51
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Chen Q, Liu C, Shulyak TS, Schneller SW. The metathesis reaction for side chain construction in carbocyclic sinefungin analogue synthesis. Tetrahedron 2014. [DOI: 10.1016/j.tet.2013.12.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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52
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Fagan RL, Wu M, Chédin F, Brenner C. An ultrasensitive high throughput screen for DNA methyltransferase 1-targeted molecular probes. PLoS One 2013; 8:e78752. [PMID: 24236046 PMCID: PMC3827244 DOI: 10.1371/journal.pone.0078752] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/20/2013] [Indexed: 12/20/2022] Open
Abstract
DNA methyltransferase 1 (DNMT1) is the enzyme most responsible for epigenetic modification of human DNA and the intended target of approved cancer drugs such as 5-aza-cytidine and 5-aza-2'-deoxycytidine. 5-aza nucleosides have complex mechanisms of action that require incorporation into DNA, and covalent trapping and proteolysis of DNMT isozymes. Direct DNMT inhibitors are needed to refine understanding of the role of specific DNMT isozymes in cancer etiology and, potentially, to improve cancer prevention and treatment. Here, we developed a high throughput pipeline for identification of direct DNMT1 inhibitors. The components of this screen include an activated form of DNMT1, a restriction enzyme-coupled fluorigenic assay performed in 384 well plates with a z-factor of 0.66, a counter screen against the restriction enzyme, a screen to eliminate DNA intercalators, and a differential scanning fluorimetry assay to validate direct binders. Using the Microsource Spectrum collection of 2320 compounds, this screen identified nine compounds with dose responses ranging from 300 nM to 11 µM, representing at least two different pharmacophores with DNMT1 inhibitory activity. Seven of nine inhibitors identified exhibited two to four-fold selectivity for DNMT1 versus DNMT3A.
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Affiliation(s)
- Rebecca L. Fagan
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Meng Wu
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, University of California Davis, Davis, California, United States of America
| | - Charles Brenner
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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53
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Gros C, Chauvigné L, Poulet A, Menon Y, Ausseil F, Dufau I, Arimondo PB. Development of a universal radioactive DNA methyltransferase inhibition test for high-throughput screening and mechanistic studies. Nucleic Acids Res 2013; 41:e185. [PMID: 23980028 PMCID: PMC3799459 DOI: 10.1093/nar/gkt753] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 07/15/2013] [Accepted: 07/30/2013] [Indexed: 12/24/2022] Open
Abstract
DNA methylation is an important epigenetic mark in eukaryotes, and aberrant pattern of this modification is involved in numerous diseases such as cancers. Interestingly, DNA methylation is reversible and thus is considered a promising therapeutic target. Therefore, there is a need for identifying new small inhibitors of C5 DNA methyltransferases (DNMTs). Despite the development of numerous in vitro DNMT assays, there is a lack of reliable tests suitable for high-throughput screening, which can also give insights into inhibitor mechanisms of action. We developed a new test based on scintillation proximity assay meeting these requirements. After optimizing our assay on human DNMT1 and calibrating it with two known inhibitors, we carried out S-Adenosyl-l-Methionine and DNA competition studies on three inhibitors and were able to determine each mechanism of action. Finally, we showed that our test was applicable to 3 other methyltransferases sources: human DNMT3A, bacterial M.SssI and cellular extracts as well.
