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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Binet R, Lambert JP, Tomkova M, Tischfield S, Baggiolini A, Picaud S, Sarkar S, Louphrasitthiphol P, Dias D, Carreira S, Humphrey TC, Fillipakopoulos P, White R, Goding CR. DNA damage remodels the MITF interactome to increase melanoma genomic instability. Genes Dev 2024; 38:70-94. [PMID: 38316520 PMCID: PMC10903946 DOI: 10.1101/gad.350740.123] [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: 04/21/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024]
Abstract
Since genome instability can drive cancer initiation and progression, cells have evolved highly effective and ubiquitous DNA damage response (DDR) programs. However, some cells (for example, in skin) are normally exposed to high levels of DNA-damaging agents. Whether such high-risk cells possess lineage-specific mechanisms that tailor DNA repair to the tissue remains largely unknown. Using melanoma as a model, we show here that the microphthalmia-associated transcription factor MITF, a lineage addition oncogene that coordinates many aspects of melanocyte and melanoma biology, plays a nontranscriptional role in shaping the DDR. On exposure to DNA-damaging agents, MITF is phosphorylated at S325, and its interactome is dramatically remodeled; most transcription cofactors dissociate, and instead MITF interacts with the MRE11-RAD50-NBS1 (MRN) complex. Consequently, cells with high MITF levels accumulate stalled replication forks and display defects in homologous recombination-mediated repair associated with impaired MRN recruitment to DNA damage. In agreement with this, high MITF levels are associated with increased single-nucleotide and copy number variant burdens in melanoma. Significantly, the SUMOylation-defective MITF-E318K melanoma predisposition mutation recapitulates the effects of DNA-PKcs-phosphorylated MITF. Our data suggest that a nontranscriptional function of a lineage-restricted transcription factor contributes to a tissue-specialized modulation of the DDR that can impact cancer initiation.
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Affiliation(s)
- Romuald Binet
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Jean-Philippe Lambert
- Department of Molecular Medicine, Cancer Research Center, Université Laval, Québec City, Québec G1V 4G2, Canada
- Endocrinology-Nephrology Axis, CHU de Québec-Université Laval Research Center, Québec City, Québec G1V 4G2, Canada
| | - Marketa Tomkova
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, USA
| | - Samuel Tischfield
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Arianna Baggiolini
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Sovan Sarkar
- Cancer Research UK, Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Diogo Dias
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Suzanne Carreira
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Timothy C Humphrey
- Cancer Research UK, Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Panagis Fillipakopoulos
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Richard White
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom;
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3
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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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4
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Binet R, Lambert JP, Tomkova M, Tischfield S, Baggiolini A, Picaud S, Sarkar S, Louphrasitthiphol P, Dias D, Carreira S, Humphrey T, Fillipakopoulos P, White R, Goding CR. DNA damage-induced interaction between a lineage addiction oncogenic transcription factor and the MRN complex shapes a tissue-specific DNA Damage Response and cancer predisposition. bioRxiv 2023:2023.04.21.537819. [PMID: 37131595 PMCID: PMC10153263 DOI: 10.1101/2023.04.21.537819] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Since genome instability can drive cancer initiation and progression, cells have evolved highly effective and ubiquitous DNA Damage Response (DDR) programs. However, some cells, in skin for example, are normally exposed to high levels of DNA damaging agents. Whether such high-risk cells possess lineage-specific mechanisms that tailor DNA repair to the tissue remains largely unknown. Here we show, using melanoma as a model, that the microphthalmia-associated transcription factor MITF, a lineage addition oncogene that coordinates many aspects of melanocyte and melanoma biology, plays a non-transcriptional role in shaping the DDR. On exposure to DNA damaging agents, MITF is phosphorylated by ATM/DNA-PKcs, and unexpectedly its interactome is dramatically remodelled; most transcription (co)factors dissociate, and instead MITF interacts with the MRE11-RAD50-NBS1 (MRN) complex. Consequently, cells with high MITF levels accumulate stalled replication forks, and display defects in homologous recombination-mediated repair associated with impaired MRN recruitment to DNA damage. In agreement, high MITF levels are associated with increased SNV burden in melanoma. Significantly, the SUMOylation-defective MITF-E318K melanoma predisposition mutation recapitulates the effects of ATM/DNA-PKcs-phosphorylated MITF. Our data suggest that a non-transcriptional function of a lineage-restricted transcription factor contributes to a tissue-specialised modulation of the DDR that can impact cancer initiation.
