3 7FZ, UK
- Current address: Structural Genomics Consortium, Department of Medicine, Karolinska Hospital and Karolinska Institute, 171 76 Stockholm, Sweden
| | - Paul E. Brennan
- Alzheimer’s Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford, OX3 7FZ, UK
| | - Allan I. Levey
- Department of Neurology, Emory Goizueta Alzheimer’s Disease Research Center, Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Alison D. Axtman
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Structural Genomics Consortium, Chapel Hill, NC 27599, USA
| | - Kenneth H. Pearce
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, NC 27599, USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Vittorio L. Katis
- Alzheimer’s Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford, OX3 7FZ, UK
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Axtman AD, Brennan PE, Frappier‐Brinton T, Betarbet R, Carter GW, Fu H, Gileadi O, Greenwood AK, Leal K, Longo FM, Mangravite LM, Edwards AM, Levey AI. Open drug discovery in Alzheimer's disease. Alzheimers Dement (N Y) 2023; 9:e12394. [PMID: 37215505 PMCID: PMC10192886 DOI: 10.1002/trc2.12394] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023]
Abstract
Alzheimer's disease (AD) drug discovery has focused on a set of highly studied therapeutic hypotheses, with limited success. The heterogeneous nature of AD processes suggests that a more diverse, systems-integrated strategy may identify new therapeutic hypotheses. Although many target hypotheses have arisen from systems-level modeling of human disease, in practice and for many reasons, it has proven challenging to translate them into drug discovery pipelines. First, many hypotheses implicate protein targets and/or biological mechanisms that are under-studied, meaning there is a paucity of evidence to inform experimental strategies as well as high-quality reagents to perform them. Second, systems-level targets are predicted to act in concert, requiring adaptations in how we characterize new drug targets. Here we posit that the development and open distribution of high-quality experimental reagents and informatic outputs-termed target enabling packages (TEPs)-will catalyze rapid evaluation of emerging systems-integrated targets in AD by enabling parallel, independent, and unencumbered research.
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Affiliation(s)
- Alison D. Axtman
- University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | | | | | | | | | - Haian Fu
- Emory University School of MedicineAtlantaGeorgiaUSA
| | - Opher Gileadi
- Structural Genomics ConsortiumKarolinska InstituteStockholmSweden
| | | | | | - Frank M. Longo
- Stanford University School of MedicineStanfordCaliforniaUSA
| | | | - Aled M. Edwards
- Structural Genomics ConsortiumUniversity of TorontoTorontoOntarioCanada
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10
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Fowkes MM, Troeberg L, Brennan PE, Vincent TL, Meldal M, Lim NH. Development of Selective ADAMTS-5 Peptide Substrates to Monitor Proteinase Activity. J Med Chem 2023; 66:3522-3539. [PMID: 36891740 PMCID: PMC10009750 DOI: 10.1021/acs.jmedchem.2c02090] [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: 12/21/2022] [Indexed: 02/25/2023]
Abstract
The dysregulation of proteinase activity is a hallmark of osteoarthritis (OA), a disease characterized by progressive degradation of articular cartilage by catabolic proteinases such as a disintegrin and metalloproteinase with thrombospondin type I motifs-5 (ADAMTS-5). The ability to detect such activity sensitively would aid disease diagnosis and the evaluation of targeted therapies. Förster resonance energy transfer (FRET) peptide substrates can detect and monitor disease-related proteinase activity. To date, FRET probes for detecting ADAMTS-5 activity are nonselective and relatively insensitive. We describe the development of rapidly cleaved and highly selective ADAMTS-5 FRET peptide substrates through in silico docking and combinatorial chemistry. The lead substrates 3 and 26 showed higher overall cleavage rates (∼3-4-fold) and catalytic efficiencies (∼1.5-2-fold) compared to the best current ADAMTS-5 substrate ortho-aminobenzoyl(Abz)-TESE↓SRGAIY-N-3-[2,4-dinitrophenyl]-l-2,3-diaminopropionyl(Dpa)-KK-NH2. They exhibited high selectivity for ADAMTS-5 over ADAMTS-4 (∼13-16-fold), MMP-2 (∼8-10-fold), and MMP-9 (∼548-2561-fold) and detected low nanomolar concentrations of ADAMTS-5.
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Affiliation(s)
- Milan M. Fowkes
- Centre
for OA Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7FY, United Kingdom
| | - Linda Troeberg
- Norwich
Medical School, Bob Champion Research and Education Building, Rosalind
Franklin Road, University of East Anglia, Norwich NR4 7UQ, United Kingdom
| | - Paul E. Brennan
- Alzheimer’s
Research UK Oxford Drug Discovery Institute, Centre for Medicines
Discovery, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, United Kingdom
| | - Tonia L. Vincent
- Centre
for OA Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7FY, United Kingdom
| | - Morten Meldal
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, Building B304, Copenhagen DK-2100, Denmark
| | - Ngee H. Lim
- Centre
for OA Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7FY, United Kingdom
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11
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Schuller M, Zarganes-Tzitzikas T, Bennett J, De Cesco S, Fearon D, von Delft F, Fedorov O, Brennan PE, Ahel I. Discovery and Development Strategies for SARS-CoV-2 NSP3 Macrodomain Inhibitors. Pathogens 2023; 12:324. [PMID: 36839595 PMCID: PMC9965906 DOI: 10.3390/pathogens12020324] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/03/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
The worldwide public health and socioeconomic consequences caused by the COVID-19 pandemic highlight the importance of increasing preparedness for viral disease outbreaks by providing rapid disease prevention and treatment strategies. The NSP3 macrodomain of coronaviruses including SARS-CoV-2 is among the viral protein repertoire that was identified as a potential target for the development of antiviral agents, due to its critical role in viral replication and consequent pathogenicity in the host. By combining virtual and biophysical screening efforts, we discovered several experimental small molecules and FDA-approved drugs as inhibitors of the NSP3 macrodomain. Analogue characterisation of the hit matter and crystallographic studies confirming binding modes, including that of the antibiotic compound aztreonam, to the active site of the macrodomain provide valuable structure-activity relationship information that support current approaches and open up new avenues for NSP3 macrodomain inhibitor development.
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Affiliation(s)
- Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | - James Bennett
- Centre for Medicines Discovery, University of Oxford, Headington OX3 7DQ, UK
| | - Stephane De Cesco
- Centre for Medicines Discovery, University of Oxford, Headington OX3 7DQ, UK
| | - Daren Fearon
- 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
| | - Frank von Delft
- Centre for Medicines Discovery, University of Oxford, Headington OX3 7DQ, UK
- 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
- Structural Genomics Consortium, University of Oxford, Headington OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Oleg Fedorov
- Centre for Medicines Discovery, University of Oxford, Headington OX3 7DQ, UK
| | - Paul E. Brennan
- Centre for Medicines Discovery, University of Oxford, Headington OX3 7DQ, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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12
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Leal K, Axtman AD, Betarbet R, Brennan PE, Carter GW, Frye SV, Fu H, Greenwood AK, Longo FM, Pearce KH, Edwards AM, Levey AI. The Emory‐Sage‐SGC TREAT‐AD Center: Tool and probe development for emerging targets in Alzheimer’s Disease. Alzheimers Dement 2022. [DOI: 10.1002/alz.064748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | | | | | - Paul E Brennan
- Alzheimer’s Research UK Oxford Drug Discovery Institute University of Oxford Oxford United Kingdom
| | | | - Stephen V. Frye
- University of North Carolina at Chapel Hill Chapel Hill NC USA
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13
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Frank N, Nugent J, Shire BR, Pickford HD, Rabe P, Sterling AJ, Zarganes-Tzitzikas T, Grimes T, Thompson AL, Smith RC, Schofield CJ, Brennan PE, Duarte F, Anderson EA. Synthesis of meta-substituted arene bioisosteres from [3.1.1]propellane. Nature 2022; 611:721-726. [PMID: 36108675 DOI: 10.1038/s41586-022-05290-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/30/2022] [Indexed: 11/08/2022]
Abstract
Small-ring cage hydrocarbons are popular bioisosteres (molecular replacements) for commonly found para-substituted benzene rings in drug design1. The utility of these cage structures derives from their superior pharmacokinetic properties compared with their parent aromatics, including improved solubility and reduced susceptibility to metabolism2,3. A prime example is the bicyclo[1.1.1]pentane motif, which is mainly synthesized by ring-opening of the interbridgehead bond of the strained hydrocarbon [1.1.1]propellane with radicals or anions4. By contrast, scaffolds mimicking meta-substituted arenes are lacking because of the challenge of synthesizing saturated isosteres that accurately reproduce substituent vectors5. Here we show that bicyclo[3.1.1]heptanes (BCHeps), which are hydrocarbons for which the bridgehead substituents map precisely onto the geometry of meta-substituted benzenes, can be conveniently accessed from [3.1.1]propellane. We found that [3.1.1]propellane can be synthesized on a multigram scale, and readily undergoes a range of radical-based transformations to generate medicinally relevant carbon- and heteroatom-substituted BCHeps, including pharmaceutical analogues. Comparison of the absorption, distribution, metabolism and excretion (ADME) properties of these analogues reveals enhanced metabolic stability relative to their parent arene-containing drugs, validating the potential of this meta-arene analogue as an sp3-rich motif in drug design. Collectively, our results show that BCHeps can be prepared on useful scales using a variety of methods, offering a new surrogate for meta-substituted benzene rings for implementation in drug discovery programmes.
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Affiliation(s)
- Nils Frank
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Jeremy Nugent
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Bethany R Shire
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Helena D Pickford
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Patrick Rabe
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Alistair J Sterling
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Tryfon Zarganes-Tzitzikas
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford, UK
| | - Thomas Grimes
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford, UK
| | - Amber L Thompson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Russell C Smith
- Abbvie Drug Discovery Science & Technology (DDST), North Chicago, IL, USA
| | | | - Paul E Brennan
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford, UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Edward A Anderson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
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14
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Fowkes MM, Das Neves Borges P, Cacho-Nerin F, Brennan PE, Vincent TL, Lim NH. Imaging articular cartilage in osteoarthritis using targeted peptide radiocontrast agents. PLoS One 2022; 17:e0268223. [PMID: 35536857 PMCID: PMC9089912 DOI: 10.1371/journal.pone.0268223] [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: 10/29/2021] [Accepted: 04/25/2022] [Indexed: 12/03/2022] Open
Abstract
Background Established MRI and emerging X-ray contrast agents for non-invasive imaging of articular cartilage rely on non-selective electrostatic interactions with negatively charged proteoglycans. These contrast agents have limited prognostic utility in diseases such as osteoarthritis (OA) due to the characteristic high turnover of proteoglycans. To overcome this limitation, we developed a radiocontrast agent that targets the type II collagen macromolecule in cartilage and used it to monitor disease progression in a murine model of OA. Methods To confer radiopacity to cartilage contrast agents, the naturally occurring tyrosine derivative 3,5-diiodo-L-tyrosine (DIT) was introduced into a selective peptide for type II collagen. Synthetic DIT peptide derivatives were synthesised by Fmoc-based solid-phase peptide synthesis and binding to ex vivo mouse tibial cartilage evaluated by high-resolution micro-CT. Di-Iodotyrosinated Peptide Imaging of Cartilage (DIPIC) was performed ex vivo and in vivo 4, 8 and 12 weeks in mice after induction of OA by destabilisation of the medial meniscus (DMM). Finally, human osteochondral plugs were imaged ex vivo using DIPIC. Results Fifteen DIT peptides were synthesised and tested, yielding seven leads with varying cartilage binding strengths. DIPIC visualised ex vivo murine articular cartilage comparably to the ex vivo contrast agent phosphotungstic acid. Intra-articular injection of contrast agent followed by in vivo DIPIC enabled delineation of damaged murine articular cartilage. Finally, the translational potential of the contrast agent was confirmed by visualisation of ex vivo human cartilage explants. Conclusion DIPIC has reduction and refinement implications in OA animal research and potential clinical translation to imaging human disease.
