151
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Wang C, Barr K, Neutel D, Roy K, Liu Y, Chanfreau GF. Stress-induced inhibition of mRNA export triggers RNase III-mediated decay of the BDF2 mRNA. RNA (NEW YORK, N.Y.) 2021; 27:1545-1556. [PMID: 34497070 PMCID: PMC8594472 DOI: 10.1261/rna.078880.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
The expression of bromodomain-containing proteins that regulate chromatin structure and accessibility must be tightly controlled to ensure the appropriate regulation of gene expression. In the yeast S. cerevisiae, Bromodomain Factor 2 (BDF2) expression is extensively regulated post-transcriptionally during stress by RNase III-mediated decay (RMD), which is triggered by cleavage of the BDF2 mRNA in the nucleus by the RNase III homolog Rnt1p. Previous studies have shown that RMD-mediated down-regulation of BDF2 is hyperactivated in osmotic stress conditions, yet the mechanisms driving the enhanced nuclear cleavage of BDF2 RNA under these conditions remain unknown. Here, we show that RMD hyperactivation can be detected in multiple stress conditions that inhibit mRNA export, and that Rnt1p remains primarily localized in the nucleus during salt stress. We show that globally inhibiting mRNA nuclear export by anchoring away mRNA biogenesis or export factors out of the nucleus can recapitulate RMD hyperactivation in the absence of stress. RMD hyperactivation requires Rnt1p nuclear localization but does not depend on the BDF2 gene endogenous promoter, and its efficiency is affected by the structure of the stem-loop cleaved by Rnt1p. Because multiple stress conditions have been shown to mediate global inhibition of mRNA export, our results suggest that the hyperactivation of RMD is primarily the result of the increased nuclear retention of the BDF2 mRNA during stress.
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Affiliation(s)
- Charles Wang
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
| | - Keaton Barr
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
| | - Dean Neutel
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
| | - Kevin Roy
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, USA
| | - Yanru Liu
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, USA
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152
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Genome-wide CRISPR-Cas9 screens identify mechanisms of BET bromodomain inhibitor sensitivity. iScience 2021; 24:103323. [PMID: 34805786 PMCID: PMC8581576 DOI: 10.1016/j.isci.2021.103323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/23/2021] [Accepted: 10/19/2021] [Indexed: 01/06/2023] Open
Abstract
BET bromodomain inhibitors hold promise as therapeutic agents in diverse indications, but their clinical progression has been challenging and none have received regulatory approval. Early clinical trials in cancer have shown heterogeneous clinical responses, development of resistance, and adverse events. Increased understanding of their mechanism(s) of action and identification of biomarkers are needed to identify appropriate indication(s) and achieve efficacious dosing. Using genome-wide CRISPR-Cas9 screens at different concentrations, we report molecular mechanisms defining cellular responses to BET inhibitors, some of which appear specific to a single compound concentration. We identify multiple transcriptional regulators and mTOR pathway members as key determinants of JQ1 sensitivity and two Ca2+/Mn2+ transporters, ATP2C1 and TMEM165, as key determinants of JQ1 resistance. Our study reveals new molecular mediators of BET bromodomain inhibitor effects, suggests the involvement of manganese, and provides a rich resource for discovery of biomarkers and targets for combination therapies. CRISPR screens identify genes regulating sensitivity to BET bromodomain inhibitors Sensitivity and resistance hit lists are concentration-dependent mTOR pathway mediates sensitivity to BET bromodomain inhibitors Manganese regulates sensitivity to BET bromodomain inhibitors
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153
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Remillard D, Savage NA, Kedves AT, Paulk J, Chen X, Garcia FJ, Romanowski MJ, Horton PA, Murphy J, Schirle M, Harrington EM, Maxwell MB, Pham HT, Maksimovic I, Thomas JR, Forrester WC. Chemoproteomics Enabled Discovery of Selective Probes for NuA4 Factor BRD8. ACS Chem Biol 2021; 16:2185-2192. [PMID: 34515462 DOI: 10.1021/acschembio.1c00256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Bromodomain-containing proteins frequently reside in multisubunit chromatin complexes with tissue or cell state-specific compositions. Recent studies have revealed tumor-specific dependencies on the BAF complex bromodomain subunit BRD9 that are a result of recurrent mutations afflicting the structure and composition of associated complex members. To enable the study of ligand engaged complex assemblies, we established a chemoproteomics approach using a functionalized derivative of the BRD9 ligand BI-9564 as an affinity matrix. Unexpectedly, in addition to known interactions with BRD9 and associated BAF complex proteins, we identify a previously unreported interaction with members of the NuA4 complex through the bromodomain-containing subunit BRD8. We apply this finding, alongside a homology-model-guided design, to develop chemical biology approaches for the study of BRD8 inhibition and to arrive at first-in-class selective and cellularly active probes for BRD8. These tools will empower further pharmacological studies of BRD9 and BRD8 within respective BAF and NuA4 complexes.
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Affiliation(s)
- David Remillard
- Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, United States
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Nikolas A. Savage
- Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, United States
| | - Alexia T. Kedves
- Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, United States
| | - Joshiawa Paulk
- Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, United States
| | - Xin Chen
- Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, United States
| | - Francisco J. Garcia
- Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, United States
| | - Michael J. Romanowski
- Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, United States
| | - Patricia A. Horton
- Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, United States
| | - Jason Murphy
- Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, United States
| | - Edmund M. Harrington
- Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, United States
| | - Matthew B. Maxwell
- Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, United States
| | - Helen Trinh Pham
- Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, United States
| | - Igor Maksimovic
- Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, United States
| | - Jason R. Thomas
- Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, United States
| | - William C. Forrester
- Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, United States
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154
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Chen IP, Longbotham JE, McMahon S, Suryawanshi RK, Carlson-Stevermer J, Gupta M, Zhang MY, Soveg FW, Hayashi JM, Taha TY, Lam VL, Li Y, Yu Z, Titus EW, Diallo A, Oki J, Holden K, Krogan N, Galonić Fujimori D, Ott M. Viral E Protein Neutralizes BET Protein-Mediated Post-Entry Antagonism of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34816261 DOI: 10.1101/2021.11.14.468537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Inhibitors of Bromodomain and Extra-terminal domain (BET) proteins are possible anti-SARS-CoV-2 prophylactics as they downregulate angiotensin-converting enzyme 2 (ACE2). Here, we show that BET proteins should not be inactivated therapeutically as they are critical antiviral factors at the post-entry level. Knockouts of BRD3 or BRD4 in cells overexpressing ACE2 exacerbate SARS-CoV-2 infection; the same is observed when cells with endogenous ACE2 expression are treated with BET inhibitors during infection, and not before. Viral replication and mortality are also enhanced in BET inhibitor-treated mice overexpressing ACE2. BET inactivation suppresses interferon production induced by SARS-CoV-2, a process phenocopied by the envelope (E) protein previously identified as a possible "histone mimetic." E protein, in an acetylated form, directly binds the second bromodomain of BRD4. Our data support a model where SARS-CoV-2 E protein evolved to antagonize interferon responses via BET protein inhibition; this neutralization should not be further enhanced with BET inhibitor treatment.
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155
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Hey J, Paulsen M, Toth R, Weichenhan D, Butz S, Schatterny J, Liebers R, Lutsik P, Plass C, Mall MA. Epigenetic reprogramming of airway macrophages promotes polarization and inflammation in muco-obstructive lung disease. Nat Commun 2021; 12:6520. [PMID: 34764283 PMCID: PMC8586227 DOI: 10.1038/s41467-021-26777-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 10/19/2021] [Indexed: 12/12/2022] Open
Abstract
Lung diseases, such as cystic fibrosis and COPD, are characterized by mucus obstruction and chronic airway inflammation, but their mechanistic link remains poorly understood. Here, we focus on the function of the mucostatic airway microenvironment on epigenetic reprogramming of airway macrophages (AM) and resulting transcriptomic and phenotypical changes. Using a mouse model of muco-obstructive lung disease (Scnn1b-transgenic), we identify epigenetically controlled, differentially regulated pathways and transcription factors involved in inflammatory responses and macrophage polarization. Functionally, AMs from Scnn1b-transgenic mice have reduced efferocytosis and phagocytosis, and excessive inflammatory responses upon lipopolysaccharide challenge, mediated through enhanced Irf1 function and expression. Ex vivo stimulation of wild-type AMs with native mucus impairs efferocytosis and phagocytosis capacities. In addition, mucus induces gene expression changes, comparable with those observed in AMs from Scnn1b-transgenic mice. Our data show that mucostasis induces epigenetic reprogramming of AMs, leading to changes favoring tissue damage and disease progression. Targeting these altered AMs may support therapeutic approaches in patients with muco-obstructive lung diseases.
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Affiliation(s)
- Joschka Hey
- grid.7497.d0000 0004 0492 0584Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Ruprecht Karl University of Heidelberg, Heidelberg, Germany ,grid.452624.3Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Michelle Paulsen
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany. .,Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany. .,Novo Nordisk Foundation Center for Stem Cell Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Reka Toth
- grid.7497.d0000 0004 0492 0584Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Weichenhan
- grid.7497.d0000 0004 0492 0584Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simone Butz
- grid.452624.3Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany
| | - Jolanthe Schatterny
- grid.452624.3Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany
| | - Reinhard Liebers
- grid.7497.d0000 0004 0492 0584Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.461742.2Present Address: National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Pavlo Lutsik
- grid.7497.d0000 0004 0492 0584Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.
| | - Marcus A. Mall
- grid.452624.3Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany ,grid.7468.d0000 0001 2248 7639Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany ,grid.452624.3German Center for Lung Research (DZL), Associated Partner, Berlin, Germany
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156
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BETter insight into PRC2-mutated T-ALL. Blood 2021; 138:1787-1788. [PMID: 34762130 DOI: 10.1182/blood.2021012677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 11/20/2022] Open
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157
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Karim RM, Bikowitz MJ, Chan A, Zhu JY, Grassie D, Becker A, Berndt N, Gunawan S, Lawrence NJ, Schönbrunn E. Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors. J Med Chem 2021; 64:15772-15786. [PMID: 34710325 DOI: 10.1021/acs.jmedchem.1c01096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BRD4 and other members of the bromodomain and extraterminal (BET) family of proteins are promising epigenetic targets for the development of novel therapeutics. Among the reported BRD4 inhibitors are dihydropteridinones and benzopyrimidodiazepinones originally designed to target the kinases PLK1, ERK5, and LRRK2. While these kinase inhibitors were identified as BRD4 inhibitors, little is known about their binding potential and structural details of interaction with the other BET bromodomains. We comprehensively characterized a series of known and newly identified dual BRD4-kinase inhibitors against all eight individual BET bromodomains. A detailed analysis of 23 novel cocrystal structures of BET-kinase inhibitor complexes in combination with direct binding assays and cell signaling studies revealed significant differences in molecular shape complementarity and inhibitory potential. Collectively, the data offer new insights into the action of kinase inhibitors across BET bromodomains, which may aid the development of drugs to inhibit certain BET proteins and kinases differentially.
