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Aggarwal R, Jha M, Shrivastava A, Jha AK. Natural Compounds: Role in Reversal of Epigenetic Changes. BIOCHEMISTRY (MOSCOW) 2016; 80:972-89. [PMID: 26547065 DOI: 10.1134/s0006297915080027] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The hallmarks of carcinogenesis are characterized by alterations in the expression of multiple genes that occur via genetic and epigenetic alterations, leading to genome rearrangements and instability. The reversible process of epigenetic regulation, which includes changes in DNA methylation, histone modifications, and alteration in microRNA (miRNA) expression that alter phenotype without any change in the DNA sequence, is recognized as a key mechanism in cancer cell metabolism. Recent advancements in the rapidly evolving field of cancer epigenetics have shown the anticarcinogenic potential of natural compounds targeting epigenetic mechanism as a common molecular approach for cancer treatment. This review summarizes the potential of natural chemopreventive agents to reverse cancer-related epigenetic aberrations by regulating the activity of histone deacetylases, histone acetyltransferases, DNA methyltransferase I, and miRNAs. Furthermore, there is impetus for determining novel and effective chemopreventive strategies, either alone or in combination with other anticancer agents that exhibit similar properties, for improving the therapeutic aspects of cancer.
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Affiliation(s)
- Ruchi Aggarwal
- Department of Biotechnology, IMS Engineering College, U. P. 201009, India.
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Cheray M, Pacaud R, Nadaradjane A, Oliver L, Vallette FM, Cartron PF. Specific Inhibition of DNMT3A/ISGF3γ Interaction Increases the Temozolomide Efficiency to Reduce Tumor Growth. Am J Cancer Res 2016; 6:1988-1999. [PMID: 27698935 PMCID: PMC5039338 DOI: 10.7150/thno.9150] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 07/16/2015] [Indexed: 11/28/2022] Open
Abstract
DNA methylation is a fundamental feature of genomes and is a candidate for pharmacological manipulation that might have important therapeutic advantage. Thus, DNA methyltransferases (DNMTs) appear to be ideal targets for drug intervention. By focusing on interactions existing between DNMT3A and DNMT3A-binding protein (D3A-BP), our work identifies the DNMT3A/ISGF3γ interaction such as a biomarker whose the presence level is associated with a poor survival prognosis and with a poor prognosis of response to the conventional chemotherapeutic treatment of glioblastoma multiforme (radiation plus temozolomide). Our data also demonstrates that the disruption of DNMT3A/ISGF3γ interactions increases the efficiency of chemotherapeutic treatment on established tumors in mice. Thus, our data opens a promising and innovative alternative to the development of specific DNMT inhibitors.
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53
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Garella D, Atlante S, Borretto E, Cocco M, Giorgis M, Costale A, Stevanato L, Miglio G, Cencioni C, Fernández-de Gortari E, Medina-Franco JL, Spallotta F, Gaetano C, Bertinaria M. Design and synthesis of N-benzoyl amino acid derivatives as DNA methylation inhibitors. Chem Biol Drug Des 2016; 88:664-676. [PMID: 27225604 DOI: 10.1111/cbdd.12794] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/02/2016] [Accepted: 05/14/2016] [Indexed: 12/11/2022]
Abstract
The inhibition of human DNA Methyl Transferases (DNMT) is a novel promising approach to address the epigenetic dysregulation of gene expression in different diseases. Inspired by the validated virtual screening hit NSC137546, a series of N-benzoyl amino acid analogues was synthesized and obtained compounds were assessed for their ability to inhibit DNMT-dependent DNA methylation in vitro. The biological screening allowed the definition of a set of preliminary structure-activity relationships and the identification of compounds promising for further development. Among the synthesized compounds, L-glutamic acid derivatives 22, 23, and 24 showed the highest ability to prevent DNA methylation in a total cell lysate. Compound 22 inhibited DNMT1 and DNMT3A activity in a concentration-dependent manner in the micromolar range. In addition, compound 22 proved to be stable in human serum and it was thus selected as a starting point for further biological studies.
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Affiliation(s)
- Davide Garella
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy.
| | - Sandra Atlante
- Division of Cardiovascular Epigenetics, Department of Cardiology, Goethe University, Frankfurt am Main, Germany
| | - Emily Borretto
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
| | - Mattia Cocco
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
| | - Marta Giorgis
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
| | - Annalisa Costale
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
| | - Livio Stevanato
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
| | - Gianluca Miglio
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
| | - Chiara Cencioni
- Division of Cardiovascular Epigenetics, Department of Cardiology, Goethe University, Frankfurt am Main, Germany
| | - Eli Fernández-de Gortari
- Facultad de Química , Departamento de Farmacia, Universidad Nacional Autónoma de México, Mexico City, México
| | - José L Medina-Franco
- Facultad de Química , Departamento de Farmacia, Universidad Nacional Autónoma de México, Mexico City, México
| | - Francesco Spallotta
- Division of Cardiovascular Epigenetics, Department of Cardiology, Goethe University, Frankfurt am Main, Germany
| | - Carlo Gaetano
- Division of Cardiovascular Epigenetics, Department of Cardiology, Goethe University, Frankfurt am Main, Germany.
| | - Massimo Bertinaria
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
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Molecular Modeling and Chemoinformatics to Advance the Development of Modulators of Epigenetic Targets: A Focus on DNA Methyltransferases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 105:1-26. [PMID: 27567482 DOI: 10.1016/bs.apcsb.2016.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In light of the emerging field of Epi-informatics, ie, computational methods applied to epigenetic research, molecular docking, and dynamics, pharmacophore and activity landscape modeling and QSAR play a key role in the development of modulators of DNA methyltransferases (DNMTs), one of the major epigenetic target families. The increased chemical information available for modulators of DNMTs has opened up the avenue to explore the epigenetic relevant chemical space (ERCS). Herein, we discuss recent progress on the identification and development of inhibitors of DNMTs as potential epi-drugs and epi-probes that have been driven by molecular modeling and chemoinformatics methods. We also survey advances on the elucidation of their structure-activity relationships and exploration of ERCS. Finally, it is illustrated how computational approaches can be applied to identify modulators of DNMTs in food chemicals.
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Joshi M, Rajpathak SN, Narwade SC, Deobagkar D. Ensemble-Based Virtual Screening and Experimental Validation of Inhibitors Targeting a Novel Site of Human DNMT1. Chem Biol Drug Des 2016; 88:5-16. [PMID: 26850820 DOI: 10.1111/cbdd.12741] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 01/16/2016] [Accepted: 01/31/2016] [Indexed: 12/29/2022]
Abstract
Human DNA methyltransferase1 (hDNMT1) is responsible for preserving DNA methylation patterns that play important regulatory roles in differentiation and development. Misregulation of DNA methylation has thus been linked to many syndromes, life style diseases, and cancers. Developing specific inhibitors of hDNMT1 is an important challenge in the area since the currently targeted cofactor and substrate binding site share structural features with various proteins. In this work, we generated a structural model of the active form of hDNMT1 and identified that the 5-methylcytosine (5-mC) binding site of the hDNMT1 is structurally unique to the protein. This site has been previously demonstrated to be critical for methylation activity. We further performed multiple nanosecond time scale atomistic molecular dynamics simulations of the structural model followed by virtual screening of the Asinex database to identify inhibitors targeting the 5-mC site. Two compounds were discovered that inhibited hDNMT1 in vitro, one of which also showed inhibition in vivo corroborating the screening procedure. This study thus identifies and attempts to validate for the first time a unique site of hDNMT1 that could be harnessed for rationally designing highly selective and potent hypomethylating agents.
