Bioinformatics

Nowadays bioinformatics is a powerful tool in the life science that has already found widespread practical application in system biology, structural biology and rational drug discovery.

Having solid knowledge and experience in the design of biologically active compounds for biomedical research Otava Institute plays a pivotal role in many drug discovery projects. Our scientists have developed more than 10 classes of novel and potent inhibitors for different biological objects: protein kinases, polymerases, synthases etc.

For  improving  research projects of our customers we propose state-of-the-art molecular modeling and computational chemistry methods in combination with an in-house collection that number more than 250,000 small organic compounds which are represented by derivatives of various types of heterocyclic systems and their fused analogues.

With more than 20 years of experience in the field of drug discovery and structural bioinformatics, we are willing to provide our customer a wide range of bioinformatics services:

  • Molecular Docking
  • Molecular Dynamics Simulation
  • Homology Modeling
  • Pharmacophore modeling
  • Protein secondary structure prediction
  • Protein disorder region prediction
  • Protein fold recognition
  • Protein structure homology modeling
  • Protein structure analysis
  • Protein spatial structure quality evaluation
  • Protein spatial structure correction
  • Protein domain prediction
  • Aptamer structure prediction
  • Protein molecular dynamics simulation
  • Nucleic acid molecular dynamic simulation
  • In silico protein modification analysis
  • In silico hit/lead development
  • In silico hit/lead prediction
  • In silico hit/lead optimization
  • Prediction of ligand binding site on protein surface
  • Accurate binding energy prediction

Completed foreign contract research:

Grants:

  • 2017 -2019: STCU Project № 6258 “Multitarget drug discovery to overcome antibiotic resistance in Mycobacterium tuberculosis”
  • 2012-2016: Project of National Academy of Sciences of Ukraine № 0112U000254 “Target-oriented search of novel antimicrobial, antiviral and anticancer remedies”
  • 2013-2014: State Agency for Science, Innovation and Informatization  № ДП/337 0113U006029 “Development of methodologies for target-oriented rational search of new anti-tuberculosis drugs”
  • 2012: State Agency for Science, Innovation and Informatization  №  ПР 059/514 0112U007642 “Development and implementation of methods of target oriented research purposes for the primary screening of molecules of potential biologically active compounds”
  • 2010 -2012: STCU Project № 5218 “Rational search for inhibitors of aminoacyl-tRNA-synthetases with selective action against causative agent of tuberculosis”
  • 2010-2014: Project of National Academy of Sciences of Ukraine № 0110U006120 “Development of technologies of target-oriented search for inhibitors of aminoacyl-tRNA-synthetases with selective action against causative agents of human infective diseases”
  • 2007-2011:  Project of National Academy of Sciences of Ukraine № 0107U000337 “Design of inhibitors of protein kinases of MAPK signaling pathway TNFR-ASK1-MKK4/7-JNK”
  • 2007-2009: STCU Project №4376 “Directional search for synthetic antibacterial compounds against specific human infections”
  • 2007-2009: Project of National Academy of Sciences of Ukraine № 0107U004939 “Optimization of protein kinase inhibitors of СК2 and estimation of their biological activity on cultures of cancer cells”
  • 2006-2008:  NASU RAS № 11-2006 “Innovative technologies in the treatment of cancer”
  • 2006-2007: SFFR № F18/12-2006 “Use of molecular genetic and structural approaches for the directed search of synthetic compounds with antibacterial activity against the specific causes of human infectious diseases”
  • 2004-2006: Project of National Academy of Sciences of Ukraine № 0106U000543 “Development of protein kinase CDK2 and СК2 inhibitors as potential drugs against cancer”

Patents:

  • Pat. 116134, 10.05.2017. Novel small-molecular organic compounds with antituberculosis activity based on benzaldehyde thiosemicarbazone. Volynets GP, Tukalo MA, Bdzhola VG, Starosyla SA, Tarnavskiy SS, Gudzera OY, Kriklivyi IA, Yarmoluk SM
  • Pat. 117279, 26.06.2017. Novel small-molecular organic compounds with antituberculosis activity based on isonicotinic acid hydrazide. Volynets GP, Tukalo MA, Bdzhola VG, Tarnavskiy SS, Starosyla SA, Gudzera OY, Yarmoluk SM

