Ukr.Biochem.J. 2014; Том 86, №2, березень-квітень, c. 50-59

doi: http://dx.doi.org/10.15407/ubj86.02.050

Взаємодія нуклеотидних основ ДНК із протипухлинним препаратом ТіоТЕФ: молекулярний докінг та квантово-механічний аналіз

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А. І. Самцевич1, Л. А. Булавін1, Л. Ф. Суходуб2, Т. Ю. Ніколаєнко1

1Київський національний університет імені Тараса Шевченка, Україна;
2Сумський державний університет, МОН України;
e-mail: samtsevichartem@gmail.com; tim_mail@ukr.net

За допомогою сучасних методів молекулярного докінгу, квантової хімії та квантової теорії атомів у молекулах досліджено взаємодію протипухлинного препарату ТіоТЕФ з окремими нуклеотидними основами та дезоксирибонуклеозидмонофосфатами ДНК. Встановлено фізичні властивості одержаних комплексів «нуклеотидна основа + ТіоТЕФ» та «дезоксирибонуклеозидмонофосфат + ТіоТЕФ» та деякі закономірності зв’язування в них. Показано, що сильні водневі зв’язки типу NH•••N є вирішальним чинником, який обумовлює високу селективність зв’язування ТіоТЕФ із гуанінвмісними ланками ДНК.