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Affiliation(s)
- Manali Joshi
- Bioinformatics Centre, S. P. Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Shriram N Rajpathak
- Center of Advanced Studies, Department of Zoology, S. P. Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Santosh C Narwade
- Center of Advanced Studies, Department of Zoology, S. P. Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Deepti Deobagkar
- Bioinformatics Centre, S. P. Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India.,Center of Advanced Studies, Department of Zoology, S. P. Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
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Stenzig J, Hirt MN, Löser A, Bartholdt LM, Hensel JT, Werner TR, Riemenschneider M, Indenbirken D, Guenther T, Müller C, Hübner N, Stoll M, Eschenhagen T. DNA methylation in an engineered heart tissue model of cardiac hypertrophy: common signatures and effects of DNA methylation inhibitors. Basic Res Cardiol 2015; 111:9. [DOI: 10.1007/s00395-015-0528-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 12/09/2015] [Indexed: 12/11/2022]
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57
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Schneeberger Y, Stenzig J, Hübner F, Schaefer A, Reichenspurner H, Eschenhagen T. Pharmacokinetics of the Experimental Non-Nucleosidic DNA Methyl Transferase Inhibitor N-Phthalyl-L-Tryptophan (RG 108) in Rats. Basic Clin Pharmacol Toxicol 2015; 118:327-32. [PMID: 26525153 DOI: 10.1111/bcpt.12514] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/20/2015] [Indexed: 12/18/2022]
Abstract
DNA methyl transferase (DNMT) inhibitors can re-establish the expression of tumour suppressor genes in malignant diseases, but might also be useful in other diseases. Inhibitors in clinical use are nucleosidic cytotoxic agents that need to be integrated into the DNA of dividing cells. Here, we assessed the in vivo kinetics of a non-nucleosidic inhibitor that is potentially free of cytotoxic effects and does not require cell division. The non-specific DNMT inhibitor N-phthalyl-L-tryptophan (RG 108) was injected subcutaneously in rats. Blood was drawn 0, 0.5, 1, 2, 4, 6, 8 and 24 hr after injection and RG 108 in plasma was measured by high-performance liquid chromatography coupled to mass spectrometry. Trough levels and area under the curve (AUC) were significantly higher with multiple-dose administration and cytochrome inhibition. In this group, time to maximal plasma concentration (tmax , mean ± S.D.) was 37.5 ± 15 min., terminal plasma half-life was approximately 3.7 h (60% CI: 2.1-15.6 h), maximal plasma concentration (Cmax) was 61.3 ± 7.6 μM, and AUC was 200 ± 54 μmol·h/l. RG 108 peak levels were not influenced by cytochrome inhibition or multiple-dose administration regimens. Maximal tissue levels (Cmax in μmol/kg) were 6.9 ± 6.7, 1.6 ± 0.4 and 3.4 ± 1.1 in liver, skeletal and heart muscle, respectively. We conclude that despite its high lipophilicity, RG 108 can be used for in vivo experiments, appears safe and yields plasma and tissue levels in the range of the described 50% inhibitory concentration of around 1 to 5 μM. RG 108 can therefore be a useful tool for in vivo DNMT inhibition.
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Affiliation(s)
- Yvonne Schneeberger
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany.,Department of Cardiovascular Surgery, University Heart Center, Hamburg, Germany
| | - Justus Stenzig
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany.,Genome Institute of Singapore, Singapore
| | - Florian Hübner
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Andreas Schaefer
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany.,Department of Cardiovascular Surgery, University Heart Center, Hamburg, Germany
| | - Hermann Reichenspurner
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany.,Department of Cardiovascular Surgery, University Heart Center, Hamburg, Germany
| | - Thomas Eschenhagen
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
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Abstract
The approval of DNA methylation inhibitors azacytidine and decitabine for the treatment of myelodysplastic syndromes and acute myeloid leukaemia has demonstrated that modulation of relatively broad epigenetic regulatory processes can show beneficial efficacy/safety profiles in defined patient groups. This chapter will focus on the biochemical mechanisms controlling DNA methylation, consequences of aberrant DNA methylation in complex chronic diseases, existing modulators of DNA methylation used in the clinic, and opportunities for new drugs targeting this central epigenetic mechanism.
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Affiliation(s)
- Tom D. Heightman
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Michael McCullar
- Astex Pharmaceuticals Inc. 4140 Dublin Boulevard, Suite 200 Dublin CA 94568 USA
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59
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Zhu B, Ge J, Yao SQ. Developing new chemical tools for DNA methyltransferase 1 (DNMT 1): A small-molecule activity-based probe and novel tetrazole-containing inhibitors. Bioorg Med Chem 2015; 23:2917-27. [DOI: 10.1016/j.bmc.2015.03.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 02/25/2015] [Accepted: 03/02/2015] [Indexed: 12/31/2022]
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60
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Cheray M, Nadaradjane A, Bonnet P, Routier S, Vallette FM, Cartron PF. Specific inhibition of DNMT1/CFP1 reduces cancer phenotypes and enhances chemotherapy effectiveness. Epigenomics 2015; 6:267-75. [PMID: 25111481 DOI: 10.2217/epi.14.18] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
AIM DNA methylation is a fundamental biologic process of genomes and is a candidate for pharmacological manipulation that might have important therapeutic advantages. Thus, DNA methyltransferases (DNMTs) appear to be ideal targets for drug intervention. MATERIALS & METHODS To develop a new generation of DNMT inhibitor, we analyzed the ability of peptides to selectively inhibit certain DNMT1-incuding complexes. RESULTS Our study demonstrates that the disruption of DNMT1/CFP1-including complexes increases the efficiency of chemotherapeutic treatment on established tumors in mice. CONCLUSION Our data opens a promising and innovative alternative to the development of DNMT inhibitors.
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61
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Li GB, Yang LL, Yuan Y, Zou J, Cao Y, Yang SY, Xiang R, Xiang M. Virtual screening in small molecule discovery for epigenetic targets. Methods 2015; 71:158-66. [DOI: 10.1016/j.ymeth.2014.11.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/27/2014] [Accepted: 11/14/2014] [Indexed: 12/31/2022] Open
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Medina-Franco JL, Méndez-Lucio O, Dueñas-González A, Yoo J. Discovery and development of DNA methyltransferase inhibitors using in silico approaches. Drug Discov Today 2014; 20:569-77. [PMID: 25526932 DOI: 10.1016/j.drudis.2014.12.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/19/2014] [Accepted: 12/10/2014] [Indexed: 01/08/2023]
Abstract
Multiple strategies have evolved during the past few years to advance epigenetic compounds targeting DNA methyltransferases (DNMTs). Significant progress has been made in HTS, lead optimization and determination of 3D structures of DNMTs. In light of the emerging concept of epi-informatics, computational approaches are employed to accelerate the development of DNMT inhibitors helping to screen chemical databases, mine the DNMT-relevant chemical space, uncover SAR and design focused libraries. Computational methods also synergize with natural-product-based drug discovery and drug repurposing. Herein, we survey the latest developments of in silico approaches to advance epigenetic drug and probe discovery targeting DNMTs.
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Affiliation(s)
- José L Medina-Franco
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico.
| | - Oscar Méndez-Lucio
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Alfonso Dueñas-González
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México and Instituto Nacional de Cancerología, Av. San Fernando 22, Mexico City 14080, Mexico
| | - Jakyung Yoo
- Life Science Research Institute, Daewoong Pharmaceutical Co. Ltd., 72 Dugye-Ro, Pogok-Eup, Gyeonggi-do 449-814, Republic of Korea
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63
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Erdmann A, Halby L, Fahy J, Arimondo PB. Targeting DNA Methylation with Small Molecules: What’s Next? J Med Chem 2014; 58:2569-83. [DOI: 10.1021/jm500843d] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Alexandre Erdmann
- Epigenetic Targeting of Cancer,
USR3388 ETaC, CNRS-Pierre Fabre, 3 Avenue H. Curien, 31035 Toulouse Cedex 01, France
| | - Ludovic Halby
- Epigenetic Targeting of Cancer,
USR3388 ETaC, CNRS-Pierre Fabre, 3 Avenue H. Curien, 31035 Toulouse Cedex 01, France
| | - Jacques Fahy
- Epigenetic Targeting of Cancer,
USR3388 ETaC, CNRS-Pierre Fabre, 3 Avenue H. Curien, 31035 Toulouse Cedex 01, France
| | - Paola B Arimondo
- Epigenetic Targeting of Cancer,
USR3388 ETaC, CNRS-Pierre Fabre, 3 Avenue H. Curien, 31035 Toulouse Cedex 01, France
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64
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Alzheimer's disease and epigenetic diet. Neurochem Int 2014; 78:105-16. [DOI: 10.1016/j.neuint.2014.09.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 09/18/2014] [Accepted: 09/29/2014] [Indexed: 01/04/2023]
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65
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Maize KM, Zhang X, Amin EA. Statistical analysis, optimization, and prioritization of virtual screening parameters for zinc enzymes including the anthrax toxin lethal factor. Curr Top Med Chem 2014; 14:2105-14. [PMID: 25373478 DOI: 10.2174/1568026614666141106163011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 09/01/2014] [Accepted: 09/09/2014] [Indexed: 11/22/2022]
Abstract
The anthrax toxin lethal factor (LF) and matrix metalloproteinase-3 (MMP-3, stromelysin-1) are popular zinc metalloenzyme drug targets, with LF primarily responsible for anthrax-related toxicity and host death, while MMP-3 is involved in cancer- and rheumatic disease-related tissue remodeling. A number of in silico screening techniques, most notably docking and scoring, have proven useful for identifying new potential drug scaffolds targeting LF and MMP-3, as well as for optimizing lead compounds and investigating mechanisms of action. However, virtual screening outcomes can vary significantly depending on the specific docking parameters chosen, and systematic statistical significance analyses are needed to prioritize key parameters for screening small molecules against these zinc systems. In the current work, we present a series of chi-square statistical analyses of virtual screening outcomes for cocrystallized LF and MMP-3 inhibitors docked into their respective targets, evaluated by predicted enzyme-inhibitor dissociation constant and root-mean-square deviation (RMSD) between predicted and experimental bound configurations, and we present a series of preferred parameters for use with these systems in the industry-standard Surflex-Dock screening program, for use by researchers utilizing in silico techniques to discover and optimize new scaffolds.
