1
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A monocyte-keratinocyte-derived co-culture assay accurately identifies efficacies of BET inhibitors as therapeutic candidates for psoriasiform dermatitis. J Dermatol Sci 2020; 100:31-38. [PMID: 32900573 DOI: 10.1016/j.jdermsci.2020.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/15/2020] [Accepted: 08/11/2020] [Indexed: 11/21/2022]
Abstract
BACKGROUND Bromodomain and extra-terminal (BET) proteins perform key roles in epigenetic control of gene expression that is involved in inflammatory conditions, including psoriasiform dermatitis (PsD). Predicting which (of many potential available BET inhibitors) will be effective in vivo is challenging. OBJECTIVE We determine if a novel in vitro assay that includes two critical cell types involved in human psoriasis can predict the therapeutic potential of specific BET inhibitors in vivo. METHODS An in vitro model consisting of U-937 and HaCaT cell co-culture was created to screen small molecule BET antagonists for inhibition of cutaneous inflammatory genes. Efficacious BET inhibitors were tested in a mouse imiquimod (IMQ)-induced PsD model. RESULTS In the co-culture system, HaCaT cells exhibited a marked increase in the secretion of a characteristic set of proinflammatory and Th17-associated cytokines. Of the ten commercially-available small molecules targeting BET proteins assayed, most compounds exhibited inhibitory functions at 1 μM against inflammatory activation, but responded variably at lower concentrations. OTX015, a typical representative for most of the compounds, barely inhibited the inflammatory reactions at 0.1 μM. By contrast, ABBV075 was effective in concentrations as low as 0.01 μM. While oral administration OTX015 in IMQ-treated mice reduced disease severity, ABBV075 equally decreased the symptoms and molecular and cellular severity markers at one-tenth of the minimal dosing required for OTX015. CONCLUSION In vitro screening system combined with an in vivo animal model, can serve as a convenient pre-clinical screening tool for the selection of BET inhibitors (and possibly other drugs) that may have clinical potential in psoriasis therapy.
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2
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Alonso VL, Tavernelli LE, Pezza A, Cribb P, Ritagliati C, Serra E. Aim for the Readers! Bromodomains As New Targets Against Chagas’ Disease. Curr Med Chem 2019; 26:6544-6563. [DOI: 10.2174/0929867325666181031132007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 12/11/2022]
Abstract
Bromodomains recognize and bind acetyl-lysine residues present in histone and non-histone
proteins in a specific manner. In the last decade they have raised as attractive targets for drug discovery
because the miss-regulation of human bromodomains was discovered to be involved in the development
of a large spectrum of diseases. However, targeting eukaryotic pathogens bromodomains
continues to be almost unexplored. We and others have reported the essentiality of diverse bromodomain-
containing proteins in protozoa, offering a new opportunity for the development of antiparasitic
drugs, especially for Trypansoma cruzi, the causative agent of Chagas’ disease. Mammalian bromodomains
were classified in eight groups based on sequence similarity but parasitic bromodomains are very
divergent proteins and are hard to assign them to any of these groups, suggesting that selective inhibitors
can be obtained. In this review, we describe the importance of lysine acetylation and bromodomains
in T. cruzi as well as the current knowledge on mammalian bromodomains. Also, we summarize
the myriad of small-molecules under study to treat different pathologies and which of them have been
tested in trypanosomatids and other protozoa. All the information available led us to propose that
T. cruzi bromodomains should be considered as important potential targets and the search for smallmolecules
to inhibit them should be empowered.
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Affiliation(s)
- Victoria Lucia Alonso
- Facultad de Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | | | - Alejandro Pezza
- Instituto de Biologia Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
| | - Pamela Cribb
- Instituto de Biologia Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
| | - Carla Ritagliati
- Instituto de Biologia Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
| | - Esteban Serra
- Instituto de Biologia Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
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3
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Zhang D, Leal AS, Carapellucci S, Zydeck K, Sporn MB, Liby KT. Chemoprevention of Preclinical Breast and Lung Cancer with the Bromodomain Inhibitor I-BET 762. Cancer Prev Res (Phila) 2017; 11:143-156. [PMID: 29246957 DOI: 10.1158/1940-6207.capr-17-0264] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/23/2017] [Accepted: 12/08/2017] [Indexed: 11/16/2022]
Abstract
Breast cancer and lung cancer remain the top two leading causes of cancer-related deaths in women. Because of limited success in reducing the high mortality of these diseases, new drugs and approaches are desperately needed. Cancer prevention is one such promising strategy that is effective in both preclinical and clinical studies. I-BET 762 is a new bromodomain inhibitor that reversibly targets BET (bromodomain and extraterminal) proteins and impairs their ability to bind to acetylated lysines on histones, thus interrupting downstream transcription. This inhibitor has anti-inflammatory effects and induces growth arrest in many cancers and is currently under clinical trials for treatment of cancer. However, few studies have investigated the chemopreventive effects of bromodomain inhibitors. Here, we found that I-BET 762 significantly delayed tumor development in preclinical breast and lung cancer mouse models. This drug not only induced growth arrest and downregulated c-Myc, pSTAT3, and pERK protein expression in tumor cells in vitro and in vivo but also altered immune populations in different organs. These results demonstrate the promising potential of using I-BET 762 for cancer prevention and suggest the striking effects of I-BET 762 are the result of targeting both tumor cells and the tumor microenvironment. Cancer Prev Res; 11(3); 143-56. ©2017 AACR.