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Affiliation(s)
- Romuald Binet
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Jean-Philippe Lambert
- Department of Molecular Medicine, Cancer Research Center and Big Data Research Center, Université Laval, Quebec, Canada; Endocrinology – Nephrology Axis, CHU de Québec – Université Laval Research Center, Quebec City, QC, Canada, G1V 4G2
| | - Marketa Tomkova
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
- Department of Biochemistry and Molecular Medicine, University of California, Davis, USA
| | - Samuel Tischfield
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Arianna Baggiolini
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Sovan Sarkar
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Diogo Dias
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Suzanne Carreira
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Timothy Humphrey
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Panagis Fillipakopoulos
- 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, Oxford OX3 7DQ, UK
| | - Richard White
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - 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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5
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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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6
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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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7
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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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8
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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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9
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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
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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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10
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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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11
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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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12
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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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13
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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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14
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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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15
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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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16
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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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17
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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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18
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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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19
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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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20
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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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21
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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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22
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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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23
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Picaud S, Trouillet A, Hadj-Saïd W, Dubus E, García-Ayuso D, Sahel J, El-Amraoui A, Petit C. Role of taurine in cone death. Acta Ophthalmol 2017. [DOI: 10.1111/j.1755-3768.2017.01363] [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: 11/29/2022]
Affiliation(s)
- S. Picaud
- INSTITUT DE LA VISION/UPMC; Paris France
| | - A. Trouillet
- Physiology; INSTITUT DE LA VISION/UPMC; Paris France
| | - W. Hadj-Saïd
- Physiology; INSTITUT DE LA VISION/UPMC; Paris France
| | - E. Dubus
- Physiology; INSTITUT DE LA VISION/UPMC; Paris France
| | - D. García-Ayuso
- Facultad de Medicina; Universidad de Murcia; Murcia Spain
- INSTITUT DE LA VISION/UPMC; UPMC; Paris France
| | - J. Sahel
- INSTITUT DE LA VISION/UPMC; UPMC; Paris France
| | - A. El-Amraoui
- Institut Pasteur; Génétique et Physiologie de l'Audition; Paris France
| | - C. Petit
- Institut Pasteur; Génétique et Physiologie de l'Audition; Paris France
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24
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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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25
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Garcia-Fernandez C, Radola B, Martin-Gondre L, Picaud S, Rayez M, Rayez J, Ouf F, Rubayo-Soneira J. A DFT study of the interaction between large PAHs and atomic chlorine or hydrogen chloride molecule: Toward a modelling of the influence of chlorinated species on the trapping of water by soot. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2016.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Navratilova I, Aristotelous T, Picaud S, Chaikuad A, Knapp S, Filappakopoulos P, Hopkins AL. Discovery of New Bromodomain Scaffolds by Biosensor Fragment Screening. ACS Med Chem Lett 2016; 7:1213-1218. [PMID: 27994766 DOI: 10.1021/acsmedchemlett.6b00154] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 04/18/2016] [Accepted: 09/20/2016] [Indexed: 12/22/2022] Open
Abstract
The discovery of novel bromodomain inhibitors by fragment screening is complicated by the presence of dimethyl sulfoxide (DMSO), an acetyl-lysine mimetic, that can compromise the detection of low affinity fragments. We demonstrate surface plasmon resonance as a primary fragment screening approach for the discovery of novel bromodomain scaffolds, by describing a protocol to overcome the DMSO interference issue. We describe the discovery of several novel small molecules scaffolds that inhibit the bromodomains PCAF, BRD4, and CREBBP, representing canonical members of three out of the seven subfamilies of bromodomains. High-resolution crystal structures of the complexes of key fragments binding to BRD4(1), CREBBP, and PCAF were determined to provide binding mode data to aid the development of potent and selective inhibitors of PCAF, CREBBP, and BRD4.
