[KSCI] Korea Science Citation Index Service

http://dx.doi.org/10.5012/bkcs.2012.33.5.1597

The Identification of Binding Mode for Arabidopsis thaliana 7-Keto-8-aminopelargonic Acid Synthase (AtKAPAS) Inhibitors

Cho, Jae-Eun (Graduate School of New Drug Discovery and Development, Chungnam National University)
Kang, Sun-Young (Graduate School of New Drug Discovery and Development, Chungnam National University)
Choi, Jung-Sup (Korea Research Institute of Chemical Technology)
Ko, Young-Kwan (Korea Research Institute of Chemical Technology)
Hwang, In-Taek (Korea Research Institute of Chemical Technology)
Kang, Nam-Sook (Graduate School of New Drug Discovery and Development, Chungnam National University)

Publication Information

Bulletin of the Korean Chemical Society / v.33, no.5, 2012 , pp. 1597-1602 More about this Journal

Abstract

In this study, we determined the 3D-structure of Arabidopsis thaliana KAPAS by homology modeling. We then investigated the binding mode of compounds obtained from in-house library using computational docking methods. From the flexible docking study, we achieved high dock scores for the active compounds denoted in this study as compound $\mathbf{3}$ and compound $\mathbf{4}$ . Thus, we highlight the flexibility of specific residues, Lys 312 and Phe 172, when used in active sites.

Keywords

KAPAS; Herbicides; Homology modeling; Docking;

Citations & Related Records

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Reference

1	Okazaki, S.; Suzuki, A.; Mizushima, T.; Kawano, T.; Komeda, H.; Asano, Y.; Yamane, T. Biochemistry 2009, 5, 941.
2	Storici, P.; Capitani, G.; Müller, R.; Schirmer, T.; Jansonius, J. N. J. Mol. Biol. 1999, 1, 297.
3	Shah, S. A.; Shen, B. W.; Brunger, A. T. Structure 1997, 8, 1067.
4	Sandmark, J.; Mann, S.; Marquet, A.; Schneider, G. J. Biol. Chem. 2002, 227, 43352.
5	Taylor, R. D.; Jewsbury, P. J.; Essex, J. W. J. Comput.-Aided Mol. Des. 2002, 16, 151. DOI ScienceOn
6	Montes, M.; Miteva, M. A.; Villoutreix, B. O. Protein 2007, 15, 712.
7	Welch, W.; Ruppert, J.; Jain, A. N. Chem. Biol. 1996, 3, 449. DOI ScienceOn
8	Koska, J.; Spassov, V. Z.; Maynard, A. J.; Yan, L.; Austin, N.; Flook, P. K.; Venkatachalam, C. M. J. Chem. Inf. Model 2008, 48, 1965. DOI ScienceOn
9	Venkatachalam, C. M.; Jiang, X.; Oldfield, T.; Waldman, M. J. Mol. Graph. Model 2003, 21, 289. DOI ScienceOn
10	Ploux, O.; Marquet, A. Biochem. J. 1992, 283, 327. DOI
11	Webster, S. P.; Alexeev, D.; Campopiano, D. J.; Watt, R. M.; Alexeeva, M.; Sawyer, L.; Baxter, R. L. Biochemistry 2000, 39, 516. DOI ScienceOn
12	Krieger, E.; Nabuurs, S. B.; Vriend, G. Structural Bioinformatics 2003, 25, 507.
13	Hwang, I. T.; Choi, J. S.; Song, H. Y.; Cho, S. J.; Lim, H. K.; Park, N. J.; Lee, D. H. Pesticide Biochemistry and Physiology 2010, 97, 24. DOI ScienceOn
14	Hwang, I. T.; Lee, D. H.; Park, N. J. InTec. 2011, 471, 22.
15	Choi, J. S.; Lim, H. K.; Seo, B. R.; Kim, J. S.; Choi, C. W.; Kim, Y. S.; Ryu, S. Y. The Korean Society of Weed Science 2011, 31, 240. DOI
16	Zhang, Y. Proteins 2007, 69, 108. DOI ScienceOn
17	Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comp. Chem. 1983, 4, 187. DOI
18	Schmidt, A.; Sivaraman, J.; Li, Y.; Larocque, R.; Barbosa, J. A.; Smith, C.; Matte, A.; Schrag, J. D.; Cygler, M. Biochemistry 2001, 40, 5151. DOI ScienceOn
19	Webster, S. P.; Alexeev, D.; Campopiano, D. J.; Watt, R. M.; Alexeeva, M.; Sawyer, L.; Baxter, R. L. Biochemistry 2000, 39, 516. DOI ScienceOn
20	Jahan, N.; Potter, J. A.; Sheikh, M. A.; Botting, C. H.; Shirran, S. L.; Westwood, N. J.; Taylor, G. L. J. Mol. Biol. 2009, 3, 763.
21	Astner, I.; Schulze, J. O.; van den Heuvel, J.; Jahn, D.; Schubert, W. D.; Heinz, D. W. EMBO J. 2005, 18, 3166.
22	Kelly, R. C.; Bolitho, M. E.; Higgins, D. A.; Lu, W.; Ng, W. L.; Jeffrey, P. D.; Rabinowitz, J. D.; Semmelhack, M. F.; Hughson, F. M.; Bassler, B. L. Nat. Chem. Biol. 2009, 12, 891.