Browse > Article
http://dx.doi.org/10.5012/bkcs.2007.28.2.211

A Simple and Efficient Docking Method to the Cyclin-Dependent Kinase 2  

Park, Kwang-Su (Division of Bioscience and Biotechnology, Institute of Biomedical Science and Technology, Konkuk University)
Kim, Jin-Young (Division of Bioscience and Biotechnology, Institute of Biomedical Science and Technology, Konkuk University)
Chong, You-Hoon (Division of Bioscience and Biotechnology, Institute of Biomedical Science and Technology, Konkuk University)
Choo, Hyun-Ah (Life Sciences Division, Korea Institute of Science and Technology)
Publication Information
Bulletin of the Korean Chemical Society / v.28, no.2, 2007 , pp. 211-219 More about this Journal
Abstract
The subtle but significant differences and thereby the lack of consensus in active site structures among the crystal structures of cyclin-dependent kinase 2 (CDK2) has hampered structure-based drug design. In this study, we devised a simple but effective ‘mutation, pharmacophore-guided docking, followed by mutation' strategy to generate an “average” CDK2 structure, which was used for ligand docking study to successfully reproduce 30 out of 32 X-ray ligand positions within 2.0 A of heavy atom RMSD. This novel docking method was applied for structure-based 3D QSAR with CoMSIA study of a series of structurally related ligands, which showed a good discrimination between CDK2 binders and nonbinders.
Keywords
CDK2; Docking; Mutation; CoMSIA;
Citations & Related Records
Times Cited By KSCI : 2  (Citation Analysis)
Times Cited By Web Of Science : 3  (Related Records In Web of Science)
Times Cited By SCOPUS : 3
연도 인용수 순위
1 Bramson, H. N.; Corona, J.; Davis, S. T.; Dickerson, S. H.; Edelstein, M.; Frye, S. V.; Gampe, Jr., R. T.; 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   DOI   ScienceOn
2 Gibson, A. E.; Arris, C. E.; Bentley, J.; Boyle, F. T.; Davies, N. J.; Curtin, T. G.; Endicott, J. A.; Golding, B. T.; Grant, S.; Griffin, R. J.; Jewsbury, P.; Johnson, L. N.; Mesguiche, V.; Newell, D. R.; Noble, M. E.; Tucker, J. A.; Whitfield, H. J. J. Med. Chem. 2002, 45, 3381   DOI   ScienceOn
3 Furet, P.; Meyer, T.; Strauss, A.; Raccuglia, S.; Rondeau, J. M. Bioorg. Med. Chem. Lett. 2002, 12, 221   DOI   ScienceOn
4 Meijer, L.; Thunnissen, A. M.; White, A. W.; Garnier, M.; Nikolic, M.; Tsai, L. H.; Walter, J.; Cleverley, K. E.; Salinas, P. C.; Wu, Y. Z.; Biernat, J.; Mandelkow, E. M.; Kim, S. H.; Pettit, G. R. Chem. Biol. 2000, 7, 51   DOI   ScienceOn
5 Arris, C. E.; Boyle, F. T.; Calvert, A. H.; Curtin, N. J.; Endicott, J. A.; Garman, E. F.; Gibson, A. E.; Golding, B. T.; Grant, S.; Griffin, R. J.; Jewsbury, P.; Johnson, L. N.; Lawrie, A. M.; Newell, D. R.; Noble, M. E.; Sausville, E. A.; Schultz, R.; Yu, W. J. Med. Chem. 2000, 43, 2797   DOI   ScienceOn
