51
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Marchand JR, Dalle Vedove A, Lolli G, Caflisch A. Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking. J Chem Inf Model 2017; 57:2584-2597. [PMID: 28862840 DOI: 10.1021/acs.jcim.7b00336] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The high-throughput docking protocol called ALTA-VS (anchor-based library tailoring approach for virtual screening) was developed in 2005 for the efficient in silico screening of large libraries of compounds by preselection of only those molecules that have optimal fragments (anchors) for the protein target. Here we present an updated version of ALTA-VS with a broader range of potential applications. The evaluation of binding energy makes use of a classical force field with implicit solvent in the continuum dielectric approximation. In about 2 days per protein target on a 96-core compute cluster (equipped with Xeon E3-1280 quad core processors at 2.5 GHz), the screening of a library of nearly 77 000 diverse molecules with the updated ALTA-VS protocol has resulted in the identification of 19, 3, 3, and 2 μM inhibitors of the human bromodomains ATAD2, BAZ2B, BRD4(1), and CREBBP, respectively. The success ratio (i.e., number of actives in a competition binding assay in vitro divided by the number of compounds tested) ranges from 8% to 13% in dose-response measurements. The poses predicted by fragment-based docking for the three ligands of the BAZ2B bromodomain were confirmed by protein X-ray crystallography.
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Affiliation(s)
- Jean-Rémy Marchand
- Department of Biochemistry, University of Zürich , CH-8057, Zürich, Switzerland
| | | | - Graziano Lolli
- Centre for Integrative Biology, University of Trento , I-38123, Povo, Italy
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich , CH-8057, Zürich, Switzerland
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52
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Hügle M, Lucas X, Ostrovskyi D, Regenass P, Gerhardt S, Einsle O, Hau M, Jung M, Breit B, Günther S, Wohlwend D. Beyond the BET Family: Targeting CBP/p300 with 4-Acyl Pyrroles. Angew Chem Int Ed Engl 2017; 56:12476-12480. [PMID: 28766825 DOI: 10.1002/anie.201705516] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/21/2017] [Indexed: 11/07/2022]
Abstract
Bromodomain and extra-terminal domain (BET) inhibitors are widely used both as chemical tools to study the biological role of their targets in living organisms and as candidates for drug development against several cancer variants and human disorders. However, non-BET bromodomains such as those in p300 and CBP are less studied. XDM-CBP is a highly potent and selective inhibitor for the bromodomains of CBP and p300 derived from a pan-selective BET BRD-binding fragment. Along with X-ray crystal-structure analysis and thermodynamic profiling, XDM-CBP was used in screenings of several cancer cell lines in vitro to study its inhibitory potential on cancer cell proliferation. XDM-CBP is demonstrated to be a potent and selective CBP/p300 inhibitor that acts on specific cancer cell lines, in particular malignant melanoma, breast cancer, and leukemia.
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Affiliation(s)
- Martin Hügle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Xavier Lucas
- School of Life Sciences, Division of Biological Chemistry and Drug Discovery, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK
| | - Dmytro Ostrovskyi
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Pierre Regenass
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Stefan Gerhardt
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
- Freiburg Institute for Advanced Studies (FRIAS), Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Mirjam Hau
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 9, 79104, Freiburg, Germany
| | - Manfred Jung
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 9, 79104, Freiburg, Germany
| | - Bernhard Breit
- Freiburg Institute for Advanced Studies (FRIAS), Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Stefan Günther
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 9, 79104, Freiburg, Germany
- Freiburg Institute for Advanced Studies (FRIAS), Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
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53
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Abstract
PURPOSE OF REVIEW This article provides an overview of anticancer therapies in various stages of clinical development as potential interventions to target HIV persistence. RECENT FINDINGS Epigenetic drugs developed for cancer have been investigated in vitro, ex vivo and in clinical trials as interventions aimed at reversing HIV latency and depleting the amount of virus that persists on antiretroviral therapy. Treatment with histone deacetylase inhibitors induced HIV expression in patients on antiretroviral therapy but did not reduce the frequency of infected cells. Other interventions that may accelerate the decay of latently infected cells, in the presence or absence of latency-reversing therapy, are now being explored. These include apoptosis-promoting agents, nonhistone deacetylase inhibitor compounds to reverse HIV latency and immunotherapy interventions to enhance antiviral immunity such as immune checkpoint inhibitors and Toll-like receptor agonists. SUMMARY A curative strategy in HIV will likely need to both reduce the amount of virus that persists on antiretroviral therapy and improve anti-HIV immune surveillance. Although we continue to explore advances in the field of oncology including cancer immunotherapy, there are major differences in the risk-benefit assessment between HIV-infected individuals and patients with malignancies. Drug development specifically targeting HIV persistence will be the key to developing effective interventions with an appropriate safety profile.
