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Laboratory of Molecular Modelling and Bioinformatics

                   

                            

   Director  -  Vladimir B. Tsvetkov, PhD

   Dir. telephone: +7 (916) 118–59–13

   Lab. telephone: +7 (812) 499–15–24

   E-mail:  v.b.tsvetkov@gmail.com

The Laboratory of Molecular Modeling and Bioinformatics at the Smorodintsev Research Institute of Influenza was founded in 2016.

Main activities:

  • Molecular modeling
  • Study of the mechanisms of action of various chemical structures (small molecules and synthetic oligomers) displaying antiviral activity, including computer-assisted design modifications aiming to enhance their activities
  • Search for new structures possessing antiviral activity among small molecules, natural oligomers, and synthetic oligomers
  • Modeling of polymer features, including participation in supramolecular complexes and study of non-canonical DNA and RNA forms
  • Simulation of metabolic pathways associated with the formation of various viruses in the cell
  • Bioinformatics, evolutionary genomics, construction of evolutionary trees, transcriptome analysis, analysis of differential expression data, analysis of NGS and microchip data
  • Research tools: quantum chemistry; docking; molecular dynamics; Monte Carlo method; kinetic modeling; and bioinformatic analysis 

Selected publications

  1. Natalya B Zakharzhevskaya, Vladimir B Tsvetkov, Anna A Vanyushkina, Anna M Varizhuk, Daria V Rakitina, Victor V Podgorsky, Innokentii E Vishnyakov, Daria D Kharlampieva, Valentin A Manuvera, Fedor V Lisitsyn, Elena A Gushina, Vassili N Lazarev, Vadim M Govorun INTERACTION OF BACTEROIDES FRAGILIS TOXIN WITH OUTER MEMBRANE VESICLES REVEALS NEW MECHANISM OF ITS SECRETION AND DELIVERY Frontiers in Cellular and Infection Microbiology 2017 7: 2. doi: 10.3389/fcimb.2017.00002
  2. Anna Varizhuk, Dmitry Ischenko, Vladimir Tsvetkov, Roman Novikov, Nikolay Kulemin, Dmitry Kaluzhny, Maria Vlasenok, Vladimir Naumov, Igor Smirnov, Galina Pozmogova THE EXPANDING REPERTOIRE OF G4 DNA STRUCTURES Biochimie 2017 135 pp 54-62 doi.org/10.1016/j.biochi.2017.01.003
  3. AA Shtil, LM Gornostaev, VB Tsvetkov, AA Markova, TI Lavrikova, YG Khalyavina, AS Kuznetsova, DN Kaluzhny, AV Shunayev, MV Tsvetkova, VA Glazunova, VV Chernyshev THE OXIME DERIVATIVES OF 1-R-1H-NAPHTHO[2.3-D][1.2.3]TRIAZOLE-4.9-DIONE 2-OXIDES: SYNTHESIS AND PROPERTIES. Anticancer Agents Med Chem. 2017 Mar 27. doi: 10.2174/1871520617666170327112216
  4. Lysenkova LN, Saveljev OY, Grammatikova NE, Tsvetkov VB, Bekker OB, Danilenko VN, Dezhenkova LG, Bykov EE, Omelchuk OA, Korolev AM, Shchekotikhin AE VERIFICATION OF OLIGOMYCIN A STRUCTURE: SYNTHESIS AND BIOLOGICAL EVALUATION OF 33-DEHYDROOLIGOMYCIN A. J Antibiot (Tokyo). 2017 Apr 19. doi: 10.1038/ja.2017.48.
