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.: (380-44) 526-11-09; 526-20-14;
: (380-44) 526-07-59.
E-mail: dhovorun@imbg.org.ua

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  1. Brovarets O.O., Tsiupa K.S., Dinets A., Hovorun D.M. Unexpected routes of the mutagenic tautomerization of the T nucleobase in the classical AT DNA base pairs: A QM/QTAIM comprehensive view. Front. Chem.,2018, 6:532; doi: 10.3389/fchem.2018.00532
  2. Brovarets, O.O., Tsiupa, K.S., Hovorun, D.M. Non-dissociative structural transitions of the Watson-Crick and reverse Watson-Crick DNA base pairs into the Hoogsteen and reverse Hoogsteen forms. Sci. Repts., 2018, V. 8, P.10371
  3. Brovarets' O.O., Hovorun D.M. Key microstructural mechanisms of the 2-aminopurine mutagenicity: Results of extensive quantum-chemical research. J. Biomol. Struct. Dynam., 2018, doi: 10.1080/07391102.2018.1495577
  4. Tolmachova, Kateryna & S. Moroz, Yurii & Konovets, Angelika & Platonov, Maxim & Vasylchenko, Olexandr & Borysko, Petro & Zozulya, Sergey & Gryniukova, Anastasia & V. Bogolubsky, Andrey & Pipko, Sergey & Mykhailiuk, Pavel & Brovarets, Volodymyr & Grygorenko, Oleksandr. (Chlorosulfonyl)benzenesulfonyl fluorides versatile building blocks for combinatorial chemistry. Design, synthesis and evaluation of a covalent inhibitor library. ACS Combinatorial Science. 2018. 10.1021/acscombsci.8b00130
  5. Zarudnaya M. I. , Kolomiets I. M., Potyahaylo A. L., Hovorun D. M. Structural transitions in poly(A), poly(C), poly(U) and poly(G) and their possible biological roles. J. Biomol. Struct. Dyn. 2018. Jul 27:1-114. doi: 10.1080/07391102.2018.1503972
  6. Golius, L Gorb, O Isayev, J Leszczynski. Diffusion of energetic compounds through biological membrane: Application of classical MD and COSMOmic approximations. Journal of Biomolecular Structure and Dynamics. 2018 Jan 19:1-9. doi: 10.1080/07391102.2018.1424037
  7. H.H. Repich, V.V. Orysyk, L.G. Palchykovska, S.I. Orysyk, Yu.L. Zborovskii, O.V. Vasylchenko, O.V. Storozhuk, A.A. Biluk, V.V. Nikulina, L.V. Garmanchuk, V.I. Pekhnyo, M.V. Vovk. Synthesis, spectral characterization of novel Pd(II), Pt(II) -coordination compounds based on N-allylthioureas. Cytotoxic properties and DNA binding ability. J. of Inorganic Biochemistry. 2017. v168. P. 98106
  8. Gorb, L., Zubatiuk, T.A., Zubatyuk, R., Hovorun, D., Leszczynski, J. d(A)3d(T)3 and d(G)3d(C)3 B-DNA mini-helixes: the DFT/M06-2x and DFT/B97-D3 comparison of geometrical and energetic characteristics. Journal of Molecular Modeling 23 (10), 289-298, 2017
  9. Zarudnaya M. I., Potyahaylo A. L., Hovorun D. M. Dependence of DNA persistence length on ionic conditions. Biopolymers and Cell. 2017. Vol. 33, N 2. P. 81-91. doi:10.7124/bc.000946
  10. Gooch, A., Sizochenko, N., Sviatenko, L., Gorb, L., Leszczynski, J. A quantum chemical based toxicity study of estimated reduction potential and hydrophobicity in series of nitroaromatic compounds. SAR and QSAR in Environmental Research 28(2), pp. 133-137, 2017
  11. Sviatenko, L.K., Gorb, L., Leszczynska, D., Okovytyy, S.I., Shukla, M.K., Leszczynski, J. In silico kinetics of alkaline hydrolysis of 1,3,5-trinitro-1,3,5-triazinane (RDX): M06-2X investigation. Environmental science. Processes & impacts, 19(3), pp. 388-392, 2017
  12. Brovarets O.O., Voiteshenko, I.S., Pérez-Sánchez H.E., & Hovorun D.M. A QM/QTAIM research under the magnifying glass of the DPT tautomerisation of the wobble mispairs involving 2-aminopurine New Journal of Chemistry. 2017. DOI: 10.1039/C7NJ00717E
  13. Brovarets O.O., Voiteshenko, I.S, Pérez-Sánchez H.E., & Hovorun D.M. A QM/QTAIM detailed look at the Watson-Crick↔wobble tautomeric transformations of the 2-aminopurinepyrimidine mispairs Journal of Biomolecular Structure & Dynamics. 2017. DOI: 10.1080/07391102.2017.1331864
  14. Brovarets O.O., Voiteshenko, I.S., & Hovorun D.M. Physico-chemical profiles of the wobble↔Watson-Crick G*2AP(w)↔G2AP(WC) and A2AP(w)↔A*2AP(WC) tautomerisations: A QM/QTAIM comprehensive survey. Physical Chemistry Chemical Physics. 2017. Crossref DOI link: https://doi.org/10.1039/C7CP05139E
  15. Glushenkov AN, Hovorun DM. Can nucleobase pairs offer a possibility of a direct 3D self-assembly? Nanoscale Res. Lett. 2016, 11(1):134. doi: 10.1186/s11671-016-1347-3.
