Docking of a novel DNA methyltransferase inhibitor identified from high-throughput screening: Insights to unveil inhibitors in chemical databases

Molecular Diversity

Volumn 17, Issue 2, 2013, Pages 337-344

  Medina Franco, José L ^a   Yoo, Jakyung ^b  

^a UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

^b Ewha Womans University   (South Korea)

Author keywords

Cancer; DNMT; Docking; Drug repurposing; Epigenetics; Natural products

Indexed keywords

5 AZA 2' DEOXYCYTIDINE; CURCUMIN; DNA METHYLTRANSFERASE 1 INHIBITOR; DNA METHYLTRANSFERASE INHIBITOR; HYDRALAZINE; ISOXAZOLINE DERIVATIVE; MAHANINE; N PHTHALOYLTRYPTOPHAN; NANAOMYCIN A; NSC 14778; PARTHENOLIDE; PROCAINAMIDE; PROCAINE; SGI 1027; SID 49645275; UNCLASSIFIED DRUG; ZEBULARINE;

ARTICLE; CHEMICAL DATABASE; CHEMICAL STRUCTURE; EPIGENETICS; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PRIORITY JOURNAL;

ALGORITHMS; BIOLOGICAL AGENTS; DATABASES, CHEMICAL; DNA (CYTOSINE-5-)-METHYLTRANSFERASE; DRUG REPOSITIONING; ENZYME INHIBITORS; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; MOLECULAR DOCKING SIMULATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SMALL MOLECULE LIBRARIES;

EID: 84880703261     PISSN: 13811991     EISSN: 1573501X     Source Type: Journal    
DOI: 10.1007/s11030-013-9428-z     Document Type: Article

References (41)