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Affiliation(s)
- Milan M. Fowkes
- Centre for OA Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Patricia Das Neves Borges
- Centre for OA Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Fernando Cacho-Nerin
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Paul E. Brennan
- Target Discovery Institute, Nuffield Department of Medicine Research Building, University of Oxford, Oxford, United Kingdom
| | - Tonia L. Vincent
- Centre for OA Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Ngee H. Lim
- Centre for OA Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
- * E-mail:
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15
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Mackinnon SR, Bezerra GA, Krojer T, Szommer T, von Delft F, Brennan PE, Yue WW. Novel Starting Points for Human Glycolate Oxidase Inhibitors, Revealed by Crystallography-Based Fragment Screening. Front Chem 2022; 10:844598. [PMID: 35601556 PMCID: PMC9114433 DOI: 10.3389/fchem.2022.844598] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Primary hyperoxaluria type I (PH1) is caused by AGXT gene mutations that decrease the functional activity of alanine:glyoxylate aminotransferase. A build-up of the enzyme’s substrate, glyoxylate, results in excessive deposition of calcium oxalate crystals in the renal tract, leading to debilitating renal failure. Oxidation of glycolate by glycolate oxidase (or hydroxy acid oxidase 1, HAO1) is a major cellular source of glyoxylate, and siRNA studies have shown phenotypic rescue of PH1 by the knockdown of HAO1, representing a promising inhibitor target. Here, we report the discovery and optimization of six low-molecular-weight fragments, identified by crystallography-based fragment screening, that bind to two different sites on the HAO1 structure: at the active site and an allosteric pocket above the active site. The active site fragments expand known scaffolds for substrate-mimetic inhibitors to include more chemically attractive molecules. The allosteric fragments represent the first report of non-orthosteric inhibition of any hydroxy acid oxidase and hold significant promise for improving inhibitor selectivity. The fragment hits were verified to bind and inhibit HAO1 in solution by fluorescence-based activity assay and surface plasmon resonance. Further optimization cycle by crystallography and biophysical assays have generated two hit compounds of micromolar (44 and 158 µM) potency that do not compete with the substrate and provide attractive starting points for the development of potent and selective HAO1 inhibitors.
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Affiliation(s)
- Sabrina R. Mackinnon
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gustavo A. Bezerra
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Tobias Krojer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Tamas Szommer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Frank von Delft
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Paul E. Brennan
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Target Discovery Institute, University of Oxford, Oxford, United Kingdom
- *Correspondence: Paul E. Brennan, ; Wyatt W. Yue,
| | - Wyatt W. Yue
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- *Correspondence: Paul E. Brennan, ; Wyatt W. Yue,
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16
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Rothweiler EM, Brennan PE, Huber KVM. Covalent fragment-based ligand screening approaches for identification of novel ubiquitin proteasome system modulators. Biol Chem 2022; 403:391-402. [PMID: 35191283 DOI: 10.1515/hsz-2021-0396] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/07/2022] [Indexed: 12/19/2022]
Abstract
Ubiquitination is a key regulatory mechanism vital for maintenance of cellular homeostasis. Protein degradation is induced by E3 ligases via attachment of ubiquitin chains to substrates. Pharmacological exploitation of this phenomenon via targeted protein degradation (TPD) can be achieved with molecular glues or bifunctional molecules facilitating the formation of ternary complexes between an E3 ligase and a given protein of interest (POI), resulting in ubiquitination of the substrate and subsequent proteolysis by the proteasome. Recently, the development of novel covalent fragment screening approaches has enabled the identification of first-in-class ligands for E3 ligases and deubiquitinases revealing so far unexplored binding sites which highlights the potential of these methods to uncover and expand druggable space for new target classes.
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Affiliation(s)
- Elisabeth M Rothweiler
- Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Target Discovery Institute, Oxford OX3 7FZ, UK
| | - Paul E Brennan
- Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Target Discovery Institute, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, Oxford OX3 7FZ, UK
| | - Kilian V M Huber
- Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Target Discovery Institute, Oxford OX3 7FZ, UK
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17
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Müller S, Ackloo S, Al Chawaf A, Al-Lazikani B, Antolin A, Baell JB, Beck H, Beedie S, Betz UAK, Bezerra GA, Brennan PE, Brown D, Brown PJ, Bullock AN, Carter AJ, Chaikuad A, Chaineau M, Ciulli A, Collins I, Dreher J, Drewry D, Edfeldt K, Edwards AM, Egner U, Frye SV, Fuchs SM, Hall MD, Hartung IV, Hillisch A, Hitchcock SH, Homan E, Kannan N, Kiefer JR, Knapp S, Kostic M, Kubicek S, Leach AR, Lindemann S, Marsden BD, Matsui H, Meier JL, Merk D, Michel M, Morgan MR, Mueller-Fahrnow A, Owen DR, Perry BG, Rosenberg SH, Saikatendu KS, Schapira M, Scholten C, Sharma S, Simeonov A, Sundström M, Superti-Furga G, Todd MH, Tredup C, Vedadi M, von Delft F, Willson TM, Winter GE, Workman P, Arrowsmith CH. Target 2035 - update on the quest for a probe for every protein. RSC Med Chem 2022; 13:13-21. [PMID: 35211674 PMCID: PMC8792830 DOI: 10.1039/d1md00228g] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 07/06/2021] [Accepted: 09/21/2021] [Indexed: 01/11/2023] Open
Abstract
Twenty years after the publication of the first draft of the human genome, our knowledge of the human proteome is still fragmented. The challenge of translating the wealth of new knowledge from genomics into new medicines is that proteins, and not genes, are the primary executers of biological function. Therefore, much of how biology works in health and disease must be understood through the lens of protein function. Accordingly, a subset of human proteins has been at the heart of research interests of scientists over the centuries, and we have accumulated varying degrees of knowledge about approximately 65% of the human proteome. Nevertheless, a large proportion of proteins in the human proteome (∼35%) remains uncharacterized, and less than 5% of the human proteome has been successfully targeted for drug discovery. This highlights the profound disconnect between our abilities to obtain genetic information and subsequent development of effective medicines. Target 2035 is an international federation of biomedical scientists from the public and private sectors, which aims to address this gap by developing and applying new technologies to create by year 2035 chemogenomic libraries, chemical probes, and/or biological probes for the entire human proteome.
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Affiliation(s)
- Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Frankfurt 60438 Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt Frankfurt 60438 Germany
| | - Suzanne Ackloo
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
| | | | - Bissan Al-Lazikani
- Department of Data Science, The Institute of Cancer Research London SM2 5NG UK
- CRUK ICR/Imperial Convergence Science Centre London SM2 5NG UK
| | - Albert Antolin
- Department of Data Science, The Institute of Cancer Research London SM2 5NG UK
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research London SM2 5NG UK
| | - Jonathan B Baell
- Monash Institute of Pharmaceutical Sciences, Monash University Parkville Victoria 3052 Australia
- School of Pharmaceutical Sciences, Nanjing Tech University No. 30 South Puzhu Road Nanjing 211816 People's Republic of China
| | - Hartmut Beck
- Research and Development, Bayer AG, Pharmaceuticals 42103 Wuppertal Germany
| | - Shaunna Beedie
- Centre for Medicines Discovery, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
| | | | - Gustavo Arruda Bezerra
- Centre for Medicines Discovery, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
| | - Paul E Brennan
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, University of Oxford Oxford OX3 7FZ UK
| | - David Brown
- Institut Recherches de Servier 125 Chemin de Ronde 78290 Croissy France
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
| | - Alex N Bullock
- Centre for Medicines Discovery, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
| | - Adrian J Carter
- Discovery Research, Boehringer Ingelheim 55216 Ingelheim am Rhein Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Frankfurt 60438 Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt Frankfurt 60438 Germany
| | - Mathilde Chaineau
- Early Drug Discovery Unit (EDDU), Montreal Neurological Institute-Hospital, McGill University Montreal QC Canada
| | - Alessio Ciulli
- School of Life Sciences, Division of Biological Chemistry and Drug Discovery, University of Dundee James Black Centre Dundee UK
| | - Ian Collins
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research London SM2 5NG UK
| | - Jan Dreher
- Research and Development, Bayer AG, Pharmaceuticals 42103 Wuppertal Germany
| | - David Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy Chapel Hill NC USA
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Kristina Edfeldt
- Structural Genomics Consortium, Department of Medicine, Karolinska University Hospital and Karolinska Institutet Stockholm Sweden
| | - Aled M Edwards
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
| | - Ursula Egner
- Nuvisan Innovation Campus Berlin GmbH Müllerstraße 178 13353 Berlin Germany
| | - Stephen V Frye
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | | | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health Rockville Maryland 20850 USA
| | - Ingo V Hartung
- Medicinal Chemistry, Global R&D, Merck Healthcare KGaA Frankfurter Straße 250 64293 Darmstadt Germany
| | - Alexander Hillisch
- Research and Development, Bayer AG, Pharmaceuticals 42103 Wuppertal Germany
| | | | - Evert Homan
- Science for Life Laboratory, Department of Oncology-Pathology Karolinska Institutet Stockholm Sweden
| | - Natarajan Kannan
- Institute of Bioinformatics and Department of Biochemistry and Molecular Biology, University of Georgia Athens GA USA
| | - James R Kiefer
- Genentech, Inc. 1 DNA Way South San Francisco California 94080 USA
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Frankfurt 60438 Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt Frankfurt 60438 Germany
| | - Milka Kostic
- Department of Cancer Biology and Chemical Biology Program, Dana-Farber Cancer Institute 450 Brookline Ave Boston MA 02215 USA
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna Austria
| | - Andrew R Leach
- European Molecular Biology Laboratory, European Bioinformatics Institute Wellcome Genome Campus, Hinxton Cambridgeshire CB10 1SD UK
| | - Sven Lindemann
- Strategic Innovation, Global R&D, Merck Healthcare KGaA Frankfurter Straße 250 64293 Darmstadt Germany
| | - Brian D Marsden
- Centre for Medicines Discovery, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford UK
| | - Hisanori Matsui
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited Fujisawa Kanagawa Japan
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick MD USA
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Frankfurt 60438 Germany
- LMU Munich, Department of Pharmacy, Chair of Pharmaceutical and Medicinal Chemistry 81377 Munich Germany
| | - Maurice Michel
- Science for Life Laboratory, Department of Oncology-Pathology Karolinska Institutet Stockholm Sweden
| | - Maxwell R Morgan
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
| | | | - Dafydd R Owen
- Discovery Network Group, Pfizer Medicine Design Cambridge MA 02139 USA
| | - Benjamin G Perry
- Drugs for Neglected Diseases initiative 15 Chemin Camille Vidart Geneva 1202 Switzerland
| | | | - Kumar Singh Saikatendu
- Global Research Externalization, Takeda California, Inc. 9625 Towne Center Drive San Diego CA 92121 USA
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
- Department of Pharmacology & Toxicology, University of Toronto Toronto Ontario M5S 1A8 Canada
| | - Cora Scholten
- Research and Development, Bayer AG, Pharmaceuticals 13353 Berlin Germany
| | - Sujata Sharma
- Structural & Protein Sciences, Discovery Sciences, Janssen Research & Development 1400 McKean Rd Spring House PA 19477 USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health Rockville Maryland 20850 USA
| | - Michael Sundström
- Division of Rheumatology, Department of Medicine Solna, Karolinska University Hospital and Karolinska Institutet Stockholm Sweden
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna Austria
- Center for Physiology and Pharmacology, Medical University of Vienna Vienna Austria
| | - Matthew H Todd
- School of Pharmacy, University College London London WC1N 1AX UK
| | - Claudia Tredup
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Frankfurt 60438 Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt Frankfurt 60438 Germany
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
- Department of Pharmacology & Toxicology, University of Toronto Toronto Ontario M5S 1A8 Canada
| | - Frank von Delft
- Centre for Medicines Discovery, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
- Diamond Light Source Ltd Harwell Science and Innovation Campus Didcot OX11 0QX UK
- Department of Biochemistry, University of Johannesburg Auckland Park 2006 South Africa
- Research Complex at Harwell Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Timothy M Willson
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna Austria
| | - Paul Workman
- CRUK ICR/Imperial Convergence Science Centre London SM2 5NG UK
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research London SM2 5NG UK
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
- Princess Margaret Cancer Centre Toronto Ontario M5G 1L7 Canada
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18
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Nizami S, Millar V, Arunasalam K, Zarganes-Tzitzikas T, Brough D, Tresadern G, Brennan PE, Davis JB, Ebner D, Di Daniel E. Author Correction: A phenotypic high-content, high-throughput screen identifies inhibitors of NLRP3 inflammasome activation. Sci Rep 2021; 11:20529. [PMID: 34635690 PMCID: PMC8505597 DOI: 10.1038/s41598-021-00202-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Sohaib Nizami
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.,Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Val Millar
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.,Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.,National Phenotypic Screening Centre, Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Kanisa Arunasalam
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.,Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Tryfon Zarganes-Tzitzikas
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.,Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - David Brough
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK.,Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, M13 9PT, UK
| | - Gary Tresadern
- Janssen Research and Development, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Paul E Brennan
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.,Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - John B Davis
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.,Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Daniel Ebner
- Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK. .,National Phenotypic Screening Centre, Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.
| | - Elena Di Daniel
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK. .,Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.
