Distinct functional and conformational states of the human lymphoid tyrosine phosphatase catalytic domain can be targeted by choice of the inhibitor chemotype

Journal of Computer-Aided Molecular Design

Volumn 25, Issue 9, 2011, Pages 873-883

  Vidović, Dušica ^a   Xie, Yuli ^b   Rinderspacher, Alison ^b   Deng, Shi Xian ^b   Landry, Donald W ^b   Chung, Caty ^a   Smith, Deborah H ^b   Tautz, Lutz ^c   Schürer, Stephan C ^a,d  

^a UNIVERSITY OF MIAMI   (United States)

^b Och Spine at New York Presbyterian Hospitals   (United States)

^c BURNHAM INSTITUTE   (United States)

^d UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

Author keywords

Docking; Drug design; Homology modeling; LYP; Protein tyrosine phosphorylation; PTPN22

Indexed keywords

AMINO ACIDS; BINDING ENERGY; BINDING SITES; CONFORMATIONS; QUALITY CONTROL;

CHEMOTYPES; DOCKING; DRUG DESIGN; FUNCTIONAL STATE; HOMOLOGY MODELING; LYMPHOID TYROSINE PHOSPHATASE; PROTEIN TYROSINE PHOSPHORYLATION; PROTEIN-TYROSINE PHOSPHATASE; PTPN22; TYROSINE PHOSPHATASE;

PHOSPHATASES;

ASPARTIC ACID; BENZOFURAN SALICYLIC ACID INHIBITOR; LYMPHOID TYROSINE PHOSPHATASE; PROTEIN TYROSINE PHOSPHATASE; PROTEIN TYROSINE PHOSPHATASE INHIBITOR; THIAZOLIDINEDIONE INHIBITOR; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVATION; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME CONFORMATION; ENZYME INACTIVATION; ENZYME STABILITY; MOLECULAR DOCKING; MOLECULAR MODEL; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN TARGETING; STRUCTURE ANALYSIS;

EID: 80054924896     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-011-9469-2     Document Type: Article

References (40)