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Affiliation(s)
- Di Zhang
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Ana S Leal
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Sarah Carapellucci
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Kayla Zydeck
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Michael B Sporn
- Department of Pharmacology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
| | - Karen T Liby
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan.
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4
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Na Z, Pan S, Uttamchandani M, Yao SQ. Protein-Protein Interaction Inhibitors of BRCA1 Discovered Using Small Molecule Microarrays. Methods Mol Biol 2017; 1518:139-156. [PMID: 27873205 DOI: 10.1007/978-1-4939-6584-7_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microarray screening technology has transformed the life sciences arena over the last decade. The platform is widely used in the area of mapping interaction networks, to molecular fingerprinting and small molecular inhibitor discovery. The technique has significantly impacted both basic and applied research. The microarray platform can likewise enable high-throughput screening and discovery of protein-protein interaction (PPI) inhibitors. Herein we demonstrate the application of microarray-guided PPI inhibitor discovery, using human BRCA1 as an example. Mutations in BRCA1 have been implicated in ~50 % of hereditary breast cancers. By targeting the (BRCT)2 domain, we showed compound 15a and its prodrug 15b inhibited BRCA1 activities in tumor cells. Unlike previously reported peptide-based PPI inhibitors of BRCA1, the compounds identified could be directly administered to tumor cells, thus making them useful in targeting BRCA1/PARP-related pathways involved in DNA damage and repair response, for cancer therapy.
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Affiliation(s)
- Zhenkun Na
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Mahesh Uttamchandani
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.,Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore, Singapore
| | - Shao Q Yao
- Department of Chemistry, Faculty of Science, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.
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5
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Bhattacharjee D, Shenoy S, Bairy KL. DNA Methylation and Chromatin Remodeling: The Blueprint of Cancer Epigenetics. SCIENTIFICA 2016; 2016:6072357. [PMID: 27119045 PMCID: PMC4826949 DOI: 10.1155/2016/6072357] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/10/2016] [Indexed: 06/05/2023]
Abstract
Epigenetics deals with the interactions between genes and the immediate cellular environment. These interactions go a long way in shaping up each and every person's individuality. Further, reversibility of epigenetic interactions may offer a dynamic control over the expression of various critical genes. Thus, tweaking the epigenetic machinery may help cause or cure diseases, especially cancer. Therefore, cancer epigenetics, especially at a molecular level, needs to be scrutinised closely, as it could potentially serve as the future pharmaceutical goldmine against neoplastic diseases. However, in view of its rapidly enlarging scope of application, it has become difficult to keep abreast of scientific information coming out of various epigenetic studies directed against cancer. Using this review, we have attempted to shed light on two of the most important mechanisms implicated in cancer, that is, DNA (deoxyribonucleic acid) methylation and histone modifications, and their place in cancer pathogenesis. Further, we have attempted to take stock of the new epigenetic drugs that have emerged onto the market as well as those in the pipeline that offer hope in mankind's fight against cancer.
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Affiliation(s)
- Dipanjan Bhattacharjee
- Department of Pharmacology, Kasturba Medical College, Manipal University, Manipal, Karnataka 576104, India
| | - Smita Shenoy
- Department of Pharmacology, Kasturba Medical College, Manipal University, Manipal, Karnataka 576104, India
| | - Kurady Laxminarayana Bairy
- Department of Pharmacology, Kasturba Medical College, Manipal University, Manipal, Karnataka 576104, India
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6
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Affiliation(s)
- Guangtao Zhang
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai , 1425 Madison Avenue, New York, New York 10029, United States
| | - Steven G Smith
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai , 1425 Madison Avenue, New York, New York 10029, United States
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai , 1425 Madison Avenue, New York, New York 10029, United States
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7
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Urick AK, Hawk LML, Cassel MK, Mishra NK, Liu S, Adhikari N, Zhang W, dos Santos CO, Hall JL, Pomerantz WCK. Dual Screening of BPTF and Brd4 Using Protein-Observed Fluorine NMR Uncovers New Bromodomain Probe Molecules. ACS Chem Biol 2015; 10:2246-56. [PMID: 26158404 PMCID: PMC4858447 DOI: 10.1021/acschembio.5b00483] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bromodomain-containing protein dysregulation is linked to cancer, diabetes, and inflammation. Selective inhibition of bromodomain function is a newly proposed therapeutic strategy. We describe a (19)F NMR dual screening method for small molecule discovery using fluorinated tryptophan resonances on two bromodomain-containing proteins. The chemical shift dispersion of (19)F resonances within fluorine-labeled proteins enables the simultaneous analysis of two fluorinated bromodomains by NMR. A library of 229 small molecules was screened against the first bromodomain of Brd4 and the BPTF bromodomain. We report the first small molecule selective for BPTF over Brd4, termed AU1. The Kd = 2.8 μM for AU1, which is active in a cell-based reporter assay. No binding is detected with Brd4. Three new Brd4 inhibitors with submicromolar affinity were also discovered. Brd4 hits were validated in a thermal stability assay and potency determined via fluorescence anisotropy. The speed, ease of interpretation, and low protein concentration needed for protein-observed (19)F NMR experiments in a multiprotein format offers a new method to discover and characterize selective ligands for bromodomain-containing proteins.