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Affiliation(s)
| | | | - Elizabeth Ambrose Amin
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St SE, Minneapolis, MN 55416 USA.
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66
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Chen S, Wang Y, Zhou W, Li S, Peng J, Shi Z, Hu J, Liu YC, Ding H, Lin Y, Li L, Cheng S, Liu J, Lu T, Jiang H, Liu B, Zheng M, Luo C. Identifying novel selective non-nucleoside DNA methyltransferase 1 inhibitors through docking-based virtual screening. J Med Chem 2014; 57:9028-41. [PMID: 25333769 DOI: 10.1021/jm501134e] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The DNA methyltransferases (DNMTs) found in mammals include DNMT1, DNMT3A, and DNMT3B and are attractive targets in cancer chemotherapy. DNMT1 was the first among the DNMTs to be characterized, and it is responsible for maintaining DNA methylation patterns. A number of DNMT inhibitors have been reported, but most of them are nucleoside analogs that can lead to toxic side effects and lack specificity. By combining docking-based virtual screening with biochemical analyses, we identified a novel compound, DC_05. DC_05 is a non-nucleoside DNMT1 inhibitor with low micromolar IC50 values and significant selectivity toward other AdoMet-dependent protein methyltransferases. Through a process of similarity-based analog searching, compounds DC_501 and DC_517 were found to be more potent than DC_05. These three potent compounds significantly inhibited cancer cell proliferation. The structure-activity relationship (SAR) and binding modes of these inhibitors were also analyzed to assist in the future development of more potent and more specific DNMT1 inhibitors.
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Affiliation(s)
- Shijie Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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Dueñas-Gonzalez A, Coronel J, Cetina L, González-Fierro A, Chavez-Blanco A, Taja-Chayeb L. Hydralazine-valproate: a repositioned drug combination for the epigenetic therapy of cancer. Expert Opin Drug Metab Toxicol 2014; 10:1433-44. [PMID: 25154405 DOI: 10.1517/17425255.2014.947263] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION DNA methylation (DNMTi) and histone deacetylase inhibitors (HDACi) are in development for cancer therapy. So far, four epigenetic drugs are approved for myelodysplastic syndrome (MDS) and cutaneous T-cell lymphoma (CTCL). The combination of hydralazine-valproate (TRANSKRIP(™)) is being repositioned as an oral DNMT and HDAC inhibitor. AREAS COVERED Brief discussion on the current status of epigenetic drugs and studies published on the preclinical and clinical development of the hydralazine-valproate combination. EXPERT OPINION Drug repositioning is a strategy for prompt and cost-efficient drug discovery. There is evidence that combining DNMTi with HDACi would be more efficacious than administering each agent on its own. Hydralazine-valproate is safe when used alone or in combination with chemotherapy or chemoradiation. The fact that both drugs are orally administered is another advantage over current epigenetic drugs. This combination is promising but larger studies are needed. Among these, the randomized Phase III trials in advanced and in locally advanced cervical cancer combined with chemotherapy and cisplatin-radiation respectively, would eventually confirm its efficacy. Studies on MDS and CTCL would also eventually prove the efficacy of hydralazine valproate so that in the coming years hydralazine-valproate could have a role in cancer epigenetic therapy.
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Affiliation(s)
- Alfonso Dueñas-Gonzalez
- Instituto de Investigaciones Biomédicas UNAM/Instituto Nacional de Cancerología Mexico, Unit of Biomedical Research on Cancer , Mexico City , Mexico
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Miceli M, Bontempo P, Nebbioso A, Altucci L. Natural compounds in epigenetics: a current view. Food Chem Toxicol 2014; 73:71-83. [PMID: 25139119 DOI: 10.1016/j.fct.2014.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 08/06/2014] [Accepted: 08/08/2014] [Indexed: 01/03/2023]
Abstract
The successful treatment of many human diseases, including cancer, has come to be considered a major challenge, as patient response to therapy is difficult to predict. Recently, considerable efforts are being focused on the development of new tools to meet the growing demand for personalized medicine. With few exceptions, synthetic compounds have been unable to meet initial expectations for their clinical use. The last twenty years have been characterized by the failure of several drugs in advanced clinical development, possibly due to the insufficient understanding of molecular pathways underlying their mechanism of action. Although the biodiversity of compounds found in nature has been poorly explored until now, the field of naturally occurring drugs is rapidly expanding. Here, we review the current knowledge on the use of natural compounds with particular emphasis on those that display a chromatin remodeling effect coupled with anticancer action.
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Affiliation(s)
- Marco Miceli
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Universita' di Napoli, Via L. De Crecchio 7, 80138 Napoli, Italy; Istituto di Genetica e Biofisica, Adriano Buzzati-Traverso, IGB, Via P. Castellino 111, 80131 Napoli, Italy
| | - Paola Bontempo
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Universita' di Napoli, Via L. De Crecchio 7, 80138 Napoli, Italy
| | - Angela Nebbioso
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Universita' di Napoli, Via L. De Crecchio 7, 80138 Napoli, Italy
| | - Lucia Altucci
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Universita' di Napoli, Via L. De Crecchio 7, 80138 Napoli, Italy; Istituto di Genetica e Biofisica, Adriano Buzzati-Traverso, IGB, Via P. Castellino 111, 80131 Napoli, Italy.
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69
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Yiannakopoulou E. Targeting epigenetic mechanisms and microRNAs by aspirin and other non steroidal anti-inflammatory agents - implications for cancer treatment and chemoprevention. Cell Oncol (Dordr) 2014; 37:167-78. [DOI: 10.1007/s13402-014-0175-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2014] [Indexed: 12/21/2022] Open
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Rationalization of activity cliffs of a sulfonamide inhibitor of DNA methyltransferases with induced-fit docking. Int J Mol Sci 2014; 15:3253-61. [PMID: 24566147 PMCID: PMC3958909 DOI: 10.3390/ijms15023253] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 02/12/2014] [Accepted: 02/14/2014] [Indexed: 12/04/2022] Open
Abstract
Inhibitors of human DNA methyltransferases (DNMT) are of increasing interest to develop novel epi-drugs for the treatment of cancer and other diseases. As the number of compounds with reported DNMT inhibition is increasing, molecular docking is shedding light to elucidate their mechanism of action and further interpret structure–activity relationships. Herein, we present a structure-based rationalization of the activity of SW155246, a distinct sulfonamide compound recently reported as an inhibitor of human DNMT1 obtained from high-throughput screening. We used flexible and induce-fit docking to develop a binding model of SW155246 with a crystallographic structure of human DNMT1. Results were in excellent agreement with experimental information providing a three-dimensional structural interpretation of ‘activity cliffs’, e.g., analogues of SW155246 with a high structural similarity to the sulfonamide compound, but with no activity in the enzymatic assay.
