1
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Kumar Sinha V, Zhang Y, Xu L, Chen YW, Picaud S, Zandian M, Biswas S, Filippakopoulos P, Wang SP, Shi X, Kutateladze TG. Histone H4K16ac Binding Function of the Triple PHD Finger Cassette of MLL4. J Mol Biol 2024; 436:168212. [PMID: 37481158 PMCID: PMC10799173 DOI: 10.1016/j.jmb.2023.168212] [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: 04/17/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 07/24/2023]
Abstract
The human methyltransferase MLL4 plays a critical role in embryogenesis and development, and aberrant activity of MLL4 is linked to neurodegenerative and developmental disorders and cancer. MLL4 contains the catalytic SET domain that catalyzes mono methylation of lysine 4 of histone H3 (H3K4me1) and seven plant homeodomain (PHD) fingers, six of which have not been structurally and functionally characterized. Here, we demonstrate that the triple PHD finger cassette of MLL4, harboring its fourth, fifth and sixth PHD fingers (MLL4PHD456) forms an integrated module, maintains the binding selectivity of the PHD6 finger toward acetylated lysine 16 of histone H4 (H4K16ac), and is capable of binding to DNA. Our findings highlight functional correlation between H4K16ac and H3K4me1, two major histone modifications that are recognized and written, respectively, by MLL4.
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Affiliation(s)
- Vikrant Kumar Sinha
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Longxia Xu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Yu-Wen Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Sarah Picaud
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Mohamad Zandian
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Soumi Biswas
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | | | - Shu-Ping Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Xiaobing Shi
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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2
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Louphrasitthiphol P, Loffreda A, Pogenberg V, Picaud S, Schepsky A, Friedrichsen H, Zeng Z, Lashgari A, Thomas B, Patton EE, Wilmanns M, Filippakopoulos P, Lambert JP, Steingrímsson E, Mazza D, Goding CR. Acetylation reprograms MITF target selectivity and residence time. Nat Commun 2023; 14:6051. [PMID: 37770430 PMCID: PMC10539308 DOI: 10.1038/s41467-023-41793-7] [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: 02/02/2022] [Accepted: 09/08/2023] [Indexed: 09/30/2023] Open
Abstract
The ability of transcription factors to discriminate between different classes of binding sites associated with specific biological functions underpins effective gene regulation in development and homeostasis. How this is achieved is poorly understood. The microphthalmia-associated transcription factor MITF is a lineage-survival oncogene that plays a crucial role in melanocyte development and melanoma. MITF suppresses invasion, reprograms metabolism and promotes both proliferation and differentiation. How MITF distinguishes between differentiation and proliferation-associated targets is unknown. Here we show that compared to many transcription factors MITF exhibits a very long residence time which is reduced by p300/CBP-mediated MITF acetylation at K206. While K206 acetylation also decreases genome-wide MITF DNA-binding affinity, it preferentially directs DNA binding away from differentiation-associated CATGTG motifs toward CACGTG elements. The results reveal an acetylation-mediated switch that suppresses differentiation and provides a mechanistic explanation of why a human K206Q MITF mutation is associated with Waardenburg syndrome.
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Affiliation(s)
- Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Alessia Loffreda
- Experimental Imaging Center, Ospedale San Raffaele, Milano, Italy
| | - Vivian Pogenberg
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
- Institute of Biochemistry and Signal Transduction, University Hamburg Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK
| | - Alexander Schepsky
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Hans Friedrichsen
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK
| | - Zhiqiang Zeng
- MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Edinburgh Cancer Research Centre, Edinburgh, UK
| | - Anahita Lashgari
- Department of Molecular Medicine and Cancer Research Center, Université Laval, Quebec, Canada; Endocrinology - Nephrology Axis, CHU de Québec - Université Laval Research Center, Quebec City, QC, Canada
| | - Benjamin Thomas
- Central Proteomics Facility, Sir William Dunn Pathology School, University of Oxford, Oxford, UK
| | - E Elizabeth Patton
- MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Edinburgh Cancer Research Centre, Edinburgh, UK
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
- University Hamburg Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK
| | - Jean-Philippe Lambert
- Department of Molecular Medicine and Cancer Research Center, Université Laval, Quebec, Canada; Endocrinology - Nephrology Axis, CHU de Québec - Université Laval Research Center, Quebec City, QC, Canada
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Davide Mazza
- Experimental Imaging Center, Ospedale San Raffaele, Milano, Italy
- Università Vita-Salulte San Raffaele, Milano, Italy
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK.
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3
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Cipriano A, Milite C, Feoli A, Viviano M, Pepe G, Campiglia P, Sarno G, Picaud S, Imaide S, Makukhin N, Filippakopoulos P, Ciulli A, Castellano S, Sbardella G. Discovery of Benzo[d]imidazole-6-sulfonamides as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with Selectivity for the First Bromodomain. ChemMedChem 2022; 17:e202200343. [PMID: 36040095 PMCID: PMC9826262 DOI: 10.1002/cmdc.202200343] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/29/2022] [Indexed: 01/11/2023]
Abstract
The bromodomain and extra-terminal (BET) family of proteins includes BRD2, BRD3, BRD4, and the testis-specific protein, BRDT, each containing two N-terminal tandem bromodomain (BRD) modules. Potent and selective inhibitors targeting the two bromodomains are required to elucidate their biological role(s), with potential clinical applications. In this study, we designed and synthesized a series of benzimidazole-6-sulfonamides starting from the azobenzene compounds MS436 (7 a) and MS611 (7 b) that exhibited preference for the first (BD1) over the second (BD2) BRD of BET family members. The most-promising compound (9 a) showed good binding potency and improved metabolic stability and selectivity towards BD1 with respect to the parent compounds.
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Affiliation(s)
- Alessandra Cipriano
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Ciro Milite
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Alessandra Feoli
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Monica Viviano
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Giacomo Pepe
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Pietro Campiglia
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Giuliana Sarno
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Sarah Picaud
- Nuffield Department of MedicineOxford UniversityOX3 7DQOxfordUK
| | - Satomi Imaide
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EH, ScotlandUK,Discovery Technology Research LaboratoriesOno Pharmaceutical Co., Ltd.618-8585OsakaJapan
| | - Nikolai Makukhin
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EH, ScotlandUK,Oncology R&DTumour Targeted DeliveryAstraZenecaQMB Innovation Centre42 New RoadLondonE1 2AXUK
| | | | - Alessio Ciulli
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EH, ScotlandUK
| | - Sabrina Castellano
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Gianluca Sbardella
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
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4
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Cipriano A, Milite C, Feoli A, Viviano M, Pepe G, Campiglia P, Sarno G, Picaud S, Imaide S, Makukhin N, Filippakopoulos P, Ciulli A, Castellano S, Sbardella G. Front Cover: Discovery of Benzo[
d
]imidazole‐6‐sulfonamides as Bromodomain and Extra‐Terminal Domain (BET) Inhibitors with Selectivity for the First Bromodomain (ChemMedChem 20/2022). ChemMedChem 2022. [DOI: 10.1002/cmdc.202200528] [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: 11/09/2022]
Affiliation(s)
- Alessandra Cipriano
- Department of Pharmacy University of Salerno via Giovanni Paolo II 132 84084 Fisciano (SA) Italy
| | - Ciro Milite
- Department of Pharmacy University of Salerno via Giovanni Paolo II 132 84084 Fisciano (SA) Italy
| | - Alessandra Feoli
- Department of Pharmacy University of Salerno via Giovanni Paolo II 132 84084 Fisciano (SA) Italy
| | - Monica Viviano
- Department of Pharmacy University of Salerno via Giovanni Paolo II 132 84084 Fisciano (SA) Italy
| | - Giacomo Pepe
- Department of Pharmacy University of Salerno via Giovanni Paolo II 132 84084 Fisciano (SA) Italy
| | - Pietro Campiglia
- Department of Pharmacy University of Salerno via Giovanni Paolo II 132 84084 Fisciano (SA) Italy
| | - Giuliana Sarno
- Department of Pharmacy University of Salerno via Giovanni Paolo II 132 84084 Fisciano (SA) Italy
| | - Sarah Picaud
- Nuffield Department of Medicine Oxford University OX3 7DQ Oxford UK
| | - Satomi Imaide
- Division of Biological Chemistry and Drug Discovery School of Life Sciences University of Dundee Dow Street Dundee DD1 5EH, Scotland UK
- Discovery Technology Research Laboratories Ono Pharmaceutical Co., Ltd. 618-8585 Osaka Japan
| | - Nikolai Makukhin
- Division of Biological Chemistry and Drug Discovery School of Life Sciences University of Dundee Dow Street Dundee DD1 5EH, Scotland UK
- Oncology R&D Tumour Targeted Delivery AstraZeneca QMB Innovation Centre 42 New Road London E1 2AX UK
| | | | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery School of Life Sciences University of Dundee Dow Street Dundee DD1 5EH, Scotland UK
| | - Sabrina Castellano
- Department of Pharmacy University of Salerno via Giovanni Paolo II 132 84084 Fisciano (SA) Italy
| | - Gianluca Sbardella
- Department of Pharmacy University of Salerno via Giovanni Paolo II 132 84084 Fisciano (SA) Italy
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5
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Piticchio SG, Martínez-Cartró M, Scaffidi S, Rachman M, Rodriguez-Arevalo S, Sanchez-Arfelis A, Escolano C, Picaud S, Krojer T, Filippakopoulos P, von Delft F, Galdeano C, Barril X. Discovery of Novel BRD4 Ligand Scaffolds by Automated Navigation of the Fragment Chemical Space. J Med Chem 2021; 64:17887-17900. [PMID: 34898210 DOI: 10.1021/acs.jmedchem.1c01108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fragment-based drug discovery (FBDD) is a very effective hit identification method. However, the evolution of fragment hits into suitable leads remains challenging and largely artisanal. Fragment evolution is often scaffold-centric, meaning that its outcome depends crucially on the chemical structure of the starting fragment. Considering that fragment screening libraries cover only a small proportion of the corresponding chemical space, hits should be seen as probes highlighting privileged areas of the chemical space rather than actual starting points. We have developed an automated computational pipeline to mine the chemical space around any specific fragment hit, rapidly finding analogues that share a common interaction motif but are structurally novel and diverse. On a prospective application on the bromodomain-containing protein 4 (BRD4), starting from a known fragment, the platform yields active molecules with nonobvious scaffold changes. The procedure is fast and inexpensive and has the potential to uncover many hidden opportunities in FBDD.
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Affiliation(s)
- Serena G Piticchio
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Míriam Martínez-Cartró
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Salvatore Scaffidi
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Moira Rachman
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Sergio Rodriguez-Arevalo
- Laboratory of Medicinal Chemistry (Associated Unit to CSIC), Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Ainoa Sanchez-Arfelis
- Laboratory of Medicinal Chemistry (Associated Unit to CSIC), Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Carmen Escolano
- Laboratory of Medicinal Chemistry (Associated Unit to CSIC), Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Tobias Krojer
- Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Frank von Delft
- Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom.,Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom.,Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom.,Centre for Medicines Discovery, University of Oxford, Oxford OX1 3QU, United Kingdom.,Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
| | - Carles Galdeano
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Xavier Barril
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
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6
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Lukacik P, Owen CD, Harris G, Bolla JR, Picaud S, Alibay I, Nettleship JE, Bird LE, Owens RJ, Biggin PC, Filippakopoulos P, Robinson CV, Walsh MA. The structure of nontypeable Haemophilus influenzae SapA in a closed conformation reveals a constricted ligand-binding cavity and a novel RNA binding motif. PLoS One 2021; 16:e0256070. [PMID: 34653190 PMCID: PMC8519434 DOI: 10.1371/journal.pone.0256070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/29/2021] [Indexed: 12/04/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) is a significant pathogen in respiratory disease and otitis media. Important for NTHi survival, colonization and persistence in vivo is the Sap (sensitivity to antimicrobial peptides) ABC transporter system. Current models propose a direct role for Sap in heme and antimicrobial peptide (AMP) transport. Here, the crystal structure of SapA, the periplasmic component of Sap, in a closed, ligand bound conformation, is presented. Phylogenetic and cavity volume analysis predicts that the small, hydrophobic SapA central ligand binding cavity is most likely occupied by a hydrophobic di- or tri- peptide. The cavity is of insufficient volume to accommodate heme or folded AMPs. Crystal structures of SapA have identified surface interactions with heme and dsRNA. Heme binds SapA weakly (Kd 282 μM) through a surface exposed histidine, while the dsRNA is coordinated via residues which constitute part of a conserved motif (estimated Kd 4.4 μM). The RNA affinity falls within the range observed for characterized RNA/protein complexes. Overall, we describe in molecular-detail the interactions of SapA with heme and dsRNA and propose a role for SapA in the transport of di- or tri-peptides.
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Affiliation(s)
- Petra Lukacik
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - C. David Owen
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - Gemma Harris
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - Jani Reddy Bolla
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Sarah Picaud
- Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom
| | - Irfan Alibay
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Joanne E. Nettleship
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Louise E. Bird
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Raymond J. Owens
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Philip C. Biggin
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Martin A. Walsh
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
- * E-mail:
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7
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Brand M, Clayton J, Moroglu M, Schiedel M, Picaud S, Bluck JP, Skwarska A, Bolland H, Chan AKN, Laurin CMC, Scorah AR, See L, Rooney TPC, Andrews KH, Fedorov O, Perell G, Kalra P, Vinh KB, Cortopassi WA, Heitel P, Christensen KE, Cooper RI, Paton RS, Pomerantz WCK, Biggin PC, Hammond EM, Filippakopoulos P, Conway SJ. Controlling Intramolecular Interactions in the Design of Selective, High-Affinity Ligands for the CREBBP Bromodomain. J Med Chem 2021; 64:10102-10123. [PMID: 34255515 PMCID: PMC8311651 DOI: 10.1021/acs.jmedchem.1c00348] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 12/22/2022]
Abstract
![]()
CREBBP (CBP/KAT3A)
and its paralogue EP300 (KAT3B) are lysine acetyltransferases
(KATs) that are essential for human development. They each comprise
10 domains through which they interact with >400 proteins, making
them important transcriptional co-activators and key nodes in the
human protein–protein interactome. The bromodomains of CREBBP
and EP300 enable the binding of acetylated lysine residues from histones
and a number of other important proteins, including p53, p73, E2F,
and GATA1. Here, we report a work to develop a high-affinity, small-molecule
ligand for the CREBBP and EP300 bromodomains [(−)-OXFBD05]
that shows >100-fold selectivity over a representative member of
the
BET bromodomains, BRD4(1). Cellular studies using this ligand demonstrate
that the inhibition of the CREBBP/EP300 bromodomain in HCT116 colon
cancer cells results in lowered levels of c-Myc and a reduction in
H3K18 and H3K27 acetylation. In hypoxia (<0.1% O2),
the inhibition of the CREBBP/EP300 bromodomain results in the enhanced
stabilization of HIF-1α.
