Nucleophilic Participation in the Transition State for Human Thymidine Phosphorylase

Journal of the American Chemical Society

Volumn 126, Issue 8, 2004, Pages 2447-2453

  Birck, Matthew R ^a   Schramm, Vern L ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSTS; CHEMICAL BONDS; COMPUTER SIMULATION; DECOMPOSITION; ELECTRONIC STRUCTURE; ENZYME KINETICS; ISOTOPES; PH EFFECTS;

KINETIC ISOTOPES; TRANSITION-STATE STRUCTURES;

ENZYMES;

2 DEOXYRIBOSE; ARSENIC ACID; ARSENIC ACID DERIVATIVE; CARBON 14; N RIBOSYL TRANSFERASE; RECOMBINANT ENZYME; THYMIDINE; THYMIDINE DERIVATIVE; THYMIDINE PHOSPHORYLASE; THYMINE; TRANSFERASE; UNCLASSIFIED DRUG;

ARTICLE; CALCULATION; CHEMICAL BOND; CHEMICAL REACTION KINETICS; COMPUTER MODEL; DECOMPOSITION; DENSITY FUNCTIONAL THEORY; DISSOCIATION; ENZYME MECHANISM; ENZYME STRUCTURE; PH; STEREOSPECIFICITY;

CATALYSIS; COMPUTER SIMULATION; ELECTROSTATICS; ENZYME INHIBITORS; HUMANS; KINETICS; MODELS, MOLECULAR; RECOMBINANT PROTEINS; THYMIDINE; THYMIDINE PHOSPHORYLASE; TRITIUM;

EID: 1542366683     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja039260h     Document Type: Article

References (70)