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71
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Méndez-Lucio O, Tran J, Medina-Franco JL, Meurice N, Muller M. Toward Drug Repurposing in Epigenetics: Olsalazine as a Hypomethylating Compound Active in a Cellular Context. ChemMedChem 2014; 9:560-5. [DOI: 10.1002/cmdc.201300555] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Indexed: 11/09/2022]
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Asgatay S, Champion C, Marloie G, Drujon T, Senamaud-Beaufort C, Ceccaldi A, Erdmann A, Rajavelu A, Schambel P, Jeltsch A, Lequin O, Karoyan P, Arimondo PB, Guianvarc’h D. Synthesis and Evaluation of Analogues of N-Phthaloyl-l-tryptophan (RG108) as Inhibitors of DNA Methyltransferase 1. J Med Chem 2014; 57:421-34. [DOI: 10.1021/jm401419p] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Saâdia Asgatay
- Laboratoire des BioMolécules,
UMR 7203, Université Pierre et Marie Curie-Paris 6, ENS, CNRS, 4, Place Jussieu, 75252 Paris Cedex 05, France
| | - Christine Champion
- MNHN CNRS
UMR 7196, INSERM U565, 43 Rue Cuvier, 75005 Paris, France
- UPMC Université Paris 6, 75005 Paris, France
| | - Gaël Marloie
- Laboratoire des BioMolécules,
UMR 7203, Université Pierre et Marie Curie-Paris 6, ENS, CNRS, 4, Place Jussieu, 75252 Paris Cedex 05, France
| | - Thierry Drujon
- Laboratoire des BioMolécules,
UMR 7203, Université Pierre et Marie Curie-Paris 6, ENS, CNRS, 4, Place Jussieu, 75252 Paris Cedex 05, France
| | | | - Alexandre Ceccaldi
- MNHN CNRS
UMR 7196, INSERM U565, 43 Rue Cuvier, 75005 Paris, France
- UPMC Université Paris 6, 75005 Paris, France
| | - Alexandre Erdmann
- USR ETaC CNRS-Pierre Fabre No. 3388, CRDPF BP 13562, 3 Avenue Hubert Curien, 31100 Toulouse, France
| | - Arumugam Rajavelu
- Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Philippe Schambel
- Institut de Recherche Pierre
Fabre, Centre de Recherche Pierre Fabre, 17 Rue Jean Moulin, 81 106, Castres Cedex, France
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Olivier Lequin
- Laboratoire des BioMolécules,
UMR 7203, Université Pierre et Marie Curie-Paris 6, ENS, CNRS, 4, Place Jussieu, 75252 Paris Cedex 05, France
| | - Philippe Karoyan
- Laboratoire des BioMolécules,
UMR 7203, Université Pierre et Marie Curie-Paris 6, ENS, CNRS, 4, Place Jussieu, 75252 Paris Cedex 05, France
| | - Paola B. Arimondo
- MNHN CNRS
UMR 7196, INSERM U565, 43 Rue Cuvier, 75005 Paris, France
- USR ETaC CNRS-Pierre Fabre No. 3388, CRDPF BP 13562, 3 Avenue Hubert Curien, 31100 Toulouse, France
| | - Dominique Guianvarc’h
- Laboratoire des BioMolécules,
UMR 7203, Université Pierre et Marie Curie-Paris 6, ENS, CNRS, 4, Place Jussieu, 75252 Paris Cedex 05, France
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Medina-Franco JL, Méndez-Lucio O, Martinez-Mayorga K. The Interplay Between Molecular Modeling and Chemoinformatics to Characterize Protein–Ligand and Protein–Protein Interactions Landscapes for Drug Discovery. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 96:1-37. [DOI: 10.1016/bs.apcsb.2014.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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74
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Yan Z, Zhang L, Fu H, Wang Z, Lin J. Design of the influenza virus inhibitors targeting the PA endonuclease using 3D-QSAR modeling, side-chain hopping, and docking. Bioorg Med Chem Lett 2013; 24:539-47. [PMID: 24365156 DOI: 10.1016/j.bmcl.2013.12.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 12/02/2013] [Accepted: 12/06/2013] [Indexed: 11/26/2022]
Abstract
With the emergence of drug resistance and the structural determination of the PA N-terminal domain (PAN), influenza endonucleases have become an attractive target for antiviral therapies for influenza infection. Here, we combined 3D-QSAR with side-chain hopping and molecular docking to produce novel structures as endonuclease inhibitors. First, a new molecular library was generated with side-chain hopping on an existing template molecule, L-742001, using an in-house fragment library that targets bivalent-cation-binding proteins. Then, the best 3D-QSAR model (AAAHR.500), with q(2)=0.76 and r(2)=0.97 from phase modeling, was constructed from 23 endonuclease inhibitors and validated with 17 test compounds. The AAAHR.500 model was then used to select effective candidates from the new molecular library. Combining 3D-QSAR with docking using Glide and Autodock, 13 compounds were considered the most likely candidate inhibitors. Docking studies showed that the binding modes of these compounds were consistent with the crystal structures of known inhibitors. These compounds could serve as potential endonuclease inhibitors for further biological activity tests.
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Affiliation(s)
- Zhihui Yan
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology, Tianjin 300457, China
| | - Lijie Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology, Tianjin 300457, China
| | - Haiyang Fu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology, Tianjin 300457, China
| | - Zhonghua Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China; High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology, Tianjin 300457, China.
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75
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Lötsch J, Schneider G, Reker D, Parnham MJ, Schneider P, Geisslinger G, Doehring A. Common non-epigenetic drugs as epigenetic modulators. Trends Mol Med 2013; 19:742-53. [PMID: 24054876 DOI: 10.1016/j.molmed.2013.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 12/15/2022]
Abstract
Epigenetic effects are exerted by a variety of factors and evidence increases that common drugs such as opioids, cannabinoids, valproic acid, or cytostatics may induce alterations in DNA methylation patterns or histone conformations. These effects occur via chemical structural interactions with epigenetic enzymes, through interactions with DNA repair mechanisms. Computational predictions indicate that one-twentieth of all drugs might potentially interact with human histone deacetylase, which was prospectively experimentally verified for the compound with the highest predicted interaction probability. These epigenetic effects add to wanted and unwanted drug effects, contributing to mechanisms of drug resistance or disease-related and unrelated phenotypes. Because epigenetic changes might be transmitted to offspring, the need for reliable and cost-effective epigenetic screening tools becomes acute.
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Affiliation(s)
- Jörn Lötsch
- Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany; Fraunhofer Institute of Molecular Biology and Applied Ecology - Project Group Translational Medicine and Pharmacology (IME-TMP), Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany.
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76
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Durrant JD, Friedman AJ, Rogers KE, McCammon JA. Comparing neural-network scoring functions and the state of the art: applications to common library screening. J Chem Inf Model 2013; 53:1726-35. [PMID: 23734946 PMCID: PMC3735370 DOI: 10.1021/ci400042y] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Indexed: 11/29/2022]
Abstract
We compare established docking programs, AutoDock Vina and Schrödinger's Glide, to the recently published NNScore scoring functions. As expected, the best protocol to use in a virtual-screening project is highly dependent on the target receptor being studied. However, the mean screening performance obtained when candidate ligands are docked with Vina and rescored with NNScore 1.0 is not statistically different than the mean performance obtained when docking and scoring with Glide. We further demonstrate that the Vina and NNScore docking scores both correlate with chemical properties like small-molecule size and polarizability. Compensating for these potential biases leads to improvements in virtual screen performance. Composite NNScore-based scoring functions suited to a specific receptor further improve performance. We are hopeful that the current study will prove useful for those interested in computer-aided drug design.
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Affiliation(s)
- Jacob D Durrant
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA.
