Toward a molecular understanding of the interaction of dual specificity phosphatases with substrates: Insights from structure-based modeling and high throughput screening

Current Medicinal Chemistry

Volumn 15, Issue 25, 2008, Pages 2536-2544

  Bakan, Ahmet ^a   Lazo, John S ^a,b   Wipf, Peter ^b   Brummond, Kay M ^b   Bahar, Ivet ^a,b  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

Computer aided drug discovery; Dual specificity phosphatases; Focused library design; High throughput screening; Intrinsic dynamics; Molecular docking; Structure based virtual screening

Indexed keywords

2,3 BIS(2 HYDROXYETHYLSULFANYL)[1,4]NAPHTHOQUINONE; CYCLIN DEPENDENT KINASE 2; MITOGEN ACTIVATED PROTEIN KINASE; MITOGEN ACTIVATED PROTEIN KINASE 1 INHIBITOR; MITOGEN ACTIVATED PROTEIN KINASE 3 INHIBITOR; MITOGEN ACTIVATED PROTEIN KINASE INHIBITOR; NSC 95397; PROTEIN TYROSINE PHOSPHATASE; PROTEIN TYROSINE PHOSPHATASE 1B; PROTEIN TYROSINE PHOSPHATASE B; PROTEIN TYROSINE PHOSPHATASE INHIBITOR; UNCLASSIFIED DRUG; DUAL SPECIFICITY PHOSPHATASE; ENZYME INHIBITOR; MITOGEN ACTIVATED PROTEIN KINASE PHOSPHATASE 1;

AMINO TERMINAL SEQUENCE; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; CELL DIVISION; COMPUTER MODEL; CONFORMATIONAL TRANSITION; DRUG MECHANISM; DRUG SCREENING; DRUG STRUCTURE; DRUG TARGETING; ENTHALPY; ENTROPY; ENZYME ACTIVATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME BINDING; ENZYME CONFORMATION; ENZYME INHIBITION; ENZYME STRUCTURE; ENZYME SUBSTRATE; GENE MUTATION; HIGH THROUGHPUT SCREENING; HUMAN; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; NEOPLASM; PROTEIN DEPHOSPHORYLATION; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; REVIEW; SCORING SYSTEM; SEQUENCE ALIGNMENT; ALGORITHM; AMINO ACID SEQUENCE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMBINATORIAL CHEMISTRY; DRUG ANTAGONISM; ENZYME SPECIFICITY; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; PROTEIN CONFORMATION; STRUCTURE ACTIVITY RELATION;

ALGORITHMS; AMINO ACID SEQUENCE; BINDING SITES; CDC25 PHOSPHATASES; COMBINATORIAL CHEMISTRY TECHNIQUES; DRUG EVALUATION, PRECLINICAL; DUAL SPECIFICITY PHOSPHATASE 1; DUAL-SPECIFICITY PHOSPHATASES; ENZYME INHIBITORS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY;

EID: 58149250722     PISSN: 09298673     EISSN: None     Source Type: Journal    
DOI: 10.2174/092986708785909003     Document Type: Review

References (86)

