Theoretical Study of Cisplatin Binding to Purine Bases: Why Does Cisplatin Prefer Guanine over Adenine?

Journal of the American Chemical Society

Volumn 125, Issue 46, 2003, Pages 14082-14092

  Baik, Mu Hyun ^a,c   Friesner, Richard A ^a   Lippard, Stephen J ^b  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; COMPUTATIONAL METHODS; CONFORMATIONS; CROSSLINKING; DNA; DRUG INTERACTIONS; ELECTROSTATICS; HYDROGEN BONDS; REACTION KINETICS; THERMODYNAMICS; TUMORS;

DENSITY FUNCTIONAL THEORY;

DRUG PRODUCTS;

ADENINE; CISPLATIN; GUANINE; PURINE DERIVATIVE;

ANTINEOPLASTIC ACTIVITY; ARTICLE; DISSOCIATION; DNA STRUCTURE; DRUG DNA BINDING; HYDROGEN BOND; HYDROLYSIS; KINETICS; MODEL; MOLECULAR INTERACTION; SOLVATION; THERMODYNAMICS;

ADENINE; CISPLATIN; GUANINE; KINETICS; MODELS, MOLECULAR; SUBSTRATE SPECIFICITY; THERMODYNAMICS;

EID: 0242582476     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja036960d     Document Type: Article

References (93)