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77
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Cheray M, Pacaud R, Nadaradjane A, Vallette FM, Cartron PF. Specific inhibition of one DNMT1-including complex influences tumor initiation and progression. Clin Epigenetics 2013; 5:9. [PMID: 23809695 PMCID: PMC3727981 DOI: 10.1186/1868-7083-5-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 06/03/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reactivation of silenced tumor suppressor genes by DNMT inhibitors has provided an alternative approach to cancer therapy. However, DNMT inhibitors have also been shown to induce or enhance tumorigenesis via DNA hypomethylation-induced oncogene activation and chromosomal instability. To develop more specific DNMT inhibitors for efficient cancer therapy, we compared the effects of peptides designed to specifically disrupt the interaction of DNMT1 with different proteins. FINDINGS Our data indicated that the use of an unspecific DNMT inhibitor (5aza-2deoxycytidine), a DNMT1 inhibitor (procainamide) or peptides disrupting the DNMT1/PCNA, DNMT1/EZH2, DNMT1/HDAC1, DNMT1/DNMT3b and DNMT1/HP1 interactions promoted or enhanced in vivo tumorigenesis in a mouse glioma model. In contrast, a peptide disrupting the DNMT1/DMAP1 interaction, which per se did not affect tumor growth, sensitized cancer cells to chemotherapy/irradiation-induced cell death. Finally, our data indicated that the peptide disrupting the DNMT1/DMAP1 interaction increased the efficiency of temozolomide treatment. CONCLUSION Our data suggest that the DNMT1/DMAP1 interaction could be an effective anti-cancer target and opens a new avenue for the development of new strategies to design DNMT inhibitors.
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Affiliation(s)
- Mathilde Cheray
- Centre de Recherche en Cancérologie Nantes-Angers, INSERM, U892, Equipe Apoptose et progression tumorale, Equipe labellisée Ligue Nationale Contre le Cancer, 8 quai moncousu, BP7021, Nantes, 44007, France.
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Yoo J, Choi S, Medina-Franco JL. Molecular modeling studies of the novel inhibitors of DNA methyltransferases SGI-1027 and CBC12: implications for the mechanism of inhibition of DNMTs. PLoS One 2013; 8:e62152. [PMID: 23637988 PMCID: PMC3636198 DOI: 10.1371/journal.pone.0062152] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Accepted: 03/18/2013] [Indexed: 12/05/2022] Open
Abstract
DNA methylation is an epigenetic modification that regulates gene expression by DNA methyltransferases (DNMTs). Inhibition of DNMTs is a promising approach for cancer therapy. Recently, novel classes of the quinolone-based compound, SGI-1027, and RG108-procainamide conjugates, CBC12, have been identified as potent DNMT inhibitors. In this work, we report comprehensive studies using induced-fit docking of SGI-1027 and CBC12 with human DNMT1 and DNMT3A. The docking was performed in the C-terminal MTase catalytic domain, which contains the substrate and cofactor binding sites, in the presence and absence of other domains. Induced-fit docking predicts possible binding modes of the ligands through the appropriate structural changes in the receptor. This work suggests a hypothesis of the inhibitory mechanisms of the new inhibitors which is in agreement with the reported autoinhibitory mechanism. The insights obtained in this work can be used to design DNMT inhibitors with novel scaffolds.
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Affiliation(s)
- Jakyung Yoo
- National Leading Research Lab of Molecular Modeling & Drug Design, College of Pharmacy, Division of Life and Pharmaceutical Sciences, and Global Top5 Research Program, Ewha Womans University, Seoul, Korea
| | - Sun Choi
- National Leading Research Lab of Molecular Modeling & Drug Design, College of Pharmacy, Division of Life and Pharmaceutical Sciences, and Global Top5 Research Program, Ewha Womans University, Seoul, Korea
- * E-mail: (SC) (SC); (JLMF) (JM)
| | - José L. Medina-Franco
- Instituto de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
- * E-mail: (SC) (SC); (JLMF) (JM)
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79
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Popovic R, Shah MY, Licht JD. Epigenetic therapy of hematological malignancies: where are we now? Ther Adv Hematol 2013; 4:81-91. [PMID: 23610616 DOI: 10.1177/2040620712466864] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A growing amount of evidence points towards alterations in epigenetic machinery as a leading cause in disease initiation and progression. Like genetic alterations, misregulation of the epigenetic regulators can lead to abnormal gene expression. However, unlike genetic events, the epigenetic machinery may be targeted pharmacologically, potentially resulting in the reversal of a particular epigenetic state. The success of DNA methyltransferase and histone deacetylase inhibitors represents a proof of concept for the use of therapies intended to target the epigenome in the treatment of hematological malignancies. Nevertheless, the molecular mechanisms underlying the efficacy of these agents have not been completely elucidated. Recently, a large number of studies sequencing cancer cell genomes identified recurring mutations of epigenetic regulators, providing new insights into the molecular underpinnings of cancer. Consequently, the efforts to identify specific epigenetic inhibitors have been expanded in order to target particular subsets of patients. This review will summarize the progress made using the currently available epigenetic therapies and discuss some of the more recently identified targets whose inhibition may present potential avenues for the treatment of hematologic malignancies.
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Affiliation(s)
- Relja Popovic
- Division of Hematology/Oncology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
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80
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Chikan NA, Bhavaniprasad V, Anbarasu K, Shabir N, Patel TN. From natural products to drugs for epimutation computer-aided drug design. Appl Biochem Biotechnol 2013; 170:164-75. [PMID: 23483409 DOI: 10.1007/s12010-013-0158-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 02/18/2013] [Indexed: 12/26/2022]
Abstract
The epimutational event, i.e., ectopic methylation in tumor suppressor genes, can lead to gene silencing, thus promoting prognosis of cancer. The progression of DNA methylation is a cycle of demethylation, de novo methylation, and maintenance methylation. The enzyme responsible for maintenance of methylation status is DNA methyltransferase 1 (DNMT1), the continuous activity of which is required to maintain the pattern of epimutation; thus, its inhibition is a promising strategy for the treatment of cancer. To the best of our knowledge, this study is the first to focus on the recently developed crystal structure of the catalytic site of DNMT1. Here in this study, we have used the crystal structure for the development of non-nucleoside DNMT1 inhibitors using virtual screening (VS), absorption, distribution, metabolism, elimination/toxicology analysis, and molecular docking studies. In this study, VS was carried out on 48,531 natural products to create a subset of lead-like natural products. Three of them were found to form hydrogen bonds with the catalytic site of the DNMT1 (Cys 1226). Thus, this study adumbrates potential lead compounds for treatment of epimutation.
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Affiliation(s)
- Naveed A Chikan
- School of Bioscience and Technology, VIT University, Vellore, Tamil Nadu, India
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81
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Medina-Franco JL, Yoo J. Docking of a novel DNA methyltransferase inhibitor identified from high-throughput screening: insights to unveil inhibitors in chemical databases. Mol Divers 2013; 17:337-44. [PMID: 23447100 DOI: 10.1007/s11030-013-9428-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Accepted: 02/07/2013] [Indexed: 12/21/2022]
Abstract
Inhibitors of DNA methyltransferase (DNMT) are attractive compounds not only as potential therapeutic agents for the treatment of cancer and other diseases, but also as research tools to investigate the role of DNMTs in epigenetic events. Recent advances in high-throughput screening (HTS) for epigenetic targets and the availability of the first crystallographic structure of human DNMT1 encourage the integration of research strategies to uncover and optimize the activity of DNMT inhibitors. Herein, we present a binding model of a novel small-molecule DNMT1 inhibitor obtained by HTS, recently released in a public database. The docking model is in agreement with key interactions previously identified for established inhibitors using extensive computational studies including molecular dynamics and structure-based pharmacophore modeling. Based on the chemical structure of the novel inhibitor, a sequential computational screening of five chemical databases was performed to identify candidate compounds for testing. Similarity searching followed by molecular docking of chemical databases such as approved drugs, natural products, a DNMT-focused library, and a general screening collection, identified at least 108 molecules with promising DNMT inhibitory activity. The chemical structures of all hit compounds are disclosed to encourage the research community working on epigenetics to test experimentally the enzymatic and demethylating activity in vivo. Five candidate hits are drugs approved for other indications and represent potential starting points of a drug repurposing strategy.
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Affiliation(s)
- José L Medina-Franco
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, 04510 México, D.F., Mexico.
