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Healy J, Rasmussen T, Miller S, Booth IR, Conway SJ. The photochemical thiol-ene reaction as a versatile method for the synthesis of glutathione S-conjugates targeting the bacterial potassium efflux system Kef. Org Chem Front 2016; 3:439-446. [PMID: 27110363 PMCID: PMC4819703 DOI: 10.1039/c5qo00436e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/15/2016] [Indexed: 01/10/2023]
Abstract
The thiol-ene coupling reaction is emerging as an important conjugation reaction that is suitable for use in a biological setting. Here, we explore the utility of this reaction for the synthesis of glutathione-S-conjugates (GSX) and present a general, operationally simple, protocol with a wide substrate scope. The GSX afforded are an important class of compounds and provide invaluable molecular tools to study glutathione-binding proteins. In this study we apply the diverse library of GSX synthesised to further our understanding of the structural requirements for binding to the glutathione-binding protein, Kef, a bacterial K+ efflux system, found in many bacterial pathogens. This system is vital to the survival of bacteria upon exposure to electrophiles, and plays an essential role in the maintenance of intracellular pH and K+ homeostasis. Consequently, Kef is an appealing target for the development of novel antibacterial drugs.
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Affiliation(s)
- Jess Healy
- Department of Chemistry , Chemistry Research Laboratory , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK . ; ; Department of Pharmaceutical and Biological Chemistry , UCL School of Pharmacy , University College London , 29/39 Brunswick Square , WC1N, 1AX , UK
| | - Tim Rasmussen
- Institute of Medical Sciences , University of Aberdeen , Foresterhill , Aberdeen , AB25 2ZD , UK
| | - Samantha Miller
- Institute of Medical Sciences , University of Aberdeen , Foresterhill , Aberdeen , AB25 2ZD , UK
| | - Ian R Booth
- Institute of Medical Sciences , University of Aberdeen , Foresterhill , Aberdeen , AB25 2ZD , UK
| | - Stuart J Conway
- Department of Chemistry , Chemistry Research Laboratory , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK . ;
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103
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Theodoulou NH, Tomkinson NCO, Prinjha RK, Humphreys PG. Progress in the Development of non-BET Bromodomain Chemical Probes. ChemMedChem 2016; 11:477-87. [PMID: 26749027 DOI: 10.1002/cmdc.201500540] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 12/09/2015] [Indexed: 12/19/2022]
Abstract
The bromodomain and extra terminal (BET) family of bromodomains have been the focus of extensive research, leading to the development of many potent, selective chemical probes and recent clinical assets. The profound biology associated with BET bromodomain inhibition has provided a convincing rationale for targeting bromodomains for the treatment of disease. However, the BET family represents just eight of the at least 56 human bromodomains identified to date. Until recently, there has been significantly less interest in non-BET bromodomains, leaving a vast area of research and the majority of this new target class yet to be thoroughly investigated. It has been widely reported that several non-BET bromodomain containing proteins are associated with various diseases including cancer and HIV. Therefore, the development of chemical probes for non-BET bromodomains will facilitate elucidation of their precise biological roles and potentially lead to the development of new medicines. This review summarises the progress made towards the development of non-BET bromodomain chemical probes to date. In addition, we highlight the potential for future work in this new and exciting area.
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Affiliation(s)
- Natalie H Theodoulou
- Epinova Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage, Hertfordshire, SG1 2NY, UK.,WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Nicholas C O Tomkinson
- WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Rab K Prinjha
- Epinova Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Philip G Humphreys
- Epinova Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage, Hertfordshire, SG1 2NY, UK.
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104
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Ferri E, Petosa C, McKenna CE. Bromodomains: Structure, function and pharmacology of inhibition. Biochem Pharmacol 2015; 106:1-18. [PMID: 26707800 DOI: 10.1016/j.bcp.2015.12.005] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/08/2015] [Indexed: 12/22/2022]
Abstract
Bromodomains are epigenetic readers of histone acetylation involved in chromatin remodeling and transcriptional regulation. The human proteome comprises 46 bromodomain-containing proteins with a total of 61 bromodomains, which, despite highly conserved structural features, recognize a wide array of natural peptide ligands. Over the past five years, bromodomains have attracted great interest as promising new epigenetic targets for diverse human diseases, including inflammation, cancer, and cardiovascular disease. The demonstration in 2010 that two small molecule compounds, JQ1 and I-BET762, potently inhibit proteins of the bromodomain and extra-terminal (BET) family with translational potential for cancer and inflammatory disease sparked intense efforts in academia and pharmaceutical industry to develop novel bromodomain antagonists for therapeutic applications. Several BET inhibitors are already in clinical trials for hematological malignancies, solid tumors and cardiovascular disease. Currently, the field faces the challenge of single-target selectivity, especially within the BET family, and of overcoming problems related to the development of drug resistance. At the same time, new trends in bromodomain inhibitor research are emerging, including an increased interest in non-BET bromodomains and a focus on drug synergy with established antitumor agents to improve chemotherapeutic efficacy. This review presents an updated view of the structure and function of bromodomains, traces the development of bromodomain inhibitors and their potential therapeutic applications, and surveys the current challenges and future directions of this vibrant new field in drug discovery.
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Affiliation(s)
- Elena Ferri
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, CA 90089, United States
| | - Carlo Petosa
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38044 Grenoble, France; Centre National de la Recherche Scientifique, IBS, 38044 Grenoble, France; Commissariat à l'Energie Atomique et aux Energies Alternatives, IBS, 38044 Grenoble, France
| | - Charles E McKenna
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, CA 90089, United States.
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105
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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: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [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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106
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Romero FA, Taylor AM, Crawford TD, Tsui V, Côté A, Magnuson S. Disrupting Acetyl-Lysine Recognition: Progress in the Development of Bromodomain Inhibitors. J Med Chem 2015; 59:1271-98. [PMID: 26572217 DOI: 10.1021/acs.jmedchem.5b01514] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bromodomains, small protein modules that recognize acetylated lysine on histones, play a significant role in the epigenome, where they function as "readers" that ultimately determine the functional outcome of the post-translational modification. Because the initial discovery of selective BET inhibitors have helped define the role of that protein family in oncology and inflammation, BET bromodomains have continued to garner the most attention of any other bromodomain. More recently, non-BET bromodomain inhibitors that are potent and selective have been disclosed for ATAD2, CBP, BRD7/9, BRPF, BRPF/TRIM24, CECR2, SMARCA4, and BAZ2A/B. Such novel inhibitors can be used to probe the physiological function of these non-BET bromodomains and further understanding of their role in certain disease states. Here, we provide an update to the progress in identifying selective bromodomain inhibitors and their use as biological tools, as well as our perspective on the field.
