Computational insight into the structure–activity relationship of novel N-substituted phthalimides with gibberellin-like activity

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• 作者：Dongling Li ; Shaoqing Du ; Weiming Tan ; Hongxia Duan
• 关键词：NSPs ; GAs ; GID1A ; Structural–activity relationship ; Plant growth regulators
• 刊名：Journal of Molecular Modeling
• 出版年：2015
• 出版时间：October 2015
• 年：2015
• 卷：21
• 期：10
• 全文大小：1,664 KB
• 参考文献：1.Davies PJ (1995) Plant hormones: physiology, biochemistry and molecular biology. Kluwer, Dordrecht, p 64
  2.Sun TP (2011) Curr Biol 21:338-45CrossRef
  3.Suttle JC (1983) News Bull Br Plant Growth Regul Grp 6:11-9
  4.Suttle JC, Schreiner DR (1982) J Plant Growth Regul 1:139-46
  5.Los M, Kust CA, Lamb G, Diehl RE (1980) HortSci 15:22-3
  6.Suttle JC, Hultstrand JF (1987) Plant Physiol 84:1068-073CrossRef
  7.Simonovic A, Grubisic D, Giba Z, Konjevic R (2000) J Plant Growth Regul 32:91-7CrossRef
  8.Yalpani N, Suttle JC, Hultstrand JF, Rodaway SJ (1989) Plant Physiol 91:823-28CrossRef
  9.Choma ME, Himelrick DG (1984) Sci Hortic 22:257-64CrossRef
  10.Li WQ, Liu XJ, Yamaguchi S (2005) Plant Physiol Commun 41:111-15 (in Chinese)
  11.Zhang GH, Zhang YJ, Cong RC, Dong KQ, Gu RZ (2009) Acta Bot Boreali-Occidentalia Sin 29:412-19 (in Chinese)
  12.Stoddart JL (1979) Planta 146:353-61CrossRef
  13.Keith B, Foster NA, Bonettemaker M, Srivastava LM (1981) Plant Physiol 68:344-48CrossRef
  14.Ueguchi-Tanaka M, Ashikari M, Nakajima M, Itoh H, Katoh E, Kobayashi M, Chow T, Hsing YC, Kitano H, Yamaguchi I, Matsuoka M (2005) Nature 437:693-98CrossRef
  15.Nakajima M, Shimada A, Takashi Y, Kim YC, Park SH, Ueguchi-Tanaka M, Suzuki H, Karoh E, Iuchi S, Kobayashi M, Maeda T, Matsuoka M, Yamaguchi I (2006) Plant Cell 46:880-89
  16.Murase K, Hirano Y, Sun TP, Hakoshima T (2008) Nature 456:459-64CrossRef
  17.Shimada A, Ueguchi-Tanaka M, Nakatsu T, Nakajima M, Naoe Y, Ohmiya H, Kato H, Matsuoka M (2008) Nature 456:520-24CrossRef
  18.Duan HX, Li DL, Liu HC, Liang DS, Yang XL (2013) J Mol Model 19:4613-624CrossRef
  19.RCSB (2015) Protein Data Bank. http://?www.?rcsb.?org/?pdb/?home/?home.?do
  20.Tripos Associates (2006) Sybyl 7.3. Tripos Associates, St. Louis
  21.Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Vreven T Jr, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Adamo C, Jaramillo J, Comperts R, Stratmann RE, Yazyey O, Austin SJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JC, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2003) Gaussian 03, revision A.1. Gaussian, Inc., Pittsburgh
  22.Jain AN (1996) J Comput Aided Mol Des 10:427-40CrossRef
  23.Welch W, Ruppert J, Jain AN (1996) Chem Biol 3:449-62CrossRef
  24.Clark RD, Strizhev A, Leonard JM, Blake JF, Matthew JB (2002) J Mol Graph Model 20:281-95CrossRef
  25.Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) J Chem Theory Comput 4:435-47CrossRef
  26.Berendsen HJC, van der Spoel D, van Drunen R (1995) Comput Phys Commun 91:43-6CrossRef
  27.Schüttelkopf AW, van Aalten DMF (2004) Acta Crystallogr D 60:1355-363
  28.Hess B, Bekker H, Berendsen HJC, Fraajie JGEM (1997) J Comput Chem 18:1463-472CrossRef
  29.Essman U, Perela L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) J Chem Phys 103:8577-592CrossRef
  30.Golbraikh A, Tropsha A (2002) J Mol Graph Model 20:269-76CrossRef
  31.Xiang HY, Takeuchi H, Tsunoda Y, Nakajima M, Murata K, Ueguchi Tanaka M, Kidokoro S, Kezuka Y, Nonaka T, Matsuoka M, Katoh E (2011) J Mol Recognit 24:275-82CrossRef
  32.Ueguchi Tanaka M, Nakajima M, Katoh E, Ohmiya H, Asano K, Saji S, Xiang HY, Ashikari M, Kitano H, Yamaguchi I, Matsuoka M (2007) Plant Cell 19:2140-155CrossRef
  
• 作者单位：Dongling Li (1)
  Shaoqing Du (1)
  Weiming Tan (2)
  Hongxia Duan (1)
  
  1. Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China, 100193
  2. Engineering Research Center of Plant Growth Regulators, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China, 100193
  
• 刊物类别：Chemistry and Materials Science
• 刊物主题：Chemistry
  Computer Applications in Chemistry
  Biomedicine
  Molecular Medicine
  Health Informatics and Administration
  Life Sciences
  Computer Application in Life Sciences
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：0948-5023

文摘

N-substituted phthalimides (NSPs) that show multiple gibberellin (GA)-like effects on the growth and development of higher plants have been reported. These NSPs may represent a potential alternative to commercial GAs. Therefore, in this work, molecular docking and molecular dynamics simulations were used to explore the mode of interaction between some NSPs and the GA receptor GID1A in order to clarify the relationship between structure and GA-like activity in the NSPs. The results obtained demonstrate that both a multiple-hydrogen-bond network and a “hat-shaped-hydrophobic interaction play important roles in the binding of the NSPs to GID1A. The carbonyl group of a phthalimide fragment in the NSPs acted in a similar manner to the pharmacophore group 6-COOH in GAs, forming multiple-hydrogen-bond interactions with residues Ser191 and Tyr322 in the binding domain of GID1A. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used to further study the 3D quantitative structure–activity relationship (3D-QSAR) of the NSPs. It was confirmed that the GA-like activity of these NSPs is strongly linked to a few H-bond donor and acceptor field contributions of the NSPs to the H-bond interactions with GID1A. Five new NSP molecules D1-strong class="EmphasisTypeBold ">D5 were designed using the binding domain of GID1A and then docked into the receptor. D1 and D4 were shown to have good docking scores due to enhanced hydrophobic contact. We hope that these results will provide useful guidance in the rational design of new NSPs.