Intercalation mechanisms with ds-DNA: Binding modes and energy contributions with benzene, naphthalene, quinoline and indole derivatives including some antimalarials

Journal of the Chemical Society. Perkin Transactions 2

Volumn , Issue 11, 1997, Pages 2319-2327

  Sartorius, Joachim ^a   Schneider, Hans Jörg ^a  

^a SAARLAND UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0347933768     PISSN: 03009580     EISSN: None     Source Type: Journal    
DOI: 10.1039/a702628e     Document Type: Article

References (115)

1. (a) W. D. Wilson, in Nucleic Acids in Chemistry and Biology, ed. G. M. Blackburn and M. J. Gait, IRL Press, Oxford, 1989, ch. 8;
2. (b) J. W. Lown, Anti-Cancer Drug Des., 1988, 3, 25;
3. (c) P. B. Dervan, Science, 1986, 232, 464.
4. (a) S. Neidle and Z. Abraham, CRC Crit. Rev. Biochem., 1984, 17, 73;
5. (b) S. Neidle and T. C. Jenkins, Molecular Design and Modeling, Part B, 1991, 203, 433.
6. (a) W. Saenger, Principles of Nucleic Acid Structure, Springer, New York, 1988;
7. (b) L. A. Basile and J. K. Barton, Met. Ions Biol. Syst., 1989, 25, 31;
8. (c) M. J. Waring, Ann. Rev. Biochem., 1981, 50, 159.
9. It has been cautioned that several methods must be applied before intercalation can be claimed, however, without consideration of the NMR method applied in the present paper: E. C. Long and J. K. Barton, Acc. Chem. Res., 1990, 23, 271.
10. For early reviews see e.g. H. W. Zimmermann, Angew. Chem., 1986, 98, 115.
11. (a) L. Kapicak and E. J. Gabbay, J. Am. Chem. Soc., 1975, 97, 403; E. J. Gabbay, R. Scofield and C. S. Baxter, J. Am. Chem. Soc., 1973, 95, 7850;
12. (a) L. Kapicak and E. J. Gabbay, J. Am. Chem. Soc., 1975, 97, 403; E. J. Gabbay, R. Scofield and C. S. Baxter, J. Am. Chem. Soc., 1973, 95, 7850;
13. (b) S. Chandrasekaran, S. Kusuma, D. W. Boykin and W. D. Wilson, Magn. Reson. Chem., 1986, 24, 630; such shifts have also been used for titrations of self-associating nucleoside derivatives;
14. (c) K. H. Scheller and H. Sigel, J. Am. Chem. Soc., 1983, 105, 5891; O. Yamauchi, A. Odani, H. Masuda and H. Sigel, Met. Ions Biol. Syst., 1996, 32, 207 and references cited therein.
15. (c) K. H. Scheller and H. Sigel, J. Am. Chem. Soc., 1983, 105, 5891; O. Yamauchi, A. Odani, H. Masuda and H. Sigel, Met. Ions Biol. Syst., 1996, 32, 207 and references cited therein.
16. J. Sartorius and H.-J. Schneider, FEBS Lett., 1995, 374, 387.
17. (a) L. Strekowski, J. L. Mokrosz, W. D. Wilson, M. J. Mokrosz and A. Strekowski, Biochemistry, 1992, 31, 10 802;
18. (b) M. W. Davidson, B. G. Griggs, D. W. Boykin and W. D. Wilson, J. Med. Chem., 1977, 20, 1117.