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Affiliation(s)
- F Anthony Romero
- Discovery Chemistry, Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Alexander M Taylor
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Terry D Crawford
- Discovery Chemistry, Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Vickie Tsui
- Discovery Chemistry, Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Alexandre Côté
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Steven Magnuson
- Discovery Chemistry, Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
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107
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Affiliation(s)
- Guangtao Zhang
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai , 1425 Madison Avenue, New York, New York 10029, United States
| | - Steven G Smith
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai , 1425 Madison Avenue, New York, New York 10029, United States
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai , 1425 Madison Avenue, New York, New York 10029, United States
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108
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Benedetti R, Conte M, Iside C, Altucci L. Epigenetic-based therapy: From single- to multi-target approaches. Int J Biochem Cell Biol 2015; 69:121-31. [PMID: 26494003 DOI: 10.1016/j.biocel.2015.10.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 12/20/2022]
Abstract
The treatment of cancer has traditionally been based on the identification of a single molecule and/or enzymatic function (target) responsible for a particular phenotype, and therefore on the ability to stimulate, attenuate or inhibit its activity through the use of selective compounds. However, cancer is no longer considered a disease caused by a single factor, but is now recognized as a multi-factorial disorder. Genetic, epigenetic and metabolic factors all contribute to neoplasia, causing significant changes in molecular networks that govern cell growth, development, death and specialization. Consequently, many antitumor therapies are no longer directed against a single target but the biological system as a whole, in which functions determining the onset and maintenance of a physio-pathological state are modulated. The field of epi-drug discovery is currently in a transitional phase where the search for putative anticancer drugs is shifting from single-target-oriented molecules to network-active compounds and to epi-drugs used in combination with other epi-agents and with traditional chemotherapeutics. This review illustrates the pros and cons of each therapeutic option, providing examples in support of single-target and multi (network)-target epi-drug approaches.
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Affiliation(s)
- Rosaria Benedetti
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Università di Napoli, Vico L. De Crecchio 7, 80138 Napoli, Italy.
| | - Mariarosaria Conte
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Università di Napoli, Vico L. De Crecchio 7, 80138 Napoli, Italy
| | - Concetta Iside
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Università di Napoli, Vico L. De Crecchio 7, 80138 Napoli, Italy
| | - Lucia Altucci
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Università di Napoli, Vico L. De Crecchio 7, 80138 Napoli, Italy; Istituto di Genetica e Biofisica, Adriano Buzzati Traverso, CNR-IGB, Via P. Castellino 111, 80131 Napoli, Italy.
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109
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Jung M, Gelato KA, Fernández-Montalván A, Siegel S, Haendler B. Targeting BET bromodomains for cancer treatment. Epigenomics 2015; 7:487-501. [PMID: 26077433 DOI: 10.2217/epi.14.91] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The bromodomain and extraterminal (BET) subfamily of bromodomain-containing proteins has emerged in the last few years as an exciting, novel target group. BRD4, the best studied BET protein, is implicated in a number of hematological and solid tumors. This is linked to its role in modulating transcription elongation of essential genes involved in cell cycle and apoptosis such as c-Myc and BCL2. Potent BET inhibitors with promising antitumor efficacy in a number of preclinical cancer models have been identified in recent years. This led to clinical studies focusing mostly on the treatment of leukemia and lymphoma, and first encouraging signs of efficacy have already been reported. Here we discuss the biology of BRD4, its known interaction partners and implication in different tumor types. Further, we summarize the current knowledge on BET bromodomain inhibitors.
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Affiliation(s)
- Marie Jung
- Global Drug Discovery, Bayer Pharma AG, D-13353 Berlin, Germany.,Institute of Chemistry & Biochemistry, Free University, D-14195 Berlin, Germany
| | - Kathy A Gelato
- Global Drug Discovery, Bayer Pharma AG, D-13353 Berlin, Germany
| | | | - Stephan Siegel
- Global Drug Discovery, Bayer Pharma AG, D-13353 Berlin, Germany
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110
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Hammitzsch A, Tallant C, Fedorov O, O'Mahony A, Brennan PE, Hay DA, Martinez FO, Al-Mossawi MH, de Wit J, Vecellio M, Wells C, Wordsworth P, Müller S, Knapp S, Bowness P. CBP30, a selective CBP/p300 bromodomain inhibitor, suppresses human Th17 responses. Proc Natl Acad Sci U S A 2015; 112:10768-73. [PMID: 26261308 PMCID: PMC4553799 DOI: 10.1073/pnas.1501956112] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Th17 responses are critical to a variety of human autoimmune diseases, and therapeutic targeting with monoclonal antibodies against IL-17 and IL-23 has shown considerable promise. Here, we report data to support selective bromodomain blockade of the transcriptional coactivators CBP (CREB binding protein) and p300 as an alternative approach to inhibit human Th17 responses. We show that CBP30 has marked molecular specificity for the bromodomains of CBP and p300, compared with 43 other bromodomains. In unbiased cellular testing on a diverse panel of cultured primary human cells, CBP30 reduced immune cell production of IL-17A and other proinflammatory cytokines. CBP30 also inhibited IL-17A secretion by Th17 cells from healthy donors and patients with ankylosing spondylitis and psoriatic arthritis. Transcriptional profiling of human T cells after CBP30 treatment showed a much more restricted effect on gene expression than that observed with the pan-BET (bromo and extraterminal domain protein family) bromodomain inhibitor JQ1. This selective targeting of the CBP/p300 bromodomain by CBP30 will potentially lead to fewer side effects than with the broadly acting epigenetic inhibitors currently in clinical trials.