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Affiliation(s)
- Iva Navratilova
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Tonia Aristotelous
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Sarah Picaud
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
- Target
Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Apirat Chaikuad
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
- Target
Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Stefan Knapp
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
- Target
Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Panagis Filappakopoulos
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
- Ludwig Institute for Cancer Research, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Andrew L. Hopkins
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
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27
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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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28
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Peynshaert K, Fradot V, Picaud S, De Smedt S, Remaut K. Toward rational design of gene carriers: a novel ex vivo
model to study the vitreoretinal interface as a barrier. Acta Ophthalmol 2016. [DOI: 10.1111/j.1755-3768.2016.0376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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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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30
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Ghari F, Quirke AM, Munro S, Kawalkowska J, Picaud S, McGouran J, Subramanian V, Muth A, Williams R, Kessler B, Thompson PR, Fillipakopoulos P, Knapp S, Venables PJ, La Thangue NB. Citrullination-acetylation interplay guides E2F-1 activity during the inflammatory response. Sci Adv 2016; 2:e1501257. [PMID: 26989780 PMCID: PMC4788482 DOI: 10.1126/sciadv.1501257] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 12/01/2015] [Indexed: 05/19/2023]
Abstract
Peptidyl arginine deiminase 4 (PAD4) is a nuclear enzyme that converts arginine residues to citrulline. Although increasingly implicated in inflammatory disease and cancer, the mechanism of action of PAD4 and its functionally relevant pathways remains unclear. E2F transcription factors are a family of master regulators that coordinate gene expression during cellular proliferation and diverse cell fates. We show that E2F-1 is citrullinated by PAD4 in inflammatory cells. Citrullination of E2F-1 assists its chromatin association, specifically to cytokine genes in granulocyte cells. Mechanistically, citrullination augments binding of the BET (bromodomain and extra-terminal domain) family bromodomain reader BRD4 (bromodomain-containing protein 4) to an acetylated domain in E2F-1, and PAD4 and BRD4 coexist with E2F-1 on cytokine gene promoters. Accordingly, the combined inhibition of PAD4 and BRD4 disrupts the chromatin-bound complex and suppresses cytokine gene expression. In the murine collagen-induced arthritis model, chromatin-bound E2F-1 in inflammatory cells and consequent cytokine expression are diminished upon small-molecule inhibition of PAD4 and BRD4, and the combined treatment is clinically efficacious in preventing disease progression. Our results shed light on a new transcription-based mechanism that mediates the inflammatory effect of PAD4 and establish the interplay between citrullination and acetylation in the control of E2F-1 as a regulatory interface for driving inflammatory gene expression.
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Affiliation(s)
- Fatemeh Ghari
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Shonagh Munro
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Sarah Picaud
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - Joanna McGouran
- University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | | | - Aaron Muth
- Ludwig Institute, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Benedikt Kessler
- University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | | | - Panagis Fillipakopoulos
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
- Target Discovery Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - Stefan Knapp
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
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31
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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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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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33
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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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Lectez S, Simon JM, Mousis O, Picaud S, Altwegg K, Rubin M, Salazar JM. A ∼32–70 K FORMATION TEMPERATURE RANGE FOR THE ICE GRAINS AGGLOMERATED BY COMET 67 P/CHURYUMOV–GERASIMENKO. ACTA ACUST UNITED AC 2015. [DOI: 10.1088/2041-8205/805/1/l1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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35
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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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36
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Matonti F, Roux S, Denis D, Picaud S, Chavane F. [Blindness and visual rehabilitation]. J Fr Ophtalmol 2015; 38:93-102. [PMID: 25595628 DOI: 10.1016/j.jfo.2014.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 06/23/2014] [Accepted: 06/30/2014] [Indexed: 10/24/2022]
Abstract
Blindness and visual impairment are a major public health problem all over the world and in all societies. A large amount of basic science and clinical research aims to rehabilitate patients and help them become more independent. Various methods are explored from cell and molecular therapy to prosthetic interfaces. We review the various treatment alternatives, describing their results and their limitations.