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82
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Link A, Balaguer F, Shen Y, Lozano JJ, Leung HCE, Boland CR, Goel A. Curcumin modulates DNA methylation in colorectal cancer cells. PLoS One 2013; 8:e57709. [PMID: 23460897 PMCID: PMC3584082 DOI: 10.1371/journal.pone.0057709] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 01/25/2013] [Indexed: 02/07/2023] Open
Abstract
Aim Recent evidence suggests that several dietary polyphenols may exert their chemopreventive effect through epigenetic modifications. Curcumin is one of the most widely studied dietary chemopreventive agents for colon cancer prevention, however, its effects on epigenetic alterations, particularly DNA methylation, remain unclear. Using systematic genome-wide approaches, we aimed to elucidate the effect of curcumin on DNA methylation alterations in colorectal cancer cells. Materials and Methods To evaluate the effect of curcumin on DNA methylation, three CRC cell lines, HCT116, HT29 and RKO, were treated with curcumin. 5-aza-2′-deoxycytidine (5-aza-CdR) and trichostatin A treated cells were used as positive and negative controls for DNA methylation changes, respectively. Methylation status of LINE-1 repeat elements, DNA promoter methylation microarrays and gene expression arrays were used to assess global methylation and gene expression changes. Validation was performed using independent microarrays, quantitative bisulfite pyrosequencing, and qPCR. Results As expected, genome-wide methylation microarrays revealed significant DNA hypomethylation in 5-aza-CdR-treated cells (mean β-values of 0.12), however, non-significant changes in mean β-values were observed in curcumin-treated cells. In comparison to mock-treated cells, curcumin-induced DNA methylation alterations occurred in a time-dependent manner. In contrast to the generalized, non-specific global hypomethylation observed with 5-aza-CdR, curcumin treatment resulted in methylation changes at selected, partially-methylated loci, instead of fully-methylated CpG sites. DNA methylation alterations were supported by corresponding changes in gene expression at both up- and down-regulated genes in various CRC cell lines. Conclusions Our data provide previously unrecognized evidence for curcumin-mediated DNA methylation alterations as a potential mechanism of colon cancer chemoprevention. In contrast to non-specific global hypomethylation induced by 5-aza-CdR, curcumin-induced methylation changes occurred only in a subset of partially-methylated genes, which provides additional mechanistic insights into the potent chemopreventive effect of this dietary nutraceutical.
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Affiliation(s)
- Alexander Link
- Gastrointestinal Cancer Research Laboratory, Division of Gastroenterology, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas, United States of America
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University, Magdeburg, Germany
| | - Francesc Balaguer
- Gastrointestinal Cancer Research Laboratory, Division of Gastroenterology, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas, United States of America
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Yan Shen
- Gastrointestinal Cancer Research Laboratory, Division of Gastroenterology, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas, United States of America
| | - Juan Jose Lozano
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Hon-Chiu E. Leung
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - C. Richard Boland
- Gastrointestinal Cancer Research Laboratory, Division of Gastroenterology, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas, United States of America
| | - Ajay Goel
- Gastrointestinal Cancer Research Laboratory, Division of Gastroenterology, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas, United States of America
- * E-mail:
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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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Aparoy P, Reddy KK, Reddanna P. Structure and ligand based drug design strategies in the development of novel 5- LOX inhibitors. Curr Med Chem 2012; 19:3763-78. [PMID: 22680930 PMCID: PMC3480706 DOI: 10.2174/092986712801661112] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 01/30/2012] [Accepted: 02/07/2012] [Indexed: 12/26/2022]
Abstract
Lipoxygenases (LOXs) are non-heme iron containing dioxygenases involved in the oxygenation of polyunsaturated fatty acids (PUFAs) such as arachidonic acid (AA). Depending on the position of insertion of oxygen, LOXs are classified into 5-, 8-, 9-, 12- and 15-LOX. Among these, 5-LOX is the most predominant isoform associated with the formation of 5-hydroperoxyeicosatetraenoic acid (5-HpETE), the precursor of non-peptido (LTB4) and peptido (LTC4, LTD4, and LTE4) leukotrienes. LTs are involved in inflammatory and allergic diseases like asthma, ulcerative colitis, rhinitis and also in cancer. Consequently 5-LOX has become target for the development of therapeutic molecules for treatment of various inflammatory disorders. Zileuton is one such inhibitor of 5-LOX approved for the treatment of asthma. In the recent times, computer aided drug design (CADD) strategies have been applied successfully in drug development processes. A comprehensive review on structure based drug design strategies in the development of novel 5-LOX inhibitors is presented in this article. Since the crystal structure of 5-LOX has been recently solved, efforts to develop 5-LOX inhibitors have mostly relied on ligand based rational approaches. The present review provides a comprehensive survey on these strategies in the development of 5-LOX inhibitors.
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85
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Zhavoronkov A, Smit-McBride Z, Guinan KJ, Litovchenko M, Moskalev A. Potential therapeutic approaches for modulating expression and accumulation of defective lamin A in laminopathies and age-related diseases. J Mol Med (Berl) 2012; 90:1361-89. [PMID: 23090008 PMCID: PMC3506837 DOI: 10.1007/s00109-012-0962-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Revised: 09/08/2012] [Accepted: 09/25/2012] [Indexed: 01/28/2023]
Abstract
Scientific understanding of the genetic components of aging has increased in recent years, with several genes being identified as playing roles in the aging process and, potentially, longevity. In particular, genes encoding components of the nuclear lamina in eukaryotes have been increasingly well characterized, owing in part to their clinical significance in age-related diseases. This review focuses on one such gene, which encodes lamin A, a key component of the nuclear lamina. Genetic variation in this gene can give rise to lethal, early-onset diseases known as laminopathies. Here, we analyze the literature and conduct computational analyses of lamin A signaling and intracellular interactions in order to examine potential mechanisms for altering or slowing down aberrant Lamin A expression and/or for restoring the ratio of normal to aberrant lamin A. The ultimate goal of such studies is to ameliorate or combat laminopathies and related diseases of aging, and we provide a discussion of current approaches in this review.
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Affiliation(s)
- Alex Zhavoronkov
- Bioinformatics and Medical Information Technology Laboratory, Center for Pediatric Hematology, Oncology and Immunology, Moscow, 119296 Russia
- The Biogerontology Research Foundation, Reading, UK
| | - Zeljka Smit-McBride
- Department of Ophthalmology and Vision Science, School of Medicine, University of California at Davis, Davis, CA 95616 USA
| | - Kieran J. Guinan
- The Biogerontology Research Foundation, Reading, UK
- BioAtlantis Ltd., Kerry Technology Park, Tralee, County Kerry Ireland
| | - Maria Litovchenko
- Bioinformatics and Medical Information Technology Laboratory, Center for Pediatric Hematology, Oncology and Immunology, Moscow, 119296 Russia
| | - Alexey Moskalev
- The Biogerontology Research Foundation, Reading, UK
- Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology, Komi Science Center of Russian Academy of Sciences, Syktyvkar, 167982 Russia
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86
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Yoo J, Kim JH, Robertson KD, Medina-Franco JL. Molecular modeling of inhibitors of human DNA methyltransferase with a crystal structure: discovery of a novel DNMT1 inhibitor. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 87:219-47. [PMID: 22607757 PMCID: PMC3837394 DOI: 10.1016/b978-0-12-398312-1.00008-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA methyltransferases (DNMTs) are promising epigenetic targets for the development of novel anticancer drugs and other diseases. Molecular modeling and experimental approaches are being used to identify and develop inhibitors of human DNMTs. Most of the computational efforts conducted so far with DNMT1 employ homology models of the enzyme. Recently, a crystallographic structure of the methyltransferase domain of human DNMT1 bound to unmethylated DNA was published. Following on our previous computational and experimental studies with DNMTs, we herein present molecular dynamics of the crystal structure of human DNMT1. Docking studies of established DNMT1 inhibitors with the crystal structure gave rise to a structure-based pharmacophore model that suggests key interactions of the inhibitors with the catalytic binding site. Results had a good agreement with the docking and pharmacophore models previously developed using a homology model of the catalytic domain of DNMT1. The docking protocol was able to distinguish active DNMT1 inhibitors from, for example, experimentally known inactive DNMT1 inhibitors. As part of our efforts to identify novel inhibitors of DNMT1, we conducted the experimental characterization of aurintricarboxylic acid (ATA) that in preliminary docking studies showed promising activity. ATA had a submicromolar inhibition (IC50 = 0.68 μM) against DNMT1. ATA was also evaluated for Dnmt3a inhibition showing an IC50 = 1.4 μM. This chapter illustrates the synergy from integrating molecular modeling and experimental methods to further advance the discovery of novel candidates for epigenetic therapies.