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Affiliation(s)
- Ariane Hammitzsch
- Botnar Research Institute, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, Oxford OX3 7LD, United Kingdom
| | - Cynthia Tallant
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom; Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom; Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Alison O'Mahony
- BioSeek Division of DiscoveRx Corporation, South San Francisco, CA 94080
| | - Paul E Brennan
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom; Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Duncan A Hay
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Fernando O Martinez
- Botnar Research Institute, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, Oxford OX3 7LD, United Kingdom
| | - M Hussein Al-Mossawi
- Botnar Research Institute, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, Oxford OX3 7LD, United Kingdom
| | - Jelle de Wit
- Botnar Research Institute, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, Oxford OX3 7LD, United Kingdom
| | - Matteo Vecellio
- Botnar Research Institute, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, Oxford OX3 7LD, United Kingdom
| | - Christopher Wells
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Paul Wordsworth
- Botnar Research Institute, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, Oxford OX3 7LD, United Kingdom
| | - Susanne Müller
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom; Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Stefan Knapp
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom; Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom; Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, 60438 Frankfurt am Main, Germany
| | - Paul Bowness
- Botnar Research Institute, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, Oxford OX3 7LD, United Kingdom;
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111
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Hu F, Szostak M. Recent Developments in the Synthesis and Reactivity of Isoxazoles: Metal Catalysis and Beyond. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500319] [Citation(s) in RCA: 220] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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112
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Xu M, Unzue A, Dong J, Spiliotopoulos D, Nevado C, Caflisch A. Discovery of CREBBP Bromodomain Inhibitors by High-Throughput Docking and Hit Optimization Guided by Molecular Dynamics. J Med Chem 2015; 59:1340-9. [PMID: 26125948 DOI: 10.1021/acs.jmedchem.5b00171] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have identified two chemotypes of CREBBP bromodomain ligands by fragment-based high-throughput docking. Only 17 molecules from the original library of two-million compounds were tested in vitro. Optimization of the two low-micromolar hits, the 4-acylpyrrole 1 and acylbenzene 9, was driven by molecular dynamics results which suggested improvement of the polar interactions with the Arg1173 side chain at the rim of the binding site. The synthesis of only two derivatives of 1 yielded the 4-acylpyrrole 6 which shows a single-digit micromolar affinity for the CREBBP bromodomain and a ligand efficiency of 0.34 kcal/mol per non-hydrogen atom. Optimization of the acylbenzene hit 9 resulted in a series of derivatives with nanomolar potencies, good ligand efficiency and selectivity (see Unzue, A.; Xu, M.; Dong, J.; Wiedmer, L.; Spiliotopoulos, D.; Caflisch, A.; Nevado, C.Fragment-Based Design of Selective Nanomolar Ligands of the CREBBP Bromodomain. J. Med. Chem. 2015, DOI: 10.1021/acs.jmedchem.5b00172). The in silico predicted binding mode of the acylbenzene derivative 10 was validated by solving the structure of the complex with the CREBBP bromodomain.
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Affiliation(s)
- Min Xu
- Department of Biochemistry, University of Zürich , Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Andrea Unzue
- Department of Chemistry, University of Zürich , Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Jing Dong
- Department of Biochemistry, University of Zürich , Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Dimitrios Spiliotopoulos
- Department of Biochemistry, University of Zürich , Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Cristina Nevado
- Department of Chemistry, University of Zürich , Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich , Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
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113
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Unzue A, Xu M, Dong J, Wiedmer L, Spiliotopoulos D, Caflisch A, Nevado C. Fragment-Based Design of Selective Nanomolar Ligands of the CREBBP Bromodomain. J Med Chem 2015; 59:1350-6. [PMID: 26043365 DOI: 10.1021/acs.jmedchem.5b00172] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Novel ligands of the CREBBP bromodomain were identified by fragment-based docking. The in silico discovered hits have been optimized by chemical synthesis into selective nanomolar compounds, thereby preserving the ligand efficiency. The selectivity for the CREBBP bromodomain over other human bromodomain subfamilies has achieved by a benzoate moiety which was predicted by docking to be involved in favorable electrostatic interactions with the Arg1173 side chain, a prediction that could be verified a posteriori by the high-resolution crystal structure of the CREBBP bromodomain in complex with ligand 6 and also by MD simulations (see Xu, M.; Unzue, A.; Dong, J.; Spiliotopoulos, D.; Nevado, C.; Caflisch, A. Discovery of CREBBP bromodomain inhibitors by high-throughput docking and hit optimization guided by molecular dynamics. J. Med. Chem. 2015, DOI: 10.1021/acs.jmedchem.5b00171).
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Affiliation(s)
- Andrea Unzue
- Department of of Chemistry, University of Zürich , Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Min Xu
- Department of of Biochemistry, University of Zürich , Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Jing Dong
- Department of of Biochemistry, University of Zürich , Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Lars Wiedmer
- Department of of Biochemistry, University of Zürich , Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Dimitrios Spiliotopoulos
- Department of of Biochemistry, University of Zürich , Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Amedeo Caflisch
- Department of of Biochemistry, University of Zürich , Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Cristina Nevado
- Department of of Chemistry, University of Zürich , Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
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114
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Chaidos A, Caputo V, Karadimitris A. Inhibition of bromodomain and extra-terminal proteins (BET) as a potential therapeutic approach in haematological malignancies: emerging preclinical and clinical evidence. Ther Adv Hematol 2015; 6:128-41. [PMID: 26137204 DOI: 10.1177/2040620715576662] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Post-translational modifications of the nucleosomal histone proteins orchestrate chromatin organization and gene expression in normal and cancer cells. Among them, the acetylation of N-terminal histone tails represents the fundamental epigenetic mark of open structure chromatin and active gene transcription. The bromodomain and extra-terminal (BET) proteins are epigenetic readers which utilize tandem bromodomains (BRD) modules to recognize and dock themselves on the acetylated lysine tails. The BET proteins act as scaffolds for the recruitment of transcription factors and chromatin organizers required in transcription initiation and elongation. The recent discovery of small molecules capable of blocking their lysine-binding pocket is the first paradigm of successful pharmacological inhibition of epigenetic readers. JQ1 is a prototype benzodiazepine molecule and a specific BET inhibitor with antineoplastic activity both in solid tumours and haematological malignancies. The quinolone I-BET151 and the suitable for clinical development I-BET762 benzodiazepine were introduced in parallel with JQ1 and have also shown potent antitumour activity in preclinical studies. I-BET762 is currently being tested in early phase clinical trials, along with a rapidly growing list of other BET inhibitors. Unlike older epigenetic therapies, the study of BET inhibitors has offered substantial, context-specific, mechanistic insights of their antitumour activity, which will facilitate optimal therapeutic targeting in future. Here, we review the development of this novel class of epigenetic drugs, the biology of BET protein inhibition, the emerging evidence from preclinical work and early phase clinical studies and we discuss their potential role in the treatment of haematological malignancies.
