In silico prediction and screening of γ-secretase inhibitors by molecular descriptors and machine learning methods

Journal of Computational Chemistry

Volumn 31, Issue 6, 2010, Pages 1249-1258

  Yang, Xue Gang ^a   Wei, L V ^a   Chen, Y U Zong ^b,c   Ying, X U E ^a,b  

^a Sichuan University   (China)

^b SICHUAN UNIVERSITY   (China)

^c NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

secretase inhibitors; Machine learning; Random forest (rf); Support vector machine (svm); Virtual screening

Indexed keywords

ALZHEIMER'S DISEASE; DEVELOPED MODEL; FEATURE SELECTION METHODS; IN-SILICO; INCOMPLETE KNOWLEDGE; MACHINE LEARNING METHODS; MACHINE-LEARNING; MOLECULAR DESCRIPTORS; OPTIMAL THRESHOLD; PHYSICOCHEMICAL FEATURES; PREDICTION ACCURACY; QUANTITATIVE ANALYSIS; RANDOM FORESTS; RECEIVER OPERATING CHARACTERISTIC CURVES; ROC CURVES; SECRETASES; THERAPEUTIC AGENTS; THREE-DIMENSIONAL STRUCTURE; TWO MACHINES; VIRTUAL SCREENING;

CURVE FITTING; FEATURE EXTRACTION; FORECASTING; LEARNING ALGORITHMS; SUPPORT VECTOR MACHINES; ZINC;

MACHINE DESIGN;

ENZYME INHIBITOR; SECRETASE;

ALZHEIMER DISEASE; ARTICLE; ARTIFICIAL INTELLIGENCE; BIOLOGICAL MODEL; CHEMISTRY; DRUG ANTAGONISM; ENZYMOLOGY; HUMAN; METABOLISM; STRUCTURE ACTIVITY RELATION;

ALZHEIMER DISEASE; AMYLOID PRECURSOR PROTEIN SECRETASES; ARTIFICIAL INTELLIGENCE; ENZYME INHIBITORS; HUMANS; MODELS, BIOLOGICAL; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 77950570306     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21411     Document Type: Article

References (73)