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54
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Igoe N, Bayle ED, Tallant C, Fedorov O, Meier JC, Savitsky P, Rogers C, Morias Y, Scholze S, Boyd H, Cunoosamy D, Andrews DM, Cheasty A, Brennan PE, Müller S, Knapp S, Fish PV. Design of a Chemical Probe for the Bromodomain and Plant Homeodomain Finger-Containing (BRPF) Family of Proteins. J Med Chem 2017; 60:6998-7011. [PMID: 28714688 DOI: 10.1021/acs.jmedchem.7b00611] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The bromodomain and plant homeodomain finger-containing (BRPF) family are scaffolding proteins important for the recruitment of histone acetyltransferases of the MYST family to chromatin. Here, we describe NI-57 (16) as new pan-BRPF chemical probe of the bromodomain (BRD) of the BRPFs. Inhibitor 16 preferentially bound the BRD of BRPF1 and BRPF2 over BRPF3, whereas binding to BRD9 was weaker. Compound 16 has excellent selectivity over nonclass IV BRD proteins. Target engagement of BRPF1B and BRPF2 with 16 was demonstrated in nanoBRET and FRAP assays. The binding of 16 to BRPF1B was rationalized through an X-ray cocrystal structure determination, which showed a flipped binding orientation when compared to previous structures. We report studies that show 16 has functional activity in cellular assays by modulation of the phenotype at low micromolar concentrations in both cancer and inflammatory models. Pharmacokinetic data for 16 was generated in mouse with single dose administration showing favorable oral bioavailability.
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Affiliation(s)
- Niall Igoe
- UCL School of Pharmacy, University College London , 29/39 Brunswick Square, London WC1N 1AX, U.K
| | - Elliott D Bayle
- UCL School of Pharmacy, University College London , 29/39 Brunswick Square, London WC1N 1AX, U.K
| | - Cynthia Tallant
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Oleg Fedorov
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Julia C Meier
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Pavel Savitsky
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Catherine Rogers
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Yannick Morias
- AstraZeneca , Innovative Medicines & Early Development, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Sarah Scholze
- AstraZeneca , Innovative Medicines & Early Development, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Helen Boyd
- AstraZeneca , Innovative Medicines & Early Development, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Danen Cunoosamy
- AstraZeneca , Innovative Medicines & Early Development, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - David M Andrews
- AstraZeneca Discovery Sciences , Darwin Building, Cambridge Science Park, Cambridge CB4 0FZ, U.K
| | - Anne Cheasty
- CRT Discovery Laboratories , Jonas Webb Building, Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Paul E Brennan
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Susanne Müller
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.,Buchmann Institute for Molecular Life Sciences , Max-von-Laue-Strasse 15, D-60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.,Buchmann Institute for Molecular Life Sciences , Max-von-Laue-Strasse 15, D-60438 Frankfurt am Main, Germany.,Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University , Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Paul V Fish
- UCL School of Pharmacy, University College London , 29/39 Brunswick Square, London WC1N 1AX, U.K
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55
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Millan DS, Kayser-Bricker KJ, Martin MW, Talbot AC, Schiller SER, Herbertz T, Williams GL, Luke GP, Hubbs S, Alvarez Morales MA, Cardillo D, Troccolo P, Mendes RL, McKinnon C. Design and Optimization of Benzopiperazines as Potent Inhibitors of BET Bromodomains. ACS Med Chem Lett 2017; 8:847-852. [PMID: 28835800 DOI: 10.1021/acsmedchemlett.7b00191] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/14/2017] [Indexed: 12/14/2022] Open
Abstract
A protein structure-guided drug design approach was employed to develop small molecule inhibitors of the BET family of bromodomains that were distinct from the known (+)-JQ1 scaffold class. These efforts led to the identification of a series of substituted benzopiperazines with structural features that enable interactions with many of the affinity-driving regions of the bromodomain binding site. Lipophilic efficiency was a guiding principle in improving binding affinity alongside drug-like physicochemical properties that are commensurate with oral bioavailability. Derived from this series was tool compound FT001, which displayed potent biochemical and cellular activity, translating to excellent in vivo activity in a mouse xenograft model (MV-4-11).
