A molecular modeling study of the interaction of 2′-fluoro-substituted analogues of dUMP/FdUMP with thymidylate synthase

Bioorganic and Medicinal Chemistry Letters

Volumn 18, Issue 8, 2008, Pages 2701-2708

  Jarmuła, Adam ^a   Dowierciał, Anna ^a   Rode, Wojciech ^a  

^a NENCKI INSTITUTE OF EXPERIMENTAL BIOLOGY   (Poland)

Author keywords

2 Fluoro substituted dUMP FdUMP analogues; MM GBSA approach; Molecular dynamics simulations; Substrate based inhibitors of thymidylate synthase; Thymidylate synthase

Indexed keywords

THYMIDYLATE SYNTHASE; THYMIDYLATE SYNTHASE INHIBITOR; URIDINE DERIVATIVE;

ARTICLE; BINDING AFFINITY; BINDING SITE; CALCULATION; ENERGY; ENZYME INHIBITION; HYDROPHOBICITY; MOLECULAR DYNAMICS; MOLECULAR MODEL; SIMULATION;

FLUORODEOXYURIDYLATE; MODELS, MOLECULAR; MOLECULAR STRUCTURE; SUBSTRATE SPECIFICITY; THYMIDYLATE SYNTHASE;

ARA;

EID: 41849144863     PISSN: 0960894X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bmcl.2008.03.016     Document Type: Article

References (39)

1. Carreras C.W., and Santi D.V. Annu. Rev. Biochem. 64 (1995) 721
2. Stroud R.M., and Finer-Moore J.S. Biochemistry 42 (2003) 239
3. Finer-Moore J.S., Santi D.V., and Stroud R.M. Biochemistry 42 (2003) 248
4. Stout T.J., Sage C.R., and Stroud R.M. Structure 6 (1998) 839
5. Liu L., and Santi D.V. Biochemistry 32 (1993) 9263
6. Finer-Moore J.S., Liu L., Schafmeister C.E., Birdsall D.L., Mau T., Santi D.V., and Stroud R.M. Biochemistry 35 (1996) 5125
7. Sage C.R., Michelitsch M.D., Stout T.J., Biermann D., Nissen R., Finer-Moore J., and Stroud R.M. Biochemistry 37 (1998) 13893
8. Chu E., Callender M.A., Farrell M.P., and Schmitz J.C. Cancer Chemother. Pharmacol. 52 (2003) S80
9. Gmeiner W.H. Curr. Med. Chem. 12 (2005) 191
10. De Clercq E., Balzarini J., Torrence P.F., Mertes M.P., Schmidt C.L., Shugar D., Barr P.J., Jones A.S., Verhelst G., and Walker R.T. Mol. Pharmacol. 19 (1981) 321
11. Grem J.L. Invest. New Drugs 18 (2000) 299
12. Santi D.V., McHenry C.S., Raines R.T., and Ivanetich K.M. Biochemistry 26 (1987) 8606
13. Washtein W.L. Mol. Pharmacol. 25 (1984) 171
14. Berger S.H., Jenh C.H., Johnson L.F., and Berger F.G. Mol. Pharmacol. 28 (1985) 461
15. Jarmuła A., Anulewicz R., Leś A., Cyrański M.K., Adamowicz L., Bretner M., Felczak K., Kulikowski T., Krygowski T.M., and Rode W. Biochim. Biophys. Acta-Protein Struct. Mol. Enzymol. 1382 (1998) 277
16. Felczak K., Miazga A., Poznański J., Bretner M., Kulikowski T., Dzik J.M., Gołos B., Zieliński Z., Cieśla J., and Rode W. J. Med. Chem. 43 (2000) 4647
17. Saxl R.L., Reston J., Nie Z., Kalman T.I., and Maley F. Biochemistry 42 (2003) 4544
18. Bijnsdorp I.V., Comijn E.M., Padron J.M., Gmeiner W.H., and Peters G.J. Oncol. Rep. 18 (2007) 287
19. Hoff P.M. Semin. Oncol. 30 (2003) 88
20. Lackey D.B., Groziak M.P., Sergeeva M., Beryt M., Boyer C., Stroud R.M., Sayre P., Park J.W., Johnston P., Slamon D., Shepard H.M., and Pegram M. Biochem. Pharmacol. 61 (2001) 179
21. Ziemkowski P., Felczak K., Poznański J., Kulikowski T., Zieliński Z., Cieśla J., and Rode W. Biochem. Biophys. Res. Commun. 362 (2007) 37
22. Almog R., Waddling C.A., Maley F., Maley G.F., and Van Roey P. Protein Sci. 10 (2001) 988
23. Balzarini J., De Clercq E., Mertes M.P., Shugar D., and Torrence P.F. Biochem. Pharmacol. 31 (1982) 3673
24. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Wang, B.; Pearlman, D. A.; Crowley, M.; Brozell, S.; Tsui, V.; Gohlke, H.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Schafmeister, C.; Caldwell, J. W.; Ross, W. S.; Kollman, P. A. AMBER 8. University of California: San Francisco, 2004.
25. Jorgensen W.L. J. Chem. Phys. 77 (1992) 5757
26. Bayly C.I., Cieplak P., Cornell W.D., and Kollman P.A. J. Phys. Chem. 97 (1993) 10269
27. Duan Y., Wu C., Chowdhury S., Lee M.C., Xiong G., Zhang W., Yang R., Cieplak P., Luo R., and Lee T. J. Comput. Chem. 24 (2003) 1999
28. Ryckaert J.P., Ciccotti G., and Berendsen H.J.C. J. Comput. Phys. 23 (1977) 327
29. Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., and Pedersen L.G. J. Chem. Phys. 103 (1995) 8577
30. Kollman P.A., Massova I., Reyes C., Kuhn B., Huo S., Chong L., Lee M., Lee T., Duan Y., Wang W., Donini O., Cieplak P., Srinivasan J., Case D.A., and Cheatham III T.E. Acc. Chem. Res. 33 (2000) 889
31. Hawkins G.D., Cramer C.J., and Truhlar D.G. Chem. Phys. Lett. 246 (1995) 122
32. Hawkins G.D., Cramer C.J., and Truhlar D.G. J. Phys. Chem. 100 (1996) 19824
33. Tsui V., and Case D.A. Biopolymers (Nucleic Acid Sci.) 56 (2001) 275
34. Weiser J., Shenkin P.S., and Still W.C. J. Comput. Chem. 20 (1999) 217
35. Weis A., Katebzadeh K., Soderhjelm P., Nilsson I., and Ryde U. J. Med. Chem. 49 (2006) 6596
36. Jarmuła A., Cieplak P., Krygowski T.M., and Rode W. Bioorg. Med. Chem. 15 (2007) 2346
37. Fritz T.A., Liu L., Finer-Moore J.S., and Stroud R.M. Biochemistry 41 (2002) 7021
38. Hong B., Haddad M., Maley F., Jensen J.H., and Kohen A. J. Am. Chem. Soc. 128 (2006) 5636
39. DeLano, W. L. The PyMOL Molecular Graphics System. DeLano Scientific LLC: San Carlos, CA, USA. Available from: http://www.pymol.org.