DOCKING STUDIES OF TYPICAL CONFORMATIONS OF PROTEIN TYROSINE PHOSPHATASE 1B

Authors

  • Volodymyr Tanin Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine
  • Vsevolod Tanchuk Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine

DOI:

https://doi.org/10.18372/2306-1472.60.7572

Keywords:

binding sites, clustering, conformations, docking, phosphatase 1B, structure similarity

Abstract

Typical conformations of protein tyrosine phosphatase 1B have been tested by docking known inhibitors.It was found that though there is no preferable conformation, there is a suitable conformation for each inhibitor.

Author Biographies

Volodymyr Tanin, Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine

Volodymyr Tanin. Engineer.Third Department, Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine,Kyiv, Ukraine.Education: Faculty of Chemistry, specialty engineer of Organic Chemistry and Technology of Organic Substances,National Technical University of Ukraine “Kyiv Polytechnic Institute”, Kyiv, Ukraine (2008).Research area: computer chemistry.

Vsevolod Tanchuk, Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine

Vsevolod Tanchuk. Candidate of Chemistry. Senior Researcher.Third Department, Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine,Kyiv, Ukraine.Education: Department of Chemistry, specialty - physic chemistry , Kyiv Taras Shevchenko University, Kyiv, Ukraine (1991).Research area: computer chemistry.

References

Adams, D.; Abraham, A.; Asano, J.; Breslin, C.; Dick, C.; Ixkes, U.; Johnston, B.; Johnston, D.; Kewnay, J.; Mackay, S. MacKenzie, S.; McFarlane, M.; Mitchell., L.; Spinks, D. Takano, Y. 2-Aryl-3,3,3-trifluoro-2-hydroxypropionic acids: A new

class of protein tyrosine phosphatase 1B inhibitors. Bioorg. Med. Chem. Lett. 2007. Vol. 17, N 23. P. 6579–6583.

Bernstein, F.; Koetzle, T.; Williams, G.; Meyer, E.; Brice, E.; Rodgers, M.; Kennard, O.; Shimanouchi, T.; Tasumi, M. The protein data bank: a computer based archival file for macromolecular structures. J. Mol. Biol. 1977. Vol. 112, N 2. P. 535–542.

Chen, Y.; Seto, C. Divalent and Trivalent a-Ketocarboxylic Acids as Inhibitors of Protein Tyrosine Phosphatases. J Med Chem. 2002. Vol. 45, N 18. P. 3946-3952.

Craig, I.; Essex, J.; Spiegel, K. Ensemble docking into multiple crystallographically derived protein structures: An evaluation based on the statistical analysis of enrichments. J. Chem. Inf.

Model. 2010. Vol.50, N 4. P. 511–524.

http://hpc-ua.org/hpc-ua-13/files/proceedings/76.pdf

http://www.chemaxon.com

Hu, X. In silico modeling of protein tyrosine phosphatase 1B inhibitors with cellular activity. Bioorg. Med. Chem. Lett. 2006. Vol. 16, N 24. P. 6321–6327.

Hu, X.; Vujanac, M.; Stebbins, C. Computational analysis of tyrosine phosphatase inhibitor selectivity for the virulence factors YopH and SptP. J. Mol. Graph Model. 2004. Vol. 23, N 2. P. 175–187.

Kasibhatla, B.; Wos, J.; Peters, K. Targeting protein tyrosine phosphatase to enhance insulin action for the potential treatment of diabetes. Curr. Opin. Invest. Drugs. 2007. Vol. 8, N 10. P. 805-813.

Koren, S.; Fantus, I. Inhibition of the protein tyrosine phosphatase PTP1B: potential therapy for obesity, insulin resistance and type-2 diabetes mellitus. Best Pract Res. Clin. Endocrinol. Metab. 2007. Vol. 21, N 4. P. 621–640.

Kumar, A.; Ahmad, P.; Maurya, R.; Singh, A.; Srivastava, A. Novel 2-aryl-naphtho[1,2-d]oxazole derivatives as potential PTP-1B inhibitors showing antihyperglycemic activities. Eur. J. Med. Chem. 2009. Vol. 44, N 1. P. 109–116.