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Affiliation(s)
- Andrew K. Urick
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE Minneapolis, MN 55455
| | - Laura M. L. Hawk
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE Minneapolis, MN 55455
| | - Melissa K. Cassel
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE Minneapolis, MN 55455
| | - Neeraj K. Mishra
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE Minneapolis, MN 55455
| | - Shuai Liu
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA 02125
| | - Neeta Adhikari
- Lillehei Heart Institute, Department of Medicine, 2231 6thStreet SE, Minneapolis, MN 55455
| | - Wei Zhang
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA 02125
| | | | - Jennifer L. Hall
- Lillehei Heart Institute, Department of Medicine, 2231 6thStreet SE, Minneapolis, MN 55455
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8
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Jung M, Gelato KA, Fernández-Montalván A, Siegel S, Haendler B. Targeting BET bromodomains for cancer treatment. Epigenomics 2015; 7:487-501. [PMID: 26077433 DOI: 10.2217/epi.14.91] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The bromodomain and extraterminal (BET) subfamily of bromodomain-containing proteins has emerged in the last few years as an exciting, novel target group. BRD4, the best studied BET protein, is implicated in a number of hematological and solid tumors. This is linked to its role in modulating transcription elongation of essential genes involved in cell cycle and apoptosis such as c-Myc and BCL2. Potent BET inhibitors with promising antitumor efficacy in a number of preclinical cancer models have been identified in recent years. This led to clinical studies focusing mostly on the treatment of leukemia and lymphoma, and first encouraging signs of efficacy have already been reported. Here we discuss the biology of BRD4, its known interaction partners and implication in different tumor types. Further, we summarize the current knowledge on BET bromodomain inhibitors.
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Affiliation(s)
- Marie Jung
- Global Drug Discovery, Bayer Pharma AG, D-13353 Berlin, Germany.,Institute of Chemistry & Biochemistry, Free University, D-14195 Berlin, Germany
| | - Kathy A Gelato
- Global Drug Discovery, Bayer Pharma AG, D-13353 Berlin, Germany
| | | | - Stephan Siegel
- Global Drug Discovery, Bayer Pharma AG, D-13353 Berlin, Germany
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9
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Jankowska AM, Millward CL, Caldwell CW. The potential of DNA modifications as biomarkers and therapeutic targets in oncology. Expert Rev Mol Diagn 2015; 15:1325-37. [PMID: 26394702 DOI: 10.1586/14737159.2015.1084229] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Knowledge of epigenetic alterations in cancer is rapidly increasing due to the development of genome-wide techniques for their identification. DNA methylation is the best understood epigenetic adaptation and disease-specific aberrant DNA methylation is a well-recognized hallmark of cancer. Recently, novel modifications, including 5-hydroxymethylation have been described, adding a new layer of complexity to understanding the epigenetic machinery and their role in cancer. There have been significant advances in techniques for the discovery and validation of DNA methylation- and hydroxymethylation-based biomarkers, each with its own advantages and limitations. With the advent of new profiling technologies, the ever-growing list of genes that show epigenetic alterations, particularly DNA methylation, emphasizes the role of these changes for early detection, diagnosis, prognosis, and prediction of response to therapies. While there are yet many challenges to the effective implementation of DNA-methylation/hydroxymethylation-based biomarkers and epigenetic therapeutics, the field is moving closer to the goal of defining personalized medicine.
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Affiliation(s)
- Anna M Jankowska
- a Lilly Research Laboratories, Eli Lilly and Company Corporate Center, Indianapolis, IN 46285 USA
| | - Carl L Millward
- a Lilly Research Laboratories, Eli Lilly and Company Corporate Center, Indianapolis, IN 46285 USA
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10
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Ran X, Zhao Y, Liu L, Bai L, Yang CY, Zhou B, Meagher JL, Chinnaswamy K, Stuckey JA, Wang S. Structure-Based Design of γ-Carboline Analogues as Potent and Specific BET Bromodomain Inhibitors. J Med Chem 2015; 58:4927-39. [PMID: 26080064 DOI: 10.1021/acs.jmedchem.5b00613] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Small-molecule inhibitors of bromodomain and extra terminal proteins (BET), including BRD2, BRD3, and BRD4 proteins have therapeutic potential for the treatment of human cancers and other diseases and conditions. In this paper, we report the design, synthesis, and evaluation of γ-carboline-containing compounds as a new class of small-molecule BET inhibitors. The most potent inhibitor (compound 18, RX-37) obtained from this study binds to BET bromodomain proteins (BRD2, BRD3, and BRD4) with Ki values of 3.2-24.7 nM and demonstrates high selectivity over other non-BET bromodomain-containing proteins. Compound 18 potently and selectively inhibits cell growth in human acute leukemia cell lines harboring the rearranged mixed lineage leukemia 1 gene. We have determined a cocrystal structure of 18 in complex with BRD4 BD2 at 1.4 Å resolution, which provides a solid structural basis for the compound's high binding affinity and for its further structure-based optimization. Compound 18 represents a promising lead compound for the development of a new class of therapeutics for the treatment of human cancer and other conditions.
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Affiliation(s)
- Xu Ran
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yujun Zhao
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Liu Liu
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Longchuan Bai
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Chao-Yie Yang
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bing Zhou
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jennifer L Meagher
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Krishnapriya Chinnaswamy
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jeanne A Stuckey
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Shaomeng Wang
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
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11
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Marchand JR, Caflisch A. Binding Mode of Acetylated Histones to Bromodomains: Variations on a Common Motif. ChemMedChem 2015; 10:1327-33. [PMID: 26033856 DOI: 10.1002/cmdc.201500141] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 11/09/2022]
Abstract
Bromodomains, epigenetic readers that recognize acetylated lysine residues in histone tails, are potential drug targets in cancer and inflammation. Herein we review the crystal structures of human bromodomains in complex with histone tails and analyze the main interaction motifs. The histone backbone is extended and occupies, in one of the two possible orientations, the bromodomain surface groove lined by the ZA and BC loops. The acetyl-lysine side chain is buried in the cavity between the four helices of the bromodomain, and its oxygen atom accepts hydrogen bonds from a structural water molecule and a conserved asparagine residue in the BC loop. In stark contrast to this common binding motif, a large variety of ancillary interactions emerge from our analysis. In 10 of 26 structures, a basic side chain (up to five residues up- or downstream in sequence with respect to the acetyl-lysine) interacts with the carbonyl groups of the C-terminal turn of helix αB. Furthermore, the complexes reveal many heterogeneous backbone hydrogen bonds (direct or water-bridged). These interactions contribute unselectively to the binding of acetylated histone tails to bromodomains, which provides further evidence that specific recognition is modulated by combinations of multiple histone modifications and multiple modules of the proteins involved in transcription.