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Affiliation(s)
- F Matonti
- Service d'ophtalmologie, hôpital Nord, chemin de Bourrely, 13915 Marseille cedex 20, France; Équipe InViBe, institut de neurosciences de la Timone, UMR 7289 CNRS, Aix-Marseille université, 13402 Marseille cedex 20, France.
| | - S Roux
- Équipe InViBe, institut de neurosciences de la Timone, UMR 7289 CNRS, Aix-Marseille université, 13402 Marseille cedex 20, France
| | - D Denis
- Service d'ophtalmologie, hôpital Nord, chemin de Bourrely, 13915 Marseille cedex 20, France; Équipe InViBe, institut de neurosciences de la Timone, UMR 7289 CNRS, Aix-Marseille université, 13402 Marseille cedex 20, France
| | - S Picaud
- Inserm, U968, CNRS, UMR 7210, institut de la vision, UPMC université Paris 06, 75012 Paris, France
| | - F Chavane
- Équipe InViBe, institut de neurosciences de la Timone, UMR 7289 CNRS, Aix-Marseille université, 13402 Marseille cedex 20, France
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37
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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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38
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Hébert C, Scorsone E, Bendali A, Kiran R, Cottance M, Girard HA, Degardin J, Dubus E, Lissorgues G, Rousseau L, Mailley P, Picaud S, Bergonzo P. Boron doped diamond biotechnology: from sensors to neurointerfaces. Faraday Discuss 2014; 172:47-59. [PMID: 25259508 DOI: 10.1039/c4fd00040d] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Boron doped nanocrystalline diamond is known as a remarkable material for the fabrication of sensors, taking advantage of its biocompatibility, electrochemical properties, and stability. Sensors can be fabricated to directly probe physiological species from biofluids (e.g. blood or urine), as will be presented. In collaboration with electrophysiologists and biologists, the technology was adapted to enable structured diamond devices such as microelectrode arrays (MEAs), i.e. common electrophysiology tools, to probe neuronal activity distributed over large populations of neurons or embryonic organs. Specific MEAs can also be used to build neural prostheses or implants to compensate function losses due to lesions or degeneration of parts of the central nervous system, such as retinal implants, which exhibit real promise as biocompatible neuroprostheses for in vivo neuronal stimulations. New electrode geometries enable high performance electrodes to surpass more conventional materials for such applications.
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Affiliation(s)
- C Hébert
- CEA, LIST, Diamond Sensors Laboratory, F-91191, Gif-sur-Yvette, France.
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39
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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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40
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Hay DA, Fedorov O, Martin S, Singleton DC, Tallant C, Wells C, Picaud S, Philpott M, Monteiro OP, Rogers CM, Conway SJ, Rooney TPC, Tumber A, Yapp C, Filippakopoulos P, Bunnage ME, Müller S, Knapp S, Schofield CJ, Brennan PE. Discovery and optimization of small-molecule ligands for the CBP/p300 bromodomains. J Am Chem Soc 2014; 136:9308-19. [PMID: 24946055 PMCID: PMC4183655 DOI: 10.1021/ja412434f] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Small-molecule inhibitors that target
bromodomains outside
of the bromodomain and extra-terminal (BET) sub-family are lacking.
Here, we describe highly potent and selective ligands for the bromodomain
module of the human lysine acetyl transferase CBP/p300, developed
from a series of 5-isoxazolyl-benzimidazoles. Our starting
point was a fragment hit, which was optimized into a more potent and
selective lead using parallel synthesis employing Suzuki couplings,
benzimidazole-forming reactions, and reductive aminations.
