Department 3

Department of Bioorganic Mechanisms

Department of Bioorganic Mechanisms

Andriy I. Vovk, Head of department,
Dr. Sc., Prof., Corr. Member of NAS of Ukraine

Directions of scientific researches

The department was created in 1963 as department of chemistry of photosynthesis of Institute of organic chemistry of NAS of Ukraine. Up to 1999, the department of chemistry of photosynthesis was headed by A.A. Yasnikov, Corr. Member of NAS of Ukraine. In 2001, the department was transformed into the department of bioorganic mechanisms.

Scientific researches of the department of bioorganic mechanisms of Institute of bioorganic chemistry and petrochemistry are directed on kinetics and mechanisms of bioorganic transformations, synthesis and biological evaluation of organic compounds in model systems, study of the relationship between the structure and activity as well as molecular docking and QSAR. Our current scientific interests are focused on design of synthetic enzyme inhibitors of non-specific alkaline phosphatases, protein tyrosine phosphatases, nucleotide pyrophosphatase/phosphodiesterase, acetylcholinesterase and butyrylcholinesterase, glutathione S-transferase, lipoxygenase and xanthine oxidase. The other part of the research work is currently proceeding on possible antioxidants and new spin probes.

The members of the department (2016) – V.V. Trush, O.L. Kobzar, O.V. Sukhoveev, L.A. Kononets, А.І. Vovk, O.V. Muzychka, V.Yu. Tanchuk, I.M. Mischenko, A.D. Ocheretnyuk, V.М. Buldenko.

The department members in the laboratory (2010) – А.І. Vovk, L.V.Babii, N.V.Samus, I.M. Mischenko, , O.V. Muzychka, L.A. Kononets, R.V. Bugas.

Dissertation defenses (from 2000)

• Babii L.V. Dissertation for the candidate degree in chemical sciences “Model oxidative transformations of thiamine and thiamine phosphates” – 2002.
• Muzychka O.V. Dissertation for the candidate degree in chemical sciences “The kinetic regularities of calf intestine alkaline phosphatase inhibition by L-cysteine, reduced glutathione, and phosphonic acids” – 2004.
  
• Bugas R.B. Dissertation for the candidate degree in chemical sciences “The modelling of transformations of vitamin В1 and its structural analogues in processes of biological transport” – 2004.
  
• Kononets L.A. Dissertation for the candidate degree in biological sciences “Sulfur-containing derivatives of phosphonic acids as inhibitors of phosphatases” – 2012.
  
• Trush V.V. Dissertation for the candidate degree in chemical sciences – Inhibition of protein tyrosine phosphatase 1B by phosphonate derivatives of calix[4]arenes– 2015.
  
• Kobzar O. L. Dissertation for the candidate degree in chemical sciences “Potential inhibitors of protein tyrosine phosphatases based on tetraazamacrocycles and fullerenes” – 2015.
  
• Tanin V.O. Dissertation for the candidate degree in chemical sciences “New approaches for in silico study of inhibitors of protein tyrosine phosphatase 1B” – 2016.

Selected publications

1. Muzychka O.V., Kobzar O.L., Popova A.V., Frasinyuk M.S., Vovk A.I. Carboxylated aurone derivatives as potent inhibitors of xanthine oxidase. Bioorg. Med. Chem. 2017, 25, 3606–3613.

2. Khilya O.V., Milokhov D.S., Kononets L.A., Kobzar O.L., Vovk A.I., Volovenko Yu.M.. Synthesis and evaluation of new 2,6-diamino-5-hetarylpyrimidines as inhibitors of dihydrofolate reductase. Monatsh. Chem. 2017, DOI 10.1007/s00706-017-2032-7.

3. Ocheretniuk A.D., Kobzar O.L., Mischenko I.M., Vovk A.I. N-Phenacylthiazolium alts as inhibitors of cholinesterases. French-Ukrainian J. Chem. 2017, 5, №2.