1. T Hunter BM Sefton 1980 Transforming gene product of Rous sarcoma virus phosphorylates tyrosine Proc Natl Acad Sci USA 77 3 1311 1315 10.1073/pnas.77.3.1311 1:CAS:528:DyaL3cXhvFChtL0%3D (Pubitemid 10072278)
2. T Hunter 2000 Signaling-2000 and beyond Cell 100 1 113 127 10.1016/S0092-8674(00)81688-8 1:CAS:528:DC%2BD3cXks1Crtg%3D%3D
3. NK Tonks 1993 Introduction: protein tyrosine phosphatases Semin Cell Biol 4 6 373 377 10.1006/scel.1993.1044 1:CAS:528:DyaK2cXpvF2qsw%3D%3D
4. ZY Zhang 1998 Protein-tyrosine phosphatases: biological function, structural characteristics, and mechanism of catalysis Crit Rev Biochem Mol Biol 33 1 1 52 10.1080/10409239891204161 (Pubitemid 28124251)
5. P Cohen 2002 Protein kinases-the major drug targets of the twenty-first century? Nat Rev Drug Discov 1 4 309 315 10.1038/nrd773 1:CAS:528: DC%2BD38XivVGmtr8%3D (Pubitemid 37361447)
6. T Hunter 1995 Protein kinases and phosphatases: the yin and yang of protein phosphorylation and signaling Cell 80 2 225 236 10.1016/0092-8674(95) 90405-0 1:CAS:528:DyaK2MXjtlGnsrs%3D
7. NK Tonks 2006 Protein tyrosine phosphatases: from genes, to function, to disease Nat Rev Mol Cell Biol 7 11 833 846 10.1038/nrm2039 1:CAS:528: DC%2BD28XhtFSms77I (Pubitemid 44627477)
8. L Tautz M Pellecchia T Mustelin 2006 Targeting the PTPome in human disease Expert Opin Ther Targets 10 1 157 177 10.1517/14728222.10.1.157 1:CAS:528:DC%2BD28XotlGgsA%3D%3D (Pubitemid 43263273)
9. KL Guan JE Dixon 1991 Evidence for protein-tyrosine-phosphatase catalysis proceeding via a cysteine-phosphate intermediate J Biol Chem 266 26 17026 17030 1:CAS:528:DyaK3MXlsFekur4%3D (Pubitemid 21907901)
10. D Barford AJ Flint NK Tonks 1994 Crystal structure of human protein tyrosine phosphatase 1B Science 263 5152 1397 1404 10.1126/science.8128219 1:CAS:528:DyaK2cXjtFyhsLo%3D (Pubitemid 24137822)
11. Z Jia D Barford AJ Flint NK Tonks 1995 Structural basis for phosphotyrosine peptide recognition by protein tyrosine phosphatase 1B Science 268 5218 1754 1758 10.1126/science.7540771 1:CAS:528:DyaK2MXmsFCitrg%3D
12. S Cohen H Dadi E Shaoul N Sharfe CM Roifman 1999 Cloning and characterization of a lymphoid-specific, inducible human protein tyrosine phosphatase, Lyp Blood 93 6 2013 2024 1:CAS:528:DyaK1MXhvFSmurw%3D (Pubitemid 29128504)
13. A Gjorloff-Wingren M Saxena S Williams D Hammi T Mustelin 1999 Characterization of TCR-induced receptor-proximal signaling events negatively regulated by the protein tyrosine phosphatase PEP Eur J Immunol 29 12 3845 3854 10.1002/(SICI)1521-4141(199912)29:12<3845::AID-IMMU3845>3.0.CO;2-U 1:CAS:528:DyaK1MXotVehsr4%3D
14. JF Cloutier A Veillette 1999 Cooperative inhibition of T-cell antigen receptor signaling by a complex between a kinase and a phosphatase J Exp Med 189 1 111 121 10.1084/jem.189.1.111 1:CAS:528:DyaK1MXjs1Ogug%3D%3D (Pubitemid 29047031)
15. J Wu A Katrekar LA Honigberg AM Smith MT Conn J Tang D Jeffery K Mortara J Sampang SR Williams J Buggy JM Clark 2006 Identification of substrates of human protein-tyrosine phosphatase PTPN22 J Biol Chem 281 16 11002 11010 10.1074/jbc.M600498200 1:CAS:528:DC%2BD28XjsFWjsrY%3D (Pubitemid 43855523)
16. N Bottini L Musumeci A Alonso S Rahmouni K Nika M Rostamkhani J MacMurray GF Meloni P Lucarelli M Pellecchia GS Eisenbarth D Comings T Mustelin 2004 A functional variant of lymphoid tyrosine phosphatase is associated with type I diabetes Nat Genet 36 4 337 338 10.1038/ng1323 1:CAS:528:DC%2BD2cXis1ahsbw%3D (Pubitemid 38437254)