1. Ducruet, A.P.; Vogt, A.; Wipf, P.; Lazo, J.S. Annu. Rev. Pharmacol. Toxicol., 2005, 45, 725.
2. Tonks, N.K. Nat. Rev. Mol. Cell Biol., 2006, 7, 833.
3. Alonso, A.; Sasin, J.; Bottini, N.; Friedberg, I.; Friedberg, I.; Osterman, A.; Godzik, A.; Hunter, T.; Dixon, J.; Mustelin T. Cell, 2004, 117, 699.
4. Boutros, R.; Lobjois, V.; Ducommun, B. Nat. Rev. Cancer, 2007, 7, 495.
5. Denu, J.M.; Dixon, J.E. Curr. Opin. Chem. Biol., 1998, 2, 633.
6. Vogt, A.; Tamewitz, A.; Skoko, J.; Sikorski, R.P.; Giuliano, K.A.; Lazo, J.S. J. Biol. Chem., 2005, 280, 19078.
7. Brisson, M.; Foster, C.; Wipf, P.; Joo, B.; Tomko, R.J.Jr; Nguyen, T.; Lazo, J.S. Mol. Pharmacol., 2006, 71, 184.
8. Lazo, J.S.; Aslan, D.C.; Southwick, E.C.; Cooley, K.A.; Ducruet, A.P.; Joo, B.; Vogt, A.; Wipf, P. J. Med. Chem., 2001, 44, 4042.
9. Lazo, J.S.; Nemoto, K.; Pestell, K.E.; Cooley, K.; Southwick, E.C.; Mitchell, D.A.; Furey, W.; Gussio, R.; Zaharevitz, D.W.; Joo, B.; Wipf, P. Mol. Pharmacol., 2002, 61, 720.
10. Vogt, A.; Cooley, K.A.; Brisson, M.; Tarpley, M.G.; Wipf, P.; Lazo, J. S. Chem. Biol., 2003, 10, 733.
11. Brisson, M.; Nguyen, T.; Vogt, A.; Yalowich, J.; Giorgianni, A.; Tobi, D.; Bahar, I.; Stephenson, C.R.; Wipf, P.; Lazo, J.S. Mol. Pharmacol., 2004, 66, 824.
12. Lazo, J.S.; Nunes, R.; Skoko, J.J.; Queiroz de Oliveira, P.E.; Vogt, A.; Wipf, P. Bioorg. Med. Chem., 2006, 14, 5643.
13. Wishart, D.S.; Knox, C.; Guo, A.C.; Cheng, D.; Shrivastava, S.; Tzur, D.; Gautam, B.; Hassanali. M. Nucleic Acids Res., 2008, 36, D901.
14. Thomas, P.D.; Campbell, M.J.; Kejariwal, A.; Mi, H.; Karlak, B.; Daverman, R.; Diemer, K.;, Muruganujan, A.; Narechania, A. Genome Res., 2003, 13, 2129.
15. Jorgensen, W.L. Science, 2004, 303, 1813.
16. Shoichet, B.K; McGovern, S.L.; Wei, B.; Irwin, J.J. Cur. Opin. Chem. Biol., 2002, 6, 439.
17. Puius, Y.A.; Zhao, Y.; Sullivan, M.; Lawrence, D.S.; Almo, S.C.; Zhang, Z.Y. Proc. Natl. Acad. Sci. USA, 1997, 94, 13420.
18. Bramson, H.N.; Corona, J.; Davis, S.T.; Dickerson, S.H.; Edelstein, M.; Frye, S.V.; Gampe, R.T.Jr; Harris, P.A.; Hassell, A.; Holmes, W.D.; Hunter, R.N.; Lackey, K.E.; Lovejoy, B.; Luzzio, M.J.; Montana, V.; Rocque, W.J.; Rusnak, D.; Shewchuk, L.; Veal, J.M.; Walker, D.H.; Kuyper, L.F. J. Med. Chem., 2001, 44, 4339.
19. Nilsson, I.; Hoffmann, I. Prog. Cell Cycle Res., 2000, 4, 107.
20. Karlsson-Rosenthal, C.; Millar, J.B. Trends Cell Biol., 2006, 16, 285.
21. Kristjánsdóttir, K.; Rudolph, J. Chem. Biol., 2004, 11, 1043.
22. Ngan, E.S.; Hashimoto, Y.; Ma, Z.Q.; Tsai, M.J.; Tsai, S.Y. Oncogene, 2003, 22, 734.
23. Ma, Z.Q.; Chua, S.S.; DeMayo, F.J.; Tsai, S.Y. Oncogene, 1999, 18, 4564.
24. Fauman, E.B.; Cogswell, J.P.; Lovejoy, B.; Rocque, W.J.; Holmes, W.; Montana, V.G.; Piwnica-Worms, H.; Rink, M.J.; Saper, M.A. Cell, 1998, 93, 617.
25. Reynolds, R.A.; Yem, A.W.; Wolfe, C.L.; Deibel Jr., M.R.; Chidester, C.G.; Watenpaugh, K.D. J. Mol. Biol., 1999, 293, 559.
26. Sohn, J.; Buhrman, G.; Rudolph, J. Biochemistry, 2007, 46, 807.