4. Burlaka Y.B., Sukhoveev O.V., Grin N.V., Khilchevskyi O.M., Verevka S.V. EPR spectroscopy studies of changes in erythrocyte membranes in patients with laryngeal cancer. Experimental Oncology 2017, 39, 49–52.

5. Tanchuk V.Yu., Tanin V.O. Vovk A.I., Poda G. A New, Improved Hybrid Scoring Function for Molecular Docking and Scoring Based on AutoDock and AutoDock Vina. Chem. Biol. Drug Des. 2016, 87, 618-625.

6. Melnyk, A. K., Sukhoveev, O. V., Kononets, L. A., Khilchevsky, O. M., Shulga, S. M., Kukhar, V. P., & Vovk, A. I. An EPR spin probe study of liposomes from sunflower and soybean phospholipids. J. Liposome Res. 2016, 26, 80-86.

7. Trush V.V., Kharchenko S.G., Tanchuk V.Yu., Kalchenko V.I., Vovk A.I. Phosphonate monoesters on a thiacalix[4]arene framework as potential inhibitors of protein tyrosine phosphatase 1B. Org. Biomol. Chem. 2015, 13, 8803-8806.

8. Trush V.V., Tanchuk V.Y., Cherenok S. O., Kalchenko V.I., Vovk A.I.. Evaluation of inhibition of protein tyrosine phosphatase 1B by calixarene-based ?-ketophosphonic acids. Chem. Biol. Lett. 2015, 2, 1-5.

9. Kobzar O.L., Shevchuk M.V., Lyashenko A.N., Tanchuk V.Yu., Romanenko V.D., Kobelev S.M., Averin A.D., Beletskaya I.P., Vovk A.I., Kukhar V.P. Phosphonate derivatives of tetraazamacrocycles as new inhibitors of protein tyrosine phosphatases. Org. Biomol. Chem. 2015, 13, 7437-7444.

10. Kobzar O.L., Trush V.V., Tanchuk V.Yu., Vovk A.I. Inhibitory potential of polyhydroxylated fullerenes against protein tyrosine phosphatase 1B. Ukr. Biochem. J. 2015, 87, 24-31.

11. Kobzar O.L. , Trush V.V. , Tanchuk V.Yu. , Voronov I.I. , Peregudov A.S. , Troshin P.A. , Vovk A.I. Polycarboxylic fullerene derivatives as protein tyrosine phosphatase inhibitors . Mendeleev Commun. 2015, 25, 199-201.

12. Tanchuk V., Tanin V., Vovk A., Poda G. A new scoring function for molecular docking based on AutoDock and AutoDock Vina . Curr. Drug Discov. Technol. 2015, 12, 170-178.

13. Mkrtchyan G., Aleshin V., Parkhomenko Y., Kaehne T., Di Salvo M. L., Parroni A., Contestabile R., Vovk A., Bettendorff L., Bunik V. Molecular mechanisms of the noncoenzyme action of thiamin in brain: biochemical, structural and pathway analysis Scientific Reports 2015, 5, Article number: 12583, doi:10.1038/srep12583.

14. Kobzar O.L., Trush V.V., Tanchuk V.Yu., Zhilenkov A.V., Troshin P.A., Vovk A.I. Fullerene derivatives as a new class of inhibitors of protein tyrosine phosphatases. Bioorg. Med. Chem. Lett. 2014, 24, 3175–3179.

15. Trush V.V., Tanchuk V.Y., Cherenok S.O., Kalchenko V.I., Vovk A.I. Calix[4]arene ?-hydroxymethylphosphonic acids as potential inhibitors of protein tyrosine phosphatases. Org. Pharm. Chem. 2014, 1, 39-42.

16. Komisarenko S.V., Kosterin S.O., Lugovskoy E.V., Cherenok S.O., Tanchuk V.Yu., Vovk A.I., Kalchenko V.I. Сalixarene methylene bisphosphonic acids as effectors of biochemical processes. In Book: “Ligands: synthesis, characterization and role im biotechnology”. Nova Science Publishers Inc. N.-Y., 2013. 304 p. pp. 67-116.