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Affiliation(s)
- Rezaul Md Karim
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States.,Department of Molecular Medicine, USF Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Melissa J Bikowitz
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States.,Department of Molecular Medicine, USF Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Alice Chan
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Jin-Yi Zhu
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Dylan Grassie
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Andreas Becker
- Chemical Biology Core, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Norbert Berndt
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Steven Gunawan
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Nicholas J Lawrence
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Ernst Schönbrunn
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
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158
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Malvezzi F, Stubbs CJ, Jowitt TA, Dale IL, Guo X, DeGnore JP, Degliesposti G, Skehel JM, Bannister AJ, McAlister MS. Phosphorylation-dependent BRD4 dimerization and implications for therapeutic inhibition of BET family proteins. Commun Biol 2021; 4:1273. [PMID: 34754068 PMCID: PMC8578508 DOI: 10.1038/s42003-021-02750-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/27/2021] [Indexed: 01/12/2023] Open
Abstract
Bromodomain-containing protein 4 (BRD4) is an epigenetic reader and oncology drug target that regulates gene transcription through binding to acetylated chromatin via bromodomains. Phosphorylation by casein kinase II (CK2) regulates BRD4 function, is necessary for active transcription and is involved in resistance to BRD4 drug inhibition in triple-negative breast cancer. Here, we provide the first biophysical analysis of BRD4 phospho-regulation. Using integrative structural biology, we show that phosphorylation by CK2 modulates the dimerization of human BRD4. We identify two conserved regions, a coiled-coil motif and the Basic-residue enriched Interaction Domain (BID), essential for the BRD4 structural rearrangement, which we term the phosphorylation-dependent dimerization domain (PDD). Finally, we demonstrate that bivalent inhibitors induce a conformational change within BRD4 dimers in vitro and in cancer cells. Our results enable the proposal of a model for BRD4 activation critical for the characterization of its protein-protein interaction network and for the development of more specific therapeutics.
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Affiliation(s)
- Francesca Malvezzi
- Structure, Biophysics and Fragment-Based Lead Generation, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Molecular Partners AG, Schlieren, Switzerland
| | - Christopher J Stubbs
- Structure, Biophysics and Fragment-Based Lead Generation, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Thomas A Jowitt
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
| | - Ian L Dale
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Xieyang Guo
- Structure, Biophysics and Fragment-Based Lead Generation, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jon P DeGnore
- Mechanistic Biology & Profiling, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Boston, USA
| | - Gianluca Degliesposti
- Biological Mass Spectrometry and Proteomics, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - J Mark Skehel
- Biological Mass Spectrometry and Proteomics, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Andrew J Bannister
- The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK
| | - Mark S McAlister
- Structure, Biophysics and Fragment-Based Lead Generation, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.
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159
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Trivalent PROTACs enhance protein degradation via combined avidity and cooperativity. Nat Chem Biol 2021; 17:1157-1167. [PMID: 34675414 PMCID: PMC7611906 DOI: 10.1038/s41589-021-00878-4] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 08/10/2021] [Indexed: 01/01/2023]
Abstract
Bivalent proteolysis-targeting chimeras (PROTACs) drive protein degradation by simultaneously binding a target protein and an E3 ligase and forming a productive ternary complex. We hypothesized that increasing binding valency within a PROTAC could enhance degradation. Here, we designed trivalent PROTACs consisting of a bivalent bromo and extra terminal (BET) inhibitor and an E3 ligand tethered via a branched linker. We identified von Hippel-Lindau (VHL)-based SIM1 as a low picomolar BET degrader with preference for bromodomain containing 2 (BRD2). Compared to bivalent PROTACs, SIM1 showed more sustained and higher degradation efficacy, which led to more potent anticancer activity. Mechanistically, SIM1 simultaneously engages with high avidity both BET bromodomains in a cis intramolecular fashion and forms a 1:1:1 ternary complex with VHL, exhibiting positive cooperativity and high cellular stability with prolonged residence time. Collectively, our data along with favorable in vivo pharmacokinetics demonstrate that augmenting the binding valency of proximity-induced modalities can be an enabling strategy for advancing functional outcomes.
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160
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Liang Y, Tian J, Wu T. BRD4 in physiology and pathology: ''BET'' on its partners. Bioessays 2021; 43:e2100180. [PMID: 34697817 DOI: 10.1002/bies.202100180] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/07/2021] [Accepted: 10/07/2021] [Indexed: 12/20/2022]
Abstract
Bromodomain-containing 4 (BRD4), a member of Bromo and Extra-Terminal (BET) family, recognizes acetylated histones and is of importance in transcription, replication, and DNA repair. It also binds non-histone proteins, DNA and RNA, contributing to development, tissue growth, and various physiological processes. Additionally, BRD4 has been implicated in driving diverse diseases, ranging from cancer, viral infection, inflammation to neurological disorders. Inhibiting its functions with BET inhibitors (BETis) suppresses the progression of several types of cancer, creating an impetus for translating these chemicals to the clinic. The diverse roles of BRD4 are largely dependent on its interaction partners in different contexts. In this review we discuss the molecular mechanisms of BRD4 with its interacting partners in physiology and pathology. Current development of BETis is also summarized. Further understanding the functions of BRD4 and its partners will facilitate resolving the liabilities of present BETis and accelerate their clinical translation.
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Affiliation(s)
- Yin Liang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Jieyi Tian
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Tao Wu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
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161
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Green AI, Burslem GM. Photochemical synthesis of an epigenetic focused tetrahydroquinoline library. RSC Med Chem 2021; 12:1780-1786. [PMID: 34778779 DOI: 10.1039/d1md00193k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/24/2021] [Indexed: 12/21/2022] Open
Abstract
Discovery of epigenetic chemical probes is an important area of research with potential to deliver drugs for a multitude of diseases. However, commercially available libraries frequently used in drug discovery campaigns contain molecules that are focused on a narrow range of chemical space primarily driven by ease of synthesis and previously targeted enzyme classes (e.g., kinases) resulting in low hit rates for epigenetic targets. Here we describe the design and synthesis of a compound collection that augments current screening collections by the inclusion of privileged isosteres for epigenetic targets.
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Affiliation(s)
- Adam I Green
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania PA 19104 USA
| | - George M Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania PA 19104 USA .,Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania PA 19104 USA
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162
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BET Proteins as Attractive Targets for Cancer Therapeutics. Int J Mol Sci 2021; 22:ijms222011102. [PMID: 34681760 PMCID: PMC8538173 DOI: 10.3390/ijms222011102] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/04/2021] [Accepted: 10/08/2021] [Indexed: 12/15/2022] Open
Abstract
Transcriptional dysregulation is a hallmark of cancer and can be an essential driver of cancer initiation and progression. Loss of transcriptional control can cause cancer cells to become dependent on certain regulators of gene expression. Bromodomain and extraterminal domain (BET) proteins are epigenetic readers that regulate the expression of multiple genes involved in carcinogenesis. BET inhibitors (BETis) disrupt BET protein binding to acetylated lysine residues of chromatin and suppress the transcription of various genes, including oncogenic transcription factors. Phase I and II clinical trials demonstrated BETis’ potential as anticancer drugs against solid tumours and haematological malignancies; however, their clinical success was limited as monotherapies. Emerging treatment-associated toxicities, drug resistance and a lack of predictive biomarkers limited BETis’ clinical progress. The preclinical evaluation demonstrated that BETis synergised with different classes of compounds, including DNA repair inhibitors, thus supporting further clinical development of BETis. The combination of BET and PARP inhibitors triggered synthetic lethality in cells with proficient homologous recombination. Mechanistic studies revealed that BETis targeted multiple essential homologous recombination pathway proteins, including RAD51, BRCA1 and CtIP. The exact mechanism of BETis’ anticancer action remains poorly understood; nevertheless, these agents provide a novel approach to epigenome and transcriptome anticancer therapy.
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163
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Bai P, Lan Y, Patnaik D, Wang H, Liu Y, Chen Z, Yuan G, Afshar S, Striar R, Zagaroli JS, Tocci DR, Langan AG, Haggarty SJ, Wang C. Design, Synthesis, and Evaluation of Thienodiazepine Derivatives as Positron Emission Tomography Imaging Probes for Bromodomain and Extra-Terminal Domain Family Proteins. J Med Chem 2021; 64:14745-14756. [PMID: 34549949 DOI: 10.1021/acs.jmedchem.1c01323] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To better understand the role of bromodomain and extra-terminal domain (BET) proteins in epigenetic mechanisms, we developed a series of thienodiazepine-based derivatives and identified two compounds, 3a and 6a, as potent BET inhibitors. Further in vivo pharmacokinetic studies and analysis of in vitro metabolic stability of 6a revealed excellent brain penetration and reasonable metabolic stability. Compounds 3a and 6a were radiolabeled with fluorine-18 in two steps and utilized in positron emission tomography (PET) imaging studies in mice. Preliminary PET imaging results demonstrated that [18F]3a and [18F]6a have good brain uptake (with maximum SUV = 1.7 and 2, respectively) and binding specificity in mice brains. These results show that [18F]6a is a potential PET radiotracer that could be applied to imaging BET proteins in the brain. Further optimization and improvement of the metabolic stability of [18F]6a are still needed in order to create optimal PET imaging probes of BET family members.
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Affiliation(s)
- Ping Bai
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Yu Lan
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Debasis Patnaik
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Hao Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Yan Liu
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Zude Chen
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Gengyang Yuan
- Gordon Center for Medical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Sepideh Afshar
- Gordon Center for Medical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Robin Striar
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Julia S Zagaroli
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Darcy R Tocci
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Amelia G Langan
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Changning Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
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164
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Feng L, Wang G, Chen Y, He G, Liu B, Liu J, Chiang CM, Ouyang L. Dual-target inhibitors of bromodomain and extra-terminal proteins in cancer: A review from medicinal chemistry perspectives. Med Res Rev 2021; 42:710-743. [PMID: 34633088 DOI: 10.1002/med.21859] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 07/14/2021] [Accepted: 09/26/2021] [Indexed: 02/05/2023]
Abstract
Bromodomain-containing protein 4 (BRD4), as the most studied member of the bromodomain and extra-terminal (BET) family, is a chromatin reader protein interpreting epigenetic codes through binding to acetylated histones and non-histone proteins, thereby regulating diverse cellular processes including cell cycle, cell differentiation, and cell proliferation. As a promising drug target, BRD4 function is closely related to cancer, inflammation, cardiovascular disease, and liver fibrosis. Currently, clinical resistance to BET inhibitors has limited their applications but synergistic antitumor effects have been observed when used in combination with other tumor inhibitors targeting additional cellular components such as PLK1, HDAC, CDK, and PARP1. Therefore, designing dual-target inhibitors of BET bromodomains is a rational strategy in cancer treatment to increase potency and reduce drug resistance. This review summarizes the protein structures and biological functions of BRD4 and discusses recent advances of dual BET inhibitors from a medicinal chemistry perspective. We also discuss the current design and discovery strategies for dual BET inhibitors, providing insight into potential discovery of additional dual-target BET inhibitors.