6 Davies, T. G.; Tunnah, P.; Meijer, L.; Marko, D.; Eisenbrand, G.; Endicott, J. A.; Noble, M. E. Structure 2001, 9, 389   DOI   ScienceOn
7 Davis, S. T.; Benson, B. G.; Bramson, H. N.; Chapman, D. E.; Dickerson, S. H.; Dold, K. M.; Eberwein, D. J.; Edelstein, M.; Frye, S. V.; Gampe Jr., R. T.; Griffin, R. J.; Harris, P. A.; Hassell, A. M.; Holmes, W. D.; Hunter, R. N.; Knick, V. B.; Lackey, K.; Lovejoy, B.; Luzzio, M. J.; Murray, D.; Parker, P.; Rocque, W. J.; Shewchuk, L.; Veal, J. M.; Walker, D. H.; Kuyper, L. F. Science 2001, 291, 134   DOI   ScienceOn
8 Kim, J.; Lee, Y.; Kim, H.; Kang, S.-Y.; Park, K.-S.; Cho, J.-H.; Lee, Y.-Y.; Kim, B.-S.; Lim, Y.; Chong, Y. Bull. Korean Chem. Soc. 2005, 26, 2065   DOI   ScienceOn
9 Wu, S. Y.; McNae, I.; Kontopidis, G.; McClue, S. J.; McInnes, C.; Stewart, K. J.; Wang, S.; Zheleva, D. I.; Marriage, H.; Lane, D. P.; Taylor, P.; Fischer, P. M.; Walkinshaw, M. D. Structure 2003, 11, 399   DOI   ScienceOn
10 Gray, N. S.; Wodicka, L.; Thunnissen, A. M.; Norman, T. C.; Kwon, S.; Espinoza, F. H.; Morgan, D. O.; Barnes, G.; LeClerc, S.; Meijer, L.; Kim, S. H.; Lockhart, D. J.; Schultz, P. G. Science 1998, 281, 533   DOI   ScienceOn
11 Bohm, M.; Sturzebecher, J.; Klebe, G. J. Med. Chem. 1999, 42, 458   DOI   ScienceOn
12 Klebe, G. Comparative Molecular Similarity Indices: CoMSIA in 3D QSAR in Drug Design; Kubinyi, H.; Folkers, G.; Martin, Y. C., Eds.; Kluwer Academic Publishers: Great Britain, 1998; Vol 3, p 87
13 Blaney, J. M.; Weiner, P. K.; Dearing, A.; Kollman, P. A.; Jorgensen, E. C.; Oatley, S. J.; Burridge, J. M.; Blake, C. C. F. J. Am. Chem. Soc. 1982, 104, 6424   DOI
14 Cramer III, R. D.; Patterson, D. E.; Bunce, J. D. J. Am. Chem. Soc. 1988, 110, 5959   DOI   ScienceOn
15 Kim, J.; Lee, M.; Kang, S.-Y.; Park, J.; Lim, Y.; Koh, D.; Park, K. H.; Chong, Y. Bull. Korean Chem. Soc. 2006, 27, 1025   DOI   ScienceOn
16 Purcell, W. P.; Singer, J. A. J. Chem. Eng. Data 1967, 12, 235   DOI
17 Wipff, G.; Dearing, A.; Weiner, P. K.; Blaney, J. M.; Kollman, P. A. J. Am. Chem. Soc. 1983, 105, 997   DOI
18 Beattie, J. F.; Breault, G. A.; Ellston, R. P. A.; Green, S.; Jewsbury, P. J.; Midgley, C. J.; Naven, R. T.; Minshull, C. A.; Pauptit, R. A.; Tucker, J. A.; Pease, J. E. Bioorg. Med. Chem. Lett. 2003, 13, 2955   DOI   ScienceOn
19 Davies, T. G.; Bentley, J.; Arris, C. E.; Boyle, F. T.; Curtin, N. J.; Endicott, J. A.; Gibson, A. E.; Golding, B. T.; Griffin, R. J.; Hardcastle, I. R.; Jewsbury, P.; Johnson, L. N.; Mesguiche, V.; Newell, D. R.; Noble, M. E. M.; Tucker, J. A.; Wang, L.; Whitfield, H. J. Nat. Struct. Biol. 2002, 9, 745   DOI   ScienceOn
20 Clare, P. M.; Poorman, R. A.; Kelley, L. C.; Watenpaugh, K. D.; Bannow, C. A.; Leach, K. L. J. Biol. Chem. 2001, 276, 48292
21 Moshinsky, D. J.; Bellamacina, C. R.; Boisvert, D. C.; Huang, P.; Hui, T.; Jancarik, J.; Kim, S. H.; Rice, A. G. Biochem. Biophys. Res. Comm. 2003, 310, 1026   DOI   ScienceOn