19. (a) See also ref. 6(a);
20. (b) C. Helène and J. C. Maurizot, CRC Crit. Rev. Biochem., 1981, 10, 213;
21. C. Helène, T. Montenay-Garestier and J.-L. Dimicoli, Biochim. Biophys. Acta, 1971, 254, 349;
22. (d) F. Brun, J.-J. Toulme and C. Helène, Biochemistry, 1975, 14, 558;
23. (e) C. Helène, J.-L. Dimicoli and F. Brun, Biochemistry, 1971, 10, 3802;
24. (f) J.-L. Dimicoli and C. Helène, Biochemistry, 1974, 13, 714;
25. (g) R. Mayer, F. Toulme, T. Montenay-Garestier and C. Helène, J. Biol. Chem., 1979, 254, 75;
26. (h) E. J. Gabbay, B. L. Gaffney and R. Glaser, Ann. N.Y. Acad. Sci., 1970, 171, 810;
27. (i) P. Adawadkar, W. D. Wilson, W. Brey and E. J. Gabbay, J. Am. Chem. Soc., 1975, 97, 1959;
28. (j) E. J. Gabbay, P. Adawadkar and W. D. Wilson, Biochemistry, 1976, 15, 146;
29. (k) E. J. Gabbay, K. Sanford and C. S. Baxter, Biochemistry, 1972, 11, 3429;
30. (l) E. J. Gabbay, P. Adawadkar, L. Kapicak, S. W. Pearce and W. D. Wilson, Biochemistry, 1976, 15, 152.
31. (a) A. J. Jacobsen and J. C. Wang, Biochim. Biophys. Acta, 1973, 335, 49;
32. (b) F. Quadrifoglio, V. Giancotti and V. Creszenzi, FEBS Lett., 1976, 65, 345.
33. H.-J. Schneider, Chem. Soc. Rev., 1994, 22, 227; H.-J. Schneider, T. Blatter, A. Eliseev, V. Rüdiger and O. A. Raevsky, Pure Applied Chem., 1993, 65, 2329.
34. H.-J. Schneider, Chem. Soc. Rev., 1994, 22, 227; H.-J. Schneider, T. Blatter, A. Eliseev, V. Rüdiger and O. A. Raevsky, Pure Applied Chem., 1993, 65, 2329.
35. T. Takita, Y. Muraoka, T. Nakatani, A. Fujii, Y. Iitaka and H. Umezawa, J. Antibiot., 1978, 65, 1673.
36. O. Kennard and W. N. Hunter, Angew. Chem., 1991, 103, 1280; Angew. Chem., Int. Ed. Engl., 1991, 30, 1254.
37. O. Kennard and W. N. Hunter, Angew. Chem., 1991, 103, 1280; Angew. Chem., Int. Ed. Engl., 1991, 30, 1254.
38. (a) F. S. Parker and J. L. Irvin, J. Biol. Chem., 1952, 199, 897;
39. (b) D. Stollar and L. Levine, Arch. Biochem. Biophys., 1963, 101, 335;
40. (c) S. N. Cohen and S. N. Yielding, J. Biol. Chem., 1965, 240, 3123;
41. (d) R. L. O'Brien and F. E. Hahn, Antimicrob. Agents Chemother., 1965, 315;
42. (e) L. W. Blodgett and K. L. Yielding, Biochim. Biophys. Acta, 1968, 169, 451;
43. (f) K. L. Yielding, L. W Blodgett, H. Sternglanz and D. Gaudin, Prog. Mol. Subcell. Biochem., 1971, 2, 69;
44. (g) S. N. Cohen and K. L. Yielding, J. Biol. Chem., 1965, 240, 3123;
45. (h) P. V. Scaria, J. C. Craig and R. H. Shafer, Biopolymers, 1993, 33, 887;
46. (i) M. W. Davidson, B. G. Griggs, D. W. Boykin and W. D. Wilson, Nature (London), 1975, 254, 632;
47. (j) M. W. Davidson, B. G. Griggs and W. D. Wilson, J. Med. Chem., 1977, 20, 1117;
48. (k) H. Auterhoff, J. Knabe and H. D. Höltje, in Lehrbuch der Pharmazeutischen Chemie, WVG, Stuttgart, 1991;
49. (l) A. Korolkovas, in Essentials of Medicinal Chemistry, Wiley, New York, 1988;
50. (m) R. L. Jones, M. W. Davidson and W. D. Wilson, Biochim. Biophys. Acta, 1979, 561, 77;
51. (n) F. E. Hahn, R. L. O'Brien, J. Ciak, J. L. Allison and J. G. Olenick, Mil. Med., 1966, 131, 1071;
52. (o) R. D. Estensen, A. K. Krey and F. E. Hahn, Mol. Pharmacol., 1969, 5, 532.