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Affiliation(s)
- Lu Feng
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Yi Chen
- State Key Laboratory of Biotherapy and Cancer Center and Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Gu He
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Bo Liu
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Jie Liu
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Cheng-Ming Chiang
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
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The nuclear ubiquitin ligase adaptor SPOP is a conserved regulator of C9orf72 dipeptide toxicity. Proc Natl Acad Sci U S A 2021; 118:2104664118. [PMID: 34593637 DOI: 10.1073/pnas.2104664118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2021] [Indexed: 12/29/2022] Open
Abstract
A hexanucleotide repeat expansion in the C9orf72 gene is the most common cause of inherited amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Unconventional translation of the C9orf72 repeat produces dipeptide repeat proteins (DPRs). Previously, we showed that the DPRs PR50 and GR50 are highly toxic when expressed in Caenorhabditis elegans, and this toxicity depends on nuclear localization of the DPR. In an unbiased genome-wide RNA interference (RNAi) screen for suppressors of PR50 toxicity, we identified 12 genes that consistently suppressed either the developmental arrest and/or paralysis phenotype evoked by PR50 expression. All of these genes have vertebrate homologs, and 7 of 12 contain predicted nuclear localization signals. One of these genes was spop-1, the C. elegans homolog of SPOP, a nuclear localized E3 ubiquitin ligase adaptor only found in metazoans. SPOP is also required for GR50 toxicity and functions in a genetic pathway that includes cul-3, which is the canonical E3 ligase partner for SPOP Genetic or pharmacological inhibition of SPOP in mammalian primary spinal cord motor neurons suppressed DPR toxicity without affecting DPR expression levels. Finally, we find that knockdown of bromodomain proteins in both C. elegans and mammalian neurons, which are known SPOP ubiquitination targets, suppresses the protective effect of SPOP inhibition. Together, these data suggest a model in which SPOP promotes the DPR-dependent ubiquitination and degradation of BRD proteins. We speculate the pharmacological manipulation of this pathway, which is currently underway for multiple cancer subtypes, could also represent an entry point for therapeutic intervention to treat C9orf72 FTD/ALS.
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166
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Liu L, Yang C, Candelario-Jalil E. Role of BET Proteins in Inflammation and CNS Diseases. Front Mol Biosci 2021; 8:748449. [PMID: 34604312 PMCID: PMC8481655 DOI: 10.3389/fmolb.2021.748449] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/06/2021] [Indexed: 01/04/2023] Open
Abstract
Bromodomain and extra-terminal domain (BET) proteins consist of four mammalian members (BRD2, BRD3, BRD4, and BRDT), which play a pivotal role in the transcriptional regulation of the inflammatory response. Dysregulated inflammation is a key pathological process in various CNS disorders through multiple mechanisms, including NF-κB and Nrf2 pathways, two well-known master regulators of inflammation. A better mechanistic understanding of the BET proteins’ role in regulating the inflammatory process is of great significance since it could reveal novel therapeutic targets to reduce neuroinflammation associated with many CNS diseases. In this minireview, we first outline the structural features of BET proteins and summarize genetic and pharmacological approaches for BET inhibition, including novel strategies using proteolysis-targeting chimeras (PROTACs). We emphasize in vitro and in vivo evidence of the interplay between BET proteins and NF-κB and Nrf2 signaling pathways. Finally, we summarize recent studies showing that BET proteins are essential regulators of inflammation and neuropathology in various CNS diseases.
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Affiliation(s)
- Lei Liu
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, United States
| | - Changjun Yang
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, United States
| | - Eduardo Candelario-Jalil
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, United States
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167
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Zhang L, Cai T, Lin X, Huang X, Bui MH, Plotnik JP, Bellin RJ, Faivre EJ, Kuruvilla VM, Lam LT, Lu X, Zha Z, Feng W, Hessler P, Uziel T, Zhang Q, Cavazos A, Han L, Ferguson DC, Mehta G, Shanmugavelandy SS, Magoc TJ, Rowe J, Goodwin NC, Dorritie KA, Boyiadzis M, Albert DH, McDaniel KF, Kati WM, Konopleva M, Shen Y. Selective Inhibition of the Second Bromodomain of BET Family Proteins Results in Robust Antitumor Activity in Preclinical Models of Acute Myeloid Leukemia. Mol Cancer Ther 2021; 20:1809-1819. [PMID: 34253595 DOI: 10.1158/1535-7163.mct-21-0029] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/31/2021] [Accepted: 06/29/2021] [Indexed: 11/16/2022]
Abstract
Dual bromodomain BET inhibitors that bind with similar affinities to the first and second bromodomains across BRD2, BRD3, BRD4, and BRDT have displayed modest activity as monotherapy in clinical trials. Thrombocytopenia, closely followed by symptoms characteristic of gastrointestinal toxicity, have presented as dose-limiting adverse events that may have prevented escalation to higher dose levels required for more robust efficacy. ABBV-744 is a highly selective inhibitor for the second bromodomain of the four BET family proteins. In contrast to the broad antiproliferative activities observed with dual bromodomain BET inhibitors, ABBV-744 displayed significant antiproliferative activities largely although not exclusively in cancer cell lines derived from acute myeloid leukemia and androgen receptor positive prostate cancer. Studies in acute myeloid leukemia xenograft models demonstrated antitumor efficacy for ABBV-744 that was comparable with the pan-BET inhibitor ABBV-075 but with an improved therapeutic index. Enhanced antitumor efficacy was also observed with the combination of ABBV-744 and the BCL-2 inhibitor, venetoclax compared with monotherapies of either agent alone. These results collectively support the clinical evaluation of ABBV-744 in AML (Clinical Trials.gov identifier: NCT03360006).
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Apoptosis
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Cell Proliferation
- Drug Therapy, Combination
- Female
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Proteins/antagonists & inhibitors
- Proto-Oncogene Proteins c-bcl-2/antagonists & inhibitors
- Pyridines/pharmacology
- Pyrroles/pharmacology
- Sulfonamides/pharmacology
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Lu Zhang
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois
| | - Tianyu Cai
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiaoyu Lin
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois
| | - Xiaoli Huang
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois
| | - Mai H Bui
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois
| | | | | | - Emily J Faivre
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois
| | - Vinitha M Kuruvilla
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lloyd T Lam
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois
| | - Xin Lu
- Genomic Research Center, AbbVie Inc., North Chicago, Illinois
| | - Zheng Zha
- Cyteir Therapeutics, 128 Spring Street, Lexington, Massachusetts
| | - Weiguo Feng
- Genomic Research Center, AbbVie Inc., North Chicago, Illinois
| | | | - Tamar Uziel
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois
| | - Qi Zhang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Antonio Cavazos
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lina Han
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Gaurav Mehta
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois
| | | | - Terrance J Magoc
- Cyteir Therapeutics, 128 Spring Street, Lexington, Massachusetts
| | - Jenny Rowe
- Charles River Laboratories, Wilmington, Massachusetts
| | | | - Kathleen A Dorritie
- Division of Hematology/Oncology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Michael Boyiadzis
- Division of Hematology/Oncology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | | | - Warren M Kati
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois
| | - Marina Konopleva
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Yu Shen
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois.
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168
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Romanelli MN, Borgonetti V, Galeotti N. Dual BET/HDAC inhibition to relieve neuropathic pain: Recent advances, perspectives, and future opportunities. Pharmacol Res 2021; 173:105901. [PMID: 34547384 DOI: 10.1016/j.phrs.2021.105901] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/15/2022]
Abstract
Despite the intense research on developing new therapies for neuropathic pain states, available treatments have limited efficacy and unfavorable safety profiles. Epigenetic alterations have a great influence on the development of cancer and neurological diseases, as well as neuropathic pain. Histone acetylation has prevailed as one of the well investigated epigenetic modifications in these diseases. Altered spinal activity of histone deacetylase (HDAC) and Bromo and Extra terminal domain (BET) have been described in neuropathic pain models and restoration of these aberrant epigenetic modifications showed pain-relieving activity. Over the last decades HDACs and BETs have been the focus of drug discovery studies, leading to the development of numerous small-molecule inhibitors. Clinical trials to evaluate their anticancer activity showed good efficacy but raised toxicity concerns that limited translation to the clinic. To maximize activity and minimize toxicity, these compounds can be applied in combination of sub-maximal doses to produce additive or synergistic interactions (combination therapy). Recently, of particular interest, dual BET/HDAC inhibitors (multi-target drugs) have been developed to assure simultaneous modulation of BET and HDAC activity by a single molecule. This review will summarize the most recent advances with these strategies, describing advantages and limitations of single drug treatment vs combination regimens. This review will also provide a focus on dual BET/HDAC drug discovery investigations as future therapeutic opportunity for human therapy of neuropathic pain.
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Affiliation(s)
- Maria Novella Romanelli
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Vittoria Borgonetti
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), Section of Pharmacology and Toxicology, University of Florence, Viale G. Pieraccini 6, 50139 Florence, Italy
| | - Nicoletta Galeotti
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), Section of Pharmacology and Toxicology, University of Florence, Viale G. Pieraccini 6, 50139 Florence, Italy.
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169
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Guo J, Liu Y, Lv J, Zou B, Chen Z, Li K, Feng J, Cai Z, Wei L, Liu M, Pang X. BCL6 confers KRAS-mutant non-small-cell lung cancer resistance to BET inhibitors. J Clin Invest 2021; 131:133090. [PMID: 33393503 DOI: 10.1172/jci133090] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/29/2020] [Indexed: 02/05/2023] Open
Abstract
The bromodomain and extra-terminal domain (BET) proteins are promising therapeutic targets to treat refractory solid tumors; however, inherent resistance remains a major challenge in the clinic. Recently, the emerging role of the oncoprotein B cell lymphoma 6 (BCL6) in tumorigenesis and stress response has been unveiled. Here, we demonstrate that BCL6 was upregulated upon BET inhibition in KRAS-mutant cancers, including non-small-cell lung cancer (NSCLC). We further found that BRD3, not BRD2 or BRD4, directly interacted with BCL6 and maintained the negative autoregulatory circuit of BCL6. Disrupting this negative autoregulation by BET inhibitors (BETi) resulted in a striking increase in BCL6 transcription, which further activated the mTOR signaling pathway through repression of the tumor suppressor death-associated protein kinase 2. Importantly, pharmacological inhibition of either BCL6 or mTOR improved the tumor response and enhanced the sensitivity of KRAS-mutant NSCLC to BETi in both in vitro and in vivo settings. Overall, our findings identify a mechanism of BRD3-mediated BCL6 autoregulation and further develop an effective combinatorial strategy to circumvent BETi resistance in KRAS-driven NSCLC.