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19
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Nizami S, Millar V, Arunasalam K, Zarganes-Tzitzikas T, Brough D, Tresadern G, Brennan PE, Davis JB, Ebner D, Di Daniel E. A phenotypic high-content, high-throughput screen identifies inhibitors of NLRP3 inflammasome activation. Sci Rep 2021; 11:15319. [PMID: 34321581 PMCID: PMC8319173 DOI: 10.1038/s41598-021-94850-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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] [Received: 12/17/2020] [Accepted: 07/13/2021] [Indexed: 12/26/2022] Open
Abstract
Inhibition of the NACHT, LRR and PYD domains-containing protein 3 (NLRP3) inflammasome has recently emerged as a promising therapeutic target for several inflammatory diseases. After priming and activation by inflammation triggers, NLRP3 forms a complex with apoptosis-associated speck-like protein containing a CARD domain (ASC) followed by formation of the active inflammasome. Identification of inhibitors of NLRP3 activation requires a well-validated primary high-throughput assay followed by the deployment of a screening cascade of assays enabling studies of structure–activity relationship, compound selectivity and efficacy in disease models. We optimized a NLRP3-dependent fluorescent tagged ASC speck formation assay in murine immortalized bone marrow-derived macrophages and utilized it to screen a compound library of 81,000 small molecules. Our high-content screening assay yielded robust assay metrics and identified a number of inhibitors of NLRP3-dependent ASC speck formation, including compounds targeting HSP90, JAK and IKK-β. Additional assays to investigate inflammasome priming or activation, NLRP3 downstream effectors such as caspase-1, IL-1β and pyroptosis form the basis of a screening cascade to identify NLRP3 inflammasome inhibitors in drug discovery programs.
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Affiliation(s)
- Sohaib Nizami
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.,Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Val Millar
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.,Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.,National Phenotypic Screening Centre, Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Kanisa Arunasalam
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.,Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Tryfon Zarganes-Tzitzikas
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.,Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - David Brough
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK.,Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, M13 9PT, UK
| | - Gary Tresadern
- Janssen Research and Development, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Paul E Brennan
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.,Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - John B Davis
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.,Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Daniel Ebner
- Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK. .,National Phenotypic Screening Centre, Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.
| | - Elena Di Daniel
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK. .,Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.
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20
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Quinlan RBA, Brennan PE. Chemogenomics for drug discovery: clinical molecules from open access chemical probes. RSC Chem Biol 2021; 2:759-795. [PMID: 34458810 PMCID: PMC8341094 DOI: 10.1039/d1cb00016k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 01/27/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
In recent years chemical probes have proved valuable tools for the validation of disease-modifying targets, facilitating investigation of target function, safety, and translation. Whilst probes and drugs often differ in their properties, there is a belief that chemical probes are useful for translational studies and can accelerate the drug discovery process by providing a starting point for small molecule drugs. This review seeks to describe clinical candidates that have been inspired by, or derived from, chemical probes, and the process behind their development. By focusing primarily on examples of probes developed by the Structural Genomics Consortium, we examine a variety of epigenetic modulators along with other classes of probe.
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Affiliation(s)
- Robert B A Quinlan
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Old Road Campus Oxford OX3 7FZ UK
| | - Paul E Brennan
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Old Road Campus Oxford OX3 7FZ UK
- Alzheimer's Research (UK) Oxford Drug Discovery Institute, Nuffield Department of Medicine, University of Oxford Oxford OX3 7FZ UK
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21
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Nie L, Pascoa TC, Pike ACW, Bushell SR, Quigley A, Ruda GF, Chu A, Cole V, Speedman D, Moreira T, Shrestha L, Mukhopadhyay SM, Burgess-Brown NA, Love JD, Brennan PE, Carpenter EP. The structural basis of fatty acid elongation by the ELOVL elongases. Nat Struct Mol Biol 2021; 28:512-520. [PMID: 34117479 PMCID: PMC7611377 DOI: 10.1038/s41594-021-00605-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/11/2021] [Indexed: 02/05/2023]
Abstract
Very long chain fatty acids (VLCFAs) are essential building blocks for the synthesis of ceramides and sphingolipids. The first step in the fatty acid elongation cycle is catalyzed by the 3-keto acyl-coenzyme A (CoA) synthases (in mammals, ELOVL elongases). Although ELOVLs are implicated in common diseases, including insulin resistance, hepatic steatosis and Parkinson's, their underlying molecular mechanisms are unknown. Here we report the structure of the human ELOVL7 elongase, which comprises an inverted transmembrane barrel surrounding a 35-Å long tunnel containing a covalently attached product analogue. The structure reveals the substrate-binding sites in the narrow tunnel and an active site deep in the membrane. We demonstrate that chain elongation proceeds via an acyl-enzyme intermediate involving the second histidine in the canonical HxxHH motif. The unusual substrate-binding arrangement and chemistry suggest mechanisms for selective ELOVL inhibition, relevant for diseases where VLCFAs accumulate, such as X-linked adrenoleukodystrophy.
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Affiliation(s)
- Laiyin Nie
- Structural Genomics Consortium, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7DQ, UK
| | - Tomas C. Pascoa
- Structural Genomics Consortium, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7DQ, UK
| | - Ashley C. W. Pike
- Structural Genomics Consortium, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7DQ, UK
| | - Simon R. Bushell
- Structural Genomics Consortium, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7DQ, UK
| | - Andrew Quigley
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK,Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Gian Filippo Ruda
- Structural Genomics Consortium, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7DQ, UK
| | - Amy Chu
- Structural Genomics Consortium, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7DQ, UK
| | - Victoria Cole
- Structural Genomics Consortium, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7DQ, UK
| | - David Speedman
- Structural Genomics Consortium, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7DQ, UK
| | - Tiago Moreira
- Structural Genomics Consortium, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7DQ, UK
| | - Leela Shrestha
- Structural Genomics Consortium, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7DQ, UK
| | | | - Nicola A. Burgess-Brown
- Structural Genomics Consortium, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7DQ, UK
| | - James D. Love
- Albert Einstein College of Medicine, Department of Biochemistry, 1300 Morris Park Avenue, Bronx, NY 10461-1602, USA
| | - Paul E. Brennan
- Structural Genomics Consortium, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7DQ, UK,Alzheimer’s Research UK Oxford Drug Discovery Institute, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Elisabeth P. Carpenter
- Structural Genomics Consortium, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7DQ, UK,Correspondence and requests for materials should be addressed to E.P.C. ()
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22
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Mackinnon S, Krojer T, Foster WR, Diaz-Saez L, Tang M, Huber KVM, von Delft F, Lai K, Brennan PE, Arruda Bezerra G, Yue WW. Fragment Screening Reveals Starting Points for Rational Design of Galactokinase 1 Inhibitors to Treat Classic Galactosemia. ACS Chem Biol 2021; 16:586-595. [PMID: 33724769 PMCID: PMC8056384 DOI: 10.1021/acschembio.0c00498] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 02/18/2021] [Indexed: 11/28/2022]
Abstract
Classic galactosemia is caused by loss-of-function mutations in galactose-1-phosphate uridylyltransferase (GALT) that lead to toxic accumulation of its substrate, galactose-1-phosphate. One proposed therapy is to inhibit the biosynthesis of galactose-1-phosphate, catalyzed by galactokinase 1 (GALK1). Existing inhibitors of human GALK1 (hGALK1) are primarily ATP-competitive with limited clinical utility to date. Here, we determined crystal structures of hGALK1 bound with reported ATP-competitive inhibitors of the spiro-benzoxazole series, to reveal their binding mode in the active site. Spurred by the need for additional chemotypes of hGALK1 inhibitors, desirably targeting a nonorthosteric site, we also performed crystallography-based screening by soaking hundreds of hGALK1 crystals, already containing active site ligands, with fragments from a custom library. Two fragments were found to bind close to the ATP binding site, and a further eight were found in a hotspot distal from the active site, highlighting the strength of this method in identifying previously uncharacterized allosteric sites. To generate inhibitors of improved potency and selectivity targeting the newly identified binding hotspot, new compounds were designed by merging overlapping fragments. This yielded two micromolar inhibitors of hGALK1 that were not competitive with respect to either substrate (ATP or galactose) and demonstrated good selectivity over hGALK1 homologues, galactokinase 2 and mevalonate kinase. Our findings are therefore the first to demonstrate inhibition of hGALK1 from an allosteric site, with potential for further development of potent and selective inhibitors to provide novel therapeutics for classic galactosemia.
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Affiliation(s)
- Sabrina
R. Mackinnon
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
| | - Tobias Krojer
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
| | - William R. Foster
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
| | - Laura Diaz-Saez
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
- Target
Discovery Institute, University of Oxford, Oxford, United Kingdom, OX3 7FZ
| | - Manshu Tang
- Department
of Pediatrics, University of Utah, Salt Lake City, Utah 84108-6500, United States
| | - Kilian V. M. Huber
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
- Target
Discovery Institute, University of Oxford, Oxford, United Kingdom, OX3 7FZ
| | - Frank von Delft
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
- Diamond
Light Source, Harwell Science and Innovation
Campus, Didcot, Oxfordshire, United Kingdom, OX11 0DE
| | - Kent Lai
- Department
of Pediatrics, University of Utah, Salt Lake City, Utah 84108-6500, United States
| | - Paul E. Brennan
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
- Target
Discovery Institute, University of Oxford, Oxford, United Kingdom, OX3 7FZ
| | - Gustavo Arruda Bezerra
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
| | - Wyatt W. Yue
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
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23
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Thompson AP, Bitsina C, Gray JL, von Delft F, Brennan PE. RHO to the DOCK for GDP disembarking: Structural insights into the DOCK GTPase nucleotide exchange factors. J Biol Chem 2021; 296:100521. [PMID: 33684443 PMCID: PMC8063744 DOI: 10.1016/j.jbc.2021.100521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 11/03/2020] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 01/16/2023] Open
Abstract
The human dedicator of cytokinesis (DOCK) family consists of 11 structurally conserved proteins that serve as atypical RHO guanine nucleotide exchange factors (RHO GEFs). These regulatory proteins act as mediators in numerous cellular cascades that promote cytoskeletal remodeling, playing roles in various crucial processes such as differentiation, migration, polarization, and axon growth in neurons. At the molecular level, DOCK DHR2 domains facilitate nucleotide dissociation from small GTPases, a process that is otherwise too slow for rapid spatiotemporal control of cellular signaling. Here, we provide an overview of the biological and structural characteristics for the various DOCK proteins and describe how they differ from other RHO GEFs and between DOCK subfamilies. The expression of the family varies depending on cell or tissue type, and they are consequently implicated in a broad range of disease phenotypes, particularly in the brain. A growing body of available structural information reveals the mechanism by which the catalytic DHR2 domain elicits nucleotide dissociation and also indicates strategies for the discovery and design of high-affinity small-molecule inhibitors. Such compounds could serve as chemical probes to interrogate the cellular function and provide starting points for drug discovery of this important class of enzymes.
