PL EN


Preferences help
enabled [disable] Abstract
Number of results
2000 | 47 | 3 | 855-866
Article title

Molecular modelling of the interaction of carbocyclic analogues of netropsin and distamycin with d(CGCGAATTCGCG)2.

Content
Title variants
Languages of publication
EN
Abstracts
EN
A molecular mechanics and molecular dynamics approach was used to examine the structure of complexes formed between the d(CGCGAATTCGCG)2 duplex and netropsin, distamycin, and four carbocyclic analogues of netropsin and distamycin (1-4). The resulting structures of the ligand-DNA model complexes and their energetics were examined. It is predicted that the compounds 1-4 should have a decreased affinity for the minor groove of AT-rich regions in comparison to netropsin and distamycin. From the energetic analysis it appears that van der Waals and electrostatic interactions are more important than specific hydrogen bonds in stabilizing the ligand-duplex complexes. We predict that compounds 1 and 2 are effectively isohelical with the DNA minor groove. The superior DNA-binding afforded by 1 and 2 in comparison to 3 and 4 results from their more effective penetration into the minor groove and smaller perturbation of molecular structure upon complex formation.
Publisher

Year
Volume
47
Issue
3
Pages
855-866
Physical description
Dates
published
2000
received
2000-01-24
accepted
2000-06-05
Contributors
  • Department of Medicinal Chemistry and Drug Technology, Medical Academy of Białystok, Białystok, Poland
  • Department of Medicinal Chemistry and Drug Technology, Medical Academy of Białystok, Białystok, Poland
  • Department of Organic Chemistry, Medical Academy of Białystok, Białystok, Poland
  • Department of Organic Chemistry, Medical Academy of Białystok, Białystok, Poland
References
  • 1. Nielsen, E.P. (1991) Sequence-selective DNA recognition by synthetic ligands. Bioconjugate Chem. 2, 1-12.
  • 2. Bailly, Ch. & Chaires, J.B. (1998) Sequence- specific DNA minor groove binders. Design and synthesis of netropsin and distamycin analogues. Bioconjugate Chem. 9, 513-538.
  • 3. Neidle, S. (1997) Crystallographic insights into DNA minor groove recognition by drugs. Biopolymers 44, 105-121
  • 4. Tanious, F.A., Spychala, J., Kumar, A., Greene, K., Boykin, D.W. & Wilson, W.D. (1994) Different binding mode in AT and GC sequences for unfused-aromatic dications. J. Biomol. Struct. Dyn. 11, 1063-1083.
  • 5. Kopka, M.L., Yoon, C., Goodsell, D., Pjura, P. & Dickerson, R.E. (1985) The molecular origin of DNA-drug specificity of netropsin and distamycin. Proc. Natl. Acad. Sci. U.S.A. 82, 1376-1380.
  • 6. Zakrzewska, K., Lavery, R. & Pullman, B. (1984) Theoretical studies of the selective binding to DNA of two nonintercalating ligands: Netropsin and SN 18071. Nucleic Acids Res. 11, 8825-8839.
  • 7. Lown, J.W. (1995) Design and development of sequence selective lexitropsin DNA minor groove binders. Drug Development Res. 34, 145-183.
  • 8. Walker, W.L., Kopka, M.L. & Goodsell, D.S. (1997) Progress in the design of DNA sequence-specific lexitropsins. Biopolymers 44, 323-334.
  • 9. Swalley, S.E., Baird, E.E. & Dervan, P.B. (1999) Effects of γ-turn and β-tail amino acids on sequence-specific recognition of DNA by hairpin polyamides. J. Am. Chem. Soc. 121, 1113-1129.
  • 10. Bartulewicz, D., Bielawski, K., Markowska, A., Zwierz, K. & Różański, A. (1998) Synthetic analogues of netropsin and distamycin synthesis of a new pyridine and carbocyclic analogues of the pyrrolecarboxamide antitumour antibiotics. Acta Biochim. Polon. 45, 41-57.
  • 11. Turner, P.R., Ferguson, L.R. & Denny, W.A. (1999) Polybenzamide mustards; Structure- activity relationships for DNA sequence-specific alkylation. Anti-Cancer Drug Des. 14, 61-70.