17. RJ Hill S Zozulya YL Lu K Ward M Gishizky B Jallal 2002 The lymphoid protein tyrosine phosphatase Lyp interacts with the adaptor molecule Grb2 and functions as a negative regulator of T-cell activation Exp Hematol 30 3 237 244 10.1016/S0301-472X(01)00794-9 1:CAS:528:DC%2BD38XhslWgtbw%3D (Pubitemid 34203730)
18. AB Begovich VE Carlton LA Honigberg SJ Schrodi AP Chokkalingam HC Alexander KG Ardlie Q Huang AM Smith JM Spoerke MT Conn M Chang SY Chang RK Saiki JJ Catanese DU Leong VE Garcia LB McAllister DA Jeffery AT Lee F Batliwalla E Remmers LA Criswell MF Seldin DL Kastner CI Amos JJ Sninsky PK Gregersen 2004 A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis Am J Hum Genet 75 2 330 337 10.1086/422827 1:CAS:528:DC%2BD2cXlvFehs74%3D (Pubitemid 38943877)
19. D Smyth JD Cooper JE Collins JM Heward JA Franklyn JM Howson A Vella S Nutland HE Rance L Maier BJ Barratt C Guja C Ionescu-Tirgoviste DA Savage DB Dunger B Widmer DP Strachan SM Ring N Walker DG Clayton RC Twells SC Gough JA Todd 2004 Replication of an association between the lymphoid tyrosine phosphatase locus (LYP/PTPN22) with type 1 diabetes, and evidence for its role as a general autoimmunity locus Diabetes 53 11 3020 3023 10.2337/diabetes.53.11. 3020 1:CAS:528:DC%2BD2cXpvV2iur4%3D (Pubitemid 39425931)
20. C Kyogoku CD Langefeld WA Ortmann A Lee S Selby VE Carlton M Chang P Ramos EC Baechler FM Batliwalla J Novitzke AH Williams C Gillett P Rodine RR Graham KG Ardlie PM Gaffney KL Moser M Petri AB Begovich PK Gregersen TW Behrens 2004 Genetic association of the R620 W polymorphism of protein tyrosine phosphatase PTPN22 with human SLE Am J Hum Genet 75 3 504 507 10.1086/423790 1:CAS:528:DC%2BD2cXnt1WgtLs%3D (Pubitemid 39095825)
21. T Vang M Congia MD Macis L Musumeci V Orru P Zavattari K Nika L Tautz K Tasken F Cucca T Mustelin N Bottini 2005 Autoimmune-associated lymphoid tyrosine phosphatase is a gain-of-function variant Nat Genet 37 12 1317 1319 10.1038/ng1673 1:CAS:528:DC%2BD2MXht1Ggsr%2FN (Pubitemid 41722185)
22. Y Xie Y Liu G Gong A Rinderspacher SX Deng DH Smith U Toebben E Tzilianos L Branden D Vidovic C Chung S Schurer L Tautz DW Landry 2008 Discovery of a novel submicromolar inhibitor of the lymphoid specific tyrosine phosphatase Bioorg Med Chem Lett 18 9 2840 2844 10.1016/j.bmcl.2008.03.079 1:CAS:528:DC%2BD1cXlvVWjs7w%3D (Pubitemid 351608878)
23. T Vang Y Xie WH Liu D Vidovic Y Liu S Wu DH Smith A Rinderspacher C Chung G Gong T Mustelin DW Landry RC Rickert SC Schurer SX Deng L Tautz 2011 Inhibition of lymphoid tyrosine phosphatase by benzofuran salicylic acids J Med Chem 54 2 562 571 10.1021/jm101004d 1:CAS:528:DC%2BC3cXhs1egu7rL
24. A Degterev A Lugovskoy M Cardone B Mulley G Wagner T Mitchison J Yuan 2001 Identification of small-molecule inhibitors of interaction between the BH3 domain and Bcl-xL Nat Cell Biol 3 2 173 182 10.1038/35055085 1:CAS:528:DC%2BD3MXht1KmsLY%3D (Pubitemid 32118371)
25. M Camps T Ruckle H Ji V Ardissone F Rintelen J Shaw C Ferrandi C Chabert C Gillieron B Francon T Martin D Gretener D Perrin D Leroy PA Vitte E Hirsch MP Wymann R Cirillo MK Schwarz C Rommel 2005 Blockade of PI3Kgamma suppresses joint inflammation and damage in mouse models of rheumatoid arthritis Nat Med 11 9 936 943 1:CAS:528:DC%2BD2MXpslelur8%3D (Pubitemid 41294438)