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Affiliation(s)
- Aristeidis Chaidos
- Centre for Haematology, Department of Medicine, Imperial College London, London, UK
| | - Valentina Caputo
- Centre for Haematology, Department of Medicine, Imperial College London, London, UK
| | - Anastasios Karadimitris
- Centre for Haematology, Department of Medicine, Imperial College London, 4th Floor Commonwealth Building, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
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115
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Ran X, Zhao Y, Liu L, Bai L, Yang CY, Zhou B, Meagher JL, Chinnaswamy K, Stuckey JA, Wang S. Structure-Based Design of γ-Carboline Analogues as Potent and Specific BET Bromodomain Inhibitors. J Med Chem 2015; 58:4927-39. [PMID: 26080064 DOI: 10.1021/acs.jmedchem.5b00613] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Small-molecule inhibitors of bromodomain and extra terminal proteins (BET), including BRD2, BRD3, and BRD4 proteins have therapeutic potential for the treatment of human cancers and other diseases and conditions. In this paper, we report the design, synthesis, and evaluation of γ-carboline-containing compounds as a new class of small-molecule BET inhibitors. The most potent inhibitor (compound 18, RX-37) obtained from this study binds to BET bromodomain proteins (BRD2, BRD3, and BRD4) with Ki values of 3.2-24.7 nM and demonstrates high selectivity over other non-BET bromodomain-containing proteins. Compound 18 potently and selectively inhibits cell growth in human acute leukemia cell lines harboring the rearranged mixed lineage leukemia 1 gene. We have determined a cocrystal structure of 18 in complex with BRD4 BD2 at 1.4 Å resolution, which provides a solid structural basis for the compound's high binding affinity and for its further structure-based optimization. Compound 18 represents a promising lead compound for the development of a new class of therapeutics for the treatment of human cancer and other conditions.
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Affiliation(s)
- Xu Ran
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yujun Zhao
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Liu Liu
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Longchuan Bai
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Chao-Yie Yang
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bing Zhou
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jennifer L Meagher
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Krishnapriya Chinnaswamy
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jeanne A Stuckey
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Shaomeng Wang
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
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116
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Sundalam SK, Stuart DR. Base Mediated Synthesis of Alkyl-aryl Ethers from the Reaction of Aliphatic Alcohols and Unsymmetric Diaryliodonium Salts. J Org Chem 2015; 80:6456-66. [DOI: 10.1021/acs.joc.5b00907] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Sunil K. Sundalam
- Department
of Chemistry, Portland State University, Portland Oregon 97201, United States
| | - David R. Stuart
- Department
of Chemistry, Portland State University, Portland Oregon 97201, United States
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117
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Theodoulou NH, Bamborough P, Bannister AJ, Becher I, Bit RA, Che KH, Chung CW, Dittmann A, Drewes G, Drewry DH, Gordon L, Grandi P, Leveridge M, Lindon M, Michon AM, Molnar J, Robson SC, Tomkinson NCO, Kouzarides T, Prinjha RK, Humphreys PG. Discovery of I-BRD9, a Selective Cell Active Chemical Probe for Bromodomain Containing Protein 9 Inhibition. J Med Chem 2015; 59:1425-39. [PMID: 25856009 DOI: 10.1021/acs.jmedchem.5b00256] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Acetylation of histone lysine residues is one of the most well-studied post-translational modifications of chromatin, selectively recognized by bromodomain "reader" modules. Inhibitors of the bromodomain and extra terminal domain (BET) family of bromodomains have shown profound anticancer and anti-inflammatory properties, generating much interest in targeting other bromodomain-containing proteins for disease treatment. Herein, we report the discovery of I-BRD9, the first selective cellular chemical probe for bromodomain-containing protein 9 (BRD9). I-BRD9 was identified through structure-based design, leading to greater than 700-fold selectivity over the BET family and 200-fold over the highly homologous bromodomain-containing protein 7 (BRD7). I-BRD9 was used to identify genes regulated by BRD9 in Kasumi-1 cells involved in oncology and immune response pathways and to the best of our knowledge, represents the first selective tool compound available to elucidate the cellular phenotype of BRD9 bromodomain inhibition.
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Affiliation(s)
- Natalie H Theodoulou
- Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K.,WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Paul Bamborough
- Computational & Structural Chemistry, Molecular Discovery Research, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Andrew J Bannister
- Department of Pathology, Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN, U.K
| | - Isabelle Becher
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline R&D , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Rino A Bit
- Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Ka Hing Che
- Department of Pathology, Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN, U.K
| | - Chun-wa Chung
- Computational & Structural Chemistry, Molecular Discovery Research, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Antje Dittmann
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline R&D , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gerard Drewes
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline R&D , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - David H Drewry
- Department of Chemical Biology, GlaxoSmithKline , Research Triangle Park, North Carolina 27709, United States
| | - Laurie Gordon
- Biological Sciences, Molecular Discovery Research, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paola Grandi
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline R&D , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Melanie Leveridge
- Biological Sciences, Molecular Discovery Research, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Matthew Lindon
- Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Anne-Marie Michon
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline R&D , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Judit Molnar
- Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Samuel C Robson
- Department of Pathology, Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN, U.K
| | - Nicholas C O Tomkinson
- WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Tony Kouzarides
- Department of Pathology, Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN, U.K
| | - Rab K Prinjha
- Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Philip G Humphreys
- Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
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118
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Observed bromodomain flexibility reveals histone peptide- and small molecule ligand-compatible forms of ATAD2. Biochem J 2015; 466:337-46. [PMID: 25486442 DOI: 10.1042/bj20140933] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Preventing histone recognition by bromodomains emerges as an attractive therapeutic approach in cancer. Overexpression of ATAD2 (ATPase family AAA domain-containing 2 isoform A) in cancer cells is associated with poor prognosis making the bromodomain of ATAD2 a promising epigenetic therapeutic target. In the development of an in vitro assay and identification of small molecule ligands, we conducted structure-guided studies which revealed a conformationally flexible ATAD2 bromodomain. Structural studies on apo-, peptide-and small molecule-ATAD2 complexes (by co-crystallization) revealed that the bromodomain adopts a 'closed', histone-compatible conformation and a more 'open' ligand-compatible conformation of the binding site respectively. An unexpected conformational change of the conserved asparagine residue plays an important role in driving the peptide-binding conformation remodelling. We also identified dimethylisoxazole-containing ligands as ATAD2 binders which aided in the validation of the in vitro screen and in the analysis of these conformational studies.