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Affiliation(s)
- Michael Brand
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - James Clayton
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Mustafa Moroglu
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Matthias Schiedel
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Sarah Picaud
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 3TA, U.K
| | - Joseph P Bluck
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Anna Skwarska
- Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, U.K
| | - Hannah Bolland
- Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, U.K
| | - Anthony K N Chan
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Corentine M C Laurin
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Amy R Scorah
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Larissa See
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Timothy P C Rooney
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Katrina H Andrews
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Oleg Fedorov
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 3TA, U.K
| | - Gabriella Perell
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Prakriti Kalra
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Kayla B Vinh
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Wilian A Cortopassi
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Pascal Heitel
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Kirsten E Christensen
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Richard I Cooper
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Robert S Paton
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.,Department of Chemistry, Colorado State University, 1301 Center Ave, Ft. Collins, Colorado 80523-1872, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Ester M Hammond
- Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, U.K
| | - Panagis Filippakopoulos
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 3TA, U.K
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
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8
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Conde J, Pumroy RA, Baker C, Rodrigues T, Guerreiro A, Sousa BB, Marques MC, de Almeida BP, Lee S, Leites EP, Picard D, Samanta A, Vaz SH, Sieglitz F, Langini M, Remke M, Roque R, Weiss T, Weller M, Liu Y, Han S, Corzana F, Morais VA, Faria C, Carvalho T, Filippakopoulos P, Snijder B, Barbosa-Morais NL, Moiseenkova-Bell VY, Bernardes GJL. Allosteric Antagonist Modulation of TRPV2 by Piperlongumine Impairs Glioblastoma Progression. ACS Cent Sci 2021; 7:868-881. [PMID: 34079902 PMCID: PMC8161495 DOI: 10.1021/acscentsci.1c00070] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Indexed: 05/04/2023]
Abstract
The use of computational tools to identify biological targets of natural products with anticancer properties and unknown modes of action is gaining momentum. We employed self-organizing maps to deconvolute the phenotypic effects of piperlongumine (PL) and establish a link to modulation of the human transient receptor potential vanilloid 2 (hTRPV2) channel. The structure of the PL-bound full-length rat TRPV2 channel was determined by cryo-EM. PL binds to a transient allosteric pocket responsible for a new mode of anticancer activity against glioblastoma (GBM) in which hTRPV2 is overexpressed. Calcium imaging experiments revealed the importance of Arg539 and Thr522 residues on the antagonistic effect of PL and calcium influx modulation of the TRPV2 channel. Downregulation of hTRPV2 reduces sensitivity to PL and decreases ROS production. Analysis of GBM patient samples associates hTRPV2 overexpression with tumor grade, disease progression, and poor prognosis. Extensive tumor abrogation and long term survival was achieved in two murine models of orthotopic GBM by formulating PL in an implantable scaffold/hydrogel for sustained local therapy. Furthermore, in primary tumor samples derived from GBM patients, we observed a selective reduction of malignant cells in response to PL ex vivo. Our results establish a broadly applicable strategy, leveraging data-motivated research hypotheses for the discovery of novel means tackling cancer.
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Affiliation(s)
- João Conde
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Ruth A. Pumroy
- Department
of Systems Pharmacology and Translational Therapeutics, Perelman School
of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Charlotte Baker
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Tiago Rodrigues
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Ana Guerreiro
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Bárbara B. Sousa
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Marta C. Marques
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Bernardo P. de Almeida
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Sohyon Lee
- Institute
of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Elvira P. Leites
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Daniel Picard
- Department
of Pediatric Neuro-Oncogenomics, DKFZ, Heidelberg 69120, Germany
- Department of Pediatric Neuro-Oncogenomics, DKTK, Essen D-45147, Germany
- Department
of Pediatric Oncology, Hematology, and Clinical Immunology, Medical
Faculty, University Hospital Düsseldorf, Düsseldorf 40225, Germany
| | - Amrita Samanta
- Department
of Systems Pharmacology and Translational Therapeutics, Perelman School
of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Sandra H. Vaz
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Florian Sieglitz
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Maike Langini
- Department
of Pediatric Neuro-Oncogenomics, DKFZ, Heidelberg 69120, Germany
- Department of Pediatric Neuro-Oncogenomics, DKTK, Essen D-45147, Germany
- Department
of Pediatric Oncology, Hematology, and Clinical Immunology, Medical
Faculty, University Hospital Düsseldorf, Düsseldorf 40225, Germany
| | - Marc Remke
- Department
of Pediatric Neuro-Oncogenomics, DKFZ, Heidelberg 69120, Germany
- Department of Pediatric Neuro-Oncogenomics, DKTK, Essen D-45147, Germany
- Department
of Pediatric Oncology, Hematology, and Clinical Immunology, Medical
Faculty, University Hospital Düsseldorf, Düsseldorf 40225, Germany
| | - Rafael Roque
- Laboratório
de Neuropatologia, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHLN) EPE, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Tobias Weiss
- Department
of Neurology and Brain Tumour Center, University
Hospital Zürich and University of Zurich, Rämistrasse 100, 8091 Zürich, Switzerland
| | - Michael Weller
- Department
of Neurology and Brain Tumour Center, University
Hospital Zürich and University of Zurich, Rämistrasse 100, 8091 Zürich, Switzerland
| | - Yuhang Liu
- Discovery
Sciences, Worldwide Research and Development, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Seungil Han
- Discovery
Sciences, Worldwide Research and Development, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Francisco Corzana
- Departamento
de Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - Vanessa A. Morais
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Cláudia
C. Faria
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Department
of Neurosurgery, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN) EPE, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Tânia Carvalho
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Panagis Filippakopoulos
- Structural
Genomics Consortium, Oxford University, Old Road Campus Research Building,
Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Berend Snijder
- Institute
of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Nuno L. Barbosa-Morais
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Vera Y. Moiseenkova-Bell
- Department
of Systems Pharmacology and Translational Therapeutics, Perelman School
of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- E-mail:
| | - Gonçalo J. L. Bernardes
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
- E-mail: ;
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9
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Vershinin Z, Feldman M, Werner T, Weil LE, Kublanovsky M, Abaev-Schneiderman E, Sklarz M, Lam EYN, Alasad K, Picaud S, Rotblat B, McAdam RA, Chalifa-Caspi V, Bantscheff M, Chapman T, Lewis HD, Filippakopoulos P, Dawson MA, Grandi P, Prinjha RK, Levy D. BRD4 methylation by the methyltransferase SETD6 regulates selective transcription to control mRNA translation. Sci Adv 2021; 7:7/22/eabf5374. [PMID: 34039605 PMCID: PMC8153730 DOI: 10.1126/sciadv.abf5374] [Citation(s) in RCA: 13] [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] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/06/2021] [Indexed: 05/14/2023]
Abstract
The transcriptional coactivator BRD4 has a fundamental role in transcription regulation and thus became a promising epigenetic therapeutic candidate to target diverse pathologies. However, the regulation of BRD4 by posttranslational modifications has been largely unexplored. Here, we show that BRD4 is methylated on chromatin at lysine-99 by the protein lysine methyltransferase SETD6. BRD4 methylation negatively regulates the expression of genes that are involved in translation and inhibits total mRNA translation in cells. Mechanistically, we provide evidence that supports a model where BRD4 methylation by SETD6 does not have a direct role in the association with acetylated histone H4 at chromatin. However, this methylation specifically determines the recruitment of the transcription factor E2F1 to selected target genes that are involved in mRNA translation. Together, our findings reveal a previously unknown molecular mechanism for BRD4 methylation-dependent gene-specific targeting, which may serve as a new direction for the development of therapeutic applications.
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Affiliation(s)
- Zlata Vershinin
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Michal Feldman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Thilo Werner
- GSK Cellzome GmbH, Functional Genomics R&D, 69117 Heidelberg, Germany
| | - Lital Estrella Weil
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Margarita Kublanovsky
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Elina Abaev-Schneiderman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Menachem Sklarz
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Enid Y N Lam
- Sir Peter MacCallum Department of Oncology and Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Khawla Alasad
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er-Sheva 84105, Israel
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Barak Rotblat
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er-Sheva 84105, Israel
| | - Ruth A McAdam
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Vered Chalifa-Caspi
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Marcus Bantscheff
- GSK Cellzome GmbH, Functional Genomics R&D, 69117 Heidelberg, Germany
| | - Trevor Chapman
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Huw D Lewis
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Mark A Dawson
- Sir Peter MacCallum Department of Oncology and Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Paola Grandi
- GSK Cellzome GmbH, Functional Genomics R&D, 69117 Heidelberg, Germany
| | - Rab K Prinjha
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Dan Levy
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel.
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
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10
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Prischi F, Filippakopoulos P. Editorial: Structural Studies of Protein Complexes in Signaling Pathways. Front Mol Biosci 2021; 8:641932. [PMID: 33996897 PMCID: PMC8119893 DOI: 10.3389/fmolb.2021.641932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/05/2021] [Indexed: 11/25/2022] Open
Affiliation(s)
- Filippo Prischi
- School of Life Sciences, University of Essex, Colchester, United Kingdom
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11
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Cribbs AP, Filippakopoulos P, Philpott M, Wells G, Penn H, Oerum H, Valge-Archer V, Feldmann M, Oppermann U. Dissecting the Role of BET Bromodomain Proteins BRD2 and BRD4 in Human NK Cell Function. Front Immunol 2021; 12:626255. [PMID: 33717143 PMCID: PMC7953504 DOI: 10.3389/fimmu.2021.626255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/13/2021] [Indexed: 12/19/2022] Open
Abstract
Natural killer (NK) cells are innate lymphocytes that play a pivotal role in the immune surveillance and elimination of transformed or virally infected cells. Using a chemo-genetic approach, we identify BET bromodomain containing proteins BRD2 and BRD4 as central regulators of NK cell functions, including direct cytokine secretion, NK cell contact-dependent inflammatory cytokine secretion from monocytes as well as NK cell cytolytic functions. We show that both BRD2 and BRD4 control inflammatory cytokine production in NK cells isolated from healthy volunteers and from rheumatoid arthritis patients. In contrast, knockdown of BRD4 but not of BRD2 impairs NK cell cytolytic responses, suggesting BRD4 as critical regulator of NK cell mediated tumor cell elimination. This is supported by pharmacological targeting where the first-generation pan-BET bromodomain inhibitor JQ1(+) displays anti-inflammatory effects and inhibit tumor cell eradication, while the novel bivalent BET bromodomain inhibitor AZD5153, which shows differential activity towards BET family members, does not. Given the important role of both cytokine-mediated inflammatory microenvironment and cytolytic NK cell activities in immune-oncology therapies, our findings present a compelling argument for further clinical investigation.
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Affiliation(s)
- Adam P Cribbs
- Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, United Kingdom
| | | | - Martin Philpott
- Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, United Kingdom
| | - Graham Wells
- Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, United Kingdom
| | - Henry Penn
- Arthritis Centre, Northwick Park Hospital, Harrow, United Kingdom
| | - Henrik Oerum
- Roche Innovation Center Copenhagen A/S, Hørsholm, Denmark
| | - Viia Valge-Archer
- Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Marc Feldmann
- Kennedy Institute of Rheumatology Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, Oxford, United Kingdom
| | - Udo Oppermann
- Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, United Kingdom.,Freiburg Institute of Advanced Studies, Freiburg, Germany.,Oxford Centre for Translational Myeloma Research, Oxford, United Kingdom
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12
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Hassell‐Hart S, Picaud S, Lengacher R, Csucker J, Millet R, Gasser G, Alberto R, Maple H, Felix R, Leśnikowski ZJ, Stewart HJS, Chevassut TJ, Morley S, Filippakopoulos P, Spencer J. Probing BRD Inhibition Substituent Effects in Bulky Analogues of (+)‐JQ1. Helv Chim Acta 2021. [DOI: 10.1002/hlca.202000214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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)
- Storm Hassell‐Hart
- Chemistry Department School of Life Sciences University of Sussex Brighton BN1 9QJ UK
| | - Sarah Picaud
- Structural Genomics Consortium (SGC) University of Oxford Oxford OX3 7DQ UK
| | - Raphael Lengacher
- University of Zurich Department of Chemistry Winterthurerstrasse 190 CH-8057 Zurich Switzerland
| | - Joshua Csucker
- University of Zurich Department of Chemistry Winterthurerstrasse 190 CH-8057 Zurich Switzerland
| | - Regis Millet
- University of Lille Inserm INFINITE U1286 ICPAL 3 rue du Professeur Laguesse, BP-83 FR-59006 Lille France
| | - Gilles Gasser
- Chimie ParisTech PSL University CNRS Institute of Chemistry for Life and Health Sciences Laboratory for Inorganic Chemical Biology FR-75005 Paris France
| | - Roger Alberto
- University of Zurich Department of Chemistry Winterthurerstrasse 190 CH-8057 Zurich Switzerland
| | - Hannah Maple
- Bio-Techne (Tocris Bioscience) The Watkins Building Atlantic Road, Avonmouth Bristol BS11 9QD UK
| | - Robert Felix
- Bio-Techne (Tocris Bioscience) The Watkins Building Atlantic Road, Avonmouth Bristol BS11 9QD UK
| | - Zbigniew J. Leśnikowski
- Laboratory of Medicinal Chemistry Institute of Medical Biology of the Polish Academy of Sciences PL 92a–232 Łodź Poland
| | | | | | - Simon Morley
- Biochemistry School of Life Sciences University of Sussex Brighton BN1 9QG UK
| | | | - John Spencer
- Chemistry Department School of Life Sciences University of Sussex Brighton BN1 9QJ UK
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13
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Crump NT, Ballabio E, Godfrey L, Thorne R, Repapi E, Kerry J, Tapia M, Hua P, Lagerholm C, Filippakopoulos P, Davies JOJ, Milne TA. BET inhibition disrupts transcription but retains enhancer-promoter contact. Nat Commun 2021; 12:223. [PMID: 33431820 PMCID: PMC7801379 DOI: 10.1038/s41467-020-20400-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [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: 12/14/2019] [Accepted: 12/01/2020] [Indexed: 12/13/2022] Open
Abstract
Enhancers are DNA sequences that enable complex temporal and tissue-specific regulation of genes in higher eukaryotes. Although it is not entirely clear how enhancer-promoter interactions can increase gene expression, this proximity has been observed in multiple systems at multiple loci and is thought to be essential for the maintenance of gene expression. Bromodomain and Extra-Terminal domain (BET) and Mediator proteins have been shown capable of forming phase condensates and are thought to be essential for super-enhancer function. Here, we show that targeting of cells with inhibitors of BET proteins or pharmacological degradation of BET protein Bromodomain-containing protein 4 (BRD4) has a strong impact on transcription but very little impact on enhancer-promoter interactions. Dissolving phase condensates reduces BRD4 and Mediator binding at enhancers and can also strongly affect gene transcription, without disrupting enhancer-promoter interactions. These results suggest that activation of transcription and maintenance of enhancer-promoter interactions are separable events. Our findings further indicate that enhancer-promoter interactions are not dependent on high levels of BRD4 and Mediator, and are likely maintained by a complex set of factors including additional activator complexes and, at some sites, CTCF and cohesin.