The selectivity of the lead compound against other bromodomain
family members was investigated using a thermal stability assay, which
revealed some inhibition of the structurally related BET family members.
To address the BET selectivity issue, X-ray crystal structures of
the lead compound bound to the CREB binding protein (CBP) and the
first bromodomain of BRD4 (BRD4(1)) were used to guide the design
of more selective compounds. The crystal structures obtained revealed
two distinct binding modes. By varying the aryl substitution pattern
and developing conformationally constrained analogues, selectivity
for CBP over BRD4(1) was increased. The optimized compound is highly
potent (Kd = 21 nM) and selective, displaying
40-fold selectivity over BRD4(1). Cellular activity was demonstrated
using fluorescence recovery after photo-bleaching (FRAP) and a p53
reporter assay. The optimized compounds are cell-active and have nanomolar
affinity for CBP/p300; therefore, they should be useful in studies
investigating the biological roles of CBP and p300 and to validate
the CBP and p300 bromodomains as therapeutic targets.
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Affiliation(s)
- Duncan A Hay
- Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3TA, U.K
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Rooney TPC, Filippakopoulos P, Fedorov O, Picaud S, Cortopassi WA, Hay DA, Martin S, Tumber A, Rogers CM, Philpott M, Wang M, Thompson AL, Heightman TD, Pryde DC, Cook A, Paton RS, Müller S, Knapp S, Brennan PE, Conway SJ. A Series of Potent CREBBP Bromodomain Ligands Reveals an Induced-Fit Pocket Stabilized by a Cation-π Interaction. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402750] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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42
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Rooney TPC, Filippakopoulos P, Fedorov O, Picaud S, Cortopassi WA, Hay DA, Martin S, Tumber A, Rogers CM, Philpott M, Wang M, Thompson AL, Heightman TD, Pryde DC, Cook A, Paton RS, Müller S, Knapp S, Brennan PE, Conway SJ. A series of potent CREBBP bromodomain ligands reveals an induced-fit pocket stabilized by a cation-π interaction. Angew Chem Int Ed Engl 2014; 53:6126-30. [PMID: 24821300 PMCID: PMC4298791 DOI: 10.1002/anie.201402750] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [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: 02/24/2014] [Indexed: 12/04/2022]
Abstract
The benzoxazinone and dihydroquinoxalinone fragments were employed as novel acetyl lysine mimics in the development of CREBBP bromodomain ligands. While the benzoxazinone series showed low affinity for the CREBBP bromodomain, expansion of the dihydroquinoxalinone series resulted in the first potent inhibitors of a bromodomain outside the BET family. Structural and computational studies reveal that an internal hydrogen bond stabilizes the protein-bound conformation of the dihydroquinoxalinone series. The side chain of this series binds in an induced-fit pocket forming a cation–π interaction with R1173 of CREBBP. The most potent compound inhibits binding of CREBBP to chromatin in U2OS cells.