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Affiliation(s)
- Andrew P Thompson
- Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Christina Bitsina
- Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Janine L Gray
- Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Frank von Delft
- Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom; Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
| | - Paul E Brennan
- Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom.
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24
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Doss PMIA, Umair M, Baillargeon J, Fazazi R, Fudge N, Akbar I, Yeola AP, Williams JB, Leclercq M, Joly-Beauparlant C, Beauchemin P, Ruda GF, Alpaugh M, Anderson AC, Brennan PE, Droit A, Lassmann H, Moore CS, Rangachari M. Male sex chromosomal complement exacerbates the pathogenicity of Th17 cells in a chronic model of central nervous system autoimmunity. Cell Rep 2021; 34:108833. [PMID: 33691111 DOI: 10.1016/j.celrep.2021.108833] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 12/13/2020] [Accepted: 02/16/2021] [Indexed: 12/13/2022] Open
Abstract
Sex differences in multiple sclerosis (MS) incidence and severity have long been recognized. However, the underlying cellular and molecular mechanisms for why male sex is associated with more aggressive disease remain poorly defined. Using a T cell adoptive transfer model of chronic experimental autoimmune encephalomyelitis (EAE), we find that male Th17 cells induce disease of increased severity relative to female Th17 cells, irrespective of whether transferred to male or female recipients. Throughout the disease course, a greater frequency of male Th17 cells produce IFNγ, a hallmark of pathogenic Th17 responses. Intriguingly, XY chromosomal complement increases the pathogenicity of male Th17 cells. An X-linked immune regulator, Jarid1c, is downregulated in pathogenic male murine Th17 cells, and functional experiments reveal that it represses the severity of Th17-mediated EAE. Furthermore, Jarid1c expression is downregulated in CD4+ T cells from MS-affected individuals. Our data indicate that male sex chromosomal complement critically regulates Th17 cell pathogenicity.
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Affiliation(s)
- Prenitha Mercy Ignatius Arokia Doss
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada
| | - Muhammad Umair
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada
| | - Joanie Baillargeon
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada
| | - Reda Fazazi
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada
| | - Neva Fudge
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL A1B 3V6, Canada
| | - Irshad Akbar
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada
| | - Asmita Pradeep Yeola
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada
| | - John B Williams
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL A1B 3V6, Canada
| | - Mickael Leclercq
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada
| | - Charles Joly-Beauparlant
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada
| | - Philippe Beauchemin
- Department of Neurology, CHU de Québec-Université Laval, Quebec City, QC G1V 4G2, Canada; Faculty of Medicine, Université Laval, 1050 ave de la Médecine, Quebec City, QC, Canada
| | - Gian Filipo Ruda
- Target Discovery Institute and NIHR, Oxford Biomedical Research Centre, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Melanie Alpaugh
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada
| | - Ana C Anderson
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham & Women's Hospital, 60 Fenwood Road, Boston, MA 02115, USA
| | - Paul E Brennan
- Target Discovery Institute and NIHR, Oxford Biomedical Research Centre, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Alzheimer's Research UK, Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Arnaud Droit
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; Faculty of Medicine, Université Laval, 1050 ave de la Médecine, Quebec City, QC, Canada
| | - Hans Lassmann
- Division of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, Vienna 1090, Austria
| | - Craig S Moore
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL A1B 3V6, Canada; Department of Neurology, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL A1B 3V6, Canada
| | - Manu Rangachari
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; Faculty of Medicine, Université Laval, 1050 ave de la Médecine, Quebec City, QC, Canada.
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25
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Vilema-Enríquez G, Quinlan R, Kilfeather P, Mazzone R, Saqlain S, Del Molino Del Barrio I, Donato A, Corda G, Li F, Vedadi M, Németh AH, Brennan PE, Wade-Martins R. Inhibition of the SUV4-20 H1 histone methyltransferase increases frataxin expression in Friedreich's ataxia patient cells. J Biol Chem 2020; 295:17973-17985. [PMID: 33028632 PMCID: PMC7939392 DOI: 10.1074/jbc.ra120.015533] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
The molecular mechanisms of reduced frataxin (FXN) expression in Friedreich's ataxia (FRDA) are linked to epigenetic modification of the FXN locus caused by the disease-associated GAA expansion. Here, we identify that SUV4-20 histone methyltransferases, specifically SUV4-20 H1, play an important role in the regulation of FXN expression and represent a novel therapeutic target. Using a human FXN-GAA-Luciferase repeat expansion genomic DNA reporter model of FRDA, we screened the Structural Genomics Consortium epigenetic probe collection. We found that pharmacological inhibition of the SUV4-20 methyltransferases by the tool compound A-196 increased the expression of FXN by ∼1.5-fold in the reporter cell line. In several FRDA cell lines and patient-derived primary peripheral blood mononuclear cells, A-196 increased FXN expression by up to 2-fold, an effect not seen in WT cells. SUV4-20 inhibition was accompanied by a reduction in H4K20me2 and H4K20me3 and an increase in H4K20me1, but only modest (1.4-7.8%) perturbation in genome-wide expression was observed. Finally, based on the structural activity relationship and crystal structure of A-196, novel small molecule A-196 analogs were synthesized and shown to give a 20-fold increase in potency for increasing FXN expression. Overall, our results suggest that histone methylation is important in the regulation of FXN expression and highlight SUV4-20 H1 as a potential novel therapeutic target for FRDA.
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Affiliation(s)
| | - Robert Quinlan
- Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Alzheimer's Research UK Oxford Drug Discovery Institute, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Peter Kilfeather
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Roberta Mazzone
- Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Alzheimer's Research UK Oxford Drug Discovery Institute, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Saba Saqlain
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Annalidia Donato
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Gabriele Corda
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom; Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Service Trust, Oxford, United Kingdom
| | - Paul E Brennan
- Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Alzheimer's Research UK Oxford Drug Discovery Institute, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Richard Wade-Martins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.
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26
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Katis V, Bradshaw W, Betarbet R, Jimenez‐Antunez C, Seyfried NT, Slakman B, Mulhern C, Guie M, Keefe A, Guilinger J, Zhang Y, Huguet C, Levey AI, Brennan PE, Mangravite LM, Gileadi O. Targeting the Moesin‐CD44 pathway for therapeutic intervention in Alzheimer’s disease. Alzheimers Dement 2020. [DOI: 10.1002/alz.045915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Vittorio Katis
- Structural Genomics Consortium University of Oxford Oxford United Kingdom
| | - William Bradshaw
- Structrual Genomics Consortium The University of Oxford Oxford United Kingdom
| | | | - Carmen Jimenez‐Antunez
- Structural Genomics Consortium University of Oxford Oxford United Kingdom
- Alzheimer’s Research UK Oxford Drug Discovery Institute University of Oxford Oxford United Kingdom
| | | | | | | | | | | | | | | | | | - Allan I. Levey
- Emory Goizueta Alzheimer's Disease Research Center Atlanta GA USA
| | - Paul E. Brennan
- Alzheimer’s Research UK Oxford Drug Discovery Institute University of Oxford Oxford United Kingdom
| | | | - Opher Gileadi
- Structural Genomics Consortium University of Oxford Oxford United Kingdom
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27
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Cottone L, Cribbs AP, Khandelwal G, Wells G, Ligammari L, Philpott M, Tumber A, Lombard P, Hookway ES, Szommer T, Johansson C, Brennan PE, Pillay N, Jenner RG, Oppermann U, Flanagan AM. Inhibition of Histone H3K27 Demethylases Inactivates Brachyury (TBXT) and Promotes Chordoma Cell Death. Cancer Res 2020; 80:4540-4551. [PMID: 32855205 DOI: 10.1158/0008-5472.can-20-1387] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 04/25/2020] [Revised: 07/08/2020] [Accepted: 08/19/2020] [Indexed: 11/16/2022]
Abstract
Expression of the transcription factor brachyury (TBXT) is normally restricted to the embryo, and its silencing is epigenetically regulated. TBXT promotes mesenchymal transition in a subset of common carcinomas, and in chordoma, a rare cancer showing notochordal differentiation, TBXT acts as a putative oncogene. We hypothesized that TBXT expression is controlled through epigenetic inhibition to promote chordoma cell death. Screening of five human chordoma cell lines revealed that pharmacologic inhibition of the histone 3 lysine 27 demethylases KDM6A (UTX) and KDM6B (JMJD3) leads to cell death. This effect was phenocopied by dual genetic inactivation of KDM6A/B using CRISPR/Cas9. Inhibition of KDM6A/B with a novel compound KDOBA67 led to a genome-wide increase in repressive H3K27me3 marks with concomitant reduction in active H3K27ac, H3K9ac, and H3K4me3 marks. TBXT was a KDM6A/B target gene, and chromatin changes at TBXT following KDOBA67 treatment were associated with a reduction in TBXT protein levels in all models tested, including primary patient-derived cultures. In all models tested, KDOBA67 treatment downregulated expression of a network of transcription factors critical for chordoma survival and upregulated pathways dominated by ATF4-driven stress and proapoptotic responses. Blocking the AFT4 stress response did not prevent suppression of TBXT and induction of cell death, but ectopic overexpression of TBXT increased viability, therefore implicating TBXT as a potential therapeutic target of H3K27 demethylase inhibitors in chordoma. Our work highlights how knowledge of normal processes in fetal development can provide insight into tumorigenesis and identify novel therapeutic approaches. SIGNIFICANCE: Pharmacologic inhibition of H3K27-demethylases in human chordoma cells promotes epigenetic silencing of oncogenic TBXT, alters gene networks critical to survival, and represents a potential novel therapy.
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Affiliation(s)
- Lucia Cottone
- Department of Pathology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Adam P Cribbs
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Garima Khandelwal
- Department of Cancer Biology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Graham Wells
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Lorena Ligammari
- Department of Pathology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Martin Philpott
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom
| | - Patrick Lombard
- Department of Pathology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Edward S Hookway
- Department of Pathology, UCL Cancer Institute, University College London, London, United Kingdom
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Tamas Szommer
- Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom
| | - Catrine Johansson
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Paul E Brennan
- Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom
| | - Nischalan Pillay
- Department of Pathology, UCL Cancer Institute, University College London, London, United Kingdom
- Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, Middlesex, United Kingdom
| | - Richard G Jenner
- Department of Cancer Biology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Udo Oppermann
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom.
- Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom
- FRIAS - Freiburg Institute of Advanced Studies, University of Freiburg, Freiburg, Germany
| | - Adrienne M Flanagan
- Department of Pathology, UCL Cancer Institute, University College London, London, United Kingdom.
- Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, Middlesex, United Kingdom
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28
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Abstract
When trying to identify new potential therapeutic protein targets, access to data and knowledge is increasingly important. In a field where new resources and data sources become available every day, it is crucial to be able to take a step back and look at the wider picture in order to identify potential drug targets. While this task is routinely performed by bespoke literature searches, it is often time-consuming and lacks uniformity when comparing multiple targets at one time. To address this challenge, we developed TargetDB, a tool that aggregates public information available on given target(s) (links to disease, safety, 3D structures, ligandability, novelty, etc.) and assembles it in an easy to read output ready for the researcher to analyze. In addition, we developed a target scoring system based on the desirable attributes of good therapeutic targets and machine learning classification system to categorize novel targets as having promising or challenging tractrability. In this manuscript, we present the methodology used to develop TargetDB as well as test cases.