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Affiliation(s)
- Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Erica Ballabio
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Laura Godfrey
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ross Thorne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Emmanouela Repapi
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Jon Kerry
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Marta Tapia
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peng Hua
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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14
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Kougnassoukou Tchara PE, Filippakopoulos P, Lambert JP. Emerging tools to investigate bromodomain functions. Methods 2020; 184:40-52. [DOI: 10.1016/j.ymeth.2019.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/30/2019] [Accepted: 11/07/2019] [Indexed: 12/21/2022] Open
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15
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Segatto M, Szokoll R, Fittipaldi R, Bottino C, Nevi L, Mamchaoui K, Filippakopoulos P, Caretti G. BETs inhibition attenuates oxidative stress and preserves muscle integrity in Duchenne muscular dystrophy. Nat Commun 2020; 11:6108. [PMID: 33257646 PMCID: PMC7705749 DOI: 10.1038/s41467-020-19839-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/31/2020] [Indexed: 12/22/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) affects 1 in 3500 live male births. To date, there is no effective cure for DMD, and the identification of novel molecular targets involved in disease progression is important to design more effective treatments and therapies to alleviate DMD symptoms. Here, we show that protein levels of the Bromodomain and extra-terminal domain (BET) protein BRD4 are significantly increased in the muscle of the mouse model of DMD, the mdx mouse, and that pharmacological inhibition of the BET proteins has a beneficial outcome, tempering oxidative stress and muscle damage. Alterations in reactive oxygen species (ROS) metabolism are an early event in DMD onset and they are tightly linked to inflammation, fibrosis, and necrosis in skeletal muscle. By restoring ROS metabolism, BET inhibition ameliorates these hallmarks of the dystrophic muscle, translating to a beneficial effect on muscle function. BRD4 direct association to chromatin regulatory regions of the NADPH oxidase subunits increases in the mdx muscle and JQ1 administration reduces BRD4 and BRD2 recruitment at these regions. JQ1 treatment reduces NADPH subunit transcript levels in mdx muscles, isolated myofibers and DMD immortalized myoblasts. Our data highlight novel functions of the BET proteins in dystrophic skeletal muscle and suggest that BET inhibitors may ameliorate the pathophysiology of DMD.
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Affiliation(s)
- Marco Segatto
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy.,Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, Pesche (Is), Italy
| | - Roberta Szokoll
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Raffaella Fittipaldi
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Cinzia Bottino
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Lorenzo Nevi
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Kamel Mamchaoui
- Sorbonne Université, Inserm, Institut de Myologie, U974, Center for Research in Myology, 47 Boulevard de l'hôpital, 75013, Paris, France
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Old Road Campus Research Building, Nuffield Department of Medicine, Oxford, OX3 7DQ, UK
| | - Giuseppina Caretti
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy.
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16
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Schröder M, Filippakopoulos P, Schwalm MP, Ferrer CA, Drewry DH, Knapp S, Chaikuad A. Crystal Structure and Inhibitor Identifications Reveal Targeting Opportunity for the Atypical MAPK Kinase ERK3. Int J Mol Sci 2020; 21:E7953. [PMID: 33114754 PMCID: PMC7663056 DOI: 10.3390/ijms21217953] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/23/2020] [Accepted: 10/23/2020] [Indexed: 12/30/2022] Open
Abstract
Extracellular signal-regulated kinase 3 (ERK3), known also as mitogen-activated protein kinase 6 (MAPK6), is an atypical member of MAPK kinase family, which has been poorly studied. Little is known regarding its function in biological processes, yet this atypical kinase has been suggested to play important roles in the migration and invasiveness of certain cancers. The lack of tools, such as a selective inhibitor, hampers the study of ERK3 biology. Here, we report the crystal structure of the kinase domain of this atypical MAPK kinase, providing molecular insights into its distinct ATP binding pocket compared to the classical MAPK ERK2, explaining differences in their inhibitor binding properties. Medium-scale small molecule screening identified a number of inhibitors, several of which unexpectedly exhibited remarkably high inhibitory potencies. The crystal structure of CLK1 in complex with CAF052, one of the most potent inhibitors identified for ERK3, revealed typical type-I binding mode of the inhibitor, which by structural comparison could likely be maintained in ERK3. Together with the presented structural insights, these diverse chemical scaffolds displaying both reversible and irreversible modes of action, will serve as a starting point for the development of selective inhibitors for ERK3, which will be beneficial for elucidating the important functions of this understudied kinase.
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Affiliation(s)
- Martin Schröder
- Structural Genomics Consortium, Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany;
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany;
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK;
| | - Martin P. Schwalm
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany;
| | - Carla A. Ferrer
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA; (C.A.F.); (D.H.D.)
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA; (C.A.F.); (D.H.D.)
| | - Stefan Knapp
- Structural Genomics Consortium, Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany;
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany;
- German Cancer network DKTK and Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Apirat Chaikuad
- Structural Genomics Consortium, Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany;
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany;
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17
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Chen Z, Wasney GA, Picaud S, Filippakopoulos P, Vedadi M, D'Angiolella V, Bullock AN. Identification of a PGXPP degron motif in dishevelled and structural basis for its binding to the E3 ligase KLHL12. Open Biol 2020; 10:200041. [PMID: 32574548 PMCID: PMC7333892 DOI: 10.1098/rsob.200041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Wnt signalling is dependent on dishevelled proteins (DVL1-3), which assemble an intracellular Wnt signalosome at the plasma membrane. The levels of DVL1-3 are regulated by multiple Cullin-RING E3 ligases that mediate their ubiquitination and degradation. The BTB-Kelch protein KLHL12 was the first E3 ubiquitin ligase to be identified for DVL1-3, but the molecular mechanisms determining its substrate interactions have remained unknown. Here, we mapped the interaction of DVL1-3 to a ‘PGXPP' motif that is conserved in other known partners and substrates of KLHL12, including PLEKHA4, PEF1, SEC31 and DRD4. To determine the binding mechanism, we solved a 2.4 Å crystal structure of the Kelch domain of KLHL12 in complex with a DVL1 peptide that bound with low micromolar affinity. The DVL1 substrate adopted a U-shaped turn conformation that enabled hydrophobic interactions with all six blades of the Kelch domain β-propeller. In cells, the mutation or deletion of this motif reduced the binding and ubiquitination of DVL1 and increased its stability confirming this sequence as a degron motif for KLHL12 recruitment. These results define the molecular mechanisms determining DVL regulation by KLHL12 and establish the KLHL12 Kelch domain as a new protein interaction module for a novel proline-rich motif.
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Affiliation(s)
- Zhuoyao Chen
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Gregory A Wasney
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College Street, Toronto, M5G 1L7, Canada
| | - Sarah Picaud
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College Street, Toronto, M5G 1L7, Canada
| | - Vincenzo D'Angiolella
- Department of Oncology, Cancer Research UK and Medical Research Council Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Alex N Bullock
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
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18
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Louphrasitthiphol P, Siddaway R, Loffreda A, Pogenberg V, Friedrichsen H, Schepsky A, Zeng Z, Lu M, Strub T, Freter R, Lisle R, Suer E, Thomas B, Schuster-Böckler B, Filippakopoulos P, Middleton M, Lu X, Patton EE, Davidson I, Lambert JP, Wilmanns M, Steingrímsson E, Mazza D, Goding CR. Tuning Transcription Factor Availability through Acetylation-Mediated Genomic Redistribution. Mol Cell 2020; 79:472-487.e10. [PMID: 32531202 PMCID: PMC7427332 DOI: 10.1016/j.molcel.2020.05.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 04/01/2020] [Accepted: 05/19/2020] [Indexed: 11/06/2022]
Abstract
It is widely assumed that decreasing transcription factor DNA-binding affinity reduces transcription initiation by diminishing occupancy of sequence-specific regulatory elements. However, in vivo transcription factors find their binding sites while confronted with a large excess of low-affinity degenerate motifs. Here, using the melanoma lineage survival oncogene MITF as a model, we show that low-affinity binding sites act as a competitive reservoir in vivo from which transcription factors are released by mitogen-activated protein kinase (MAPK)-stimulated acetylation to promote increased occupancy of their regulatory elements. Consequently, a low-DNA-binding-affinity acetylation-mimetic MITF mutation supports melanocyte development and drives tumorigenesis, whereas a high-affinity non-acetylatable mutant does not. The results reveal a paradoxical acetylation-mediated molecular clutch that tunes transcription factor availability via genome-wide redistribution and couples BRAF to tumorigenesis. Our results further suggest that p300/CREB-binding protein-mediated transcription factor acetylation may represent a common mechanism to control transcription factor availability. Reducing transcription factor DNA-binding affinity increases activity in vivo Acetylation is triggered by MAPK signaling Acetylation leads to genome-wide transcription factor redistribution Acetylation of MITF drives tumorigenesis and melanocyte development
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Affiliation(s)
- Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK; Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Robert Siddaway
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Alessia Loffreda
- Experimental Imaging Center, Cancer Imaging Unit, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy; Fondazione CEN, European Center for Nanomedicine, 20133 Milan, Italy
| | - Vivian Pogenberg
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 25a, 22607 Hamburg, Germany & University Hamburg Medical Centre Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Hans Friedrichsen
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Alexander Schepsky
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK; Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Zhiqiang Zeng
- MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit and Edinburgh Cancer Research UK Centre, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Min Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Thomas Strub
- Institut de Génetique et Biologie Moléculaire et Cellulaire (IGBMC), Equipe labéllisée Ligue contre le Cancer, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Rasmus Freter
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Richard Lisle
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Eda Suer
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Benjamin Thomas
- Central Proteomics Facility, Sir William Dunn Pathology School, Oxford University, Oxford OX1 3RE, UK
| | - Benjamin Schuster-Böckler
- Ludwig Institute for Cancer Research, Big Data Institute, University of Oxford, Headington, Oxford OX3 7LF, UK
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Mark Middleton
- Oxford NIHR Biomedical Research Centre, Department of Oncology, Churchill Hospital, Oxford OX3 7LE, UK
| | - Xin Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - E Elizabeth Patton
- MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit and Edinburgh Cancer Research UK Centre, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Irwin Davidson
- Institut de Génetique et Biologie Moléculaire et Cellulaire (IGBMC), Equipe labéllisée Ligue contre le Cancer, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Jean-Philippe Lambert
- Department of Molecular Medicine and Cancer Research Centre, Université Laval, Quebec, QC, Canada; CHU de Québec Research Center, CHUL, 2705 Boulevard Laurier, Quebec G1V 4G2, QC, Canada
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 25a, 22607 Hamburg, Germany & University Hamburg Medical Centre Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Davide Mazza
- Experimental Imaging Center, Cancer Imaging Unit, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy; Fondazione CEN, European Center for Nanomedicine, 20133 Milan, Italy.
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK.
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19
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Affiliation(s)
| | - Stefan Knapp
- Goethe-University Frankfurt, Institute of Pharmaceutical Chemistry, Frankfurt, Germany
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20
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Lines KE, Filippakopoulos P, Stevenson M, Müller S, Lockstone HE, Wright B, Knapp S, Buck D, Bountra C, Thakker RV. Effects of epigenetic pathway inhibitors on corticotroph tumour AtT20 cells. Endocr Relat Cancer 2020; 27:163-174. [PMID: 31935194 PMCID: PMC7040567 DOI: 10.1530/erc-19-0448] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/13/2020] [Indexed: 12/13/2022]
Abstract
Medical treatments for corticotrophinomas are limited, and we therefore investigated the effects of epigenetic modulators, a new class of anti-tumour drugs, on the murine adrenocorticotropic hormone (ACTH)-secreting corticotrophinoma cell line AtT20. We found that AtT20 cells express members of the bromo and extra-terminal (BET) protein family, which bind acetylated histones, and therefore, studied the anti-proliferative and pro-apoptotic effects of two BET inhibitors, referred to as (+)-JQ1 (JQ1) and PFI-1, using CellTiter Blue and Caspase Glo assays, respectively. JQ1 and PFI-1 significantly decreased proliferation by 95% (P < 0.0005) and 43% (P < 0.0005), respectively, but only JQ1 significantly increased apoptosis by >50-fold (P < 0.0005), when compared to untreated control cells. The anti-proliferative effects of JQ1 and PFI-1 remained for 96 h after removal of the respective compound. JQ1, but not PFI-1, affected the cell cycle, as assessed by propidium iodide staining and flow cytometry, and resulted in a higher number of AtT20 cells in the sub G1 phase. RNA-sequence analysis, which was confirmed by qRT-PCR and Western blot analyses, revealed that JQ1 treatment significantly altered expression of genes involved in apoptosis, such as NFκB, and the somatostatin receptor 2 (SSTR2) anti-proliferative signalling pathway, including SSTR2. JQ1 treatment also significantly reduced transcription and protein expression of the ACTH precursor pro-opiomelanocortin (POMC) and ACTH secretion by AtT20 cells. Thus, JQ1 treatment has anti-proliferative and pro-apoptotic effects on AtT20 cells and reduces ACTH secretion, thereby indicating that BET inhibition may provide a novel approach for treatment of corticotrophinomas.
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Affiliation(s)
- K E Lines
- OCDEM, Radcliffe Department of Medicine, University of Oxford, Churchill Hospital, Oxford, UK
| | | | - M Stevenson
- OCDEM, Radcliffe Department of Medicine, University of Oxford, Churchill Hospital, Oxford, UK
| | - S Müller
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Frankfurt, Germany
| | - H E Lockstone
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - B Wright
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - S Knapp
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Frankfurt, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - D Buck
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - C Bountra
- Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - R V Thakker
- OCDEM, Radcliffe Department of Medicine, University of Oxford, Churchill Hospital, Oxford, UK
- Correspondence should be addressed to R V Thakker:
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21
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Hassell-Hart S, Runcie A, Krojer T, Doyle J, Lineham E, Ocasio CA, Neto BAD, Fedorov O, Marsh G, Maple H, Felix R, Banks R, Ciulli A, Picaud S, Filippakopoulos P, von Delft F, Brennan P, Stewart HJS, Chevassut TJ, Walker M, Austin C, Morley S, Spencer J. Synthesis and Biological Investigation of (+)-JD1, an Organometallic BET Bromodomain Inhibitor. Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00750] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Storm Hassell-Hart
- Chemistry Department, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, U.K
| | - Andrew Runcie
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH Scotland, U.K
| | - Tobias Krojer
- Structural Genomics Consortium (SGC), University of Oxford, Oxford OX3 7DQ, U.K
| | - Jordan Doyle
- Chemistry Department, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, U.K
| | - Ella Lineham
- Biochemistry Department, School of Life Sciences, University of Sussex, Brighton BN1 9QQ, U.K
| | - Cory A. Ocasio
- Chemistry Department, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, U.K
| | - Brenno A. D. Neto
- Laboratory of Medicinal and Technological Chemistry, University of Brasília, Chemistry Institute (IQ-UnB), Campus Universitário Darcy
Ribeiro, Brasília, Q3 Distrito Federal 70904-970, Brazil
| | - Oleg Fedorov
- Structural Genomics Consortium (SGC), University of Oxford, Oxford OX3 7DQ, U.K
| | - Graham Marsh
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road,
Avonmouth, Bristol BS11 9QD, U.K
| | - Hannah Maple
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road,
Avonmouth, Bristol BS11 9QD, U.K
| | - Robert Felix
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road,
Avonmouth, Bristol BS11 9QD, U.K
| | - Rebecca Banks
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road,
Avonmouth, Bristol BS11 9QD, U.K
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH Scotland, U.K
| | - Sarah Picaud
- Structural Genomics Consortium (SGC), University of Oxford, Oxford OX3 7DQ, U.K
| | | | - Frank von Delft
- Diamond Light Source (DLS), Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
| | - Paul Brennan
- Structural Genomics Consortium (SGC), University of Oxford, Oxford OX3 7DQ, U.K
| | - Helen J. S. Stewart
- Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PS, U.K
| | | | - Martin Walker
- Eurofins Integrated Discovery UK Ltd., Fyfield Business & Research Park, Fyfield Road, Ongar, Essex CM5 0GS, U.K
| | - Carol Austin
- Eurofins Integrated Discovery UK Ltd., Fyfield Business & Research Park, Fyfield Road, Ongar, Essex CM5 0GS, U.K
| | - Simon Morley
- Biochemistry Department, School of Life Sciences, University of Sussex, Brighton BN1 9QQ, U.K
| | - John Spencer
- Chemistry Department, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, U.K
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22
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Shiota H, Barral S, Buchou T, Tan M, Couté Y, Charbonnier G, Reynoird N, Boussouar F, Gérard M, Zhu M, Bargier L, Puthier D, Chuffart F, Bourova-Flin E, Picaud S, Filippakopoulos P, Goudarzi A, Ibrahim Z, Panne D, Rousseaux S, Zhao Y, Khochbin S. Nut Directs p300-Dependent, Genome-Wide H4 Hyperacetylation in Male Germ Cells. Cell Rep 2019; 24:3477-3487.e6. [PMID: 30257209 DOI: 10.1016/j.celrep.2018.08.069] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 04/20/2018] [Revised: 07/19/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022] Open
Abstract
Nuclear protein in testis (Nut) is a universal oncogenic driver in the highly aggressive NUT midline carcinoma, whose physiological function in male germ cells has been unclear. Here we show that expression of Nut is normally restricted to post-meiotic spermatogenic cells, where its presence triggers p300-dependent genome-wide histone H4 hyperacetylation, which is essential for the completion of histone-to-protamine exchange. Accordingly, the inactivation of Nut induces male sterility with spermatogenesis arrest at the histone-removal stage. Nut uses p300 and/or CBP to enhance acetylation of H4 at both K5 and K8, providing binding sites for the first bromodomain of Brdt, the testis-specific member of the BET family, which subsequently mediates genome-wide histone removal. Altogether, our data reveal the detailed molecular basis of the global histone hyperacetylation wave, which occurs before the final compaction of the male genome.
