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 our team 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:

BIOINFORMATICS

  • Protein sequence analysis and alignment
  • Gene expression data analysis and reporting
  • Systems network analysis
  • Protein modeling (homology modeling, Ab Initio spatial structure prediction, structure analysis)
  • Nucleic acids modeling (spatial structure prediction and optimization, analysis)
  • Prediction of aptamer structure
  • Identification and analysis of binding sites

Computer-Aided Drug Discovery (CADD)

  • Molecular docking and reverse molecular docking
  • Pharmacophore modeling and reverse pharmacophore modeling
  • Prediction of compounds activity using machine learning (QSAR, artificial neural networks and bayesian modeling)
  • Virtual high-throughput screening and design of targeted compound libraries with high affinity to the molecular targets
  • Hit identification and optimization
  • Structure-activity relationship (SAR) analysis
  • In silico ADME predictions
  • Computational studies of drug-receptor, protein-protein, nucleic acids-protein and other interactions
  • Molecular dynamics of proteins, nucleic acids, extra large heterogeneous systems
  • Accurate prediction of binding energy

Completed foreign contract research:

Grants:

  • 2017 -2019: STCU Project № 6258 “Multitarget drug discovery to overcome antibiotic resistance in Mycobacterium tuberculosis”
  • 2010 -2012: STCU Project № 5218 “Rational search for inhibitors of aminoacyl-tRNA-synthetases with selective action against causative agent of tuberculosis”
  • 2007-2009: STCU Project №4376 “Directional search for synthetic antibacterial compounds against specific human infections”
  • 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”

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
  • Pat. UА68984 А, C07D215/00, 2004-08-16. Application of 4-substituted 3-carboxyquinolines as protein kinase CK2 inhibitors. Sapelkin VM, Lukashov SS, Golub AG, Bdzhola VG, Yakovenko OYa, Yarmoluk SM, Dubinina GG
  • Pat. UA69165 А, С07D215/00, 2004-08-16. Application of 4,5,6,7-tetrahalogeno-1,3-isoindolinediones as protein kinase CK2 inhibitors. Golub AG, Yakovenko OYa, Yarmoluk SM, Dubinina GG, Bdzhola VG, Prykhod'ko AO
  • Pat. 86041, 10.12.2013. Low-molecular organic ATP-competitive inhibitors of serine/threonine kinase CK2 based on 4-aminothieno-[2,3-d]pyrimidine heterocycle. Ostrynska OV, Balanda AO, Bdzhola VG, Kotey IM, Kukharenko OP, 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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