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Acta Chimica Sinica ›› 2011, Vol. 69 ›› Issue (20): 2427-2433. Previous Articles     Next Articles

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洋刀豆脲酶与抑制剂相互作用的分子对接和分子动力学研究

吕婧1，蒋勇军*,2，俞庆森1,2，邹建卫2   

  1. (1浙江大学化学系 杭州 310027)
    (2浙江大学宁波理工学院分子设计与营养工程市重点实验室 宁波 315104)
  • 投稿日期:2011-01-17 修回日期:2011-05-18 发布日期:2011-06-16
  • 通讯作者: 蒋勇军 E-mail:yjjiang@nit.net.cn
  • 基金资助:

    GSK3β激酶结构功能的分子模拟研究

Molecular Docking and Molecular Dynamics Simulations of Inhibitors Binding to Jack Bean Urease

Lü Jing1 Jiang Yongjun*,2 Yu Qingsen1,2 Zou Jianwei2   

  1. (1 Department of Chemistry, Zhejiang University, Hangzhou 310027)
    (2 Key Laboratory for Molecular Design and Nutrition Engineering of Ningbo City, Ningbo Institute of Technology, Zhejiang University, Ningbo 315104)
  • Received:2011-01-17 Revised:2011-05-18 Published:2011-06-16

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From the bioassay tests, compound 2-acetyl-γ-hydroxybutyric (COM) showed good inhibitory activity against Jack bean urease with IC50＝375 μmol•L－l. Then the molecular docking and molecular dynamics (MD) simulations were performed to investigate the interactions between Jack bean urease and inhibitor aceto hydroxamic acid (AHA) and COM. GOLD3.0 program was used to perform the docking, and Amber was used to model the docking complex structures of inhibitor-Jack bean urease. Nonbonded model used for the nickel ions provided good reproduction of the active site of Jack bean urease during the MD simulations. The results confirmed that both nickel ions were pentacoordinated in AHA-Jack bean urease model. The binding model of the COM-Jack bean urease showed that Ni(1) was pentacoordinated while Ni(2) was hexacoordinated. The models provided useful information for understanding of the interactions between inhibitors and the protein.

Key words: Jack bean urease, molecular docking, molecular dynamics simulation, MM_GBSA, Nickel ion