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Affiliation(s)
- Hitoshi Shiota
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France
| | - Sophie Barral
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France
| | - Thierry Buchou
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France
| | - Minjia Tan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P.R. China
| | - Yohann Couté
- Université Grenoble Alpes, CEA, Inserm U1038, CEA, BIG-BGE, Grenoble 38000, France
| | - Guillaume Charbonnier
- TGML, platform IbiSA, Aix Marseille Université, Inserm U1090, TAGC, Marseille, France
| | - Nicolas Reynoird
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France
| | - Fayçal Boussouar
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France
| | | | - Mingrui Zhu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P.R. China
| | - Lisa Bargier
- TGML, platform IbiSA, Aix Marseille Université, Inserm U1090, TAGC, Marseille, France
| | - Denis Puthier
- TGML, platform IbiSA, Aix Marseille Université, Inserm U1090, TAGC, Marseille, France
| | - Florent Chuffart
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France
| | - Ekaterina Bourova-Flin
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France
| | - Sarah Picaud
- Structural Genomics Consortium & Ludwig Institute for Cancer Research, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Panagis Filippakopoulos
- Structural Genomics Consortium & Ludwig Institute for Cancer Research, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Afsaneh Goudarzi
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France
| | - Ziad Ibrahim
- EMBL Grenoble, BP 181, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Daniel Panne
- EMBL Grenoble, BP 181, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France; Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK
| | - Sophie Rousseaux
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Saadi Khochbin
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France.
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23
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Ivanochko D, Halabelian L, Henderson E, Savitsky P, Jain H, Marcon E, Duan S, Hutchinson A, Seitova A, Barsyte-Lovejoy D, Filippakopoulos P, Greenblatt J, Lima-Fernandes E, Arrowsmith CH. Direct interaction between the PRDM3 and PRDM16 tumor suppressors and the NuRD chromatin remodeling complex. Nucleic Acids Res 2019; 47:1225-1238. [PMID: 30462309 PMCID: PMC6379669 DOI: 10.1093/nar/gky1192] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 08/02/2018] [Revised: 10/31/2018] [Accepted: 11/15/2018] [Indexed: 01/01/2023] Open
Abstract
Aberrant isoform expression of chromatin-associated proteins can induce epigenetic programs related to disease. The MDS1 and EVI1 complex locus (MECOM) encodes PRDM3, a protein with an N-terminal PR-SET domain, as well as a shorter isoform, EVI1, lacking the N-terminus containing the PR-SET domain (ΔPR). Imbalanced expression of MECOM isoforms is observed in multiple malignancies, implicating EVI1 as an oncogene, while PRDM3 has been suggested to function as a tumor suppressor through an unknown mechanism. To elucidate functional characteristics of these N-terminal residues, we compared the protein interactomes of the full-length and ΔPR isoforms of PRDM3 and its closely related paralog, PRDM16. Unlike the ΔPR isoforms, both full-length isoforms exhibited a significantly enriched association with components of the NuRD chromatin remodeling complex, especially RBBP4. Typically, RBBP4 facilitates chromatin association of the NuRD complex by binding to histone H3 tails. We show that RBBP4 binds to the N-terminal amino acid residues of PRDM3 and PRDM16, with a dissociation constant of 3.0 μM, as measured by isothermal titration calorimetry. Furthermore, high-resolution X-ray crystal structures of PRDM3 and PRDM16 N-terminal peptides in complex with RBBP4 revealed binding to RBBP4 within the conserved histone H3-binding groove. These data support a mechanism of isoform-specific interaction of PRDM3 and PRDM16 with the NuRD chromatin remodeling complex.
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Affiliation(s)
- Danton Ivanochko
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2M9, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Elizabeth Henderson
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Pavel Savitsky
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Harshika Jain
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Edyta Marcon
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Shili Duan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2M9, Canada
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | | | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Jack Greenblatt
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Evelyne Lima-Fernandes
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2M9, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Cheryl H Arrowsmith
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2M9, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
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24
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Lines K, Stevenson M, Filippakopoulos P, Muller S, Lockstone H, Wright B, Knapp S, Buck D, Bountra C, Thakker R. MON-468 Selective Inhibition of Epigenetic Pathways Has Anti-Proliferative and Pro-Apoptotic Effects on the Mouse Corticotroph Tumor Cells, AtT20. J Endocr Soc 2019. [PMCID: PMC6551103 DOI: 10.1210/js.2019-mon-468] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Corticotrophinomas, which are neuroendocrine tumors (NETs) and represent >10% of all surgically removed pituitary adenomas, cause Cushing’s disease that is associated with hypersecretion of adrenocorticotropic hormone (ACTH) leading to excessive production of glucocorticoids by the adrenal cortex. Trans-sphenoidal hypophysectomy is the treatment of choice for corticotrophinomas, with medical treatments being reserved for patients who have contraindications for surgery. However, these treatments are often ineffective. Improved therapeutic approaches are required, and we have therefore assessed the efficacy of epigenetic modulators, a new class of anti-cancer drugs that have been reported to be effective in treating pancreatic NETs. Specifically, we assessed the anti-proliferative and pro-apoptotic effects of the bromo and extra terminal domain (BET) inhibitors JQ1 and PFI-1, in the mouse corticotrophinoma cell line AtT20, using Cell Titer Blue and Caspase Glo assays, respectively. JQ1, after 96h treatment, was more efficacious than PFI-1. Thus, JQ1 significantly decreased proliferation by 95%, (p<0.0005), and significantly increased apoptosis >50-fold (p<0.0005), compared to control treated cells; whereas PFI-1 decreased proliferation by 43% (p<0.0005), but did not significantly alter apoptosis. Furthermore, AtT20 cells did not resume proliferating for up to 96 hours after the removal of JQ1 from the media. In addition, RNA-sequence (RNA-Seq) analysis revealed that JQ1 treatment significantly altered the expression of genes involved in apoptosis, including Nuclear Factor Kappa B Subunit 1 (Nfκb1) and Baculoviral IAP Repeat Containing 3 (Birc3), as well as genes associated with the somatostatin receptor type 2 (SSTR2) anti-proliferative signaling pathway, including Sstr2. The down regulation of these genes was confirmed using quantitative PCR, which showed decreases in Nfkb1, Birc3 and Sstr2 mRNA of 2.9-fold (p<0.0009), 1.7-fold (p<0.005), and 1.5-fold (p<0.005), respectively. In addition, Western blot analysis showed decreases in Nfkb1, cIAP2 and SSTR2 protein expression of 1.5-fold (p<0.05), 1.9-fold (p<0.05), and 2.3-fold (p<0.05), respectively. Thus our results, which demonstrate that JQ1 treatment is both anti-proliferative and pro-apoptotic in ACTH-secreting cells, reveal that BET inhibition may provide a novel approach for the treatment of corticotrophinomas.
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Affiliation(s)
- Kate Lines
- OCDEM, University of Oxford, Oxford, , United Kingdom
| | | | | | - Susanne Muller
- Structural Genomics Consortium, University of Oxford, Oxford, , United Kingdom
| | - Helen Lockstone
- Oxford Genomics Centre, University of Oxford, Oxford, , United Kingdom
| | - Benjamin Wright
- Oxford Genomics Centre, University of Oxford, Oxford, , United Kingdom
| | - Stefan Knapp
- Structural Genomics Consortium, University of Oxford, Oxford, , United Kingdom
| | - David Buck
- Oxford Genomics Centre, University of Oxford, Oxford, , United Kingdom
| | - Chas Bountra
- Structural Genomics Consortium, University of Oxford, Oxford, , United Kingdom
| | - Rajesh Thakker
- Nuffield Dept of Med, OCDEM, University of Oxford, Oxford, , United Kingdom
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25
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Marabelli C, Marrocco B, Pilotto S, Chittori S, Picaud S, Marchese S, Ciossani G, Forneris F, Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S, Mattevi A. A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex. Cell Rep 2019; 27:387-399.e7. [PMID: 30970244 DOI: 10.1016/j.celrep.2019.03.061] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/28/2019] [Accepted: 03/15/2019] [Indexed: 12/25/2022] Open
Abstract
LSD1 and LSD2 are homologous histone demethylases with opposite biological outcomes related to chromatin silencing and transcription elongation, respectively. Unlike LSD1, LSD2 nucleosome-demethylase activity relies on a specific linker peptide from the multidomain protein NPAC. We used single-particle cryoelectron microscopy (cryo-EM), in combination with kinetic and mutational analysis, to analyze the mechanisms underlying the function of the human LSD2/NPAC-linker/nucleosome complex. Weak interactions between LSD2 and DNA enable multiple binding modes for the association of the demethylase to the nucleosome. The demethylase thereby captures mono- and dimethyl Lys4 of the H3 tail to afford histone demethylation. Our studies also establish that the dehydrogenase domain of NPAC serves as a catalytically inert oligomerization module. While LSD1/CoREST forms a nucleosome docking platform at silenced gene promoters, LSD2/NPAC is a multifunctional enzyme complex with flexible linkers, tailored for rapid chromatin modification, in conjunction with the advance of the RNA polymerase on actively transcribed genes.
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Affiliation(s)
- Chiara Marabelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Biagina Marrocco
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Simona Pilotto
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Sagar Chittori
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Sara Marchese
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Giuseppe Ciossani
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Federico Forneris
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Guy Schoehn
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Daniela Rhodes
- Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Sriram Subramaniam
- The University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada.
| | - Andrea Mattevi
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, via Ferrata 9, 27100 Pavia, Italy.
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26
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Song Y, Park PMC, Wu L, Ray A, Picaud S, Li D, Wimalasena VK, Du T, Filippakopoulos P, Anderson KC, Qi J, Chauhan D. Development and preclinical validation of a novel covalent ubiquitin receptor Rpn13 degrader in multiple myeloma. Leukemia 2019; 33:2685-2694. [PMID: 30962579 DOI: 10.1038/s41375-019-0467-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 03/25/2019] [Indexed: 12/13/2022]
Abstract
Proteasome inhibition is an effective treatment for multiple myeloma (MM); however, targeting different components of the ubiquitin-proteasome system (UPS) remains elusive. Our RNA-interference studies identified proteasome-associated ubiquitin-receptor Rpn13 as a mediator of MM cell growth and survival. Here, we developed the first degrader of Rpn13, WL40, using a small-molecule-induced targeted protein degradation strategy to selectively degrade this component of the UPS. WL40 was synthesized by linking the Rpn13 covalent inhibitor RA190 with the cereblon (CRBN) binding ligand thalidomide. We show that WL40 binds to both Rpn13 and CRBN and triggers degradation of cellular Rpn13, and is therefore first-in-class in exploiting a covalent inhibitor for the development of degraders. Biochemical and cellular studies show that WL40-induced Rpn13 degradation is both CRBN E3 ligase- and Rpn13-dependent. Importantly, WL40 decreases viability in MM cell lines and patient MM cells, even those resistant to bortezomib. Mechanistically, WL40 interrupts Rpn13 function and activates caspase apoptotic cascade, ER stress response and p53/p21 signaling. In animal model studies, WL40 inhibits xenografted human MM cell growth and prolongs survival. Overall, our data show the development of the first UbR Rpn13 degrader with potent anti-MM activity, and provide proof of principle for the development of degraders targeting components of the UPS for therapeutic application.
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Affiliation(s)
- Yan Song
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Paul M C Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Lei Wu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Arghya Ray
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Deyao Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Virangika K Wimalasena
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Ting Du
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Kenneth C Anderson
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Dharminder Chauhan
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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27
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Traquete R, Henderson E, Picaud S, Cal PMSD, Sieglitz F, Rodrigues T, Oliveira R, Filippakopoulos P, Bernardes GJL. Evaluation of linker length effects on a BET bromodomain probe. Chem Commun (Camb) 2019; 55:10128-10131. [DOI: 10.1039/c9cc05054j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A systematic study of the biological effects of introducing linkers of different chemical nature and length into BET bromodomain benzodiazepine ligands.
