Bulletin of the Korean Chemical Society

  • 제28권7호
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  • Pages.1141-1150
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  • 2007
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  • 0253-2964(pISSN)
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  • 1229-5949(eISSN)
대한화학회 (Korean Chemical Society)
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Docking Studies on Formylchromone Derivatives as Protein Tyrosine Phosphatase 1B (PTP1B) Inhibitors

  • 발행 : 2007.07.20
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초록

Molecular modeling study has been performed to assist in the design of PTP1B inhibitors using FlexX. FlexX dockings with 19 test ligands, whose structures have been determined by X-ray crystallography, were successful in reproducing the experimental conformations within the protein. An increase in biological activity is observed as hydrophobic character of formylchromone derivatives increases. Most ligands bind to the activesite regions of the protein successfully in two different score runs. The Drug score run gave better results than the FlexX score run based on the score, rank, binding modes and bond distance of docked structures. Consensus values from the CScore scoring function are between 3 and 5, suggesting that the scoring scheme is reliable. All formylchromone inhibitors considered in this work show unidirectional binding modes in the active site pocket, which is contrary to the bidirectional X-ray results by Malamas et al. and amino acid residues responsible for such orientation are identified to help further development of the inhibitors.

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참고문헌

  1. Zhan, X.-L.; Wishart, M. J.; Guan, K.-L. Chem. Rev. 2001, 101, 2477
  2. Ostman, A.; Böhmer, F. D. Trends Cell Biol. 2001, 11, 258 https://doi.org/10.1016/S0962-8924(01)01990-0
  3. Cohen, P. Trends Biochem. Sci. 2000, 25, 596 https://doi.org/10.1016/S0968-0004(00)01712-6
  4. Neel, B. G.; Tonks, N. K. Curr. Opin. Cell Biol. 1997, 9, 193 https://doi.org/10.1016/S0955-0674(97)80063-4
  5. Tonks, N. K.; Neel, B. G. Curr. Opin. Cell Biol. 2001, 13, 182 https://doi.org/10.1016/S0955-0674(00)00196-4
  6. Denu, J. M.; Dixon, J. E. Curr. Biol. 1998, 2, 633 https://doi.org/10.1016/S1367-5931(98)80095-1
  7. Zhang, Z.-Y. Curr. Opin. Chem. Biol. 2001, 5, 416
  8. Van Huijsduijnen, R. H.; Bombrun, A.; Swinnen, D. Drug Discov. Today 2002, 7, 1013 https://doi.org/10.1016/S1359-6446(02)02438-8
  9. Li, L.; Dixon, J. E. Semin. Immunol. 2000, 12, 75 https://doi.org/10.1006/smim.2000.0209
  10. Tonks, N. K.; Charbonneau, H.; Diltz, C. D.; Fischer, E. H.; Walsh, K. A. Biochemistry 1998, 27, 8695 https://doi.org/10.1021/bi00424a001