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  1. Gerl R, Vaux DL. Apoptosis in the development and treatment of cancer. Carcinogenesis. 2005 Feb;26(2):263-70. Review. PubMed
  2. Kasibhatla S, Tseng B. Why target apoptosis in cancer treatment? Mol Cancer Ther. 2003 Jun;2(6):573-80. Review. PubMed
  3. Lind MJ. Principles of cytotoxic chemotherapy. Medicine. 2004:32(3):20–25.
  4. Thurston DE. Chemistry and pharmacology of anticancer drugs.  CRC press, 2006.  290 p.
  5. Palchaudhuri R, Hergenrother PJ. DNA as a target for anticancer compounds: methods to determine the mode of binding and the mechanism of action. Curr Opin Biotechnol. 2007 Dec;18(6):497-503. Review. PubMed
  6. Nussbaumer S, Bonnabry P, Veuthey JL, Fleury-Souverain S. Analysis of anticancer drugs: a review. Talanta. 2011 Oct 15;85(5):2265-89. Review. PubMed, CrossRef
  7. Laurent G, Tew KD. Cancer Management in Man: Chemotherapy, Biological Therapy, Hyperthermia and Supporting Measures.  Springer: Netherlands, 2011. P. 61–85.
  8. Jorgensen WL. The many roles of computation in drug discovery. Science. 2004 Mar 19;303(5665):1813-8. Review. PubMed
  9. Burchenal JH, Murphy ML, Ellison RR, Sykes MP, Tan TC, Leone LA, Karnofsky DA, Craver LF, Dargeon HW, Rhoads CP. Clinical evaluation of a new antimetabolite, 6-mercaptopurine, in the treatment of leukemia and allied diseases. Blood. 1953 Nov;8(11):965-99. PubMed
  10.  Maanen MJ, Smeets CJ, Beijnen JH. Chemistry, pharmacology and pharmacokinetics of N,N’,N” -triethylenethiophosphoramide (ThioTEPA). Cancer Treat Rev. 2000 Aug;26(4):257-68. Review. PubMed
  11. Siddik ZH. Mechanisms of action of cancer chemotherapeutic agents: DNA interactive alkylaating agents and antitumour platinum-base drugs. In: The Cancer Handbook. Ed. Aliso MR. London: Nature Publishing Group, 2002. P. 1295–1313.
  12. Torabifard H, Fattahi A. DFT study on Thiotepa and Tepa interactions with their DNA receptor. Struct. Chem. 2013;24(1):1–11. CrossRef
  13. Sukhodub LF. Soft-ionization mass spectrometry study of deoxynucleoside bioclusters and deoxynucleoside-antitumor medicinal preparation clusters. Mass Spectrometry Reviews. 1995;14(4–5):235-254. CrossRef
  14. Sukhodub LF, Grebenik LI, Chivanov VD. Study of anticancer drug interaction with DNA by means of particle-induced desorption mass spectrometry: prospydine and deoxyguanosine-5′-monophosphate. Rapid Commun Mass Spectrom. 1994 Feb;8(2):195-8. PubMed
  15. Bader RFW. Atoms in molecules. A quantum theory. M.: Mir, 2001. 532 p.
  16. Spyrakis F, Cozzini P, Kellogg GE. Docking and Scoring in Drug Discovery. in: Burger’s Medicinal Chemistry, Drug Discovery and Development. John Wiley & Sons, Inc: 2010. P. 601–684.
  17. Hobza P. The calculation of intermolecular interaction energies.  Annu Rep Prog Chem Sect C. 2011;107:148–168. CrossRef
  18. Raha K, Peters MB, Wang B, Yu N, Wollacott AM, Westerhoff LM, Merz KM Jr. The role of quantum mechanics in structure-based drug design. Drug Discov Today. 2007 Sep;12(17-18):725-31. Review. PubMed
  19. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009 Dec;30(16):2785-91. PubMed, PubMedCentral, CrossRef
  20. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated dockingusinga Lamarckian genetic algorithm andan empirical binding freeenergy function. JComputChem. 1998;19(14):1639–1662. CrossRef
  21. Frisch MJ, Trucks GW, Schlegel HB. et al. Gaussian 03, Revision E.01. Gaussian, Inc., Wallingford CT, 2004.
  22. Nikolaienko TYu, Bulavin LA, Hovorun DM. Quantum-mechanical conformational analysis of the 5′-thymidilic acid molecule. Ukr Biokhim Zhurn. 2010 Nov-Dec;82(6):76-86. Ukrainian. PubMed
  23. Nikolaienko TYu, Bulavin LA, Hovorun D M. The 5′-deoxyadenylic acid molecule conformational capacity: quant um-mechanical investigation using density funct ional theory (DFT). Ukr Biokhim Zhurn. 2011 Jul-Sep;83(4):16-28. Ukrainian. PubMed
  24. Nikolaienko TYu, Bulavin LA, Hovorun DM, Missura OO. Conformational variety and physical properties of the 1,2-dideoxyribofuranose-5-phosphate, the model DNA monomer structural unit. Ukr Biokhim Zhurn. 2011 Jan-Feb;83(1):54-62. Ukrainian. PubMed
  25. Nikolaienko TYu, Bulavin LA, Hovorun DM. Analysis of 2-deoxy-D-ribofuranose molecule conformational capacity with the quantum-mechanical density functional method. Biopolym. Cell. 2011;27(1):74–81.
  26. Neese F. The ORCA program system. WIREs Comput. Mol. Sci. 2012;2(1):73–78. DOI: 10.1002/wcms.81
  27. Cremer D. Møller–Plesset perturbation theory: from small molecule methods to methods for thousands of atoms. WIREs Comput Mol Sci. 2011;1(4):509-530. CrossRef
  28. Kalinowski R, Dittrich B, Hübschle CB, Paulmann C, Luger P. Experimental charge density of L-alanyl-L-prolyl-L-alanine hydrate: classical multipole and invariom approach, analysis of intra- and intermolecular topological properties. Acta Crystallogr B. 2007 Oct;63(Pt 5):753-67.  PubMed
  29. AIMAll (Version 08.11.29), Todd A. Keith, TK Gristmill Software, Overland Park KS, USA, 2012 (aim.tkgristmill.com).
  30. Nikolaienko TY, Bulavin LA, Hovorun DM. Bridging QTAIM with vibrational spectroscopy: the energy of intramolecular hydrogen bonds in DNA-related biomolecules. Phys Chem Chem Phys. 2012 May 28;14(20):7441-7. PubMed, CrossRef
  31. Espinosa E, Molins E, Lecomte C. Hydrogen bond strengths revealed by topological analyses of experimentrally observed electrons densities. Chem Phys Lett. 1998;285:170-173. CrossRef
  32. Jurecka P, Hobza P. True stabilization energies for the optimal planar hydrogen-bonded and stacked structures of guanine…cytosine, adenine…thymine, and their 9- and 1-methyl derivatives: complete basis set calculations at the MP2 and CCSD(T) levels and comparison with experiment. J Am Chem Soc. 2003 Dec 17;125(50):15608-13. PubMed
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