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学科主题: 药学
题名:
Flexible computational docking studies of new aminoglycosides targeting RNA 16S bacterial ribosome site
作者: Barbault, Florent1; Ren, Bo2; Rebehmed, Joseph1; Teixeira, Catia1; Luo, Yun1; Smila-Castro, Ornella1; Maurel, Francois1; Fan, BoTao1; Zhang, Liangren2; Zhang, Lihe2
关键词: RNA ; aminoglycoside ; antibiotics ; molecular dynamics ; docking
刊名: EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
发表日期: 2008-08-01
DOI: 10.1016/j.ejmech.2007.10.022
卷: 43, 期:8, 页:1648-1656
收录类别: SCI
文章类型: Article
WOS标题词: Science & Technology
类目[WOS]: Chemistry, Medicinal
研究领域[WOS]: Pharmacology & Pharmacy
关键词[WOS]: AMBER FORCE-FIELD ; MOLECULAR-DYNAMICS ; DRUG TARGET ; MECHANICAL CALCULATIONS ; CATIONIC ANTIBIOTICS ; A-SITE ; BINDING ; PROTEINS ; MODEL ; SIMULATIONS
英文摘要:

Ribonucleic acids (RNAs) have only recently been viewed as a target for small-molecules drug discovery. Aminoglycoside compounds are antibiotics which bind the ribosomal A site (16S fragment) and cause misreading of the bacterial genetic code and inhibit translocation. In this work, a complete molecular modeling study is done for 16 newly derived anninoglycoside compounds where diverse nucleoside fragments are linked. Docking calculations are applied to 16S RNA target and a weak linear correlation, between experimental and calculated data, is obtained. However, one particularity of RNA is its high flexibility. To mimic this behavior, all docking calculations are followed by small molecular dynamic simulations. This last computational step improves significantly the correlation with experimental data and allowed us to establish structure-activity relationships. The overall results showed that the consideration of the RNA dynamic behavior is of great interest. (c) 2007 Elsevier Masson SAS. All rights reserved.

语种: 英语
所属项目编号: 2004CB518904 ; 90713005
项目资助者: Ministry of Science and Technology of China ; National Natural Science Foundation of China
WOS记录号: WOS:000259161600009
Citation statistics:
内容类型: 期刊论文
URI标识: http://ir.bjmu.edu.cn/handle/400002259/58467
Appears in Collections:北京大学药学院_期刊论文

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作者单位: 1.Univ Paris Diderot, ITODYS, CNRS UMR 7086, F-75005 Paris, France
2.Peking Univ, Sch Pharmaceut Sci, State Key Lab Nat & Biomimet Drugs, Beijing 100083, Peoples R China

Recommended Citation:
Barbault, Florent,Ren, Bo,Rebehmed, Joseph,et al. Flexible computational docking studies of new aminoglycosides targeting RNA 16S bacterial ribosome site[J]. EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY,2008,43(8):1648-1656.
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