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Affiliation(s)
- Stephane De Cesco
- Nuffield Department of Medicine, ARUK Oxford Drug Discovery Institute, Target Discovery Institute, University of Oxford, Oxford, United-Kingdom
- * E-mail: (PEB); (SDC)
| | - John B. Davis
- Nuffield Department of Medicine, ARUK Oxford Drug Discovery Institute, Target Discovery Institute, University of Oxford, Oxford, United-Kingdom
| | - Paul E. Brennan
- Nuffield Department of Medicine, ARUK Oxford Drug Discovery Institute, Target Discovery Institute, University of Oxford, Oxford, United-Kingdom
- * E-mail: (PEB); (SDC)
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29
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Abstract
The Ras superfamily of small GTPases are guanine-nucleotide-dependent switches essential for numerous cellular processes. Mutations or dysregulation of these proteins are associated with many diseases, but unsuccessful attempts to target the small GTPases directly have resulted in them being classed as "undruggable". The GTP-dependent signaling of these proteins is controlled by their regulators; guanine nucleotide exchange factors (GEFs), GTPase activating proteins (GAPs), and in the Rho and Rab subfamilies, guanine nucleotide dissociation inhibitors (GDIs). This review covers the recent small molecule and biologics strategies to target the small GTPases through their regulators. It seeks to critically re-evaluate recent chemical biology practice, such as the presence of PAINs motifs and the cell-based readout using compounds that are weakly potent or of unknown specificity. It highlights the vast scope of potential approaches for targeting the small GTPases in the future through their regulatory proteins.
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Affiliation(s)
- Janine L. Gray
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordOld Road CampusOxfordOX3 7FZUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0QXUK
| | - Frank von Delft
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0QXUK
- Department of BiochemistryUniversity of JohannesburgAuckland Park2006South Africa
| | - Paul E. Brennan
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordOld Road CampusOxfordOX3 7FZUK
- Alzheimer's Research (UK) Oxford Drug Discovery InstituteNuffield Department of MedicineUniversity of OxfordOxfordOX3 7FZUK
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30
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Affiliation(s)
- Janine L. Gray
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Old Road Campus Oxford OX3 7FZ Großbritannien
- Diamond Light Source Harwell Science and Innovation Campus Didcot OX11 0QX Großbritannien
| | - Frank Delft
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Diamond Light Source Harwell Science and Innovation Campus Didcot OX11 0QX Großbritannien
- Department of BiochemistryUniversity of Johannesburg Auckland Park 2006 Südafrika
| | - Paul E. Brennan
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Old Road Campus Oxford OX3 7FZ Großbritannien
- Alzheimer's Research (UK) Oxford Drug Discovery InstituteNuffield Department of MedicineUniversity of Oxford Oxford OX3 7FZ Großbritannien
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31
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Ni X, Heidenreich D, Christott T, Bennett J, Moustakim M, Brennan PE, Fedorov O, Knapp S, Chaikuad A. Structural Insights into Interaction Mechanisms of Alternative Piperazine-urea YEATS Domain Binders in MLLT1. ACS Med Chem Lett 2019; 10:1661-1666. [PMID: 31857843 DOI: 10.1021/acsmedchemlett.9b00460] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022] Open
Abstract
YEATS-domain-containing MLLT1 is an acetyl/acyl-lysine reader domain, which is structurally distinct from well-studied bromodomains and has been strongly associated in development of cancer. Here, we characterized piperazine-urea derivatives as an acetyl/acyl-lysine mimetic moiety for MLLT1. Crystal structures revealed distinct interaction mechanisms of this chemotype compared to the recently described benzimidazole-amide based inhibitors, exploiting different binding pockets within the protein. Thus, the piperazine-urea scaffold offers an alternative strategy for targeting the YEATS domain family.
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Affiliation(s)
- Xiaomin Ni
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Structural Genomics Consortium, BMLS, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - David Heidenreich
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Structural Genomics Consortium, BMLS, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Thomas Christott
- Target Discovery Institute and Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
| | - James Bennett
- Target Discovery Institute and Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
| | - Moses Moustakim
- Target Discovery Institute and Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
| | | | - Oleg Fedorov
- Target Discovery Institute and Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Structural Genomics Consortium, BMLS, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Structural Genomics Consortium, BMLS, Goethe-University Frankfurt, 60438 Frankfurt, Germany
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32
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Fagan V, Johansson C, Gileadi C, Monteiro O, Dunford JE, Nibhani R, Philpott M, Malzahn J, Wells G, Faram R, Cribbs AP, Halidi N, Li F, Chau I, Greschik H, Velupillai S, Allali-Hassani A, Bennett J, Christott T, Giroud C, Lewis AM, Huber KVM, Athanasou N, Bountra C, Jung M, Schüle R, Vedadi M, Arrowsmith C, Xiong Y, Jin J, Fedorov O, Farnie G, Brennan PE, Oppermann U. A Chemical Probe for Tudor Domain Protein Spindlin1 to Investigate Chromatin Function. J Med Chem 2019; 62:9008-9025. [PMID: 31550156 DOI: 10.1021/acs.jmedchem.9b00562] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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] [Indexed: 02/06/2023]
Abstract
Modifications of histone tails, including lysine/arginine methylation, provide the basis of a "chromatin or histone code". Proteins that contain "reader" domains can bind to these modifications and form specific effector complexes, which ultimately mediate chromatin function. The spindlin1 (SPIN1) protein contains three Tudor methyllysine/arginine reader domains and was identified as a putative oncogene and transcriptional coactivator. Here we report a SPIN1 chemical probe inhibitor with low nanomolar in vitro activity, exquisite selectivity on a panel of methyl reader and writer proteins, and with submicromolar cellular activity. X-ray crystallography showed that this Tudor domain chemical probe simultaneously engages Tudor domains 1 and 2 via a bidentate binding mode. Small molecule inhibition and siRNA knockdown of SPIN1, as well as chemoproteomic studies, identified genes which are transcriptionally regulated by SPIN1 in squamous cell carcinoma and suggest that SPIN1 may have a role in cancer related inflammation and/or cancer metastasis.
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Affiliation(s)
- Vincent Fagan
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Catrine Johansson
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Carina Gileadi
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Octovia Monteiro
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - James E Dunford
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Reshma Nibhani
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Martin Philpott
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Jessica Malzahn
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Graham Wells
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Ruth Faram
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Adam P Cribbs
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Nadia Halidi
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Fengling Li
- Structural Genomics Consortium , University of Toronto , 101 College Street , Toronto , Ontario M5G 1L7 , Canada
| | - Irene Chau
- Structural Genomics Consortium , University of Toronto , 101 College Street , Toronto , Ontario M5G 1L7 , Canada
| | - Holger Greschik
- Department of Urology, Center for Clinical Research, Medical Center, Signalling Research Centres BIOSS and CIBSS , University of Freiburg , D-79106 Freiburg , Germany
| | - Srikannathasan Velupillai
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
| | - Abdellah Allali-Hassani
- Structural Genomics Consortium , University of Toronto , 101 College Street , Toronto , Ontario M5G 1L7 , Canada
| | - James Bennett
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Thomas Christott
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Charline Giroud
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Andrew M Lewis
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Kilian V M Huber
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Nick Athanasou
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Chas Bountra
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
| | - Manfred Jung
- FRIAS-Freiburg Institute of Advanced Studies , University of Freiburg , 79104 Freiburg , Germany
- Institute of Pharmaceutical Sciences , University of Freiburg , Albertstraße 25 , 79104 Freiburg , Germany
| | - Roland Schüle
- Department of Urology, Center for Clinical Research, Medical Center, Signalling Research Centres BIOSS and CIBSS , University of Freiburg , D-79106 Freiburg , Germany
| | - Masoud Vedadi
- Structural Genomics Consortium , University of Toronto , 101 College Street , Toronto , Ontario M5G 1L7 , Canada
| | - Cheryl Arrowsmith
- Structural Genomics Consortium , University of Toronto , 101 College Street , Toronto , Ontario M5G 1L7 , Canada
| | - Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences , Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences , Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States
| | - Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Gillian Farnie
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Paul E Brennan
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
- Alzheimer's Research UK Oxford Drug Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Udo Oppermann
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
- FRIAS-Freiburg Institute of Advanced Studies , University of Freiburg , 79104 Freiburg , Germany
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33
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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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34
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Fang H, De Wolf H, Knezevic B, Burnham KL, Osgood J, Sanniti A, Lledó Lara A, Kasela S, De Cesco S, Wegner JK, Handunnetthi L, McCann FE, Chen L, Sekine T, Brennan PE, Marsden BD, Damerell D, O'Callaghan CA, Bountra C, Bowness P, Sundström Y, Milani L, Berg L, Göhlmann HW, Peeters PJ, Fairfax BP, Sundström M, Knight JC. A genetics-led approach defines the drug target landscape of 30 immune-related traits. Nat Genet 2019; 51:1082-1091. [PMID: 31253980 PMCID: PMC7124888 DOI: 10.1038/s41588-019-0456-1] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [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: 11/22/2018] [Accepted: 05/24/2019] [Indexed: 12/22/2022]
Abstract
Most candidate drugs currently fail later-stage clinical trials, largely due to poor prediction of efficacy on early target selection1. Drug targets with genetic support are more likely to be therapeutically valid2,3, but the translational use of genome-scale data such as from genome-wide association studies for drug target discovery in complex diseases remains challenging4-6. Here, we show that integration of functional genomic and immune-related annotations, together with knowledge of network connectivity, maximizes the informativeness of genetics for target validation, defining the target prioritization landscape for 30 immune traits at the gene and pathway level. We demonstrate how our genetics-led drug target prioritization approach (the priority index) successfully identifies current therapeutics, predicts activity in high-throughput cellular screens (including L1000, CRISPR, mutagenesis and patient-derived cell assays), enables prioritization of under-explored targets and allows for determination of target-level trait relationships. The priority index is an open-access, scalable system accelerating early-stage drug target selection for immune-mediated disease.
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Affiliation(s)
- Hai Fang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Bogdan Knezevic
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Katie L Burnham
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Julie Osgood
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Anna Sanniti
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alicia Lledó Lara
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Silva Kasela
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Stephane De Cesco
- Alzheimer's Research UK Oxford Drug Discovery Institute, Target Discovery Institute, University of Oxford, Oxford, UK
| | | | | | - Fiona E McCann
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Liye Chen
- Botnar Research Centre, University of Oxford, Oxford, UK
| | - Takuya Sekine
- Botnar Research Centre, University of Oxford, Oxford, UK
| | - Paul E Brennan
- Alzheimer's Research UK Oxford Drug Discovery Institute, Target Discovery Institute, University of Oxford, Oxford, UK
- Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Brian D Marsden
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - David Damerell
- Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Chris A O'Callaghan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Chas Bountra
- Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Paul Bowness
- Botnar Research Centre, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Yvonne Sundström
- Structural Genomics Consortium, Department of Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Lili Milani
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Louise Berg
- Structural Genomics Consortium, Department of Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | | | | | - Benjamin P Fairfax
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Michael Sundström
- Structural Genomics Consortium, Department of Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.
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35
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Resnick E, Bradley A, Gan J, Douangamath A, Krojer T, Sethi R, Geurink PP, Aimon A, Amitai G, Bellini D, Bennett J, Fairhead M, Fedorov O, Gabizon R, Gan J, Guo J, Plotnikov A, Reznik N, Ruda GF, Díaz-Sáez L, Straub VM, Szommer T, Velupillai S, Zaidman D, Zhang Y, Coker AR, Dowson CG, Barr HM, Wang C, Huber KVM, Brennan PE, Ovaa H, von Delft F, London N. Rapid Covalent-Probe Discovery by Electrophile-Fragment Screening. J Am Chem Soc 2019; 141:8951-8968. [PMID: 31060360 PMCID: PMC6556873 DOI: 10.1021/jacs.9b02822] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [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: 12/24/2022]
Abstract
Covalent probes can display unmatched potency, selectivity, and duration of action; however, their discovery is challenging. In principle, fragments that can irreversibly bind their target can overcome the low affinity that limits reversible fragment screening, but such electrophilic fragments were considered nonselective and were rarely screened. We hypothesized that mild electrophiles might overcome the selectivity challenge and constructed a library of 993 mildly electrophilic fragments. We characterized this library by a new high-throughput thiol-reactivity assay and screened them against 10 cysteine-containing proteins. Highly reactive and promiscuous fragments were rare and could be easily eliminated. In contrast, we found hits for most targets. Combining our approach with high-throughput crystallography allowed rapid progression to potent and selective probes for two enzymes, the deubiquitinase OTUB2 and the pyrophosphatase NUDT7. No inhibitors were previously known for either. This study highlights the potential of electrophile-fragment screening as a practical and efficient tool for covalent-ligand discovery.
