Classification of Binding Site Conformations of Protein Tyrosine Phosphatase 1B

Chemical Biology and Drug Design

Volumn 80, Issue 1, 2012, Pages 121-128

  Tanchuk, Vsevolod Yu ^a   Tanin, Volodymyr O ^a   Vovk, Andriy I ^a  

^a INSTITUTE OF BIOORGANIC CHEMISTRY AND PETROCHEMISTRY   (Ukraine)

Author keywords

Binding sites; Clustering; Conformations; Docking; Protein tyrosine phosphatase 1B; Structure similarity

Indexed keywords

PROTEIN TYROSINE PHOSPHATASE 1B;

ARTICLE; BINDING SITE; COMPUTER PROGRAM; ENZYME ANALYSIS; ENZYME BINDING; ENZYME METABOLISM; ENZYME STRUCTURE; PRIORITY JOURNAL;

BINDING SITES; CATALYTIC DOMAIN; COMPUTER SIMULATION; DATABASES, PROTEIN; PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1;

EID: 84862129938     PISSN: 17470277     EISSN: 17470285     Source Type: Journal    
DOI: 10.1111/j.1747-0285.2012.01370.x     Document Type: Article

References (47)

1. Tonks N.K. (2006) Protein tyrosine phosphatases: from genes, to function, to disease. Nat Rev Mol Cell Biol;7:833-846.
2. Vintonyak V.V., Antonchick A.P., Rauh D., Waldmann H. (2009) The therapeutic potential of phosphatase inhibitors. Curr Opin Chem Biol;13:272-283.
3. Tabernero L., Aricescu A.R., Jones E.Y., Szedlacsek S.E. (2008) Protein tyrosine phosphatases: structure-function relationships. FEBS J;275:867-882.
4. Kasibhatla B., Wos J., Peters K.G. (2007) Targeting protein tyrosine phosphatase to enhance insulin action for the potential treatment of diabetes. Curr Opin Investig Drugs;8:805-813.
5. Koren S., Fantus I.G. (2007) Inhibition of the protein tyrosine phosphatase PTP1B: potential therapy for obesity, insulin resistance and type-2 diabetes mellitus. Best Pract Res Clin Endocrinol Metab;21:621-640.
6. Zhang S., Zhang Z.Y. (2007) PTP1B as a drug target: recent developments in PTP1B inhibitor discovery. Drug Discovery Today;12:373-381.
7. Chen Y.T., Seto C.T. (2002) Divalent and trivalent a-ketocarboxylic acids as inhibitors of protein tyrosine phosphatases. J Med Chem;45:3946-3952.
8. Zhang Z.Y. (2005) Functional studies of protein tyrosine phosphatases with chemical approaches. Biochim Biophys Acta;1754:100-107.
9. Li X., Bhandari A., Holmes C.P., Szardenings A.K. (2004) α, α-Difluoro-β-ketophosphonates as potent inhibitors of protein tyrosine phosphatase 1B. Bioorg Med Chem Lett;14:4301-4306.
10. Tautz L., Mustelin T. (2007) Strategies for developing protein tyrosine phosphatase inhibitors. Methods;42:250-260.
11. Kumar A., Ahmad P., Maurya R.A., Singh A.B., Srivastava A.K. (2009) Novel 2-aryl-naphtho[1, 2-d]oxazole derivatives as potential PTP-1B inhibitors showing antihyperglycemic activities. Eur J Med Chem;44:109-116.
12. Lau C.K., Bayly C.I., Gauthier J.Y., Li C.S., Therien M., Asante-Appiah E., Cromlish W. et al. (2004) Structure based design of a series of potent and selective non peptidic PTP-1B inhibitors. Bioorg Med Chem Lett;14:1043-1048.
13. Hu X., Vujanac M., Stebbins C.E. (2004) Computational analysis of tyrosine phosphatase inhibitor selectivity for the virulence factors YopH and SptP. J Mol Graph Model;23:175-187.
14. Hu X. (2006) In silico modeling of protein tyrosine phosphatase 1B inhibitors with cellular activity. Bioorg Med Chem Lett;16:6321-6327.
