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Structure, Thermodynamics and Energetics of Drug-DNA Interactions: Computer Modeling and Experiment

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Application of Computational Techniques in Pharmacy and Medicine

Part of the book series: Challenges and Advances in Computational Chemistry and Physics ((COCH,volume 17))

Abstract

In this chapter we demonstrate the large usefulness of using complex approach for understanding the mechanism of binding of biologically active compounds (antitumour antibiotics, mutagens etc.) with nucleic acids (NA). The applications of various biophysical methods and computer modeling to determination of structural (Infra-red and Raman vibrational spectroscopies, computer modeling by means of Monte-Carlo, molecular docking and molecular dynamics methods) and thermodynamic (UV-VIS spectrophotometry, microcalorimetry, molecular dynamics simulation) parameters of NA-ligand complexation with estimation of the role of water environment in this process, are discussed. The strategy of energy analysis of the NA-ligand binding reactions in solution is described, which is based on decomposition of experimentally measured net Gibbs free energy of binding in terms of separate energetic contributions from particular physical factors. The main outcome of such analysis is to answer the questions “What physical factors and to what extent stabilize/destabilize NA-ligand complexes?” and “What physical factors most strongly affect the bioreceptor binding affinity?”

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Acknowledgments

The authors express their special thanks to the following people which, in part, created the background, contributed and stimulated further the results reviewed in this chapter: Professor Vladimir Ya. Maleev (IRE NASU), Professor Mikhail A. Semenov (IRE NASU), Dr. Elena B. Kruglova (IRE NASU), Dr. Ekaterina G. Bereznyak (IRE NASU), Dr. Viktor V. Kostjukov (SevNTU). Support from the Ministry of Education and National Academy of Sciences of Ukraine via the grants 0103U002268 (2002–2006), 0107U001331 (2007–2009), 0107U001079 (2007–2011), 0110U001683 (2010–2012), F27/60-2010 is greatly acknowledged.

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Authors and Affiliations

  1. Sevastopol National Technical University (SevNTU), Universitetskaya Str., 33, 99053, Sevastopol, Ukraine

    Maxim P. Evstigneev

  2. A.Usikov Institute for Radiophysics and Electronics National Academy of Sciences of Ukraine (IRE NASU), Ak. Proskura str., 12, 61085, Kharkov, Ukraine

    Anna V. Shestopalova

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  1. Maxim P. Evstigneev
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  2. Anna V. Shestopalova
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Correspondence to Maxim P. Evstigneev .

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Editors and Affiliations

  1. Department of Molecular Biophysics, Laboratory of Computational Structural Biology, Kiev, Ukraine

    Leonid Gorb

  2. Department of Molecular Structure and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute, National Academy of Sciences of Ukraine, Odessa, Ukraine

    Victor Kuz'min

  3. Department of Chemical Biology and Medicinal Chemistry, University of North Carolina, Laboratory for Molecular Modeling, Chapel Hill, North Carolina, USA

    Eugene Muratov

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Evstigneev, M., Shestopalova, A. (2014). Structure, Thermodynamics and Energetics of Drug-DNA Interactions: Computer Modeling and Experiment. In: Gorb, L., Kuz'min, V., Muratov, E. (eds) Application of Computational Techniques in Pharmacy and Medicine. Challenges and Advances in Computational Chemistry and Physics, vol 17. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9257-8_2

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