Novel and selective DNA methyltransferase inhibitors: Docking-based virtual screening and experimental evaluation

Bioorganic and Medicinal Chemistry

Volumn 18, Issue 2, 2010, Pages 822-829

  Kuck, Dirk ^a   Singh, Narender ^b   Lyko, Frank ^a   Medina Franco, Jose L ^b  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^b TORREY PINES INSTITUTE FOR MOLECULAR STUDIES   (United States)

Author keywords

Cancer; DNA methyltransferases; Docking; Drug discovery; Epigenetics; Structure activity relationships

Indexed keywords

ADENOSYLHOMOCYSTEINASE INHIBITOR; ANTINEOPLASTIC AGENT; CURCUMIN; CYTOSINE; DNA METHYLTRANSFERASE; DNA METHYLTRANSFERASE 1; DNA METHYLTRANSFERASE 1 INHIBITOR; DNA METHYLTRANSFERASE 3B; DNA METHYLTRANSFERASE INHIBITOR; HYDRALAZINE; METHYLTRANSFERASE INHIBITOR; N PHTHALOYLTRYPTOPHAN; NSC 106084; NSC 137546; NSC 138419; NSC 14778; NSC 154957; NSC 158324; NSC 319745; NSC 345763; NSC 348926; NSC 408488; NSC 54162; NSC 56071; NSC 57893; NSC 622444; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; CHEMICAL ANALYSIS; CONTROLLED STUDY; DNA METHYLATION; DRUG DESIGN; DRUG SCREENING; DRUG SELECTIVITY; ENZYME INHIBITION; ENZYME SPECIFICITY; EVALUATION; HUMAN; HUMAN CELL; MOLECULAR DOCKING; MOLECULAR MODEL; MOLECULE; NATIONAL HEALTH ORGANIZATION; PROTEIN DOMAIN;

CLONING, MOLECULAR; CRYSTALLOGRAPHY, X-RAY; DNA (CYTOSINE-5-)-METHYLTRANSFERASE; DOSE-RESPONSE RELATIONSHIP, DRUG; DRUG EVALUATION, PRECLINICAL; ENZYME INHIBITORS; HUMANS; MODELS, MOLECULAR; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 76449100936     PISSN: 09680896     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bmc.2009.11.050     Document Type: Article

References (48)