  16. Sviatenko, L.K., Gorb, L., Hill, F.C., Leszczynska, D., Shukla, M.K., Okovytyy, S.I., Hovorun, D., Leszczynski, J. In Silico Alkaline Hydrolysis of Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine: Density Functional Theory Investigation. Environmental Science and Technology. 2016, 50(18):10039-10046.
  17. Brovarets O.O., Pérez-Sánchez H.E., Hovorun D.M. Structural grounds for the 2-aminopurine mutagenicity: A novel insight into the old problem of the replication errors. RS Adv. 2016, 6(101): 99546-99557.
  18. T. Yu. Nikolaienko, L. A. Bulavin, D. M. Hovorun. Can we treat ab initio atomic charges and bond orders as conformation-independent electronic structure descriptors? RSC Adv. 2016, 6(78):74785-74796.
  19. Brovarets OO, Hovorun DM. The physicochemical essence of the purinepyrimidine transition mismatches with Watson-Crick geometry in DNA: AC* versa A*C. A QM and QTAIM atomistic understanding. J. Biomol. Struct. & Dynam. 2015;33(1):28-55.
  20. Brovarets OO, Hovorun DM. Tautomeric transition between wobble DNA base mispair and Watson-Crick-like AC* mismatch: miscrostructural mechanism and biological significance. Phys. Chem. Chem. Phys. 2015;17(23):15103-15110.
  21. Brovarets OO, Hovorun DM. How do long improper purine-purine pairs of DNA bases adapt their enzymatically competent conformation? Structural mechanism and its quantum-mechanical grounds. Ukr. J. Phys. (Special Issue devoted to Acad. L.A. Bulavin). 2015;60(8):748-756.
  22. Brovarets OO, Hovorun DM. A novel conception for spontaneous transversions caused by homo-pyrimidine DNA mismatches: A QM/QTAIM highlight. Phys. Chem. Chem. Phys. 2015;17(33):21381-21388.
  23. Brovarets OO, Hovorun DM. Novel physico-chemical mechanism of the mutagenic tautomerisation of the Watson-Crick-like AG and CT DNA base mispairs: a quantum-chemical picture. RS Adv. 2015;5(81):66318-66333.
  24. Kolomiets IN, Zarudnaya MI, Potyahaylo AL, Hovorun DM. Structural insight into HIV-1 reverse transcription initiation in MAL-like templates (CRF01_AE, subtype G and CRF02_AG). J. Biomol. Struct. Dyn. 2015;33(2):418-433.
  25. Alexeeva I, Nosach L, Palchykovska L, Usenko L, Povnitsa O. Synthesis and Comparative Study of Anti-Adenoviral Activity of 6-Azacytidine and Its Analogues. Nucleosides, Nucleotides and Nucleic Acids. 2015;34:565578.
  26. Zahanich I, Kondratov I, Naumchyk V, Kheylik Yu, Platonov M, Zozulya S, Krasavin M. Phenoxymethyl 1,3-oxazoles and 1,2,4-oxadiazoles as potent and selective agonists of free fatty acid receptor 1 (GPR40). Bioorganic & medicinal chemistry letters. 2015;25(6):3105-3111.
