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Inhibition of C5-cytosine-DNA-methyltransferases

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Abstract

Changes in the methylation pattern of genomic DNA, particularly hypermethylation of tumor suppressor genes, occur at early stages of tumor development. Errors in DNA methylation contribute to both initiation and progression of various cancers. This stimulates significant interest in searching for inhibitors of C5-DNA-methyltransferases (MTases). Here we review the known nucleoside mechanism-based reversible and irreversible inhibitors of the MTases, as well as non-nucleoside ones, and discuss their inhibitory mechanisms and application for MTase investigations and cancer therapy.

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Abbreviations

AdoHcy:

S-(5′-adenosyl)-L-homocysteine

AdoMet:

S-(5′-adenosyl)-L-methionine

d4HCyd:

1-(2′-deoxy-β-D-ribofuranosyl)-2-pyrimidinone

DTT:

dithiothreitol

DZdCyd:

5,6-dihydro-5-aza-2′-deoxycytidine

EGCG:

(−)-epigallocatechin-3-gallate

FdCyd:

5-fluoro-2′-deoxycytidine

MTase:

DNA-methyltransferase

NEM:

N-ethylmaleimide

P:

2-pyrimidinone

4′-SdCyd:

4′-thio-2′-deoxycytidine

sinefungin:

S-adenosyl-L-ornithine

XRSA:

X-ray structural analysis

ZCyd:

5-azacytidine

ZdCyd:

5-aza-2′-deoxycytidine

References

  1. Gromova, E. S., and Khoroshaev, A. V. (2003) Mol. Biol. (Moscow), 37, 260–272.

    CAS  Google Scholar 

  2. Jeltsch, A. (2002) Chembiochem., 3, 274–293.

    Article  PubMed  CAS  Google Scholar 

  3. Cheng, X., and Roberts, R. J. (2001) Nucleic Acids Res., 29, 3784–3795.

    Article  PubMed  CAS  Google Scholar 

  4. Bird, A. (2002) Genes Dev., 16, 6–21.

    Article  PubMed  CAS  Google Scholar 

  5. Goll, M. G., and Bestor, T. H. (2005) Annu. Rev. Biochem., 74, 481–514.

    Article  PubMed  CAS  Google Scholar 

  6. Roberts, R. J., Vincze, T., Posfai, J., and Macelis, D. (2007) Nucleic Acids Res., 35, D269–D270.

    Article  PubMed  CAS  Google Scholar 

  7. Hermann, A., Gowher, H., and Jeltsch, A. (2004) Cell Mol. Life Sci., 61, 2571–2587.

    Article  PubMed  CAS  Google Scholar 

  8. Kumar, S., Cheng, X., Klimasauskas, S., Mi, S., Posfai, J., Roberts, R. J., and Wilson, G. G. (1994) Nucleic Acids Res., 22, 1–10.

    Article  PubMed  CAS  Google Scholar 

  9. Posfai, J., Bhagwat, A. S., Posfai, G., and Roberts, R. J. (1989) Nucleic Acids Res., 17, 2421–2435.

    Article  PubMed  CAS  Google Scholar 

  10. Klimasauskas, S., Kumar, S., Roberts, R. J., and Cheng, X. (1994) Cell, 76, 357–369.

    Article  PubMed  CAS  Google Scholar 

  11. Sankpal, U. T., and Rao, D. N. (2002) Crit. Rev. Biochem. Mol. Biol., 37, 167–197.

    Article  PubMed  CAS  Google Scholar 

  12. Lee, Y. F., Tawfik, D. S., and Griffiths, A. D. (2002) Nucleic Acids Res., 30, 4937–4944.

    Article  PubMed  CAS  Google Scholar 

  13. Eden, A., Gaudet, F., Waghmare, A., and Jaenisch, R. (2003) Science, 300, 455.

    Article  PubMed  CAS  Google Scholar 

  14. Jones, P. A., and Baylin, S. B. (2002) Nat. Rev. Genet., 3, 415–428.

    Article  PubMed  CAS  Google Scholar 

  15. Baylin, S. B., Esteller, M., Rountree, M. R., Bachman, K. E., Schuebel, K., and Herman, J. G. (2001) Hum. Mol. Genet., 10, 687–692.