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Affiliation(s)
- Rui Traquete
- Instituto de Medicina Molecular João Lobo Antunes
- Faculdade de Medicina
- Universidade de Lisboa
- Lisboa
- Portugal
| | - Elizabeth Henderson
- Structural Genomics Consortium
- Nuffield Department of Clinical Medicine
- Oxford University
- ORCRB
- Roosevelt Drive
| | - Sarah Picaud
- Structural Genomics Consortium
- Nuffield Department of Clinical Medicine
- Oxford University
- ORCRB
- Roosevelt Drive
| | - Pedro M. S. D. Cal
- Instituto de Medicina Molecular João Lobo Antunes
- Faculdade de Medicina
- Universidade de Lisboa
- Lisboa
- Portugal
| | - Florian Sieglitz
- Instituto de Medicina Molecular João Lobo Antunes
- Faculdade de Medicina
- Universidade de Lisboa
- Lisboa
- Portugal
| | - Tiago Rodrigues
- Instituto de Medicina Molecular João Lobo Antunes
- Faculdade de Medicina
- Universidade de Lisboa
- Lisboa
- Portugal
| | | | - Panagis Filippakopoulos
- Structural Genomics Consortium
- Nuffield Department of Clinical Medicine
- Oxford University
- ORCRB
- Roosevelt Drive
| | - Gonçalo J. L. Bernardes
- Instituto de Medicina Molecular João Lobo Antunes
- Faculdade de Medicina
- Universidade de Lisboa
- Lisboa
- Portugal
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28
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Lambert JP, Picaud S, Fujisawa T, Hou H, Savitsky P, Uusküla-Reimand L, Gupta GD, Abdouni H, Lin ZY, Tucholska M, Knight JDR, Gonzalez-Badillo B, St-Denis N, Newman JA, Stucki M, Pelletier L, Bandeira N, Wilson MD, Filippakopoulos P, Gingras AC. Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains. Mol Cell 2018; 73:621-638.e17. [PMID: 30554943 PMCID: PMC6375729 DOI: 10.1016/j.molcel.2018.11.006] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [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: 04/25/2018] [Revised: 09/06/2018] [Accepted: 11/02/2018] [Indexed: 12/20/2022]
Abstract
Targeting bromodomains (BRDs) of the bromo-and-extra-terminal (BET) family offers opportunities for therapeutic intervention in cancer and other diseases. Here, we profile the interactomes of BRD2, BRD3, BRD4, and BRDT following treatment with the pan-BET BRD inhibitor JQ1, revealing broad rewiring of the interaction landscape, with three distinct classes of behavior for the 603 unique interactors identified. A group of proteins associate in a JQ1-sensitive manner with BET BRDs through canonical and new binding modes, while two classes of extra-terminal (ET)-domain binding motifs mediate acetylation-independent interactions. Last, we identify an unexpected increase in several interactions following JQ1 treatment that define negative functions for BRD3 in the regulation of rRNA synthesis and potentially RNAPII-dependent gene expression that result in decreased cell proliferation. Together, our data highlight the contributions of BET protein modules to their interactomes allowing for a better understanding of pharmacological rewiring in response to JQ1.
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Affiliation(s)
- Jean-Philippe Lambert
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Takao Fujisawa
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Huayun Hou
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, Canada
| | - Pavel Savitsky
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Liis Uusküla-Reimand
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, Canada; Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Gagan D Gupta
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Hala Abdouni
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Monika Tucholska
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - James D R Knight
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | | | - Nicole St-Denis
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Joseph A Newman
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Manuel Stucki
- Department of Gynecology, University of Zurich, Wagistrasse 14, 8952 Schlieren, Switzerland
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, Canada; Heart & Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto, ON, Canada
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK; Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK.
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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29
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Hrdinka M, Schlicher L, Dai B, Pinkas DM, Bufton JC, Picaud S, Ward JA, Rogers C, Suebsuwong C, Nikhar S, Cuny GD, Huber KV, Filippakopoulos P, Bullock AN, Degterev A, Gyrd-Hansen M. Small molecule inhibitors reveal an indispensable scaffolding role of RIPK2 in NOD2 signaling. EMBO J 2018; 37:embj.201899372. [PMID: 30026309 PMCID: PMC6120666 DOI: 10.15252/embj.201899372] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 06/17/2018] [Accepted: 06/22/2018] [Indexed: 01/06/2023] Open
Abstract
RIPK2 mediates inflammatory signaling by the bacteria‐sensing receptors NOD1 and NOD2. Kinase inhibitors targeting RIPK2 are a proposed strategy to ameliorate NOD‐mediated pathologies. Here, we reveal that RIPK2 kinase activity is dispensable for NOD2 inflammatory signaling and show that RIPK2 inhibitors function instead by antagonizing XIAP‐binding and XIAP‐mediated ubiquitination of RIPK2. We map the XIAP binding site on RIPK2 to the loop between β2 and β3 of the N‐lobe of the kinase, which is in close proximity to the ATP‐binding pocket. Through characterization of a new series of ATP pocket‐binding RIPK2 inhibitors, we identify the molecular features that determine their inhibition of both the RIPK2‐XIAP interaction, and of cellular and in vivoNOD2 signaling. Our study exemplifies how targeting of the ATP‐binding pocket in RIPK2 can be exploited to interfere with the RIPK2‐XIAP interaction for modulation of NOD signaling.
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Affiliation(s)
- Matous Hrdinka
- Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Lisa Schlicher
- Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Bing Dai
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Daniel M Pinkas
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Joshua C Bufton
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Sarah Picaud
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Jennifer A Ward
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Oxford, UK.,Nuffield Department of Clinical Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Catherine Rogers
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Oxford, UK.,Nuffield Department of Clinical Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
| | | | - Sameer Nikhar
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX, USA
| | - Gregory D Cuny
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX, USA
| | - Kilian Vm Huber
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Oxford, UK.,Nuffield Department of Clinical Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Panagis Filippakopoulos
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Alex N Bullock
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Alexei Degterev
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Mads Gyrd-Hansen
- Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
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30
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Jennings LE, Schiedel M, Hewings DS, Picaud S, Laurin CMC, Bruno PA, Bluck JP, Scorah AR, See L, Reynolds JK, Moroglu M, Mistry IN, Hicks A, Guzanov P, Clayton J, Evans CNG, Stazi G, Biggin PC, Mapp AK, Hammond EM, Humphreys PG, Filippakopoulos P, Conway SJ. BET bromodomain ligands: Probing the WPF shelf to improve BRD4 bromodomain affinity and metabolic stability. Bioorg Med Chem 2018; 26:2937-2957. [PMID: 29776834 DOI: 10.1016/j.bmc.2018.05.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 02/23/2018] [Revised: 04/30/2018] [Accepted: 05/02/2018] [Indexed: 12/20/2022]
Abstract
Ligands for the bromodomain and extra-terminal domain (BET) family of bromodomains have shown promise as useful therapeutic agents for treating a range of cancers and inflammation. Here we report that our previously developed 3,5-dimethylisoxazole-based BET bromodomain ligand (OXFBD02) inhibits interactions of BRD4(1) with the RelA subunit of NF-κB, in addition to histone H4. This ligand shows a promising profile in a screen of the NCI-60 panel but was rapidly metabolised (t½ = 39.8 min). Structure-guided optimisation of compound properties led to the development of the 3-pyridyl-derived OXFBD04. Molecular dynamics simulations assisted our understanding of the role played by an internal hydrogen bond in altering the affinity of this series of molecules for BRD4(1). OXFBD04 shows improved BRD4(1) affinity (IC50 = 166 nM), optimised physicochemical properties (LE = 0.43; LLE = 5.74; SFI = 5.96), and greater metabolic stability (t½ = 388 min).
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Affiliation(s)
- Laura E Jennings
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Matthias Schiedel
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - David S Hewings
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sarah Picaud
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 3TA, United Kingdom
| | - Corentine M C Laurin
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Paul A Bruno
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, United States; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109-2216, United States
| | - Joseph P Bluck
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Amy R Scorah
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Larissa See
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jessica K Reynolds
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Mustafa Moroglu
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Ishna N Mistry
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, United Kingdom
| | - Amy Hicks
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Pavel Guzanov
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - James Clayton
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Charles N G Evans
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Giulia Stazi
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Anna K Mapp
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, United States; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109-2216, United States
| | - Ester M Hammond
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, United Kingdom
| | - Philip G Humphreys
- Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage Hertfordshire SG1 2NY, United Kingdom
| | - Panagis Filippakopoulos
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 3TA, United Kingdom
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom.
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Li L, Friedrichsen HJ, Andrews S, Picaud S, Volpon L, Ngeow K, Berridge G, Fischer R, Borden KLB, Filippakopoulos P, Goding CR. A TFEB nuclear export signal integrates amino acid supply and glucose availability. Nat Commun 2018; 9:2685. [PMID: 29992949 PMCID: PMC6041281 DOI: 10.1038/s41467-018-04849-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 05/22/2018] [Indexed: 02/04/2023] Open
Abstract
How cells coordinate the response to fluctuating carbon and nitrogen availability required to maintain effective homeostasis is a key issue. Amino acid limitation that inactivates mTORC1 promotes de-phosphorylation and nuclear translocation of Transcription Factor EB (TFEB), a key transcriptional regulator of lysosome biogenesis and autophagy that is deregulated in cancer and neurodegeneration. Beyond its cytoplasmic sequestration, how TFEB phosphorylation regulates its nuclear-cytoplasmic shuttling, and whether TFEB can coordinate amino acid supply with glucose availability is poorly understood. Here we show that TFEB phosphorylation on S142 primes for GSK3β phosphorylation on S138, and that phosphorylation of both sites but not either alone activates a previously unrecognized nuclear export signal (NES). Importantly, GSK3β is inactivated by AKT in response to mTORC2 signaling triggered by glucose limitation. Remarkably therefore, the TFEB NES integrates carbon (glucose) and nitrogen (amino acid) availability by controlling TFEB flux through a nuclear import-export cycle.
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Affiliation(s)
- Linxin Li
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Hans J Friedrichsen
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Sarah Andrews
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Laurent Volpon
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal, Pavillon Marcel-Coutou, Chemin de la Polytechnique, Montréal, QC, H3T 1J4, Canada
| | - Kaochin Ngeow
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Georgina Berridge
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
- Discovery Proteomics Facility, Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7FZ, UK
| | - Roman Fischer
- Discovery Proteomics Facility, Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7FZ, UK
| | - Katherine L B Borden
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal, Pavillon Marcel-Coutou, Chemin de la Polytechnique, Montréal, QC, H3T 1J4, Canada
| | - Panagis Filippakopoulos
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK.
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33
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Bulbrook D, Brazier H, Mahajan P, Kliszczak M, Fedorov O, Marchese FP, Aubareda A, Chalk R, Picaud S, Strain-Damerell C, Filippakopoulos P, Gileadi O, Clark AR, Yue WW, Burgess-Brown NA, Dean JLE. Tryptophan-Mediated Interactions between Tristetraprolin and the CNOT9 Subunit Are Required for CCR4-NOT Deadenylase Complex Recruitment. J Mol Biol 2017; 430:722-736. [PMID: 29291391 DOI: 10.1016/j.jmb.2017.12.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 07/26/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 12/27/2022]
Abstract
The zinc-finger protein tristetraprolin (TTP) binds to AU-rich elements present in the 3' untranslated regions of transcripts that mainly encode proteins of the inflammatory response. TTP-bound mRNAs are targeted for destruction via recruitment of the eight-subunit deadenylase complex "carbon catabolite repressor protein 4 (CCR4)-negative on TATA-less (NOT)," which catalyzes the removal of mRNA poly-(A) tails, the first obligatory step in mRNA decay. Here we show that a novel interaction between TTP and the CCR4-NOT subunit, CNOT9, is required for recruitment of the deadenylase complex. In addition to CNOT1, CNOT9 is now included in the identified CCR4-NOT subunits shown to interact with TTP. We find that both the N- and C-terminal domains of TTP are involved in an interaction with CNOT9. Through a combination of SPOT peptide array, site-directed mutagenesis, and bio-layer interferometry, we identified several conserved tryptophan residues in TTP that serve as major sites of interaction with two tryptophan-binding pockets of CNOT9, previously found to interact with another modulator GW182. We further demonstrate that these interactions are also required for recruitment of the CCR4-NOT complex and TTP-directed decay of an mRNA containing an AU-rich element in its 3'-untranslated region. Together the results reveal new molecular details for the TTP-CNOT interaction that shape an emerging mechanism whereby TTP targets inflammatory mRNAs for deadenylation and decay.
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Affiliation(s)
- D Bulbrook
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FY, United Kingdom
| | - H Brazier
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FY, United Kingdom; Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, United Kingdom
| | - P Mahajan
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, United Kingdom
| | - M Kliszczak
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, United Kingdom
| | - O Fedorov
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, United Kingdom
| | - F P Marchese
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FY, United Kingdom
| | - A Aubareda
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FY, United Kingdom
| | - R Chalk
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, United Kingdom
| | - S Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, United Kingdom
| | - C Strain-Damerell
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, United Kingdom
| | - P Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, United Kingdom; Ludwig Institute for Cancer Research, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - O Gileadi
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, United Kingdom
| | - A R Clark
- Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, B15 2TT, United Kingdom
| | - W W Yue
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, United Kingdom.
| | - N A Burgess-Brown
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, United Kingdom.
| | - J L E Dean
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FY, United Kingdom.
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Segatto M, Fittipaldi R, Pin F, Sartori R, Dae Ko K, Zare H, Fenizia C, Zanchettin G, Pierobon ES, Hatakeyama S, Sperti C, Merigliano S, Sandri M, Filippakopoulos P, Costelli P, Sartorelli V, Caretti G. Epigenetic targeting of bromodomain protein BRD4 counteracts cancer cachexia and prolongs survival. Nat Commun 2017; 8:1707. [PMID: 29167426 PMCID: PMC5700099 DOI: 10.1038/s41467-017-01645-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 10/05/2017] [Indexed: 02/08/2023] Open
Abstract
Cancer cachexia is a devastating metabolic syndrome characterized by systemic inflammation and massive muscle and adipose tissue wasting. Although it is responsible for approximately one-third of cancer deaths, no effective therapies are available and the underlying mechanisms have not been fully elucidated. We previously identified the bromodomain and extra-terminal domain (BET) protein BRD4 as an epigenetic regulator of muscle mass. Here we show that the pan-BET inhibitor (+)-JQ1 protects tumor-bearing mice from body weight loss and muscle and adipose tissue wasting. Remarkably, in C26-tumor-bearing mice (+)-JQ1 administration dramatically prolongs survival, without directly affecting tumor growth. By ChIP-seq and ChIP analyses, we unveil that BET proteins directly promote the muscle atrophy program during cachexia. In addition, BET proteins are required to coordinate an IL6-dependent AMPK nuclear signaling pathway converging on FoxO3 transcription factor. Overall, these findings indicate that BET proteins may represent a promising therapeutic target in the management of cancer cachexia.
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Affiliation(s)
- Marco Segatto
- Department of Biosciences, Universita' degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Raffaella Fittipaldi
- Department of Biosciences, Universita' degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Fabrizio Pin
- Department of Clinical and Biological Sciences, Unit of General and Clinical Pathology, University of Turin, 10124, Torino, Italy
| | - Roberta Sartori
- Department of Biomedical Sciences, University of Padova, 35131, Padova, Italy
- Venetian Institute of Molecular Medicine, 35131, Padova, Italy
| | - Kyung Dae Ko
- Laboratory of Muscle Stem Cells and Gene Regulation, NIH/NIAMS, 50 South Drive, Bethesda, MD, USA
| | - Hossein Zare
- Laboratory of Muscle Stem Cells and Gene Regulation, NIH/NIAMS, 50 South Drive, Bethesda, MD, USA
| | - Claudio Fenizia
- Department of Biosciences, Universita' degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Gianpietro Zanchettin
- Department of Surgery, Oncology and Gastroenterology, 3rd Surgical Clinic, University of Padua, 35122, Padova, Italy
| | - Elisa Sefora Pierobon
- Department of Surgery, Oncology and Gastroenterology, 3rd Surgical Clinic, University of Padua, 35122, Padova, Italy
| | - Shinji Hatakeyama
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research Basel, Novartis Pharma AG, 4056, Basel, Switzerland
| | - Cosimo Sperti
- Department of Surgery, Oncology and Gastroenterology, 3rd Surgical Clinic, University of Padua, 35122, Padova, Italy
| | - Stefano Merigliano
- Department of Surgery, Oncology and Gastroenterology, 3rd Surgical Clinic, University of Padua, 35122, Padova, Italy
| | - Marco Sandri
- Venetian Institute of Molecular Medicine, 35131, Padova, Italy
- Laboratory of Muscle Stem Cells and Gene Regulation, NIH/NIAMS, 50 South Drive, Bethesda, MD, USA
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Old Road Campus Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Ludwig Institute for Cancer Research, Old Road Campus Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Paola Costelli
- Department of Clinical and Biological Sciences, Unit of General and Clinical Pathology, University of Turin, 10124, Torino, Italy
| | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, NIH/NIAMS, 50 South Drive, Bethesda, MD, USA
| | - Giuseppina Caretti
- Department of Biosciences, Universita' degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy.
