The effect of 5-substitution in the pyrimidine ring of dUMP on the interaction with thymidylate synthase: Molecular modeling and QSAR

Bioorganic and Medicinal Chemistry

Volumn 15, Issue 6, 2007, Pages 2346-2358

  Jarmuła, Adam ^a   Cieplak, Piotr ^b   Krygowski, Tadeusz M ^c   Rode, Wojciech ^a  

^a NENCKI INSTITUTE OF EXPERIMENTAL BIOLOGY   (Poland)

^b BURNHAM INSTITUTE   (United States)

^c UNIVERSITY OF WARSAW   (Poland)

Author keywords

Binding affinity; dUMP analogues; Ligand binding; Molecular dynamics; Molecular modeling; QSAR; Thymidylate synthase (TS); TS inhibitors

Indexed keywords

ANTINEOPLASTIC AGENT; DEOXYURIDINE PHOSPHATE; FLUOROURACIL; PROPANE; PYRIMIDINE DERIVATIVE; THYMIDYLATE SYNTHASE;

ARTICLE; BINDING AFFINITY; BINDING KINETICS; COMPLEX FORMATION; DNA SYNTHESIS; DRUG POTENCY; DRUG SYNTHESIS; ENZYME BINDING; ENZYME SUBSTRATE; MOLECULAR DYNAMICS; MOLECULAR MODEL; QUANTITATIVE ANALYSIS; QUANTITATIVE STRUCTURE ACTIVITY RELATION; SIMULATION; STEREOSPECIFICITY; SUBSTITUTION REACTION;

BINDING SITES; COMPUTER SIMULATION; DEOXYURACIL NUCLEOTIDES; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; PROTEIN BINDING; PYRIMIDINES; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; TETRAHYDROFOLATES; THYMIDYLATE SYNTHASE;

EID: 33846933540     PISSN: 09680896     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bmc.2007.01.021     Document Type: Article

References (71)