26. HM Albers A Dong LA van Meeteren DA Egan M Sunkara EW van Tilburg K Schuurman O van Tellingen AJ Morris SS Smyth WH Moolenaar H Ovaa 2010 Boronic acid-based inhibitor of autotaxin reveals rapid turnover of LPA in the circulation Proc Natl Acad Sci USA 107 16 7257 7262 10.1073/pnas.1001529107 1:CAS:528:DC%2BC3cXlsFWhsr0%3D
27. MC Wolf AN Freiberg T Zhang Z Akyol-Ataman A Grock PW Hong J Li NF Watson AQ Fang HC Aguilar M Porotto AN Honko R Damoiseaux JP Miller SE Woodson S Chantasirivisal V Fontanes OA Negrete P Krogstad A Dasgupta A Moscona LE Hensley SP Whelan KF Faull MR Holbrook ME Jung B Lee 2010 A broad-spectrum antiviral targeting entry of enveloped viruses Proc Natl Acad Sci USA 107 7 3157 3162 10.1073/pnas.0909587107 1:CAS:528:DC%2BC3cXis1Clu7c%3D
28. C Knox V Law T Jewison P Liu S Ly A Frolkis A Pon K Banco C Mak V Neveu Y Djoumbou R Eisner AC Guo DS Wishart 2011 DrugBank 3.0: a comprehensive resource for 'omics' research on drugs Nucleic Acids Res 39 Database issue D1035 D1041 10.1093/nar/gkq1126
29. X Yu JP Sun Y He X Guo S Liu B Zhou A Hudmon ZY Zhang 2007 Structure, inhibitor, and regulatory mechanism of Lyp, a lymphoid-specific tyrosine phosphatase implicated in autoimmune diseases Proc Natl Acad Sci USA 104 50 19767 19772 10.1073/pnas.0706233104 1:CAS:528:DC%2BD1cXitFSktQ%3D%3D
30. LigPrep (2009) Schrödinger LLC. Portland, OR
31. W Jorgensen J Tirado-Rives 1988 The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin J Am Chem Soc 110 6 1657 1666 10.1021/ja00214a001 1:CAS:528:DyaL1cXht1yjt7Y%3D
32. PJ Ala L Gonneville MC Hillman M Becker-Pasha M Wei BG Reid R Klabe EW Yue B Wayland B Douty P Polam Z Wasserman M Bower AP Combs TC Burn GF Hollis R Wynn 2006 Structural basis for inhibition of protein-tyrosine phosphatase 1B by isothiazolidinone heterocyclic phosphonate mimetics J Biol Chem 281 43 32784 32795 10.1074/jbc.M606873200 1:CAS:528:DC%2BD28XhtFSrtr3E (Pubitemid 46036834)
33. M Andrec Y Harano MP Jacobson RA Friesner RM Levy 2002 Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction J Struct Funct Genomics 2 2 103 111 10.1023/A:1020435630054 1:CAS:528:DC%2BD38XosValsb4%3D (Pubitemid 34975806)
34. MP Jacobson DL Pincus CS Rapp TJ Day B Honig DE Shaw RA Friesner 2004 A hierarchical approach to all-atom protein loop prediction Proteins 55 2 351 367 10.1002/prot.10613 1:CAS:528:DC%2BD2cXjtFKhsrc%3D (Pubitemid 38437493)
35. Maestro (2009) Schrödinger LLC. Portland, OR
36. RA Friesner JL Banks RB Murphy TA Halgren JJ Klicic DT Mainz MP Repasky EH Knoll M Shelley JK Perry DE Shaw P Francis PS Shenkin 2004 Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy J Med Chem 47 7 1739 1749 10.1021/jm0306430 1:CAS:528:DC%2BD2cXhsFyit74%3D (Pubitemid 38380917)
37. TA Halgren RB Murphy RA Friesner HS Beard LL Frye WT Pollard JL Banks 2004 Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening J Med Chem 47 7 1750 1759 10.1021/jm030644s 1:CAS:528:DC%2BD2cXhsFyit78%3D (Pubitemid 38380918)
38. DeLano WL (2009) PyMOL. Schrödinger LLC, Portland, OR
39. D Vidovic SC Schurer 2009 Knowledge-based characterization of similarity relationships in the human protein-tyrosine phosphatase family for rational inhibitor design J Med Chem 52 21 6649 6659 10.1021/jm9008899 1:CAS:528:DC%2BD1MXht1artL%2FP
40. AJ Barr E Ugochukwu WH Lee ON King P Filippakopoulos I Alfano P Savitsky NA Burgess-Brown S Muller S Knapp 2009 Large-scale structural analysis of the classical human protein tyrosine phosphatome Cell 136 2 352 363 10.1016/j.cell.2008.11.038 1:CAS:528:DC%2BD1MXhs1Kiu7o%3D