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Affiliation(s)
| | | | | | | | | | - Isabelle Dufau
- CNRS-Pierre Fabre USR n° 3388 ETaC, CRDPF, 3 Avenue H. Curien, 31035 Toulouse Cedex 01, France
| | - Paola B. Arimondo
- CNRS-Pierre Fabre USR n° 3388 ETaC, CRDPF, 3 Avenue H. Curien, 31035 Toulouse Cedex 01, France
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54
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Fagan RL, Cryderman DE, Kopelovich L, Wallrath LL, Brenner C. Laccaic acid A is a direct, DNA-competitive inhibitor of DNA methyltransferase 1. J Biol Chem 2013; 288:23858-67. [PMID: 23839987 DOI: 10.1074/jbc.m113.480517] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Methylation of cytosines in CpG dinucleotides is the predominant epigenetic mark on vertebrate DNA. DNA methylation is associated with transcriptional repression. The pattern of DNA methylation changes during development and with disease. Human DNA methyltransferase 1 (Dnmt1), a 1616-amino acid multidomain enzyme, is essential for maintenance of DNA methylation in proliferating cells and is considered an important cancer drug target. Using a fluorogenic, endonuclease-coupled DNA methylation assay with an activated form of Dnmt1 engineered to lack the replication foci targeting sequence domain, we discovered that laccaic acid A (LCA), a highly substituted anthraquinone natural product, is a direct inhibitor with a 310 nm Ki. LCA is competitive with the DNA substrate in in vitro methylation assays and alters the expression of methylated genes in MCF-7 breast cancer cells synergistically with 5-aza-2'-deoxycytidine. LCA represents a novel class of Dnmt-targeted molecular probes, with biochemical properties that allow it to distinguish between non DNA-bound and DNA-bound Dnmt1.
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Affiliation(s)
- Rebecca L Fagan
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
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55
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Florent JC. [Small compounds libraries: a research tool for chemical biology]. Biol Aujourdhui 2013; 207:39-54. [PMID: 23694724 DOI: 10.1051/jbio/2013006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Indexed: 06/02/2023]
Abstract
Obtaining and screening collections of small molecules remain a challenge for biologists. Recent advances in analytical techniques and instrumentation now make screening possible in academia. The history of the creation of such public or commercial collections and their accessibility is related. It shows that there is interest for an academic laboratory involved in medicinal chemistry, chemogenomics or "chemical biology" to organize its own collection and make it available through existing networks such as the French National chimiothèque or the European partner network "European Infrastructure of open screening platforms for Chemical Biology" EU-OpenScreen under construction.
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Affiliation(s)
- Jean-Claude Florent
- Laboratoire de Conception, Synthèse et Vectorisation de Biomolécules (CSVB), UMR 176 CNRS-Institut Curie, Institut Curie Centre de Recherche, 75248 Paris Cedex, France.
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56
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Ceccaldi A, Rajavelu A, Ragozin S, Sénamaud-Beaufort C, Bashtrykov P, Testa N, Dali-Ali H, Maulay-Bailly C, Amand S, Guianvarc’h D, Jeltsch A, Arimondo PB. Identification of novel inhibitors of DNA methylation by screening of a chemical library. ACS Chem Biol 2013; 8:543-8. [PMID: 23294304 DOI: 10.1021/cb300565z] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In order to discover new inhibitors of the DNA methyltransferase 3A/3L complex, we used a medium-throughput nonradioactive screen on a random collection of 1120 small organic compounds. After a primary hit detection against DNA methylation activity of the murine Dnmt3A/3L catalytic complex, we further evaluated the EC50 of the 12 most potent hits as well as their cytotoxicity on DU145 prostate cancer cultured cells. Interestingly, most of the inhibitors showed low micromolar activities and little cytotoxicity. Dichlone, a small halogenated naphthoquinone, classically used as pesticide and fungicide, showed the lowest EC50 at 460 nM. We briefly assessed the selectivity of a subset of our new inhibitors against hDNMT1 and bacterial Dnmts, including M. SssI and EcoDam, and the protein lysine methyltransferase PKMT G9a and the mode of inhibition. Globally, the tested molecules showed a clear preference for the DNA methyltransferases, but poor selectivity among them. Two molecules including Dichlone efficiently reactivated YFP gene expression in a stable HEK293 cell line by promoter demethylation. Their efficacy was comparable to the DNMT inhibitor of reference 5-azacytidine.