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119
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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] [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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120
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Affiliation(s)
| | - Philip A. Cole
- Department
of Pharmacology
and Molecular Sciences, The Johns Hopkins
University School of Medicine, 725 North Wolfe Street, Hunterian 316, Baltimore, Maryland 21205, United States
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121
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Hewitt MC, Leblanc Y, Gehling VS, Vaswani RG, Côté A, Nasveschuk CG, Taylor AM, Harmange JC, Audia JE, Pardo E, Cummings R, Joshi S, Sandy P, Mertz JA, Sims RJ, Bergeron L, Bryant BM, Bellon S, Poy F, Jayaram H, Tang Y, Albrecht BK. Development of methyl isoxazoleazepines as inhibitors of BET. Bioorg Med Chem Lett 2015; 25:1842-8. [PMID: 25851940 DOI: 10.1016/j.bmcl.2015.03.045] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 12/26/2022]
Abstract
In this report we detail the evolution of our previously reported thiophene isoxazole BET inhibitor chemotype exemplified by CPI-3 to a novel bromodomain selective chemotype (the methyl isoxazoleazepine chemotype) exemplified by carboxamide 23. The methyl isoxazoleazepine chemotype provides potent inhibition of the bromodomains of the BET family, excellent in vivo PK across species, low unbound clearance, and target engagement in a MYC PK-PD model.
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Affiliation(s)
- Michael C Hewitt
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA.
| | - Yves Leblanc
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA
| | - Victor S Gehling
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA
| | - Rishi G Vaswani
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA
| | - Alexandre Côté
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA
| | | | - Alexander M Taylor
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA
| | | | - James E Audia
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA
| | - Eneida Pardo
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA
| | - Rich Cummings
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA
| | - Shivangi Joshi
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA
| | - Peter Sandy
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA
| | - Jennifer A Mertz
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA
| | - Robert J Sims
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA
| | - Louise Bergeron
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA
| | - Barbara M Bryant
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA
| | - Steve Bellon
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA
| | - Florence Poy
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA
| | | | - Yong Tang
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA
| | - Brian K Albrecht
- Constellation Pharmaceuticals, 215 First St., Suite 200, Cambridge, MA 02142, USA
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122
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Brand M, Measures AM, Wilson BG, Cortopassi WA, Alexander R, Höss M, Hewings DS, Rooney TPC, Paton RS, Conway SJ. Small molecule inhibitors of bromodomain-acetyl-lysine interactions. ACS Chem Biol 2015; 10:22-39. [PMID: 25549280 DOI: 10.1021/cb500996u] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bromodomains are protein modules that bind to acetylated lysine residues. Their interaction with histone proteins suggests that they function as "readers" of histone lysine acetylation, a component of the proposed "histone code". Bromodomain-containing proteins are often found as components of larger protein complexes with roles in fundamental cellular process including transcription. The publication of two potent ligands for the BET bromodomains in 2010 demonstrated that small molecules can inhibit the bromodomain-acetyl-lysine protein-protein interaction. These molecules display strong phenotypic effects in a number of cell lines and affect a range of cancers in vivo. This work stimulated intense interest in developing further ligands for the BET bromodomains and the design of ligands for non-BET bromodomains. Here we review the recent progress in the field with particular attention paid to ligand design, the assays employed in early ligand discovery, and the use of computational approaches to inform ligand design.
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Affiliation(s)
- Michael Brand
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Angelina M. Measures
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Brian G. Wilson
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Wilian A. Cortopassi
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | | | | | - David S. Hewings
- 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
| | - Robert S. Paton
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, 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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123
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Zhao L, Wang Y, Cao D, Chen T, Wang Q, Li Y, Xu Y, Zhang N, Wang X, Chen D, Chen L, Chen YL, Xia G, Shi Z, Liu YC, Lin Y, Miao Z, Shen J, Xiong B. Fragment-based drug discovery of 2-thiazolidinones as BRD4 inhibitors: 2. Structure-based optimization. J Med Chem 2015; 58:1281-97. [PMID: 25559428 DOI: 10.1021/jm501504k] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The signal transduction of acetylated histone can be processed through a recognition module, bromodomain. Several inhibitors targeting BRD4, one of the bromodomain members, are in clinical trials as anticancer drugs. Hereby, we report our efforts on discovery and optimization of a new series of 2-thiazolidinones as BRD4 inhibitors along our previous study. In this work, guided by crystal structure analysis, we reversed the sulfonamide group and identified a new binding mode. A structure-activity relationship study on this new series led to several potent BRD4 inhibitors with IC50 of about 0.05-0.1 μM in FP binding assay and GI50 of 0.1-0.3 μM in cell based assays. To complete the lead-like assessment of this series, we further checked its effects on BRD4 downstream protein c-Myc, investigated its selectivity among five different bromodomain proteins, as well as the metabolic stability test, and reinforced the utility of 2-thiazolidinone scaffold as BET bromodomain inhibitors in novel anticancer drug development.
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Affiliation(s)
- Lele Zhao
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, ‡Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, and §Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China
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124
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Hett EC, Piatnitski Chekler EL, Basak A, Bonin PD, Denny RA, Flick AC, Geoghegan KF, Liu S, Pletcher MT, Sahasrabudhe P, Salter SC, Stock IA, Taylor AP, Jones LH. Direct photocapture of bromodomains using tropolone chemical probes. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00070j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tropolone probes directly photoaffinity label bromodomains.
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Affiliation(s)
| | | | | | | | | | | | - Kieran F. Geoghegan
- Structural Biology and Biophysics
- Worldwide Medicinal Chemistry
- Pfizer
- Groton
- USA
| | - Shenping Liu
- Structural Biology and Biophysics
- Worldwide Medicinal Chemistry
- Pfizer
- Groton
- USA
| | | | - Parag Sahasrabudhe
- Structural Biology and Biophysics
- Worldwide Medicinal Chemistry
- Pfizer
- Groton
- USA
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125
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Abstract
A review of fragment-based approaches to finding and optimising bromodomain inhibitors. Early successes against the BET subfamily are now being extended to other members of the target class.