Lau, C.; Bayly, C.; Gauthier, J.; Li, C.; Therien, M.; Asante-Appiah, E.; Cromlish, W.; Boie, Y.; Forghani, F.; Desmarais, S.; Wang, Q.; Skorey, K.; Waddleton, D.; Payette, P.; Ramachandran, C.; Kennedy, B.; Scapin, G. Structure based design of a series of potent and selective non peptidic PTP-1B

inhibitors. Bioorg. Med. Chem. Lett. 2004. Vol. 14, N 4. P. 1043–1048.

Li, X.; Bhandari, A.; Holmes, C.; Szardenings, A. α,α-Difluoro-β-ketophosphonates as potent inhibitors of protein tyrosine phosphatase 1B. Bioorg. Med. Chem. Lett. 2004. Vol. 14, N 16.

P. 4301–4306.

Liu, T.; Lin, Y.; Wen, X.; Jorrisen, R.; Gilson, M. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Research. 2007. Vol. 35, N Database issue. P. D198–D201.

Maccari, R.; Paoli, P.; Ottana, R.; Jacomelli, M.; Ciurleo, R.; Manao, G.; Steindl, T.; Langer, T.; Vigorita, M.; Camici, G. 5-Arylidene-2,4-thiazolidinediones as inhibitors of protein

tyrosine phosphatases. Bioorg. Med. Chem. 2007. Vol. 15, N 15. P. 5137–5149.

Saxena, A.; Pandey, G.; Gupta, S.; Singh, A.; Srivastava A. Synthesis of protein tyrosine phosphatase 1B inhibitors: Model validation and docking studies. Bioorg. Med. Chem. Lett. 2009.

Vol. 19, N 8. P. 2320–2323.

Shim, Y.; Kim, K.; Lee, K.; Shrestha, S.; Lee, K.; Kim, C.; Cho, H. Formylchromone derivatives as irreversible and selective inhibitors of human protein tyrosine phosphatase 1B. Kinetic and modeling studies. Bioorg Med Chem. 2005. Vol. 13, N 4. P. 1325–1332.

Shrestha, S.; Bhattarai, B.; Lee, K.; Cho, H. Mono- and disalicylic acid derivatives. PTP1B inhibitors as potential anti-obesity drugs. Bioorg. Med. Chem. 2007. Vol. 15, N 20. P. 6535–6548.

Tabernero, L.; Aricescu, A.; Jones, E.; Szedlacsek, S. Protein tyrosine phosphatases: structure–function relationships. FEBS J. 2008. Vol. 275, N 5. P. 867–882.

Tanchuk, V.; Tanin, V.; Vovk, A. Classification of binding site conformations of rotein tyrosine phosphatase 1B. Chem. Biol. Drug Des. 2012. Vol. 80, N 1. P. 121–128.

Tautz, L.; Mustelin, T. Strategies for developing protein tyrosine phosphatase inhibitors. Methods. 2007. Vol. 42, N 3. P. 250–260.

Tonks, N. Protein tyrosine phosphatases: From genes, to function, to disease. Nat Rev Mol Cell Biol. 2006. Vol. 7, N 11. P. 833–846.

Totrov, M.; Abagyan, R. Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol. 2008. Vol. 18, N 2. P. 178–184.

Vintonyak, V.; Antonchick, A.; Rauh, D.; Waldmann, H. The therapeutic potential of phosphatase inhibitors. Curr Opin Chem Biol. 2009. Vol. 13, N 3. P. 13272–13283.

Zhang, S.; Zhang, Z. PTP1B as a drug target: recent developments in PTP1B inhibitor discovery. Drug Discovery Today. 2007. Vol. 12, N 9-10. P. 373-381.

Zhang, Z. Functional studies of protein tyrosine phosphatases with chemical approaches. Biochim Biophys Acta. 2005. Vol. 1754, N 1–2. P. 100–107.

Published

01-10-2014

How to Cite

Tanin, V., & Tanchuk, V. (2014). DOCKING STUDIES OF TYPICAL CONFORMATIONS OF PROTEIN TYROSINE PHOSPHATASE 1B. Proceedings of National Aviation University, 60(3), 87–92. https://doi.org/10.18372/2306-1472.60.7572

Issue

Section

CHEMICAL TECHNOLOGY, HIMMOTOLOGY