53. (a) J. Sponer, J. Lesczynski and P. Hobza, J. Phys. Chem., 1996, 100, 5590;
54. (b) J. Sponer and P. Hobza, Int. J. Quant. Chem., 1996, 57, 959;
55. (c) J. Sponer, J. Lesczynski, V. Vetter and P. Hobza, J. Biomol. Struct. Dynamics, 1996, 13, 695;
56. (d) see also P. Hobza, J. Sponer and M. Polasek, J. Am. Chem. Soc., 1995, 117, 792.
57. See also (a) R. L. Jernigan, A. Sarai, K.-L. Ting and R. J. Nussinov, J. Biomol. Struct. Dyn., 1986, 4, 41; (b) R. A. Friedmann and B. Honig, Biopolymers, 1992, 32, 145; (c) R. C. Maroun and W. K. Olson, Biopolymers, 1988, 27, 585; (d) A. Sarai, J. Mazur, R. Nussinov and R. L. Jernigan, Biochemistry, 1988, 27, 8498; (e) C. A. Hunter, J. Mol. Biol., 1993, 230, 1025.
58. See also (a) R. L. Jernigan, A. Sarai, K.-L. Ting and R. J. Nussinov, J. Biomol. Struct. Dyn., 1986, 4, 41; (b) R. A. Friedmann and B. Honig, Biopolymers, 1992, 32, 145; (c) R. C. Maroun and W. K. Olson, Biopolymers, 1988, 27, 585; (d) A. Sarai, J. Mazur, R. Nussinov and R. L. Jernigan, Biochemistry, 1988, 27, 8498; (e) C. A. Hunter, J. Mol. Biol., 1993, 230, 1025.
59. See also (a) R. L. Jernigan, A. Sarai, K.-L. Ting and R. J. Nussinov, J. Biomol. Struct. Dyn., 1986, 4, 41; (b) R. A. Friedmann and B. Honig, Biopolymers, 1992, 32, 145; (c) R. C. Maroun and W. K. Olson, Biopolymers, 1988, 27, 585; (d) A. Sarai, J. Mazur, R. Nussinov and R. L. Jernigan, Biochemistry, 1988, 27, 8498; (e) C. A. Hunter, J. Mol. Biol., 1993, 230, 1025.
60. See also (a) R. L. Jernigan, A. Sarai, K.-L. Ting and R. J. Nussinov, J. Biomol. Struct. Dyn., 1986, 4, 41; (b) R. A. Friedmann and B. Honig, Biopolymers, 1992, 32, 145; (c) R. C. Maroun and W. K. Olson, Biopolymers, 1988, 27, 585; (d) A. Sarai, J. Mazur, R. Nussinov and R. L. Jernigan, Biochemistry, 1988, 27, 8498; (e) C. A. Hunter, J. Mol. Biol., 1993, 230, 1025.
61. See also (a) R. L. Jernigan, A. Sarai, K.-L. Ting and R. J. Nussinov, J. Biomol. Struct. Dyn., 1986, 4, 41; (b) R. A. Friedmann and B. Honig, Biopolymers, 1992, 32, 145; (c) R. C. Maroun and W. K. Olson, Biopolymers, 1988, 27, 585; (d) A. Sarai, J. Mazur, R. Nussinov and R. L. Jernigan, Biochemistry, 1988, 27, 8498; (e) C. A. Hunter, J. Mol. Biol., 1993, 230, 1025.
62. (a) C. E. Bugg, J. M. Thomas, M. Sundaralingam and T. S. Rao, Biopolymers, 1971, 10, 175;
63. (b) U. Heinemann and C. Alings, J. Mol. Biol., 1989, 210, 369.