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Affiliation(s)
- David S. Millan
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | | | - Matthew W. Martin
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - Adam C. Talbot
- FORMA Therapeutics Inc., 35 Northeast Industrial Road, Branford, Connecticut 06405, United States
| | - Shawn E. R. Schiller
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - Torsten Herbertz
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - Grace L. Williams
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - George P. Luke
- FORMA Therapeutics Inc., 35 Northeast Industrial Road, Branford, Connecticut 06405, United States
| | - Stephen Hubbs
- FORMA Therapeutics Inc., 35 Northeast Industrial Road, Branford, Connecticut 06405, United States
| | - Monica A. Alvarez Morales
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - Daniel Cardillo
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - Paul Troccolo
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - Rachel L. Mendes
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - Crystal McKinnon
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
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56
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Hasvold LA, Sheppard GS, Wang L, Fidanze SD, Liu D, Pratt JK, Mantei RA, Wada CK, Hubbard R, Shen Y, Lin X, Huang X, Warder SE, Wilcox D, Li L, Buchanan FG, Smithee L, Albert DH, Magoc TJ, Park CH, Petros AM, Panchal SC, Sun C, Kovar P, Soni NB, Elmore SW, Kati WM, McDaniel KF. Methylpyrrole inhibitors of BET bromodomains. Bioorg Med Chem Lett 2017; 27:2225-2233. [DOI: 10.1016/j.bmcl.2017.02.057] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/17/2017] [Accepted: 02/23/2017] [Indexed: 11/30/2022]
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57
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Bouché L, Christ CD, Siegel S, Fernández-Montalván AE, Holton SJ, Fedorov O, Ter Laak A, Sugawara T, Stöckigt D, Tallant C, Bennett J, Monteiro O, Díaz-Sáez L, Siejka P, Meier J, Pütter V, Weiske J, Müller S, Huber KVM, Hartung IV, Haendler B. Benzoisoquinolinediones as Potent and Selective Inhibitors of BRPF2 and TAF1/TAF1L Bromodomains. J Med Chem 2017; 60:4002-4022. [PMID: 28402630 PMCID: PMC5443610 DOI: 10.1021/acs.jmedchem.7b00306] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
Bromodomains
(BD) are readers of lysine acetylation marks present
in numerous proteins associated with chromatin. Here we describe a
dual inhibitor of the bromodomain and PHD finger (BRPF) family member
BRPF2 and the TATA box binding protein-associated factors TAF1 and
TAF1L. These proteins are found in large chromatin complexes and play
important roles in transcription regulation. The substituted benzoisoquinolinedione
series was identified by high-throughput screening, and subsequent
structure–activity relationship optimization allowed generation
of low nanomolar BRPF2 BD inhibitors with strong selectivity against
BRPF1 and BRPF3 BDs. In addition, a strong inhibition of TAF1/TAF1L
BD2 was measured for most derivatives. The best compound of the series
was BAY-299, which is a very potent, dual inhibitor with an IC50 of 67 nM for BRPF2 BD, 8 nM for TAF1 BD2, and 106 nM for
TAF1L BD2. Importantly, no activity was measured for BRD4 BDs. Furthermore,
cellular activity was evidenced using a BRPF2– or TAF1–histone
H3.3 or H4 interaction assay.