  5. Maria Prokofjeva Vladimir Tsvetkov, Dmitry Basmanov, Anna Varizhuk, Maria Lagarkova, Igor Smirnov, Kirill Prusakov, Dmitry Klinov, Vladimir Prassolov, Galina Pozmogova, and Sergey N. Mikhailov ANTI-HIV ACTIVITIES OF INTRAMOLECULAR G4 AND NON-G4 OLIGONUCLEOTIDES Nucleic Acid Therapeutics Online Ahead of Print: October 20, 2016
  6. Durandin NA, Tsvetkov VB, Bykov EE, Kaluzhny DN, Lavrenov SN, Tevyashova AN, Preobrazhenskaya MN. QUANTITATIVE PARAMETERS OF COMPLEXES OF TRIS(1-ALKYLINDOL-3-L) METHYLIUM SALTS WITH SERUM ALBUMIN: RELEVANCE FOR THE DESIGN OF DRUG CANDIDATES. Journal of Photochemistry and Photobiology B: Biology 2016 Volume 162, September 2016, Pages 570–576
  7. K. V. Sivak , A. V. Vasin, V. V. Egorov , V. B. Tsevtkov ,N. N. Kuzmich , V. A. Savina , and O. I. KiselevADENOSINE A2A RECEPTOR AS A DRUG TARGET FOR TREATMENT OF SEPSIS Molecular Biology, 2016, Vol. 50, No. 2, pp. 200–212.
  8. Andrey E. Shchekotikhin, Lyubov G. Dezhenkova, Vladimir B. Tsvetkov, Yuri N. Luzikov, Yulia L. Volodina, Victor V. Tatarskiy Jr., Anastasia A. Kalinina, Michael I. Treshalin, Helen M. Treshalina, Vladimir I. Romanenko, Dmitry N. Kaluzhny, Michael Kubbutat, Dominique Schols, Yves Pommier, Alexander A. Shtil, Maria N. Preobrazhenskaya DISCOVERY OF ANTITUMOR ANTHRA[2,3-B]FURAN-3-CARBOXAMIDES: OPTIMIZATION OF SYNTHESIS AND EVALUATION OF ANTITUMOR PROPERTIES. European Journal of Medicinal Chemistry Volume 112, 13 April 2016, Pages 114–129
  9. Tsvetkov V.B., Shtil A.A. THE INTRACELLULAR TARGETS OF ANTICANCER THERAPY: THE INCREASING COMPLEXITY OF THE PATH TO THE RATIONAL DESIGN OF DRUGS Russian Chemical Bulletin 2015 Issue 9 pp 2269-2272
  10. VY Grinberg, VB Tsvetkov, AA Markova, LG Dezhenkova, TV Burova, NV Grinberg, AS Dubovik, NV Plyavnik, AA Shtil INTERACTIONS OF NON-PHOSPHOROUS GLYCEROLIPIDS WITH DNA: ENERGETICS, MOLECULAR DOCKING AND TOPOISOMERASE I ATTENUATION. Anti-cancer agents in medicinal chemistry 2016;16(3):335-46 
  11. Vladimir B Tsvetkov, Anna M Varizhuk, Galina E Pozmogova, Igor P Smirnov, Natalia A Kolganova, Edward N Timofeev. A UNIVERSAL BASE IN A SPECIFIC ROLE: TUNING UP A THROMBIN APTAMER WITH 5-NITROINDOLE Scientific reports 2015 5: 16337
  12. Oleg I Kiselev, Andrey V Vasin, M P Shevyreva, Ella G Deeva, Konstantin V Sivak, Vladimir V Egorov, Vladimir B Tsvetkov, Andrey Yu Egorov, Ekaterina A Romanovskaya-Romanko, Ludmila A Stepanova, Andrey B Komissarov, Ludmila M Tsybalova, G M Ignatjev., EBOLA HEMORRHAGIC FEVER: PROPERTIES OF THE PATHOGEN AND DEVELOPMENT OF VACCINES AND CHEMOTHERAPEUTIC AGENTS Molecular Biology 2015, V.49, Issue 4, с.480-493
  13. Vladimir Tsvetkov, Galina Pozmogova, Anna Varizhuk., THE SYSTEMATIC APPROACH TO DESCRIBING CONFORMATIONAL REARRANGEMENTS IN G-QUADRUPLEXES Journal of Biomolecular Structure and Dynamics 2016 2016 Apr;34(4):705-15
  14. Mikhail A Grin, Philip V Toukach, Vladimir B Tsvetkov, Roman I Reshetnikov, Olga V Kharitonova, Anton S Kozlov, Alexander A Krasnovsky, Andrey F Mironov., BACTERIOCHLORIN-CONTAINING TRIAD: STRUCTURE AND PHOTOPHYSICAL PROPERTIES Dyes and Pigments 2015 121 p 21-29
