Electrostatic contribution to the energy of complexation of aromatic antitumor antibiotics with DNA
Keywords:
aromatic antitumor antibiotics, electrostatic contribution to the energy of complexation, nonlinear Poisson-Boltzmann equation
Abstract
The study of electrostatic interactions during the complexation of actinomycin D, daunomycin, novatron, and nogalamycin with oligonucleotide duplexes containing from 4 to 16 base pairs was carried out. The analysis of the main components of electrostatic energy is carried out. The influence of the length of the DNA double helix on the energy of electrostatic interactions has been studied.It was shown that the calculation results for DNA duplexes with 8 and more base pairs are in good agreement with each other. A correlation was established between changes in the values of the angle of helical rotation and electrostatic interactions during intercalation unwinding of the insertion site, as well as a change in the electrostatic energy of interactions in the DNA duplex, similar for all antibiotics. In the same time intermolecular electrostatic interactions of neutral actinomycin D and novanthrone molecules with DNA oligomers differ significantly from those for DNA binding of positively charged daunomycin and nogalamycin. It has been shown that, in general, electrostatic interactions prevent the complexation of all four considered anti-tumor antibiotics with DNA.
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References
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3. Brana M.F. Cacho M., Gradillas A., Pascual-Teresa B., Ramos A. Intercalators as Anticancer Drugs// Curr. Pharm. Des. - 2001. - Vol.7. - p. 1745 - 1780.
4. Ren. J., Jenkins T.C. Chaires J. B. Energetics of DNA Intercalation Reactions // Biochemistry-2000.-Vol.39.-P. 8439-8447.
5. Haq I. Thermodynamics of drug-DNA interactions // Arch. Biochem. Biophys.-2002.-Vol.403-P. 1-15.
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7. Sharp K.A. Electrostatic interactions in macromolecules // Curr. Opin. Struct. Biol. - 1994. - Vol.4. - P. 234-239.
8. Baginski M., Fogolari F., Briggs J.M. Electrostatic and Non-electrostatic Contributions to the Binding Free Energies of Anthracycline Antibiotics to DNA // J. Mol. Biol - 1997.-Vol.274.-P. 253-267.
9. Chaires J.B. Dissecting the free energy of drug binding to DNA // Anti-Cancer Drug Des.- 1996-Vol. 11 -P. 569-580.
10. Yang X.-L., Wang A.H.-J. Structural studies of atom-specific anticancer drugs acting on DNA // Pharm. Ther.-1999.-Vol.83.-P. 181-215.
11. Sharp K.A., Honig B. Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation // J. Chem. Phys.-1990.-VoI.94.-P. 7684-7692.
12. Lee В., Richards F.M. The interpretation of protein structures: estimation of static accessibility // J. Mol. Biol.-1971.-Vol.55.-P. 379-400.
13. Rocchia W., Alexov E., Honig B. Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions // J. Phys. Chem. B.-2001.-Vol.105.-P. 6507-6514.
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15. Brunger A.T. X-PLOR. A system for X-ray crystallography and NMR-Yale: Univ. Press, 1992.-382 p.
16. Cornell W.D., Cieplak P.,. Bayly C.I, Gould I.R., Merz K.M.J., Ferguson D.M., Spellmeyer D.C., Fox Т., Caldwell J.W., Kollman P.A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules // J. Am. Chem. Soc. 1995.-Vol.117.-P. 5179-5197.
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18. Allison S.A. End effects in electrostatic potentials of cylinders: models for DNA fragments // J. Phys. Chem.-1994.-V. 98.-P. 12091-12096.
19. Neidle S., Pearl L.H., Herzyk P., Berman H.M. A molecular model for proflavine-DNA intercalation // Nucleic Acids Res.-1988.-Vol.16.-P. 8999-9016.
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22. Snyder J.G., Hartman N.G., D'Estantoit B.L., Kennard O., Remeta D.P., Breslauer K.J. Binding of actino-mycin D to DNA: Evidence for a nonclassical high-affinity binding mode that does not require GpC sites // Proc. Natl. Acad. Sci. USA.-1989.-Vol.86.-P. 3968-3972.
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26. Medhi С, Mitchell J.B.O., Price S.L., Tabor A.B. Electrostatic Factors in DNA Intercalation // Biopolymers.-1999.-Vol.52.-P. 84-93.
27. Rudnicki W.R., Kurzepa M., Szczepanik Т., Priebe W., Lesyng B.A. Simple model for predicting the free energy of binding between anthracycline antibiotics and DNA // Acta Biochim. Polon.-2000.-Vol.47.-P. 1 -9.
Published
2008-06-03
Cited
How to Cite
Kostjukov, V. V., Khomutova, N. M., & Evstigneev, M. P. (2008). Electrostatic contribution to the energy of complexation of aromatic antitumor antibiotics with DNA. Biophysical Bulletin, 1(20), 5-16. Retrieved from https://periodicals.karazin.ua/biophysvisnyk/article/view/1524
Section
Molecular biophysics
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