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Affiliation(s)
- Jean-Rémy Marchand
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich (Switzerland)
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich (Switzerland).
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12
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Brand M, Measures AM, Wilson BG, Cortopassi WA, Alexander R, Höss M, Hewings DS, Rooney TPC, Paton RS, Conway SJ. Small molecule inhibitors of bromodomain-acetyl-lysine interactions. ACS Chem Biol 2015; 10:22-39. [PMID: 25549280 DOI: 10.1021/cb500996u] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bromodomains are protein modules that bind to acetylated lysine residues. Their interaction with histone proteins suggests that they function as "readers" of histone lysine acetylation, a component of the proposed "histone code". Bromodomain-containing proteins are often found as components of larger protein complexes with roles in fundamental cellular process including transcription. The publication of two potent ligands for the BET bromodomains in 2010 demonstrated that small molecules can inhibit the bromodomain-acetyl-lysine protein-protein interaction. These molecules display strong phenotypic effects in a number of cell lines and affect a range of cancers in vivo. This work stimulated intense interest in developing further ligands for the BET bromodomains and the design of ligands for non-BET bromodomains. Here we review the recent progress in the field with particular attention paid to ligand design, the assays employed in early ligand discovery, and the use of computational approaches to inform ligand design.
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Affiliation(s)
- Michael Brand
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Angelina M. Measures
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Brian G. Wilson
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Wilian A. Cortopassi
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | | | | | - David S. Hewings
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Timothy P. C. Rooney
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Robert S. Paton
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Stuart J. Conway
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
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13
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Ran T, Zhang Z, Liu K, Lu Y, Li H, Xu J, Xiong X, Zhang Y, Xu A, Lu S, Liu H, Lu T, Chen Y. Insight into the key interactions of bromodomain inhibitors based on molecular docking, interaction fingerprinting, molecular dynamics and binding free energy calculation. MOLECULAR BIOSYSTEMS 2015; 11:1295-304. [DOI: 10.1039/c4mb00723a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The interaction mechanism of bromodomain inhibitors was investigated using interaction fingerprinting and binding free energy based methods.
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14
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Cortés-Ciriano I, Ain QU, Subramanian V, Lenselink EB, Méndez-Lucio O, IJzerman AP, Wohlfahrt G, Prusis P, Malliavin TE, van Westen GJP, Bender A. Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00216d] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteochemometric (PCM) modelling is a computational method to model the bioactivity of multiple ligands against multiple related protein targets simultaneously.
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Affiliation(s)
- Isidro Cortés-Ciriano
- Unité de Bioinformatique Structurale
- Institut Pasteur and CNRS UMR 3825
- Structural Biology and Chemistry Department
- 75 724 Paris
- France
| | - Qurrat Ul Ain
- Unilever Centre for Molecular Informatics
- Department of Chemistry
- CB2 1EW Cambridge
- UK
| | | | - Eelke B. Lenselink
- Division of Medicinal Chemistry
- Leiden Academic Centre for Drug Research
- Leiden
- The Netherlands
| | - Oscar Méndez-Lucio
- Unilever Centre for Molecular Informatics
- Department of Chemistry
- CB2 1EW Cambridge
- UK
| | - Adriaan P. IJzerman
- Division of Medicinal Chemistry
- Leiden Academic Centre for Drug Research
- Leiden
- The Netherlands
| | - Gerd Wohlfahrt
- Computer-Aided Drug Design
- Orion Pharma
- FIN-02101 Espoo
- Finland
| | - Peteris Prusis
- Computer-Aided Drug Design
- Orion Pharma
- FIN-02101 Espoo
- Finland
| | - Thérèse E. Malliavin
- Unité de Bioinformatique Structurale
- Institut Pasteur and CNRS UMR 3825
- Structural Biology and Chemistry Department
- 75 724 Paris
- France
| | - Gerard J. P. van Westen
- European Molecular Biology Laboratory
- European Bioinformatics Institute
- Wellcome Trust Genome Campus
- Hinxton
- UK
| | - Andreas Bender
- Unilever Centre for Molecular Informatics
- Department of Chemistry
- CB2 1EW Cambridge
- UK
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15
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Mishra NK, Urick AK, Ember SWJ, Schönbrunn E, Pomerantz WC. Fluorinated aromatic amino acids are sensitive 19F NMR probes for bromodomain-ligand interactions. ACS Chem Biol 2014; 9:2755-60. [PMID: 25290579 PMCID: PMC4273984 DOI: 10.1021/cb5007344] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
We describe a 19F NMR method for detecting bromodomain–ligand
interactions using fluorine-labeled aromatic amino acids due to the
conservation of aromatic residues in the bromodomain binding site.