  15. Varizhuk A., Ischenko D., Smirnov I., Tatarinova O., Severov V., Novikov R., Tsvetkov V., Naumov V., Kaluzhny D., Pozmogova G., AN IMPROVED SEARCH ALGORITHM TO FIND G-QUADRUPLEXES IN GENOME SEQUENCES, BIORXIV (the preprint server for biology - Cold Spring Harbor Labs Journals), 2014, Preprint N. 2014/1/23 – P. 1-10 and figures
  16. Kovaleva OA, Tsvetkov VB, Mamaeva OK, Ol’shevskaya VA, Makarenkov AV, Dezhenkova LG, Semeikin AS, Borisova OF, Shtil AA, Shchyolkina AK, Kaluzhny DN. PREFERENTIAL DNA PHOTOCLEAVAGE POTENCY OF ZN(II) OVER NI(II) DERIVATIVES OF CARBOXYMETHYL TETRACATIONIC PORPHYRIN: THE ROLE OF THE MODE OF BINDING TO DNA. European Biophysics Journal. 2014 Nov;43(10-11):545-54.
  17. Vladimir B. Tsvetkov, Alexander V. Serbin MOLECULAR DYNAMICS MODELING THE SYNTHETIC AND BIOLOGICAL POLYMERS INTERACTIONS PRE-STUDIED VIA DOCKING: ANCHORS MODIFIED POLYANIONS INTERFERENCE WITH THE HIV-1 FUSION MEDIATOR. Journal of Computer-Aided Molecular Design 2014 June, Volume 28, Issue 6, pp 647-673
  18. Tsvetkov VB, Solov’eva AB, Melik-Nubarov NS. COMPUTER MODELING OF THE COMPLEXES OF CHLORIN E6 WITH AMPHIPHILIC POLYMERS. Physical Chemistry Chemical Physics. 2014 Jun 14;16(22):10903-13
  19. O. Tatarinova, V. Tsvetkov, D. Basmanov, N. Barinov, I. Smirnov, E. Timofeev, D. Kaluzhny, A. Chuvilin, D. Klinov, A. Varizhuk, G. Pozmogova. COMPARISON OF THE ‘CHEMICAL’ AND ‘STRUCTURAL’ APPROACHES TO THE OPTIMIZATION OF THE THROMBIN-BINDING APTAMER. PLoS One 9, e89383 (2014)
  20. Dezhenkova L.G., Tsvetkov V.B., Shtil A.A., TOPOISOMERASE I AND II INHIBITORS: CHEMICAL STRUCTURE, MECHANISMS OF ACTION AND ROLE IN CANCER CHEMOTHERAPY, Russian Chemical Reviews, 2014, V. 83 – N. 1 - P.82 -94
  21. Anna M. Varizhuk, Vladimir B. Tsvetkov, Olga N. Tatarinova, Dmitry N. Kaluzhny, Vladimir L. Florentiev, Edward N. Timofeev, Anna K. Shchyolkina, Olga F. Borisova, Igor P. Smirnov, Sergei L. Grokhovsky, Anton V. Aseychev, Galina E. Pozmogova SYNTHESIS, CHARACTERIZATION AND IN VITRO ACTIVITY OF THROMBIN-BINDING DNA APTAMERS WITH TRIAZOLE INTERNUCLEOTIDE LINKAGESEuropean Journal of Medicinal Chemistry 06/2013; 67C:90-97
  22. Vladimir B. Tsvetkov, Alexander V. Serbin A NOVEL VIEW OF MODELLING INTERACTIONS BETWEEN SYNTHETIC AND BIOLOGICAL POLYMERS VIA DOCKING Journal of Computer-Aided Molecular Design (2012) 26:1369–1388
  23. Kovaleva O. A., Tsvetkov V. B., Shchyolkina A. K., Borisova O. F., Ol’shevskaya V. A., Makarenkov A. V., Semeikin A. S., Shtil A. A., Kaluzhny D. N. THE ROLE OF CARBOXYMETHYL SUBSTITUENTS IN THE INTERACTION OF TETRACATIONIC PORPHYRINS WITH DNA Eur Biophys J. – 2012 – V. 41 – P. 723–732
  24. Serbin A.V., Veselovsky A.V., Tsvetkov V.B. IN VITRO AND IN SILICO INVESTIGATION OF INTERFERONOGENIC ANALOGUES OF NUCLEIC ACIDS, ARTIFICIALLY PROGRAMMED TO BLOCK THE INITIAL STAGES OF HIV INFECTION OF CELLS Applied Biochemistry and Microbiology – 2012. - N 9. – P. 723-739.