  27. Zubatiuk T, Shishkin O, Gorb L, Hovorun D, Leszczynski J. Structural Waters in the Minor and Major Grooves of DNAA Major Factor Governing Structural Adjustments of the A−T Mini-Helix. J. Phys. Chem. B. 2015;119(2):381−391.
  28. Zubatiuk T, Kukuev M, Korolyova A, Gorb L, Nyporko A, Hovorun D, Leszczynski J. Structure and Binding Energy of Double-Stranded A-DNA Mini-helices: Quantum-Chemical Study. J. Phys. Chem. B. 2015;119(40):1274112749.
  29. , , . m1Thym1Thy. - . Ukrainica Bioorganica Acta. 2015; 1:9-12.
  30. Leonid Gorb, Victor Kuz'min, Eugene Muratov. Application of Computational Techniques in Pharmacy and Medicine. Springer. 2014;:550. ISBN 978-94-017-9257-8
  31. Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Hovorun DM. Phylogenetic study on structural elements of HIV-1 poly(A) region. 2. USE domain and TAR hairpin. Biopolym. Cell. 2014; 30(1):29-36.
  32. Kolomiets IN, Zarudnaya MI, Potyahaylo AL, Hovorun DM. Structural insight into HIV-1 reverse transcription initiation in MAL-liketemplates (CRF01_AE, subtype G and CRF02_AG). J. Biomol. Struct. Dyn. 2014; Epub ahead of print, Feb 21.
  33. Hurmach V. V., Balinskyi O. M., Platonov M. O., et al. Design of potentially active ligands for SH2 domains by molecular modeling methods. Biopolym. Cell. 2014;30(4):321-325.
  34. Ammosova T, Platonov M, Ivanov A, et al. 1E7-03, a low MW compound targeting host protein phosphatase-1, inhibits HIV-1 transcription. British Journal of Pharmacology. 2014;171:50595075.
  35. Paytakov G, Gorb L, Stepanyugin A, et al. Homodimers of cytosine and 1-methylcytosine. A DFT study of geometry, relative stability and H-NMR shifts in gas-phase and selected solvents. Journal of Molecular Modeling. 2014;20:2115-2119.
  36. Sviatenko LK, Gorb L, Hovorun D, Leszczynski J. In Silico kinetics and mechanism of interaction of cis-2-butene-1,4-dial with 2′-deoxycytidine. Chem Res Toxicol. 2014;27(6):981-9.
  37. Brovarets OO, Hovorun DM. Why the tautomerization of the GC Watson-Crick base pair via the DPT does not cause point mutations during DNA replication? QM and QTAIM comprehensive analysis. Journal of Biomolecular Structure & Dynamics. 2014;32:1474-1499.
  38. Brovarets'OO, Zhurakivsky RO, Hovorun DM. Is the DPT tautomerisation of the long AG Watson-Crick DNA base mispair a source of the adenine and guanine mutagenic tautomers? A QM and QTAIM response to the biologically important question. Journal of Computional Chemistry. 2014;35:451-466.
  39. Brovarets OO, Zhurakivsky RO, Hovorun DM. Does the tautomeric status of the adenine bases change under the dissociation of the *syn Topal-Fresco DNA mismatch? A combined QM and QTAIM atomistic insight. Physical Chemistry Chemical Physics. 2014;16:3715-372.
  40. Brovarets OO, Zhurakivsky RO, Hovorun DM. Structural, energetic and tautomeric properties of the TT*/T*T DNA mismatch involving mutagenic tautomer of thymine: A QM and QTAIM insight. Chemical Physics Letters. 2014;592:247-255.
  41. Brovarets'OO, Zhurakivsky RO, Hovorun DM. A QM/QTAIM microstructural analysis of the tautomerisation via the DPT of the hypoxanthineadenine nucleobase pair. Molecular Physics. 2014;112:2005-2016.
  42. Nikolaienko TYu, Bulavin LA, Hovorun DM. JANPA: An open source cross-platform implementation of the Natural Population Analysis on the Java platform. Theoretical and Computational Chemistry. 2014; DOI: 10.1016/j.comptc.2014.10.002.
  43. Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Hovorun DM. Phylogenetic study on structural elements of HIV-1 poly(A) region. 1. PolyA and DSE hairpins. Biopolym. Cell. 2013; 29(6):454-462.