1. Mount, C.; Downton, C. Nat Med 2006, 12, 780.
2. Takahashi, Y.; Fuwa, H.; Raneko, A.; Sasaki, M.; Yokoshima, S.; Koizumi, H.; Takebe, T.; Kan, T.; Iwatsubo, T.; Tomita, T.; Natsugari, H.; Fukuyama, T. Bioorg Med Chem Lett 2006, 16, 3813.
3. Blennow, K.; De Leon, M. J.; Zetterberg, H. Lancet 2006, 368, 387.
4. Selkoe, D. J. Ann Intern Med 2004, 140, 627.
5. Guo, T.; Gu, H. Z.; Hobbs, D. W.; Rokosz, L. L.; Stauffer, T. M.; Jacob, B.; Clader, J. W. Bioorg Med Chem Lett 2007, 17, 3010.
6. Hardy, J.; Selkoe, D. J. Science 2002, 297, 353.
7. Lundkvist, J.; Näslund, J. Curr Opin Pharmacol 2007, 7, 112.
8. Wolfe, M. S. J Med Chem 2001, 44, 2039.
9. Tomita, T. Naunyn-Schmiedeberg's Arch. Pharmacol 2008, 377, 295.
10. Mullarcl, A. Nat Rev Mol Cell Biol 2007, 8, 272.
11. Kimberly, W. T.; Lavoie, M. J.; Ostaszewsk!, B. L.; Ye, W.; Wolfe, M. S.; Selkoe, D. J. Proc Natl Acad Sci USA 2003, 100, 6382.
12. Takashima, A.; Shimojo, M.; Wolozin, B. Nat Med 2006, 12, 766.
13. Petit, A.; Bihel, F.; Da Costa, C. A.; Pourquié, O.; Checler, F.; Rraus, J. L. Nat Cell Biol 2001, 3, 507.
14. Peters, J. U.; Galley, G.; Jacobsen, H.; Czech, C.; David-Pierson, P.; Ritas, E. A.; Ozmen, L. Bioorg Med Chem Lett 2007, 17, 5918.
15. Josien, H.; Bara, T.; Rajagopalan, M., Asberom, T.; Clader, J. W.; Favreau, L.; Greenlee, W. J.; Hyde, L. A.; Nomeir, A. A.; Parker, E. M.; Pissarnitski, D. A.; Song, L. X.; Wong, G. T.; Zhang, L. L.; Zhang, Q.; Zhao, Z. Q. Bioorg Med Chem Lett 2007, 17, 5330.
16. Li, H. M.; Asberom, T.; Bara, T. A.; Clader, J. W.; Greenlee, W. J.; Josien, H. B.; Mcbriar, M. D.; Nomeir, A.; Pissarnitski, D. A.; Rajagopalan, M.; Xu, R.; Zhao, Z. Q.; Song, L. X.; Zhang, L. L. Bioorg Med Chem Lett 2007, 17, 6290.
17. Chen, Y. L.; Cherry, K., Corman, M. L.; Ebbinghaus, C. F.; Gamlath, C. B.; Liston, D.; Martin, B. A.; Oborski, C. E.; Sahagan, B. G. Bioorg Med Chem Lett 2007, 17, 5518.
18. Asberom, T.; Bara, T. A.; Clader, J. W.; Greenlee, W. J.; Guzik, H. S.; Josien, H. B.; Li, W.; Parker, E. M.; Pissarnitski, D. A.; Song, L. X.; Zhang, L. L.; Zhao, Z. Q. Bioorg Med Chem. Lett 2007, 17, 205.
19. Fuwa, H., Hiromoto, R.; Takahashi, Y.; Yokoshima, S.; Kan, T.; Fukuyama, T.; Iwatsubo, T.; Tomita, T.; Natsugari, H. Bioorg Med Chem Lett 2006, 16, 4184.
20. Teall, M.; Oakley, P.; Harrison, T.; Shaw, D.; Kay, E.; Elliott, J.; Gerhard, U.; Castro, J. L.; Shearman, M.; Ball, R. G.; Tsou, N. N. Bioorg Med Chem. Lett 2005, 15, 2685.
21. Shaw, D.; Best, J.; Dinnell, K.; Nadin, A.; Shearman, M.; Pattison, C.; Peachey, J.; Reilly, M.; Williams, B.; Wrigley, J.; Harrison, T. Bioorg Med Chem Lett 2006, 16, 3073.
22. Thompson, L. A.; Liauw, A. Y.; Ramanjulu, M. M.; KasireddyPolam, P.; Mercer, S. E.; Maduskuie, T. P.; Glicksman, M., Roach, A. H.; Meredith, J. E.; Liu, R. Q.; Combs, A. P.; Higaki, J. N.; Cordell, B.; Seiffert, D.; Zaczek, R. C.; Robertson, D. W.; Olson, R. E. Bioorg Med Chem. Lett 2006, 16, 2357.