27. Buhrman, G.K.; Parker, B.; Sohn, J.; Rudolph, J.; Mattos, C. Biochemistry, 2005, 44, 5307.
28. Lyon, M.A.; Ducruet, A.P.; Wipf, P.; Lazo, J.S. Nat. Rev. Drug. Discov., 2002, 1, 961.
29. Contour-Galcera, M.O.; Sidhu, A.; Prévost, G.; Bigg, D.; Ducommun, B. Pharmacol. Ther., 2007, 115, 1.
30. Tautz, L.; Mustelin, T. Methods, 2007, 42, 250.
31. González-Ruiz, D.; Gohlke, H. Curr. Med. Chem., 2006, 13, 2607.
32. Wells, J.A.; McClendon, C.L. Nature, 2007, 450, 1001.
33. Sohn, J.; Kristjánsdóttir, K.; Safi, A.; Parker, B.; Kiburz, B.; Rudolph, J. Proc. Natl. Acad. Sci. U.S.A., 2004, 101, 16437.
34. Sohn, J.; Parks, J.M.; Buhrman, G.; Brown, P.; Kristjánsdóttir, K.; Safi, A.; Edelsbrunner, H.; Yang, W.; Rudolph, J. Biochemistry, 2005, 44, 16563.
35. McConkey, B.J.; Sobolev, V.; Edelman, M. Bioinformatics, 2002, 18, 1365.
36. Theodosiou, A.; Ashworth, A. Genome Biology, 2002, 3, 1.
37. Jeffrey, K.L.; Camps, M.; Rommel, C.; Mackay, C.R. Nat. Rev. Drug. Discov., 2007, 6, 391.
38. Camps, M.; Nichols, A.; Arkinstall, S. FASEB J., 2000, 14, 6.
39. Wu, G.S. Cancer Metastasis Rev., 2007, 26, 579.
40. Wang, H.Y.; Cheng, Z.; Malbon, C.C. Cancer Lett., 2003, 191, 229.
41. Vicent, S.; Garayoa, M.; López-Picazo, J.M.; Lozano, M.D.; Toledo, G.; Thunnissen, F.B.; Manzano, R.G.; Montuenga, L.M. Clin. Cancer Res., 2004, 10, 3639.
42. Chen, H.Y.; Yu, S.L.; Chen, C.H.; Chang, G.C.; Chen, C.Y.; Yuan, A.; Cheng, C.L.; Wang, C.H.; Terng, H.J.; Kao, S.F.; Chan, W.K.; Li, H.N.; Liu, C.C.; Singh, S.; Chen, W.J.; Chen, J.J.; Yang, P.C. N. Engl. J. Med., 2007, 356, 11.
43. Furukawa, T.; Sunamura, M.; Motoi, F.; Matsuno, S.; Horii, A. Am. J. Pathol., 2003, 162, 1807.
44. Farooq, A.; Zhou, M.M. Cell Signal., 2004, 16, 769.
45. Stewart, A.E.; Dowd, S.; Keyse, S.; Mcdonald, N.Q. Nat. Struct. Biol., 1999, 6, 174.
46. Farooq, A.; Plotnikova, O.; Chaturvedi, G.; Yan, S.; Zeng, L.; Zhang, Q.; Zhou, M.-M. Structure, 2003, 11, 155.
47. Jeong, D.G.; Yoon, T.S.; Kim, J.H.; Shim, M.Y.; Jeong, S.K.; Son, J.H.; Ryu, S.E.; Kim, S.J. J. Mol. Biol., 2006, 360, 946.
48. Jeong, D.G.; Cho, Y.H.; Yoon, T.S.; Kim, J.H.; Ryu, S.E.; Kim, S.J. Proteins, 2007, 66, 253.
49. Bahar, I.; Chennubhotla, C.; Tobi, D. Curr. Opin. Struct. Biol., 2007, 17, 633.
50. Farooq, A.; Chaturvedi, G.; Mujtaba, S.; Plotnikova, O.; Zeng, L.; Dhalluin, C.; Ashton, R.; Zhou, M.M. Mol. Cell, 2001, 7, 387.
51. Tao, X.; Tong, L. Protein Sci., 2007, 16, 880.
52. Hutter, D.; Chen, P.; Barnes, J.; Liu, Y. Biochem. J., 2000, 352, 155.
53. Camps, M.; Nichols, A.; Gillieron, C.; Antonsson, B.; Muda, M.; Chabert, C.; Boschert, U.; Arkinstall, S. Science, 1998, 280, 1262.
54. Zhang, Q.; Muller, M.; Chen, C.H.; Zeng, L.; Farooq, A.; Zhou, M.M. J. Mol. Biol., 2005, 354, 777.
55. Wiesmann, C.; Barr, K.J.; Kung, J.; Zhu, J.; Erlanson, D.A.; Shen, W.; Fahr, B.J.; Zhong, M.; Taylor, L.; Randal, M.; McDowell, R.S.; Hansen, S.K. Nat. Struct. Mol. Biol., 2004, 11, 730.
56. Liu, S.; Sun, J.P.; Zhou, B.; Zhang, Z.Y. Proc. Natl. Acad. Sci. USA, 2006, 103, 5326.
57. Zhou, B.; Wu, L.; Shen, K.; Zhang, J.; Lawrence, D.S.; Zhang, Z.Y. J. Biol. Chem., 2001, 276, 6506.