  11. Lander, E. S.; Linton, L. M.; Birren, B.; Nusbaum, C.; Zody, M. C.; Baldwin, J.; Devon, K.; Dewar, K.; Doyle, M.; FitzHugh, W.; Funke, R.; Gage, D.; Harris, K.; Heaford, A.; Howland, J.; Kann, L.; Lehoczky, J.; LeVine, R.; McEwan, P.; McKernan, K.; Meldrim, J.; Mesirov, J. P.; Miranda, C.; Morris, W.; Naylor, J.; Raymond, C.; Rosetti, M.; Santos, R.; Sheridan, A.; Sougnez, C.; Stange-Thomann, N.; Stojanovic, N.; Subramanian, A.; Wyman, D.; Rogers, J.; Sulston, J.; Ainscough, R.; Beck, S.; Bentley, D.; Burton, J.; Clee, C.; Carter, N.; Coulson, A.; Deadman, R.; Deloukas, P.; Dunham, A.; Dunham, I.; Durbin, R.; French, L.; Grafham, D.; Gregory, S.; Hubbard, T.; Humphray, S.; Hunt, A.; Jones, M.; Lloyd, C.; McMurray, A.; Matthews, L.; Mercer, S.; Milne, S.; Mullikin, J. C.; Mungall, A.; Plumb, R.; Ross, M.; Shownkeen, R.; Sims, S.; Waterston, R. H.; Wilson, R. K.; Hillier, L. W.; McPherson, J. D.; Marra, M. A.; Mardis, E. R.; Fulton, L. A.; Chinwalla, A. T.; Pepin, K. H.; Gish, W. R.; Chissoe, S. L.; Wendl, M. C.; Delehaunty, K. D.; Miner, T. L.; Delehaunty, A.; Kramer, J. B.; Cook, L. L.; Fulton, R. S.; Johnson, D. L.; Minx, P. J.; Clifton, S. W.; Hawkins, T.; Branscomb, E.; Predki, P.; Richardson, P.; Wenning, S.; Slezak, T.; Doggett, N.; Cheng, J. F.; Olsen, A.; Lucas, S.; Elkin, C.; Uberbacher, E.; Frazier, M.; Gibbs, R. A.; Muzny, D. M.; Scherer, S. E.; Bouck, J. B.; Sodergren, E. J.; Worley, K. C.; Rives, C. M.; Gorrell, J. H.; Metzker, M. L.; Naylor, S. L.; Kucherlapati, R. S.; Nelson, D. L.; Weinstock, G. M.; Sakaki, Y.; Fujiyama, A.; Hattori, M.; Yada, T.; Toyoda, A.; Itoh, T.; Kawagoe, C.; Watanabe, H.; Totoki, Y.; Taylor, T.; Weissenbach, J.; Heilig, R.; Saurin, W.; Artiguenave, F.; Brottier, P.; Bruls, T.; Pelletier, E.; Robert, C.; Wincker, P.; Smith, D. R.; Doucette-Stamm, L.; Rubenfield, M.; Weinstock, K.; Lee, H. M.; Dubois, J.; Rosenthal, A.; Platzer, M.; Nyakatura, G.; Taudien, S.; Rump, A.; Yang, H.; Yu, J.; Wang, J.; Huang, G.; Gu, J.; Hood, L.; Rowen, L.; Madan, A.; Qin, S.; Davis, R. W.; Federspiel, N. A.; Abola, A. P.; Proctor, M. J.; Myers, R. M.; Schmutz, J.; Dickson, M.; Grimwood, J.; Cox, D. R.; Olson, M. V.; Kaul, R.; Raymond, C.; Shimizu, N.; Kawasaki, K.; Minoshima, S.; Evans, G. A.; Athanasiou, M.; Schultz, R.; Roe, B. A.; Chen, F.; Pan, H.; Ramser, J.; Lehrach, H.; Reinhardt, R.; McCombie, W. R.; de la Bastide, M.; Dedhia, N.; Blocker, H.; Hornischer, K.; Nordsiek, G.; Agarwala, R.; Aravind, L.; Bailey, J. A.; Bateman, A.; Batzoglou, S.; Birney, E.; Bork, P.; Brown, D. G.; Burge, C. B.; Cerutti, L.; Chen, H. C.; Church, D.; Clamp, M.; Copley, R. R.; Doerks, T.; Eddy, S. R.; Eichler, E. E.; Furey, T. S.; Galagan, J.; Gilbert, J. G.; Harmon, C.; Hayashizaki, Y.; Haussler, D.; Hermjakob, H. Nature 2001, 409, 860