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Affiliation(s)
- Timothy P C Rooney
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA (UK) http://conway.chem.ox.ac.uk/
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43
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Garcia-Fernandez C, Picaud S, Rayez MT, Rayez JC, Rubayo-Soneira J. First-Principles Study of the Interaction between NO and Large Carbonaceous Clusters Modeling the Soot Surface. J Phys Chem A 2014; 118:1443-50. [DOI: 10.1021/jp412217q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- C. Garcia-Fernandez
- Institut UTINAM—UMR 6213, CNRS/Université de Franche-Comté, 16 Route de Gray F-25030 Besançon Cedex, France
- Instituto
Superior de Tecnologias y Ciencias Aplicadas (InSTEC), Ave. Salvador Allende y Luaces, Quinta de los Molinos Plaza, Habana 10600, Cuba
| | - S. Picaud
- Institut UTINAM—UMR 6213, CNRS/Université de Franche-Comté, 16 Route de Gray F-25030 Besançon Cedex, France
| | - M. T. Rayez
- Institut des Sciences Moléculaires − UMR 5255/CNRS, Université de Bordeaux I, 351 cours
de la Libération, F-33405 Talence Cedex, France
| | - J. C. Rayez
- Institut des Sciences Moléculaires − UMR 5255/CNRS, Université de Bordeaux I, 351 cours
de la Libération, F-33405 Talence Cedex, France
| | - J. Rubayo-Soneira
- Instituto
Superior de Tecnologias y Ciencias Aplicadas (InSTEC), Ave. Salvador Allende y Luaces, Quinta de los Molinos Plaza, Habana 10600, Cuba
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44
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Fedorov O, Lingard H, Wells C, Monteiro OP, Picaud S, Keates T, Yapp C, Philpott M, Martin SJ, Felletar I, Marsden BD, Filippakopoulos P, Müller S, Knapp S, Brennan PE. [1,2,4]triazolo[4,3-a]phthalazines: inhibitors of diverse bromodomains. J Med Chem 2013; 57:462-76. [PMID: 24313754 PMCID: PMC3906316 DOI: 10.1021/jm401568s] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [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] [Indexed: 12/24/2022]
Abstract
Bromodomains are gaining increasing interest as drug targets. Commercially sourced and de novo synthesized substituted [1,2,4]triazolo[4,3-a]phthalazines are potent inhibitors of both the BET bromodomains such as BRD4 as well as bromodomains outside the BET family such as BRD9, CECR2, and CREBBP. This new series of compounds is the first example of submicromolar inhibitors of bromodomains outside the BET subfamily. Representative compounds are active in cells exhibiting potent cellular inhibition activity in a FRAP model of CREBBP and chromatin association. The compounds described are valuable starting points for discovery of selective bromodomain inhibitors and inhibitors with mixed bromodomain pharmacology.
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Affiliation(s)
- Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
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45
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Kempen HJ, Bellus D, Fedorov O, Nicklisch S, Filippakopoulos P, Picaud S, Knapp S. Stimulation of Hepatic Apolipoprotein A-I Production by Novel Thieno-Triazolodiazepines: Roles of the Classical Benzodiazepine Receptor, PAF Receptor, and Bromodomain Binding. Lipid Insights 2013; 6:47-54. [PMID: 25278768 PMCID: PMC4147775 DOI: 10.4137/lpi.s13258] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/17/2013] [Accepted: 11/21/2013] [Indexed: 12/19/2022] Open
Abstract
Expression and secretion of apolipoprotein A-I (apoA-I) by cultured liver cells can be markedly stimulated by triazolodiazepines (TZDs). It has been shown previously that the thieno-TZD Ro 11-1464 increases plasma levels of apoA-I and in vivomacrophage reverse cholesterol transport in mice. However, these effects were only seen at high doses, at which the compound could act on central benzodiazepine (BZD) receptors or platelet activating factor (PAF) receptors, interfering with its potential utility. In this work, we describe 2 new thieno-TZDs MDCO-3770 and MDCO-3783, both derived from Ro 11-1464. These compounds display the same high efficacy on apoA-I production, metabolic stability, and lack of cytotoxicity in cultured hepatocytes as Ro 11-1464, but they do not bind to the central BZD receptor and PAF receptor. The quinazoline RVX-208 was less efficacious in stimulating apoA-I production and displayed signs of cytotoxicity. Certain TZDs stimulating apoA-I production are now known to be inhibitors of bromodomain (BRD) extra-terminal (BET) proteins BRDT, BRD2, BRD3, and BRD4, and this inhibition was inferred as a main molecular mechanism for their effect on apoA-I expression. We show here that the thieno-TZD (+)-JQ1, a potent BET inhibitor, strongly stimulated apoA-I production in Hep-G2 cells, but that its enantiomer (−)-JQ1, which has no BET inhibitor activity, also showed considerable effect on apoA-I production. MDCO-3770 and MDCO-3783 also inhibited BRD3 and BRD4 in vitro, with potency somewhat below that of (+)-JQ1. We conclude that the effect of thieno-TZDs on apoA-I expression is not due to inhibition of the BZD or PAF receptors and is not completely explained by transcriptional repression by BET proteins.