23. Prasad, C. V. C.; Noonan, J. W.; Sloan, C. P.; Lau, W.; Vig, S.; Parker, M. F.; Smith, D. W.; Hansel, S. B.; Poison, C. T.; Barten, D. M.; Felsenstein, K. M.; Roberts, S. B. Bioorg Med Chem Lett 2004, 14, 1917.
24. Best, J. D.; Smith, D. W.; Reilly, M. A.; O'donneli, R.; Lewis, H. D.; Ellis, S.; Wilkie, N.; Rosahl, T. W.; Laroque, P. A.; BoussiquetLeroux, C.; Churcher, I.; Atack, J. R.; Harrison, T.; Shearman, M. S. J Pharmacol Exp Ther 2007, 320, 552.
25. Siemers, E. R.; Quinn, J. F.; Raye, J.; Farlow, M. R.; Porsteinsson, A.; Tariot, P.; Zoulnouni, P.; Galvin, J. E.; Holtzman, D. M.; Knopman, D. S.; Satterwhite, J.; Gonzales, C.; Dean, R. A.; May, P. C. Neurology 2006, 66, 602.
26. Hadland, B. K.; Manley, N. R.; Su, D.; Longmore, G. D.; Moore, C. L.; Wolfe, M. S.; Schroeter, E. H.; Kopan, R. Proc Natl Acad Sci USA 2001, 98, 7487.
27. Searfoss, G. H.; Jordan, W. H.; Calligaro, D. O.; Galbreath, E. J.; Schirtzinger, L. M.; Berridge, B. R.; Gao, H.; Higgins, M. A.; May, P. C.; Ryan, T. P. J Biol Chem 2003, 278, 46107.
28. Van Es, J. H.; Van Gijn, M. E.; Riccio, O.; Van Den Born, M.; Vooijs, M.; Begthel, H.; Cozijnsen, M.; Robine, S.; Winton, D. J.; Radtke, F.; Clevers, H. Nature 2005, 435, 959.
29. Milano, J.; Mckay, J.; Dagenais, C.; Foster-Brown, L.; Pognan, F.; Gadient, R.; Jacobs, R. T.; Zaceo, A.; Greenberg, B.; Ciaccio, P. J. Toxicol Sci 2004, 82, 341.
30. Wong, G. T.; Manfra, D.; Poulet, F. M.; Zhang, Q.; Josien, H.; Bara, T.; Engstrom, L.; Pinzon-Ortiz, M.; Fine, J. S.; Lee, H. J. J.; Zhang, L. L.; Higgins, G. A.; Parker, E. M. J Biol Chem 2004, 279, 12876.
31. Xue, Y.; Yap, C. W.; Sun, L. Z.; Cao, Z. W.; Wang, J. F.; Chen, Y. Z. J Chem Inf Comput Sci 2004, 44, 1497.
32. Xue, Y.; Li, H.; Ung, C. Y.; Yap, C. W.; Chen, Y. Z. Chem Res Toxicol 2006, 19, 1030.
33. Yang, X.-G.; Chen, D.; Wang, M.; Xue, Y.; Chen, Y.-Z. J Comput Chem 2009, 30, 1202.
34. Bruce, C. L.; Melville, J. L.; Pickett, S. D.; Hirst, J. D. J Chem Inf Model 2007, 47, 219.
35. Boiani, M.; Cerecetto, H.; González, M.; Gasteiger, J. J Chem Inf Model 2008, 48, 213.
36. Debeljak, Ž.; Škrbo, A.; Jasprica, I.; Mornar, A.; Plečko, V.; Banjanac, M.; Medić-Šarić, M. J Chem. Inf Model 2007, 47, 918.
37. Vapnik, V. N. The Nature of Statistical Learning Theory, Springer: New York, 1995.
38. Burges, C. J. C. Data Min Knowl Disc 1998, 2, 121.
39. Svetnik, V.; Liaw, A.; Tong, C.; Culberson, J. C.; Sheridan, R. P.; Feuston, B. P. J Chem Inf Comput Sci 2003, 43, 1947.
40. Breiman, L. Mach Learn. 2001, 45, 5.
41. Duda, R. O.; Hart, P. E.; Stork, D. G. Unsupervised Learning and Clustering, In Pattern Classification, 2nd ed.; John Wiley & Sons: New York, 2001.
42. Koch, M. A.; Schuffenhauer, A.; Scheck, M.; Wetzel, S.; Casaulta, M.; Odermatt, A.; Ertl, P.; Waldmann, H. Proc Natl Acad. Sci USA 2005, 102, 17272.