We test the sensitivity, accuracy, and speed of this method with small
molecule ligands (+)-JQ1, BI2536, Dinaciclib, TG101348, and acetaminophen
using three bromodomains Brd4, BrdT, and BPTF. Simplified 19F NMR spectra allowed for simultaneous testing of multiple bromodomains
to assess selectivity and identification of a new BPTF ligand. Fluorine
labeling only modestly affected the Brd4 structure and function assessed
by isothermal titration calorimetry, circular dichroism, and X-ray
crystallography. The speed, ease of interpretation, and low concentration
of protein needed for binding experiments affords a new method to
discover and characterize both native and new ligands.
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Affiliation(s)
- Neeraj K. Mishra
- Department
of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Andrew K. Urick
- Department
of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Stuart W. J. Ember
- Drug
Discovery Department, Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, Florida 33612, United States
| | - Ernst Schönbrunn
- Drug
Discovery Department, Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, Florida 33612, United States
| | - William C. Pomerantz
- Department
of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
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Gosmini R, Nguyen VL, Toum J, Simon C, Brusq JMG, Krysa G, Mirguet O, Riou-Eymard AM, Boursier EV, Trottet L, Bamborough P, Clark H, Chung CW, Cutler L, Demont EH, Kaur R, Lewis AJ, Schilling MB, Soden PE, Taylor S, Walker AL, Walker MD, Prinjha RK, Nicodème E. The discovery of I-BET726 (GSK1324726A), a potent tetrahydroquinoline ApoA1 up-regulator and selective BET bromodomain inhibitor. J Med Chem 2014; 57:8111-31. [PMID: 25249180 DOI: 10.1021/jm5010539] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Through their function as epigenetic readers of the histone code, the BET family of bromodomain-containing proteins regulate expression of multiple genes of therapeutic relevance, including those involved in tumor cell growth and inflammation. BET bromodomain inhibitors have profound antiproliferative and anti-inflammatory effects which translate into efficacy in oncology and inflammation models, and the first compounds have now progressed into clinical trials. The exciting biology of the BETs has led to great interest in the discovery of novel inhibitor classes. Here we describe the identification of a novel tetrahydroquinoline series through up-regulation of apolipoprotein A1 and the optimization into potent compounds active in murine models of septic shock and neuroblastoma. At the molecular level, these effects are produced by inhibition of BET bromodomains. X-ray crystallography reveals the interactions explaining the structure-activity relationships of binding. The resulting lead molecule, I-BET726, represents a new, potent, and selective class of tetrahydroquinoline-based BET inhibitors.
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Affiliation(s)
- Romain Gosmini
- Candidate Discovery, ‡Discovery Biology, §DMPK, GlaxoSmithKline Les Ulis, Centre de Recherches François Hyafil, GlaxoSmithKline R&D , 25 Avenue du Québec, 91140 Villebon-sur-Yvette, France
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17
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Phenotypic screening and fragment-based approaches to the discovery of small-molecule bromodomain ligands. Future Med Chem 2014; 6:179-204. [PMID: 24467243 DOI: 10.4155/fmc.13.197] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Bromodomains are protein modules that bind to acetylated lysine residues and hence facilitate protein-protein interactions. These bromodomain-mediated interactions often play key roles in transcriptional regulation and their dysfunction is implicated in a large number of diseases. The discovery of potent and selective small-molecule bromodomain and extra C-terminal domain bromodomain ligands, which show promising results for the treatment of cancers and atherosclerosis, has promoted intense interest in this area. Here we describe the progress that has been made to date in the discovery of small-molecule bromodomain ligands, with particular emphasis on the roles played by phenotypic screening and fragment-based approaches. In considering the future of the field we discuss the prospects for development of molecular probes and drugs for the non-bromodomain and extra C-terminal domain bromodomains.
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18
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Na Z, Pan S, Uttamchandani M, Yao SQ. Discovery of Cell-Permeable Inhibitors That Target the BRCT Domain of BRCA1 Protein by Using a Small-Molecule Microarray. Angew Chem Int Ed Engl 2014; 53:8421-6. [DOI: 10.1002/anie.201405169] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 05/28/2014] [Indexed: 11/12/2022]
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19
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Na Z, Pan S, Uttamchandani M, Yao SQ. Discovery of Cell-Permeable Inhibitors That Target the BRCT Domain of BRCA1 Protein by Using a Small-Molecule Microarray. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405169] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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20
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Owen DR, Trzupek JD. Epigenetic drugs that do not target enzyme activity. DRUG DISCOVERY TODAY. TECHNOLOGIES 2014; 12:e29-e34. [PMID: 25027371 DOI: 10.1016/j.ddtec.2012.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
While the installation and removal of epigenetic post-translational modifications or ‘marks’ on both DNA and histone proteins are the tangible outcome of enzymatically catalyzed processes, the role of the epigenetic reader proteins looks, at first, less obvious. As they do not catalyze a chemical transformation or process as such, their role is not enzymatic. However, this does not preclude them from being potential targets for drug discovery as their function is clearly correlated to transcriptional activity and as a class of proteins, they appear to have binding sites of sufficient definition and size to be inhibited by small molecules. This suggests that this third class of epigenetic proteins that are involved in the interpretation of post-translational marks (as opposed to the creation or deletion of marks) may represent attractive targets for drug discovery efforts. This review mainly summarizes selected publications, patent literature and company disclosures on these non-enzymatic epigenetic reader proteins from 2009 to the present.