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Affiliation(s)
- Léa Bouché
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Clara D Christ
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Stephan Siegel
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | | | - Simon J Holton
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | | | - Tatsuo Sugawara
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Detlef Stöckigt
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Cynthia Tallant
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - James Bennett
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Octovia Monteiro
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Laura Díaz-Sáez
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Paulina Siejka
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Julia Meier
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Vera Pütter
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Jörg Weiske
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Susanne Müller
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Kilian V M Huber
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Ingo V Hartung
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Bernard Haendler
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
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58
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Gul S. Epigenetic assays for chemical biology and drug discovery. Clin Epigenetics 2017; 9:41. [PMID: 28439316 PMCID: PMC5399855 DOI: 10.1186/s13148-017-0342-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 04/12/2017] [Indexed: 12/27/2022] Open
Abstract
The implication of epigenetic abnormalities in many diseases and the approval of a number of compounds that modulate specific epigenetic targets in a therapeutically relevant manner in cancer specifically confirms that some of these targets are druggable by small molecules. Furthermore, a number of compounds are currently in clinical trials for other diseases including cardiovascular, neurological and metabolic disorders. Despite these advances, the approved treatments for cancer only extend progression-free survival for a relatively short time and being associated with significant side effects. The current clinical trials involving the next generation of epigenetic drugs may address the disadvantages of the currently approved epigenetic drugs. The identification of chemical starting points of many drugs often makes use of screening in vitro assays against libraries of synthetic or natural products. These assays can be biochemical (using purified protein) or cell-based (using for example, genetically modified, cancer cell lines or primary cells) and performed in microtiter plates, thus enabling a large number of samples to be tested. A considerable number of such assays are available to monitor epigenetic target activity, and this review provides an overview of drug discovery and chemical biology and describes assays that monitor activities of histone deacetylase, lysine-specific demethylase, histone methyltransferase, histone acetyltransferase and bromodomain. It is of critical importance that an appropriate assay is developed and comprehensively validated for a given drug target prior to screening in order to improve the probability of the compound progressing in the drug discovery value chain.
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Affiliation(s)
- Sheraz Gul
- Fraunhofer Institute for Molecular Biology and Applied Ecology - ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
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59
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Remillard D, Buckley DL, Paulk J, Brien GL, Sonnett M, Seo HS, Dastjerdi S, Wühr M, Dhe-Paganon S, Armstrong SA, Bradner JE. Degradation of the BAF Complex Factor BRD9 by Heterobifunctional Ligands. Angew Chem Int Ed Engl 2017; 56:5738-5743. [PMID: 28418626 DOI: 10.1002/anie.201611281] [Citation(s) in RCA: 192] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/24/2017] [Indexed: 12/12/2022]
Abstract
The bromodomain-containing protein BRD9, a subunit of the human BAF (SWI/SNF) nucleosome remodeling complex, has emerged as an attractive therapeutic target in cancer. Despite the development of chemical probes targeting the BRD9 bromodomain, there is a limited understanding of BRD9 function beyond acetyl-lysine recognition. We have therefore created the first BRD9-directed chemical degraders, through iterative design and testing of heterobifunctional ligands that bridge the BRD9 bromodomain and the cereblon E3 ubiquitin ligase complex. Degraders of BRD9 exhibit markedly enhanced potency compared to parental ligands (10- to 100-fold). Parallel study of degraders with divergent BRD9-binding chemotypes in models of acute myeloid leukemia resolves bromodomain polypharmacology in this emerging drug class. Together, these findings reveal the tractability of non-BET bromodomain containing proteins to chemical degradation, and highlight lead compound dBRD9 as a tool for the study of BRD9.