    Article  PubMed  CAS  Google Scholar 

  16. Baylin, S. B., and Herman, J. G. (2000) Trends Genet., 16, 168–174.

    Article  PubMed  CAS  Google Scholar 

  17. Jones, P. A., and Laird, P. W. (1999) Nat. Genet., 21, 163–167.

    Article  PubMed  CAS  Google Scholar 

  18. Jones, P. A., and Baylin, S. B. (2007) Cell, 128, 683–692.

    Article  PubMed  CAS  Google Scholar 

  19. Kumar, R., Srivastava, R., Singh, R. K., Surolia, A., and Rao, D. N. (2008) Bioorg. Med. Chem., 16, 2276–2285.

    Article  PubMed  CAS  Google Scholar 

  20. Zingg, J. M., Shen, J. C., Yang, A. S., Rapoport, H., and Jones, P. A. (1996) Nucleic Acids Res., 24, 3267–3275.

    Article  PubMed  CAS  Google Scholar 

  21. Gowher, H., and Jeltsch, A. (2004) Cancer Biol. Ther., 3, 1062–1068.

    PubMed  CAS  Google Scholar 

  22. Christman, J. K. (2002) Oncogene, 21, 5483–5495.

    Article  PubMed  CAS  Google Scholar 

  23. Gabbara, S., and Bhagwat, A. S. (1995) Biochem. J., 307, 87–92.

    PubMed  CAS  Google Scholar 

  24. Palii, S. S., van Emburgh, B. O., Sankpal, U. T., Brown, K. D., and Robertson, K. D. (2008) Mol. Cell Biol., 28, 752–771.

    Article  PubMed  CAS  Google Scholar 

  25. Sheikhnejad, G., Brank, A., Christman, J. K., Goddard, A., Alvarez, E., Ford, H., Jr., Marquez, V. E., Marasco, C. J., Sufrin, J. R., O’Gara, M., and Cheng, X. (1999) J. Mol. Biol., 285, 2021–2034.

    Article  PubMed  CAS  Google Scholar 

  26. Osterman, D. G., DePillis, G. D., Wu, J. C., Matsuda, A., and Santi, D. V. (1988) Biochemistry, 27, 5204–5210.

    Article  PubMed  CAS  Google Scholar 

  27. Taylor, C., Ford, K., and Connolly, B. A. (1993) Biochem. J., 291, 493–504.

    PubMed  CAS  Google Scholar 

  28. Hurd, P. J., Whitmarsh, A. J., and Baldwin, G. S. (1999) J. Mol. Biol., 286, 389–401.

    Article  PubMed  CAS  Google Scholar 

  29. Zhou, L., Cheng, X., and Connolly, B. A. (2002) J. Mol. Biol., 321, 591–599.

    Article  PubMed  CAS  Google Scholar 

  30. Kumar, S., Horton, J. R., Jones, G. D., Walker, R. T., Roberts, R. J., and Cheng, X. (1997) Nucleic Acids Res., 25, 2773–2783.

    Article  PubMed  CAS  Google Scholar 

  31. Flynn, J., Fang, J. Y., Mikovits, J. A., and Reich, N. O. (2003) J. Biol. Chem., 278, 8238–8243.

    Article  PubMed  CAS  Google Scholar 

  32. Knox, J. D., Araujo, F. D., Bigey, P., Slack, A. D., Price, G. B., Zannis-Hadjopoulos, M., and Szyf, M. (2000) J. Biol. Chem., 275, 17986–17990.

    Article  PubMed  CAS  Google Scholar 

  33. Milutinovic, S., Knox, J. D., and Szyf, M. (2000) J. Biol. Chem., 275, 6353–6359.

    Article  PubMed  CAS  Google Scholar 

  34. Fang, M. Z., Wang, Y., Ai, N., Hou, Z., Sun, Y., Lu, H., Welsh, W., and Yang, C. S. (2003) Cancer Res., 63, 7563–7570.

    PubMed  CAS  Google Scholar 

  35. Fang, M. Z., Chen, D., Sun, Y., Jin, Z., Christman, J. K., and Yang, C. S. (2005) Clin. Cancer Res., 11, 7033–7041.

    Article  PubMed  CAS  Google Scholar 

  36. Pina, I. C., Gautschi, J. T., Wang, G. Y., Sanders, M. L., Schmitz, F. J., France, D., Cornell-Kennon, S., Sambucetti, L. C., Remiszewski, S. W., Perez, L. B., Bair, K. W., and Crews, P. (2003) J. Org. Chem., 68, 3866–3873.

