Department of Molecular and Quantum Biophysics

Head

Leonid G. Gorb

Dr. Sci. (Chem.), Senior Staff Scientist

Phone: (380-44) 526-11-09
fax: (380-44) 526-07-59
E-mail: leonid.gorb@gmail.com

LG Gorb is the author of more than 240 scientific publications, including monographs. He is a winner of S. M. Gershenzon award of the National Academy of Sciences of Ukraine. His scientific papers are cited in prestigious international journals (more than 4,500 citations according to the Web of Science database). The worst index is 39 (according to Scopus).

Membership:

Member of Ukrainian Biophysical Society

Member of the editorial board of Biopolymers and Cell, International Journal of Applied Nanotechnology Research (IJANR)

Member of the Scientific Council of the IMBG NASU

Education and Degrees:

1971–1976 Dnipropetrovsk State University (Chemistry)

1983 Ph. D. (Organic Chemistry, Physical Chemistry)

1994 Senior Researcher (Physical Chemistry)

2009 Dr. Sci. (Physical Chemistry)

Professional Employment:

11976–1978 engineer, Ukrainian Institute of Plastics

1980–1983 graduate student, Institute of Organic Chemistry of the USSR Academy of Sciences

1984–1986 Junior Research Fellow, Institute of Colloid Chemistry, National Academy of Sciences of Ukraine

1986–1998 Senior Research Fellow, Institute of Colloid Chemistry, National Academy of Sciences of Ukraine

1998–2005 Visiting Professor, Jackson University, USA

2005–2008 Senior Research Fellow, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine

2008-2009 Leading Researcher, IMBG NAS of Ukraine

2009-2014 Head, Laboratory of Computational Structural Biology, IMBG NAS of Ukraine

2014-2021 Leading researcher, IMBG NAS of Ukraine

since 2021 Head, Department of Molecular and Quantum Biophysics, IMBG NAS of Ukraine

Scientific Directions of the Department:

  • Search of universal physicochemical foundations for the specificity of interaction between components of nucleoprotein complexes; establishment of the role of prototropic tautomerism and conformational variability of nucleic acid components and and the role of proton transfer in elementary acts of protein-nucleic and nucleic-nucleon recognition.
  • Research by computational biology methods of physicochemical properties of DNA, its components and protein-nucleic complexes; search for physicochemical mechanisms responsible for the accuracy of DNA synthesis.
  • Identification of polypharmacological profile and activity profile of new biologically active substances (BAS), identification of new protein targets for known BAS and drugs, determination of universal structural domains - target-ligand binding sites for different families of enzymes using in vitro methods and in silico.
  • In silico study of primary, secondary and higher order structures of signaling elements in the genomic RNA of HIV-1 and SARS-CoV-2 viruses.

Scientific Achievements of the Department:

The change of tautomeric state of nucleo- bases due to the influence of hydrogen bonds forming with ligands of peptide nature and alkali metal cations is investigated by means of physicochemical methods and quantum chemical calculations of different degrees of complexity. Similar changes in the tautomeric state of nucleo-bases are expected under the action of a heterogeneous environment in a cell. They are postulated as one of the mechanisms responsible for structural and dynamic transformations in protein-nucleic complexes.
Experimental and theoretical results revealing polypharmacological properties of some pharmaceutically important compounds have beeng obtained.
By using modern methods of electrophoresis, proton buffer capacity, molecular modeling and bioinformatics, the patterns of spatial organization - the secondary and tertiary structures of cellular and viral RNA and their signal sequences are obtained.

Selected publications:

  1. Brovarets O., Voiteshenko I. S., Pérez-Sánchez H., 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, 41 (15), 7232-7243. DOI: 10.1039/c7nj00717e.
  2. Zarudnaya M. I., Potyahaylo A. L., Hovorun D. M. Dependence of DNA persistence length on ionic conditions. Biopolymers and Cell. –2017,33, N 2. – P. 81-91. doi:10.7124/bc.000946.
  3. 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 2017, 23 (10), 289-298.
  4. 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. 98–106.
  5. 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, 2017, 19(3), pp. 388-392.
  6. 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 2017б 28(2), pp. 133-137.
  7. Brovarets’ O.O., Voiteshenko, I.S., & Hovorun D.M. Physico-chemical profiles of the wobble↔Watson-Crick G*•2AP(w)↔G•2AP(WC) and A•2AP(w)↔A*•2AP(WC) tautomerisations: A QM/QTAIM comprehensive survey. Physical Chemistry Chemical Physics. – 2018, 20, 623-636. DOI: 10.1039/C7CP05139E
  8. 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, 19:1-9. doi:10.1080/07391102.2018.1424037.
  9. 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, 27:1-114. doi: 10.1080/07391102.2018.1503972.
  10. 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.
  11. 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.
  12. Brovarets’, O.O., Tsiupa, K.S., Hovorun, D.M. Non-dissociative structural transitions of the Watson-Crick and reverse Watson-Crick А•Т DNA base pairs into the Hoogsteen and reverse Hoogsteen forms. Sci. Repts., 2018, V. 8, P.10371.
  13. Brovarets’ O.O., Tsiupa K.S., Dinets A., Hovorun D.M. Unexpected routes of the mutagenic tautomerization of the T nucleobase in the classical A•T DNA base pairs: A QM/QTAIM comprehensive view. Front. Chem.,2018, 6:532; doi: 10.3389/fchem.2018.00532.
  14. Brovarets’ O.O., Tsiupa K.S., Dinets A., Hovorun D.M. Unexpected routes of the mutagenic tautomerization of the T nucleobase in the classical A•T DNA base pairs: A QM/QTAIM comprehensive view. Front. Chem.,2018, 6:532; doi: 10.3389/fchem.2018.00532.
  15. Brovarets’, O.O., Oliynyk, T.O. & Hovorun, D.M. Novel tautomerisation mechanisms of the biologically important conformers of the reverse Löwdin, Hoogsteen and reverse Hoogsteen G*∙C* DNA base pairs via proton transfer: A quantum-mechanical survey. Front. Chem., 7, 2019, doi: 10.3389/fchem.2019.00597.
  16. Zarudnaya MI, Kolomiets IM, Potyahaylo AL, Hovorun DM. Structural transitions in poly(A), poly(C), poly(U), and poly(G) and their possible biological roles. J Biomol Struct Dyn. 2019; 37(11): 2837-2866. doi:10.1080/07391102.2018.1503972.
  17. Brovarets', O.O., Hovorun, D.M. A hidden side of the conformational mobility of the quercetin molecule caused by the rotations of the O3H, O5H and O7H hydroxyl groups: In Silico scrupulous study. Symmetry,2020, 12(2), 230.
  18. Leonid Gorb, Anatoliy Pekh, Alexey Nyporko, Mykola Ilchenko, Anastasia Golius, Tetiana Zubatiuk, Roman Zubatyuk, Igor Dubey, Dmytro M. Hovorun and Jerzy Leszczynski. Effect of micro-environment on the geometrical structure of d(A)5 d(T)5, d(G)5 d(C)5 DNA mini-helixes and Dickerson dodecamer: A density functional theory study” J. Phys. Chem. B 2020, 124, 42, 9343–9353.