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Affiliation(s)
- Dafydd R Owen
- Pfizer Worldwide Research and Development, 200 Cambridgepark Drive, Cambridge, MA 02140, USA.
| | - John D Trzupek
- Pfizer Worldwide Research and Development, 200 Cambridgepark Drive, Cambridge, MA 02140, USA
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21
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Tolani B, Gopalakrishnan R, Punj V, Matta H, Chaudhary PM. Targeting Myc in KSHV-associated primary effusion lymphoma with BET bromodomain inhibitors. Oncogene 2014; 33:2928-37. [PMID: 23792448 PMCID: PMC4892892 DOI: 10.1038/onc.2013.242] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 05/03/2013] [Accepted: 05/09/2013] [Indexed: 01/22/2023]
Abstract
Primary effusion lymphoma (PEL) is an aggressive form of non-Hodgkin's B-cell lymphoma associated with infection by Kaposi's sarcoma-associated herpes virus (KSHV). (+)-JQ1 and I-BET151 are two recently described novel small-molecule inhibitors of BET bromodomain chromatin-associated proteins that have shown impressive preclinical activity in cancers in which MYC is overexpressed at the transcriptional level due to chromosomal translocations that bring the MYC gene under the control of a super-enhancer. PEL cells, in contrast, lack structural alterations in the MYC gene, but have deregulated Myc protein due to the activity of KSHV-encoded latent proteins. We report that PEL cell lines are highly sensitive to bromodomain and extra-terminal (BET) bromodomain inhibitors-induced growth inhibition and undergo G0/G1 cell-cycle arrest, apoptosis and cellular senescence, but without the induction of lytic reactivation, upon treatment with these drugs. Treatment of PEL cell lines with BET inhibitors suppressed the expression of MYC and resulted in a genome-wide perturbation of MYC-dependent genes. Silencing of BRD4 and MYC expression blocked cell proliferation and cell-cycle progression, while ectopic expression of MYC from a retroviral promoter rescued cells from (+)-JQ1-induced growth arrest. In a xenograft model of PEL, (+)-JQ1 significantly reduced tumor growth and improved survival. Taken collectively, our results demonstrate that the utility of BET inhibitors may not be limited to cancers in which genomic alterations result in extremely high expression of MYC and they may have equal or perhaps greater activity against cancers in which the MYC genomic locus is structurally intact and c-Myc protein is deregulated at the post-translational level and is only modestly overexpressed.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Apoptosis/drug effects
- Azepines/pharmacology
- Cell Cycle Checkpoints/drug effects
- Cell Cycle Proteins
- Cell Line, Tumor
- Cell Nucleus/metabolism
- Cell Proliferation/drug effects
- Cell Survival/drug effects
- Cell Survival/genetics
- Cellular Senescence/drug effects
- Disease Models, Animal
- Dose-Response Relationship, Drug
- Female
- Gene Expression Regulation, Neoplastic/genetics
- Herpesvirus 8, Human
- Heterocyclic Compounds, 4 or More Rings/pharmacology
- Humans
- Inhibitory Concentration 50
- Lymphoma, Primary Effusion/genetics
- Lymphoma, Primary Effusion/metabolism
- Lymphoma, Primary Effusion/pathology
- Lymphoma, Primary Effusion/virology
- Nuclear Proteins/antagonists & inhibitors
- Protein Binding/drug effects
- Protein Transport
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- Transcription Factors/antagonists & inhibitors
- Transcription, Genetic
- Triazoles/pharmacology
- Tumor Burden/drug effects
- Virus Replication/drug effects
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Bhairavi Tolani
- Jane Anne Nohl Division of Hematology and Center for the Study of Blood Diseases, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Ramakrishnan Gopalakrishnan
- Jane Anne Nohl Division of Hematology and Center for the Study of Blood Diseases, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Vasu Punj
- Jane Anne Nohl Division of Hematology and Center for the Study of Blood Diseases, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Hittu Matta
- Jane Anne Nohl Division of Hematology and Center for the Study of Blood Diseases, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Preet M. Chaudhary
- Jane Anne Nohl Division of Hematology and Center for the Study of Blood Diseases, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
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22
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Molecular Dynamics Simulations of Bromodomains Reveal Binding-Site Flexibility and Multiple Binding Modes of the Natural Ligand Acetyl-Lysine. Isr J Chem 2014. [DOI: 10.1002/ijch.201400009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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23
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Jung M, Philpott M, Müller S, Schulze J, Badock V, Eberspächer U, Moosmayer D, Bader B, Schmees N, Fernández-Montalván A, Haendler B. Affinity map of bromodomain protein 4 (BRD4) interactions with the histone H4 tail and the small molecule inhibitor JQ1. J Biol Chem 2014; 289:9304-19. [PMID: 24497639 PMCID: PMC3979416 DOI: 10.1074/jbc.m113.523019] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Bromodomain protein 4 (BRD4) is a member of the bromodomain and extra-terminal domain (BET) protein family. It binds to acetylated histone tails via its tandem bromodomains BD1 and BD2 and forms a complex with the positive transcription elongation factor b, which controls phosphorylation of RNA polymerase II, ultimately leading to stimulation of transcription elongation. An essential role of BRD4 in cell proliferation and cancer growth has been reported in several recent studies. We analyzed the binding of BRD4 BD1 and BD2 to different partners and showed that the strongest interactions took place with di- and tetra-acetylated peptides derived from the histone 4 N-terminal tail. We also found that several histone 4 residues neighboring the acetylated lysines significantly influenced binding. We generated 10 different BRD4 BD1 mutants and analyzed their affinities to acetylated histone tails and to the BET inhibitor JQ1 using several complementary biochemical and biophysical methods. The impact of these mutations was confirmed in a cellular environment. Altogether, the results show that Trp-81, Tyr-97, Asn-140, and Met-149 play similarly important roles in the recognition of acetylated histones and JQ1. Pro-82, Leu-94, Asp-145, and Ile-146 have a more differentiated role, suggesting that different kinds of interactions take place and that resistance mutations compatible with BRD4 function are possible. Our study extends the knowledge on the contribution of individual BRD4 amino acids to histone and JQ1 binding and may help in the design of new BET antagonists with improved pharmacological properties.