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Affiliation(s)
- Herman J Kempen
- Dybly AG, Basel, Switzerland. ; The Medicines Company (Schweiz) GmbH, Zürich, Switzerland
| | | | - Oleg Fedorov
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford, UK. ; Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, Oxford, UK
| | | | - Panagis Filippakopoulos
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford, UK. ; Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, Oxford, UK
| | - Sarah Picaud
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford, UK
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford, UK. ; Nuffield Department of Clinical Medicine, Target Discovery Institute, Oxford, UK
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46
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Vidler LR, Filippakopoulos P, Fedorov O, Picaud S, Martin S, Tomsett M, Woodward H, Brown N, Knapp S, Hoelder S. Discovery of novel small-molecule inhibitors of BRD4 using structure-based virtual screening. J Med Chem 2013; 56:8073-88. [PMID: 24090311 PMCID: PMC3807807 DOI: 10.1021/jm4011302] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Bromodomains
(BRDs) are epigenetic readers that recognize acetylated-lysine
(KAc) on proteins and are implicated in a number of diseases. We describe
a virtual screening approach to identify BRD inhibitors. Key elements
of this approach are the extensive design and use of substructure
queries to compile a set of commercially available compounds featuring
novel putative KAc mimetics and docking this set for final compound
selection. We describe the validation of this approach by applying
it to the first BRD of BRD4. The selection and testing of 143 compounds
lead to the discovery of six novel hits, including four unprecedented
KAc mimetics. We solved the crystal structure of four hits, determined
their binding mode, and improved their potency through synthesis and
the purchase of derivatives. This work provides a validated virtual
screening approach that is applicable to other BRDs and describes
novel KAc mimetics that can be further explored to design more potent
inhibitors.
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Affiliation(s)
- Lewis R Vidler
- Division of Cancer Therapeutics, Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research , 15 Cotswold Road, Sutton, Surrey SM2 5NG, United Kingdom
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47
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48
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Hewings D, Fedorov O, Filippakopoulos P, Martin S, Picaud S, Tumber A, Wells C, Olcina MM, Freeman K, Gill A, Ritchie AJ, Sheppard DW, Russell AJ, Hammond EM, Knapp S, Brennan PE, Conway SJ. Optimization of 3,5-dimethylisoxazole derivatives as potent bromodomain ligands. J Med Chem 2013; 56:3217-27. [PMID: 23517011 PMCID: PMC3640414 DOI: 10.1021/jm301588r] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [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: 10/28/2012] [Indexed: 12/14/2022]
Abstract
The bromodomain protein module, which binds to acetylated lysine, is emerging as an important epigenetic therapeutic target. We report the structure-guided optimization of 3,5-dimethylisoxazole derivatives to develop potent inhibitors of the BET (bromodomain and extra terminal domain) bromodomain family with good ligand efficiency. X-ray crystal structures of the most potent compounds reveal key interactions required for high affinity at BRD4(1). Cellular studies demonstrate that the phenol and acetate derivatives of the lead compounds showed strong antiproliferative effects on MV4;11 acute myeloid leukemia cells, as shown for other BET bromodomain inhibitors and genetic BRD4 knockdown, whereas the reported compounds showed no general cytotoxicity in other cancer cell lines tested.
