Structure-affinity relationships for the binding of actinomycin D to DNA

Journal of Computer-Aided Molecular Design

Volumn 11, Issue 2, 1997, Pages 114-128

  Gallego, José ^a,b   Ortiz, Angel R ^a,c   De Pascual Teresa, Beatriz ^a,d   Gago, Federico ^a  

^a UNIVERSITY OF ALCALÁ   (Spain)

^b UNIVERSITY OF WASHINGTON   (United States)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

^d UNIVERSIDAD SAN PABLO CEU   (Spain)

Author keywords

Actinomycin D; DNA intercalation; Electrostatic interactions; Stacking interactions

Indexed keywords

BINDING ENERGY; BINDING SITES; CHROMOPHORES; COMPLEXATION; CRYSTAL STRUCTURE; DNA; ELECTROSTATICS; HYDROGEN BONDS; PRINCIPAL COMPONENT ANALYSIS; VAN DER WAALS FORCES;

ACTINOMYCIN D; BASE PAIRS; BINDING-SITES; DNA INTERCALATIONS; GOOD CORRELATIONS; HEXAMERS; INTERMOLECULAR INTERACTION ENERGIES; STACKING INTERACTION; STRUCTURE-AFFINITY RELATIONSHIPS; X RAY CRYSTAL STRUCTURES;

DNA SEQUENCES;

ANTIINFECTIVE AGENT; DACTINOMYCIN; DNA; OLIGODEOXYRIBONUCLEOTIDE;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; CONFORMATION; DNA BASE COMPOSITION; DRUG DESIGN; ELECTRICITY; HYDROGEN BOND; IN VITRO STUDY; METABOLISM; NUCLEOTIDE SEQUENCE; PROTEIN CONFORMATION; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

ANTI-BACTERIAL AGENTS; BASE COMPOSITION; BASE SEQUENCE; BINDING SITES; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DACTINOMYCIN; DNA; DRUG DESIGN; ELECTROSTATICS; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES; PROTEIN CONFORMATION; SOFTWARE; THERMODYNAMICS;

EID: 0031088081     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1008018106064     Document Type: Article

References (62)

