Molecular dynamic and quantum mechanics study of drug recognition for the extremity of DNA G-quadruplex groove

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• 作者：Jinlian Li (1) (2) (3)
  Jia Fu (3)
  Jianping Wang (2)
  Donghua Hu (2)
  Zhongmin Su (1) (2)
  Xiaoqiang Jin (3)
  
• 关键词：Molecular dynamics (MD) ; Density functional theory (DFT) ; G ; quadruplex groove ; Distamycin A ; Electronic property
• 刊名：Medicinal Chemistry Research
• 出版年：2012
• 出版时间：December 2012
• 年：2012
• 卷：21
• 期：12
• 页码：4010-4016
• 全文大小：545KB
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• 作者单位：Jinlian Li (1) (2) (3)
  Jia Fu (3)
  Jianping Wang (2)
  Donghua Hu (2)
  Zhongmin Su (1) (2)
  Xiaoqiang Jin (3)
  
  1. Department of Chemistry, College of Science, Yanbian University, Yanji, 133002, People鈥檚 Republic of China
  2. Institute of Functional Material Chemistry, Department of Chemistry, Northeast Normal University, Changchun, 130024, People鈥檚 Republic of China
  3. Department of Chemistry, College of Pharmaceutical Sciences, Jiamusi University, Jiamusi, 154007, People鈥檚 Republic of China
  

文摘

Human DNA G-quadruplex has been an attractive drug target for cancer therapeutic intervention. Especially the G-quadruplex groove has been paid growing attention to because of its selectivity. In this work, molecular dynamics (MD) simulations of the complexes of parallel G-quadruplexes ([d(TGGGGT)]4 and [d(GGGGGG)]4) with distamycin A (Dist-A) dimmers were performed. The characteristic of drug binding in G-quadruplex grooves was investigated. The simulations reveal the propensity of Dist-A dimmer toward the end of the groove. The electronic properties of three successive G-tetrads are estimated by density functional theory (DFT) method at the B3LYP/6-31G (d, p) level. The results show that the N3 atoms in two terminal G-tetrads possess more negative charges than it in the middle G-tetrad, which is one reason for driving cation ligand toward the end of groove. This study provides the factors of affecting the binding of drugs in the G-quadruplex groove and is of significance for drug design based on the structure of G-quadruplex groove.