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Affiliation(s)
- David Remillard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gerard L Brien
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew Sonnett
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shiva Dastjerdi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
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60
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Remillard D, Buckley DL, Paulk J, Brien GL, Sonnett M, Seo HS, Dastjerdi S, Wühr M, Dhe-Paganon S, Armstrong SA, Bradner JE. Degradation of the BAF Complex Factor BRD9 by Heterobifunctional Ligands. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611281] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- David Remillard
- Department of Medical Oncology; Dana-Farber Cancer Institute; Boston MA USA
| | - Dennis L. Buckley
- Department of Medical Oncology; Dana-Farber Cancer Institute; Boston MA USA
| | - Joshiawa Paulk
- Department of Medical Oncology; Dana-Farber Cancer Institute; Boston MA USA
| | - Gerard L. Brien
- Department of Pediatric Oncology; Dana-Farber Cancer Institute; Boston MA USA
| | - Matthew Sonnett
- Department of Systems Biology; Harvard Medical School; Boston MA USA
- Lewis-Sigler Institute for Integrative Genomics; Princeton University; Princeton NJ USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology; Dana-Farber Cancer Institute; Boston MA USA
| | - Shiva Dastjerdi
- Department of Medical Oncology; Dana-Farber Cancer Institute; Boston MA USA
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics; Princeton University; Princeton NJ USA
- Department of Molecular Biology; Princeton University; Princeton NJ USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology; Dana-Farber Cancer Institute; Boston MA USA
| | - Scott A. Armstrong
- Department of Pediatric Oncology; Dana-Farber Cancer Institute; Boston MA USA
| | - James E. Bradner
- Department of Medical Oncology; Dana-Farber Cancer Institute; Boston MA USA
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61
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Wan S, Bhati AP, Zasada SJ, Wall I, Green D, Bamborough P, Coveney PV. Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: A Computational Study. J Chem Theory Comput 2017; 13:784-795. [PMID: 28005370 PMCID: PMC5312866 DOI: 10.1021/acs.jctc.6b00794] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Binding free energies of bromodomain inhibitors are calculated with recently formulated approaches, namely ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling). A set of compounds is provided by GlaxoSmithKline, which represents a range of chemical functionality and binding affinities. The predicted binding free energies exhibit a good Spearman correlation of 0.78 with the experimental data from the 3-trajectory ESMACS, and an excellent correlation of 0.92 from the TIES approach where applicable. Given access to suitable high end computing resources and a high degree of automation, we can compute individual binding affinities in a few hours with precisions no greater than 0.2 kcal/mol for TIES, and no larger than 0.34 and 1.71 kcal/mol for the 1- and 3-trajectory ESMACS approaches.
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Affiliation(s)
- Shunzhou Wan
- Centre for Computational Science, Department of Chemistry, University College London , London WC1H 0AJ, United Kingdom
| | - Agastya P Bhati
- Centre for Computational Science, Department of Chemistry, University College London , London WC1H 0AJ, United Kingdom
| | - Stefan J Zasada
- Centre for Computational Science, Department of Chemistry, University College London , London WC1H 0AJ, United Kingdom
| | - Ian Wall
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
| | - Darren Green
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
| | - Paul Bamborough
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
| | - Peter V Coveney
- Centre for Computational Science, Department of Chemistry, University College London , London WC1H 0AJ, United Kingdom
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Humphreys PG, Bamborough P, Chung CW, Craggs PD, Gordon L, Grandi P, Hayhow TG, Hussain J, Jones KL, Lindon M, Michon AM, Renaux JF, Suckling CJ, Tough DF, Prinjha RK. Discovery of a Potent, Cell Penetrant, and Selective p300/CBP-Associated Factor (PCAF)/General Control Nonderepressible 5 (GCN5) Bromodomain Chemical Probe. J Med Chem 2017; 60:695-709. [DOI: 10.1021/acs.jmedchem.6b01566] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | | | | | | | - Paola Grandi
- Cellzome
GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | | | | | | | - Anne-Marie Michon
- Cellzome
GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Colin J. Suckling
- WestCHEM,
Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, G1 1XL, United Kingdom
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63