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Affiliation(s)
- Paul Bamborough
- Molecular Discovery Research
- GlaxoSmithKline Medicines Research Centre
- UK
| | - Chun-wa Chung
- Molecular Discovery Research
- GlaxoSmithKline Medicines Research Centre
- UK
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126
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Li GB, Yang LL, Yuan Y, Zou J, Cao Y, Yang SY, Xiang R, Xiang M. Virtual screening in small molecule discovery for epigenetic targets. Methods 2015; 71:158-66. [DOI: 10.1016/j.ymeth.2014.11.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/27/2014] [Accepted: 11/14/2014] [Indexed: 12/31/2022] Open
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127
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Ran T, Zhang Z, Liu K, Lu Y, Li H, Xu J, Xiong X, Zhang Y, Xu A, Lu S, Liu H, Lu T, Chen Y. Insight into the key interactions of bromodomain inhibitors based on molecular docking, interaction fingerprinting, molecular dynamics and binding free energy calculation. MOLECULAR BIOSYSTEMS 2015; 11:1295-304. [DOI: 10.1039/c4mb00723a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The interaction mechanism of bromodomain inhibitors was investigated using interaction fingerprinting and binding free energy based methods.
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128
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Abstract
The druggability of a target is defined by the likelihood of a certain target binding site to be amendable to functional modulation by a small molecule in vivo. Thus, druggability depends on the ability of the developed small molecule to reach the target site, the properties of the ligand binding pocket and our ability to develop chemical matter that efficiently interact with the drug binding site of interest. Historically enzymes have been the main drug targets because the inhibition of their activity can be easily assayed and catalytic centres are often attractive drug binding sites. However, despite considerable effort, a number of classical enzyme families have not been successfully targeted. More recently protein-protein interactions received considerable attention and several clinical inhibitors have now been developed. Despite the considerable progress made expanding target space, a large number of targets with a very strong rationale for targeting remain intractable. In the following chapter I will summarize progress made in developing inhibitors for challenging drug binding sites and emerging target families.
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129
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McKeown MR, Shaw DL, Fu H, Liu S, Xu X, Marineau JJ, Huang Y, Zhang X, Buckley DL, Kadam A, Zhang Z, Blacklow SC, Qi J, Zhang W, Bradner JE. Biased multicomponent reactions to develop novel bromodomain inhibitors. J Med Chem 2014; 57:9019-27. [PMID: 25314271 PMCID: PMC4234447 DOI: 10.1021/jm501120z] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BET bromodomain inhibition has contributed new insights into gene regulation and emerged as a promising therapeutic strategy in cancer. Structural analogy of early methyl-triazolo BET inhibitors has prompted a need for structurally dissimilar ligands as probes of bromodomain function. Using fluorous-tagged multicomponent reactions, we developed a focused chemical library of bromodomain inhibitors around a 3,5-dimethylisoxazole biasing element with micromolar biochemical IC50. Iterative synthesis and biochemical assessment allowed optimization of novel BET bromodomain inhibitors based on an imidazo[1,2-a]pyrazine scaffold. Lead compound 32 (UMB-32) binds BRD4 with a Kd of 550 nM and 724 nM cellular potency in BRD4-dependent lines. Additionally, compound 32 shows potency against TAF1, a bromodomain-containing transcription factor previously unapproached by discovery chemistry. Compound 32 was cocrystallized with BRD4, yielding a 1.56 Å resolution crystal structure. This research showcases new applications of fluorous and multicomponent chemical synthesis for the development of novel epigenetic inhibitors.
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Affiliation(s)
- Michael R McKeown
- Department of Medical Oncology, Dana-Farber Cancer Institute , 450 Brookline Avenue, Boston, Massachusetts 02215, United States
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130
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Gosmini R, Nguyen VL, Toum J, Simon C, Brusq JMG, Krysa G, Mirguet O, Riou-Eymard AM, Boursier EV, Trottet L, Bamborough P, Clark H, Chung CW, Cutler L, Demont EH, Kaur R, Lewis AJ, Schilling MB, Soden PE, Taylor S, Walker AL, Walker MD, Prinjha RK, Nicodème E. The discovery of I-BET726 (GSK1324726A), a potent tetrahydroquinoline ApoA1 up-regulator and selective BET bromodomain inhibitor. J Med Chem 2014; 57:8111-31. [PMID: 25249180 DOI: 10.1021/jm5010539] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Through their function as epigenetic readers of the histone code, the BET family of bromodomain-containing proteins regulate expression of multiple genes of therapeutic relevance, including those involved in tumor cell growth and inflammation. BET bromodomain inhibitors have profound antiproliferative and anti-inflammatory effects which translate into efficacy in oncology and inflammation models, and the first compounds have now progressed into clinical trials. The exciting biology of the BETs has led to great interest in the discovery of novel inhibitor classes. Here we describe the identification of a novel tetrahydroquinoline series through up-regulation of apolipoprotein A1 and the optimization into potent compounds active in murine models of septic shock and neuroblastoma. At the molecular level, these effects are produced by inhibition of BET bromodomains. X-ray crystallography reveals the interactions explaining the structure-activity relationships of binding. The resulting lead molecule, I-BET726, represents a new, potent, and selective class of tetrahydroquinoline-based BET inhibitors.
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Affiliation(s)
- Romain Gosmini
- Candidate Discovery, ‡Discovery Biology, §DMPK, GlaxoSmithKline Les Ulis, Centre de Recherches François Hyafil, GlaxoSmithKline R&D , 25 Avenue du Québec, 91140 Villebon-sur-Yvette, France
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131
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Phenotypic screening and fragment-based approaches to the discovery of small-molecule bromodomain ligands. Future Med Chem 2014; 6:179-204. [PMID: 24467243 DOI: 10.4155/fmc.13.197] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Bromodomains are protein modules that bind to acetylated lysine residues and hence facilitate protein-protein interactions. These bromodomain-mediated interactions often play key roles in transcriptional regulation and their dysfunction is implicated in a large number of diseases. The discovery of potent and selective small-molecule bromodomain and extra C-terminal domain bromodomain ligands, which show promising results for the treatment of cancers and atherosclerosis, has promoted intense interest in this area. Here we describe the progress that has been made to date in the discovery of small-molecule bromodomain ligands, with particular emphasis on the roles played by phenotypic screening and fragment-based approaches. In considering the future of the field we discuss the prospects for development of molecular probes and drugs for the non-bromodomain and extra C-terminal domain bromodomains.