22 Hindle, S. A.; Rarey, M.; Buning, C.; Lengaue, T. J. Comput.-Aided Mol. Des. 2002, 16, 129
23 Dreyer, M. K.; Borcherding, D. R.; Dumont, J. A.; Peet, N. P.; Tsay, J. T.; Wright, P. S.; Bitonti, A. J.; Shen, J.; Kim, S. H. J. Med. Chem. 2001, 44, 524   DOI   ScienceOn
24 Gasteiger, J.; Marsili, M. Tetrahedron 1980, 36, 3219   DOI   ScienceOn
25 Sayle, K. L.; Bentley, J.; Boyle, F. T.; Calvert, A. H.; Cheng, Y.; Curtin, N. J.; Endicott, J. A.; Golding, B. T.; Hardcastle, I. R.; Jewsbury, P.; Mesguiche, V.; Newell, D. R.; Noble, M. E. M.; Parsons, R. J.; Pratt, D. J.; Wang, L. Z.; Griffin, R. J. Bioorg. Med. Chem. Lett. 2003, 13, 3079   DOI   ScienceOn
26 Brown, N. R.; Noble, M. E.; Lawrie, A. M.; Morris, M. C.; Tunnah, P.; Divita, G.; Johnson, L. N.; Endicott, J. A. J. Biol. Chem. 1999, 274, 8746   DOI   ScienceOn
27 Sims, P. A.; Wong, C. F.; McCammon, J. A. J. Med. Chem. 2003, 46, 3314   DOI   ScienceOn
28 Zavodszky, M. I.; Kuhn, L. A. Protein Sci. 2005, 14, 1104   DOI   ScienceOn
29 Barril, X.; Morley, S. D. J. Med. Chem. 2005, 48, 4432   DOI   ScienceOn
30 Sciabola, S.; Carosati, E.; Baroni, M.; Mannhold, R. J. Med. Chem. 2005, 48, 3756   DOI   ScienceOn
31 Liu, J.-J.; Dermatakis, A.; Lukacs, C. M.; Konzelmann, F.; Chen, Y.; Kammlott, U.; Depinto, W.; Yang, H.; Yin, X.; Chen, Y.; Schutt, A.; Simcox, M. E.; Luk, K.-C. Bioorg. Med. Chem. 2003, 13, 2465   DOI   ScienceOn
32 Wang, S.; Meades, C.; Wood, G.; Osnowski, A.; Anderson, S.; Yuill, R.; Thomas, M.; Mezna, M.; Jackson, W.; Midgley, C.; Griffiths, G.; Fleming, I.; Green, S.; McNae, I.; Wu, S.-Y.; McInnes, C.; Zheleva, D.; Walkinshaw, M. D.; Fischer, P. M. J. Med. Chem. 2004, 47, 1662   DOI   ScienceOn
33 Wold, S.; Albano, C.; Dunn, W.; Edlund, U.; Esbensen, K.; Geladi, P.; Hellberg, S.; Johansson, E.; Lindberg, W.; Sjosstrom, M. Mathematics and Statistics in Chemistry in Chemometrics; Kowalski, B., Ed.; Reidel: Dordrecht, 1987
34 Anderson, M.; Beattie, J.; Breault, G.; Breed, J.; Byth, K.; Culshaw, J.; Ellston, R.; Green, S.; Minshull, C.; Norman, R.; Pauptit, R.; Stanway, J.; Thomas, A.; Jewsbury, P. Bioorg. Med. Chem. Lett. 2003, 13, 3021   DOI   ScienceOn
35 Huse, M.; Kuriyan, J. Cell 2002, 109, 275   DOI   ScienceOn
36 Erickson, J. A.; Jalaie, M.; Robertson, D. H.; Lewis, R. A.; Vieth, M. J. Med. Chem. 2004, 47, 45   DOI   ScienceOn
37 Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res. 2000, 28, 235   DOI   ScienceOn
38 Thomas, M. P.; McInnes, C.; Fischer, P. M. J. Med. Chem. 2006, 49, 92   DOI   ScienceOn
39 Subramanian, J.; Sharma, S.; B-Rao, C. J. Med. Chem. 2006, 49, 5434   DOI   ScienceOn
40 Shewchuk, L.; Hassell, A.; Wisely, B.; Rocque, W.; Holmes, W.; Veal, J.; Kuyper, L. F. J. Med. Chem. 2000, 43, 133   DOI   ScienceOn