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35
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Lines KE, Stevenson M, Filippakopoulos P, Müller S, Lockstone HE, Wright B, Grozinsky-Glasberg S, Grossman AB, Knapp S, Buck D, Bountra C, Thakker RV. Epigenetic pathway inhibitors represent potential drugs for treating pancreatic and bronchial neuroendocrine tumors. Oncogenesis 2017; 6:e332. [PMID: 28504695 PMCID: PMC5523063 DOI: 10.1038/oncsis.2017.30] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 03/24/2017] [Accepted: 03/28/2017] [Indexed: 02/06/2023] Open
Abstract
Cancer is associated with alterations in epigenetic mechanisms such as histone modifications and methylation of DNA, and inhibitors targeting epigenetic mechanisms represent a novel class of anti-cancer drugs. Neuroendocrine tumors (NETs) of the pancreas (PNETs) and bronchus (BNETs), which may have 5-year survivals of <50% and as low as 5%, respectively, represent targets for such drugs, as >40% of PNETs and ~35% of BNETs have mutations of the multiple endocrine neoplasia type 1 (MEN1) gene, which encodes menin that modifies histones by interacting with histone methyltransferases. We assessed 9 inhibitors of epigenetic pathways, for their effects on proliferation, by CellTiter Blue assay, and apoptosis, by CaspaseGlo assay, using 1 PNET and 2 BNET cell lines. Two inhibitors, referred to as (+)-JQ1 (JQ1) and PFI-1, targeting the bromo and extra terminal (BET) protein family which bind acetylated histone residues, were most effective in decreasing proliferation (by 40-85%, P<0.001) and increasing apoptosis (by 2-3.6 fold, P<0.001) in all 3 NET cell lines. The anti-proliferative effects of JQ1 and PFI-1 remained present for at least 48 hours after removal of the compound. JQ1, but not PFI-1, had cell cycle effects, assessed by propidium iodide staining and flow cytometry, resulting in increased and decreased proportions of NET cells in G1, and S and G2 phases, respectively. RNA Sequencing analysis revealed that these JQ1 effects were associated with increased histone 2B expression, and likely mediated through altered activity of bromodomain-containing (Brd) proteins. Assessment of JQ1 in vivo, using a pancreatic beta cell-specific conditional Men1 knockout mouse model that develops PNETs, revealed that JQ1 significantly reduced proliferation (by ~50%, P<0.0005), assessed by bromodeoxyuridine incorporation, and increased apoptosis (by ~3 fold, P<0.0005), assessed by terminal deoxynucleotidyl transferase dUTP nick end labelling, of PNETs. Thus, our studies demonstrate that BET protein inhibitors may provide new treatments for NETs.
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Affiliation(s)
- K E Lines
- Academic Endocrine Unit, OCDEM, University of Oxford, Churchill Hospital, Headington, Oxford, UK
| | - M Stevenson
- Academic Endocrine Unit, OCDEM, University of Oxford, Churchill Hospital, Headington, Oxford, UK
| | - P Filippakopoulos
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Headington, Oxford, UK
| | - S Müller
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Headington, Oxford, UK
| | - H E Lockstone
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - B Wright
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - S Grozinsky-Glasberg
- Neuroendocrine Tumor Unit, Endocrinology & Metabolism Service, Department of Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - A B Grossman
- Academic Endocrine Unit, OCDEM, University of Oxford, Churchill Hospital, Headington, Oxford, UK
| | - S Knapp
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Headington, Oxford, UK
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University and Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Strasse 9, Frankfurt am Main, Jerusalem, Germany
| | - D Buck
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - C Bountra
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Headington, Oxford, UK
| | - R V Thakker
- Academic Endocrine Unit, OCDEM, University of Oxford, Churchill Hospital, Headington, Oxford, UK
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36
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Couzens AL, Xiong S, Knight JDR, Mao DY, Guettler S, Picaud S, Kurinov I, Filippakopoulos P, Sicheri F, Gingras AC. MOB1 Mediated Phospho-recognition in the Core Mammalian Hippo Pathway. Mol Cell Proteomics 2017; 16:1098-1110. [PMID: 28373298 PMCID: PMC5461540 DOI: 10.1074/mcp.m116.065490] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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: 11/13/2016] [Revised: 04/03/2017] [Indexed: 01/13/2023] Open
Abstract
The Hippo tumor suppressor pathway regulates organ size and tissue homoeostasis in response to diverse signaling inputs. The core of the pathway consists of a short kinase cascade: MST1 and MST2 phosphorylate and activate LATS1 and LATS2, which in turn phosphorylate and inactivate key transcriptional coactivators, YAP1 and TAZ (gene WWTR1). The MOB1 adapter protein regulates both phosphorylation reactions firstly by concurrently binding to the upstream MST and downstream LATS kinases to enable the trans phosphorylation reaction, and secondly by allosterically activating the catalytic function of LATS1 and LATS2 to directly stimulate phosphorylation of YAP and TAZ. Studies of yeast Mob1 and human MOB1 revealed that the ability to recognize phosphopeptide sequences in their interactors, Nud1 and MST2 respectively, was critical to their roles in regulating the Mitotic Exit Network in yeast and the Hippo pathway in metazoans. However, the underlying rules of phosphopeptide recognition by human MOB1, the implications of binding specificity for Hippo pathway signaling, and the generality of phosphopeptide binding function to other human MOB family members remained elusive. Employing proteomics, peptide arrays and biochemical analyses, we systematically examine the phosphopeptide binding specificity of MOB1 and find it to be highly complementary to the substrate phosphorylation specificity of MST1 and MST2. We demonstrate that autophosphorylation of MST1 and MST2 on several threonine residues provides multiple MOB1 binding sites with varying binding affinities which in turn contribute to a redundancy of MST1-MOB1 protein interactions in cells. The crystal structures of MOB1A in complex with two favored phosphopeptide sites in MST1 allow for a full description of the MOB1A phosphopeptide-binding consensus. Lastly, we show that the phosphopeptide binding properties of MOB1A are conserved in all but one of the seven MOB family members in humans, thus providing a starting point for uncovering their elusive cellular functions.
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Affiliation(s)
- Amber L Couzens
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5
| | - Shawn Xiong
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5.,§Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada, M5S 1A8
| | - James D R Knight
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5
| | - Daniel Y Mao
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5
| | - Sebastian Guettler
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5.,¶New address: The Institute of Cancer Research, Divisions of Structural Biology and Cancer Biology, London, UK, SW7 3RP
| | - Sarah Picaud
- ‖Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Igor Kurinov
- **NE-CAT APS, Building 436E, Argonne National Lab, 9700 S. Cass Avenue, Argonne, Illinois 60439
| | - Panagis Filippakopoulos
- ‖Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.,‡‡Ludwig Institute for Cancer Research, University of Oxford, Oxford OX3 7DQ, U.K
| | - Frank Sicheri
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5, .,§Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada, M5S 1A8.,§§Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 1A8
| | - Anne-Claude Gingras
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5, .,§§Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 1A8
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37
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Abstract
Bromodomains (BRDs) are evolutionarily conserved protein-protein interaction modules that are found in a wide range of proteins with diverse catalytic and scaffolding functions and are present in most tissues. BRDs selectively recognize and bind to acetylated Lys residues - particularly in histones - and thereby have important roles in the regulation of gene expression. BRD-containing proteins are frequently dysregulated in cancer, they participate in gene fusions that generate diverse, frequently oncogenic proteins, and many cancer-causing mutations have been mapped to the BRDs themselves. Importantly, BRDs can be targeted by small-molecule inhibitors, which has stimulated many translational research projects that seek to attenuate the aberrant functions of BRD-containing proteins in disease.
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Affiliation(s)
- Takao Fujisawa
- Ludwig Institute for Cancer Research, Old Road Campus Research Building, Roosevelt Drive, Oxford
| | - Panagis Filippakopoulos
- Ludwig Institute for Cancer Research, Old Road Campus Research Building, Roosevelt Drive, Oxford.,Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
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38
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Myrianthopoulos V, Gaboriaud-Kolar N, Tallant C, Hall ML, Grigoriou S, Brownlee P, Fedorov O, Rogers C, Heidenreich D, Wanior M, Drosos N, Mexia N, Savitsky P, Bagratuni T, Kastritis E, Terpos E, Filippakopoulos P, Müller S, Skaltsounis AL, Downs J, Knapp S, Mikros E. Discovery and Optimization of a Selective Ligand for the Switch/Sucrose Nonfermenting-Related Bromodomains of Polybromo Protein-1 by the Use of Virtual Screening and Hydration Analysis. J Med Chem 2016; 59:8787-8803. [PMID: 27617704 PMCID: PMC5301280 DOI: 10.1021/acs.jmedchem.6b00355] [Citation(s) in RCA: 37] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Indexed: 12/21/2022]
Abstract
Bromodomains (BRDs) are epigenetic interaction domains currently recognized as emerging drug targets for development of anticancer or anti-inflammatory agents. In this study, development of a selective ligand of the fifth BRD of polybromo protein-1 (PB1(5)) related to switch/sucrose nonfermenting (SWI/SNF) chromatin remodeling complexes is presented. A compound collection was evaluated by consensus virtual screening and a hit was identified. The biophysical study of protein-ligand interactions was performed using X-ray crystallography and isothermal titration calorimetry. Collective data supported the hypothesis that affinity improvement could be achieved by enhancing interactions of the complex with the solvent. The derived SAR along with free energy calculations and a consensus hydration analysis using WaterMap and SZmap algorithms guided rational design of a set of novel analogues. The most potent analogue demonstrated high affinity of 3.3 μM and an excellent selectivity profile, thus comprising a promising lead for the development of chemical probes targeting PB1(5).
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Affiliation(s)
| | - Nicolas Gaboriaud-Kolar
- Department
of Pharmacy, University of Athens, Panepistimiopolis Zografou, GR-15771 Athens, Greece
| | - Cynthia Tallant
- Nuffield
Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Nuffield
Department of Clinical Medicine, Target Discovery Institute (TDI), University of Oxford, Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Michelle-Lynn Hall
- Schrödinger
Inc., 222 Third Street, Cambridge, Massachusetts 02139, United States
| | - Stylianos Grigoriou
- Department
of Pharmacy, University of Athens, Panepistimiopolis Zografou, GR-15771 Athens, Greece
| | - Peter
Moore Brownlee
- Genome
Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, U.K.
| | - Oleg Fedorov
- Nuffield
Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Nuffield
Department of Clinical Medicine, Target Discovery Institute (TDI), University of Oxford, Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Catherine Rogers
- Nuffield
Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Nuffield
Department of Clinical Medicine, Target Discovery Institute (TDI), University of Oxford, Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - David Heidenreich
- Institute
for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Marek Wanior
- Institute
for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Nikolaos Drosos
- Department
of Pharmacy, University of Athens, Panepistimiopolis Zografou, GR-15771 Athens, Greece
| | - Nikitia Mexia
- Department
of Pharmacy, University of Athens, Panepistimiopolis Zografou, GR-15771 Athens, Greece
| | - Pavel Savitsky
- Nuffield
Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Nuffield
Department of Clinical Medicine, Target Discovery Institute (TDI), University of Oxford, Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Tina Bagratuni
- Department
of Clinical Therapeutics, School of Medicine, University of Athens, Mikras Asias 75, GR-11527 Athens, Greece
| | - Efstathios Kastritis
- Department
of Clinical Therapeutics, School of Medicine, University of Athens, Mikras Asias 75, GR-11527 Athens, Greece
| | - Evangelos Terpos
- Department
of Clinical Therapeutics, School of Medicine, University of Athens, Mikras Asias 75, GR-11527 Athens, Greece
| | - Panagis Filippakopoulos
- Nuffield
Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Nuffield
Department of Clinical Medicine, Target Discovery Institute (TDI), University of Oxford, Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Susanne Müller
- Nuffield
Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Nuffield
Department of Clinical Medicine, Target Discovery Institute (TDI), University of Oxford, Roosevelt Drive, Oxford OX3 7BN, U.K.
- Institute
for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | | | - Jessica
Ann Downs
- Genome
Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, U.K.
| | - Stefan Knapp
- Nuffield
Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Nuffield
Department of Clinical Medicine, Target Discovery Institute (TDI), University of Oxford, Roosevelt Drive, Oxford OX3 7BN, U.K.
- Institute
for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Emmanuel Mikros
- Department
of Pharmacy, University of Athens, Panepistimiopolis Zografou, GR-15771 Athens, Greece
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39
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Picaud S, Leonards K, Lambert JP, Dovey O, Wells C, Fedorov O, Monteiro O, Fujisawa T, Wang CY, Lingard H, Tallant C, Nikbin N, Guetzoyan L, Ingham R, Ley SV, Brennan P, Muller S, Samsonova A, Gingras AC, Schwaller J, Vassiliou G, Knapp S, Filippakopoulos P. Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia. Sci Adv 2016; 2:e1600760. [PMID: 27757418 PMCID: PMC5061470 DOI: 10.1126/sciadv.1600760] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 08/22/2016] [Indexed: 06/06/2023]
Abstract
Bromodomains (BRDs) have emerged as compelling targets for cancer therapy. The development of selective and potent BET (bromo and extra-terminal) inhibitors and their significant activity in diverse tumor models have rapidly translated into clinical studies and have motivated drug development efforts targeting non-BET BRDs. However, the complex multidomain/subunit architecture of BRD protein complexes complicates predictions of the consequences of their pharmacological targeting. To address this issue, we developed a promiscuous BRD inhibitor [bromosporine (BSP)] that broadly targets BRDs (including BETs) with nanomolar affinity, creating a tool for the identification of cellular processes and diseases where BRDs have a regulatory function. As a proof of principle, we studied the effects of BSP on leukemic cell lines known to be sensitive to BET inhibition and found, as expected, strong antiproliferative activity. Comparison of the modulation of transcriptional profiles by BSP after a short exposure to the inhibitor resulted in a BET inhibitor signature but no significant additional changes in transcription that could account for inhibition of other BRDs. Thus, nonselective targeting of BRDs identified BETs, but not other BRDs, as master regulators of context-dependent primary transcription response.