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Affiliation(s)
- David
S. Hewings
- Department of Chemistry, Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 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
| | - 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
| | - Sarah Martin
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 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
| | - Anthony Tumber
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Christopher Wells
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Monica M. Olcina
- Department of Oncology, Cancer
Research UK/MRC Gray Institute for Radiation Oncology and Biology, University of Oxford, Old Road Campus Research Building,
Oxford, OX3 7DQ, U.K
| | - Katherine Freeman
- Department of Chemistry, Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Andrew Gill
- BioFocus, Chesterford Research Park, Saffron Walden,
Essex, CB10 1XL, U.K
| | - Alison J. Ritchie
- BioFocus, Chesterford Research Park, Saffron Walden,
Essex, CB10 1XL, U.K
| | - David W. Sheppard
- BioFocus, Chesterford Research Park, Saffron Walden,
Essex, CB10 1XL, U.K
| | - Angela J. Russell
- Department of Chemistry, Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Ester M. Hammond
- Department of Oncology, Cancer
Research UK/MRC Gray Institute for Radiation Oncology and Biology, University of Oxford, Old Road Campus Research Building,
Oxford, OX3 7DQ, U.K
| | - Stefan Knapp
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Paul E. Brennan
- 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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49
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Picaud S, Da Costa D, Thanasopoulou A, Filippakopoulos P, Fish PV, Philpott M, Fedorov O, Brennan P, Bunnage ME, Owen DR, Bradner JE, Taniere P, O'Sullivan B, Müller S, Schwaller J, Stankovic T, Knapp S. PFI-1, a highly selective protein interaction inhibitor, targeting BET Bromodomains. Cancer Res 2013; 73:3336-46. [PMID: 23576556 DOI: 10.1158/0008-5472.can-12-3292] [Citation(s) in RCA: 195] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Bromo and extra terminal (BET) proteins (BRD2, BRD3, BRD4, and BRDT) are transcriptional regulators required for efficient expression of several growth promoting and antiapoptotic genes as well as for cell-cycle progression. BET proteins are recruited on transcriptionally active chromatin via their two N-terminal bromodomains (BRD), a protein interaction module that specifically recognizes acetylated lysine residues in histones H3 and H4. Inhibition of the BET-histone interaction results in transcriptional downregulation of a number of oncogenes, providing a novel pharmacologic strategy for the treatment of cancer. Here, we present a potent and highly selective dihydroquinazoline-2-one inhibitor, PFI-1, which efficiently blocks the interaction of BET BRDs with acetylated histone tails. Cocrystal structures showed that PFI-1 acts as an acetyl-lysine (Kac) mimetic inhibitor efficiently occupying the Kac binding site in BRD4 and BRD2. PFI-1 has antiproliferative effects on leukemic cell lines and efficiently abrogates their clonogenic growth. Exposure of sensitive cell lines with PFI-1 results in G1 cell-cycle arrest, downregulation of MYC expression, as well as induction of apoptosis and induces differentiation of primary leukemic blasts. Intriguingly, cells exposed to PFI-1 showed significant downregulation of Aurora B kinase, thus attenuating phosphorylation of the Aurora substrate H3S10, providing an alternative strategy for the specific inhibition of this well-established oncology target.
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Affiliation(s)
- Sarah Picaud
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, USA
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50
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Hay D, Fedorov O, Filippakopoulos P, Martin S, Philpott M, Picaud S, Hewings DS, Uttakar S, Heightman TD, Conway SJ, Knapp S, Brennan PE. The design and synthesis of 5- and 6-isoxazolylbenzimidazoles as selective inhibitors of the BET bromodomains. Medchemcomm 2013; 4:140-144. [PMID: 26682033 DOI: 10.1039/c2md20189e] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Simple 1-substituted 5- and 6-isoxazolyl-benzimidazoles have been shown to be potent inhibitors of the BET bromodomains with selectivity over the related bromodomain of CBP. The reported inhibitors were prepared from simple starting materials in two steps followed by separation of the regioisomers or regioselectively in three steps.
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Affiliation(s)
- Duncan Hay
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, 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
| | - Sarah Martin
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Martin Philpott
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - David S Hewings
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Sagar Uttakar
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Tom D Heightman
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Stefan Knapp
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Paul E Brennan
- 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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