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Zhubanchaliyev A, Temirbekuly A, Kongrtay K, Wanshura LC, Kunz J. Targeting Mechanotransduction at the Transcriptional Level: YAP and BRD4 Are Novel Therapeutic Targets for the Reversal of Liver Fibrosis. Front Pharmacol 2016; 7:462. [PMID: 27990121 PMCID: PMC5131002 DOI: 10.3389/fphar.2016.00462] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/16/2016] [Indexed: 12/14/2022] Open
Abstract
Liver fibrosis is the result of a deregulated wound healing process characterized by the excessive deposition of extracellular matrix. Hepatic stellate cells (HSCs), which are activated in response to liver injury, are the major source of extracellular matrix and drive the wound healing process. However, chronic liver damage leads to perpetual HSC activation, progressive formation of pathological scar tissue and ultimately, cirrhosis and organ failure. HSC activation is triggered largely in response to mechanosignaling from the microenvironment, which induces a profibrotic nuclear transcription program that promotes HSC proliferation and extracellular matrix secretion thereby setting up a positive feedback loop leading to matrix stiffening and self-sustained, pathological, HSC activation. Despite the significant progress in our understanding of liver fibrosis, the molecular mechanisms through which the extracellular matrix promotes HSC activation are not well understood and no effective therapies have been approved to date that can target this early, reversible, stage in liver fibrosis. Several new lines of investigation now provide important insight into this area of study and identify two nuclear targets whose inhibition has the potential of reversing liver fibrosis by interfering with HSC activation: Yes-associated protein (YAP), a transcriptional co-activator and effector of the mechanosensitive Hippo pathway, and bromodomain-containing protein 4 (BRD4), an epigenetic regulator of gene expression. YAP and BRD4 activity is induced in response to mechanical stimulation of HSCs and each protein independently controls waves of early gene expression necessary for HSC activation. Significantly, inhibition of either protein can revert the chronic activation of HSCs and impede pathological progression of liver fibrosis in clinically relevant model systems. In this review we will discuss the roles of these nuclear co-activators in HSC activation, their mechanism of action in the fibrotic process in the liver and other organs, and the potential of targeting their activity with small molecule drugs for fibrosis reversal.
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Affiliation(s)
- Altynbek Zhubanchaliyev
- Department of Biology, School of Science and Technology, Nazarbayev UniversityAstana, Kazakhstan; Department of Biotechnology and Microbiology, Faculty of Natural Sciences, L.N.Gumilyov Eurasian National UniversityAstana, Kazakhstan
| | - Aibar Temirbekuly
- Department of Biology, School of Science and Technology, Nazarbayev University Astana, Kazakhstan
| | - Kuralay Kongrtay
- Department of Biology, School of Science and Technology, Nazarbayev University Astana, Kazakhstan
| | | | - Jeannette Kunz
- Department of Biology, School of Science and Technology, Nazarbayev University Astana, Kazakhstan
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64
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Moustakim M, Clark PGK, Hay DA, Dixon DJ, Brennan PE. Chemical probes and inhibitors of bromodomains outside the BET family. MEDCHEMCOMM 2016; 7:2246-2264. [PMID: 29170712 PMCID: PMC5644722 DOI: 10.1039/c6md00373g] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/06/2016] [Indexed: 01/03/2023]
Abstract
Significant progress has been made in discovering inhibitors and chemical probes of bromodomains, epigenetic readers of lysine acetylation.
In the last five years, the development of inhibitors of bromodomains has emerged as an area of intensive worldwide research. Emerging evidence has implicated a number of non-BET bromodomains in the onset and progression of diseases such as cancer, HIV infection and inflammation. The development and use of small molecule chemical probes has been fundamental to pre-clinical evaluation of bromodomains as targets. Recent efforts are described highlighting the development of potent, selective and cell active non-BET bromodomain inhibitors and their therapeutic potential. Over half of typical bromodomains now have reported ligands, but those with atypical binding site residues remain resistant to chemical probe discovery efforts.
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Affiliation(s)
- Moses Moustakim
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Structural Genomics Consortium, University of Oxford, OX3 7DQ, UK. .,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK
| | - Peter G K Clark
- Department of Chemistry, Simon Fraser University, Burnaby V5A 1S6, Canada
| | - Duncan A Hay
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK
| | - Darren J Dixon
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Paul E Brennan
- Structural Genomics Consortium, University of Oxford, OX3 7DQ, UK. .,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK
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