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Affiliation(s)
- Jiawei Guo
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.,Department of Thoracic Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Yanan Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jing Lv
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Bin Zou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zhi Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.,Medical Research Institute, Wuhan University, Wuhan, China
| | - Kun Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Juanjuan Feng
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Zhenyu Cai
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Xiufeng Pang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
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170
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Cheung KL, Kim C, Zhou MM. The Functions of BET Proteins in Gene Transcription of Biology and Diseases. Front Mol Biosci 2021; 8:728777. [PMID: 34540900 PMCID: PMC8446420 DOI: 10.3389/fmolb.2021.728777] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/31/2021] [Indexed: 12/25/2022] Open
Abstract
The BET (bromodomain and extra-terminal domain) family proteins, consisting of BRD2, BRD3, BRD4, and testis-specific BRDT, are widely acknowledged as major transcriptional regulators in biology. They are characterized by two tandem bromodomains (BDs) that bind to lysine-acetylated histones and transcription factors, recruit transcription factors and coactivators to target gene sites, and activate RNA polymerase II machinery for transcriptional elongation. Pharmacological inhibition of BET proteins with BD inhibitors has been shown as a promising therapeutic strategy for the treatment of many human diseases including cancer and inflammatory disorders. The recent advances in bromodomain protein biology have further uncovered the complex and versatile functions of BET proteins in the regulation of gene expression in chromatin. In this review article, we highlight our current understanding of BET proteins' functions in mediating protein-protein interactions required for chromatin-templated gene transcription and splicing, chromatin remodeling, DNA replication, and DNA damage repair. We further discuss context-dependent activator vs. repressor functions of individual BET proteins, isoforms, and bromodomains that may be harnessed for future development of BET bromodomain inhibitors as emerging epigenetic therapies for cancer and inflammatory disorders.
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171
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Sasca D, Guezguez B, Kühn MWM. Next generation epigenetic modulators to target myeloid neoplasms. Curr Opin Hematol 2021; 28:356-363. [PMID: 34267079 DOI: 10.1097/moh.0000000000000673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
PURPOSE OF REVIEW Comprehensive sequencing studies aimed at determining the genetic landscape of myeloid neoplasms have identified epigenetic regulators to be among the most commonly mutated genes. Detailed studies have also revealed a number of epigenetic vulnerabilities. The purpose of this review is to outline these vulnerabilities and to discuss the new generation of drugs that exploit them. RECENT FINDINGS In addition to deoxyribonucleic acid-methylation, novel epigenetic dependencies have recently been discovered in various myeloid neoplasms and many of them can be targeted pharmacologically. These include not only chromatin writers, readers, and erasers but also chromatin movers that shift nucleosomes to allow access for transcription. Inhibitors of protein-protein interactions represent a novel promising class of drugs that allow disassembly of oncogenic multiprotein complexes. SUMMARY An improved understanding of disease-specific epigenetic vulnerabilities has led to the development of second-generation mechanism-based epigenetic drugs against myeloid neoplasms. Many of these drugs have been introduced into clinical trials and synergistic drug combination regimens have been shown to enhance efficacy and potentially prevent drug resistance.
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Affiliation(s)
- Daniel Sasca
- Department of Hematology, Oncology, and Pulmonary Medicine, University Medical Center, Johannes Gutenberg-University Mainz, Mainz
| | - Borhane Guezguez
- Department of Hematology, Oncology, and Pulmonary Medicine, University Medical Center, Johannes Gutenberg-University Mainz, Mainz
- German Cancer Research Center (DKFZ), Heidelberg
- German Cancer Consortium (DKTK), Mainz, Germany
| | - Michael W M Kühn
- Department of Hematology, Oncology, and Pulmonary Medicine, University Medical Center, Johannes Gutenberg-University Mainz, Mainz
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172
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Cao S, Liu M, Sehrawat TS, Shah VH. Regulation and functional roles of chemokines in liver diseases. Nat Rev Gastroenterol Hepatol 2021; 18:630-647. [PMID: 33976393 PMCID: PMC9036964 DOI: 10.1038/s41575-021-00444-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/18/2021] [Indexed: 02/03/2023]
Abstract
Inflammation is a major contributor to the pathogenesis of almost all liver diseases. Low-molecular-weight proteins called chemokines are the main drivers of liver infiltration by immune cells such as macrophages, neutrophils and others during an inflammatory response. During the past 25 years, tremendous progress has been made in understanding the regulation and functions of chemokines in the liver. This Review summarizes three main aspects of the latest advances in the study of chemokine function in liver diseases. First, we provide an overview of chemokine biology, with a particular focus on the genetic and epigenetic regulation of chemokine transcription as well as on the cell type-specific production of chemokines by liver cells and liver-associated immune cells. Second, we highlight the functional roles of chemokines in liver homeostasis and their involvement in progression to disease in both human and animal models. Third, we discuss the therapeutic opportunities targeting chemokine production and signalling in the treatment of liver diseases, such as alcohol-associated liver disease and nonalcoholic steatohepatitis, including the relevant preclinical studies and ongoing clinical trials.
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173
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Wang Q, Shao X, Leung ELH, Chen Y, Yao X. Selectively targeting individual bromodomain: Drug discovery and molecular mechanisms. Pharmacol Res 2021; 172:105804. [PMID: 34450309 DOI: 10.1016/j.phrs.2021.105804] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 12/21/2022]
Abstract
Bromodomain-containing proteins include bromodomain and extra-terminal (BET) and non-BET families. Due to the conserved bromodomain (BD) module between BD-containing proteins, and especially BETs with each member having two BDs (BD1 and BD2), the high degree of structural similarity makes BD-selective inhibitors much difficult to be designed. However, increasing evidences emphasized that individual BDs had distinct functions and different cellular phenotypes after pharmacological inhibition, and selectively targeting one of the BDs could result in a different efficacy and tolerability profile. This review is to summarize the pioneering progress of BD-selective inhibitors targeting BET and non-BET proteins, focusing on their structural features, biological activity, therapeutic application and experimental/theoretical mechanisms. The present proteolysis targeting chimeras (PROTAC) degraders targeting BDs, and clinical status of BD-selective inhibitors were also analyzed, providing a new insight into future direction of bromodomain-selective drug discovery.
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Affiliation(s)
- Qianqian Wang
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China
| | - Xiaomin Shao
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China
| | - Elaine Lai Han Leung
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau(SAR) 999078, China
| | - Yingqing Chen
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China.
| | - Xiaojun Yao
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau(SAR) 999078, China.
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174
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Blasl AT, Schulze S, Qin C, Graf LG, Vogt R, Lammers M. Post-translational lysine ac(et)ylation in health, ageing and disease. Biol Chem 2021; 403:151-194. [PMID: 34433238 DOI: 10.1515/hsz-2021-0139] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022]
Abstract
The acetylation/acylation (ac(et)ylation) of lysine side chains is a dynamic post-translational modification (PTM) regulating fundamental cellular processes with implications on the organisms' ageing process: metabolism, transcription, translation, cell proliferation, regulation of the cytoskeleton and DNA damage repair. First identified to occur on histones, later studies revealed the presence of lysine ac(et)ylation in organisms of all kingdoms of life, in proteins covering all essential cellular processes. A remarkable finding showed that the NAD+-dependent sirtuin deacetylase Sir2 has an impact on replicative lifespan in Saccharomyces cerevisiae suggesting that lysine acetylation has a direct role in the ageing process. Later studies identified sirtuins as mediators for beneficial effects of caloric/dietary restriction on the organisms' health- or lifespan. However, the molecular mechanisms underlying these effects are only incompletely understood. Progress in mass-spectrometry, structural biology, synthetic and semi-synthetic biology deepened our understanding of this PTM. This review summarizes recent developments in the research field. It shows how lysine ac(et)ylation regulates protein function, how it is regulated enzymatically and non-enzymatically, how a dysfunction in this post-translational machinery contributes to disease development. A focus is set on sirtuins and lysine acyltransferases as these are direct sensors and mediators of the cellular metabolic state. Finally, this review highlights technological advances to study lysine ac(et)ylation.
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Affiliation(s)
- Anna-Theresa Blasl
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Sabrina Schulze
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Chuan Qin
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Leonie G Graf
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Robert Vogt
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Michael Lammers
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
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Unraveling the IGF System Interactome in Sarcomas Exploits Novel Therapeutic Options. Cells 2021; 10:cells10082075. [PMID: 34440844 PMCID: PMC8392407 DOI: 10.3390/cells10082075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 12/15/2022] Open
Abstract
Aberrant bioactivity of the insulin-like growth factor (IGF) system results in the development and progression of several pathologic conditions including cancer. Preclinical studies have shown promising anti-cancer therapeutic potentials for anti-IGF targeted therapies. However, a clear but limited clinical benefit was observed only in a minority of patients with sarcomas. The molecular complexity of the IGF system, which comprises multiple regulators and interactions with other cancer-related pathways, poses a major limitation in the use of anti-IGF agents and supports the need of combinatorial therapeutic strategies to better tackle this axis. In this review, we will initially highlight multiple mechanisms underlying IGF dysregulation in cancer and then focus on the impact of the IGF system and its complexity in sarcoma development and progression as well as response to anti-IGF therapies. We will also discuss the role of Ephrin receptors, Hippo pathway, BET proteins and CXCR4 signaling, as mediators of sarcoma malignancy and relevant interactors with the IGF system in tumor cells. A deeper understanding of these molecular interactions might provide the rationale for novel and more effective therapeutic combinations to treat sarcomas.
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176
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Xiang W, Wang Q, Ran K, Ren J, Shi Y, Yu L. Structure-guided discovery of novel potent and efficacious proteolysis targeting chimera (PROTAC) degrader of BRD4. Bioorg Chem 2021; 115:105238. [PMID: 34390970 DOI: 10.1016/j.bioorg.2021.105238] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/27/2021] [Accepted: 08/02/2021] [Indexed: 02/08/2023]
Abstract
Bromodomain-containing protein 4 (BRD4) has been identified as a potential target in the treatment of many cancers and several BRD4 inhibitors have entered clinical studies. Previous studies have shown that BRD4 degraders have potential to overcome resistance to BRD4 inhibitors. However, most of the BRD4 degraders have poor solubility and bioavailability, one of which the reason is large molecular weight. Here, we describe the design, synthesis, and evaluation studies of a BRD4 degrader based on the proteolysis targeting chimeras (PROTAC) concept. Our efforts have led to the discovery of compound 15, which is a weak inhibitor and potent BRD4 degrader with a molecular weight of 821.8. In vitro, 15 can completely degrade BRD4 at nanomolar concentration, with DC50 = 0.25 and 3.15 nM in MV4-11 and RS4-11 cell lines, respectively. Further optimization of compound 15 may reduce its molecular weight and improve druggabillity, and provide a new choice for the treatment of cancer.
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Affiliation(s)
- Wang Xiang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Qiwei Wang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Kai Ran
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Jing Ren
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Yaojie Shi
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, PR China.
| | - Luoting Yu
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, PR China.