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Affiliation(s)
- Marie Jung
- From the Global Drug Discovery, Bayer HealthCare, 13353 Berlin, Germany
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24
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Lucas X, Wohlwend D, Hügle M, Schmidtkunz K, Gerhardt S, Schüle R, Jung M, Einsle O, Günther S. 4-Acyl pyrroles: mimicking acetylated lysines in histone code reading. Angew Chem Int Ed Engl 2013; 52:14055-9. [PMID: 24272870 DOI: 10.1002/anie.201307652] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 10/04/2013] [Indexed: 01/21/2023]
Affiliation(s)
- Xavier Lucas
- Pharmazeutische Bioinformatik, Institut für Pharmazeutische, Wissenschaften, Albert-Ludwigs-Universität, Hermann-Herder-Strasse 9, 79104 Freiburg (Germany) http://www.pharmaceutical-bioinformatics.org
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25
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Lucas X, Wohlwend D, Hügle M, Schmidtkunz K, Gerhardt S, Schüle R, Jung M, Einsle O, Günther S. 4-Acyl Pyrroles: Mimicking Acetylated Lysines in Histone Code Reading. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307652] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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26
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Zhang CJ, Tan CYJ, Ge J, Na Z, Chen GYJ, Uttamchandani M, Sun H, Yao SQ. Preparation of Small-Molecule Microarrays bytrans-Cyclooctene Tetrazine Ligation and Their Application in the High-Throughput Screening of Protein-Protein Interaction Inhibitors of Bromodomains. Angew Chem Int Ed Engl 2013; 52:14060-4. [DOI: 10.1002/anie.201307803] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 09/30/2013] [Indexed: 01/29/2023]
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27
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Zhang CJ, Tan CYJ, Ge J, Na Z, Chen GYJ, Uttamchandani M, Sun H, Yao SQ. Preparation of Small-Molecule Microarrays bytrans-Cyclooctene Tetrazine Ligation and Their Application in the High-Throughput Screening of Protein-Protein Interaction Inhibitors of Bromodomains. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307803] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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28
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Plass C, Pfister SM, Lindroth AM, Bogatyrova O, Claus R, Lichter P. Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer. Nat Rev Genet 2013; 14:765-80. [DOI: 10.1038/nrg3554] [Citation(s) in RCA: 315] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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29
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Abstract
The second half of the 20th century has been dominated by genetic models of tumors that provided conceptual tools explaining tumor genesis and its evolution. Other domains--epigenetics, cell metabolism--appeared that generated a more complex landscape of tumor physiopathology. Moreover, the discovery of tumor stem cells and intratumoral heterogeneity are likely to explain recurrence. A major difficulty is that every tumor behaves as an organ that evolves in function of its microenvironment. By integrating all the new data in more and more sophisticated models, the major goals may emerge from the characterisation of new markers for diagnosis and prognosis and from the selection of pertinent and efficient new therapeutic targets.
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30
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Duan Z, Zou JX, Yang P, Wang Y, Borowsky AD, Gao AC, Chen HW. Developmental and androgenic regulation of chromatin regulators EZH2 and ANCCA/ATAD2 in the prostate Via MLL histone methylase complex. Prostate 2013; 73:455-66. [PMID: 23038103 DOI: 10.1002/pros.22587] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 08/16/2012] [Indexed: 02/03/2023]
Abstract
BACKGROUND Chromatin regulators ANCCA and EZH2 are overexpressed in prostate cancer and play crucial roles in androgen-stimulated and castration-refractory prostate tumor growth and survival. However, how their expression is regulated in the tumors and whether they play a role in prostate development remains unclear. METHODS Prostate tissue from different developmental stages of mouse and human were examined by IHC, qRT-PCR and Western for expression of ANCCA, EZH2, and Ki-67. Animals were castrated and T-implanted for the expression response in normal prostate and tumors. siRNA knockdown and ChIP were performed for the mechanism of ANCCA regulation of EZH2. RESULTS In contrast to their very low level expression in adult prostate, ANCCA and EZH2 are strongly expressed in the epithelium and mesenchyme of mouse and human UGS. Their expression becomes more restricted to epithelial cells during later development and displays a second peak during puberty, which correlates with the proliferative status of the epithelium. Importantly, their expression in normal prostate and tumors is strongly suppressed by castration and markedly induced by testosterone replacement. While androgen suppresses EZH2 in CRPC cells, in LNCaP cells, physiological concentrations of androgen stimulate expression of PRC2 genes (EZH2, SUZ12, and EED), which is mediated by androgen-induced ANCCA and involves E2F and histone H3K4me3 methylase MLL1 complex. CONCLUSION EZH2 and ANCCA are androgen regulated and strongly expressed in early prostate morphogenesis and during puberty, suggesting their important role in prostate development. Regulation of EZH2 by ANCCA emphasizes bromodomain protein ANCCA as a potential therapeutic target against prostate cancer.