  12. Zick, Y. Trends Cell Biol. 2001, 11, 437 https://doi.org/10.1016/S0962-8924(01)02129-8
  13. Bailey, C. J. Biochem. Pharm. 1999, 58, 1511 https://doi.org/10.1016/S0006-2952(99)00191-4
  14. Taylor, S. I. Cell 1999, 97, 9 https://doi.org/10.1016/S0092-8674(00)80709-6
  15. Kido, Y.; Burks, D. J.; Withers, D.; Bruning, J. C.; Kahn, C. R.; White, M. F. J. Clinical Invest. 2000, 105, 199 https://doi.org/10.1172/JCI7917
  16. Cheng, A.; Dube, N.; Gu, F.; Tremblay, M. L. Eur. J. Biochem. 2002, 269, 1050 https://doi.org/10.1046/j.0014-2956.2002.02756.x
  17. Elchebly, M.; Payette, P.; Michaliszyn, E.; Cromlish, W.; Collins, S.; Loy, A. L.; Normandin, D.; Cheng, A.; Himms-Hagen, J.; Chan, C. C.; Ramachandran, C.; Gresser, M. J.; Tremblay, M. L.; Kennedy, B. P. Science 1999, 283, 1544
  18. Klaman, L. D.; Boss, O.; Peroni, O. D.; Kim, J. K.; Martino, J. L.; Zabotny, J. M.; Moghal, N.; Lubkin, M.; Kim, Y.-B.; Sharpe, A. H.; Stricket- Krongrad, A.; Shulman, G. I.; Neel, B. G.; Kahn, B. B. Mol. Cell. Biol. 2000, 20, 5479
  19. Zinker, B. A.; Rondinone, C. M.; Trevillyan, J. M.; Gum, R. J.; Clampit, J. E.; Waring, J. F.; Xie, N.; Wilcox, D.; Jacobson, P.; Frost, L.; Kroeger, P. E.; Reilly, R. M.; Koterski, S.; Opgenorth, T. J.; Ulrich, R. G.; Crosby, S.; Butler, M.; Murray, S. F.; Mckay, R. A.; Bhanot, S.; Monia, B. P.; Jirousek, M. R. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11357 https://doi.org/10.1073/pnas.142298199
  20. Rondinone, C. M.; Trevillyan, J. M.; Clampit, J.; Gum, R. J.; Berg, C.; Kroeger, P.; Frost, L.; Zinker, B. A.; Reilly, R.; Ulrich, R.; Butler, M.; Monia, B. P.; Jirousek, M. R.; Waring, J. F. Diabetes 2002, 51, 2405 https://doi.org/10.2337/diabetes.51.8.2405
  21. Ramachandran, C.; Kennedy, B. P. Curr. Top. Med. Chem. 2003, 3, 749 https://doi.org/10.2174/1568026033452276
  22. Lee, D. Y.; Hyun, K. H.; Park, H. Y.; Lee, B.-S.; Kim, C. K. Bull. Korean Chem. Soc. 2006, 27, 273 https://doi.org/10.5012/bkcs.2006.27.2.273
  23. Lee, I. Y.; Lee, K. A.; Lee, B.-S.; Chi, D. Y.; Kim, C. K. Bull Korean Chem. Soc. 2006, 27, 1969 https://doi.org/10.5012/bkcs.2006.27.12.1969
  24. Shim, Y. S.; Kim, K. C.; Chi, D. Y.; Lee, K.-H.; Cho, H. Bioorg. Med. Chem. Lett. 2003, 13, 2561 https://doi.org/10.1016/S0960-894X(03)00479-7
  25. Shim, Y. S.; Kim, K. C.; Lee, K. A.; Shrestha, S.; Lee, K.-H.; Kim, C. K.; Cho, H. Bioorg. Med. Chem. 2005, 13, 1325 https://doi.org/10.1016/j.bmc.2004.11.006
  26. Berman, H. M.; Wilson, I. B. J. Biol. Chem. 1962, 237, 3245