1. Santi D.V., and Danenberg P.V. Folates in pyrimidine nucleotide biosynthesis. In: Blakely R.L., and Benkovic S.J. (Eds). Folates and Pteridines Vol. 1 (1984), Wiley, New York 345-398
2. Carreras C.W., and Santi D.V. Annu. Rev. Biochem. 64 (1995) 721-762
3. Stroud R.M., and Finer-Moore J.S. Biochemistry 42 (2003) 239-247
4. Finer-Moore J.S., Santi D.V., and Stroud R.M. Biochemistry 42 (2003) 248-256
5. Papamichael D. Stem Cells 18 (2000) 166-175
6. Chu E., Callender M.A., Farrell M.P., and Schmitz J.C. Cancer Chemother. Pharmacol. 52 (2003) S80-S89
7. Grem J.L. Invest. New Drugs 18 (2000) 299-313
8. Beale P., and Clark S. Tomudex. Clinical Development. In: Jackman A.L. (Ed). Anticancer Drug Development (1999), Humana Press, Inc, Totowa, NJ 167-181
9. Bavetsias V., and Jackman A.L. Curr. Med. Chem. 5 (1998) 265-288
10. Jackman A.L., Theti D.S., and Gibbs D.D. Adv. Drug Deliv. Rev. 56 (2004) 1111-1125
11. Sergeeva M.V., and Cathers B.E. Biochem. Pharmacol. 65 (2003) 823-831
12. 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) 321-330
13. Balzarini J., De Clercq E., Mertes M.P., Shugar D., and Torrence P.F. Biochem. Pharmacol. 31 (1982) 3673-3682
14. Balzarini J., and De Clercq E. Biochim. Biophys. Acta 785 (1984) 36-45
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 1382 (1998) 277-286
16. Jarmuła A., Cyrański M.K., Leś A., Krygowski T.M., and Rode W. Pol. J. Chem. 72 (1998) 1958-1962
17. Kalman T.I., and Nie Z. Nucleosides Nucleotides 19 (2000) 357-369
18. Kalman T.I., Nie Z., and Kamat A. Nucleosides Nucleotides Nucleic Acid 20 (2001) 869-871
19. Saxl R.L., Reston J., Nie Z., Kalman T.I., and Maley F. Biochemistry 42 (2003) 4544-4551
20. Wataya Y., Santi D.V., and Hansch C. J. Med. Chem. 20 (1977) 1469-1473
21. Parker W.B., and Cheng Y.C. Pharmacol. Ther. 48 (1990) 381-395
22. Eckstein J.W., Foster P.G., Finer-Moore J., Wataya Y., and Santi D.V. Biochemistry 33 (1994) 15086-15094
23. Matsuda A., Wataya Y., and Santi D.V. Biochem. Biophys. Res. Commun. 84 (1978) 654-659
24. Wataya Y., Matsuda A., and Santi D.V. J. Biol. Chem. 255 (1980) 5538-5544
25. Mertes M.P., Chang C.T., De Clercq E., Huang G.F., and Torrence P.F. Biochem. Biophys. Res. Commun. 84 (1978) 1054-1059
26. Kampf A., Barfknecht R.L., Shaffer P.J., Osaki S., and Mertes M.P. J. Med. Chem. 19 (1976) 903-908
27. Santi D.V., and Sakai T.T. Biochem. Biophys. Res. Commun. 46 (1972) 1320-1325
28. Santi D.V., and Sakai T.T. Biochem. Biophys. Res. Commun. 42 (1971) 813-817
29. Barr P.J., Nolan P.A., Santi D.V., and Robins M.J. J. Med. Chem. 24 (1981) 1385-1388
30. Barr P.J., Robins M.J., and Santi D.V. Biochemistry 22 (1983) 1696-1703
31. Rode W., Kulikowski T., Ke{ogonek}dzierska B., Jastreboff M., and Shugar D. Biochem. Pharmacol. 33 (1984) 2699-2705
32. Edelman M.S., Barfknecht R.L., Huet-Rose R., Boguslawski S., and Mertes M.P. J. Med. Chem. 20 (1977) 669-673
33. Barfknecht R.L., Huet-Rose R.A., Kampf A., and Mertes M.P. J. Am. Chem. Soc. 98 (1976) 5041-5043
34. Al-Razzak L.A., Schwepler D., Decedue C.J., Balzarini J., and De Clercq E. J. Med. Chem. 30 (1987) 409-419
35. Jarmuła A., Leś A., and Rode W. Bioorg. Chem. 28 (2000) 156-162
36. Stout T.J., Sage C.R., and Stroud R.M. Structure 6 (1998) 839-848
37. Hyatt D.C., Maley F., and Montfort W.R. Biochemistry 36 (1997) 4585-4594
38. Fritz T.A., Liu L., Finer-Moore J.S., and Stroud R.M. Biochemistry 41 (2002) 7021-7025
39. Fauman E.B., Rutenber E.E., Maley G.F., Maley F., and Stroud R.M. Biochemistry 33 (1994) 1502-1511
40. Copur S., Aiba K., Drake J.C., Allegra C.J., and Chu E. Biochem. Pharmacol. 49 (1995) 1419-1426
41. van de Waterbeemd, H. http://www.ndsu.nodak.edu/qsar_soc/resource/datasets/vdw1.htm.
42. Charton M. Progr. Phys. Org. Chem. 8 (1971) 235-317
43. Hansch C., Leo A., and Hoekman D. Exploring QSAR: Hydrophobic, Electronic, and Steric Constants (1995), American Chemical Society, Washington
44. Garrett C., Wataya Y., and Santi D.V. Biochemistry 13 (1979) 2798-2804
45. Liu L., and Santi D.V. Biochemistry 32 (1993) 9263-9267
46. Finer-Moore J.S., Liu L., Schafmeister C.E., Birdsall D.L., Mau T., Santi D.V., and Stroud R.M. Biochemistry 35 (1996) 5125-5136
47. Saenger W. Principles of Nucleic Acid Structure (1984), Springer, New York
48. Finer-Moore J., Montfort W.R., and Stroud R.M. Biochemistry 29 (1990) 6977-6986
49. Matthews D.A., Villafranca J.E., Janson C.A., Smith W.W., Welsh K., and Freer S. J. Mol. Biol. 214 (1990) 923-936
50. Wallace A.C., Laskowski R.A., and Thornton J.M. Protein Eng. 8 (1995) 127-134
51. DeLano, W. L. The PyMOL Molecular Graphics System. DeLano Scientific LLC, San Carlos, CA, USA. http://www.pymol.org.
52. Montfort W.R., Perry K.M., Fauman E.B., Finer-Moore J.S., Maley G.F., Hardy L., Maley F., and Stroud R.M. Biochemistry 29 (1990) 6964-6977
53. Sergeeva O.A., Khambatta H.G., Cathers B.E., and Sergeeva M.V. Biochem. Biophys. Res. Commun. 307 (2003) 297-300
54. Costi M.P., Ferrari S., Venturelli A., Calo S., Tondi D., and Barlocco D. Curr. Med. Chem. 12 (2005) 2241-2258
55. Gmeiner W.H. Curr. Med. Chem. 12 (2005) 191-202
56. 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) 4647-4656
57. Oliveira D.B., and Gaudio A.C. Quant. Struct.-Act. Relat. 19 (2000) 599-601
58. Cronin M.T.D., and Schultz T.W. J. Mol. Struct. (THEOCHEM) 622 (2003) 39-51
59. Hansch C., and Leo A. Exploring QSAR: Fundamentals and Applications in Chemistry and Biology (1995), American Chemical Society, Washington
60. Sjöström M., and Wold S. Chem. Scr. 9 (1976) 200-210
61. Case, D. A.; Pearlman, D. A.; Caldwell J. W.; Cheatham, T. E.; Ross, W. S., III; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton R. V.; Cheng, A. L.; Vincent, J. J.; Crowley, M.; Tsui, V.; Radmer, R. J.; Duan, Y.; Pitera, J.; Massova, I.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P.A. AMBER 6, 1999 University of California, San Francisco.
62. Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., and Klein M.L. J. Chem. Phys. 79 (1983) 926-935
63. Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., and Kollman P.A. J. Am. Chem. Soc. 117 (1995) 5179-5197
64. Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., and Pedersen L.G. J. Chem. Phys. 103 (1995) 8577-8593
65. York D.M., Darden T.A., and Pedersen L.G. J. Chem. Phys. 99 (1993) 8345-8348
66. Ryckaert J.P., Ciccotti G., and Berendsen H.J.C. J. Comput. Phys. 23 (1977) 327-341
67. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Baboul, A. G.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B. G.; Chen, W.; Wong, M. W.; Andres, J. L.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98 (Revision A.1), Gaussian, Inc., Pittsburgh, PA, 1998.
68. Bayly C.I., Cieplak P., Cornell W.D., and Kollman P.A. J. Phys. Chem. 97 (1993) 10269-10280
69. Cieplak P., Bayly C.I., Cornell W.D., and Kollman P.A. J. Comput. Chem. 16 (1995) 1357-1377
70. Discovery Studio, Accelrys, Inc., San Diego, CA, 2005. http://www.accelrys.com/dstudio/.
71. Finer-Moore J.S., Liu L., Birdsall D.L., Brem R., Apfeld J., Santi D.V., and Stroud R.M. J. Mol. Biol. 276 (1998) 113-129