1. Rius M, Lyko F (2012) Epigenetic cancer therapy: rationales, targets and drugs. Oncogene 31:4257-4265. doi: 10.1038/onc.2011.601
2. Jones PA, Baylin SB (2007) The epigenomics of cancer. Cell 128:683-692. doi: 10.1016/j.cell.2007.01.029
3. Yoo J, Medina-Franco JL (2012) Inhibitors of DNA methyltransferases: insights from computational studies. Curr Med Chem 19:3475-3487
4. Martinet N, Michel BY, Bertrand P, Benhida R (2012) Small molecules DNA methyltransferases inhibitors. MedChemComm 3: 263-273. doi: 10.1039/c1md00194a
5. Foulks JM, Parnell KM, Nix RN, Chau S, Swierczek K, Saunders M, Wright K, Hendrickson TF, Ho K-K, McCullar MV, Kanner SB (2012) Epigenetic drug discovery: targeting DNA methyltransferases. J Biomol Screen 17:2-17. doi: 10.1177/1087057111421212
6. Halby L, Champion C, Sénamaud-Beaufort C, Ajjan S, Drujon T, Rajavelu A, Ceccaldi A, Jurkowska R, Lequin O, Nelson WG, Guy A, Jeltsch A, Guianvarc'h D, Ferroud C, Arimondo PB (2012) Rapid synthesis of new DNMT inhibitors derivatives of procainamide. ChemBioChem 13:157-165. doi: 10.1002/cbic.201100522
7. Kuck D, Singh N, Lyko F, Medina-Franco JL (2010) Novel and selective DNA methyltransferase inhibitors: docking-based virtual screening and experimental evaluation. Bioorg Med Chem 18:822-829. doi: 10.1016/j.bmc.2009.11.050
8. Nicola G, Liu T, Gilson MK (2012) Public domain databases for medicinal chemistry. J Med Chem 55:6987-7002. doi: 10.1021/jm300501t
9. Medina-Franco JL, Caulfield T (2011) Advances in the computational development of DNA methyltransferase inhibitors. Drug Discov Today 16:418-425. doi: 10.1016/j.drudis.2011.02.003
10. Ye Y, Stivers JT (2010) Fluorescence-based high-throughput assay for human DNA (cytosine-5)-methyltransferase 1. Anal Biochem 401:168-172. doi: 10.1016/j.ab.2010.02.032
11. Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, Overington JP (2012) ChEMBL: a large-scale bioactivity database for drug discovery. Nucl Acids Res 40:D1100-D1107. doi: 10.1093/nar/gkr777
12. Wang YL, Xiao JW, Suzek TO, Zhang J, Wang JY, Zhou ZG, Han LY, Karapetyan K, Dracheva S, Shoemaker BA, Bolton E, Gindulyte A, Bryant SH (2012) PubChem's bioassay database. Nucl Acids Res 40:D400-D412. doi: 10.1093/nar/gkr1132
13. Song J, Rechkoblit O, Bestor TH, Patel DJ (2011) Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation. Science 331:1036-1040. doi: 10.1126/science.1195380
14. Cheng XD, Blumenthal RM (2008) Mammalian DNA methyltransferases: a structural perspective. Structure 16:341-350. doi: 10.1016/j.str.2008.01.004
15. Sippl W, Jung M (2009) DNA methyltransferase inhibitors. In:, Sippl W, Jung M (eds) Epigenetic targets in drug discovery. Wiley-VCH, Weinheim, pp. 163-183. doi: 10.1002/9783527627073.ch8
16. Lan J, Hua S, He XN, Zhang Y (2010) DNA methyltransferases and methyl-binding proteins of mammals. Acta Biochim Biophys Sin 42:243-252. doi: 10.1093/abbs/gmq015
17. Yoo J, Kim JH, Robertson KD, Medina-Franco JL (2012) Molecular modeling of inhibitors of human DNA methyltransferase with a crystal structure: discovery of a novel DNMT1 inhibitor. Adv Protein Chem Struct Biol 87:219-247. doi: 10.1016/B978-0-12-398312-1.00008-1
18. Yoo J, Medina-Franco JL (2011) Homology modeling, docking, and structure-based pharmacophore of inhibitors of DNA methyltransferase. J Comput Aided Mol Des 25:555-567. doi: 10.1007/s10822-011-9441-1
19. Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727-748. doi: 10.1006/jmbi.1996.0897
20. Yoo J, Medina-Franco JL (2013) Molecular modeling and virtual screening of DNA methyltransferase inhibitors. Curr Pharm Des (in press)
21. Hernández-Campos A, Velázquez-Martínez I, Castillo R, López-Vallejo F, Jia P, Yu Y, Giulianotti MA, Medina-Franco JL (2010) Docking of protein kinase B inhibitors: implications in the structure-based optimization of a novel scaffold. Chem Biol Drug Des 76:269-276. doi: 10.1111/j.1747-0285.2010.01002.x
22. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M (2008) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucl Acids Res 36:D901-D906. doi: 10.1093/nar/gkm958
23. Chen CYC (2011) TCM Database@Taiwan: the world's largest traditional chinese medicine database for drug screening in silico. PLoS ONE 6:e15939. doi: 10.1371/journal.pone.0015939
24. López-Vallejo F, Giulianotti MA, Houghten RA, Medina-Franco JL (2012) Expanding the medicinally relevant chemical space with compound libraries. Drug Discov Today 17:718-726. doi: 10.1016/j.drudis.2012.04.001
25. Yongye AB, Waddell J, Medina-Franco JL (2012) Molecular scaffold analysis of natural products databases in the public domain. Chem Biol Drug Des 80:717-724. doi: 10.1111/cbdd.12011
26. Medina-Franco JL, Martínez-Mayorga K, Peppard TL, Del Rio A (2013) Chemoinformatic analysis of GRAS (Generally Recognized as Safe) flavor chemicals and natural products. PLoS ONE 7:e50798. doi: 10.1371/journal.pone. 0050798
27. Maggiora GM (2006) On outliers and activity cliffs - why QSAR often disappoints. J Chem Inf Model 46:1535-1535. doi: 10.1021/ci060117s
28. Medina-Franco JL (2012) Scanning structure-activity relationships with structure-activity similarity and related maps: from consensus activity cliffs to selectivity switches. J Chem Inf Model 52:2485-2493. doi: 10.1021/ci300362x
29. Holliday JD, Kanoulas E, Malim N, Willett P (2011) Multiple search methods for similarity-based virtual screening: analysis of search overlap and precision. J Cheminform 3:29. doi: 10.1186/1758-2946-3-29
30. Yongye A, Byler K, Santos R, Martínez-Mayorga K, Maggiora GM, Medina-Franco JL (2011) Consensus models of activity landscapes with multiple chemical, conformer and property representations. J Chem Inf Model 51:1259-1270. doi: 10.1021/ci200081k
31. Kuck D, Caulfield T, Lyko F, Medina-Franco JL (2010) Nanaomycin a selectively inhibits DNMT3B and reactivates silenced tumor suppressor genes in human cancer cells. Mol Cancer Ther 9:3015-3023. doi: 10.1158/1535-7163.MCT-10- 0609
32. Singh N, Dueñas-González A, Lyko F, Medina-Franco JL (2009) Molecular modeling and dynamics studies of hydralazine with human DNA methyltransferase 1. ChemMedChem 4:792-799. doi: 10.1002/cmdc.200900017
33. Gabbara S, Sheluho D, Bhagwat A (1995) Cytosine methyltransferase from Escherichia coli in which active site cysteine is replaced with serine is partially active. Biochemistry 34:8914-8923. doi: 10.1021/bi00027a044
34. Zangi R, Arrieta A, Cossio FP (2010) Mechanism of DNA methylation: the double role of DNA as a substrate and as a cofactor. J Mol Biol 400:632-644. doi: 10.1016/j.jmb.2010.05.021
35. Santi DV, Garrett CE, Barr PJ (1983) On the mechanism of inhibition of DNA cytosine methyltransferases by cytosine analogs. Cell 33:9-10. doi: 10.1016/0092-8674(83)90327-6
36. Wu JC, Santi DV (1987) Kinetic and catalytic mechanism of HhaI methyltransferase. J Biol Chem 262:4778-4786
37. Jeltsch A (2002) Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases. ChemBioChem 3:274-293. doi: 10.1002/1439-7633(20020402)3:4<274:AID-CBIC274>3.0.CO;2-S
38. Ashburn TT, Thor KB (2004) Drug repositioning: identifying and developing new uses for existing drugs. Nat Rev Drug Discov 3:673-683. doi: 10.1038/nrd1468
39. Duenas-Gonzalez A, Garcia-Lopez P, Herrera LA, Medina-Franco JL, Gonzalez-Fierro A, Candelaria M (2008) The prince and the pauper. A tale of anticancer targeted agents. Mol Cancer 7:82. doi: 10.1186/1476-4598-7-82
40. Yoo J, Medina-Franco JL (2012) Towards the chemoinformatic-based identification of DNA methyltransferase inhibitors: 2D- and 3D-similarity profile of screening libraries. Curr Comput Aided Drug Des 8:317-329. doi: 10.2174/157340912803519606
41. Candelaria M, Herrera A, Labardini J, González-Fierro A, Trejo-Becerril C, Taja-Chayeb L, Pérez-Cárdenas E, de la Cruz-Hernández E, Arias-Bofill D, Vidal S, Cervera E, Dueñas-Gonzalez A (2011) Hydralazine and magnesium valproate as epigenetic treatment for myelodysplastic syndrome. Preliminary results of a phase-II trial. Ann Hematol 90:379-387. doi: 10.1007/s00277-010-1090-2