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Affiliation(s)
- Sarah Picaud
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Katharina Leonards
- Laboratory of Childhood Leukemia, Department of Biomedicine, University of Basel and Basel University Children’s Hospital, Hebelstrasse 20, CH-4031 Basel, Switzerland
| | - Jean-Philippe Lambert
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Oliver Dovey
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, U.K
| | - Christopher Wells
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Oleg Fedorov
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, U.K
| | - Octovia Monteiro
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, U.K
| | - Takao Fujisawa
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX3 7DQ, U.K
| | - Chen-Yi Wang
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX3 7DQ, U.K
| | - Hannah Lingard
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Cynthia Tallant
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, U.K
| | - Nikzad Nikbin
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Lucie Guetzoyan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Richard Ingham
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Steven V. Ley
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Paul 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, Oxford OX3 7FZ, U.K
- Alzheimer’s Research UK Oxford, Nuffield Department of Medicine Research Building, University of Oxford, Oxford OX3 7FZ, U.K
| | - Susanne Muller
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, U.K
| | - Anastasia Samsonova
- Department of Oncology, CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, U.K
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Juerg Schwaller
- Laboratory of Childhood Leukemia, Department of Biomedicine, University of Basel and Basel University Children’s Hospital, Hebelstrasse 20, CH-4031 Basel, Switzerland
| | - George Vassiliou
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, U.K
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge CB2 0QQ, U.K
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, U.K
| | - Stefan Knapp
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, U.K
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, Goethe University, Max-von Laue Str. 9, 60438 Frankfurt am Main, Germany
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX3 7DQ, U.K
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40
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Gerstenberger BS, Trzupek JD, Tallant C, Fedorov O, Filippakopoulos P, Brennan PE, Fedele V, Martin S, Picaud S, Rogers C, Parikh M, Taylor A, Samas B, O'Mahony A, Berg E, Pallares G, Torrey AD, Treiber DK, Samardjiev IJ, Nasipak BT, Padilla-Benavides T, Wu Q, Imbalzano AN, Nickerson JA, Bunnage ME, Müller S, Knapp S, Owen DR. Identification of a Chemical Probe for Family VIII Bromodomains through Optimization of a Fragment Hit. J Med Chem 2016; 59:4800-11. [PMID: 27115555 DOI: 10.1021/acs.jmedchem.6b00012] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The acetyl post-translational modification of chromatin at selected histone lysine residues is interpreted by an acetyl-lysine specific interaction with bromodomain reader modules. Here we report the discovery of the potent, acetyl-lysine-competitive, and cell active inhibitor PFI-3 that binds to certain family VIII bromodomains while displaying significant, broader bromodomain family selectivity. The high specificity of PFI-3 for family VIII was achieved through a novel bromodomain binding mode of a phenolic headgroup that led to the unusual displacement of water molecules that are generally retained by most other bromodomain inhibitors reported to date. The medicinal chemistry program that led to PFI-3 from an initial fragment screening hit is described in detail, and additional analogues with differing family VIII bromodomain selectivity profiles are also reported. We also describe the full pharmacological characterization of PFI-3 as a chemical probe, along with phenotypic data on adipocyte and myoblast cell differentiation assays.
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Affiliation(s)
- Brian S Gerstenberger
- Pfizer Worldwide Medicinal Chemistry , 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - John D Trzupek
- Pfizer Worldwide Medicinal Chemistry , 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Cynthia Tallant
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Oleg Fedorov
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Panagis Filippakopoulos
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Ludwig Institute for Cancer Research, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Paul E Brennan
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Vita Fedele
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Sarah Martin
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Sarah Picaud
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Catherine Rogers
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Mihir Parikh
- Pfizer Pharmaceutical Sciences , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Alexandria Taylor
- Pfizer Pharmaceutical Sciences , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Brian Samas
- Pfizer Worldwide Medicinal Chemistry , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Alison O'Mahony
- Bioseek Inc., Division of DiscoveRx , 310 Utah Avenue, South San Francisco, California 94080, United States
| | - Ellen Berg
- Bioseek Inc., Division of DiscoveRx , 310 Utah Avenue, South San Francisco, California 94080, United States
| | - Gabriel Pallares
- KinomeScan, Division of DiscoveRx , 11180 Roselle Street, Suite D, San Diego, California 92121, United States
| | - Adam D Torrey
- KinomeScan, Division of DiscoveRx , 11180 Roselle Street, Suite D, San Diego, California 92121, United States
| | - Daniel K Treiber
- KinomeScan, Division of DiscoveRx , 11180 Roselle Street, Suite D, San Diego, California 92121, United States
| | - Ivan J Samardjiev
- Eurofins Lancaster PPS , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Brian T Nasipak
- Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States
| | - Teresita Padilla-Benavides
- Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States
| | - Qiong Wu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States
| | - Anthony N Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States
| | - Jeffrey A Nickerson
- Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States
| | - Mark E Bunnage
- Pfizer Worldwide Medicinal Chemistry , 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Susanne Müller
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Stefan Knapp
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom.,Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences (BMLS), Johann Wolfgang Goethe University , Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Dafydd R Owen
- Pfizer Worldwide Medicinal Chemistry , 610 Main Street, Cambridge, Massachusetts 02139, United States
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41
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Tögel L, Nightingale R, Chueh AC, Jayachandran A, Tran H, Phesse T, Wu R, Sieber OM, Arango D, Dhillon AS, Dawson MA, Diez-Dacal B, Gahman TC, Filippakopoulos P, Shiau AK, Mariadason JM. Dual Targeting of Bromodomain and Extraterminal Domain Proteins, and WNT or MAPK Signaling, Inhibits c-MYC Expression and Proliferation of Colorectal Cancer Cells. Mol Cancer Ther 2016; 15:1217-26. [PMID: 26983878 DOI: 10.1158/1535-7163.mct-15-0724] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 03/06/2016] [Indexed: 12/28/2022]
Abstract
Inhibitors of the bromodomain and extraterminal domain (BET) protein family attenuate the proliferation of several tumor cell lines. These effects are mediated, at least in part, through repression of c-MYC. In colorectal cancer, overexpression of c-MYC due to hyperactive WNT/β-catenin/TCF signaling is a key driver of tumor progression; however, effective strategies to target this oncogene remain elusive. Here, we investigated the effect of BET inhibitors (BETi) on colorectal cancer cell proliferation and c-MYC expression. Treatment of 20 colorectal cancer cell lines with the BETi JQ1 identified a subset of highly sensitive lines. JQ1 sensitivity was higher in cell lines with microsatellite instability but was not associated with the CpG island methylator phenotype, c-MYC expression or amplification status, BET protein expression, or mutation status of TP53, KRAS/BRAF, or PIK3CA/PTEN Conversely, JQ1 sensitivity correlated significantly with the magnitude of c-MYC mRNA and protein repression. JQ1-mediated c-MYC repression was not due to generalized attenuation of β-catenin/TCF-mediated transcription, as JQ1 had minimal effects on other β-catenin/TCF target genes or β-catenin/TCF reporter activity. BETi preferentially target super-enhancer-regulated genes, and a super-enhancer in c-MYC was recently identified in HCT116 cells to which BRD4 and effector transcription factors of the WNT/β-catenin/TCF and MEK/ERK pathways are recruited. Combined targeting of c-MYC with JQ1 and inhibitors of these pathways additively repressed c-MYC and proliferation of HCT116 cells. These findings demonstrate that BETi downregulate c-MYC expression and inhibit colorectal cancer cell proliferation and identify strategies for enhancing the effects of BETi on c-MYC repression by combinatorial targeting the c-MYC super-enhancer. Mol Cancer Ther; 15(6); 1217-26. ©2016 AACR.
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Affiliation(s)
- Lars Tögel
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia. Ludwig Institute for Cancer Research, Melbourne, Victoria, Australia
| | - Rebecca Nightingale
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia. Ludwig Institute for Cancer Research, Melbourne, Victoria, Australia
| | - Anderly C Chueh
- Ludwig Institute for Cancer Research, Melbourne, Victoria, Australia
| | | | - Hoanh Tran
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia. Ludwig Institute for Cancer Research, Melbourne, Victoria, Australia
| | - Toby Phesse
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
| | - Rui Wu
- Ludwig Institute for Cancer Research, Melbourne, Victoria, Australia
| | - Oliver M Sieber
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Diego Arango
- CIBBIM-Nanomedicine, Vall d'Hebron University Hospital Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Mark A Dawson
- Peter MacCallum Cancer Institute, Melbourne, Victoria, Australia
| | - Beatriz Diez-Dacal
- Ludwig Institute for Cancer Research and UK and Structural Genomics Consortium, Oxford, United Kingdom
| | - Timothy C Gahman
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, California
| | - Panagis Filippakopoulos
- Ludwig Institute for Cancer Research and UK and Structural Genomics Consortium, Oxford, United Kingdom
| | - Andrew K Shiau
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, California
| | - John M Mariadason
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia. Ludwig Institute for Cancer Research, Melbourne, Victoria, Australia.
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42
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Picaud S, Fedorov O, Thanasopoulou A, Leonards K, Jones K, Meier J, Olzscha H, Monteiro O, Martin S, Philpott M, Tumber A, Filippakopoulos P, Yapp C, Wells C, Che KH, Bannister A, Robson S, Kumar U, Parr N, Lee K, Lugo D, Jeffrey P, Taylor S, Vecellio ML, Bountra C, Brennan PE, O’Mahony A, Velichko S, Müller S, Hay D, Daniels DL, Urh M, La Thangue NB, Kouzarides T, Prinjha R, Schwaller J, Knapp S. Generation of a Selective Small Molecule Inhibitor of the CBP/p300 Bromodomain for Leukemia Therapy. Cancer Res 2015; 75:5106-5119. [PMID: 26552700 PMCID: PMC4948672 DOI: 10.1158/0008-5472.can-15-0236] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [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: 01/28/2015] [Accepted: 08/07/2015] [Indexed: 01/11/2023]
Abstract
The histone acetyltransferases CBP/p300 are involved in recurrent leukemia-associated chromosomal translocations and are key regulators of cell growth. Therefore, efforts to generate inhibitors of CBP/p300 are of clinical value. We developed a specific and potent acetyl-lysine competitive protein-protein interaction inhibitor, I-CBP112, that targets the CBP/p300 bromodomains. Exposure of human and mouse leukemic cell lines to I-CBP112 resulted in substantially impaired colony formation and induced cellular differentiation without significant cytotoxicity. I-CBP112 significantly reduced the leukemia-initiating potential of MLL-AF9(+) acute myeloid leukemia cells in a dose-dependent manner in vitro and in vivo. Interestingly, I-CBP112 increased the cytotoxic activity of BET bromodomain inhibitor JQ1 as well as doxorubicin. Collectively, we report the development and preclinical evaluation of a novel, potent inhibitor targeting CBP/p300 bromodomains that impairs aberrant self-renewal of leukemic cells. The synergistic effects of I-CBP112 and current standard therapy (doxorubicin) as well as emerging treatment strategies (BET inhibition) provide new opportunities for combinatorial treatment of leukemia and potentially other cancers.
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Affiliation(s)
- Sarah Picaud
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Ludwig Institute for Cancer Research (LICR), Roosevelt Drive, Oxford OX3 7DQ,
UK
| | - Oleg Fedorov
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Angeliki Thanasopoulou
- Laboratory of Childhood Leukemia, Department of Biomedicine,
University of Basel and Basel University Children’s Hospital, Hebelstrasse 20
CH - 4031 Basel, Switzerland
| | - Katharina Leonards
- Laboratory of Childhood Leukemia, Department of Biomedicine,
University of Basel and Basel University Children’s Hospital, Hebelstrasse 20
CH - 4031 Basel, Switzerland
| | - Katherine Jones
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline,
Medicines Research Centre, Stevenage SG1 2NY, UK
| | - Julia Meier
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Heidi Olzscha
- Laboratory of Cancer Biology, Department of Oncology, Medical
Sciences Division, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Octovia Monteiro
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Sarah Martin
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Martin Philpott
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Anthony Tumber
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Panagis Filippakopoulos
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Ludwig Institute for Cancer Research (LICR), Roosevelt Drive, Oxford OX3 7DQ,
UK
| | - Clarence Yapp
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christopher Wells
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Ka Hing Che
- Gurdon Institute and Department of Pathology, University of
Cambridge, Cambridge CB2 1QN, UK
| | - Andrew Bannister
- Gurdon Institute and Department of Pathology, University of
Cambridge, Cambridge CB2 1QN, UK
| | - Samuel Robson
- Gurdon Institute and Department of Pathology, University of
Cambridge, Cambridge CB2 1QN, UK
| | - Umesh Kumar
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline,
Medicines Research Centre, Stevenage SG1 2NY, UK
| | - Nigel Parr
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline,
Medicines Research Centre, Stevenage SG1 2NY, UK
| | - Kevin Lee
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline,
Medicines Research Centre, Stevenage SG1 2NY, UK
| | - Dave Lugo
- Experimental Medicines Unit, GlaxoSmithKline, Medicines Research
Centre, Stevenage, UK
| | - Philip Jeffrey
- Experimental Medicines Unit, GlaxoSmithKline, Medicines Research
Centre, Stevenage, UK
| | - Simon Taylor
- Experimental Medicines Unit, GlaxoSmithKline, Medicines Research
Centre, Stevenage, UK
| | - Matteo L. Vecellio
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Chas Bountra
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
| | - Paul E. Brennan
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Alison O’Mahony
- BioSeek Division of DiscoveRx Corporation, 310 Utah Street, Suite
100, South San Francisco, CA, 94080, USA
| | - Sharlene Velichko
- BioSeek Division of DiscoveRx Corporation, 310 Utah Street, Suite
100, South San Francisco, CA, 94080, USA
| | - Susanne Müller
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Duncan Hay
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Danette L. Daniels
- Promega Corporation, 2800 Woods Hollow Road, Madison, Wisconsin,
U.S.A 53711
| | - Marjeta Urh
- Promega Corporation, 2800 Woods Hollow Road, Madison, Wisconsin,
U.S.A 53711
| | - Nicholas B. La Thangue
- Laboratory of Cancer Biology, Department of Oncology, Medical
Sciences Division, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Tony Kouzarides
- Gurdon Institute and Department of Pathology, University of
Cambridge, Cambridge CB2 1QN, UK
| | - Rab Prinjha
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline,
Medicines Research Centre, Stevenage SG1 2NY, UK
| | - Jürg Schwaller
- Laboratory of Childhood Leukemia, Department of Biomedicine,
University of Basel and Basel University Children’s Hospital, Hebelstrasse 20
CH - 4031 Basel, Switzerland
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
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43
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Lambert JP, Zhou Y, Couzens A, Tsou CC, Picaud S, Ivosev G, Tate S, Nesvizhskii A, Filippakopoulos P, Gingras AC. Abstract IA19: Regulation of signaling interactomes in cancer. Cancer Res 2015. [DOI: 10.1158/1538-7445.compsysbio-ia19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
With the advent of next generation DNA sequencing technologies, the pace of discovery of cancer-associated sequence variants has greatly accelerated, leading to the realization that tumors (and especially solid tumors) harbor hundreds of mutations. Ongoing statistical analysis across multiple laboratories worldwide is progressing rapidly, helping to identify which of these mutations are likely drivers of the cancer phenotype. However, in spite of rapid progress in mapping of cancer related signaling and interaction networks, there has been an increasing disconnect between the identification of a cancer variant, and the mechanistic understanding of transformation induced by the mutation. Such molecular understanding is crucial for developing therapeutic interventions. In particular, frequent consequences of cancer-related mutations are specific alterations of protein-protein interactions affecting downstream signaling networks: an analysis of these altered interactions offers novel therapeutic avenues. At the same time, we still need to gain more knowledge regarding the protein-protein interactions targeted by anticancer drugs, in order to validate on-target effects and identify potential off-target modulation. For both of these objectives, we require the development of approaches that can quantify both gain and loss of interactions, in a sensitive manner, and as much as possible, under conditions that recapitulate the cellular context.