1. Klose R.J., and Bird A.P. Trends Biochem. Sci. 31 (2006) 89
2. Jones P.A., and Baylin S.B. Nat. Rev. Genet. 3 (2002) 415
3. Lister R., Pelizzola M., Dowen R.H., Hawkins R.D., Hon G., Tonti-Filippini J., Nery J.R., Lee L., Ye Z., Ngo Q.M., Edsall L., Antosiewicz-Bourget J., Stewart R., Ruotti V., Millar A.H., Thomson J.A., Ren B., and Ecker. J. R. Nature 462 (2009) 315
4. Esteller M. Nat. Rev. Genet. 8 (2007) 286
5. Jones P.A., and Baylin S.B. Cell 128 (2007) 683
6. Baylin S.B., and Ohm J.E. Nat. Rev. Cancer 6 (2006) 107
7. Goll M.G., and Bestor T.H. Annu. Rev. Biochem. 74 (2005) 481
8. Rhee I., Bachman K.E., Park B.H., Jair K.W., Yen R.W., Schuebel K.E., Cui H., Feinberg A.P., Lengauer C., Kinzler K.W., Baylin S.B., and Vogelstein B. Nature 416 (2002) 552
9. Egger G., Liang G., Aparicio A., and Jones P.A. Nature 429 (2004) 457
10. Svedruzic Z.M. Curr. Med. Chem. 15 (2008) 92
11. Yu N., and Wang M. Curr. Med. Chem. 15 (2008) 1350
12. Liu K., Wang Y.F., Cantemir C., and Muller M.T. Mol. Cell. Biol. 23 (2003) 2709
13. Stresemann C., and Lyko F. Int. J. Cancer 123 (2008) 8
14. Schermelleh L., Spada F., Easwaran H.P., Zolghadr K., Margot J.B., Cardoso M.C., and Leonhardt H. Nat. Methods 2 (2005) 751
15. Lyko F., and Brown R.J. Natl. Cancer Inst. 97 (2005) 1498
16. Segura-Pacheco B., Trejo-Becerril C., Pérez-Cárdenas E., Taja-Chayeb L., Mariscal I., Chávez A., Acuña C., Salazar A.M., Lizano M., and Dueñas-González A. Clin. Cancer Res. 9 (2003) 1596
17. Segura-Pacheco B., Pérez-Cárdenas E., Taja-Chayeb L., Chávez-Blanco A., Revilla-Vázquez A., Benítez-Bribiesca L., and Dueñas-González A. J. Transl. Med. 4 (2006) 32
18. Lee B.H., Yegnasubramanian S., Lin X.H., and Nelson W.G. J. Biol. Chem. 280 (2005) 40749
19. Fang M.Z., Wang Y., Ai N., Hou Z., Sun Y., Lu H., Welsh W., and Yang C.S. Cancer Res. 63 (2003) 7563
20. Liu Z.F., Xie Z.L., Jones W., Pavlovicz R.E., Liu S.J., Yu J.H., Li P.K., Lin J.Y., Fuchs J.R., Marcucci G., Li C.L., and Chan K.K. Bioorg. Med. Chem. Lett. 19 (2009) 706
21. Isakovic L., Saavedra O.M., Llewellyn D.B., Claridge S., Zhan L., Bernstein N., Vaisburg A., Elowe N., Petschner A.J., Rahil J., Beaulieu N., Gauthier F., MacLeod A.R., Delorme D., Besterman J.M., and Wahhab A. Bioorg. Med. Chem. Lett. 19 (2009) 2742
22. Saavedra O.M., Isakovic L., Llewellyn D.B., Zhan L., Bernstein N., Claridge S., Raeppel F., Vaisburg A., Elowe N., Petschner A.J., Rahil J., Beaulieu N., MacLeod A.R., Delorme D., Besterman J.M., and Wahhab A. Bioorg. Med. Chem. Lett. 19 (2009) 2747
23. Brueckner B., and Lyko F. Trends Pharmacol. Sci. 25 (2004) 551
24. Scior T., Bernard P., Medina-Franco J.L., and Maggiora G.M. Mini-Rev. Med. Chem. 7 (2007) 851
25. Jorgensen W.L. Science 303 (2004) 1813
26. Guido R.V.C., Oliva G., and Andricopulo A.D. Curr. Med. Chem. 15 (2008) 37
27. Muegge I. Mini-Rev. Med. Chem. 8 (2008) 927
28. Singh N., Dueñas-González A., Lyko F., and Medina-Franco J.L. ChemMedChem 4 (2009) 792
29. Siedlecki P., Boy R.G., Comagic S., Schirrmacher R., Wiessler M., Zielenkiewicz P., Suhai S., and Lyko F. Biochem. Biophys. Res. Commun. 306 (2003) 558
30. Siedlecki P., Boy R.G., Musch T., Brueckner B., Suhai S., Lyko F., and Zielenkiewicz P. J. Med. Chem. 49 (2006) 678
31. Developmental Therapeutics Program, National Cancer Institute. http://dtp.cancer.gov (accessed Sep 2009).
32. Irwin J.J., and Shoichet B.K. J. Chem. Inf. Model. 45 (2005) 177
33. Charifson P.S., and Walters W.P. J. Comput.-Aided Mol. Des. 16 (2002) 311
34. Oprea T.I., Bologa C., and Olah M. In: Alvarez J., and Shoichet B. (Eds). Virtual Screening in Drug Discovery (2005), Taylor & Francis, Boca Raton 89-106
35. filter, version 2.0.1; OpenEye Scientific Software Inc.: Santa Fe, NM. http://www.eyesopen.com (accessed Sep 2009).
36. ligprep, version 2.2, Schrödinger, LLC, New York, NY, 2005.
37. glide, version 5.0, Schrödinger, LLC, New York, NY, 2008.
38. Jones G., Willett P., Glen R.C., Leach A.R., and Taylor R. J. Mol. Biol. 267 (1997) 727
39. Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., and Olson A.J. J. Comput. Chem. 19 (1998) 1639
40. Singh N., Guha R., Giulianotti M.A., Pinilla C., Houghten R.A., and Medina-Franco J.L. J. Chem. Inf. Model. 49 (2009) 1010
41. Medina-Franco J.L., Martinez-Mayorga K., Giulianotti M.A., Houghten R.A., and Pinilla C. Curr. Comput.-Aided Drug Des. 4 (2008) 322
42. Molecular Operating Environment (moe), version 2008.10; Chemical Computing Group Inc.: Montreal, Quebec, Canada. http://www.chemcomp.com (accessed Sep 2009).
43. Jia D., Jurkowska R.Z., Zhang X., Jeltsch A., and Cheng X. Nature 449 (2007) 248
44. Chenna R., Sugawara H., Koike T., López R., Gibson T.J., Higgins D.G., and Thompson J.D. Nucleic Acids Res. 31 (2003) 3497
45. Prime, version 2.1.108, Schrödinger LLC, New York, NY, 2009.
46. Jacobson M.P., Pincus D.L., Rapp C.S., Day T.J., Honig B., Shaw D.E., and Friesner R.A. Proteins 55 (2004) 351
47. Kaminski G.A., Friesner R.A., Tirado-Rives J., and Jorgensen W.L. J. Phys. Chem. B 105 (2001) 6474
48. Castellano S., Kuck D., Sala M., Novellino E., Lyko F., and Sbardella G. J. Med. Chem. 51 (2008) 2321