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177
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Li J, Zou W, Yu K, Liu B, Liang W, Wang L, Lu Y, Jiang Z, Wang A, Zhu J. Discovery of the natural product 3',4',7,8-tetrahydroxyflavone as a novel and potent selective BRD4 bromodomain 2 inhibitor. J Enzyme Inhib Med Chem 2021; 36:903-913. [PMID: 33820450 PMCID: PMC8032343 DOI: 10.1080/14756366.2021.1906663] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bromodomain-containing protein 4 (BRD4) binds acetylated lysine residues on the N-terminal tails of histones through two bromodomains (BD1 and BD2) to regulate gene transcription. Inhibiting one or both of bromodomains resulted in different phenotypes, suggesting BD1 and BD2 may have different functions. Here we report the characterisation of a natural product 3',4',7,8-tetrahydroxyflavone as a novel and potent selective BRD4 inhibitor. The compound is 100-fold more selective for BRD4-BD2 (IC50 = 204 nM) than BRD4-BD1 (IC50=17.9 µM). Co-crystal structures show 3',4',7,8-tetrahydroxyflavone binds to the acetylated lysine binding pocket of BRD4-BD1 or BRD4-BD2, but establishes more interactions with BRD4-BD2 than BRD4-BD1. Our data suggest 3',4',7,8-tetrahydroxyflavone as a potent selective inhibitor of BRD4-BD2 with a novel chemical scaffold. Given its distinct chemical structure from current BRD4 inhibitors, this compound may open the door for a novel class of anti-BRD4 inhibitors by serving as a lead compound.
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Affiliation(s)
- Jiao Li
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Wei Zou
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Koukou Yu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Bing Liu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Weifeng Liang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Lisha Wang
- Department of Medicinal Chemistry, PharmaBlock Sciences (Nanjing), Inc., Nanjing, China
| | - Yin Lu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Zequn Jiang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Aiyun Wang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Jiapeng Zhu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
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178
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Abstract
There is no nonhormonal contraceptive pill for men, although hundreds of genes have been identified to play roles during spermatogenesis and fertilization in the male reproductive tract. To address the absence of contraceptive drugs for men, we established a DNA-encoded chemistry technology (DEC-Tec) platform. Our drug discovery campaign on BRDT, a validated spermatogenic-specific contraceptive target, yielded rapid discovery of potent and specific inhibitors of the second bromodomain of BRDT that have unique binding characteristics to BRDT-BD2 relative to BRDT-BD1. Our study emphasizes the robustness and validation of the DEC-Tec platform where the obtained structure–affinity relationship data would allow us to identify specific protein binders immediately without performing exhaustive medicinal chemistry optimization of compounds with potential as male contraceptives. Bromodomain testis (BRDT), a member of the bromodomain and extraterminal (BET) subfamily that includes the cancer targets BRD2, BRD3, and BRD4, is a validated contraceptive target. All BET subfamily members have two tandem bromodomains (BD1 and BD2). Knockout mice lacking BRDT-BD1 or both bromodomains are infertile. Treatment of mice with JQ1, a BET BD1/BD2 nonselective inhibitor with the highest affinity for BRD4, disrupts spermatogenesis and reduces sperm number and motility. To assess the contribution of each BRDT bromodomain, we screened our collection of DNA-encoded chemical libraries for BRDT-BD1 and BRDT-BD2 binders. High-enrichment hits were identified and resynthesized off-DNA and examined for their ability to compete with JQ1 in BRDT and BRD4 bromodomain AlphaScreen assays. These studies identified CDD-1102 as a selective BRDT-BD2 inhibitor with low nanomolar potency and >1,000-fold selectivity over BRDT-BD1. Structure–activity relationship studies of CDD-1102 produced a series of additional BRDT-BD2/BRD4-BD2 selective inhibitors, including CDD-1302, a truncated analog of CDD-1102 with similar activity, and CDD-1349, an analog with sixfold selectivity for BRDT-BD2 versus BRD4-BD2. BROMOscan bromodomain profiling confirmed the great affinity and selectivity of CDD-1102 and CDD-1302 on all BET BD2 versus BD1 with the highest affinity for BRDT-BD2. Cocrystals of BRDT-BD2 with CDD-1102 and CDD-1302 were determined at 2.27 and 1.90 Å resolution, respectively, and revealed BRDT-BD2 specific contacts that explain the high affinity and selectivity of these compounds. These BD2-specific compounds and their binding to BRDT-BD2 are unique compared with recent reports and enable further evaluation of their nonhormonal contraceptive potential in vitro and in vivo.
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179
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Lara-Ureña N, García-Domínguez M. Relevance of BET Family Proteins in SARS-CoV-2 Infection. Biomolecules 2021; 11:1126. [PMID: 34439792 PMCID: PMC8391731 DOI: 10.3390/biom11081126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022] Open
Abstract
The recent pandemic we are experiencing caused by the coronavirus disease 2019 (COVID-19) has put the world's population on the rack, with more than 191 million cases and more than 4.1 million deaths confirmed to date. This disease is caused by a new type of coronavirus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A massive proteomic analysis has revealed that one of the structural proteins of the virus, the E protein, interacts with BRD2 and BRD4 proteins of the Bromodomain and Extra Terminal domain (BET) family of proteins. BETs are essential to cell cycle progression, inflammation and immune response and have also been strongly associated with infection by different types of viruses. The fundamental role BET proteins play in transcription makes them appropriate targets for the propagation strategies of some viruses. Recognition of histone acetylation by BET bromodomains is essential for transcription control. The development of drugs mimicking acetyl groups, and thereby able to displace BET proteins from chromatin, has boosted interest on BETs as attractive targets for therapeutic intervention. The success of these drugs against a variety of diseases in cellular and animal models has been recently enlarged with promising results from SARS-CoV-2 infection studies.
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Affiliation(s)
| | - Mario García-Domínguez
- Andalusian Centre for Molecular Biology and Regenerative Medicine (CABIMER), CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain;
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180
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Liu M, Cao S, He L, Gao J, Arab JP, Cui H, Xuan W, Gao Y, Sehrawat TS, Hamdan FH, Ventura-Cots M, Argemi J, Pomerantz WCK, Johnsen SA, Lee JH, Gao F, Ordog T, Mathurin P, Revzin A, Bataller R, Yan H, Shah VH. Super enhancer regulation of cytokine-induced chemokine production in alcoholic hepatitis. Nat Commun 2021; 12:4560. [PMID: 34315876 PMCID: PMC8316465 DOI: 10.1038/s41467-021-24843-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/01/2021] [Indexed: 02/08/2023] Open
Abstract
Alcoholic hepatitis (AH) is associated with liver neutrophil infiltration through activated cytokine pathways leading to elevated chemokine expression. Super-enhancers are expansive regulatory elements driving augmented gene expression. Here, we explore the mechanistic role of super-enhancers linking cytokine TNFα with chemokine amplification in AH. RNA-seq and histone modification ChIP-seq of human liver explants show upregulation of multiple CXCL chemokines in AH. Liver sinusoidal endothelial cells (LSEC) are identified as an important source of CXCL expression in human liver, regulated by TNFα/NF-κB signaling. A super-enhancer is identified for multiple CXCL genes by multiple approaches. dCas9-KRAB-mediated epigenome editing or pharmacologic inhibition of Bromodomain and Extraterminal (BET) proteins, transcriptional regulators vital to super-enhancer function, decreases chemokine expression in vitro and decreases neutrophil infiltration in murine models of AH. Our findings highlight the role of super-enhancer in propagating inflammatory signaling by inducing chemokine expression and the therapeutic potential of BET inhibition in AH treatment.
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Affiliation(s)
- Mengfei Liu
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Sheng Cao
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Li He
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinhang Gao
- Lab of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China
| | - Juan P Arab
- Department of Gastroenterology and Hepatology, School of Medicine of the Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Huarui Cui
- Department of Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Weixia Xuan
- Department of Respiratory and Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, China
- Department of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Yandong Gao
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Tejasav S Sehrawat
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Feda H Hamdan
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Meritxell Ventura-Cots
- Department of Gastroenterology Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Josepmaria Argemi
- Department of Gastroenterology Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Steven A Johnsen
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Jeong-Heon Lee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Fei Gao
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tamas Ordog
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Alexander Revzin
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Ramon Bataller
- Department of Gastroenterology Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Huihuang Yan
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Vijay H Shah
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA.
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181
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Paakinaho V, Palvimo JJ. Genome-wide crosstalk between steroid receptors in breast and prostate cancers. Endocr Relat Cancer 2021; 28:R231-R250. [PMID: 34137734 PMCID: PMC8345902 DOI: 10.1530/erc-21-0038] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022]
Abstract
Steroid receptors (SRs) constitute an important class of signal-dependent transcription factors (TFs). They regulate a variety of key biological processes and are crucial drug targets in many disease states. In particular, estrogen (ER) and androgen receptors (AR) drive the development and progression of breast and prostate cancer, respectively. Thus, they represent the main specific drug targets in these diseases. Recent evidence has suggested that the crosstalk between signal-dependent TFs is an important step in the reprogramming of chromatin sites; a signal-activated TF can expand or restrict the chromatin binding of another TF. This crosstalk can rewire gene programs and thus alter biological processes and influence the progression of disease. Lately, it has been postulated that there may be an important crosstalk between the AR and the ER with other SRs. Especially, progesterone (PR) and glucocorticoid receptor (GR) can reprogram chromatin binding of ER and gene programs in breast cancer cells. Furthermore, GR can take the place of AR in antiandrogen-resistant prostate cancer cells. Here, we review the current knowledge of the crosstalk between SRs in breast and prostate cancers. We emphasize how the activity of ER and AR on chromatin can be modulated by other SRs on a genome-wide scale. We also highlight the knowledge gaps in the interplay of SRs and their complex interactions with other signaling pathways and suggest how to experimentally fill in these gaps.
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Affiliation(s)
- Ville Paakinaho
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Jorma J Palvimo
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
- Correspondence should be addressed to J J Palvimo:
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182
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Boyson SP, Gao C, Quinn K, Boyd J, Paculova H, Frietze S, Glass KC. Functional Roles of Bromodomain Proteins in Cancer. Cancers (Basel) 2021; 13:3606. [PMID: 34298819 PMCID: PMC8303718 DOI: 10.3390/cancers13143606] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 12/31/2022] Open
Abstract
Histone acetylation is generally associated with an open chromatin configuration that facilitates many cellular processes including gene transcription, DNA repair, and DNA replication. Aberrant levels of histone lysine acetylation are associated with the development of cancer. Bromodomains represent a family of structurally well-characterized effector domains that recognize acetylated lysines in chromatin. As part of their fundamental reader activity, bromodomain-containing proteins play versatile roles in epigenetic regulation, and additional functional modules are often present in the same protein, or through the assembly of larger enzymatic complexes. Dysregulated gene expression, chromosomal translocations, and/or mutations in bromodomain-containing proteins have been correlated with poor patient outcomes in cancer. Thus, bromodomains have emerged as a highly tractable class of epigenetic targets due to their well-defined structural domains, and the increasing ease of designing or screening for molecules that modulate the reading process. Recent developments in pharmacological agents that target specific bromodomains has helped to understand the diverse mechanisms that bromodomains play with their interaction partners in a variety of chromatin processes, and provide the promise of applying bromodomain inhibitors into the clinical field of cancer treatment. In this review, we explore the expression and protein interactome profiles of bromodomain-containing proteins and discuss them in terms of functional groups. Furthermore, we highlight our current understanding of the roles of bromodomain-containing proteins in cancer, as well as emerging strategies to specifically target bromodomains, including combination therapies using bromodomain inhibitors alongside traditional therapeutic approaches designed to re-program tumorigenesis and metastasis.
