Quantitative structure-activity relationship analysis and a combined ligand-based/structure-based virtual screening study for glycogen synthase kinase-3

Molecular Informatics

Volumn 33, Issue 9, 2014, Pages 627-640

  Fu, Gang ^a,b   Liu, Sheng ^b   Nan, Xiaofei ^b   Dale, Olivia R ^a   Zhao, Zhendong ^b   Chen, Yixin ^b   Wilkins, Dawn E ^b   Manly, Susan P ^a   Cutler, Stephen J ^a   Doerksen, Robert J ^a  

^a UNIVERSITY OF MISSISSIPPI   (United States)

^b The University of Mississippi   (United States)

Author keywords

Glycogen synthase kinase 3 inhibitors; High throughput screening; Random forests; Structure activity relationships; Support vector machines

Indexed keywords

1 (4 METHOXYBENZYL) 3 (5 NITRO 2 THIAZOLYL)UREA; 2 (2,4 DICHLOROPHENYL) 3 (1 METHYL 3 INDOLYL)MALEIMIDE; 2 (3 CHLORO 4 HYDROXYANILINO) 3 (2 NITROPHENYL)MALEIMIDE; ALSTERPAULLONE; GLYCOGEN SYNTHASE KINASE 3; GLYCOGEN SYNTHASE KINASE 3 INHIBITOR; INDIRUBIN 3' MONOXIME; KENPAULLONE; LIGAND; STAUROSPORINE; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; BINDING AFFINITY; BIOASSAY; BIOLOGICAL ACTIVITY; CHEMICAL STRUCTURE; DECISION TREE; DRUG STRUCTURE; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; RANDOM FOREST; SUPPORT VECTOR MACHINE;

EID: 85027923367     PISSN: 18681743     EISSN: 18681751     Source Type: Journal    
DOI: 10.1002/minf.201400045     Document Type: Article

References (61)