17. Tanchuk V.Yu., Tanin V.O., Vovk A.I.. Analysis of сonformational flexibility of loop 110-120 of protein tyrosine phosphatase 1B. Ukr. Biochim. J., 2013, 85, 73-80.

18. Kalchenko V. I., Cherenok S.O., Kosterin S.O., Lugovskoy E.V., Komisarenko S.V., Vovk A.I., Tanchuk V.Y., Kononets L.A., Kukhar V.P. Calixarene phosphonous acids: synthesis and biological activity. Phosphorus, Sulfur, and Silicon 2013, 188, 232-237.

19. Tanchuk V.Yu., Tanin V.O., Vovk A.I. QSAR models for predicting protein tyrosine phosphatase 1B inhibition by structurally diverse inhibitors. Org. Pharm. Chem. 2013, 11, 51-56.

20. Trush V.V., Cherenok S.O., Tanchuk V.Yu., Kukhar V.P., Kalchenko V.I., Vovk A.I. Calix[4]arene methylenebisphosphonic acids as inhibitors of protein tyrosine phosphatase 1B Bioorg. Med. Chem. Lett. 2013, 23, 5619–5623.

21. Khakina E.A., Yurkova A.A., Peregudov A.A., Troyanov S.I., Trush V.V., Vovk A.I., Mumyatov A.V., Martynenko V.M., Balzarini J. , Troshin P.A. Highly selective reactions of C60Cl6 with thiols for synthesis of functionalized [60]fullerene derivatives. Chem. Commun. 2012, 48, 7158-7160.

22. Tanchuk V.Y., Tanin V.O., Vovk A.I. Classification of binding site conformations of protein tyrosine phosphatase 1B. Chem Biol Drug Des. 2012, 80, 121-128.

23. Cherenok S.O., Yushchenko O.A., Tanchuk V.Yu., Mischenko I.M., Samus N.V., Ruban O.V., Matvieiev Y.I., Karpenko J.A., Kukhar V.P., Vovk A.I., Kalchenko V.I. Calix[4]arene-?-hydroxyphosphonic acids. Synthesis, stereochemistry, and inhibition of glutathione S-transferase. ARKIVOC 2012, 278 – 298.

24. Vovk A.I., Mischenko I.M., Cherenok S.O., Tanchuk V.Yu., Kalchenko V.I., Kukhar V.P. Phosphorylated calix[4]arenes as inhibitors of glutathione S-transferase. Phosphorus, Sulfur, and Silicon 2011, 186, 961-963.

25. Vovk A.I., Tanchuk V.Yu., Kononets L.A., Cherenok S.O., Drapailo A.B., Kalchenko V.I., Kukhar V.P. A novel approach to the design of phosphonate inhibitors of protein tyrosine phosphatase. Phosphorus, Sulfur, and Silicon 2011, 186, 958-960.

26. Kachkovskyi G.O., Kononets L.A., Tanchuk V.Yu., Vovk A.I., Kolodiazhnyi O.I. Synthesis and Evaluation of 1-Aryl-1-(7-carboxyisoindolin-1-one-2-yl)methyl-phosphonic Acid Derivatives as Inhibitors of Protein Tyrosine Phosphatase. Phosphorus, Sulfur, and Silicon 2011, 186, 956-957.

27. Shapoval G.S., Babii L.V., Kruglyak O.S., Vovk A.I. Antioxidant activity of thiamine and its structural analogs in reactions with electrochemically generated hydroxyl radicals and hydrogen peroxide. Theor. Exp. Chem. 2011, 47, 55-60.

28. Vovk A.I., Kononets L.A., Tanchuk V.Yu., Cherenok S.O., Drapailo A.B., Kalchenko V.I., Kukhar V.P. Inhibition of Yersinia protein tyrosine phosphatase by phosphonate derivatives of calixarenes. Bioorg. Med. Chem. Lett. 2010, 20, 483-487.