15. Shim Y.S., Kim K.C., Lee K.A., Shrestha S., Lee K.-H., Kim C.K., Cho H. (2005) Formylchromone derivatives as irreversible and selective inhibitors of human protein tyrosine phosphatase 1B. Kinetic and modeling studies. Bioorg Med Chem;13:1325-1332.
16. Maccari R., Paoli P., Ottana R., Jacomelli M., Ciurleo R., Manao G., Steindl T., Langer T., Vigorita M.G., Camici G. (2007) 5-Arylidene-2, 4-thiazolidinediones as inhibitors of protein tyrosine phosphatases. Bioorg Med Chem;15:5137-5149.
17. Saxena A.K., Pandey G., Gupta S., Singh A.B., Srivastava A.K. (2009) Synthesis of protein tyrosine phosphatase 1B inhibitors: model validation and docking studies. Bioorg Med Chem Lett;19:2320-2323.
18. Adams D.R., Abraham A., Asano J., Breslin C., Dick C.A.J., Ixkes U., Johnston B.F., Johnston D., Kewnay J., Mackay S.P., MacKenzie S.J., McFarlane M., Mitchell L., Spinks D., Takano Y. (2007) 2-Aryl-3, 3, 3-trifluoro-2-hydroxypropionic acids: a new class of protein tyrosine phosphatase 1B inhibitors. Bioorg Med Chem Lett;17:6579-6583.
19. Shrestha S., Bhattarai B.R., Lee K.-H., Cho H. (2007) Mono- and disalicylic acid derivatives: PTP1B inhibitors as potential anti-obesity drugs. Bioorg Med Chem;15:6535-6548.
20. Montalibet J., Skorey K., McKay D., Scapin G., Asante-Appiah E., Kennedy B.P. (2006) Residues distant from the active site influence protein-tyrosine phosphatase 1B inhibitor binding. J Biol Chem;281:5258-5266.
21. Scapin G., Patel S.B., Becker J.W., Wang Q., Desponts C., Waddleton D., Skorey K. et al. (2003) The structural basis for the selectivity of benzotriazole inhibitors of PTP1B. Biochemistry;42:11451-11459.
22. Sun J.-P., Fedorov A.A., Lee S.-Y., Guo X.-L., Shen K., Lawrence D.S., Almo S.C., Zhang Z.-Y. (2003) Crystal structure of PTP1B complexed with a potent and selective bidentate inhibitor. J Biol Chem;278:12406-12414.
23. Liu S., Zeng L.-F., Wu L., Yu X., Xue T., Gunawan A.M., Ya-Qiu L., Zhang Z.-Y. (2008) Targeting inactive enzyme conformation: aryl diketoacid derivatives as a new class of PTP1B inhibitors. J Am Chem Soc;130:17075-17084.
24. Xin Z., Oost T.K., Abad-Zapatero C., Hajduk P.J., Pei Z., Szczepankiewicz B.G., Hutchins C.W., Ballaron S.J., Stashko M.A., Lubben T., Trevillyan J.M., Jirousek M.R., Liu G. (2003) Potent, selective inhibitors of protein tyrosine phosphatase 1B. Bioorg Med Chem Lett;13:1887-1890.
25. Lund I.K., Andersen H.S., Iversen L.F., Olsen O.H., Møller K.B., Pedersen A.K., Ge Y., Holsworth D.D., Newman M.J., Axe F.U., Møller N.P. (2004) Structure-based design of selective and potent inhibitors of protein-tyrosine phosphatase β. J Biol Chem;279:24226-24235.
26. Ottana R., Maccari R., Ciurleo R., Paoli P., Jacomelli M., Manao G., Camici G., Laggner C., Langer T. (2009) 5-Arylidene-2-phenylimino-4-thiazolidinones as PTP1B and LMW-PTP inhibitors. Bioorg Med Chem;17:1928-1937.
27. Comeau A.B., Critton D.A., Page R., Seto C.T. (2010) A focused library of protein tyrosine phosphatase inhibitors. J Med Chem;53:6768-6772.
28. Rao G.S., Ramachandran M.V., Bajaj J.S. (2006) In silico structure-based design of a potent and selective small peptide inhibitor of protein tyrosine phosphatase 1B, a novel therapeutic target for obesity and type 2 diabetes mellitus: a computer modeling approach. J Biomol Struct Dyn;23:377-384.
