Department of Synthetic Bioregulators

Head

Igor Ya. Dubey

Dr. Sci. (Bioorg. Chem.), Senior Staff Scientist
Phone: (380-44) 526–07-09; 526-55-98;
Fax: (380-44) 526-07-59;
E-mail: dubey@imbg.org.ua

Education and Degrees:

1979–1984 Graduate Student, Department of Chemistry, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine, M.Sc. (organic chemistry of natural compounds)

1984–1987 Postgraduate Student, Laboratory of Genetic Engineering, M. M. Shemyakin Institute of Bioorganic Chemistry, Moscow, Russia

1990 Ph.D. (bioorganic chemistry)

2009 Dr.Sci. (bioorganic chemistry)

Professional Employment:

1987–1990 Junior Research Scientist, Laboratory of Nucleic Acids Chemistry (LNAC), Institute of Bioorganic Chemistry and Petrochemistry (IBCP), NASU, Kyiv, Ukraine

1990–1992 Research Scientist, LNAC, IBCP NASU, Kyiv, Ukraine

1992–1998 Senior Research Scientist, LNAC, IBCP NASU, Kyiv, Ukraine

1998–2009 Leading Research Scientist, Department of the Structure and Function of Nucleic Acids, IMBG NASU, Kyiv, Ukraine

Since 2009 Head of the Department of Synthetic Bioregulators, IMBG NASU, Kyiv, Ukraine

Membership:

Since 2002 Member of International Society of Nucleosides, Nucleotides and Nucleic Acids

Since 2005 Editorial Board member of Journal “Ukrainica Bioorganica Acta” (Ukraine)

Since 2009 Member of the American Chemical Society

Since 2010 Editorial Board member of Journal “Biopolymers and Cell” (Ukraine)

Honours, Prizes, Awards:

1992, 1993 Personal grants from the Soros International Science Foundation

1993 Honorary Diploma from the NASU

2001 State Prize of Ukraine in Science and Technology

Research Area:

Design, synthesis and study of biologically active heterocyclic compounds

Specific ligands of quadruplex DNA

Chemistry and biological properties of nucleosides, nucleotides and oligonucleotides, their analogs and conjugates

Polymers for biomedical applications and solid phase synthesis

Current Research Activities and Recent:

Achievements Design of low-molecular ligands of G-quadruplexes and study on their interaction with quadruplex DNA. Telomerase inhibitors.

Design, synthesis and structure optimization of heterocyclic ligands of G-quadruplex DNA (G4) is being performed. The enzymatic test system TRAP (Telomeric Repeat Amplification Protocol) has been introduced to analyze the effect of new compounds on telomerase activity in vitro. A number of compounds (porphyrins, cyanines, phenazine derivatives) have been found to efficiently inhibit telomerase at micromolar concentrations. Enzyme inhibition by these compounds is based on their binding to G-quadruplex structures of telomeric DNA (Fig. 1).

Fig. 1. Scheme of telomerase inhibition by specific ligands of quadruplex DNA

Spectral-fluorescent studies of the interaction of some inhibitors (first of all, porphyrin derivatives) with quadruplex DNA allowed determining their binding modes that include intercalation and external binding, as well as aggregation. Simple G-quadruplex models, G-quartets and octets, have been developed that allowed computer modelling of ligand–quadruplex interactions using semi-empirical and non-empirical quantum chemistry approaches. An optimized model of full 22-mer DNA quadruplex Tel22 (PDB 1KF1) has been introduced to determine the geometries and energies of G4 complexes with low-molecular ligands. In addition to semiempirical methods, a hybrid QM/MM approach ONIOM2 has been successfully applied for molecular modelling of this complex system (Fig. 2).

Fig. 2. Interaction of Tel22 DNA quadruplex with acridone derivative (ONIOM2 model; high layer atoms are presented as spheres)
Inhibitors of topoisomerase I based on condensed heterocyclic systems.