Our research team has coupled affinity purification of a protein to quantitative mass spectrometry approaches. Key to our success has been the expression at near endogenous levels of a recombinant bait protein (as wild type or sequence variants) in human cells, followed by affinity purification using an antibody directed against the epitope tag and simultaneous identification and quantification by mass spectrometry.
In particular, we are reporting here on our efforts to apply the novel data-independent mass spectrometric acquisition (DIA) method known as SWATH to these questions (see Lambert et al., Nature Methods, 2013; Tsou et al., Nature Methods, 2015). We are demonstrating how the approach can be used to profile the differential interactomes of cancer-associated mutants of kinase and phosphatase proteins (CDK4, PPP2R1A, PPP6C), and identify potentially actionable interactions. We are further demonstrating, using JQ1, an inhibitor of the interaction between acetyl-lysine modified histones and the bromodomain and extra-terminal (BET) protein family, (BRD2, BRD3, BRD4 and BRDT) that our approach permits to globally study the modulation of interactions following exposure to an anticancer agent. We reveal that JQ1 induces a rapid rewiring of the interactome of each BET protein, both decreasing interactions with acetylated histones as expected, but also modulating BET association with numerous interaction partners. Furthermore, multiple new interactions were induced upon JQ1 treatment that may alter the compound's potency. Taken together, our results demonstrate that the AP-SWATH-MS allows for the characterization of dynamically modulated interactomes for a wide array of cancer-associated proteins.
Citation Format: Jean-Philippe Lambert, Yiwang Zhou, Amber Couzens, Chih-Chiang Tsou, Sarah Picaud, Gordana Ivosev, Stephen Tate, Alexey Nesvizhskii, Panagis Filippakopoulos, Anne-Claude Gingras. Regulation of signaling interactomes in cancer. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr IA19.
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Affiliation(s)
| | - Yiwang Zhou
- 1Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada,
| | - Amber Couzens
- 1Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada,
| | | | - Sarah Picaud
- 3Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom,
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44
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Fedorov O, Castex J, Tallant C, Owen DR, Martin S, Aldeghi M, Monteiro O, Filippakopoulos P, Picaud S, Trzupek JD, Gerstenberger BS, Bountra C, Willmann D, Wells C, Philpott M, Rogers C, Biggin PC, Brennan PE, Bunnage ME, Schüle R, Günther T, Knapp S, Müller S. Selective targeting of the BRG/PB1 bromodomains impairs embryonic and trophoblast stem cell maintenance. Sci Adv 2015; 1:e1500723. [PMID: 26702435 PMCID: PMC4681344 DOI: 10.1126/sciadv.1500723] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 08/31/2015] [Indexed: 05/13/2023]
Abstract
Mammalian SWI/SNF [also called Brg/Brahma-associated factors (BAFs)] are evolutionarily conserved chromatin-remodeling complexes regulating gene transcription programs during development and stem cell differentiation. BAF complexes contain an ATP (adenosine 5'-triphosphate)-driven remodeling enzyme (either BRG1 or BRM) and multiple protein interaction domains including bromodomains, an evolutionary conserved acetyl lysine-dependent protein interaction motif that recruits transcriptional regulators to acetylated chromatin. We report a potent and cell active protein interaction inhibitor, PFI-3, that selectively binds to essential BAF bromodomains. The high specificity of PFI-3 was achieved on the basis of a novel binding mode of a salicylic acid head group that led to the replacement of water molecules typically maintained in other bromodomain inhibitor complexes. We show that exposure of embryonic stem cells to PFI-3 led to deprivation of stemness and deregulated lineage specification. Furthermore, differentiation of trophoblast stem cells in the presence of PFI-3 was markedly enhanced. The data present a key function of BAF bromodomains in stem cell maintenance and differentiation, introducing a novel versatile chemical probe for studies on acetylation-dependent cellular processes controlled by BAF remodeling complexes.
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Affiliation(s)
- Oleg Fedorov
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Josefina Castex
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Breisacher Strasse 66, 79106 Freiburg, Germany
| | - Cynthia Tallant
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Dafydd R. Owen
- Pfizer Worldwide Medicinal Chemistry, 610 Main Street, Cambridge, MA 02139, USA
| | - Sarah Martin
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Matteo Aldeghi
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Octovia Monteiro
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX3 7DQ, UK
| | - Sarah Picaud
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - John D. Trzupek
- Pfizer Worldwide Medicinal Chemistry, 610 Main Street, Cambridge, MA 02139, USA
| | | | - Chas Bountra
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Dominica Willmann
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Breisacher Strasse 66, 79106 Freiburg, Germany
| | - Christopher Wells
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Martin Philpott
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Catherine Rogers
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Philip C. Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Paul E. Brennan
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Mark E. Bunnage
- Pfizer Worldwide Medicinal Chemistry, 610 Main Street, Cambridge, MA 02139, USA
| | - Roland Schüle
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Breisacher Strasse 66, 79106 Freiburg, Germany
- Deutsches Konsortium für Translationale Krebsforschung, Standort Freiburg, 79106 Freiburg, Germany
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Thomas Günther
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Breisacher Strasse 66, 79106 Freiburg, Germany
- Corresponding author. E-mail: (T.G.); (S.M.); (S.K.)
| | - Stefan Knapp
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Corresponding author. E-mail: (T.G.); (S.M.); (S.K.)
| | - Susanne Müller
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
- Corresponding author. E-mail: (T.G.); (S.M.); (S.K.)
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Abstract
Control of histone acetylation is a part of the epigenetic mechanism that regulates gene expression and chromatin architecture. The members of the bromodomain and extra terminal domain (BET) protein family are a group of epigenetic readers that recognize histone acetylation, whereas histone deacetyl- ases such as sirtuin 1 (SIRT1) function as epigenetic erasers. We observed that BET inhibition by the specific inhibitor JQ1 upregulated SIRT1 expression and activated SIRT1. Moreover, we observed that BET inhibition functionally reversed the pro-inflammatory effect of SIRT1 inhibition in a cellular lung disease model. SIRT1 activation is desirable in many age-related, metabolic and inflammatory diseases; our results suggest that BET protein inhibition would be beneficial in treatment of those conditions. Most importantly, our findings demonstrate a novel mechanism of SIRT1 activation by inhibition of the BET proteins.
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Affiliation(s)
- Tarja Kokkola
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1C, 70211, Kuopio, Finland. .,Institute of Clinical Medicine, University of Eastern Finland, Yliopistonranta 1C, 70211, Kuopio, Finland.
| | - Tiina Suuronen
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1C, 70211, Kuopio, Finland
| | - Maija Pesonen
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1C, 70211, Kuopio, Finland
| | | | - Antero Salminen
- Institute of Clinical Medicine, University of Eastern Finland, Yliopistonranta 1C, 70211, Kuopio, Finland
| | - Elina M Jarho
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1C, 70211, Kuopio, Finland
| | - Maija Lahtela-Kakkonen
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1C, 70211, Kuopio, Finland
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Wang CY, Filippakopoulos P. Beating the odds: BETs in disease. Trends Biochem Sci 2015; 40:468-79. [PMID: 26145250 DOI: 10.1016/j.tibs.2015.06.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/01/2015] [Accepted: 06/04/2015] [Indexed: 01/16/2023]
Abstract
Bromodomains (BRDs) are evolutionarily conserved protein interaction modules that specifically recognise acetyl-lysine on histones and other proteins, facilitating roles in regulating gene transcription. BRD-containing proteins bound to chromatin loci such as enhancers are often deregulated in disease leading to aberrant expression of proinflammatory cytokines and growth-promoting genes. Recent developments targeting the bromo and extraterminal (BET) subset of BRD proteins demonstrated remarkable efficacy in murine models providing a compelling rationale for drug development and translation to the clinic. Here we summarise recent advances in our understanding of the roles of BETs in regulating gene transcription in normal and diseased tissue as well as the current status of their clinical translation.
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Affiliation(s)
- Chen-Yi Wang
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Panagis Filippakopoulos
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK; Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK.
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47
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Picaud S, Strocchia M, Terracciano S, Lauro G, Mendez J, Daniels D, Riccio R, Bifulco G, Bruno I, Filippakopoulos P. 9H-purine scaffold reveals induced-fit pocket plasticity of the BRD9 bromodomain. J Med Chem 2015; 58:2718-36. [PMID: 25703523 PMCID: PMC4403932 DOI: 10.1021/jm501893k] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Indexed: 12/20/2022]
Abstract
The 2-amine-9H-purine scaffold was identified as a weak bromodomain template and was developed via iterative structure based design into a potent nanomolar ligand for the bromodomain of human BRD9 with small residual micromolar affinity toward the bromodomain of BRD4. Binding of the lead compound 11 to the bromodomain of BRD9 results in an unprecedented rearrangement of residues forming the acetyllysine recognition site, affecting plasticity of the protein in an induced-fit pocket. The compound does not exhibit any cytotoxic effect in HEK293 cells and displaces the BRD9 bromodomain from chromatin in bioluminescence proximity assays without affecting the BRD4/histone complex. The 2-amine-9H-purine scaffold represents a novel template that can be further modified to yield highly potent and selective tool compounds to interrogate the biological role of BRD9 in diverse cellular systems.
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Affiliation(s)
- Sarah Picaud
- Nuffield
Department of Clinical Medicine, Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Maria Strocchia
- Department
of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Stefania Terracciano
- Department
of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Gianluigi Lauro
- Department
of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Jacqui Mendez
- Promega
Corporation, 2800 Woods
Hollow Road, Madison, Wisconsin 53711, United States
| | - Danette
L. Daniels
- Promega
Corporation, 2800 Woods
Hollow Road, Madison, Wisconsin 53711, United States
| | - Raffaele Riccio
- Department
of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Giuseppe Bifulco
- Department
of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Ines Bruno
- Department
of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Panagis Filippakopoulos
- Nuffield
Department of Clinical Medicine, Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Nuffield
Department of Clinical Medicine, Ludwig
Cancer Research, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.
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48
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Tallant C, Valentini E, Fedorov O, Overvoorde L, Ferguson FM, Filippakopoulos P, Svergun DI, Knapp S, Ciulli A. Molecular basis of histone tail recognition by human TIP5 PHD finger and bromodomain of the chromatin remodeling complex NoRC. Structure 2014; 23:80-92. [PMID: 25533489 PMCID: PMC4291147 DOI: 10.1016/j.str.2014.10.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/24/2014] [Accepted: 10/13/2014] [Indexed: 12/22/2022]
Abstract
Binding of the chromatin remodeling complex NoRC to RNA complementary to the rDNA promoter mediates transcriptional repression. TIP5, the largest subunit of NoRC, is involved in recruitment to rDNA by interactions with promoter-bound TTF-I, pRNA, and acetylation of H4K16. TIP5 domains that recognize posttranslational modifications on histones are essential for recruitment of NoRC to chromatin, but how these reader modules recognize site-specific histone tails has remained elusive. Here, we report crystal structures of PHD zinc finger and bromodomains from human TIP5 and BAZ2B in free form and bound to H3 and/or H4 histones. PHD finger functions as an independent structural module in recognizing unmodified H3 histone tails, and the bromodomain prefers H3 and H4 acetylation marks followed by a key basic residue, KacXXR. Further low-resolution analyses of PHD-bromodomain modules provide molecular insights into their trans histone tail recognition, required for nucleosome recruitment and transcriptional repression of the NoRC complex. TIP5 and BAZ2B PHD zinc fingers recognize unmodified H3K4 TIP5 and BAZ2B bromodomain recognize H4K16ac and H3K14ac with specific motif KacXXR Cocrystal structures of individual domains define the basis for histone recognition SAXS data for BAZ2B suggest independent PTM recognition
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Affiliation(s)
- Cynthia Tallant
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK; Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Erica Valentini
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK; Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Lois Overvoorde
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Fleur M Ferguson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK; Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Stefan Knapp
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK; Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Alessio Ciulli
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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49
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Quinn ER, Ciceri P, Müller-Knapp S, O'Mahony A, Fedorov O, Filippakopoulos P, Hunt JP, Lasater EA, Pallares G, Picaud S, Wells C, Wodicka LM, Shah NP, Knapp S, Treiber DK. Abstract 5387: Dual kinase/bromodomain inhibitors for rationally designed polypharmacology. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-5387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Concomitant inhibition of multiple cancer-driving kinases is an established strategy to improve the durability of clinical responses to targeted therapies. The difficulty of discovering kinase inhibitors with an appropriate multi-target profile has, however, necessitated the application of combination therapies, which can pose significant clinical development challenges. Epigenetic reader domains of the bromodomain family have recently emerged as novel targets for cancer therapy. Here we have used BROMOscan™ bromodomain ligand binding assays to identify several clinical kinase inhibitors that also inhibit bromodomains with therapeutically relevant potencies and are best classified as dual kinase/bromodomain inhibitors. Nanomolar activity on BRD4 by clinical PLK1 and JAK2/FLT3 kinase inhibitors is particularly noteworthy as these combinations of activities on independent oncogenic pathways exemplify a novel strategy for rational single agent polypharmacological targeting. Importantly, cell-based data show that these dual inhibitors suppress c-Myc expression (a hallmark of BRD4 inhibition) and induce complex polypharmacological phenotypes reflecting dual kinase/bromodomain inhibition across a panel of primary human cell assay systems that model complex tissue and disease state environments (BioMap™). Furthermore, rich structure-activity relationships for related inhibitors and co-crystal structures identify design features that enable a general platform for the rational design of dual kinase/bromodomain inhibitors.
Citation Format: Elizabeth R. Quinn, Pietro Ciceri, Susanne Müller-Knapp, Alison O'Mahony, Oleg Fedorov, Panagis Filippakopoulos, Jeremy P. Hunt, Elisabeth A. Lasater, Gabriel Pallares, Sarah Picaud, Christopher Wells, Lisa M. Wodicka, Neil P. Shah, Stefan Knapp, Daniel K. Treiber. Dual kinase/bromodomain inhibitors for rationally designed polypharmacology. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5387. doi:10.1158/1538-7445.AM2014-5387
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Neil P. Shah
- 3University of California, San Francisco, San Francisco, CA
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50
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Ciceri P, Müller S, O'Mahony A, Fedorov O, Filippakopoulos P, Hunt JP, Lasater EA, Pallares G, Picaud S, Wells C, Martin S, Wodicka LM, Shah NP, Treiber DK, Knapp S. Erratum: Corrigendum: Dual kinase-bromodomain inhibitors for rationally designed polypharmacology. Nat Chem Biol 2014. [DOI: 10.1038/nchembio0814-692d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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