1. Bailly, C. and Waring, M.J., Nucleic Acids Res., 23 (1995) 885.
2. Müller, W. and Crothers, D.M., J. Mol. Biol., 35 (1968) 251.
3. Van Dycke, M.W., Hertzberg, R.P. and Dervan, P.B., Proc. Natl. Acad. Sci. USA, 79 (1982) 5470.
4. Lane, M.J., Dabrowiak, J.C. and Vournakis, J.N., Proc. Natl. Acad. Sci. USA, 80 (1983) 3260.
5. Scamrov, A.V. and Beabealashvilli, R.Sh., FEBS Lett., 164 (1983) 97.
6. Fox, K.R. and Waring, M.J., Nucleic Acids Res., 12 (1984) 9271.
7. Waterloh, K. and Fox, K.R., Biochim. Biophys. Acta, 1131 (1992) 300.
8. Goodisman, J., Rehfuss, R., Ward, B. and Dabrowiak, J.C., Biochemistry, 31 (1992) 1046.
9. Snyder, J.G., Hartman, N.G., D'Estantoit, B.L., Kennard, O., Remeta, D.P. and Breslauer, K.J., Proc. Natl. Acad. Sci. USA, 86 (1989) 3968.
10. Bailey, S.A., Graves, D.E., Rill, R. and Marsch, G., Biochemistry, 32 (1993) 5881.
11. Bailey, S.A., Graves, D.E. and Rill, R., Biochemistry, 33 (1994) 11493.
12. Sobell, H.M., Jain, S.C., Sakore, T.D. and Nordman, C.E., Nat. New Biol., 231 (1971) 200.
13. Takusagawa, F., Dabrow, M., Neidle, S. and Berman, H.M., Nature, 296 (1982) 466.
14. Kamitori, S. and Takusagawa, F., J. Mol. Biol., 225 (1992) 445.
15. Kamitori, S. and Takusagawa, F., J. Am. Chem. Soc., 116 (1994) 4154.
16. Patel, D.J., Biochemistry, 13 (1974) 2396.
17. Lybrand, T.P., Brown, S.C., Creighton, S., Shafer, R.H. and Kollman, P.A., J. Mol. Biol., 191 (1986) 495.
18. Crothers, D.M. and Müller, W., Cancer Chemother. Rep., 58 (1974) 97.
19. Krugh, T.R., Mooberry, E.S. and Chiao, Y.-C.C., Biochemistry, 16 (1977) 740.
20. Chiao, Y.-C.C. and Krugh, T.R., Biochemistry, 16 (1977) 747.
21. Kopka, M.L., Goodsell, D.S., Baikalov, I., Grzeskowiak, K., Cascio, D. and Dickerson, R.E., Biochemistry, 33 (1994) 13593.
22. Cerami, A., Reich, E., Ward, D.C. and Goldberg, I.H., Proc. Natl. Acad. Sci. USA, 57 (1967) 1038.
23. Bailly, C., Marchand, C. and Waring, M.J., J. Am. Chem. Soc., 115 (1993) 3784.
24. Chen, F.-M., Biochemistry, 27 (1988) 6393.
25. Chen, F-M., Biochemistry, 31 (1992) 6223.
26. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer Jr., E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M., J. Mol. Biol., 112 (1977) 535.
27. Ginell, S., Lessinger, L. and Berman, H.M., Biopolymers, 27 (1988) 843.
28. Gallego, J., Ph.D. Thesis, Universidad de Alcalá de Henares, Madrid, Spain, 1994.
29. AMBER, v. 4.0, Pearlman, D.A., Case, D.A., Caldwell, J., Seibel, G., Singh, U.C., Weiner, P. and Kollman, P.A., Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, U.S.A., 1991.
30. Gago, F., Reynolds, C.A. and Richards, W.G., Mol. Pharmacol., 35 (1989) 232.
31. Gallego, J., Luque, F.J., Orozco, M., Burgos, C., Alvarez-Builla, J., Rodrigo, M.M. and Gago, F., J. Med. Chem., 37 (1994) 1602.
32. Jain, S.C. and Sobell, H.M., J. Mol. Biol., 68 (1972) 1.
33. Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ohio, C., Alagona, G., Profeta, S. and Weiner, P., J. Am. Chem. Soc., 106 (1984) 765.
34. Hopfinger, A.J. and Pearlstein, R.A., J. Comput. Chem., 5 (1984) 486.
35. Dewar, M.J.S., Zoebisch, E.G., Healy, E.F. and Stewart, J.J.P., J. Am. Chem. Soc., 107 (1985) 3902.
36. Chirlian, L.E. and Francl, M.M., J. Comput. Chem., 8 (1987) 894.
37. SPARTAN, v. 3.0.1, Wavefunction Inc., Irvine, CA, U.S.A., 1993.
38. Sanz, F., Manaut, F., Rodríguez, J., Lozoya, E. and López-de-Briñas, E., J. Comput.-Aided Mol. Design, 7 (1993) 337.
39. INSIGHT II, v. 2.3.0, Biosym Technologies, San Diego, CA, U.S.A., 1993.
40. Friedman, R.A. and Honig, B., Biopolymers, 32 (1992) 145.
41. Klapper, I., Hagstrom, R., Fine, R., Sharp, K. and Honig, B., Proteins, 1 (1986) 47.
42. Lee, B. and Richards, F.M., J. Mol. Biol., 55 (1971) 379.
43. Gilson, M.K., Sharp, K.A. and Honig, B., J. Comput. Chem., 9 (1988) 327.
44. Wold, S., Esbensen, K. and Geladi, P., Chemometr. Intell. Lab. Syst., 2 (1987) 37.
45. Wold, H., In David, F. (Ed.), Research Papers in Statistics, Wiley, New York, NY, U.S.A., 1966, pp. 411-444.
46. Boobyer, D.N.A., Goodford, P.J., McWhinnie, P.M. and Wade, R., J. Med. Chem., 32 (1989) 1083.
47. Gallego, J., de Pascual, B., Ortiz, A.R., Pisabarro, M.T. and Gago, F., In Sanz, F., Giraldo, J. and Manaut, F. (Eds.), QSAR and Molecular Modelling: Concepts, Computational Tools and Biological Applications, Prous Science, Barcelona, Spain, 1995, pp. 274-281.
48. Gallego, J., Ortiz, A.R. and Gago, F., J. Med. Chem., 36 (1993) 1548.
49. Lavery, R. and Pullman, B., Int. J. Quantum Chem., 20 (1981) 259.
50. Fox, K.R. and Waring, M.J., Eur. J. Biochem., 145 (1984) 579.
51. Bailly, C., Graves, D.E., Ridge, G. and Waring, M.J., Biochemistry, 33 (1994) 8736.
52. Dean, P.M. and Wakelin, L.P.G., Proc. R. Soc. London, B209 (1980) 473.
53. Wang, A.H.-J., Ughetto, G., Quigley, G.J., Hakoshima, T., Van der Marel, G.A., Van Boom, J.H. and Rich, A., Science, 225 (1984) 1115.
54. Marky, L.A., Snyder, J.G., Remeta, D.P. and Breslauer, K.J., J. Biomol. Struct. Dyn., 1 (1983) 487.
55. Quadrifoglio, F., Ciana, A. and Crescenzi, V., Biopolymers, 15 (1976) 595.
56. Gago, F. and Richards, W.G., Mol. Pharmacol., 37 (1990) 341.
57. Hunter, C.A., J. Mol. Biol., 230 (1993) 1025.
58. Gallego, J., Luque, F.J., Orozco, M. and Gago, F., J. Biomol. Struct. Dyn., 12 (1994) 111.
59. Krugh, T.R. and Reinhardt, C.G., J. Mol. Biol., 97 (1975) 133.
60. Müller, W. and Crothers, D.M., Eur. J. Biochem., 54 (1975) 267.
61. Cruciani, G. and Goodford, P.J., J. Mol. Graph., 12 (1994) 116.
62. Geierstanger, B.H., Mrksich, M., Dervan, P.B. and Wemmer, D.E., Science, 266 (1994) 646.