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Affiliation(s)
- Jakyung Yoo
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida, USA
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87
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García-Domínguez P, Weiss M, Lepore I, Álvarez R, Altucci L, Gronemeyer H, de Lera ÁR. A DNA Methyltransferase Modulator Inspired by Peyssonenyne Natural Product Structures. ChemMedChem 2012; 7:2101-12. [DOI: 10.1002/cmdc.201200366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/10/2012] [Indexed: 01/04/2023]
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88
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Thomas X. DNA methyltransferase inhibitors in acute myeloid leukemia: discovery, design and first therapeutic experiences. Expert Opin Drug Discov 2012; 7:1039-51. [PMID: 22950862 DOI: 10.1517/17460441.2012.722618] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION DNA methylation is an epigenetic change mediated by DNA methyltranferases (DNMTs), which are promising epigenetic targets for the treatment of acute myeloid leukemia (AML). This is evidenced by the two DNMT inhibitors (azacitidine and decitabine) approved by the Food and Drug Administration of the United States for the treatment of high-risk myelodysplastic syndromes and the first clinical data available in AML. AREAS COVERED This paper reviews data from the international literature regarding the design, sites of impact and pharmacodynamic characteristics of DNMT inhibitors, and their first clinical experiences in AML. EXPERT OPINION The strongest advances in epigenetic therapy have been in the treatment of AML. There are now an increasing number of DNMT inhibitors. These agents may be potentially administered at different times of leukemia therapy: before or instead of chemotherapy, as maintenance therapy, prior to allogeneic stem cell transplant (SCT) or after relapse following SCT.
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Affiliation(s)
- Xavier Thomas
- Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, Service d'Hématologie Clinique, Pierre Bénite, France.
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89
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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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90
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Van De Voorde L, Speeckaert R, Van Gestel D, Bracke M, De Neve W, Delanghe J, Speeckaert M. DNA methylation-based biomarkers in serum of patients with breast cancer. Mutat Res 2012; 751:304-325. [PMID: 22698615 DOI: 10.1016/j.mrrev.2012.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 06/03/2012] [Accepted: 06/05/2012] [Indexed: 12/18/2022]
Abstract
Alterations of genetic and epigenetic features can provide important insights into the natural history of breast cancer. Although DNA methylation analysis is a rapidly developing field, a reproducible epigenetic blood-based assay for diagnosis and follow-up of breast cancer has yet to be successfully developed into a routine clinical test. The aim of this study was to review multiple serum DNA methylation assays and to highlight the value of those novel biomarkers in diagnosis, prognosis and prediction of therapeutic outcome. Serum is readily accessible for molecular diagnosis in all individuals from a peripheral blood sample. The list of hypermethylated genes in breast cancer is heterogeneous and no single gene is methylated in all breast cancer types. There is increasing evidence that a panel of epigenetic markers is essential to achieve a higher sensitivity and specificity in breast cancer detection. However, the reported percentages of methylation are highly variable, which can be partly explained by the different sensitivities and the different intra-/inter-assay coefficients of variability of the analysis methods. Moreover, there is a striking lack of receiver operating characteristic (ROC) curves of the proposed biomarkers. Another point of criticism is the fact that 'normal' patterns of DNA methylation of some tumor suppressor and other cancer-related genes are influenced by several factors and are often poorly characterized. A relatively frequent methylation of those genes has been observed in high-risk asymptomatic women. Finally, there is a call for larger prospective cohort studies to determine methylation patterns during treatment and follow-up. Identification of patterns specific for a differential response to therapeutic interventions should be useful. Only in this way, it will be possible to evaluate the predictive and prognostic characteristics of those novel promising biomarkers.
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Affiliation(s)
- Lien Van De Voorde
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | | | - Dirk Van Gestel
- Department of Radiation Oncology, Antwerp University Hospital, Antwerp, Belgium
| | - Marc Bracke
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | - Wilfried De Neve
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | - Joris Delanghe
- Department of Clinical Chemistry, Ghent University Hospital, Ghent, Belgium
| | - Marijn Speeckaert
- Department of Clinical Chemistry, Ghent University Hospital, Ghent, Belgium; Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium.
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91
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Abstract
A number of bioactive dietary components are of particular interest in the field of epigenetics. Many of these compounds display anticancer properties and may play a role in cancer prevention. Numerous studies suggest that a number of nutritional compounds have epigenetic targets in cancer cells. Importantly, emerging evidence strongly suggests that consumption of dietary agents can alter normal epigenetic states as well as reverse abnormal gene activation or silencing. Epigenetic modifications induced by bioactive dietary compounds are thought to be beneficial. Substantial evidence is mounting proclaiming that commonly consumed bioactive dietary factors act to modify the epigenome and may be incorporated into an 'epigenetic diet'. Bioactive nutritional components of an epigenetic diet may be incorporated into one's regular dietary regimen and used therapeutically for medicinal or chemopreventive purposes. This article will primarily focus on dietary factors that have been demonstrated to influence the epigenome and that may be used in conjunction with other cancer prevention and chemotherapeutic therapies.
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Affiliation(s)
- Tabitha M Hardy
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA
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92
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Baud MGJ, Leiser T, Haus P, Samlal S, Wong AC, Wood RJ, Petrucci V, Gunaratnam M, Hughes SM, Buluwela L, Turlais F, Neidle S, Meyer-Almes FJ, White AJP, Fuchter MJ. Defining the Mechanism of Action and Enzymatic Selectivity of Psammaplin A against Its Epigenetic Targets. J Med Chem 2012; 55:1731-50. [DOI: 10.1021/jm2016182] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Matthias G. J. Baud
- Department of Chemistry, Imperial
College London, London SW7 2AZ, United Kingdom
| | - Thomas Leiser
- Department of Chemical Engineering
and Biotechnology, University of Applied Sciences, Schnittspahnstrasse 12, 64287 Darmstadt, Germany
| | - Patricia Haus
- Department of Chemical Engineering
and Biotechnology, University of Applied Sciences, Schnittspahnstrasse 12, 64287 Darmstadt, Germany
| | - Sharon Samlal
- Cancer Research Technology Discovery
Laboratories, Wolfson Institute for Biomedical Research, The Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
| | - Ai Ching Wong
- Cancer Research Technology Discovery
Laboratories, Wolfson Institute for Biomedical Research, The Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
| | - Robert J. Wood
- Cancer Research Technology Discovery
Laboratories, Wolfson Institute for Biomedical Research, The Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
| | - Vanessa Petrucci
- Cancer Research UK Biomolecular Structure
Group, The School of Pharmacy, University of London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Mekala Gunaratnam
- Cancer Research UK Biomolecular Structure
Group, The School of Pharmacy, University of London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Siobhan M. Hughes
- Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 0NN,
United Kingdom
| | - Lakjaya Buluwela
- Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 0NN,
United Kingdom
| | - Fabrice Turlais
- Cancer Research Technology Discovery
Laboratories, Wolfson Institute for Biomedical Research, The Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
| | - Stephen Neidle
- Cancer Research UK Biomolecular Structure
Group, The School of Pharmacy, University of London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering
and Biotechnology, University of Applied Sciences, Schnittspahnstrasse 12, 64287 Darmstadt, Germany
| | - Andrew J. P. White
- Department of Chemistry, Imperial
College London, London SW7 2AZ, United Kingdom
| | - Matthew J. Fuchter
- Department of Chemistry, Imperial
College London, London SW7 2AZ, United Kingdom
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93
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Abstract
The fundamental role of altered epigenetic modification patterns in tumorigenesis establishes epigenetic regulatory enzymes as important targets for cancer therapy. Over the past few years, several drugs with an epigenetic activity have received approval for the treatment of cancer patients, which has led to a detailed characterization of their modes of action. The results showed that both established drug classes, the histone deacetylase (HDAC) inhibitors and the DNA methyltransferase inhibitors, show substantial limitations in their epigenetic specificity. HDAC inhibitors are highly specific drugs, but the enzymes have a broad substrate specificity and deacetylate numerous proteins that are not associated with epigenetic regulation. Similarly, the induction of global DNA demethylation by non-specific inhibition of DNA methyltransferases shows pleiotropic effects on epigenetic regulation with no apparent tumor-specificity. Second-generation azanucleoside drugs have integrated the knowledge about the cellular uptake and metabolization pathways, but do not show any increased specificity for cancer epigenotypes. As such, the traditional rationale of epigenetic cancer therapy appears to be in need of refinement, as we move from the global inhibition of epigenetic modifications toward the identification and targeting of tumor-specific epigenetic programs. Recent studies have identified epigenetic mechanisms that promote self-renewal and developmental plasticity in cancer cells. Druggable somatic mutations in the corresponding epigenetic regulators are beginning to be identified and should facilitate the development of epigenetic therapy approaches with improved tumor specificity.