64. A. Sen, A. Ray and M. Maiti, Biophys. Chem., 1996, 59, 155; D. B. Davies and A. N. Veselkov, J. Chem. Soc., Faraday Trans., 1996, 92, 3545; I. Haq, J. E. Ladbury, B. Z. Chowdhry and T. C. Jenkins, J. Am. Chem. Soc., 1996, 118, 10 693; and references cited therein.
65. A. Sen, A. Ray and M. Maiti, Biophys. Chem., 1996, 59, 155; D. B. Davies and A. N. Veselkov, J. Chem. Soc., Faraday Trans., 1996, 92, 3545; I. Haq, J. E. Ladbury, B. Z. Chowdhry and T. C. Jenkins, J. Am. Chem. Soc., 1996, 118, 10 693; and references cited therein.
66. A. Sen, A. Ray and M. Maiti, Biophys. Chem., 1996, 59, 155; D. B. Davies and A. N. Veselkov, J. Chem. Soc., Faraday Trans., 1996, 92, 3545; I. Haq, J. E. Ladbury, B. Z. Chowdhry and T. C. Jenkins, J. Am. Chem. Soc., 1996, 118, 10 693; and references cited therein.
67. A. J. Hopfinger, M. G. Cardozo and Y. Kawakami, J. Chem. Soc., Faraday Trans., 1995, 91, 2315.
68. L. F. Newcomb and S. H. Gellman, J. Am. Chem Soc. 1994, 116, 4993.
69. J. D. McGhee and P. H. von Hippel, J. Mol. Biol., 1974, 86, 469.
70. See also: NMR of Macromolecules, ed. G. C. K. Roberts, Oxford University Press, New York, 1993, ch. 8.
71. (a) G. Scatchard, Ann. N. Y. Acad. Sci., 1949, 51, 660;
72. (b) see also ref. 5;
73. (c) J. Pauluhn and H. W. Zimmermann, Ber. Bunsenges. Phys. Chem., 1978, 82, 1265;
74. (d) J. Pauluhn, R. Grezes and H. W. Zimmermann. Acta Histochemica Suppl., 1981, 24, 169.
75. (a) See also ref. 5;
76. (b) M. S. Whittingham and A. J. Jacobsen, in Intercalation Chemistry, Academic Press, New York, 1982, ch. 14.
77. (a) L. S. Lerman, J. Mol. Biol., 1961, 3, 18;
78. (b) A. R. Peacocke and J. N. H. Skerrett, Trans. Faraday Soc., 1956, 52, 261.
79. (a) K. D. Stewart, J. Phys. Org. Chem., 1992, 5;
80. (b) M. Cory, D. D. McKee, J. Kagan, D. W. Henry and J. A. Miller, J. Am. Chem. Soc., 1985, 107, 2528.
81. H.-J. Schneider and T. Blatter, Angew. Chem., 1988, 100, 1211; Angew. Chem., Int. Ed. Engl., 1988, 27, 1163.
82. H.-J. Schneider and T. Blatter, Angew. Chem., 1988, 100, 1211; Angew. Chem., Int. Ed. Engl., 1988, 27, 1163.
83. See D. L. Boger and D. S. Johnson, Angew. Chem., 1996, 108, 1543; Angew. Chem., Int. Ed. Engl., 1996, 35, 1438, and references cited therein.
84. See D. L. Boger and D. S. Johnson, Angew. Chem., 1996, 108, 1543; Angew. Chem., Int. Ed. Engl., 1996, 35, 1438, and references cited therein.
85. C. R. Cantor and P. R. Schimmel, in Biophysical Chemistry, Freeman, San Francisco, 1980, vol. 3, pp. 1199ff.
86. (a) S. R. Meshnick, Parasitology Today, 1990, 6, 87;
87. (b) F. Kwakye-Berko and S. R. Meshnick, Mol. Biochem. Parasitol., 1989, 35, 51.