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Affiliation(s)
| | - Anthony Bradley
- Department of Chemistry , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , U.K.,Diamond Light Source Ltd., Harwell Science and Innovation Campus , Didcot OX11 0QX , U.K
| | | | - Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus , Didcot OX11 0QX , U.K
| | | | - Ritika Sethi
- Structural Biology Research Center , VIB , Brussels , Belgium.,Structural Biology Brussels , Vrije Universiteit Brussel , Brussels , Belgium
| | - Paul P Geurink
- Oncode Institute and Department of Cell and Chemical Biology , Leiden University Medical Center , Einthovenweg 20 , 2333 ZC Leiden , The Netherlands
| | - Anthony Aimon
- Department of Chemistry , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , U.K.,Diamond Light Source Ltd., Harwell Science and Innovation Campus , Didcot OX11 0QX , U.K
| | | | - Dom Bellini
- School of Life Sciences , University of Warwick , Coventry , U.K
| | | | | | | | | | - Jin Gan
- Oncode Institute and Department of Cell and Chemical Biology , Leiden University Medical Center , Einthovenweg 20 , 2333 ZC Leiden , The Netherlands
| | - Jingxu Guo
- Division of Medicine , University College London , Gower Street , London WC1E 6BT , U.K
| | | | | | | | | | | | | | | | | | | | - Alun R Coker
- Division of Medicine , University College London , Gower Street , London WC1E 6BT , U.K
| | | | | | | | | | - Paul E Brennan
- School of Life Sciences , University of Warwick , Coventry , U.K.,Alzheimer's Research UK Oxford Drug Discovery Institute , University of Oxford , NDMRB, Roosevelt Drive , Oxford OX3 7FZ , U.K
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology , Leiden University Medical Center , Einthovenweg 20 , 2333 ZC Leiden , The Netherlands
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus , Didcot OX11 0QX , U.K.,Department of Biochemistry , University of Johannesburg , Auckland Park 2006 , South Africa
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36
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Carvalho D, Taylor KR, Olaciregui NG, Molinari V, Clarke M, Mackay A, Ruddle R, Henley A, Valenti M, Hayes A, Brandon ADH, Eccles SA, Raynaud F, Boudhar A, Monje M, Popov S, Moore AS, Mora J, Cruz O, Vinci M, Brennan PE, Bullock AN, Carcaboso AM, Jones C. ALK2 inhibitors display beneficial effects in preclinical models of ACVR1 mutant diffuse intrinsic pontine glioma. Commun Biol 2019; 2:156. [PMID: 31098401 PMCID: PMC6509210 DOI: 10.1038/s42003-019-0420-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [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: 03/05/2019] [Accepted: 04/08/2019] [Indexed: 02/07/2023] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG) is a lethal childhood brainstem tumour, with a quarter of patients harbouring somatic mutations in ACVR1, encoding the serine/threonine kinase ALK2. Despite being an amenable drug target, little has been done to-date to systematically evaluate the role of ACVR1 in DIPG, nor to screen currently available inhibitors in patient-derived tumour models. Here we show the dependence of DIPG cells on the mutant receptor, and the preclinical efficacy of two distinct chemotypes of ALK2 inhibitor in vitro and in vivo. We demonstrate the pyrazolo[1,5-a]pyrimidine LDN-193189 and the pyridine LDN-214117 to be orally bioavailable and well-tolerated, with good brain penetration. Treatment of immunodeprived mice bearing orthotopic xenografts of H3.3K27M, ACVR1R206H mutant HSJD-DIPG-007 cells with 25 mg/kg LDN-193189 or LDN-214117 for 28 days extended survival compared with vehicle controls. Development of ALK2 inhibitors with improved potency, selectivity and advantageous pharmacokinetic properties may play an important role in therapy for DIPG patients.
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Grants
- Wellcome Trust
- C13468/A14078 Cancer Research UK
- 106169/ZZ14/Z Wellcome Trust
- CHILDREN with CANCER UK
- This work was supported by Children with Cancer UK, Abbie’s Army and the DIPG Collaborative, the Lyla Nsouli Foundation and Lucas’ Legacy, the McKenna Claire Foundation and Fondo Alicia Pueyo. The Queensland Children’s Tumour Bank is supported by the Children’s Hospital Foundation. We thank Louise Howell (ICR) for excellent technical assistance. This work was supported by the Xarxa de Bancs de Tumors de Catalunya (XBTC), sponsored by Pla Director d’Oncologia de Catalunya. AMC acknowledges funding from ISCIII-FEDER (CP13/00189). A.B. and A.N.B acknowledge funding from the Amateurs Trust, Roemex Ltd and FOP Friends. The SGC is a registered charity (number 1097737) that receives funds from AbbVie, Bayer Pharma AG, Boehringer Ingelheim, Canada Foundation for Innovation, Eshelman Institute for Innovation, Genome Canada, Innovative Medicines Initiative (EU/EFPIA) [ULTRA-DD grant no. 115766], Janssen, MSD, Merck KGaA, Novartis Pharma AG, Ontario Ministry of Economic Development and Innovation, Pfizer, São Paulo Research Foundation-FAPESP, Takeda and Wellcome [106169/ZZ14/Z]. This study makes use of data generated by Cancer Research UK Genomics Initiative (C13468/A14078). The authors acknowledge NHS funding to the NIHR Biomedical Research Centre at The Royal Marsden and the ICR.
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Affiliation(s)
- Diana Carvalho
- Divisions of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | - Kathryn R. Taylor
- Divisions of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
- Stanford University School of Medicine, Stanford, 94305 CA USA
| | | | - Valeria Molinari
- Divisions of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | - Matthew Clarke
- Divisions of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | - Alan Mackay
- Divisions of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | - Ruth Ruddle
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | - Alan Henley
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | - Melanie Valenti
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | - Angela Hayes
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | | | - Suzanne A. Eccles
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | - Florence Raynaud
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | - Aicha Boudhar
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Michelle Monje
- Stanford University School of Medicine, Stanford, 94305 CA USA
| | - Sergey Popov
- Divisions of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
- Department of Cellular Pathology, University Hospital of Wales, Cardiff, CF14 4XW UK
| | - Andrew S. Moore
- Diamantina Institute and Child Health Research Centre, The University of Queensland, Brisbane, QLD 4101 Australia
- Oncology Service, Queensland Children’s Hospital, Brisbane, QLD 4029 Australia
| | - Jaume Mora
- Institut de Recerca Sant Joan de Deu, Barcelona, 08950 Esplugues de Llobregat Spain
| | - Ofelia Cruz
- Institut de Recerca Sant Joan de Deu, Barcelona, 08950 Esplugues de Llobregat Spain
| | - Mara Vinci
- Divisions of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
- Bambino Gesù Children’s Hospital, Rome, 00165 Roma RM Italy
| | - 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
| | - Alex N. Bullock
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ UK
| | | | - Chris Jones
- Divisions of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
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37
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Huang L, Li H, Li L, Niu L, Seupel R, Wu C, Cheng W, Chen C, Ding B, Brennan PE, Yang S. Discovery of Pyrrolo[3,2-d]pyrimidin-4-one Derivatives as a New Class of Potent and Cell-Active Inhibitors of P300/CBP-Associated Factor Bromodomain. J Med Chem 2019; 62:4526-4542. [PMID: 30998845 DOI: 10.1021/acs.jmedchem.9b00096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Luyi Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Hui Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Linli Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, P. R. China
| | - Lu Niu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Raina Seupel
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Chengyong Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Wei Cheng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Chong Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Bisen Ding
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Paul E. Brennan
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Shengyong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
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38
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D'Ascenzio M, Pugh KM, Konietzny R, Berridge G, Tallant C, Hashem S, Monteiro O, Thomas JR, Schirle M, Knapp S, Marsden B, Fedorov O, Bountra C, Kessler BM, Brennan PE. An Activity-Based Probe Targeting Non-Catalytic, Highly Conserved Amino Acid Residues within Bromodomains. Angew Chem Int Ed Engl 2019; 58:1007-1012. [PMID: 30589164 PMCID: PMC6492141 DOI: 10.1002/anie.201807825] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 07/09/2018] [Revised: 10/20/2018] [Indexed: 12/27/2022]
Abstract
Bromodomain-containing proteins are epigenetic modulators involved in a wide range of cellular processes, from recruitment of transcription factors to pathological disruption of gene regulation and cancer development. Since the druggability of these acetyl-lysine reader domains was established, efforts were made to develop potent and selective inhibitors across the entire family. Here we report the development of a small molecule-based approach to covalently modify recombinant and endogenous bromodomain-containing proteins by targeting a conserved lysine and a tyrosine residue in the variable ZA or BC loops. Moreover, the addition of a reporter tag allowed in-gel visualization and pull-down of the desired bromodomains.
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Affiliation(s)
- Melissa D'Ascenzio
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| | - Kathryn M. Pugh
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| | | | - Georgina Berridge
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| | - Cynthia Tallant
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| | - Shaima Hashem
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
| | - Octovia Monteiro
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| | - Jason R. Thomas
- Novartis Institute for BioMedical Research (NIBR)180 Massachusetts AveCambridgeMA02139USA
| | - Markus Schirle
- Novartis Institute for BioMedical Research (NIBR)180 Massachusetts AveCambridgeMA02139USA
| | - Stefan Knapp
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life SciencesJohann Wolfgang Goethe-University60438Frankfurt am MainGermany
| | - Brian Marsden
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
| | - Oleg Fedorov
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| | - Chas Bountra
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
| | | | - Paul E. Brennan
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
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39
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Vazquez‐Rodriguez S, Wright M, Rogers CM, Cribbs AP, Velupillai S, Philpott M, Lee H, Dunford JE, Huber KVM, Robers MB, Vasta JD, Thezenas M, Bonham S, Kessler B, Bennett J, Fedorov O, Raynaud F, Donovan A, Blagg J, Bavetsias V, Oppermann U, Bountra C, Kawamura A, Brennan PE. Design, Synthesis and Characterization of Covalent KDM5 Inhibitors. Angew Chem Int Ed Engl 2019; 58:515-519. [PMID: 30431220 PMCID: PMC6391970 DOI: 10.1002/anie.201810179] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 09/11/2018] [Revised: 10/30/2018] [Indexed: 01/05/2023]
Abstract
Histone lysine demethylases (KDMs) are involved in the dynamic regulation of gene expression and they play a critical role in several biological processes. Achieving selectivity over the different KDMs has been a major challenge for KDM inhibitor development. Here we report potent and selective KDM5 covalent inhibitors designed to target cysteine residues only present in the KDM5 sub-family. The covalent binding to the targeted proteins was confirmed by MS and time-dependent inhibition. Additional competition assays show that compounds were non 2-OG competitive. Target engagement and ChIP-seq analysis showed that the compounds inhibited the KDM5 members in cells at nano- to micromolar levels and induce a global increase of the H3K4me3 mark at transcriptional start sites.