A series of potential topoisomerase I inhibitors have been synthesized and tested in enzymatic DNA relaxation system in vitro. New compounds include benzimidazole and phenazine derivatives and amino-substituted cyanines. A number of compounds were found to completely inhibit the enzyme at 1-2 μM concentration. Investigation of their interaction with DNA and topoisomerase complex using biophysical and electrophoretic methods allowed identifying inhibitors that bind efficiently to DNA, as well as compounds interacting with enzyme or enzymatic complex. Some cyanines form highly fluorescent complexes with DNA and RNA and thus are suitable for sensitive visualization and quantification of picogram quantities of nucleic acids in electrophoretic gels (Fig. 3).

Fig. 3. Agarose gel analysis of relaxation of supercoiled pTZ19R plasmid DNA by E. coli topoisomerase I in the presence of compounds 1-6 (10 μM). C – control reaction (DNA+TopoI in the absence of inhibitors), relDNA and scDNA – relaxed and supercoiled DNA, respectively. Compounds 4, 5 efficiently inhibit enzymatic reaction
Modification, conjugation, labeling and immobilization of biomolecules.

Novel aminespecific dioxaborine polymethine dye was successfully applied for the fluorescent labeling of proteins, both in the solution and in electrophoretic gels. Conjugation of this stable dye to proteins does not require any activation and results in ca. 80fold emission increase that makes it a convenient label for protein staining in the gel (Fig. 4).

Fig. 4. PAGE analysis of proteins labeled with amine-reactive dioxaborine fluorescent dye. 1, 2 – bovine serum albumin (1 and 5 μg); 3, 4 – lysozyme (1 and 5 μg)

We have developed efficient methods for the preparation of oligonucleotide conjugates with imidazo[4,5b] phenazine dye. Spectroscopic studies of complexes formed by these conjugates with complementary oligonucleotides have demonstrated that the dye chromophore intercalates into the DNA duplex to stabilize it (Fig. 5,a). A series of new 3hetarylcoumarinbased reagents were prepared for the fluorescent labeling of oligonucleotides and other biomolecules.

Polymer supports for affinity chromatography, drug delivery and solid phase synthesis.

A number of new silica-based supports for solid phase oligonucleeotide synthesis containing efficient linker groups were proposed. Polymeric carriers for the delivery of various therapeutic oligonucleotides and proteins including e.g. interferons have been developed which are mainly based on functionalized and cross-linked polysaccharide matrices (dextran, hyaluronic acid, heparin etc) or polyethylene glycol. We have introduced a new simple method for the preparation of amine-modified polysaccharide hydrogels based on periodate oxidation of sugar residues followed by a partial cross-linking of the formed aldehyde groups with aliphatic diamines. Dextran hydrogel nanoconjugates containing covalently attached telomerase inhibitor, TMP3 porphyrin (drug content 10-20 μM/g), have been obtained. A number of organic and inorganic affinity sorbents with immobilized proteins, antibodies and low-molecular ligands were developed for biotechnology and molecular biology research (Fig. 5,b).

Fig. 5. The structure of bioconjugates: a – imidazophenazine-oligonucleotide; b – cross-linked dextran modified with telomerase inhibitor TMP3

National Grants:

Projects of National Academy of Sciences of Ukraine

  • 2012–2015 N 30–12 Project: “Design, synthesis and biological testing of new heterocyclic inhibitors of topoisomerase I as potential antitumor agents” (scientific supervisor – I. Ya. Dubey)
  • 2010–2014 N 5.16.3.36 Project: “Nanoconjugates of novel antitumor agents based on the specific ligands of quadruplex DNA – inhibitors of telomerase” (scientific supervisor – I. Ya. Dubey)
  • 2010–2014 N 43/10 Project: “New generation antitumor drugs based on heterocyclic telomerase inhibitors, specific ligands of quadruplex DNA” (scientific supervisor – I. Ya. Dubey)

Projects of State Fund for Fundamental Researches

  • 2011–2012 N F40.4/078 Project: “Clathrochelates of transition metals as inhibitors of some enzymes of nucleic acids biosynthesis system and prospective antitumor and antiviral pharmaceuticals” (scientific supervisor – I. Ya. Dubey)

Collaboration:

with Ukrainian organizations:

  • Institute of Organic Chemistry, NASU (Kyiv)
  • ²nstitute of Bioorganic Chemistry and Petrochemistry, NASU (Êyiv)
  • B. Verkin Institute for Low Temperature Physics and Engineering, NASU (Kharkiv)
  • R. E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, NASU (Kyiv)
  • D. K. Zabolotny Institute of Microbiology and Virology, NASU (Kyiv)
  • State Institution “L. V. Gromashevsky Institute of Epidemiology and Infectious Diseases of NAMS of Ukraine” (Kyiv)
  • O. V. Palladin Institute of Biochemistry, NASU (Kyiv)
  • V. M. Glushkov Institute of Cybernetics, NASU (Kyiv)
  • Taras Shevchenko National University of Kyiv (Kyiv)

with foreign organizations:

  • Laboratory of Coordination Chemistry of CNRS (Toulouse, France)

Selected publications:

  1. Kostina V.G., Alexeeva I.V., Lysenko N.A., Negrutska V.V., Dubey I.Ya. Synthesis and biological evaluation of new derivatives of tricyclic heteroaromatic carboxamides as potential topoisomerase I inhibitors. Ukr. Bioorg. Acta. 2016, 14(1): 3-8.
  2. Ryazanova O., Zozulya V., Voloshin I., Glamazda A., Dubey I., Dubey L., Karachevtsev V. Interaction of a tricationic meso-substituted porphyrin with guanine-containing polyribonucleotides of various structures. Meth. Appl. Fluoresc. 2016, 4(3): 034005.
  3. Boyarshin K.S., Priss A.E., Rayevskiy A.V., Ilchenko M.M., Dubey I.Ya., Kriklivyi I.A., Yaremchuk A.D., Tukalo M.A. A new mechanism of post-transfer editing by aminoacyl-tRNA synthetases: Catalysis of hydrolytic reaction by bacterial-type prolyl-tRNA synthetase. J. Biomol. Struct. Dynam. 2016, 34. doi:10.1080/07391102.2016.1155171.
  4. Ryazanova O, Zozulya V, Voloshin I, Dubey L, Dubey I, Karachevtsev V. Spectroscopic studies on binding of porphyrin-phenazine conjugate to four-stranded poly(G). J. Fluorescence. 2015;25(4):1013-1021.
  5. 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(8):565-578.
  6. Gorbatiuk OB, Bakhmachuk AO, Dubey LV, Usenko MO, Irodov DM, Okunev OV, Kostenko OM, Rachkov AE, Kordium VA. Recombinant Staphylococcal protein A with cysteine residue for affinity chromatography stationary phase and immunosensor applications. Biopolym. Cell. 2015;31(2):115-122.
  7. Kuperman MV, Chernii SV, Losytskyy MYu, Kryvorotenko DV, Derevyanko NO, Slominskii YuL, Kovalska VB, Yarmoluk SM. Trimethine cyanine dyes as fluorescent probes for amyloid fibrils: The effect of N,N'-substituents. Anal. Biochem. 2015;484:9-17.
  8. Ryazanova O, Zozulya V, Voloshin I, Dubey L, Dubey I, Karachevtsev V. Interaction of metallated porphyrin-imidazophenazine conjugate with tetramolecular quadruplex formed by poly(G): a spectroscopic investigation. J. Fluorescence. 2015;25. DOI: 10.1007/s10895-015-1682-2.
  9. Zozulya V, Ryazanova O, Voloshin I, et al. Self-assemblies of tricationic porphyrin on inorganic polyphosphate. Biophys. Chem. 2014;185:39-46.
  10. Levchenko SM, Rebriev AW, Tkachuk VV,...Dubey IYa. The detection of interaction between oligonucleotides and interferon, a key protein of antiviral cell defence system. Mol. Cryst. Liq. Cryst. 2014;590(1):213-220.
  11. Demianenko E, Ilchenko M, Grebenyuk A, et al. A theoretical study on ascorbic acid dissociation in water clusters. J. Mol. Model. 2014;20(3):2128-2135.