88. (a) T. Maniatis, J. H. Venable and L. S. Lerman, J. Mol. Biol., 1974, 84, 37;
89. (b) see also ref. 3(a);
90. (c) V. I. Ivanov, A. T. Karapetyan, E. E. Minyat and J. Sagi, Molecular Biology, 1993, 27, 713;
91. (d) I. S. Haworth, A. Rodger and W. G. Richards, J. Biomol. Struct. Dyn., 1992, 10, 195;
92. (e) W. Zacharias, J. C. Martin and R. D. Wells, Biochemistry, 1983, 22, 2398;
93. (f) W. Zacharias, J. E. Larson, J. Klysik, S. M. Stirdivant and R. D. Wells, J. Biol. Chem., 1982, 257, 2775;
94. (g) D. M. Soumpasis, M. Robert-Nicoud and T. M. Jovin, FEBS Lett., 1987, 213, 341;
95. (h) H. S. Basu, H. C. A. Schwietert, B. G. Feuerstein and L. J. Marton, Biochem. J., 1990, 269, 329;
96. (i) A. Rich, A. Nordheim and A. H. J. Wang, Ann. Rev. Biochem., 1984, 53, 791;
97. (j) F. E. Rossetto and E. Nieboer, J. Inorg. Biochem., 1994, 54, 167;
98. (k) F. M. Pohl, Nature, 1976, 260, 365;
99. (l) J. C. Girod, W. C. Johnson, S. K. Huntington and M. F. Maestre, Biochemistry, 1973, 12, 5092.
100. Further data see J. Sartorius, PhD Dissertation, Universität des Saarlandes, Saarbrücken, 1996.
101. (a) M.-A. Schwaller, G. Dodin and J. Aubard, Biopolymers, 1991, 31, 519;
102. (b) A. Kagemoto, A. Kunihiro and Y. Baba, Thermochim. Acta, 1994, 242, 65.
103. (a) J. Bach, M. J. Blandamer, K. Bijma, B. F. N. EnJan, P. A. Kooreman, A. Kacperska, K. Rao and C. S. Marata, J. Chem. Soc., Faraday Trans., 1995, 91, 1229;
104. (b) L. Giorgio Solid, Y. Marcus, M. J. Blandamer and P. M. Cullis, J. Solution Chem., 1995, 24, 201.
105. (a) G. S. Manning, Acc. Chem. Res., 1979, 12, 443;
106. (b) for the application on DNA intercalation complexes see also refs. 2(a), 5 and 25(ft).
107. B. P. Hudson, C. M. Dupureur and J. K. Barton, J. Am. Chem. Soc., 1995, 117, 9379.
108. H.-J. Schneider and M. Wang, J. Org. Chem., 1994, 59, 7464.
109. D. L. Boger, J.-H. Chen and K. W. Saionz, J. Am. Chem. Soc., 1996, 118, 1629.
110. K. M. Guckian, B. A. Schweitzer, R. X.-F. Ren, C. J. Sheils, P. L. Paris, D. C. Tahmassebi and E. T. Kool, J. Am. Chem. Soc., 1996, 118, 8182.
111. L.-F. Tietze and T. Eicher, in Reaktionen und Synthesen im organischchemischen Praktikum, Thieme, Stuttgart, 1981, and references cited therein.
112. K. Fukudome, K. Yamaoka, K. Nishikori, T. Takahashi and O. Yamamoto, Polym. J., 1986, 18, 71.
113. A. P. Gray, D. C. Schliefer, E. E. Spinner and C. J. Cavallito, J. Am. Chem. Soc., 1955, 77, 3648.
114. (a) C. S. Wilcox, in Frontiers on Supramolecular Organic Chemistry and Photochemistry, ed. H.-J. Schneider and H. Dürr, VCH, Weinheim, 1991, pp. 122ff;
115. (b) H.-J. Schneider, R. Kramer, S. Simora and U. Schneider, J. Am. Chem. Soc., 1988, 110, 6442.