29. Vovk A.I., Kononets L.A., Tanchuk V.Yu., Drapailo A.B., Kalchenko V.I., Kukhar V.P. Thiacalix[4]arene as Molecular Platform for Design of Alkaline Phosphatase Inhibitors. J. Incl. Phenom. Macrocycl. Chem. 2010, 66, 271-277.

30. Vovk A.I., Shivanyuk A.M., Bugas, R.V., Muzychka, O.V., Melnyk, A.K. Antioxidant and antiradical activities of resorcinarene tetranitroxides. Bioorg. Med. Chem. Lett. 2009, 19, 1314-1317.

31. Vovk A.I., Mischenko I.M., Tanchuk V.Yu., Kachkovskii G.A., Sheiko S.Yu., Kolodyazhnyi O.I., Kukhar V.P. Stereoselectivity of binding of (N-benzylamino)benzylphosphonic acids to prostatic acid phosphatase. Bioorg. Med. Chem. Lett. 2008, 18, 4620–4623.

32. Vovk A.I., Chuiko A.L., Kononets L.A., Tanchuk V.Yu., Muravyova I.V., Lozynsky M.O., Kukhar V.P. Inhibition of alkaline phosphatase by thioureido derivatives of methylenebisphosphonic acid. Russ. J. Bioorg. Chem. 2008, 34, 60-66.

33. Vovk A., Kalchenko V., Tanchuk V., Muzychka O., Muravyova I., Shivanyuk A., Cherenok S., Kukhar V. Сalixarene methylenebisphosphonic acids: alkaline phosphatase inhibition and docking studies. Phosphorus, Sulfur, and Silicon 2008, 183, 625-626.

34. Garazd M.M., Muzychka O.V., Vovk A.I., Nagorichna I.V., Ogorodniichuk A.S. Modified coumarins. 27. Synthesis and antioxidant activity of 3-substituted 5,7-dihydroxy-4-methylcoumarins. Chem. Nat. Comp. 2007, 43, 19-23.

35. Kochubey S.M., Vovk A.I., Bondarenko O.Yu., Shevchenko V.V., Bugas R.V., Melnyk A. K., Tanchuk V.Yu. Heterogeneity of thylakoid membranes studied by EPR spin probe. Biochemistry (Moscow) 2007, 72, 558-564.

36. Cherenok S., Vovk A., Muravyova I., Shivanyuk A., Kukhar V., Lipkowski J., Kalchenko V. Calix[4]arene ?-aminophosphonic acids: asymmetric synthesis and enantioselective inhibition of an alkaline phosphatase. Org. Lett. 2006, 8, 549-552.

37. Vovk A.I., Kharhenko O.V., Kharitonenko A.I., Kukhar V.P., Babiy L.V., Kazachkov M.G., Melnyk A.K., Khichevsky О.M. Hydrophobic nitroxyl radicals inhibit linoleyl alcohol oxidation by 5-lipoxygenase. Russ. J. Bioorg. Chem. 2004, 30, 391-395.

38. Vovk A.I., Kalchenko V.I., Cherenok S.A., Kukhar V.P., Muzychka O.V., Lozynsky M.O. Calix[4]arene methylenebisphosphonic acids as calf intestine alkaline phosphatase inhibitors. Org. Biomol. Chem. 2004, 2, 3162-3166.

In the cafeteria. V.М. Buldenko, O.L. Kobzar, А.І. Vovk, Ocheretnyuk, O.V. Muzychka,
I.M. Mischenko, L.A. Kononets.

At work in the morning – O.L. Kobzar, A.D. Ocheretnyuk, V.М. Buldenko.

A.D. Ocheretnyuk, PhD student.

V.М. Buldenko, PhD student.

V.V. Tanin and V.Yu. Tanchuk

Yu. V. Shulga – the youngest student in the department (2017).

Contact information

02660, Kyiv-94, Murmanska Str., 1, Ukraine
Tel. +38 (044) 2732553
Fax: +38 (044) 5732552
E-mail: vovk@bpci.kiev.ua