58. Zhou, B.; Zhang, J.; Liu, S.; Reddy, S.; Wang, F.; Zhang, Z.Y. J. Biol. Chem., 2006, 281, 38834.
59. Brooijmans, N.; Kuntz, I.D. Annu. Rev. Biophys. Biomol. Struct., 2003, 32, 335.
60. Sousa, S.F.; Fernandes, P.A.; Ramos, M.J. Proteins, 2006, 65, 15.
61. Warren, G.L.; Andrews, C.W.; Capelli, A.M.; Clarke, B.; LaLonde, J.; Lambert, M.H.; Lindvall, M.; Nevins, N.; Semus, S.F.; Senger, S.; Tedesco, G.; Wall, I.D.; Woolven, J.M.; Peishoff, C.E.; Head, M.S. J. Med. Chem., 2006, 49, 5912.
62. Leach, A.R.; Shoichet, B.K.; Peishoff, C.E. J. Med. Chem., 2006, 49, 5851.
63. Brem, R.; Dill, K.A. Protein Sci., 1999, 8, 1134.
64. Totrov, M.; Abagyan, R. Curr. Opin. Struct. Biol., 2008, 18, 178.
65. Gilson, M.K.; Given, J.A.; Head, M.S. Chem. Biol., 1997, 4, 87.
66. Chang, C.E.; Chen, W.; Gilson, M.K. Proc. Natl. Acad. Sci. USA, 2007, 104, 1534.
67. Mobley, D.L.; Graves, A.P.; Chodera, J.D.; McReynolds, A.C.; Shoichet, B.K.; Dill, K.A. J. Mol. Biol., 2007, 371, 1118.
68. Ruvinsky, A.M. J. Comput. Aided. Mol. Des., 2007, 21, 361.
69. Prasad, J C.; Goldstone, J.V.; Camacho, C.J.; Vajda, S.; Stegeman, J.J. Biochemistry, 2007, 46, 2640.
70. Carlson, H.A.; McCammon, J.A. Mol. Pharmacol., 2000, 57, 213.
71. Cavasotto, C.N.; Abagyan, R.A. J. Mol. Biol., 2004, 337, 209.
72. Cavasotto, C.N.; Kovacs, J.A.; Abagyan R.A. J. Am. Chem. Soc, 2005, 127, 9632.
73. Cui, Q.; Bahar, I. Normal mode analysis. Theory and applications to biological and chemical systems, Chapman & Hall/CRC, 2006.
74. Henzler-Wildman, K.A.; Thai, V.; Lei, M.; Ott, M.; Wolf-Watz, M.; Fenn, T.; Pozharski, E.; Wilson, M.A.; Petsko, G.A.; Karplus, M.; Hübner, C.G.; Kern, D. Nature, 2007, 450, 838.
75. Henzler-Wildman, K.A.; Lei, M.; Thai, V.; Kerns, S.J.; Karplus, M.; Kern, D. Nature, 2007, 450, 913.
76. Floquet, N.; Marechal, J.D.; Badet-Denisot, M.A.; Robert, C.H.; Dauchez, M.; Perahia, D. FEBS Lett., 2006, 580, 5130.
77. Lavecchia, A.; Cosconati, S.; Limongelli, V.; Novellino, E. Chem. Med. Chem., 2006, 1, 540.
78. Park, H.; Carr, B.I.; Li, M.; Ham, S.W. Bioorg. Med. Chem. Lett., 2007, 17, 2351.
79. Montes, M.; Braud, E.; Miteva, M.A.; Goddard, M.L.; Mondésert, O.; Kolb, S.; Brun, M.P.; Ducommun, B.; Garbay, C.; Villoutreix, B.O. J. Chem. Inf. Model., 2007, 48, 157.
80. Werner, S.; Iyer, P.S.; Fodor, M.D.; Coleman, C.M.; Twining, L.A.; Mitasev, B. Brummond, K.M. J. Comb. Chem., 2006, 8, 368.
81. Lazo, J.S.; Skoko, J.J.; Werner, S.; Mitasev, B.; Bakan, A.; Koizumi, F.; Yellow-Duke, A.; Bahar, I.; Brummond, K.M. J. Pharmacol. Exp. Ther., 2007, 322, 940.
82. Morris, G.M.; Goodsell, D.S.; Halliday, R.S.; Huey, R.; Hart, W.E.; Belew, R.K.; Olson, A.J. J. Comp. Chem., 1998, 19, 1639.
83. Sali, A.; Blundell, T.L. J. Mol. Biol., 1993, 234, 779.
84. Jones, G.; Willett, P.; Glen, R.C.; Leach, A.R.; Taylor, R. J. Mol. Biol., 1997, 267, 727.
85. Bialy, L.; Waldmann, H. Angew. Chem. Int. Ed., 2005, 44, 3814.
86. Tautz, T.; Pellecchia, M; Mustelin, T. Expert Opin. Ther. Targets, 2006, 10, 157.