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Affiliation(s)
- Samuel P. Boyson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA;
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
| | - Cong Gao
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Kathleen Quinn
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Joseph Boyd
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Hana Paculova
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
- University of Vermont Cancer Center, Burlington, VT 05405, USA
| | - Karen C. Glass
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA;
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
- University of Vermont Cancer Center, Burlington, VT 05405, USA
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183
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He MY, Halford MM, Liu R, Roy JP, Grant ZL, Coultas L, Thio N, Gilan O, Chan YC, Dawson MA, Achen MG, Stacker SA. Three-dimensional CRISPR screening reveals epigenetic interaction with anti-angiogenic therapy. Commun Biol 2021; 4:878. [PMID: 34267311 PMCID: PMC8282794 DOI: 10.1038/s42003-021-02397-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 06/23/2021] [Indexed: 12/13/2022] Open
Abstract
Angiogenesis underlies development, physiology and pathogenesis of cancer, eye and cardiovascular diseases. Inhibiting aberrant angiogenesis using anti-angiogenic therapy (AAT) has been successful in the clinical treatment of cancer and eye diseases. However, resistance to AAT inevitably occurs and its molecular basis remains poorly understood. Here, we uncover molecular modifiers of the blood endothelial cell (EC) response to a widely used AAT bevacizumab by performing a pooled genetic screen using three-dimensional microcarrier-based cell culture and CRISPR–Cas9. Functional inhibition of the epigenetic reader BET family of proteins BRD2/3/4 shows unexpected mitigating effects on EC survival and/or proliferation upon VEGFA blockade. Moreover, transcriptomic and pathway analyses reveal an interaction between epigenetic regulation and anti-angiogenesis, which may affect chromosomal structure and activity in ECs via the cell cycle regulator CDC25B phosphatase. Collectively, our findings provide insight into epigenetic regulation of the EC response to VEGFA blockade and may facilitate development of quality biomarkers and strategies for overcoming resistance to AAT. Through three-dimensional CRISPR screening, He et al. report that functional inhibition of BET family of proteins BRD2/3/4 shows mitigating effects on blood endothelial cell (EC) survival and/or proliferation upon VEGFA blockade. An interaction between epigenetic regulation and anti-angiogenesis, which may affect chromosomal structure and activity in ECs through CDC25B phosphatase, is potentially involved with EC resistance to anti-angiogenic therapy.
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Affiliation(s)
- Michael Y He
- Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michael M Halford
- Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Ruofei Liu
- Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - James P Roy
- Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Zoe L Grant
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Gladstone Institutes, San Francisco, CA, USA
| | - Leigh Coultas
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Niko Thio
- Bioinformatics Core, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Omer Gilan
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.,Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Yih-Chih Chan
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Mark A Dawson
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.,Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Centre for Cancer Research, The University of Melbourne, Parkville, VIC, Australia.,Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Marc G Achen
- Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.,Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia.,St Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Steven A Stacker
- Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia. .,Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia.
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184
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Lucas SCC, Atkinson SJ, Chung CW, Davis R, Gordon L, Grandi P, Gray JJR, Grimes T, Phillipou A, Preston AG, Prinjha RK, Rioja I, Taylor S, Tomkinson NCO, Wall I, Watson RJ, Woolven J, Demont EH. Optimization of a Series of 2,3-Dihydrobenzofurans as Highly Potent, Second Bromodomain (BD2)-Selective, Bromo and Extra-Terminal Domain (BET) Inhibitors. J Med Chem 2021; 64:10711-10741. [PMID: 34260229 DOI: 10.1021/acs.jmedchem.1c00344] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Herein, a series of 2,3-dihydrobenzofurans have been developed as highly potent bromo and extra-terminal domain (BET) inhibitors with 1000-fold selectivity for the second bromodomain (BD2) over the first bromodomain (BD1). Investment in the development of two orthogonal synthetic routes delivered inhibitors that were potent and selective but had raised in vitro clearance and suboptimal solubility. Insertion of a quaternary center into the 2,3-dihydrobenzofuran core blocked a key site of metabolism and improved the solubility. This led to the development of inhibitor 71 (GSK852): a potent, 1000-fold-selective, highly soluble compound with good in vivo rat and dog pharmacokinetics.
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Affiliation(s)
| | | | | | | | | | - Paola Grandi
- IVIVT Cellzome, Platform Technology and Science, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | | | | | | | | | | | | | - Nicholas C O Tomkinson
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 259 Cathedral Street, Glasgow G1 1XL, U.K
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185
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Seal JT, Atkinson SJ, Bamborough P, Bassil A, Chung CW, Foley J, Gordon L, Grandi P, Gray JRJ, Harrison LA, Kruger RG, Matteo JJ, McCabe MT, Messenger C, Mitchell D, Phillipou A, Preston A, Prinjha RK, Rianjongdee F, Rioja I, Taylor S, Wall ID, Watson RJ, Woolven JM, Wyce A, Zhang XP, Demont EH. Fragment-based Scaffold Hopping: Identification of Potent, Selective, and Highly Soluble Bromo and Extra Terminal Domain (BET) Second Bromodomain (BD2) Inhibitors. J Med Chem 2021; 64:10772-10805. [PMID: 34255512 DOI: 10.1021/acs.jmedchem.1c00365] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The profound efficacy of pan-BET inhibitors is well documented, but these epigenetic agents have shown pharmacology-driven toxicity in oncology clinical trials. The opportunity to identify inhibitors with an improved safety profile by selective targeting of a subset of the eight bromodomains of the BET family has triggered extensive medicinal chemistry efforts. In this article, we disclose the identification of potent and selective drug-like pan-BD2 inhibitors such as pyrazole 23 (GSK809) and furan 24 (GSK743) that were derived from the pyrrole fragment 6. We transpose the key learnings from a previous pyridone series (GSK620 2 as a representative example) to this novel class of inhibitors, which are characterized by significantly improved solubility relative to our previous research.
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Affiliation(s)
| | | | | | | | | | - James Foley
- Cancer Epigenetics Research Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | | | - Paola Grandi
- IVIVT Cellzome, Platform Technology and Science, GlaxoSmithKline, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | | | | | - Ryan G Kruger
- Cancer Epigenetics Research Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Jeanne J Matteo
- Cancer Epigenetics Research Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Michael T McCabe
- Cancer Epigenetics Research Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | | | | | | | | | | | | | | | | | | | | | | | - Anastasia Wyce
- Cancer Epigenetics Research Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Xi-Ping Zhang
- Cancer Epigenetics Research Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
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186
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Rianjongdee F, Atkinson SJ, Chung CW, Grandi P, Gray JRJ, Kaushansky LJ, Medeiros P, Messenger C, Phillipou A, Preston A, Prinjha RK, Rioja I, Satz AL, Taylor S, Wall ID, Watson RJ, Yao G, Demont EH. Discovery of a Highly Selective BET BD2 Inhibitor from a DNA-Encoded Library Technology Screening Hit. J Med Chem 2021; 64:10806-10833. [PMID: 34251219 DOI: 10.1021/acs.jmedchem.1c00412] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Second-generation bromodomain and extra terminal (BET) inhibitors, which selectively target one of the two bromodomains in the BET proteins, have begun to emerge in the literature. These inhibitors aim to help determine the roles and functions of each domain and assess whether they can demonstrate an improved safety profile in clinical settings compared to pan-BET inhibitors. Herein, we describe the discovery of a novel BET BD2-selective chemotype using a structure-based drug design from a hit identified by DNA-encoded library technologies, showing a structural differentiation from key previously reported greater than 100-fold BD2-selective chemotypes GSK620, GSK046, and ABBV-744. Following a structure-based hypothesis for the selectivity and optimization of the physicochemical properties of the series, we identified 60 (GSK040), an in vitro ready and in vivo capable BET BD2-inhibitor of unprecedented selectivity (5000-fold) against BET BD1, excellent selectivity against other bromodomains, and good physicochemical properties. This novel chemical probe can be added to the toolbox used in the advancement of epigenetics research.
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Affiliation(s)
| | | | | | - Paola Grandi
- IVIVT Cellzome, Platform Technology and Science, GlaxoSmithKline, Meyerhofstr. 1, Heidelberg 69117, Germany
| | | | - Laura J Kaushansky
- Encoded Library Technologies, R&D Medicinal Science and Technology, GSK, 200 Cambridge Park Drive, Cambridge 02140, Massachusetts, United States
| | - Patricia Medeiros
- Encoded Library Technologies, R&D Medicinal Science and Technology, GSK, 200 Cambridge Park Drive, Cambridge 02140, Massachusetts, United States
| | | | | | | | | | | | | | | | | | | | - Gang Yao
- Encoded Library Technologies, R&D Medicinal Science and Technology, GSK, 200 Cambridge Park Drive, Cambridge 02140, Massachusetts, United States
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187
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Cui H, Carlson AS, Schleiff MA, Divakaran A, Johnson JA, Buchholz CR, Zahid H, Vail NR, Shi K, Aihara H, Harki DA, Miller GP, Topczewski JJ, Pomerantz WCK. 4-Methyl-1,2,3-Triazoles as N-Acetyl-Lysine Mimics Afford Potent BET Bromodomain Inhibitors with Improved Selectivity. J Med Chem 2021; 64:10497-10511. [PMID: 34236185 DOI: 10.1021/acs.jmedchem.1c00933] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The bromodomain and extra terminal (BET) protein family recognizes acetylated lysines within histones and transcription factors using two N-terminal bromodomains, D1 and D2. The protein-protein interactions between BET bromodomains, acetylated histones, and transcription factors are therapeutic targets for BET-related diseases, including inflammatory disease and cancer. Prior work demonstrated that methylated-1,2,3-triazoles are suitable N-acetyl lysine mimetics for BET inhibition. Here we describe a structure-activity relationship study of triazole-based inhibitors that improve affinity, D1 selectivity, and microsomal stability. These outcomes were accomplished by targeting a nonconserved residue, Asp144 and a conserved residue, Met149, on BRD4 D1. The lead inhibitors DW34 and 26 have a BRD4 D1 Kd of 12 and 6.4 nM, respectively. Cellular activity was demonstrated through suppression of c-Myc expression in MM.1S cells and downregulation of IL-8 in TNF-α-stimulated A549 cells. These data indicate that DW34 and 26 are new leads to investigate the anticancer and anti-inflammatory activity of BET proteins.