1. Ishikawa, F.; Miyazono, K.; Hellman, U.; Drexler, H.; Wernstedt, C.; Usuki, K.; Takaku, F.; Risau, W.; Heldin, C.-H. Nature 1989, 338, 557-562.
2. Furukawa, T.; Yoshimura, A.; Sumizawa, T.; Haraguchi, M.; Akiyama, S.-I. ; Fukui, K.; Ishizawa, M.; Yamada, Y. Nature (London) 1992, 356, 668-.
3. Haraguchi, M.; Miyadera, K.; Uemura, K.; Sumizawa, T.; Furukawa, T.; Yamada, K.; Akiyama, S.; Yamada, Y. Nature 1994, 368, 198.
4. Matshushita, S.; Nitanda, T.; Furukawa, T.; Sumizawa, T.; Tani, A.; Nishimoto, K.; Akiba, S.; Miyadera, K.; Fukushima, M.; Yamada, Y.; Yoshida, H.; Kanzaki, T.; Akiyama, S. Cancer Res. 1999, 59, 1911-1916.
5. Kitazono, M.; Takebayashi, Y.; Ishitsuka, K.; Takao, S.; Tani, A.; Furukawa, T.; Miyadera, K.; Yamada, Y.; Aikou, T.; Akiyama, S. Biochem. Biophys. Res. Commun. 1998, 253, 797-803.
6. Ikeda, R.; Furukawa, T.; Kitazono, M.; Ishitsuka, K.; Okumura, H.; Tani, A.; Sumizawa, T.; Haraguchi, M.; Komatsu, M.; Uchimiya, H.; Ren, X. Q.; Motoya, T.; Yamada, K.; Akiyama, S. Biochem. Biophys. Res. Commun. 2002, 291, 806-812.
7. Saeki, T.; Tanada, M.; Takashima, S.; Saeki, H.; Takiyama, W.; Nishimoto, N.; Moriwaki, S. Jpn. J. Clin. Oncol. 1997, 27, 227-230.
8. Relf, M.; LeJeune, S.; Scott, P. A.; Fox, S.; Smith, K.; Leek, R.; Moghaddam, A.; Whitehouse, R.; Bicknell, R.; Harris, A. L. Cancer Res. 1997, 57, 963-969.
9. Giatromanolaki, A.; Koukourakis, M. I.; Comley, M.; Kaklamanis, L.; Turley, H.; O'Byrne, K.; Harris, A. L.; Gatter, K. C. J. Pathol. 1997, 181, 196-199.
10. Takebayashi, Y.; Natsugoe, S.; Baba, M.; Akiba, S.; Fukumoto, T.; Miyadera, K.; Yamada, Y.; Takao, S.; Akiyama, S.; Aikou, T. Cancer 1999, 85, 282-289.
11. Tokunaga, Y.; Hosogi, H.; Hoppou, T.; Nakagami, M.; Tokuka, A.; Ohsumi, K. Surgery 2002, 131, 541-547.
12. Shimada, H.; Takeda, A.; Shiratori, T.; Nabeya, Y.; Okazumi, S.; Matsubara, H.; Funami, Y.; Hayashi, H.; Gunji, Y.; Kobayashi, S.; Suzuki, T.; Ochiai, T. Cancer 2002, 94, 1947-1954.
13. Miyadera, K.; Sumizawa, T.; Haraguchi, M.; Yoshida, H.; Konstanty, W.; Yamada, Y.; Akiyama, S. Cancer Res. 1995, 55, 1687-1690.
14. Takao, S.; Takebayashi, Y.; Che, X.; Shinchi, H.; Natsugoe, S.; Miyadera, K.; Yamada, Y.; Akiyama, S.; Aikou, T. Clin. Cancer Res. 1944, 4, 1619-1624.
15. Manson, L. A. In September 1948 Meeting of the American Chemical Society.
16. Manson, L. A.; Lampen, J. O. Fed. Proc. 1949, 8.
17. Razzell, W. E.; Khorana, H. G. Biochim. Biophys. Acta 1958, 28, 562-566.
18. Nakayama, C.; Wataya, Y.; Rich B, Meyer, J.; Santi, D. V.; Saneyoshi, M. ; Ueda, T. J. Med. Chem. 1980, 23, 962-964.
19. Avraham, Y.; Grossowicz, N.; Yashphe, J. Biochim. Biophys. Acta 1990, 1040, 287-293.
20. Moghaddam, A.; Bicknell, R. Biochemistry 1992, 31, 12141-12146.
21. Hotchkiss, K. A.; Ashton, A. W.; Schwartz, E. L. J. Biol. Chem. 2003, 278, 19272-19279.
22. Hotchkiss, K. A.; Ashton, A. W.; Klein, R. S.; Lenzi, M. L.; Shu, G. H.; Schwartz, E. L. Cancer Res. 2003, 63, 527-533.
23. de Bruin, M.; Smid, K.; Laan, A. C.; Noordhuis, P.; Fukushima, M.; Hoekman, K.; Pinedo, H. M.; Peters, G. J. Biochem. Biophys. Res. Commun. 2003, 301, 675-679.
24. Sengupta, S.; Sellers, L. A.; Matheson, H. B.; Fan, T. P. Br. J. Pharmacol. 2003, 139, 219-231.
25. Focher, F.; Spadari, S. Curr. Cancer Drug Targets 2001, 1, 141-153.
26. Kline, P. C.; Schramm, V. L. Biochemistry 1993, 32, 13212-13219.
27. Mentch, F.; Parkin, D. W.; Schramm, V. L. Biochemistry 1987, 26, 921-930.
28. Werner, R. M.; Stivers, J. T. Biochemistry 2000, 39, 14054-14064.
29. Schramm, V. L.; Horenstein, B. A.; Bagdassarian, C. K.; Schwartz, S. D.; Berti, P. J.; Rising, K. A.; Scheuring, J.; Kline, P. C.; Parkin, D. W.; Merkler, D. J. Journal of Quantum Chemistry: Quantum Biology Symposium 1996, 23, 1805-1813.
30. Santi, D. V.; McHenry, C. S.; Raines, R. T.; Ivanetich, K. M. Biochemistry 1987, 26, 8606-8613.
31. Santi, D. V.; McHenry, C. S.; Sommer, H. Biochemistry 1974, 13, 3.
32. Foth, H.; Hellkamp, J.; Kunellis, E.-M.; Kahl, G. F. Drug Metab. Dispos. 1990, 18, 1011-1017.