1. B. W. Doble, J. R. Woodgett, J. Cell Sci. 2003, 116, 1175-1186
2. P. Cohen, M. Goedert, Nat. Rev. Drug Discov. 2004, 3, 479-487.
3. A. J. Harwood, Cell 2001, 105, 821-824.
4. A. Martinez, A. Castro, I. Dorronsoro, M. Alonso, Med. Res. Rev. 2002, 22, 373-384.
5. G. V. Johnson, W. H. Stoothoff, J. Cell Sci. 2004, 117, 5721-5729.
6. M. Medina, A. Castro, Curr. Opin. Drug Discov. De. 2008, 11, 533-543.
7. D. S. Patel, N. Dessalew, P. Iqbal, P. V. Bharatam, Curr. Protein Pept. Sci. 2007, 8, 352-364.
8. P. K. Gadakar, S. Phukan, P. Dattatreya, V. N. Balaji, J. Chem. Inf. Model. 2007, 47, 1446-1459.
9. J. L. Melville, E. K. Burke, J. D. Hirst, Comb. Chem. High Through. Scr. 2009, 12, 332-343.
10. J. C. Dearden, M. T. D. Cronin, K. L. E. Kaiser, SAR QSAR Environ. Res. 2009, 20, 241-266.
11. M. P. Coghlan, A. A. Culbert, D. A. Cross, S. L. Corcoran, J. W. Yates, N. J. Pearce, O. L. Rausch, G. J. Murphy, P. S. Carter, L. R. Cox, D. Mills, M. J. Brown, D. Haigh, R. W. Ward, D. G. Smith, K. J. Murray, A. D. Reith, J. C. Holder, Chem. Biol. 2000, 7, 793-803.
12. A. P. Kozikowski, I. N. Gaisina, P. A. Petukhov, J. Sridhar, L. T. King, S. Y. Blond, T. Duka, M. Rusnak, A. Sidhu, ChemMedChem 2006, 1, 256-266.
13. D. G. Smith, M. Buffet, A. E. Fenwick, D. Haigh, R. J. Ife, M. Saunders, B. P. Slingsby, R. Stacey, R. W. Ward, Bioorg. Med. Chem. Lett. 2001, 11, 635-639.
14. R. Bhat, Y. Xue, S. Berg, S. Hellberg, M. Ormo, Y. Nilsson, A. Radesater, E. Jerning, P. Markgren, T. Borgegard, M. Nylof, A. Gimenez-Cassina, F. Hernandez, J. J. Lucas, J. Diaz-Nido, J. Avila, J. Biol. Chem. 2003, 278, 45937-45945.
15. I. N. Gaisina, F. Gallier, A. V. Ougolkov, K. H. Kim, T. Kurome, S. Guo, D. Holzle, D. N. Luchini, S. Y. Blond, D. D. Billadeau, A. P. Kozikowski, J. Med. Chem. 2009, 52, 1853-1863.
16. S. Leclerc, M. Garnier, R. Hoessel, D. Marko, J. A. Bibb, G. L. Snyder, P. Greengard, J. Biernat, Y. Z. Wu, E. M. Mandelkow, G. Eisenbrand, L. Meijer, J. Biol. Chem. 2001, 276, 251-260.
17. T. A. Engler, J. R. Henry, S. Malhotra, B. Cunningham, K. Furness, J. Brozinick, T. P. Burkholder, M. P. Clay, J. Clayton, C. Diefenbacher, E. Hawkins, P. W. Iversen, Y. Li, T. D. Lindstrom, A. L. Marquart, J. McLean, D. Mendel, E. Misener, D. Briere, J. C. O'Toole, W. J. Porter, S. Queener, J. K. Reel, R. A. Owens, R. A. Brier, T. E. Eiessalu, J. R. Wagner, R. M. Campbell, R. Vaughn, J. Med. Chem. 2004, 47, 3934-3937.
18. L. Meijer, A. L. Skaltsounis, P. Magiatis, P. Polychronopoulos, M. Knockaert, M. Leost, X. P. Ryan, C. A. Vonica, A. Brivanlou, R. Dajani, C. Crovace, C. Tarricone, A. Musacchio, S. M. Roe, L. Pearl, P. Greengard, Chem. Biol. 2003, 10, 1255-1266.
19. J. Bain, H. McLauchlan, M. Elliott, P. Cohen, Biochem. J. 2003, 371, 199-204.
20. M. Leost, C. Schultz, A. Link, Y. Z. Wu, J. Biernat, E. M. Mandelkow, J. A. Bibb, G. L. Snyder, P. Greengard, D. Zaharevitz, R. Gussio, A. M. Senderowicz, E. A. Sausville, C. Kunick, L. Meijer, Eur. J. Biochem. 2000, 267, 5983-5994.
21. Version 2.4 ed., Schrödinger, LLC, New York, NY, 2010.
22. G. Fu, P. Sivaprakasam, O. R. Dale, S. P. Manly, S. J. Cutler, R. J. Doerksen, Molec. Inf. 2014, 33, 635.
23. Chemical Computing Group, Montreal, Quebec, Canada, 2009.
24. Version 1.4 ed., Talete srl, Milano, Italy, 2010, p. Software for Molecular Descriptor Calculations.
25. P. Polychronopoulos, P. Magiatis, A. L. Skaltsounis, V. Myrianthopoulos, E. Mikros, A. Tarricone, A. Musacchio, S. M. Roe, L. Pearl, M. Leost, P. Greengard, L. Meijer, J. Med. Chem. 2004, 47, 935-946
26. K. Vougogiannopoulou, Y. Ferandin, K. Bettayeb, V. Myrianthopoulos, O. Lozach, Y. Z. Fan, C. H. Johnson, P. Magiatis, A. L. Skaltsounis, E. Mikros, L. Meijer, J. Med. Chem. 2008, 51, 6421-6431.
27. C. Kunich, K. Lauenroth, K. Wieking, X. Xie, C. Schultz, R. Gussio, D. Zaharevitz, M. Leost, L. Meijer, A. Weber, F. S. Jorgensen, T. Lemcke, J. Med. Chem. 2004, 47
28. H. Stukenbrock, R. Mussmann, M. Geese, Y. Ferandin, O. Lozach, T. Lemcke, S. Kegel, A. Lomow, U. Burk, C. Dohrmann, L. Meijer, M. Austen, C. Kunick, J. Med. Chem. 2008, 51, 2196-2207.