29. Bernstein F., Koetzle T., Williams G., Meyer E., Brice E.J., Rodgers M., Kennard O., Shimanouchi T., Tasumi M. (1977) The protein data bank: a computer based archival file for macromolecular structures. J Mol Biol;112:535-542.
30. Craig I.R., Essex J.W., Spiegel K. (2010) Ensemble docking into multiple crystallographically derived protein structures: an evaluation based on the statistical analysis of enrichments. J Chem Inf Model;50:511-524.
31. Totrov M., Abagyan R. (2008) Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol;18:178-184.
32. Feig M., Karanicolas J., Brooks C.L. III (2004) MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model;22:377-395.
33. Press W.H., Teukolsky S.A., Vetterling W.T., Flannery B.P. (1995) Numerical Recipes in C: The Art of Scientific Computing. Cambridge University Press: New York, USA.
34. Duda R.O., Hart P.E. (1973) Pattern Classification and Scene Analysis. New York, USA: John Wiley & Sons, Inc.
35. Keller P.A., Leach S.P., Luu T.T.T., Titmuss S.J., Griffith R. (2000) Development of computational and graphical tools for analysis of movement and flexibility in large molecules. J Mol Graph Model;18:235-241.
36. Kamerlin S.C.L., Rucker R., Boresch S. (2006) A targeted molecular dynamics study of WPD loop movement in PTP1B. Biochem Biophys Res Commun;345:1161-1166.
37. Kamerlin S.C.L., Rucker R., Boresch S. (2007) A molecular dynamics study of WPD-loop flexibility in PTP1B. Biochem Biophys Res Commun;356:1011-1016.
38. Guex N., Peitsch M.C. (1995) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis;18:2714-2723.
39. Barford D., Flint A.J., Tonks N.K. (1994) Crystal structure of human protein tyrosine phosphatase 1B. Science;263:1397-1404.
40. Asante-Appiah E., Ball K., Bateman K., Skorey K., Friesen R., Desponts C., Payette P., Bayly C., Zamboni R., Scapini G., Ramachandran C., Kennedy B.P. (2001) The YRD motif is a major determinant of substrate and inhibitor specificity in T-cell protein-tyrosine phosphatase. J Biol Chem;276:26036-26043.
41. Sarmiento M., Puius Y.A., Vetter S.W., Keng Y.F., Wu L., Zhao Y., Lawrence D.S., Almo S.C., Zhang Z.Y. (2000) Structural basis of plasticity in protein tyrosine phosphatase 1B substrate recognition. Biochemistry;39:8171-8179.
42. Asante-Appiah E., Patel S., Desponts C., Taylor J.M., Lau C., Dufresne C., Therien M., Friesen R., Becker J.W., Leblanc Y., Kennedy B.P., Scapin G. (2006) Conformation-assisted inhibition of protein-tyrosine phosphatase-1B elicits inhibitor selectivity over T-cell protein-tyrosine phosphatase. J Biol Chem;281:8010-8015.
43. Puius Y.A., Zhao Y., Sulvivan M., Lawrence D.S., Almo S.C., Zhang Z.-Y. (1997) Identification of a second aryl phosphate-binding site in protein-tyrosine phosphatase 1B: a paradigm for inhibitor design. Proc Natl Acad Sci USA;94:13420-13425.
44. Shoichet B.K., McGovern S.L., Wei B., Irwin J.J. (2002) Lead discovery using molecular docking. Curr Opin Chem Biol;6:439-446.
45. Sarmiento M., Zhao Y., Gordon S.J., Zhang Z.-Y. (1998) Molecular basis for substrate specificity of protein-tyrosine phosphatase 1B. J Biol Chem;273:26368-26374.
46. Erickson J.A., Jalaie M., Robertson D.H., Lewis R.A., Vieth M. (2004) Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy. J Med Chem;47:45-55.
47. Murthy V.S., Kulkarni V.M. (2002) Molecular modeling of protein tyrosine phosphatase 1B (PTP 1B) inhibitors. Bioorg Med Chem;10:897-906.