43. Han, L. Y.; Ma, X. H.; Lin, H. H.; Jia, J.; Zhu, F.; Xue, Y.; Li, Z. R.; Cao, Z. W.; Ji, Z. L.; Chen, Y. Z. J Mol Graph Model. 2008, 26, 1276.
44. Liew, C. Y.; Ma, X. H.; Liu, X.; Yap, C. W. J Chem Inf Model 2009, 49, 877.
45. Todeschini, R.; Consonni, V. Handbook of Molecular Descriptors; Wiley-VCH: Weinheim, 2000.
46. Katritzky, A. R.; Gordeeva, E. V. J Chem Inf Comput Sci 1993, 33, 835.
47. Kier, L. B.; Hall, L. H. Molecular Structure Description: The Electrotopological. State; Academic Press: San Diego, 1999.
48. Karelson, M.; Lobanov, V. S.; Katritzky, A. R. Chem. Rev 1996, 96, 1027.
49. Doucet, J.-P.; Barbault, F.; Xia, H., Panaye, A.; Fan, B. Curr Comput Aided Drug Des 2007, 3, 263.
50. Li, S. Q.; Fedorowicz, A.; Singh, H.; Soderholm, S. C. J Chem Inf Model 2005, 45, 952.
51. Khandelwal, A.; Krasowski, M. D.; Reschly, E. J.; Sinz, M. W.; Swaan, P. W.; Ekins, S. Chem Res Toxicol. 2008, 21, 1457.
52. Degroeve, S.; De Baets, B.; Van De Peer, Y.; Rouzé, P. Bioinformatics 2002, 18, S75.
53. Furey, T. S.; Cristianini, N.; Duffy, N.; Bednarski, D. W.; Schummer, M.; Haussler, D. Bioinformatics 20CK), 16, 906.
54. Yu, H.; Yang, J.; Wang, W.; Han, J. Proc IEEE Comput Soc Bioinform Conf 2003, 2, 220.
55. Guyon, I.; Weston, J.; Bamhill, S.; Vapnik, V. Mach Learn 2002, 46, 389.
56. Irwin, J. J.; Shoichet, B. K. J Chem Inf Model 2005, 45, 177.
57. Roulston, J. E. Mol Biotechnol 2002, 20, 153.
58. Matthews, B. W. Biochim Biophys Acta 1975, 405, 442.
59. Perez, J. J. Chem Soc Rev 2005, 34, 143.
60. Willett, P.; Barnard, J. M.; Downs, G. M. J Chem Inf Comput Sci 1998, 38, 983.
61. Willett, P.; Winterman, V. Quant Struct Act Relat 1986, 5, 18.
62. The NCI Diversity Set II. Available at http://dtp.nci.nih.gov/ branches/dscb/div2-exp.lanation.html (accessed on April 5, 2009).
63. Li, C.; Xu, L.; Wolan, D. W.; Wilson, I. A.; Olson, A. J. J Med Chem 2004, 47, 6681.
64. Breiman, L.; Cutler, A. Random Forests; version 51, 2004. Available at http://stat-www.berkeley.edu/users/breiman/Random.Forests/ cc-home.htm (accessed on June 25, 2008).
65. Zweig, M. H.; Campbell, G. Clin Chem 1993, 39, 561.
66. Triballeau, N.; Acher, F.; Brabet, I.; Pin, J. P.; Bertrand, H. O. J Med Chem 2005, 48, 2534.
67. Ferri, C.; Flach, P.; Hernández-Orallo, J. Learning Decision Trees Using the Area Under the ROC Curve. In Proceedings of the 19th International Conference on Machine Learning, 2002; p 139.
68. Bradley, A. P. Pattem.Recognit 1997, 30, 1145.
69. Zhang, Q. Y.; Aires-De-Sousa, J. J Chem. Inf Model 2007, 47, 1.
70. Youden, W. J. Cancer 1950, 3, 32.
71. Schisterman, E. F.; Perkins, N. J.; Liu, A.; Bondell, H. Epidemiology 2005, 16, 73.
72. Carosati, E.; Mannhold, R.; Wahl, P.; Hansen, J. B.; Fremming, T.; Zamora, I.; Cianchetta, G.; Baroni, M. J Med Chem 2007, 50, 2117.
73. Jorissen, R. N.; Gilson, M. R. J Chem Inf Model 2005, 45, 549.