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Affiliation(s)
- Huarui Cui
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Angela S Carlson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Mary A Schleiff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 W. Markham Street, Little Rock, Arkansas 72205, United States
| | - Anand Divakaran
- Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
| | - Jorden A Johnson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Caroline R Buchholz
- Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
| | - Huda Zahid
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Nora R Vail
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Daniel A Harki
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.,Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
| | - Grover P Miller
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 W. Markham Street, Little Rock, Arkansas 72205, United States
| | - Joseph J Topczewski
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.,Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
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188
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Harrison LA, Atkinson SJ, Bassil A, Chung CW, Grandi P, Gray JRJ, Levernier E, Lewis A, Lugo D, Messenger C, Michon AM, Mitchell DJ, Preston A, Prinjha RK, Rioja I, Seal JT, Taylor S, Wall ID, Watson RJ, Woolven JM, Demont EH. Identification of a Series of N-Methylpyridine-2-carboxamides as Potent and Selective Inhibitors of the Second Bromodomain (BD2) of the Bromo and Extra Terminal Domain (BET) Proteins. J Med Chem 2021; 64:10742-10771. [PMID: 34232650 DOI: 10.1021/acs.jmedchem.0c02155] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Domain-specific BET bromodomain ligands represent an attractive target for drug discovery with the potential to unlock the therapeutic benefits of antagonizing these proteins without eliciting the toxicological aspects seen with pan-BET inhibitors. While we have reported several distinct classes of BD2 selective compounds, namely, GSK620, GSK549, and GSK046, only GSK046 shows high aqueous solubility. Herein, we describe the lead optimization of a further class of highly soluble compounds based upon a picolinamide chemotype. Focusing on achieving >1000-fold selectivity for BD2 over BD1 ,while retaining favorable physical chemical properties, compound 36 was identified as being 2000-fold selective for BD2 over BD1 (Brd4 data) with >1 mg/mL solubility in FaSSIF media. 36 represents a valuable new in vivo ready molecule for the exploration of the BD2 phenotype.
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Affiliation(s)
- Lee A Harrison
- Epigenetics Discovery Performance Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Stephen J Atkinson
- Epigenetics Discovery Performance Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Anna Bassil
- Epigenetics Discovery Performance Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Chun-Wa Chung
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paola Grandi
- IVIVT Cellzome, Platform Technology and Science, GlaxoSmithKline, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - James R J Gray
- Quantitative Pharmacology, Immunoinflammation Therapy Area Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Etienne Levernier
- Epigenetics Discovery Performance Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Antonia Lewis
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - David Lugo
- Quantitative Pharmacology, Immunoinflammation Therapy Area Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Cassie Messenger
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Anne-Marie Michon
- IVIVT Cellzome, Platform Technology and Science, GlaxoSmithKline, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Darren J Mitchell
- Epigenetics Discovery Performance Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Alex Preston
- Epigenetics Discovery Performance Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Rab K Prinjha
- Epigenetics Discovery Performance Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Inmaculada Rioja
- Epigenetics Discovery Performance Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Jonathan T Seal
- Epigenetics Discovery Performance Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Simon Taylor
- Quantitative Pharmacology, Immunoinflammation Therapy Area Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Ian D Wall
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Robert J Watson
- Epigenetics Discovery Performance Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - James M Woolven
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Emmanuel H Demont
- Epigenetics Discovery Performance Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
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189
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Wang X, Kutschat AP, Yamada M, Prokakis E, Böttcher P, Tanaka K, Doki Y, Hamdan FH, Johnsen SA. Bromodomain protein BRDT directs ΔNp63 function and super-enhancer activity in a subset of esophageal squamous cell carcinomas. Cell Death Differ 2021; 28:2207-2220. [PMID: 33658703 PMCID: PMC8257622 DOI: 10.1038/s41418-021-00751-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 12/21/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is the predominant subtype of esophageal cancer with a particularly high prevalence in certain geographical regions and a poor prognosis with a 5-year survival rate of 15-25%. Despite numerous studies characterizing the genetic and transcriptomic landscape of ESCC, there are currently no effective targeted therapies. In this study, we used an unbiased screening approach to uncover novel molecular precision oncology targets for ESCC and identified the bromodomain and extraterminal (BET) family member bromodomain testis-specific protein (BRDT) to be uniquely expressed in a subgroup of ESCC. Experimental studies revealed that BRDT expression promotes migration but is dispensable for cell proliferation. Further mechanistic insight was gained through transcriptome analyses, which revealed that BRDT controls the expression of a subset of ΔNp63 target genes. Epigenome and genome-wide occupancy studies, combined with genome-wide chromatin interaction studies, revealed that BRDT colocalizes and interacts with ΔNp63 to drive a unique transcriptional program and modulate cell phenotype. Our data demonstrate that these genomic regions are enriched for super-enhancers that loop to critical ΔNp63 target genes related to the squamous phenotype such as KRT14, FAT2, and PTHLH. Interestingly, BET proteolysis-targeting chimera, MZ1, reversed the activation of these genes. Importantly, we observed a preferential degradation of BRDT by MZ1 compared with BRD2, BRD3, and BRD4. Taken together, these findings reveal a previously unknown function of BRDT in ESCC and provide a proof-of-concept that BRDT may represent a novel therapeutic target in cancer.
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Affiliation(s)
- Xin Wang
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Ana P Kutschat
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Moyuru Yamada
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Evangelos Prokakis
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Patricia Böttcher
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Koji Tanaka
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Feda H Hamdan
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Steven A Johnsen
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany.
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA.
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190
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Guest EE, Pickett SD, Hirst JD. Structural variation of protein-ligand complexes of the first bromodomain of BRD4. Org Biomol Chem 2021; 19:5632-5641. [PMID: 34105560 DOI: 10.1039/d1ob00658d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The bromodomain-containing protein 4 (BRD4), a member of the bromodomain and extra-terminal domain (BET) family, plays a key role in several diseases, especially cancers. With increased interest in BRD4 as a therapeutic target, many X-ray crystal structures of the protein in complex with small molecule inhibitors are publicly available over the recent decade. In this study, we use this structural information to investigate the conformations of the first bromodomain (BD1) of BRD4. Structural alignment of 297 BRD4-BD1 complexes shows a high level of similarity between the structures of BRD4-BD1, regardless of the bound ligand. We employ WONKA, a tool for detailed analyses of protein binding sites, to compare the active site of over 100 of these crystal structures. The positions of key binding site residues show a high level of conformational similarity, with the exception of Trp81. A focused analysis on the highly conserved water network in the binding site of BRD4-BD1 is performed to identify the positions of these water molecules across the crystal structures. The importance of the water network is illustrated using molecular docking and absolute free energy perturbation simulations. 82% of the ligand poses were better predicted when including water molecules as part of the receptor. Our analysis provides guidance for the design of new BRD4-BD1 inhibitors and the selection of the best structure of BRD4-BD1 to use in structure-based drug design, an important approach for faster and more cost-efficient lead discovery.
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Affiliation(s)
- Ellen E Guest
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Stephen D Pickett
- GlaxoSmithKline R&D Pharmaceuticals, Computational Chemistry, Stevenage, UK
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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191
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Zhang H, Zhang M, Zheng YC, Zhang JG, Xu H. The design, synthesis and cellular imaging of a tumor-anchored, potent and cell-permeable BRD4-targeted fluorescent ligands. Bioorg Chem 2021; 114:105120. [PMID: 34216895 DOI: 10.1016/j.bioorg.2021.105120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/17/2021] [Accepted: 06/20/2021] [Indexed: 12/13/2022]
Abstract
Bromodomain 4 (BRD4) proteins play an important role in histone post-translational modifications and facilitate several important physiological and pathological processes, including cancers. The inhibition of BRD4 by small molecule inhibitors shows promise as a therapeutic strategy for cancer treatment. However, their clinical applications were limited, which is largely hampered by off-target effects-induced toxicity. We herein report the design, synthesis, and cellular imaging of a set of tumor-anchored and BRD4-targeted fluorescent ligands by introducing selective and potent BRD4 inhibitor into different fluorophores via variable linkers. One of the fluorescent conjugates (compound 6) was demonstrated to be cell-permeable and low cytotoxic, preferentially accumulated in cancer cells, and display pronounced fluorescent signal. More importantly, 6 was identified to show specific BRD4 engagement in the cellular content. Collectively, this study provides a pathway for developing labeled BRD4 ligands and highlights that compound 6 may represent a valuable tool for explorative learning and target delivery study of BRD4.
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Affiliation(s)
- Hang Zhang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Mingliang Zhang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Yi-Chao Zheng
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Jin-Ge Zhang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Haiwei Xu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China.
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192
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Bai P, Lan Y, Wang H, Liu Y, Striar R, Yuan G, Afshar S, Zagaroli JS, Tocci DR, Langan AG, Wang C. Synthesis and Characterization of a Positron Emission Tomography Imaging Probe Selectively Targeting the Second Bromodomain of Bromodomain Protein BRD4. Bioconjug Chem 2021; 32:1711-1718. [PMID: 34139120 DOI: 10.1021/acs.bioconjchem.1c00245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Two tandem bromodomains (BD1 and BD2) of bromodomain and extraterminal domain (BET) family proteins have shown distinct roles in mediating gene transcription and expression. Inhibitors that interact with a specific bromodomain may contribute to a specific therapeutic potential with fewer side effects. However, little is known about this disease-related target. Positron emission tomography (PET) imaging could allow us to achieve in-depth knowledge of the BD2 bromodomain. Herein we describe the radiosynthesis and evaluation of [11C]1 as a BRD4 BD2 bromodomain PET imaging radioligand. Our preliminary PET imaging results in rodents demonstrated that [11C]1 had suitable biodistribution in peripheral organs and tissues. Further blocking studies indicated that [11C]1 had good binding specificity toward the BD2 bromodomain. This study may pave the way for the development of a PET radioligand specifically targeting BD1/2 bromodomains as well as for the biological mechanism investigation of BD1/2 bromodomains.
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193
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Donczew R, Hahn S. BET family members Bdf1/2 modulate global transcription initiation and elongation in Saccharomyces cerevisiae. eLife 2021; 10:e69619. [PMID: 34137374 PMCID: PMC8266393 DOI: 10.7554/elife.69619] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/16/2021] [Indexed: 01/10/2023] Open
Abstract
Human bromodomain and extra-terminal domain (BET) family members are promising targets for therapy of cancer and immunoinflammatory diseases, but their mechanisms of action and functional redundancies are poorly understood. Bdf1/2, yeast homologues of the human BET factors, were previously proposed to target transcription factor TFIID to acetylated histone H4, analogous to bromodomains that are present within the largest subunit of metazoan TFIID. We investigated the genome-wide roles of Bdf1/2 and found that their important contributions to transcription extend beyond TFIID function as transcription of many genes is more sensitive to Bdf1/2 than to TFIID depletion. Bdf1/2 co-occupy the majority of yeast promoters and affect preinitiation complex formation through recruitment of TFIID, Mediator, and basal transcription factors to chromatin. Surprisingly, we discovered that hypersensitivity of genes to Bdf1/2 depletion results from combined defects in transcription initiation and early elongation, a striking functional similarity to human BET proteins, most notably Brd4. Our results establish Bdf1/2 as critical for yeast transcription and provide important mechanistic insights into the function of BET proteins in all eukaryotes.