  • 12. Bartulewicz, D., Wolczynski, S., Dabrowska, M. & Rozanski, A. (2000) Molecular modelling, synthesis and antitumor activity of carbocyclic analogues of netropsin and distamycin new carriers of alkylating elements. Acta Biochim. Polon. 47, 23-35.
  • 13. Dickerson, R.E. & Drew, H.R. (1981) Structure of a B-DNA dodecamer II. Influence of base sequence on helix structure. J. Mol. Biol. 149, 761-786.
  • 14. Flatters, D., Zakrzewska, K. & Lavery, R. (1997) Internal coordinate modeling of DNA: Force field comparisons. J. Comput. Chem. 18, 1043-1055.
  • 15. Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, G., Alagano, G., Profeta, S. & Weiner, P. (1984) A new force-field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 108, 765- 784.
  • 16. Weiner, S.J., Kollman, P.A., Nguyen, D.T. & Case, D.A. (1986) An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem. 7, 230-252.
  • 17. Orozco, M. & Luque, F.J. (1990) On the use of AM1 and MNDO wavefunctions to compute accurate electrostatic charges. J. Comput. Chem. 11, 909-923.
  • 18. Orozco, M., Laughton, C.A., Herzyk, P. & Neidle, S. (1990) Molecular modelling of drug-DNA structures: The effects of differing dielectric treatment on helix parameters and comparison with a fully solvated structural model. J. Biomol. Struct. Dyn. 8, 359-373.
  • 19. Lipton, M. & Still, W.C. (1988) The multiple minimum problem in molecular modeling. Tree searching internal coordinate conformational space. J. Comput. Chem. 9, 345-355.
  • 20. Neidle, S. (1992) Minor-groove width and accessibility in B-DNA drug and protein complexes. FEBS Lett. 298, 97-99.
  • 21. Berman, H.M. (1997) Crystal studies of B-DNA: The answers and the questions. Biopolymers 44, 23-44.
  • 22. Laughton, Ch. & Luisi, B. (1999) The mechanics of minor groove width variation in DNA, and its implications for the accommodation of ligands. J. Mol. Biol. 288, 953-963.
  • 23. Marky, L. & Breslauer, K.J. (1987) Origins of netropsin binding affinity and specificity: Correlations of the thermodynamic and structural data. Proc. Natl. Acad. Sci. U.S.A. 84, 4359- 4363.
  • 24. Young, M.A., Jayaram, B. & Beveridge, D.L. (1997) Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: Fractional occupancy of electronegative pockets. J. Am. Chem. Soc. 119, 59-69.
  • 25. Singh, S.B. & Kollman, P.A. (1999) Calculating the absolute free energy of association of netropsin and DNA. J. Am. Chem. Soc. 121, 3267-3271.
  • 26. Goodsell, D.S., Kopka, M.L. & Dickerson, R.E. (1995) Refinement of netropsin bound to DNA: Bias and feedback in electron density map interpretation. Biochemistry 34, 4983- 4993.
  • 27. Kopka, M.L., Yoon, C., Goodsell, D., Pjura, P. & Dickerson, R.E. (1985) The molecular origin of DNA-drug specificity in netropsin and distamycin. Proc. Natl. Acad. Sci. U.S.A. 82, 1376-1380.
  • 28. Mazur, A.K. (1999) Internal correlations in minor groove profiles of experimental and computed B-DNA conformations. J. Mol. Biol. 290, 373-377.
  • 29. Dasgupta, D., Rajagopalan, M. & Sasisekharan, V. (1986) DNA-binding characteristics of a synthetic analogue of distamycin. Biochim. Biophys. Res. Commun. 140, 626-631.
  • 30. Yan, Y., Liu, M. & Gong, B. (1997) Two-ring DNA minor-groove binders consisting of readily available, di-substituted benzene derivatives. Bioorg. Med. Chem. Lett. 7, 1469-1474.
  • 31. Johannesson, H. & Halle, B. (1998) Minor groove hydration of DNA in solution: Dependence on base composition and sequence. J. Am. Chem. Soc. 120, 6859-6870.
  • 32. Tereshko, V., Minasov, G. & Egli, M. (1999) A hydration spine in a B-DNA minor groove. J. Am. Chem. Soc. 121, 3590-3595.
Document Type
Publication order reference
Identifiers
YADDA identifier
bwmeta1.element.bwnjournal-article-abpv47i3p855kz
JavaScript is turned off in your web browser. Turn it on to take full advantage of this site, then refresh the page.