  12. Pokholenko Ia, Chetyrkina M, Dubey L, Dubey I, et al. Development and characterization of porous functionalized collagen scaffold for the delivery of FGF-2. Biopolym. Cell. 2014;30(3):216-222.
  13. Belov AS, Vologzhanina AV, Novikov VV, et al. Synthesis of the first morpholine-containing iron(II) clathrochelates: A new class of efficient functionalized transcription inhibitors. Inorg. Chim. Acta. 2014;421:300-306.
  14. Tsendra O, Scott AM, Gorb L, et al. Adsorption of nitrogen-containing compounds on the (100) α-quartz surface: ab initio cluster approach. J. Phys. Chem. C. 2014;118(6):3023-3034.
  15. Varzatskii OA, Novikov VV, Shulga SV, et al. Copper-promoted reductive homocoupling of quasi-aromatic iron(II) clathrochelates: boosting the inhibitory activity in a transcription assay. ChemComm. 2014;50(24):3166-3168.
  16. Negrutska VV, Dubey LV, Ilchenko MM, Dubey IYa. Design and study of telomerase inhibitors based on G-quadruplex ligands Biopolym. Cell. 2013; 29(3):169-176 doi:10.7124/bc.000817
  17. Lebed EG, Belov AS, Dolganov AV, Vologzhanina AV, et al. First clathrochelate iron and cobalt(II) trisdioximates with reactive apical substituents. Inorg. Chem. Commun. 2013; 30:53–57 doi:10.1016/j.inoche.2013.01.020
  18. Ryazanova O, Dubey L, Dubey I, Zozulya V. Spectroscopic study on the effect of imidazophenazine tethered to 5'­end of pentadecathymidilate on stability of poly(dA)•(dT)15 duplex. J Fluoresc. 2012; 22(6):1431–9 doi:10.1007/s10895-012-1080-y
  19. Gerasov A, Shandura M, Kovtun Y, Losytskyy M, Negrutska V, Dubey I. Fluorescent labeling of proteins with amine­specific 1,3,2­(2H)­dioxaborine polymethine dye. Anal Biochem. 2012; 420(2):115–20 doi:10.1016/j.ab.2011.09.018
  20. Zozulya VN, Ryazanova OA, Voloshin IM, Dubey LV, Dubey IYa. Spectroscopic studies on binding of porphyrinphenazine conjugate to intramolecular Gquadruplex formed by 22mer oligonucleotide. Int Rev Biophys Chem. 2011; 2(4):1129.
  21. Tkachuk ZYu, Dubey LV, Tkachuk VV, et al. Studying the interaction of 2'5'oligoadenylates and their analogues with proteins by fluorescence spectroscopy. Ukr. Biokhim. Zh. 2011; 83(1):45–53
  22. Palchykovska LG, Alexeeva IV, Negrutska VV, et al. In vitro transcription inhibition by 2arylidene derivatives of thiazolo[3,2a] benzimidazol3(2H)one. Biopolym. Cell. 2010; 26(6):508–11 doi:10.7124/bc.00017B
  23. Piletsky SA, Piletska OV, Turner APF, Dubey I, Dubey L. Polymeric binding materials US Patent Application N20090082480, 26.03.2009.
  24. De Logu A, Palchykovska LH, Kostina VH, et al. Novel N­aryl­ and N­heteryl phenazine­ 1­carboxamides as potential agents for the treatment of infections sustained by drug­resistant and multidrug­resistant Mycobacterium tuberculosis. Int J Antimicrob Agents. 2009; 33(3):223–9 doi:10.1016/j.ijantimicag.2008.09.016
  25. Ryazanova O, Voloshin I, Dubey I, Dubey L, Zozulya V. Fluorescent studies on cooperative binding of cationic pheophorbide­a derivative to polyphosphate. Ann N Y Acad Sci. 2008;1130:293–9 doi: 10.1196/annals.1430.033
  26. Stankiewicz­Drogon A, Palchykovska LG, Kostina VG, Alexeeva IV, Shved AD, Boguszewska­Chachulska AM. New acridone­ 4­carboxylic acid derivatives as potential inhibitors of hepatitis C virus infection. Bioorg Med Chem. 2008; 16(19):8846–52 doi:10.1016/j.bmc.2008.08.074