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Flexible computational docking studies of new aminoglycosides targeting RNA 16S bacterial ribosome site
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
2008-08-01
DOI10.1016/j.ejmech.2007.10.022
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
WOS记录号WOS:000259161600009
项目编号2004CB518904 ; 90713005
资助机构Ministry of Science and Technology of China ; National Natural Science Foundation of China
引用统计
被引频次:18[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.bjmu.edu.cn/handle/400002259/58467
专题北京大学药学院
北京大学药学院_药物化学系
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
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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.
APA Barbault, Florent.,Ren, Bo.,Rebehmed, Joseph.,Teixeira, Catia.,Luo, Yun.,...&Zhang, Lihe.(2008).Flexible computational docking studies of new aminoglycosides targeting RNA 16S bacterial ribosome site.EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY,43(8),1648-1656.
MLA Barbault, Florent,et al."Flexible computational docking studies of new aminoglycosides targeting RNA 16S bacterial ribosome site".EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY 43.8(2008):1648-1656.
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