  44. Brovarets' OO, Yurenko YP, Hovorun DM. Intermolecular CHO/N Hbonds in the biologically important pairs of natural nucleobases: a thorough quantumchemical study. J Biomol Struct Dyn. 2013 Jun 03. doi:10.1080/07391102.2013.799439
  45. Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Hovorun DM. Structural model of the complete poly(A) region of HIV1 pre mRNA. J Biomol Struct Dyn. 2013;31(10):10441056. doi: 10.1080/07391102.2012.718530
  46. FordGreen J, Isayev O, Gorb L, Perkins EJ, Leszczynski J. Evaluation of natural and nitramine binding energies to 3D models of the S1S2 domains in the NmethylDaspartate receptor. J Mol Model. 2012;18(4):127384. doi: 10.1007/s00894-011-1152-y
  47. Isayev O, CrespoHernandez CE, Gorb L, Hill FC, Leszczynski J. In silico structurefunction analysis of E. cloacae nitroreductase. Proteins. 2012;80(12):272841. doi:10.1002/prot.24157
  48. Sviatenko L, Gorb L, Hovorun D, Leszczynski J. Interaction of 2'deoxyadenosine with cis2butene1,4dial: computational approach to analysis of multistep chemical reactions. J Phys Chem A. 2012;116(9):233342. doi:10.1021/jp211911u
  49. Brovarets' OO, Yurenko YP, Dubey IY, Hovorun DM. Can DNAbinding proteins of replisome tautomerize nucleotide bases? Ab initio model study. J Biomol Struct Dyn. 2012;29(6):597605. doi:10.1080/07391102.2011.672624
  50. Shishkin OV, Dopieralski P, Omelchenko IV, Gorb L, Latajka Z, Leszczynski J. Dynamical Nonplanarity of Benzene. Evidences from the CarParrinello Molecular Dynamics Study. J. Phys. Chem. Lett. 2011;2(22):28814. doi: 10.1021/jz201327t
  51. Yurenko YP, Zhurakivsky RO, Samijlenko SP, Hovorun DM. Intramolecular CHO hydrogen bonds in the AI and BI DNAlike conformers of canonical nucleosides and their WatsonCrick pairs. Quantum chemical and AIM analysis. J Biomol Struct Dyn. 2011;29(1):5165. doi:10.1080/07391102.2011.10507374
  52. Furmanchuk A, Isayev O, Gorb L, Shishkin OV, Hovorun DM, Leszczynski J. Novel view on the mechanism of waterassisted proton transfer in the DNA bases: bulk water hydration. Phys Chem Chem Phys. 2011;13(10):43117. doi:10.1039/c0cp02177f
  53. Samijlenko SP, Yurenko YP, Stepanyugin AV, Hovorun DM. Tautomeric equilibrium of uracil and thymine in model protein nucleic acid contacts. Spectroscopic and quantum chemical approach. J Phys Chem B. 2010;114(3):145461. doi: 10.1021/jp909099a
  54. Danilov VI, van Mourik T, Kurita N, Wakabayashi H, Tsukamoto T, Hovorun DM. On the mechanism of the mutagenic action of 5bromouracil: a DFT study of uracil and 5bromouracil in a water cluster. J Phys Chem A. 2009;113(11):22335. doi: 10.1021/jp811007j
  55. De Logu A, Palchykovska LH, Kostina VH, et al. Novel Naryland Nheteryl phenazine1carboxamides as potential agents for the treatment of infections sustained by drugresistant and multidrugresistant Mycobacterium tuberculosis. Int J Antimicrob Agents. 2009;33(3):2239. doi:10.1016/j.ijantimicag.2008.09.016
  56. StankiewiczDrogon A, Palchykovska LG, Kostina VG, Alexeeva IV, Shved AD, BoguszewskaChachulska AM. New acridone4carboxylic acid derivatives as potential inhibitors of hepatitis C virus infection. Bioorg. Med. Chem. 2008; 6(19):88468852. doi:10.1016/j.bmc.2008.08.074
  57. Zarudnaya MI, Kolomiets IM, Potyahaylo AL, Hovorun DM. Downstream elements of mammalian premRNA polyadenylation signals: primary, secondary and higherorder structures. Nucleic Acids Res. 2003;31(5):137586. doi: 10.1093/nar/gkg241
  58. ..; . . , 2012. 260 . ISBN 978-966-00-1264-6.