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化学学报
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化学学报 ›› 2007, Vol. 65 ›› Issue (4): 284-288. 上一篇    下一篇

研究论文

诺氟沙星-DNA复合物的分子动力学模拟

马国正*,1, 蒋勇军2, 俞庆森2   

  1. (1华南师范大学化学与环境学院 广州 510006)
    (2浙江大学宁波理工学院药物分子设计与营养工程重点实验室 宁波 315100)
  • 投稿日期:2006-07-03 修回日期:2006-08-28 发布日期:2007-02-28
  • 通讯作者: 马国正

Molecular Dynamics Simulation of the Norfloxacin-DNA Complex

MA Guo-Zheng*,1; JIANG Yong-Jun2; YU Qing-Sen2   

  1. (1 School of Chemistry & Environment, South China Normal University, Guangzhou 510006)
    (2 Key Laboratory for Molecular Design and Nutrition Engineering of Ningbo City, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100)
  • Received:2006-07-03 Revised:2006-08-28 Published:2007-02-28
  • Contact: MA Guo-Zheng

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1199

被引次数

13 | 5

采用分子模建的方法构建了诺氟沙星-DNA复合物的初始结构, 通过2 ns的分子动力学(MD)模拟研究表明: 诺氟沙星能够和双螺旋d[ATATCGATAT]2形成稳定的复合物, 药物分子可紧密结合在DNA的小沟区域, 并且能够与DNA的鸟嘌呤碱基形成两个稳定的氢键. 在分子水平上提供了诺氟沙星直接与双螺旋DNA相互作用的结构及复合物的动态变化情况.

关键词: 诺氟沙星, DNA, 分子模建, 分子动力学模拟

Molecular dynamics (MD) simulations were used to investigate the interaction of norfloxacin with the DNA oligonucleotide d[ATATCGATAT]2. The initial binding structure was built with molecular modeling based on the experimental results. A 2 ns MD calculation was performed to study the norflox-acin-DNA complex and the results indicated that norfloxacin was inserted in the minor groove of DNA, binding to the region of duplex TCGA bases. The possible H-bonds between carbonyl and carboxyl group of norfloxacin and amine group of the guanine base support a minor-groove complex for the compound in GC DNA sequence. Molecular dynamics studies complement the structural analysis and provide a clear picture of the norfloxacin-DNA complex.

Key words: norfloxacin, DNA, molecular modeling, molecular dynamics simulation