Selected publications:

  • Dihydrobenzo[4,5]imidazo[1,2-a]pyrimidine-4-ones as a new class of CK2 inhibitors (2018). Protopopov MV, Ostrynska OV, Starosyla SA, Vodolazhenko MA, Sirko SM, Gorobets NY, Bdzhola V, Desenko SM, Yarmoluk SM. Molecular Diversity. doi: 10.1007/s11030-018-9836-1.
  • Identification of 1,3-thiazole-5-carboxylic acid derivatives as inhibitors of protein kinase CK2 (2018) Protopopov MV, Volynets GP, Starosyla SA, Vdovin VS, Lukashov SS, Bilokin YV, Bdzhola VG, Yarmoluk SM. Current Enzyme Inhibition 14(2): 152-159
  • Hit identification of CK2 inhibitors by methods of virtual screening (2017). Protopopov MV, Starosyla SA, Borovykov OV, Sapelkin VN, Bilokin YV, Bdzhola VG, Yarmoluk SM. Biopolymers and Cell 33(4): 291-301.
  • Structural hypervariability of the two human protein kinase CK2 catalytic subunit paralogs revealed by complex structures with a flavonol- and a thieno[2,3-d]pyrimidine-based inhibitor (2017). Niefind K, Bischoff N, Golub AG, Bdzhola VG, Balanda AO, Prykhod’ko AO, Yarmoluk SM. Pharmaceuticals (Basel) 10(1): pii: E9.
  • Syniugin AR, Ostrynska OV, Chekanov MO, Volynets GP, Starosyla SA, Bdzhola VG, Yarmoluk SM (2016) Design, synthesis and evaluation of 3-quinoline carboxylic acids as new inhibitors of protein kinase CK2. J Enzyme Inhib Med Chem doi: 10.1080/14756366.2016.1222584.
  • Gudzera OI, Golub AG, Bdzhola VG, Volynets GP, Lukashov SS, Kovalenko OP, Kriklivyi IA, Yaremchuk AD, Starosyla SA, Yarmoluk SM, Tukalo MA (2016) Discovery of potent anti-tuberculosis agents targeting leucyl-tRNA synthetase. Bioorg Med Chem 24(5):1023-1031.
  • Starosyla SA, Volynets GP, Bdzhola VG, Golub AG, Yarmoluk SM (2014) Pharmacophore approaches in protein kinase inhibitors design. World J Pharmacol 3(4):162-173.
  • Starosyla SA, Volynets GP, Bdzhola VG, Golub AG, Protopopov MV, Yarmoluk SM (2014) ASK1 pharmacophore model derived from diverse classes of inhibitors. Bioorg Med Chem Lett 24(18):4418-4423.
  • Ostrynska OV, Balanda AO, Bdzhola VG, Golub AG, Kotey IM, Kukharenko OP, Gryshchenko AA, Briukhovetska NV, Yarmoluk SM (2016) Design and synthesis of novel protein kinase CK2 inhibitors on the base of 4-aminothieno[2,3-d]pyrimidines. Eur J Med Chem 115:148-160.
  • Starosyla SA, Volynets GP, Lukashov SS, Gorbatiuk OB, Golub AG, Bdzhola VG, Yarmoluk SM (2015) Identification of apoptosis signal-regulating kinase 1 (ASK1) inhibitors among the derivatives of benzothiazol-2-yl-3-hydroxy-5-phenyl-1,5-dihydro-pyrrol-2-one. Bioorg Med Chem 23(10):2489-2497.
  • Guerra B, Bischoff N, Bdzhola VG, Yarmoluk SM, Issinger OG, Golub AG, Niefind K (2015) A note of caution on the role of halogen bonds for protein kinase/inhibitor recognition suggested by high- and low-salt CK2α complex structures. ACS Chem Biol 10(7):1654-1660.

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