1. Platinum and Other Metal Coordination Compounds in Cancer Chemotherapy; Pinedo, H. M., Schornagel, J. H., Eds.; Plenum Press: New York, 1996.
2. For example, see: Go, R. S.; Adjei, A. A. J. Clin. Oncol. 1999, 17, 409-422.
3. Rosenberg, B.; Van Camp, L.; Krigas, T. Nature 1965, 205, 698.
4. Rosenberg, B.; Van Camp, L.; Trosko, J. E.; Mansour, V. H. Nature 1969, 222, 385.
5. Jamieson, E. R.; Lippard, S. J. Chem. Rev. 1999, 99, 2467.
6. Fuertes, M. A.; Alonso, C.; Perez, J. M. Chem. Rev. 2003, 103, 645.
7. Bancroft, D. P.; Lepre, C. A.; Lippard, S. J. J. Am. Chem. Soc. 1990, 112, 6860.
8. Sherman, S. E.; Lippard, S. J. Chem. Rev. 1987, 87, 1153.
9. Mello, J. A.; Lippard, S. J.; Essigmann, J. M. Biochemistry 1995, 34, 14783.
10. Fichtinger-Schepman, A. M. J.; van der Veer, J. L.; den Hartog, J. H. J. ; Lohman, P. H. M.; Reedijk, J. Biochemistry 1985, 24, 707.
11. Eastman, A. Biochemistry 1986, 25, 3912.
12. Wong, E.; Giandomenico, C. M. Chem. Rev. 1999, 99, 2451.
13. Weiss, R. B.; Christian, M. C. Drugs 1993, 46, 360.
14. Clarke, M. J.; Zhu, F. C.; Frasca, D. R. Chem. Rev. 1999, 99, 2511.
15. Kelland, L. R. Drugs 2000, 59, 1.
16. Giaccone, G. Drugs 2000, 59, 9.
17. Judson, I.; Kelland, L. R. Drugs 2000, 59, 29.
18. Raymond, E.; Chaney, S. G.; Taamma, A.; Cvitkovic, E. Ann. Oncol. 1998, 9, 1053.
19. Spingler, B.; Whittington, D. A.; Lippard, S. J. Inorg. Chem. 2001. 40, 5596.
20. Wagstaff, A. J.; Ward, A.; Benfield, P.; Heel, R. C. Drugs 1989, 37, 162.
21. Teuben, J. M.; Bauer, C.; Wang, A. H. J.; Reedijk, J. Biochemistry 1999, 38, 12305.
22. Piccart, M. J.; Lamb, H.; Vermorken, J. B. Ann. Oncol. 2001, 12. 1195.
23. Reedijk, J. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 3611.
24. Deeth, R. J.; Elding, L. 1. Inorg. Chem. 1996, 35, 5019.
25. Legendre, F.; Bas, V.; Kozelka, J.; Chottard, J. C. Chem.-Eur. J. 2000, 6, 2002.
26. Kozelka, J.; Legendre, F.; Reeder, F.; Chottard, J. C. Coord. Chem. Rev. 1999, 192, 61.
27. Legendre, F.; Kozelka, J.; Chottard, J. C. Inorg. Chem. 1998, 37, 3964.
28. Reedijk, J. Pure Appl. Chem. 1987, 59, 181.
29. Scovell, W. M.; O'Connor, T. J. Am. Chem. Soc. 1977, 99, 120.
30. Carloni, P.; Sprik, M.; Andreoni, W. J. Phys. Chem. B 2000, 104, 823.
31. Zhang, Y.; Guo, Z. J.; You, X. Z. J. Am. Chem. Soc. 2001, 123, 9378.
32. Tsipis, A. C.; Sigalas, M. P. THEOCHEM 2002, 584, 235.
33. Langlet, J.; Berges, J.; Caillet, J.; Kozelka, J. Theor. Chem. Acc. 2000, 104, 247.
34. Chval, Z.; Sip, M. THEOCHEM 2000, 532, 59.
35. Basch, H.; Krauss, M.; Stevens, W. J.; Cohen, D. Inorg. Chem. 1985, 24, 3313.
36. Basch, H.; Krauss, M.; Stevens, W. J.; Cohen, D. Inorg. Chem. 1986, 25, 684.
37. Hill, G. A.; Forde, G.; Gorb, L.; Leszczynski. J. Int. J. Quantum Chem. 2002, 90, 1121.
38. Cochran, K.; Forde, G.; Hill, G. A.; Gorb, L.; Leszczynski, J. Struct. Chem. 2002, 13, 133.
39. Pelmenschikov, A.; Zilberberg, I.; Leszczynski, J.; Famulari, A.; Sironi, M.; Raimondi, M. Chem. Phys. Lett. 1999, 314, 496.
40. Burda, J. V.; Sponer, J.; Leszczynski, J. Phys. Chem. Chem. Phys. 2001, 3, 4404.
41. Sponer, J. E.; Leszczynski, J.; Glahe, F.; Lippert, B.; Sponer, J. Inorg. Chem. 2001, 40, 3269.
42. Burda, J. V.; Sponer, J.; Hrabakova, J.; Zeizinger, M.; Leszczynski, J. J. Phys. Chem. B 2003, 107, 5349.
43. Burda, J. V.; Sponer, J.; Leszczynski, J. J. Biol. Inorg. Chem. 2000, 5, 178.
44. Deubel, D. V. J. Am. Chem. Soc. 2002, 124, 5834.
45. Sponer, J. E.; Glahe, F.; Leszczynski, J.; Lippert, B.; Sponer, J. J. Phys. Chem. B 2001, 105, 12171.
46. Sponer, J.; Sponer, J. E.; Gorb, L.; Leszczynski, J.; Lippert, B. J. Phys. Chem. A 1999, 103, 11406.
47. Kozelka, J.; Berges, J. J. Chito. Phys. Phys. Chim. Biol. 1998, 95, 2226.
48. Monjardet-Bas, V.; Elizondo-Riojas, M.-A.; Chottard, J.-C.; Kozelka, J. Angew. Chem., Int. Ed. 2002, 41, 2998.
49. Carloni, P.; Andreoni, W. J. Phys. Chem. 1996, 100, 17797.
50. Carloni, P.; Andreoni, W.; Hutter, J.; Curioni, A.; Giannozzi, P.; Parrinello, M. Chem. Phys. Lett. 1995, 234, 50.
51. Tomaghi, E.; Andreoni, W.; Carloni, P.; Hutter, J.; Parrinello, M. Chem. Phys. Lett. 1995, 246, 469.