    Article  PubMed  CAS  Google Scholar 

  37. Brueckner, B., Boy, R. G., Siedlecki, P., Musch, T., Kliem, H. C., Zielenkiewicz, P., Suhai, S., Wiessler, M., and Lyko, F. (2005) Cancer Res., 65, 6305–6311.

    Article  PubMed  CAS  Google Scholar 

  38. Siedlecki, P., Boy, R. G., Musch, T., Brueckner, B., Suhai, S., Lyko, F., and Zielenkiewicz, P. (2006) J. Med. Chem., 49, 678–683.

    Article  PubMed  CAS  Google Scholar 

  39. Lin, X., Asgari, K., Putzi, M. J., Gage, W. R., Yu, X., Cornblatt, B. S., Kumar, A., Piantadosi, S., DeWeese, T. L., De Marzo, A. M., and Nelson, W. G. (2001) Cancer Res., 61, 8611–8616.

    PubMed  CAS  Google Scholar 

  40. Villar-Garea, A., Fraga, M. F., Espada, J., and Esteller, M. (2003) Cancer Res., 63, 4984–4989.

    PubMed  CAS  Google Scholar 

  41. Lee, B. H., Yegnasubramanian, S., Lin, X., and Nelson, W. G. (2005) J. Biol. Chem., 280, 40749–40756.

    Article  PubMed  CAS  Google Scholar 

  42. Castellano, S., Kuck, D., Sala, M., Novellino, E., Lyko, F., and Sbardella, G. (2008) J. Med. Chem., 51, 2321–2325.

    Article  PubMed  CAS  Google Scholar 

  43. Lin, R. K., Hsu, C. H., and Wang, Y. C. (2007) Anticancer Drugs, 18, 1157–1164.

    Article  PubMed  CAS  Google Scholar 

  44. Yokochi, T., and Robertson, K. D. (2004) Mol. Pharmacol., 66, 1415–1420.

    Article  PubMed  CAS  Google Scholar 

  45. Adams, R. L., and Rinaldi, A. (1987) FEBS Lett., 215, 266–268.

    Article  PubMed  CAS  Google Scholar 

  46. Shvachko, L. P. (2008) Exp. Oncol., 30, 230–234.

    PubMed  CAS  Google Scholar 

  47. Milicic, A., Harrison, L. A., Goodlad, R. A., Hardy, R. G., Nicholson, A. M., Presz, M., Sieber, O., Santander, S., Pringle, J. H., Mandir, N., East, P., Obszynska, J., Sanders, S., Piazuelo, E., Shaw, J., Harrison, R., Tomlinson, I. P., McDonald, S. A., Wright, N. A., and Jankowski, J. A. (2008) Cancer Res., 68, 7760–7768.

    Article  PubMed  CAS  Google Scholar 

  48. Kisseljova, N. P., and Kisseljov, F. L. (2005) Biochemistry (Moscow), 70, 743–752.

    Article  CAS  Google Scholar 

  49. Vilkaitis, G., Merkiene, E., Serva, S., Weinhold, E., and Klimasauskas, S. (2001) J. Biol. Chem., 276, 20924–20934.

    Article  PubMed  CAS  Google Scholar 

  50. Bender, C. M., Zingg, J. M., and Jones, P. A. (1998) Pharm. Res., 15, 175–187.

    Article  PubMed  CAS  Google Scholar 

  51. Wu, J. C., and Santi, D. V. (1987) J. Biol. Chem., 262, 4778–4786.

    PubMed  CAS  Google Scholar 

  52. Chen, L., MacMillan, A. M., and Verdine, G. L. (1993) J. Am. Chem. Soc., 115, 5318–5319.

    Article  CAS  Google Scholar 

  53. Jones, P. A., and Tailor, S. M. (1980) Cell, 20, 85–93.

    Article  PubMed  CAS  Google Scholar 

  54. Constantinides, P. G., Jones, P. A., and Gevers, W. (1977) Nature, 267, 364–366.

    Article  PubMed  CAS  Google Scholar 

  55. Cheng, J. C., Matsen, C. B., and Gonzales, F. A. (2003) J. Natl. Cancer Inst., 95, 3399–3409.

    Google Scholar 

  56. Lee, W. J., and Kim, H. J. (2007) Mol. Cells, 24, 441–444.

    PubMed  CAS  Google Scholar 

  57. Santi, D. V., Norment, A., and Garret, C. E. (1984) Proc. Natl. Acad. Sci. USA, 81, 6993–6997.

    Article  PubMed  CAS  Google Scholar 

  58. Subach, O. M., Khoroshaev, A. V., Gerasimov, D. N., Baskunov, V. B., Shchyolkina, A. K., and Gromova, E. S. (2004) Eur. J. Biochem., 271, 2391–2399.