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94
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Caulfield T, Medina-Franco JL. Molecular dynamics simulations of human DNA methyltransferase 3B with selective inhibitor nanaomycin A. J Struct Biol 2011; 176:185-91. [PMID: 21839172 DOI: 10.1016/j.jsb.2011.07.015] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 07/25/2011] [Accepted: 07/27/2011] [Indexed: 02/08/2023]
Abstract
DNA methyltransferases (DNMTs) are involved in epigenetic regulation of the genome and are promising targets for therapeutic intervention in cancer and other diseases. Until now, very limited information is available concerning the molecular dynamics of DNMTs. The natural product nanaomycin A is the first selective inhibitor of DNMT3B that induce genomic demethylation. Herein we report long (>100ns) molecular dynamics simulations for human DNMT3B bound to nanaomycin A with and without the presence of the cofactor S-adenosyl-L-methionine (SAM). We concluded that SAM favors the binding of nanaomycin A to DNMT3B. Key interactions of nanaomycin A with DNMT3B involve long lasting interactions with Arg731, Arg733, Arg832, and the catalytic Cys651. Results further support the previous hypothesis that nanaomycin A has key interactions with amino acid residues involved in the mechanism of methylation. This work represents one of the first molecular dynamics studies of DNMT3B. Results of this work shed light on the structure and binding recognition process of a key epigenetic enzyme with a small molecule inhibitor.
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Affiliation(s)
- Thomas Caulfield
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, FL 34987, USA
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95
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Eglen RM, Reisine T. Screening for Compounds That Modulate Epigenetic Regulation of the Transcriptome. ACTA ACUST UNITED AC 2011; 16:1137-52. [DOI: 10.1177/1087057111417871] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Epigenetic control of the transciptome is a complex and highly coordinated cellular process. One critical mechanism involves DNA methylation, mediated by distinct but related DNA methyltransferases (DNMTs). Although several DNMT inhibitors are available, most are nonselective; selective DNMT inhibitors, therefore, could be optimal as therapeutics, as well acting as chemical probes to elucidate the fundamental biology of individual DNMTs. DNA methylation is a stable chemical modification, yet posttranslational modification of histones is transitory, with reversible effects on gene expression. Histone posttranslational modifications influence access of transcription factors to DNA target sites to affect gene activity. Histones are regulated by several enzymes, including acetylases (HATs), deacetylases (HDACs), methyltransferases (HMTs), and demethylases (HDMTs). Generally, HATs activate, whereas HDACs suppress gene activity. Specifically, HMTs and HDMTs can either activate or inhibit gene expression, depending on the site and extent of the methylation pattern. There is growing interest in drugs that target enzymes involved in epigenetic control. Currently, a range of high-throughput screening (HTS) technologies are used to identify selective compounds against these enzymes. This review focuses on the rationale for drug development of these enzymes, as well the utility of HTS methods used in identifying and optimizing novel selective compounds that modulate epigenetic control of the human transcriptome.
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96
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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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97
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Foulks JM, Parnell KM, Nix RN, Chau S, Swierczek K, Saunders M, Wright K, Hendrickson TF, Ho KK, McCullar MV, Kanner SB. Epigenetic drug discovery: targeting DNA methyltransferases. ACTA ACUST UNITED AC 2011; 17:2-17. [PMID: 21965114 DOI: 10.1177/1087057111421212] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Epigenetic modification of DNA leads to changes in gene expression. DNA methyltransferases (DNMTs) comprise a family of nuclear enzymes that catalyze the methylation of CpG dinucleotides, resulting in an epigenetic methylome distinguished between normal cells and those in disease states such as cancer. Disrupting gene expression patterns through promoter methylation has been implicated in many malignancies and supports DNMTs as attractive therapeutic targets. This review focuses on the rationale of targeting DNMTs in cancer, the historical approach to DNMT inhibition, and current marketed hypomethylating therapeutics azacytidine and decitabine. In addition, we address novel DNMT inhibitory agents emerging in development, including CP-4200 and SGI-110, analogs of azacytidine and decitabine, respectively; the oligonucleotides MG98 and miR29a; and a number of reversible inhibitors, some of which appear to be selective against particular DNMT isoforms. Finally, we discuss future opportunities and challenges for next-generation therapeutics.
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Affiliation(s)
- Jason M Foulks
- Astex Pharmaceuticals, Inc., Salt Lake City, UT 84109, USA.
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98
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Yoo J, Medina-Franco JL. Trimethylaurintricarboxylic acid inhibits human DNA methyltransferase 1: insights from enzymatic and molecular modeling studies. J Mol Model 2011; 18:1583-9. [PMID: 21805123 PMCID: PMC7087970 DOI: 10.1007/s00894-011-1191-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 07/18/2011] [Indexed: 01/09/2023]
Abstract
DNA methyltransferase 1 (DNMT1) is an emerging target for the treatment of cancer, brain disorders, and other diseases. Currently, there are only a few DNMT1 inhibitors with potential application as therapeutic agents or research tools. 5,5-Methylenedisalicylic acid is a novel scaffold previously identified by virtual screening with detectable although weak inhibitory activity of DNMT1 in biochemical assays. Herein, we report enzyme inhibition of a structurally related compound, trimethylaurintricarboxylic acid (NSC97317) that showed a low micromolar inhibition of DNMT1 (IC50 = 4.79 μM). Docking studies of the new inhibitor with the catalytic domain of DNMT1 suggest that NSC97317 can bind into the catalytic site. Interactions with amino acid residues that participate in the mechanism of DNA methylation contribute to the binding recognition. In addition, NSC97317 had a good match with a structure-based pharmacophore model recently developed for inhibitors of DNMT1. Trimethylaurintricarboxylic acid can be a valuable biochemical tool to study DNMT1 inhibition in cancer and other diseases related to DNA methylation. Trimethylaurintricarboxylic acid (NSC97317) is a novel and low micromolar inhibitor of DNMT1 ![]()
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Affiliation(s)
- Jakyung Yoo
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, FL 34987, USA
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99
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Mutations in epigenetic modifiers in myeloid malignancies and the prospect of novel epigenetic-targeted therapy. Adv Hematol 2011; 2012:469592. [PMID: 21811504 PMCID: PMC3145345 DOI: 10.1155/2012/469592] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 06/02/2011] [Indexed: 11/17/2022] Open
Abstract
In the recent years, the discovery of a series of mutations in patients with myeloid malignancies has provided insight into the pathogenesis of myelodysplastic syndromes (MDSs), myeloproliferative neoplasms (MPNs), and acute myeloid leukemia (AML). Among these alterations have been mutations in genes, such as IDH1/2, TET2, DNMT3A, and EZH2, which appear to affect DNA and/or histone lysine methylation. Large clinical correlative studies are beginning to decipher the clinical importance, prevalence, and potential prognostic significance of these mutations. Additionally, burgeoning insight into the role of epigenetics in the pathogenesis of myeloid malignancies has prompted increased interest in development of novel therapies which target DNA and histone posttranslational modifications. DNA demethylating agents have been demonstrated to be clinically active in a subset of patients with MDS and AML and are used extensively. However, newer, more specific agents which alter DNA and histone modification are under preclinical study and development and are likely to expand our therapeutic options for these diseases in the near future. Here, we review the current understanding of the clinical importance of these newly discovered mutations in AML and MDS patients. We also discuss exciting developments in DNA methyltransferase inhibitor strategies and the prospect of novel histone lysine methyltransferase inhibitors.
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100
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Yoo J, Medina-Franco JL. Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase. J Comput Aided Mol Des 2011; 25:555-67. [DOI: 10.1007/s10822-011-9441-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 05/30/2011] [Indexed: 11/28/2022]
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