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Affiliation(s)
- Zhijian Duan
- Cancer Center/Basic Sciences, University of California at Davis, Sacramento, California 95817, USA
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31
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Hewings DS, Rooney TPC, Jennings LE, Hay DA, Schofield CJ, Brennan PE, Knapp S, Conway SJ. Progress in the development and application of small molecule inhibitors of bromodomain-acetyl-lysine interactions. J Med Chem 2012; 55:9393-413. [PMID: 22924434 DOI: 10.1021/jm300915b] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bromodomains, protein modules that recognize and bind to acetylated lysine, are emerging as important components of cellular machinery. These acetyl-lysine (KAc) "reader" domains are part of the write-read-erase concept that has been linked with the transfer of epigenetic information. By reading KAc marks on histones, bromodomains mediate protein-protein interactions between a diverse array of partners. There has been intense activity in developing potent and selective small molecule probes that disrupt the interaction between a given bromodomain and KAc. Rapid success has been achieved with the BET family of bromodomains, and a number of potent and selective probes have been reported. These compounds have enabled linking of the BET bromodomains with diseases, including cancer and inflammation, suggesting that bromodomains are druggable targets. Herein, we review the biology of the bromodomains and discuss the SAR for the existing small molecule probes. The biology that has been enabled by these compounds is summarized.
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Affiliation(s)
- David S Hewings
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
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Abstract
The epigenetic regulation of DNA-templated processes has been intensely studied over the last 15 years. DNA methylation, histone modification, nucleosome remodeling, and RNA-mediated targeting regulate many biological processes that are fundamental to the genesis of cancer. Here, we present the basic principles behind these epigenetic pathways and highlight the evidence suggesting that their misregulation can culminate in cancer. This information, along with the promising clinical and preclinical results seen with epigenetic drugs against chromatin regulators, signifies that it is time to embrace the central role of epigenetics in cancer.
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Affiliation(s)
- Mark A Dawson
- Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
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33
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Chung CW. Small molecule bromodomain inhibitors: extending the druggable genome. PROGRESS IN MEDICINAL CHEMISTRY 2012; 51:1-55. [PMID: 22520470 DOI: 10.1016/b978-0-12-396493-9.00001-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chun-Wa Chung
- Computational and Structural Sciences, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
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34
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Quy VC, Pantano S, Rossetti G, Giacca M, Carloni P. HIV-1 Tat Binding to PCAF Bromodomain: Structural Determinants from Computational Methods. BIOLOGY 2012; 1:277-96. [PMID: 24832227 PMCID: PMC4009784 DOI: 10.3390/biology1020277] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 07/09/2012] [Accepted: 07/26/2012] [Indexed: 12/13/2022]
Abstract
The binding between the HIV-1 trans-activator of transcription (Tat) and p300/(CREB-binding protein)-associated factor (PCAF) bromodomain is a crucial step in the HIV-1 life cycle. However, the structure of the full length acetylated Tat bound to PCAF has not been yet determined experimentally. Acetylation of Tat residues can play a critical role in enhancing HIV-1 transcriptional activation. Here, we have combined a fully flexible protein-protein docking approach with molecular dynamics simulations to predict the structural determinants of the complex for the common HIV-1BRU variant. This model reproduces all the crucial contacts between the Tat peptide 46SYGR(AcK)KRRQRC56 and the PCAF bromodomain previously reported by NMR spectroscopy. Additionally, inclusion of the entire Tat protein results in additional contact points at the protein-protein interface. The model is consistent with the available experimental data reported and adds novel information to our previous structural predictions of the PCAF bromodomain in complex with the rare HIVZ2 variant, which was obtained with a less accurate computational method. This improved characterization of Tat.PCAF bromodomain binding may help in defining the structural determinants of other protein interactions involving lysine acetylation.
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Affiliation(s)
- Vo Cam Quy
- Computational Biophysics, German Research School for Simulation Sciences, Computational Biomedicine, Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich, Jülich D-52425, Germany.
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP 11400, Uruguay.
| | - Giulia Rossetti
- Computational Biophysics, German Research School for Simulation Sciences, Computational Biomedicine, Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich, Jülich D-52425, Germany.
| | - Mauro Giacca
- International Centre for Genetic Engineering and Biotechnology, Trieste 34149, Italy.
| | - Paolo Carloni
- Computational Biophysics, German Research School for Simulation Sciences, Computational Biomedicine, Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich, Jülich D-52425, Germany.
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35
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Lu Q, Quinn AM, Patel MP, Semus SF, Graves AP, Bandyopadhyay D, Pope AJ, Thrall SH. Perspectives on the discovery of small-molecule modulators for epigenetic processes. ACTA ACUST UNITED AC 2012; 17:555-71. [PMID: 22392809 DOI: 10.1177/1087057112437763] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Epigenetic gene regulation is a critical process controlling differentiation and development, the malfunction of which may underpin a variety of diseases. In this article, we review the current landscape of small-molecule epigenetic modulators including drugs on the market, key compounds in clinical trials, and chemical probes being used in epigenetic mechanistic studies. Hit identification strategies for the discovery of small-molecule epigenetic modulators are summarized with respect to writers, erasers, and readers of histone marks. Perspectives are provided on opportunities for new hit discovery approaches, some of which may define the next generation of therapeutic intervention strategies for epigenetic processes.
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Affiliation(s)
- Quinn Lu
- GlaxoSmithKline, Collegeville, Pennsylvania, USA.
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Heightman T, Pope A. Epigenetic-targeted drug discovery: from the guest editors. JOURNAL OF BIOMOLECULAR SCREENING 2011; 16:1135-1136. [PMID: 22156584 DOI: 10.1177/1087057111425979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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