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Affiliation(s)
- Rafal Donczew
- Fred Hutchinson Cancer Research Center, Division of Basic SciencesSeattleUnited States
| | - Steven Hahn
- Fred Hutchinson Cancer Research Center, Division of Basic SciencesSeattleUnited States
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194
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Choi HI, An GY, Baek M, Yoo E, Chai JC, Lee YS, Jung KH, Chai YG. BET inhibitor suppresses migration of human hepatocellular carcinoma by inhibiting SMARCA4. Sci Rep 2021; 11:11799. [PMID: 34083693 PMCID: PMC8175750 DOI: 10.1038/s41598-021-91284-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 05/24/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent and poorly responsive cancers worldwide. Bromodomain and extraterminal (BET) inhibitors, such as JQ1 and OTX-015, inhibit BET protein binding to acetylated residues in histones. However, the physiological mechanisms and regulatory processes of BET inhibition in HCC remain unclear. To explore BET inhibitors’ potential role in the molecular mechanisms underlying their anticancer effects in HCC, we analyzed BET inhibitor-treated HCC cells’ gene expression profiles with RNA-seq and bioinformatics analysis. BET inhibitor treatment significantly downregulated genes related to bromodomain-containing proteins 4 (BRD4), such as ACSL5, SLC38A5, and ICAM2. Importantly, some cell migration-related genes, including AOC3, CCR6, SSTR5, and SCL7A11, were significantly downregulated. Additionally, bioinformatics analysis using Ingenuity Knowledge Base Ingenuity Pathway Analysis (IPA) revealed that SMARCA4 regulated migration response molecules. Furthermore, knockdown of SMARCA4 gene expression by siRNA treatment significantly reduced cell migration and the expression of migration-related genes. In summary, our results indicated that BET inhibitor treatment in HCC cell lines reduces cell migration through the downregulation of SMARCA4.
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Affiliation(s)
- Hae In Choi
- Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea
| | - Ga Yeong An
- Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea
| | - Mina Baek
- Institute of Natural Science and Technology, Hanyang University, Ansan, 15588, Republic of Korea.,Department of Molecular and Life Science, Hanyang University, Ansan, 15588, Republic of Korea
| | - Eunyoung Yoo
- Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea
| | - Jin Choul Chai
- College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Young Seek Lee
- College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Kyoung Hwa Jung
- Convergence Technology Campus of Korea Polytechnic II, Incheon, 21417, Republic of Korea. .,Department of Biopharmaceutical System, Gwangmyeong Convergence Technology Campus of Korea Polytechnic II, Gwangmyeong , 14222, Republic of Korea.
| | - Young Gyu Chai
- Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea. .,Department of Molecular and Life Science, Hanyang University, Ansan, 15588, Republic of Korea.
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195
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Green AI, Burslem GM. Focused Libraries for Epigenetic Drug Discovery: The Importance of Isosteres. J Med Chem 2021; 64:7231-7240. [PMID: 34042449 DOI: 10.1021/acs.jmedchem.1c00592] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epigenetic drug discovery provides a wealth of opportunities for the discovery of new therapeutics but has been hampered by low hit rates, frequent identification of false-positives, and poor synthetic tractability. A key reason for this is that few screening collections consider the unique requirements of epigenetic targets despite significant medicinal chemistry interest. Here we analyze the suitability of some commercially available screening collections in the context of epigenetic drug discovery, with a particular focus on lysine post-translational modifications, and show that even privileged motifs found in U.S. Food and Drug Administration (FDA)-approved drugs are not present in these collections. We propose that the incorporation of epigenetic bioisosteres should become central in the design of new focused screening collections and highlight some opportunities for the development of synthetic methods which may improve the tractability of hit molecules.
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Affiliation(s)
- Adam I Green
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - George M Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Department of Cancer Biology and Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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196
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Epigenetic Modulation of Radiation-Induced Diacylglycerol Kinase Alpha Expression Prevents Pro-Fibrotic Fibroblast Response. Cancers (Basel) 2021; 13:cancers13102455. [PMID: 34070078 PMCID: PMC8158145 DOI: 10.3390/cancers13102455] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/04/2021] [Accepted: 05/12/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary To reduce long-term fibrosis risk after radiotherapy, we demonstrated with different experimental approaches that modulation of the epigenetic pattern at the DGKA enhancer can attenuate pro-fibrotic reactions in human fibroblasts. We used (epi)genomic editing of the DGKA enhancer and administration of various epigenetic drugs and were able to modulate radiation-induced expression of DGKA and pro-fibrotic collagens. Based on our results, clinical application of bromodomain inhibitors will open promising ways to epigenetically modulate DGKA expression and might provide novel therapeutic options to prevent or even reverse radiotherapy-induced fibrotic reactions. Abstract Radiotherapy, a common component in cancer treatment, can induce adverse effects including fibrosis in co-irradiated tissues. We previously showed that differential DNA methylation at an enhancer of diacylglycerol kinase alpha (DGKA) in normal dermal fibroblasts is associated with radiation-induced fibrosis. After irradiation, the transcription factor EGR1 is induced and binds to the hypomethylated enhancer, leading to increased DGKA and pro-fibrotic marker expression. We now modulated this DGKA induction by targeted epigenomic and genomic editing of the DGKA enhancer and administering epigenetic drugs. Targeted DNA demethylation of the DGKA enhancer in HEK293T cells resulted in enrichment of enhancer-related histone activation marks and radiation-induced DGKA expression. Mutations of the EGR1-binding motifs decreased radiation-induced DGKA expression in BJ fibroblasts and caused dysregulation of multiple fibrosis-related pathways. EZH2 inhibitors (GSK126, EPZ6438) did not change radiation-induced DGKA increase. Bromodomain inhibitors (CBP30, JQ1) suppressed radiation-induced DGKA and pro-fibrotic marker expression. Similar drug effects were observed in donor-derived fibroblasts with low DNA methylation. Overall, epigenomic manipulation of DGKA expression may offer novel options for a personalized treatment to prevent or attenuate radiotherapy-induced fibrosis.
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Design, synthesis, biological evaluation, and molecular docking of 1,7-dibenzyl-substituted theophylline derivatives as novel BRD4-BD1-selective inhibitors. Med Chem Res 2021. [DOI: 10.1007/s00044-021-02737-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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198
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Henley MJ, Koehler AN. Advances in targeting 'undruggable' transcription factors with small molecules. Nat Rev Drug Discov 2021; 20:669-688. [PMID: 34006959 DOI: 10.1038/s41573-021-00199-0] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2021] [Indexed: 02/07/2023]
Abstract
Transcription factors (TFs) represent key biological players in diseases including cancer, autoimmunity, diabetes and cardiovascular disease. However, outside nuclear receptors, TFs have traditionally been considered 'undruggable' by small-molecule ligands due to significant structural disorder and lack of defined small-molecule binding pockets. Renewed interest in the field has been ignited by significant progress in chemical biology approaches to ligand discovery and optimization, especially the advent of targeted protein degradation approaches, along with increasing appreciation of the critical role a limited number of collaborators play in the regulation of key TF effector genes. Here, we review current understanding of TF-mediated gene regulation, discuss successful targeting strategies and highlight ongoing challenges and emerging approaches to address them.
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Affiliation(s)
- Matthew J Henley
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,The Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Angela N Koehler
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,The Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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199
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Enhancer rewiring in tumors: an opportunity for therapeutic intervention. Oncogene 2021; 40:3475-3491. [PMID: 33934105 DOI: 10.1038/s41388-021-01793-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/30/2021] [Accepted: 04/12/2021] [Indexed: 02/06/2023]
Abstract
Enhancers are cis-regulatory sequences that fine-tune expression of their target genes in a spatiotemporal manner. They are recognized by sequence-specific transcription factors, which in turn recruit transcriptional coactivators that facilitate transcription by promoting assembly and activation of the basal transcriptional machinery. Their functional importance is underscored by the fact that they are often the target of genetic and nongenetic events in human disease that disrupt their sequence, interactome, activation potential, and/or chromatin environment. Dysregulation of transcription and addiction to transcriptional effectors that interact with and modulate enhancer activity are common features of cancer cells and are amenable to therapeutic intervention. Here, we discuss the current knowledge on enhancer biology, the broad spectrum of mechanisms that lead to their malfunction in tumor cells, and recent progress in developing drugs that efficaciously target their dependencies.
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200
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Vershinin Z, Feldman M, Werner T, Weil LE, Kublanovsky M, Abaev-Schneiderman E, Sklarz M, Lam EYN, Alasad K, Picaud S, Rotblat B, McAdam RA, Chalifa-Caspi V, Bantscheff M, Chapman T, Lewis HD, Filippakopoulos P, Dawson MA, Grandi P, Prinjha RK, Levy D. BRD4 methylation by the methyltransferase SETD6 regulates selective transcription to control mRNA translation. SCIENCE ADVANCES 2021; 7:7/22/eabf5374. [PMID: 34039605 PMCID: PMC8153730 DOI: 10.1126/sciadv.abf5374] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/06/2021] [Indexed: 05/14/2023]
Abstract
The transcriptional coactivator BRD4 has a fundamental role in transcription regulation and thus became a promising epigenetic therapeutic candidate to target diverse pathologies. However, the regulation of BRD4 by posttranslational modifications has been largely unexplored. Here, we show that BRD4 is methylated on chromatin at lysine-99 by the protein lysine methyltransferase SETD6. BRD4 methylation negatively regulates the expression of genes that are involved in translation and inhibits total mRNA translation in cells. Mechanistically, we provide evidence that supports a model where BRD4 methylation by SETD6 does not have a direct role in the association with acetylated histone H4 at chromatin. However, this methylation specifically determines the recruitment of the transcription factor E2F1 to selected target genes that are involved in mRNA translation. Together, our findings reveal a previously unknown molecular mechanism for BRD4 methylation-dependent gene-specific targeting, which may serve as a new direction for the development of therapeutic applications.
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Affiliation(s)
- Zlata Vershinin
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Michal Feldman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Thilo Werner
- GSK Cellzome GmbH, Functional Genomics R&D, 69117 Heidelberg, Germany
| | - Lital Estrella Weil
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Margarita Kublanovsky
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Elina Abaev-Schneiderman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Menachem Sklarz
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Enid Y N Lam
- Sir Peter MacCallum Department of Oncology and Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Khawla Alasad
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er-Sheva 84105, Israel
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Barak Rotblat
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er-Sheva 84105, Israel
| | - Ruth A McAdam
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Vered Chalifa-Caspi
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Marcus Bantscheff
- GSK Cellzome GmbH, Functional Genomics R&D, 69117 Heidelberg, Germany
| | - Trevor Chapman
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Huw D Lewis
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Mark A Dawson
- Sir Peter MacCallum Department of Oncology and Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Paola Grandi
- GSK Cellzome GmbH, Functional Genomics R&D, 69117 Heidelberg, Germany
| | - Rab K Prinjha
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Dan Levy
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel.
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
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