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132
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Tatsuno T, Miyazaki K, Yamashiro H. Multiple solvent, N-methyl-2-pyrrolidone, acts as a novel adjuvant for enhancing cutaneous immune responses. Biosci Biotechnol Biochem 2014; 78:954-9. [PMID: 25036119 DOI: 10.1080/09168451.2014.912114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
N-methyl-2-pyrrolidone (NMP) is known for its multi-solvent properties. However, its biological, especially immunological significance still remains to be elucidated. In this study, we show for the first time that NMP stimulates the skin immune system by activating epidermal Langerhans cells (LCs). In contrast with the placebo tape, when the NMP-containing adhesive tape was applied on murine skin, LCs were stimulated immediately. Activated LCs not only exhibited enhanced expression of major histocompatibility complex class II and morphological changes, including the loss of dendrites, but also migrated effectively to draining lymph nodes. In addition, application of the tyrosine-related protein-2 peptide, which is the cytotoxic T lymphocyte (CTL) epitope against B16 melanoma, in combination with the NMP tape, resulted in explosive expansion of specific CTLs in mouse spleens. Taken together, these results demonstrate a novel role of NMP as an adjuvant in percutaneous peptide immunization.
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Affiliation(s)
- Tomoko Tatsuno
- a Research Laboratory , LINTEC Corporation , Warabi-shi , Japan
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133
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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: 222] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [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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134
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Muvva C, Singam ERA, Raman SS, Subramanian V. Structure-based virtual screening of novel, high-affinity BRD4 inhibitors. MOLECULAR BIOSYSTEMS 2014; 10:2384-97. [DOI: 10.1039/c4mb00243a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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135
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Owen DR, Trzupek JD. Epigenetic drugs that do not target enzyme activity. DRUG DISCOVERY TODAY. TECHNOLOGIES 2014; 12:e29-e34. [PMID: 25027371 DOI: 10.1016/j.ddtec.2012.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
While the installation and removal of epigenetic post-translational modifications or ‘marks’ on both DNA and histone proteins are the tangible outcome of enzymatically catalyzed processes, the role of the epigenetic reader proteins looks, at first, less obvious. As they do not catalyze a chemical transformation or process as such, their role is not enzymatic. However, this does not preclude them from being potential targets for drug discovery as their function is clearly correlated to transcriptional activity and as a class of proteins, they appear to have binding sites of sufficient definition and size to be inhibited by small molecules. This suggests that this third class of epigenetic proteins that are involved in the interpretation of post-translational marks (as opposed to the creation or deletion of marks) may represent attractive targets for drug discovery efforts. This review mainly summarizes selected publications, patent literature and company disclosures on these non-enzymatic epigenetic reader proteins from 2009 to the present.
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Affiliation(s)
- Dafydd R Owen
- Pfizer Worldwide Research and Development, 200 Cambridgepark Drive, Cambridge, MA 02140, USA.
| | - John D Trzupek
- Pfizer Worldwide Research and Development, 200 Cambridgepark Drive, Cambridge, MA 02140, USA
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136
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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137
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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] [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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138
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Shortt J, Hsu A, Martin B, Doggett K, Matthews G, Doyle M, Ellul J, Jockel T, Andrews D, Hogg S, Reitsma A, Faulkner D, Bergsagel P, Chesi M, Heath J, Denny W, Thompson P, Neeson P, Ritchie D, McArthur G, Johnstone R. The Drug Vehicle and Solvent N-Methylpyrrolidone Is an Immunomodulator and Antimyeloma Compound. Cell Rep 2014; 7:1009-19. [DOI: 10.1016/j.celrep.2014.04.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 03/12/2014] [Accepted: 04/07/2014] [Indexed: 01/03/2023] Open
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139
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Abstract
Lysine acetylation is a key mechanism that regulates chromatin structure; aberrant acetylation levels have been linked to the development of several diseases. Acetyl-lysine modifications create docking sites for bromodomains, which are small interaction modules found on diverse proteins, some of which have a key role in the acetylation-dependent assembly of transcriptional regulator complexes. These complexes can then initiate transcriptional programmes that result in phenotypic changes. The recent discovery of potent and highly specific inhibitors for the BET (bromodomain and extra-terminal) family of bromodomains has stimulated intensive research activity in diverse therapeutic areas, particularly in oncology, where BET proteins regulate the expression of key oncogenes and anti-apoptotic proteins. In addition, targeting BET bromodomains could hold potential for the treatment of inflammation and viral infection. Here, we highlight recent progress in the development of bromodomain inhibitors, and their potential applications in drug discovery.
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140
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Smith SG, Sanchez R, Zhou MM. Privileged diazepine compounds and their emergence as bromodomain inhibitors. ACTA ACUST UNITED AC 2014; 21:573-83. [PMID: 24746559 DOI: 10.1016/j.chembiol.2014.03.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/02/2014] [Accepted: 03/15/2014] [Indexed: 12/23/2022]
Abstract
Chemical compounds built on a diazepine scaffold have recently emerged as potent inhibitors of the acetyl-lysine binding activity of bromodomain-containing proteins, which is required for gene transcriptional activation in cancer and inflammation. Not only have these chemical compounds validated bromodomains as attractive epigenetic drug targets, but they have also brought to the forefront another application of the diazepine, which had already been regarded as a versatile chemical scaffold in rational drug design. This article reviews the success of diazepine compounds as therapeutic agents and examines the unique chemical and geometric features of this privileged scaffold that make it an excellent template for developing potent and selective molecules that control bromodomain-related gene expression in human diseases.
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Affiliation(s)
- Steven G Smith
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Roberto Sanchez
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA.
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141
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Zhao H, Gartenmann L, Dong J, Spiliotopoulos D, Caflisch A. Discovery of BRD4 bromodomain inhibitors by fragment-based high-throughput docking. Bioorg Med Chem Lett 2014; 24:2493-6. [PMID: 24767840 DOI: 10.1016/j.bmcl.2014.04.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 04/02/2014] [Accepted: 04/03/2014] [Indexed: 12/13/2022]
Abstract
Bromodomains (BRDs) recognize acetyl-lysine modified histone tails mediating epigenetic processes. BRD4, a protein containing two bromodomains, has emerged as an attractive therapeutic target for several types of cancer as well as inflammatory diseases. Using a fragment-based in silico screening approach, we identified two small molecules that bind to the first bromodomain of BRD4 with low-micromolar affinity and favorable ligand efficiency (0.37 kcal/mol per non-hydrogen atom), selectively over other families of bromodomains. Notably, the hit rate of the fragment-based in silico approach is about 10% as only 24 putative inhibitors, from an initial library of about 9 million molecules, were tested in vitro.