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Affiliation(s)
- Alexandre Ceccaldi
- CNRS-MNHN UMR 7196, 43 rue Cuvier, 75005
Paris, France
- INSERM UR565, 43 rue Cuvier, 75005 Paris, France
- Université Pierre et Marie Curie, Paris 6, place Jussieu, 75005
Paris, France
| | - Arumugam Rajavelu
- Institute
of Biochemistry, Faculty
of Chemistry, University Stuttgart, Pfaffenwaldring
55, 70569 Stuttgart, Germany
| | - Sergey Ragozin
- Institute
of Biochemistry, Faculty
of Chemistry, University Stuttgart, Pfaffenwaldring
55, 70569 Stuttgart, Germany
| | | | - Pavel Bashtrykov
- Institute
of Biochemistry, Faculty
of Chemistry, University Stuttgart, Pfaffenwaldring
55, 70569 Stuttgart, Germany
| | - Noé Testa
- CNRS-MNHN UMR 7196, 43 rue Cuvier, 75005
Paris, France
- INSERM UR565, 43 rue Cuvier, 75005 Paris, France
| | - Hana Dali-Ali
- CNRS-MNHN UMR 7196, 43 rue Cuvier, 75005
Paris, France
- INSERM UR565, 43 rue Cuvier, 75005 Paris, France
| | | | - Séverine Amand
- CNRS-MNHN UMR 7245 RDDM, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Dominique Guianvarc’h
- UPMC Paris 06−ENS−CNRS,
UMR 7203, Laboratoire des Biomolécules and FR2769 Chimie Moléculaire, Université Pierre et Marie Curie, 4 place Jussieu,
75005 Paris, France
| | - Albert Jeltsch
- Institute
of Biochemistry, Faculty
of Chemistry, University Stuttgart, Pfaffenwaldring
55, 70569 Stuttgart, Germany
| | - Paola B. Arimondo
- CNRS-MNHN UMR 7196, 43 rue Cuvier, 75005
Paris, France
- INSERM UR565, 43 rue Cuvier, 75005 Paris, France
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57
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Terriente J, Pujades C. Use of Zebrafish Embryos for Small Molecule Screening Related to Cancer. Dev Dyn 2013. [DOI: 10.1002/dvdy.23912] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Javier Terriente
- Department of Experimental and Health Sciences; Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona; PRBB; Barcelona; Spain
| | - Cristina Pujades
- Department of Experimental and Health Sciences; Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona; PRBB; Barcelona; Spain
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58
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Kabro A, Lachance H, Marcoux-Archambault I, Perrier V, Doré V, Gros C, Masson V, Gregoire JM, Ausseil F, Cheishvili D, Laulan NB, St-Pierre Y, Szyf M, Arimondo PB, Gagnon A. Preparation of phenylethylbenzamide derivatives as modulators of DNMT3 activity. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00214d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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59
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DNA methylation inhibitors in cancer: recent and future approaches. Biochimie 2012; 94:2280-96. [PMID: 22967704 DOI: 10.1016/j.biochi.2012.07.025] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Accepted: 07/30/2012] [Indexed: 12/14/2022]
Abstract
This review presents the different human DNA methyltransferases (DNMTs), their biological roles, their mechanisms of action and their role in cancer. The description of assays for detecting DNMT inhibitors (DNMTi) follows. The different known DNMTi are reported along with their advantages, drawbacks and clinical trials. A discussion on the features of the future DNMT inhibitors will conclude this review.
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60
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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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61
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Castellano S, Kuck D, Viviano M, Yoo J, López-Vallejo F, Conti P, Tamborini L, Pinto A, Medina-Franco JL, Sbardella G. Synthesis and Biochemical Evaluation of Δ2-Isoxazoline Derivatives as DNA Methyltransferase 1 Inhibitors. J Med Chem 2011; 54:7663-77. [DOI: 10.1021/jm2010404] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Sabrina Castellano
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Dirk Kuck
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Monica Viviano
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Jakyung Yoo
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Fabian López-Vallejo
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Paola Conti
- Dipartimento di Scienze Farmaceutiche “Pietro Pratesi”, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy
| | - Lucia Tamborini
- Dipartimento di Scienze Farmaceutiche “Pietro Pratesi”, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy
| | - Andrea Pinto
- Dipartimento di Scienze Farmaceutiche “Pietro Pratesi”, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy
| | - José L. Medina-Franco
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Gianluca Sbardella
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
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