52. Burda, J. V.; Sponer, J.; Hrabadkova, J.; Zeizinger, M.; Leszczynski, J. J. Phys. Chem. B 2003, 107, 5349.
53. Miller, S. E.; House, D. A. Inorg. Chim. Acta 1990, 173, 53.
54. Miller, S. E.; House, D. A. Inorg. Chim. Acta 1989, 166, 189.
55. Chval, Z.; Sip, M. Collect. Czech. Chem. Commun. 2003, 68, 1105.
56. Parr, R. G.; Yang, W. Density Functional Theory of Atoms and Molecules: Oxford University Press: New York, 1989.
57. Ziegler, T. Chem. Rev. 1991, 91, 651.
58. Jaguar 4.1: Schrödinger, Inc.: Portland. OR, 2000.
59. Velde, G. T.; Bickelhaupt, F. M.; Baerends, E. J.; Guerra, C. F.; Van Gisbergen, S. J. A.; Snijders, J. G.; Ziegler, T. J. Comput. Chem. 2001, 22, 931.
60. Becke, A. D. J. Chem. Phys. 1993, 98, 5648.
61. Lee, C. T.; Yang, W. T.; Parr, R. G. Phys. Rev. B 1988, 37, 785.
62. Hay, P. J.; Wadt, W. R. J. Chem. Phys. 1985, 82, 270.
63. Wadt, W. R.; Hay, P. J. J. Chem. Phys. 1985, 82, 284.
64. Hay, P. J.; Wadt, W. R. J. Chem. Phys. 1985, 82, 299.
65. Dunning, T. H. J. Chem. Phys. 1989, 90, 1007.
66. Tomasi, J.; Persico, M. Chem. Rev. 1994, 94, 2027.
67. Cramer, C. J.; Truhlar, D. G. Structure and Reactivity in Aqueous Solution, ACS Symposium Series 568: American Chemical Society: Washington, D.C., 1994.
68. Cramer, C. J.; Truhlar, D. G. Chem. Rev. 1999, 99, 2161.
69. Tannor, D. J.; Marten, B.; Murphy, R. B.; Friesner, R. A.; Sitkoff, D.; Nicholls, A.; Ringnalda, M. N.; Goddard, W. A., III.; Honig, B. J. Am. Chem. Soc. 1994, 116, 11875.
70. Marten, B.; Kim, K.; Cortis, C.; Friesner, R. A.; Murphy, R. B.; Ringnalda, M. N.; Sitkoff, D.; Honig, B. J. Phys. Chem. 1996, 100, 11775.
71. Ziegler, T.; Rauk, A. Theor. Chim. Acta 1977, 46, 1.
72. Ziegler, T.; Rauk, A. Inorg. Chem. 1979, 18, 1755.
73. Ziegler, T.; Rauk, A. Inorg. Chem. 1979, 18, 1558.
74. Becke, A. D. Phys. Rev. A 1988, 38, 3098.
75. van Lenthe, E.; Baerends, E. J.; Snijders, J. G. J. Chem. Phys. 1993, 99, 4597.
76. van Lenthe, E.; van Leeuwen, R.; Baerends, E. J.; Snijders, J. G. Int. J. Quantum Chem. 1996, 57, 281.
77. Peng, C. Y.; Schlegel, H. B. Isr. J. Chem. 1993, 33, 449.
78. Brammer, L.; Charnock, J. M.; Goggin, P. L.; Goodfellow, R. J.; Koetzle, T. F.; Orpen, A. G. J. Chem. Soc., Chem. Commun. 1987, 443.
79. Aullon, G.; Bellamy, D.; Brammer, L.; Bruton, E. A.; Orpen, A. G. Chem. Commun. 1998, 653.
80. Reedijk, J. Inorg. Chim. Acta 1992, 200, 873.
81. Luisi, B.; Orozco, M.; Sponer, J.; Luque, F. J.; Shakked, Z. J. Mol. Biol. 1998, 279, 1123.
82. Vargas, R.; Garza, J.; Friesner, R. A.; Stern, H.; Hay, B. P.; Dixon, D. A. J. Phys. Chem. A 2001, 105, 4963.
83. Dixon, D. A.; Dobbs, K. D.; Valentini, J. J. J. Phys. Chem. 1994, 98, 13435.
84. Lorant, F.; Behar, F.; Goddard, W. A.; Tang, Y. C. J. Phys. Chem. A 2001, 105, 7896.
85. Truhlar, D. G.; Garrett, B. C.; Klippenstein, S. J. J. Phys. Chem. 1996, 100, 12771.
86. Attempts to optimize the transition state geometry consistently produced the structure 1TS.
87. Structure 4TS is equivalent to the transition state structure TSAdelb reported previously.55
88. Arpalahti, J.; Lippert, B. Inorg. Chem. 1990, 29, 104.
89. Frenking, G.; Fröhlich, N. Chem. Rev. 2000, 100, 717.
90. Baik, M. H.; Friesner, R. A.; Lippard, S. J. J. Am. Chem. Soc. 2002, 124, 4495.
91. total for the same species is -42.5 kcal/mol (Table 5). All of the relative energy trends observed for the four transition states above are reproduced in this protocol, however. The energy difference between 1TS and 4TS, for example, is predicted to be 19.4 kcal/mol using ADF which compares well with the energy difference of 19.7 kcal/mol mentioned above (Table 4).
92. For a more detailed discussion, see: Baik, M.-H.; Friesner, R. A.; Lippard, S. J. Inorg. Chem., in press.
93. Because the distortion towards the trigonal-bipyramidal structure in the transition state is more pronounced in the case of guanine, the orbital energy of this orbital is slightly higher by 0.024 eV, as indicated in Figure 5, but this detail is probably not of practical significance.