29. Y. Mettey, M. Gompel, V. Thomas, M. Garnier, M. Leost, I. Ceballos-Picot, M. Noble, J. Endicott, J. M. Vierfond, L. Meijer, J. Med. Chem. 2003, 46, 222-236.
30. J. Witherington, V. Bordas, S. L. Garland, D. M. B. Hickey, R. J. Ife, J. Liddle, M. Saunders, D. G. Smith, R. W. Ward, Bioorg. Med. Chem. Lett. 2003, 13, 1577-1580.
31. J. Witherington, V. Bordas, D. Haigh, D. M. B. Hickey, R. J. Ife, A. D. Rawlings, B. P. Slingsby, D. G. Smith, R. W. Ward, Bioorg. Med. Chem. Lett. 2003, 13, 1581-1584.
32. J. Witherington, V. Bordas, A. Gaiba, N. S. Garton, A. Naylor, A. D. Rawlings, B. P. Slingsby, D. G. Smith, A. K. Takle, R. W. Ward, Bioorg. Med. Chem. Lett. 2003, 13, 3055-3057.
33. J. Witherington, V. Bordas, A. Gaiba, A. Naylor, A. D. Rawlings, B. P. Slingsby, D. G. Smith, A. K. Takle, R. W. Ward, Bioorg. Med. Chem. Lett. 2003, 13, 3059-3062.
34. A. J. Peat, J. A. Boucheron, S. H. Dickerson, D. Garrido, W. Mills, J. Peckham, F. Preugschat, T. Smalley, S. L. Schweiker, J. R. Wilson, T. Y. Wang, H. Q. Zhou, S. A. Thomas, Bioorg. Med. Chem. Lett. 2004, 14, 2121-2125
35. A. J. Peat, D. Garrido, J. A. Boucheron, S. L. Schweiker, S. H. Dickerson, J. R. Wilson, T. Y. Wang, S. A. Thomas, Bioorg. Med. Chem. Lett. 2004, 14, 2127-2130.
36. Y. Maeda, M. Nakano, H. Sato, Y. Miyazaki, S. L. Schweiker, J. L. Smith, A. T. Truesdale, Bioorg. Med. Chem. Lett. 2004, 14, 3907-3911.
37. A. P. Kozikowski, I. N. Gaisina, H. B. Yuan, P. A. Petukhov, S. Y. Blond, A. Fedolak, B. Caldarone, P. McGonigle, J. Am. Chem. Soc. 2007, 129, 8328-8332.
38. M. Arnost, A. Pierce, E. T. Haar, D. Lauffer, J. Madden, K. Tanner, J. Green, Bioorg. Med. Chem. Lett. 2010, 20, 1661-1664.
39. M. Saitoh, J. Kunitomo, E. Kimura, Y. Hayase, H. Kobayashi, N. Uchiyama, T. Kawamoto, T. Tanaka, C. D. Mol, D. R. Dougan, G. S. Textor, G. P. Snell, F. Itoh, Bioorg. Med. Chem. 2009, 17, 2017-2029
40. M. Saitoh, J. Kunitomo, E. Kimura, H. Iwashita, Y. Uno, T. Onishi, N. Uchiyama, T. Kawamoto, T. Tanaka, C. D. Mol, D. R. Dougan, G. P. Textor, G. P. Snell, M. Takizawa, F. Itoh, M. Kori, J. Med. Chem. 2009, 52, 6270-6286.
41. D. Lesuisse, G. Dutruc-Rosset, G. Tiraboschi, M. Dreyer, S. Maignan, A. Chevalier, F. Halley, P. Bertrand, M. C. Burgevin, D. Quarteronet, T. Rooney, Bioorg. Med. Chem. Lett. 2010, 20, 1985-1989.
42. E. W. Forgy, Biometrics 1965, 21, 768-769.
43. A. Golbraikh, A. Tropsha, J. Mol. Graph. Model. 2002, 20, 269-276.
44. V. Vapnik, The Nature of Statistical Learning Theory, Springer, New York, 1995.
45. C. Cortes, V. Vapnik, Mach. Learn. 1995, 20, 273-297.
46. H. Drucker, C. Burges, L. Kaufman, A. Smola, V. Vapnik, in Advances in Neural Information Processing Systems, Vol. 9 (Eds:, M. Mozer, M. Jordan, T. Petsche,), MIT Press, 1997, pp. 155-161.
47. R2011a ed., The Mathworks Inc., Natick, MA, 2011.
48. C. C. Chang, C. J. Lin, 2011, Software available at http://www.csie.ntu.edu.tw/cjlin/libsvm
49. Y. Saeys, I. Inza, P. Larranaga, Bioinformatics 2007, 23, 2507-2517.
50. J. Kennedy, R. C. Eberhart, in Proc. IEEE Int. Conf. Neural Networks, Perth, 1995, pp. 1942-1948
51. J. Kennedy, R. C. Eberhart, in 6th Int. Symp. Micro Machine and Human Science, Nagoya, 1995, pp. 39-43.
52. Y. Shi, R. C. Eberhart, in Proc. IEEE Int. Conf. Evolutionary Computation, Anchorage, AK, USA, 1998, pp. 69-73
53. R. C. Eberhart, Y. Shi, in Proc. of IEEE Int. Conf. Evolutionary Computation, Seoul, 2001, pp. 81-86.
54. X. Y. Wang, J. Yang, X. L. Teng, W. J. Xia, R. Jensen, Pattern Recogn. Lett. 2007, 28, 459-471.
55. D. K. Agrafiotis, W. Cedeno, J. Med. Chem. 2002, 45, 1098-1107
56. J. Huang, G. Ma, I. Muhammad, Y. Cheng, J. Chem. Inf. Model. 2007, 47, 1638-1647.
57. L. Breiman, Mach. Learn. 2001, 45, 5-32.
58. V. Svetnik, A. Liaw, C. Tong, J. C. Culberson, R. P. Sheridan, B. P. Feuston, J. Chem. Inf. Comput. Sci. 2003, 43, 1947-1958.
59. A. Jaiantilal, 2009, pp. Software available at http://code.google.com/p/randomforest-matlab.
60. J. Jaworska, N. Nikolova-Jeliazkova, T. Aldenberg, ATLA Altern. Lab. Anim. 2005, 33, 445-459.
61. version 5.6 ed., Schrödinger, LLC, New York, NY, 2010.