  27. PDB files are downloadable from http://www.rcsb.org/pdb
  28. Groves, M. R.; Yao, Z.-J.; Burke, T. R. Jr.; Barford, D. Biochemistry 1998, 37, 17773
  29. Andersen, H. S.; Iversen, L. F.; Jeppesen, C. B.; Branner, S.; Norris, K.; Rasmussen, H. B.; Moller, K. B.; Moller, N. P. J. Biol. Chem. 2000, 275, 7101 https://doi.org/10.1074/jbc.275.10.7101
  30. Iversen, L. F.; Andersen, H. S.; Branner, S.; Mortensen, S. B.; Peters, G. H.; Norris, K.; Olsen, O. H.; Jeppesen, C. B.; Lundt, B. F.; Ripka, W.; Moller, K. B.; Moller, N. P. J. Biol. Chem. 2000, 275, 10300 https://doi.org/10.1074/jbc.275.14.10300
  31. Iversen, L. F.; Andersen, H. S.; Moller, K. B.; Olsen, O. H.; Peters, G. H.; Branner, S.; Mortensen, S. B.; Hansen, T. K.; Lau, J.; Ge, Y.; Holsworth, D. D.; Newman, M. J.; Moller, N. P. Biochemistry 2001, 40, 14812 https://doi.org/10.1021/bi011389l
  32. Szczepankiewicz, B. G.; Liu, G.; Hajduk, P. J.; Abad-Zapatero, C.; Pei, Z.; Xin, Z.; Lubben, T.; Trevillyan, J. M.; Stashko, M. A.; Bballaron, S. J.; Liang, H.; Huang, F.; Hutchins, C. W.; Fesik, S. W.; Jirousek, M. R. J. Am. Chem. Soc. 2003, 125, 4087 https://doi.org/10.1021/ja0296733
  33. Liu, G.; Xin, Z.; Pei, Z.; Hajduk, P. J.; Abad-Zapatero, C.; Hutchins, C. W.; Zhao, H.; Lubben, T. H.; Ballaron, S. J.; Haasch, D. L.; Kaszubska, W.; Rondinone, C. M.; Trevillyan, J. M.; Jirousek, M. R. J. Med. Chem. 2003, 46, 4232 https://doi.org/10.1021/jm034122o
  34. Xin, Z.; Liu, G.; Abad-Zapatero, C.; Pei, Z.; Szczepankiewick, B. G.; Li, X.; Zhang, T.; Hutchins, C. W.; Hajduk, P. J.; Ballaron, S. J.; Stashko, M. A.; Lubben, T. H.; Trevillyan, J. M.; Jirousek, M. R. Bioorg. Med. Chem. Lett. 2003, 13, 3947 https://doi.org/10.1016/j.bmcl.2003.08.064
  35. Zhao, H.; Liu, G.; Xin, Z.; Serby, M.; Pei, Z.; Szczepankiewicz, B. G.; Hajduk, P. J.; Abad-Zapatero, C.; Hutchins, C. W.; Lubben, T. H.; Ballaron, S. J.; Hassach, D. L.; Kaszubska, W.; Rondinone, C. M.; Trevillyan, J. M.; Jirousek, M. R. Bioorg. Med. Chem. Lett. 2004, 14, 5543 https://doi.org/10.1016/j.bmcl.2004.08.063
  36. Groves, M. R.; Yao, Z. J.; Roller, P. P.; Jr Bruke, T. R.; Barford, D. Biochemistry 1998, 37, 17773 https://doi.org/10.1021/bi9816958
  37. Jia, Z.; Ye, Q.; Dinaut, A. N.; Wang, Q.; Waddleton, D.; Payette, P.; Ramachandran, C.; Kennedy, B.; Hum, G.; Taylor, S. D. J. Med. Chem. 2001, 44, 4584 https://doi.org/10.1021/jm010266w
  38. Scapin, G.; Patel, S. B.; Becker, J. W.; Wang, Q.; Desponts, C.; Waddleton, D.; Skorey, K.; Cromlish, W.; Bayly, C.; Therien, M.; Gauthier, J. Y.; Li, C. S.; Lau, C. K.; Ramachandran, C.; Kennedy, B. P.; Asante-Appiah, E. Biochemistry 2003, 42, 11451 https://doi.org/10.1021/bi035098j