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Affiliation(s)
- Saleta Vazquez‐Rodriguez
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
| | - Miranda Wright
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Catherine M. Rogers
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
| | - Adam P. Cribbs
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of OxfordOxfordOX3 7DQUK
| | - Srikannathasan Velupillai
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
| | - Martin Philpott
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of OxfordOxfordOX3 7DQUK
| | - Henry Lee
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of OxfordOxfordOX3 7DQUK
| | - James E. Dunford
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of OxfordOxfordOX3 7DQUK
| | - Kilian V. M. Huber
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
| | | | - James D. Vasta
- Promega Corporation2800 Woods Hollow RoadFitchburgWI53711USA
| | - Marie‐Laetitia Thezenas
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOX3 7FZOxfordUK
| | - Sarah Bonham
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOX3 7FZOxfordUK
| | - Benedikt Kessler
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOX3 7FZOxfordUK
| | - James Bennett
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
| | - Oleg Fedorov
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
| | - Florence Raynaud
- Cancer Research (UK) Cancer Therapeutics UnitThe Institute of Cancer Research15 Cotswold RoadLondonSM2 5NGUK
| | - Adam Donovan
- Cancer Research (UK) Cancer Therapeutics UnitThe Institute of Cancer Research15 Cotswold RoadLondonSM2 5NGUK
| | - Julian Blagg
- Cancer Research (UK) Cancer Therapeutics UnitThe Institute of Cancer Research15 Cotswold RoadLondonSM2 5NGUK
| | - Vassilios Bavetsias
- Cancer Research (UK) Cancer Therapeutics UnitThe Institute of Cancer Research15 Cotswold RoadLondonSM2 5NGUK
| | - Udo Oppermann
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of OxfordOxfordOX3 7DQUK
- FRIAS—Freiburg Institute of Advanced Studies79104FreiburgGermany
| | - Chas Bountra
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
| | - Akane Kawamura
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Paul E. Brennan
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
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40
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D'Ascenzio M, Pugh KM, Konietzny R, Berridge G, Tallant C, Hashem S, Monteiro O, Thomas JR, Schirle M, Knapp S, Marsden B, Fedorov O, Bountra C, Kessler BM, Brennan PE. An Activity‐Based Probe Targeting Non‐Catalytic, Highly Conserved Amino Acid Residues within Bromodomains. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807825] [Citation(s) in RCA: 6] [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] [Indexed: 11/09/2022]
Affiliation(s)
- Melissa D'Ascenzio
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Kathryn M. Pugh
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Rebecca Konietzny
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Georgina Berridge
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Cynthia Tallant
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Shaima Hashem
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
| | - Octovia Monteiro
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Jason R. Thomas
- Novartis Institute for BioMedical Research (NIBR) 180 Massachusetts Ave Cambridge MA 02139 USA
| | - Markus Schirle
- Novartis Institute for BioMedical Research (NIBR) 180 Massachusetts Ave Cambridge MA 02139 USA
| | - Stefan Knapp
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life SciencesJohann Wolfgang Goethe-University 60438 Frankfurt am Main Germany
| | - Brian Marsden
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
| | - Oleg Fedorov
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Chas Bountra
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
| | | | - Paul E. Brennan
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
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41
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Moustakim M, Christott T, Monteiro OP, Bennett J, Giroud C, Ward J, Rogers CM, Smith P, Panagakou I, Díaz‐Sáez L, Felce SL, Gamble V, Gileadi C, Halidi N, Heidenreich D, Chaikuad A, Knapp S, Huber KVM, Farnie G, Heer J, Manevski N, Poda G, Al‐awar R, Dixon DJ, Brennan PE, Fedorov O. Discovery of an MLLT1/3 YEATS Domain Chemical Probe. Angew Chem Int Ed Engl 2018; 57:16302-16307. [PMID: 30288907 PMCID: PMC6348381 DOI: 10.1002/anie.201810617] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [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: 09/14/2018] [Indexed: 11/10/2022]
Abstract
YEATS domain (YD) containing proteins are an emerging class of epigenetic targets in drug discovery. Dysregulation of these modified lysine-binding proteins has been linked to the onset and progression of cancers. We herein report the discovery and characterisation of the first small-molecule chemical probe, SGC-iMLLT, for the YD of MLLT1 (ENL/YEATS1) and MLLT3 (AF9/YEATS3). SGC-iMLLT is a potent and selective inhibitor of MLLT1/3-histone interactions. Excellent selectivity over other human YD proteins (YEATS2/4) and bromodomains was observed. Furthermore, our probe displays cellular target engagement of MLLT1 and MLLT3. The first small-molecule X-ray co-crystal structures with the MLLT1 YD are also reported. This first-in-class probe molecule can be used to understand MLLT1/3-associated biology and the therapeutic potential of small-molecule YD inhibitors.
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Affiliation(s)
- Moses Moustakim
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
| | - Thomas Christott
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - Octovia P. Monteiro
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - James Bennett
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - Charline Giroud
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - Jennifer Ward
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - Catherine M. Rogers
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - Paul Smith
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - Ioanna Panagakou
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - Laura Díaz‐Sáez
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - Suet Ling Felce
- Structural Genomics Consortium & Botnar Research CentreUniversity of OxfordWindmill RoadOxfordOX3 7LDUK
| | - Vicki Gamble
- Structural Genomics Consortium & Botnar Research CentreUniversity of OxfordWindmill RoadOxfordOX3 7LDUK
| | - Carina Gileadi
- Structural Genomics Consortium & Botnar Research CentreUniversity of OxfordWindmill RoadOxfordOX3 7LDUK
| | - Nadia Halidi
- Structural Genomics Consortium & Botnar Research CentreUniversity of OxfordWindmill RoadOxfordOX3 7LDUK
| | - David Heidenreich
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life SciencesJohann Wolfgang Goethe-University60438Frankfurt am MainGermany
| | - Apirat Chaikuad
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life SciencesJohann Wolfgang Goethe-University60438Frankfurt am MainGermany
| | - Stefan Knapp
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life SciencesJohann Wolfgang Goethe-University60438Frankfurt am MainGermany
| | - Kilian V. M. Huber
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - Gillian Farnie
- Structural Genomics Consortium & Botnar Research CentreUniversity of OxfordWindmill RoadOxfordOX3 7LDUK
| | | | | | - Gennady Poda
- Drug Discovery ProgramOntario Institute for Cancer ResearchTorontoONCanada
- Leslie Dan Faculty of PharmacyUniversity of TorontoTorontoONCanada
| | - Rima Al‐awar
- Drug Discovery ProgramOntario Institute for Cancer ResearchTorontoONCanada
- Department of Pharmacology and ToxicologyUniversity of TorontoTorontoONCanada
| | - Darren J. Dixon
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
| | - Paul E. Brennan
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
- Alzheimer's Research (UK) Oxford Drug Discovery InstituteNuffield Department of MedicineUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7FZUK
| | - Oleg Fedorov
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
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42
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Moustakim M, Christott T, Monteiro OP, Bennett J, Giroud C, Ward J, Rogers CM, Smith P, Panagakou I, Díaz-Sáez L, Felce SL, Gamble V, Gileadi C, Halidi N, Heidenreich D, Chaikuad A, Knapp S, Huber KVM, Farnie G, Heer J, Manevski N, Poda G, Al-awar R, Dixon DJ, Brennan PE, Fedorov O. Entdeckung einer chemischen Sonde für MLLT1/3-YEATS-Domänen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Moses Moustakim
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
- Department of Chemistry; University of Oxford; Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA Großbritannien
| | - Thomas Christott
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - Octovia P. Monteiro
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - James Bennett
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - Charline Giroud
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - Jennifer Ward
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - Catherine M. Rogers
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - Paul Smith
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - Ioanna Panagakou
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - Laura Díaz-Sáez
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - Suet Ling Felce
- Structural Genomics Consortium & Botnar Research Centre; University of Oxford; Windmill Road Oxford OX3 7LD Großbritannien
| | - Vicki Gamble
- Structural Genomics Consortium & Botnar Research Centre; University of Oxford; Windmill Road Oxford OX3 7LD Großbritannien
| | - Carina Gileadi
- Structural Genomics Consortium & Botnar Research Centre; University of Oxford; Windmill Road Oxford OX3 7LD Großbritannien
| | - Nadia Halidi
- Structural Genomics Consortium & Botnar Research Centre; University of Oxford; Windmill Road Oxford OX3 7LD Großbritannien
| | - David Heidenreich
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences; Johann Wolfgang Goethe-University; 60438 Frankfurt am Main Deutschland
| | - Apirat Chaikuad
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences; Johann Wolfgang Goethe-University; 60438 Frankfurt am Main Deutschland
| | - Stefan Knapp
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences; Johann Wolfgang Goethe-University; 60438 Frankfurt am Main Deutschland
| | - Kilian V. M. Huber
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - Gillian Farnie
- Structural Genomics Consortium & Botnar Research Centre; University of Oxford; Windmill Road Oxford OX3 7LD Großbritannien
| | - Jag Heer
- UCB Pharma Ltd; Slough SL1 3WE UK
| | | | - Gennady Poda
- Drug Discovery Program; Ontario Institute for Cancer Research; Toronto ON Kanada
- Leslie Dan Faculty of Pharmacy; University of Toronto; Toronto ON Kanada
| | - Rima Al-awar
- Drug Discovery Program; Ontario Institute for Cancer Research; Toronto ON Kanada
- Department of Pharmacology and Toxicology; University of Toronto; Toronto ON Kanada
| | - Darren J. Dixon
- Department of Chemistry; University of Oxford; Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA Großbritannien
| | - Paul E. Brennan
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
- Alzheimer's Research (UK) Oxford Drug Discovery Institute; Nuffield Department of Medicine; University of Oxford; NDM Research Building; Roosevelt Drive Oxford OX3 7FZ Großbritannien
| | - Oleg Fedorov
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
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43
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Vazquez‐Rodriguez S, Wright M, Rogers CM, Cribbs AP, Velupillai S, Philpott M, Lee H, Dunford JE, Huber KVM, Robers MB, Vasta JD, Thezenas M, Bonham S, Kessler B, Bennett J, Fedorov O, Raynaud F, Donovan A, Blagg J, Bavetsias V, Oppermann U, Bountra C, Kawamura A, Brennan PE. Design, Synthesis and Characterization of Covalent KDM5 Inhibitors. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Saleta Vazquez‐Rodriguez
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
| | - Miranda Wright
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
- Chemistry Research LaboratoryUniversity of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Catherine M. Rogers
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
| | - Adam P. Cribbs
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of Oxford Oxford OX3 7DQ UK
| | - Srikannathasan Velupillai
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
| | - Martin Philpott
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of Oxford Oxford OX3 7DQ UK
| | - Henry Lee
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of Oxford Oxford OX3 7DQ UK
| | - James E. Dunford
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of Oxford Oxford OX3 7DQ UK
| | - Kilian V. M. Huber
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
| | | | - James D. Vasta
- Promega Corporation 2800 Woods Hollow Road Fitchburg WI 53711 USA
| | - Marie‐Laetitia Thezenas
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Roosevelt Drive OX3 7FZ Oxford UK
| | - Sarah Bonham
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Roosevelt Drive OX3 7FZ Oxford UK
| | - Benedikt Kessler
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Roosevelt Drive OX3 7FZ Oxford UK
| | - James Bennett
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
| | - Oleg Fedorov
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
| | - Florence Raynaud
- Cancer Research (UK) Cancer Therapeutics UnitThe Institute of Cancer Research 15 Cotswold Road London SM2 5NG UK
| | - Adam Donovan
- Cancer Research (UK) Cancer Therapeutics UnitThe Institute of Cancer Research 15 Cotswold Road London SM2 5NG UK
| | - Julian Blagg
- Cancer Research (UK) Cancer Therapeutics UnitThe Institute of Cancer Research 15 Cotswold Road London SM2 5NG UK
| | - Vassilios Bavetsias
- Cancer Research (UK) Cancer Therapeutics UnitThe Institute of Cancer Research 15 Cotswold Road London SM2 5NG UK
| | - Udo Oppermann
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of Oxford Oxford OX3 7DQ UK
- FRIAS—Freiburg Institute of Advanced Studies 79104 Freiburg Germany
| | - Chas Bountra
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
| | - Akane Kawamura
- Chemistry Research LaboratoryUniversity of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Paul E. Brennan
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
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44
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Heidenreich D, Moustakim M, Schmidt J, Merk D, Brennan PE, Fedorov O, Chaikuad A, Knapp S. Structure-Based Approach toward Identification of Inhibitory Fragments for Eleven-Nineteen-Leukemia Protein (ENL). J Med Chem 2018; 61:10929-10934. [DOI: 10.1021/acs.jmedchem.8b01457] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- David Heidenreich
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Structural Genomics Consortium, BMLS, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Moses Moustakim
- Target Discovery Institute and Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
| | - Jurema Schmidt
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Paul E. Brennan
- Target Discovery Institute and Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
| | - Oleg Fedorov
- Target Discovery Institute and Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Structural Genomics Consortium, BMLS, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Structural Genomics Consortium, BMLS, Goethe-University Frankfurt, 60438 Frankfurt, Germany
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45
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Abstract
Chemical probes are small molecules with potency and selectivity for a single or small number of protein targets. A good chemical probe engages its target intracellularly and is accompanied by a chemically similar, but inactive molecule to be used as a negative control in cellular phenotypic screening. The utility of these chemical probes is ultimately governed by how well they are developed and characterized. Chemical probes either as single entities, or in chemical probes sets are being increasingly used to interrogate the biological relevance of a target in a disease model. This chapter lays out the core properties of chemical probes, summarizes the seminal and emerging techniques used to demonstrate robust intracellular target engagement. Translation of target engagement assays to disease-relevant phenotypic assays using primary patient-derived cells and tissues is also reviewed. Two examples of epigenetic chemical probe discovery and utility are presented whereby target engagement pointed to novel disease associations elucidated from poorly understood protein targets. Finally, a number of examples are discussed whereby chemical probe sets, or "chemogenomic libraries" are used to illuminate new target-disease links which may represent future directions for chemical probe utility.