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Affiliation(s)
- Hongtao Zhao
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Lisa Gartenmann
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Jing Dong
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Dimitrios Spiliotopoulos
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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142
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Molecular Dynamics Simulations of Bromodomains Reveal Binding-Site Flexibility and Multiple Binding Modes of the Natural Ligand Acetyl-Lysine. Isr J Chem 2014. [DOI: 10.1002/ijch.201400009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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143
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Sanchez R, Meslamani J, Zhou MM. The bromodomain: from epigenome reader to druggable target. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:676-85. [PMID: 24686119 DOI: 10.1016/j.bbagrm.2014.03.011] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 03/15/2014] [Accepted: 03/23/2014] [Indexed: 10/25/2022]
Abstract
Lysine acetylation is a fundamental post-translational modification that plays an important role in the control of gene transcription in chromatin in an ordered fashion. The bromodomain, the conserved structural module present in transcription-associated proteins, functions exclusively to recognize acetyl-lysine on histones and non-histone proteins. The structural analyses of bromodomains' recognition of lysine-acetylated peptides derived from histones and cellular proteins provide detailed insights into the differences and unifying features of biological ligand binding selectivity by the bromodomains. Newly developed small-molecule inhibitors targeting bromodomain proteins further highlight the functional importance of bromodomain/acetyl-lysine binding as a key mechanism in orchestrating molecular interactions and regulation in chromatin biology and gene transcription. These new studies argue that modulating bromodomain/acetyl-lysine interactions with small-molecule chemicals offer new opportunities to control gene expression in a wide array of human diseases including cancer and inflammation. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Roberto Sanchez
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jamel Meslamani
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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144
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Gallenkamp D, Gelato KA, Haendler B, Weinmann H. Bromodomains and their pharmacological inhibitors. ChemMedChem 2014; 9:438-64. [PMID: 24497428 DOI: 10.1002/cmdc.201300434] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/23/2013] [Indexed: 12/15/2022]
Abstract
Over 60 bromodomains belonging to proteins with very different functions have been identified in humans. Several of them interact with acetylated lysine residues, leading to the recruitment and stabilization of protein complexes. The bromodomain and extra-terminal domain (BET) proteins contain tandem bromodomains which bind to acetylated histones and are thereby implicated in a number of DNA-centered processes, including the regulation of gene expression. The recent identification of inhibitors of BET and non-BET bromodomains is one of the few examples in which effective blockade of a protein-protein interaction can be achieved with a small molecule. This has led to major strides in the understanding of the function of bromodomain-containing proteins and their involvement in diseases such as cancer and inflammation. Indeed, BET bromodomain inhibitors are now being clinically evaluated for the treatment of hematological tumors and have also been tested in clinical trials for the relatively rare BRD-NUT midline carcinoma. This review gives an overview of the newest developments in the field, with a focus on the biology of selected bromodomain proteins on the one hand, and on reported pharmacological inhibitors on the other, including recent examples from the patent literature.
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145
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Müller S, Knapp S. Discovery of BET bromodomain inhibitors and their role in target validation. MEDCHEMCOMM 2014. [DOI: 10.1039/c3md00291h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Publicly available bromodomain inhibitors led to discoveries of key functions of BET-proteins in disease and development of new therapeutic strategies.
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Affiliation(s)
- S. Müller
- Nuffield Department of Clinical Medicine
- University of Oxford
- Old Road Campus Research Building
- Structural Genomics Consortium
- Oxford OX3 7DQ
| | - S. Knapp
- Nuffield Department of Clinical Medicine
- University of Oxford
- Old Road Campus Research Building
- Structural Genomics Consortium
- Oxford OX3 7DQ
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146
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Selective Inhibition of Acetyl-Lysine Effector Domains of the Bromodomain Family in Oncology. NUCLEAR SIGNALING PATHWAYS AND TARGETING TRANSCRIPTION IN CANCER 2014. [DOI: 10.1007/978-1-4614-8039-6_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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147
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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] [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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148
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Ferguson FM, Fedorov O, Chaikuad A, Philpott M, Muniz JRC, Felletar I, von Delft F, Heightman T, Knapp S, Abell C, Ciulli A. Targeting low-druggability bromodomains: fragment based screening and inhibitor design against the BAZ2B bromodomain. J Med Chem 2013; 56:10183-7. [PMID: 24304323 PMCID: PMC3905694 DOI: 10.1021/jm401582c] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Bromodomains are epigenetic reader domains that have recently become popular targets. In contrast to BET bromodomains, which have proven druggable, bromodomains from other regions of the phylogenetic tree have shallower pockets. We describe successful targeting of the challenging BAZ2B bromodomain using biophysical fragment screening and structure-based optimization of high ligand-efficiency fragments into a novel series of low-micromolar inhibitors. Our results provide attractive leads for development of BAZ2B chemical probes and indicate the whole family may be tractable.
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Affiliation(s)
- Fleur M Ferguson
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge, CB2 1EW, U.K
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149
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Pachaiyappan B, Woster PM. Design of small molecule epigenetic modulators. Bioorg Med Chem Lett 2013; 24:21-32. [PMID: 24300735 DOI: 10.1016/j.bmcl.2013.11.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 10/28/2013] [Accepted: 11/04/2013] [Indexed: 12/16/2022]
Abstract
The field of epigenetics has expanded rapidly to reveal multiple new targets for drug discovery. The functional elements of the epigenomic machinery can be categorized as writers, erasers and readers, and together these elements control cellular gene expression and homeostasis. It is increasingly clear that aberrations in the epigenome can underly a variety of diseases, and thus discovery of small molecules that modulate the epigenome in a specific manner is a viable approach to the discovery of new therapeutic agents. In this Digest, the components of epigenetic control of gene expression will be briefly summarized, and efforts to identify small molecules that modulate epigenetic processes will be described.
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Affiliation(s)
- Boobalan Pachaiyappan
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, SC 29425, United States
| | - Patrick M Woster
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, SC 29425, United States.
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150
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Zhang CJ, Tan CYJ, Ge J, Na Z, Chen GYJ, Uttamchandani M, Sun H, Yao SQ. Preparation of Small-Molecule Microarrays bytrans-Cyclooctene Tetrazine Ligation and Their Application in the High-Throughput Screening of Protein-Protein Interaction Inhibitors of Bromodomains. Angew Chem Int Ed Engl 2013; 52:14060-4. [DOI: 10.1002/anie.201307803] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 09/30/2013] [Indexed: 01/29/2023]
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