33. Patterson, A. V.; Zhang, H. T.; Moghaddam, A.; Bicknell, R.; Talbot, D. C.; Stratford, I. J.; Harris, A. L. Br. J. Cancer 1995, 72, 669-675.
34. de Bruin, M.; van Capel, T.; Van der Born, K.; Kruyt, F. A.; Fukushima, M.; Hoekman, K.; Pinedo, H. M.; Peters, G. J. Br. J. Cancer 2003, 88, 957-964.
35. Parkin, D. W.; Leung, H. B.; Schramm, V. L. J. Biol. Chem. 1984, 259, 9411-9417.
36. Parkin, D. W.; Schramm, V. L. Biochemistry 1987, 26, 913-920.
37. Berti, P. J.; Blanke, S. R.; Schramm, V. L. J. Am. Chem. Soc. 1997, 119, 12079-12088.
38. The calculated TS, along with frequency tables and, where appropriate, calculated KIEs are included in the Supporting Information.
39. Electron density at the attacking oxygen of dianionic phosphate and arsenate differ by 0.02. This alters the nucleophile/leaving group distances by less than 0.05 Å.
40. Peng, C.; Schlegel, H. B. Isr. J. Chem. 1993, 33, 449-454.
41. Anisimov, V.; Paneth, P. J. Math. Chem. 1999, 26, 75-86.
42. Peng, C.; Ayala, P. Y.; Schlegel, H. B.; Frish, M. J. J. Comput. Chem. 1996, 17, 49.
43. Northrop, D. B. Annu. Rev. Biochem. 1981, 50, 103-131.
44. Parks, R. E.; Agarwal, R. P. In The Enzymes; Boyer, P. D., Ed.; Academic Press: New York, 1972; Vol. 7, pp 483-514.
45. Rose, I. Methods Enzymol. 1980, 64, 47-59.
46. Markham, G. D.; Parkin, D. W.; Mentch, F.; Schramm, V. L. J. Biol. Chem. 1987, 262, 5609-5615.
47. Scheuring, J.; Berti, P. J.; Schramm, V. L. Biochemistry 1998, 37, 2748-2758.
48. Rising, K. A.; Schramm, V. L. J. Am. Chem. Soc. 1997, 119, 27-37.
49. Chen, X.-Y.; Berti, P. J.; Schramm, V. L. J. Am. Chem. Soc. 2000, 122, 6527-6534.
50. Chen, C. Y.; Berti, P. J.; Schramm, V. J. Am. Chem. Soc. 2000, 122, 1609-1617.
51. Yamataka, H.; Ando, T. Tetrahedron Lett. 1975, 1059-1062.
52. Bender, M. L.; Hoeg, D. F. J. Am. Chem. Soc. 1957, 79, 5649-5654.
53. Raaen, V. F.; Juhlke, T.; Brown, F. J.; Collins, C. J. J. Am. Chem. Soc. 1974, 96, 5928-5930.
54. Melander, L.; Saunders, W. H. Reaction Rates of Isotopic Molecules; Robert E. Krieger Publishing Company: Malabar, Florida, 1987.
55. Cole, C.; Reigan, P.; Gbaj, A.; Edwards, P. N.; Douglas, K. T.; Stratford, I. J.; Freeman, S.; Jaffer, M. J. Med. Chem. 2003, 46, 207-209.
56. Mendieta, J.; Martin-Santamaria, S.; Priego, E. M.; Balzarini, J.; Camarasa, M. J.; Perez-Perez, M. J.; Gago, F. Biochemistry 2004, 43, 405-414.
57. Lewis, B. E.; Schramm, V. L. J. Am. Chem. Soc. 2003, 125, 4785-4798.
58. Fedorov, A.; Shi, W.; Kicska, G.; Fedorov, E.; Tyler, P. C.; Furneaux, R. H.; Hanson, J. C.; Gainsford, G. J.; Larese, J. Z.; Schramm, V. L.; Almo, S. C. Biochemistry 2001, 40, 853-860.
59. Heguzi, M. F.; Borehardt, R. T.; Schowen, R. L. J. Am. Chem. Soc. 1979, 101, 4359-4365.
60. Price, M. L.; Guida, W. C.; Jackson, T. E.; Nydick, J. A.; Gladstone, P. L.; Juarez, J. C.; Donate, F.; Ternansky, R. J. Bioorg. Med. Chem. Lett. 2003, 13, 107-110.
61. Walter, M. R.; Cook, W. J.; Cole, L. B.; Short, S. A.; Koszalka, G. W.; Krenitsky, T. A.; Ealick, S. E. J. Biol. Chem. 1990, 265, 14016-14022.
62. Reliability of models generate by SWISS-MODEL. http://www.expasy.org/swissmod/SM_likelyprecision.html.
63. Chothia, C.; Lesk, A. M. EMBO J. 1986, 5, 823-826.
64. Harrison, R. W.; Chatterjee, D.; Weber, I. T. Proteins: Struct., Funct., Genet. 1995, 23, 463-471.
65. Guex, N.; Peitsch, M. C. Electrophoresis 1997, 18, 2714-2723.
66. Bajorath, J.; Stenkamp, R.; Aruffo, A. Protein Sci. 1993, 2.
67. Uracil derivatives and antitumor effect potentiator and antitumor agent containing the same. U.S. Patent 5,744,475, April 28, 1998.
68. Basso, L. A.; Santos, D. S.; Shi, W.; Furneaux, R. H.; Tyler, P. C.; Schramm, V. L.; Blanchard, J. S. Biochemistry 2001, 40, 8196-8203.
69. Poulter, C. D.; Fredrick, G. D. Tetrahedron Lett. 1975, 26, 2171.
70. Dawson, R. M. C.; Elliott, D. C.; Elliott, W. H.; Jones, K. M. Data for Biochemical Research, 3rd ed.; Clarendon Press: Oxford, UK, 1986.