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Affiliation(s)
- Moses Moustakim
- Nuffield Department of Medicine, Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom; Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Suet Ling Felce
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - Nancy Zaarour
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom; Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Gillian Farnie
- Nuffield Department of Medicine, Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom.
| | - Fiona E McCann
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom; Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom.
| | - Paul E Brennan
- Nuffield Department of Medicine, Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford, United Kingdom.
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46
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Wright M, Martínez-Lamenca C, Leenaerts JE, Brennan PE, Trabanco AA, Oehlrich D. Bench-Stable Transfer Reagent Facilitates the Generation of Trifluoromethyl-sulfonimidamides. J Org Chem 2018; 83:9510-9516. [DOI: 10.1021/acs.joc.8b01244] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Miranda Wright
- Structural Genomics Consortium & Target Discovery Institute, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Carolina Martínez-Lamenca
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Joseph E. Leenaerts
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Paul E. Brennan
- Structural Genomics Consortium & Target Discovery Institute, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Andrés A. Trabanco
- Neuroscience Medicinal Chemistry, Janssen Research & Development, C/Jarama 75A, 45007 Toledo, Spain
| | - Daniel Oehlrich
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium
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47
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Bowkett D, Talon R, Tallant C, Schofield C, von Delft F, Knapp S, Bruton G, Brennan PE. Identifying Small-Molecule Binding Sites for Epigenetic Proteins at Domain-Domain Interfaces. ChemMedChem 2018; 13:1051-1057. [PMID: 29578648 PMCID: PMC6001751 DOI: 10.1002/cmdc.201800030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 01/15/2018] [Revised: 03/16/2018] [Indexed: 12/27/2022]
Abstract
Epigenetics is a rapidly growing field in drug discovery. Of particular interest is the role of post-translational modifications to histones and the proteins that read, write, and erase such modifications. The development of inhibitors for reader domains has focused on single domains. One of the major difficulties of designing inhibitors for reader domains is that, with the notable exception of bromodomains, they tend not to possess a well-enclosed binding site amenable to small-molecule inhibition. As many of the proteins in epigenetic regulation have multiple domains, there are opportunities for designing inhibitors that bind at a domain-domain interface which provide a more suitable interaction pocket. Examination of X-ray structures of multiple domains involved in recognising and modifying post-translational histone marks using the SiteMap algorithm identified potential binding sites at domain-domain interfaces. For the tandem plant homeodomain-bromodomain of SP100C, a potential inter-domain site identified computationally was validated experimentally by the discovery of ligands by X-ray crystallographic fragment screening.
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Affiliation(s)
- David Bowkett
- Structural Genomics Consortium (SGC) & Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford, NDM Research BuildingRoosevelt DriveOxfordOX3 7FZUK
| | - Romain Talon
- Structural Genomics Consortium (SGC) & Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford, NDM Research BuildingRoosevelt DriveOxfordOX3 7FZUK
| | - Cynthia Tallant
- Structural Genomics Consortium (SGC) & Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford, NDM Research BuildingRoosevelt DriveOxfordOX3 7FZUK
| | - Chris Schofield
- Chemistry Research LaboratoryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Frank von Delft
- Structural Genomics Consortium (SGC) & Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford, NDM Research BuildingRoosevelt DriveOxfordOX3 7FZUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0DEUK
- Department of BiochemistryUniversity of JohannesburgAuckland Park2006South Africa
| | - Stefan Knapp
- Structural Genomics Consortium (SGC) & Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford, NDM Research BuildingRoosevelt DriveOxfordOX3 7FZUK
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life SciencesJohann Wolfgang Goethe University60438Frankfurt am MainGermany
| | - Gordon Bruton
- GlaxoSmithKlineMedicines Research CentreGunnels Wood RoadStevenageHertfordshireSG1 2NYUK
| | - Paul E. Brennan
- Structural Genomics Consortium (SGC) & Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford, NDM Research BuildingRoosevelt DriveOxfordOX3 7FZUK
- Alzheimer's Research (UK) Oxford Drug Discovery InstituteNuffield Department of MedicineUniversity of Oxford, NDM Research BuildingRoosevelt DriveOxfordOX3 7FZUK
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48
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Gerken PA, Wolstenhulme JR, Tumber A, Hatch SB, Zhang Y, Müller S, Chandler SA, Mair B, Li F, Nijman SMB, Konietzny R, Szommer T, Yapp C, Fedorov O, Benesch JLP, Vedadi M, Kessler BM, Kawamura A, Brennan PE, Smith MD. Discovery of a Highly Selective Cell-Active Inhibitor of the Histone Lysine Demethylases KDM2/7. Angew Chem Int Ed Engl 2017; 56:15555-15559. [PMID: 28976073 PMCID: PMC5725665 DOI: 10.1002/anie.201706788] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [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: 07/05/2017] [Revised: 09/07/2017] [Indexed: 12/13/2022]
Abstract
Histone lysine demethylases (KDMs) are of critical importance in the epigenetic regulation of gene expression, yet there are few selective, cell-permeable inhibitors or suitable tool compounds for these enzymes. We describe the discovery of a new class of inhibitor that is highly potent towards the histone lysine demethylases KDM2A/7A. A modular synthetic approach was used to explore the chemical space and accelerate the investigation of key structure-activity relationships, leading to the development of a small molecule with around 75-fold selectivity towards KDM2A/7A versus other KDMs, as well as cellular activity at low micromolar concentrations.
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Affiliation(s)
- Philip A. Gerken
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | | | - Anthony Tumber
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Stephanie B. Hatch
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Yijia Zhang
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Susanne Müller
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Shane A. Chandler
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Barbara Mair
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Fengling Li
- Structural Genomics ConsortiumUniversity of TorontoTorontoOntarioM5G 1L7Canada
| | - Sebastian M. B. Nijman
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Rebecca Konietzny
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Tamas Szommer
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Clarence Yapp
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Oleg Fedorov
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Justin L. P. Benesch
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Masoud Vedadi
- Structural Genomics ConsortiumUniversity of TorontoTorontoOntarioM5G 1L7Canada
| | - Benedikt M. Kessler
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Akane Kawamura
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Paul E. Brennan
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Martin D. Smith
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
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49
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Gerken PA, Wolstenhulme JR, Tumber A, Hatch SB, Zhang Y, Müller S, Chandler SA, Mair B, Li F, Nijman SMB, Konietzny R, Szommer T, Yapp C, Fedorov O, Benesch JLP, Vedadi M, Kessler BM, Kawamura A, Brennan PE, Smith MD. Discovery of a Highly Selective Cell-Active Inhibitor of the Histone Lysine Demethylases KDM2/7. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Philip A. Gerken
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Jamie R. Wolstenhulme
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Anthony Tumber
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Stephanie B. Hatch
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Yijia Zhang
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Susanne Müller
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Shane A. Chandler
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Barbara Mair
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Fengling Li
- Structural Genomics Consortium; University of Toronto; Toronto Ontario M5G 1L7 Canada
| | - Sebastian M. B. Nijman
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Rebecca Konietzny
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Tamas Szommer
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Clarence Yapp
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Oleg Fedorov
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Justin L. P. Benesch
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Masoud Vedadi
- Structural Genomics Consortium; University of Toronto; Toronto Ontario M5G 1L7 Canada
| | - Benedikt M. Kessler
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Akane Kawamura
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Paul E. Brennan
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Martin D. Smith
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
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50
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Meier JC, Tallant C, Fedorov O, Witwicka H, Hwang SY, van Stiphout RG, Lambert JP, Rogers C, Yapp C, Gerstenberger BS, Fedele V, Savitsky P, Heidenreich D, Daniels DL, Owen DR, Fish PV, Igoe NM, Bayle ED, Haendler B, Oppermann UC, Buffa F, Brennan PE, Müller S, Gingras AC, Odgren PR, Birnbaum MJ, Knapp S. Selective Targeting of Bromodomains of the Bromodomain-PHD Fingers Family Impairs Osteoclast Differentiation. ACS Chem Biol 2017; 12:2619-2630. [PMID: 28849908 PMCID: PMC5662925 DOI: 10.1021/acschembio.7b00481] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/29/2017] [Indexed: 01/16/2023]
Abstract
Histone acetyltransferases of the MYST family are recruited to chromatin by BRPF scaffolding proteins. We explored functional consequences and the therapeutic potential of inhibitors targeting acetyl-lysine dependent protein interaction domains (bromodomains) present in BRPF1-3 in bone maintenance. We report three potent and selective inhibitors: one (PFI-4) with high selectivity for the BRPF1B isoform and two pan-BRPF bromodomain inhibitors (OF-1, NI-57). The developed inhibitors displaced BRPF bromodomains from chromatin and did not inhibit cell growth and proliferation. Intriguingly, the inhibitors impaired RANKL-induced differentiation of primary murine bone marrow cells and human primary monocytes into bone resorbing osteoclasts by specifically repressing transcriptional programs required for osteoclastogenesis. The data suggest a key role of BRPF in regulating gene expression during osteoclastogenesis, and the excellent druggability of these bromodomains may lead to new treatment strategies for patients suffering from bone loss or osteolytic malignant bone lesions.
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Affiliation(s)
- Julia C. Meier
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Cynthia Tallant
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Oleg Fedorov
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Hanna Witwicka
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States
| | - Sung-Yong Hwang
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States
| | - Ruud G. van Stiphout
- Department of Oncology, Oxford University, Old Road Campus Research Building, Oxford OX3 7DQ, United Kingdom
| | - Jean-Philippe Lambert
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Catherine Rogers
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Clarence Yapp
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Brian S. Gerstenberger
- Pfizer Worldwide Medicinal
Chemistry, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Vita Fedele
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Pavel Savitsky
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - David Heidenreich
- Goethe-University Frankfurt, Institute of Pharmaceutical Chemistry, Riedberg Campus, 60438 Frankfurt am Main, Germany
| | | | - Dafydd R. Owen
- Pfizer Worldwide Medicinal
Chemistry, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Paul V. Fish
- Department
of Pharmaceutical & Biological Chemistry, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, United
Kingdom
| | - Niall M. Igoe
- Department
of Pharmaceutical & Biological Chemistry, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, United
Kingdom
| | - Elliott D. Bayle
- Department
of Pharmaceutical & Biological Chemistry, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, United
Kingdom
| | - Bernard Haendler
- Drug Discovery, Bayer Pharma
AG, Müllerstrasse
178, D-13353 Berlin, Germany
| | | | - Francesca Buffa
- Department of Oncology, Oxford University, Old Road Campus Research Building, Oxford OX3 7DQ, United Kingdom
| | - Paul E. Brennan
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Susanne Müller
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
- Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, 60438 Frankfurt am Main, Germany
| | - Anne Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Paul R. Odgren
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States
| | - Mark J. Birnbaum
- Department of Biology, Merrimack College, North Andover, Massachusetts, United States
| | - Stefan Knapp
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
- Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, 60438 Frankfurt am Main, Germany
- Goethe-University Frankfurt, Institute of Pharmaceutical Chemistry, Riedberg Campus, 60438 Frankfurt am Main, Germany
- German Cancer Network (DKTK), Frankfurt site, 60438 Frankfurt am Main, Germany
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