    Article  PubMed  CAS  Google Scholar 

  59. Abeles, R. H., and Alston, T. A. (1990) J. Biol. Chem., 265, 16705–16708.

    PubMed  CAS  Google Scholar 

  60. Chen, L., MacMillan, A. M., Chang, W., Ezaz-Nikpay, K., Lane, W. S., and Verdine, G. L. (1991) Biochemistry, 30, 11018–11025.

    Article  PubMed  CAS  Google Scholar 

  61. Friedman, S., and Ansari, N. (1992) Nucleic Acids Res., 20, 3241–3248.

    Article  PubMed  CAS  Google Scholar 

  62. Smith, S. S., Kaplan, B. E., Sowers, L. C., and Newman, E. M. (1992) Proc. Natl. Acad. Sci. USA, 89, 4744–4748.

    Article  PubMed  CAS  Google Scholar 

  63. Sorm, F., Piskala, A., Cihak, A., and Vesely, J. (1964) Experientia, 20, 202–203.

    Article  PubMed  CAS  Google Scholar 

  64. Issa, J. P. (2005) Nat. Clin. Pract. Oncol., 2,Suppl. 1, S24–S29.

    Article  PubMed  CAS  Google Scholar 

  65. Herman, J. G., and Baylin, S. B. (2003) N. Engl. J. Med., 349, 2042–2054.

    Article  PubMed  CAS  Google Scholar 

  66. Juttermann, R., Li, E., and Jaenisch, R. (1994) Proc. Natl. Acad. Sci. USA, 91, 797–801.

    Article  Google Scholar 

  67. Li, L. H., Olin, E. J., Buskirk, H. H., and Reineke, L. M. (1970) Cancer Res., 30, 2760–2769.

    PubMed  CAS  Google Scholar 

  68. Yoo, C. B., Jeong, S., Egger, G., Liang, G., Phiasivongsa, P., Tang, C., Redkar, S., and Jones, P. A. (2007) Cancer Res., 67, 6400–6408.

    Article  PubMed  CAS  Google Scholar 

  69. Beisler, J. A. (1978) J. Med. Chem., 21, 204–208.

    Article  PubMed  CAS  Google Scholar 

  70. McGregor, D. B., Brown, A. G., Cattanach, P., Shepherd, W., Riach, C., Daston, D. S., and Caspary, W. J. (1989) Carcinogenesis, 10, 2003–2008.

    Article  PubMed  CAS  Google Scholar 

  71. Cheng, J. C., Matsen, C. B., Gonzales, F. A., Ye, W., Greer, S., Marquez, V. E., Jones, P. A., and Selker, E. U. (2003) J. Natl. Cancer Inst., 95, 399–409.

    Article  PubMed  CAS  Google Scholar 

  72. Cheng, J. C., Weisenberger, D. J., Gonzales, F. A., Liang, G., Xu, G. L., Hu, Y. G., Marquez, V. E., and Jones, P. A. (2004) Mol. Cell Biol., 24, 1270–1278.

    Article  PubMed  CAS  Google Scholar 

  73. Cheng, J. C., Yoo, C. B., Weisenberger, D. J., Chuang, J., Wozniak, C., Liang, G., Marquez, V. E., Greer, S., Orntoft, T. F., Thykjaer, T., and Jones, P. A. (2004) Cancer Cell, 6, 151–158.

    Article  PubMed  CAS  Google Scholar 

  74. Newman, E. M., and Santi, D. V. (1982) Proc. Natl. Acad. Sci. USA, 79, 6419–6423.

    Article  PubMed  CAS  Google Scholar 

  75. O’Gara, M., Roberts, R. J., and Cheng, X. (1996) J. Mol. Biol., 263, 597–606.

    Article  PubMed  Google Scholar 

  76. O’Gara, M., Klimasauskas, S., Roberts, R. J., and Cheng, X. (1996) J. Mol. Biol., 261, 634–645.

    Article  PubMed  Google Scholar 

  77. Wyszynski, M. W., Gabbara, S., and Bhagwat, A. S. (1992) Nucleic Acids Res., 20, 319–326.

    Article  PubMed  CAS  Google Scholar 

  78. Wyszynski, M. W., Gabbara, S., Kubareva, E. A., Romanova, E. A., Oretskaya, T. S., Gromova, E. S., Shabarova, Z. A., and Bhagwat, A. S. (1993) Nucleic Acids Res., 21, 295–301.