  39. Kim, C. K.; Lee, K. A.; Hyun, K. H.; Park, H. J.; Kwack, I. Y.; Kim, C. K.; Lee, H. W.; Lee, B.-S. J. Comput. Chem. 2004, 25, 2073 https://doi.org/10.1002/jcc.20129
  40. Malamas, M. S.; Sredy, J.; Moxham, C.; Katz, A.; Xu, W.; McDevitt, R.; Adebayo, F. O.; Sawicki, D. R.; Seestaller, L.; Sullivan, D.; Taylor, J. R. J. Med. Chem. 2000, 43, 1293 https://doi.org/10.1021/jm990560c
  41. SYBYL 6.9; TRIPOS Inc.: St Louis, USA
  42. Powell, M. J. D. Mathematical Programming 1977, 12, 241 https://doi.org/10.1007/BF01593790
  43. Clark, M.; Crammer, R. D.; Opdenbosch, N. V. J. Comp. Chem. 1989, 10, 982 https://doi.org/10.1002/jcc.540100804
  44. Dixon, D. A.; Zeroka, D. J.; Wendoloski, J. J.; Wasserman, Z. R. J. Phys. Chem. 1985, 89, 5334 https://doi.org/10.1021/j100271a005
  45. Streitwieser, A. Molecular Orbital Theory for Organic Chemists; Wiley: NY, 1961
  46. Purcel, W. P.; Singer, J. A. J. Chem. Eng. Data 1967, 12, 235 https://doi.org/10.1021/je60033a020
  47. Hoffmann, D.; Kramer, B.; Washio, T.; Steinmetzer, T.; Rarey, M.; Lengauer, T. J. Med. Chem. 1999, 42, 4422 https://doi.org/10.1021/jm991090p
  48. Szczepankiewicz, B. G.; Liu, G.; Hajduk, P. J.; Abad-Zapater, C.; Pei, Z.; Xin, Z.; Lubben, T.; Trevillyan, J. M.; Stashko, M. A.; Ballaron, S. J.; Linag, H.; Huang, F.; Hutchins, C. W.; Fesik, S. W.; Jirousek, M. R. J. Am. Chem. Soc. 2003, 125, 4087 https://doi.org/10.1021/ja0296733
  49. Bohm, H. J. J. Comput. Aided Mol. Des. 1994, 8, 243 https://doi.org/10.1007/BF00126743
  50. Klebe, G. J. Mol. Biol. 1994, 237, 212 https://doi.org/10.1006/jmbi.1994.1223
  51. Gohlke, H.; Hendlich, M.; Klebe, G. J. Mol. Biol. 2000, 295, 337 https://doi.org/10.1006/jmbi.1999.3371
  52. Clark, R. D.; Strizhev, A.; Leonard, J. M.; Blake, F. F.; Matthew, J. B. J. Mol. Graph. Modelling 2002, 20, 281 https://doi.org/10.1016/S1093-3263(01)00125-5
  53. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. J. Mol. Biol. 1997, 267, 727 https://doi.org/10.1006/jmbi.1996.0897
  54. Muegge, I.; Martin, Y. C.; Hajduk, P. J.; Fesik, S. W. J. Med. Chem. 1999, 42, 2398
  55. Kuntz, I. D.; Blaney, J. M.; Oatley, S. J.; Langridge, R. L.; Ferrin, T. E. J. Mol. Biol. 1982, 161, 269 https://doi.org/10.1016/0022-2836(82)90153-X
  56. Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. J. Compt. Aided Mol. Des. 1997, 11, 425 https://doi.org/10.1023/A:1007996124545
  57. Connolly, M. L. J. Appl. Crystallogr. 1983, 16, 548 https://doi.org/10.1107/S0021889883010985
  58. Lorensen, W.; Cline, H. Computer Graphics 1987, 21, 163 https://doi.org/10.1145/37402.37422
  59. Heiden, W.; Goetze, T.; Brickmann, J. J. Comput. Chem. 1993, 14, 246 https://doi.org/10.1002/jcc.540140212

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