    Article  PubMed  CAS  Google Scholar 

  79. Gabbara, S., Sheluho, D., and Bhagwat, A. S. (1995) Nucleic Acids Res., 27, 8914–8923.

    Google Scholar 

  80. Robert, M. F., Morin, S., Beaulieu, N., Gauthier, F., Chute, I. C., Barsalou, A., and MacLeod, A. R. (2003) Nat. Genet., 33, 61–65.

    Article  PubMed  CAS  Google Scholar 

  81. Brueckner, B., and Lyko, F. (2004) Trends Pharmacol. Sci., 25, 551–554.

    Article  PubMed  CAS  Google Scholar 

  82. Lyko, F., and Brown, R. (2005) J. Natl. Cancer Inst., 97, 1498–1506.

    Article  PubMed  CAS  Google Scholar 

  83. Stresemann, C., Brueckner, B., Musch, T., Stopper, H., and Lyko, F. (2006) Cancer Res., 66, 2794–2800.

    Article  PubMed  CAS  Google Scholar 

  84. Wang, Y., Fang, M. Z., Liao, J., Yang, G. Y., Nie, Y., Song, Y., So, C., Xu, X., Wang, L. D., and Yang, C. S. (2003) Clin. Cancer Res., 9, 5257–5263.

    PubMed  CAS  Google Scholar 

  85. Kim, D., Lee, I. S., Jung, J. H., Lee, C. O., and Choi, S. U. (1999) Anticancer Res., 19, 4085–4090.

    PubMed  CAS  Google Scholar 

  86. Siedlecki, P., Boy, R. G., Comagic, S., Schirrmacher, R., Wiessler, M., Zielenkiewicz, P., Suhai, S., and Lyko, F. (2003) Biochem. Biophys. Res. Commun., 306, 558–563.

    Article  PubMed  CAS  Google Scholar 

  87. Brana, M. F., Cacho, M., Gradillas, A., de Pascual-Teresa, B., and Ramos, A. (2001) Curr. Pharm. Des., 7, 1745–1780.

    Article  PubMed  CAS  Google Scholar 

  88. Carter, S. K. (1975) J. Natl. Cancer Inst., 55, 1265–1274.

    PubMed  CAS  Google Scholar 

  89. Hickman, J. A. (1992) Cancer Metastasis Rev., 11, 121–139.

    Article  PubMed  CAS  Google Scholar 

  90. Kiechle, F. L., and Zhang, X. (2002) Clin. Chim. Acta, 326, 27–45.

    Article  PubMed  CAS  Google Scholar 

  91. Yokochi, T., and Robertson, K. D. (2004) Mol. Pharmacol., 66, 1415–1420.

    Article  PubMed  CAS  Google Scholar 

  92. Shieh, F. K., and Reich, N. O. (2007) J. Mol. Biol., 373, 1157–1168.

    Article  PubMed  CAS  Google Scholar 

  93. Friedman, S., and Ansari, N. (1992) Nucleic Acids Res., 20, 3241–3248.

    Article  PubMed  CAS  Google Scholar 

  94. Hanck, T., Schmidt, S., and Fritz, H.-J. (1993) Nucleic Acids Res., 21, 303–309.

    Article  PubMed  CAS  Google Scholar 

  95. Reither, S., Li, F., Gowher, H., and Jeltsch, A. (2003) J. Mol. Biol., 329, 675–684.

    Article  PubMed  CAS  Google Scholar 

  96. Dong, A., Yoder, J. A., Zhang, X., Zhou, L., Bestor, T. H., and Cheng, X. (2001) Nucleic Acids Res., 29, 439–448.

    Article  PubMed  CAS  Google Scholar 

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Correspondence to E. S. Gromova.

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Original Russian Text © O. V. Kirsanova, N. A. Cherepanova, E. S. Gromova, 2009, published in Biokhimiya, 2009, Vol. 74, No. 11, pp. 1445–1458.

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Kirsanova, O.V., Cherepanova, N.A. & Gromova, E.S. Inhibition of C5-cytosine-DNA-methyltransferases. Biochemistry Moscow 74, 1175–1186 (2009). https://doi.org/10.1134/S0006297909110017

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