[1]于明珠),张鹏莉),吕思凡),等.小分子化合物3D结构数据库的构建[J].郑州大学学报(医学版),2019,(01):46-50.[doi:10.13705/j.issn.1671-6825.2018.05.113]
 YU Mingzhu),ZHANG Pengli),LYU Sifan),et al.Construction of a 3D structural platform of small molecule compounds[J].JOURNAL OF ZHENGZHOU UNIVERSITY(MEDICAL SCIENCES),2019,(01):46-50.[doi:10.13705/j.issn.1671-6825.2018.05.113]
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小分子化合物3D结构数据库的构建()
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《郑州大学学报(医学版)》[ISSN:1671-6825/CN:41-1340/R]

卷:
期数:
2019年01期
页码:
46-50
栏目:
应用研究
出版日期:
2019-01-20

文章信息/Info

Title:
Construction of a 3D structural platform of small molecule compounds
作者:
于明珠1)张鹏莉1)吕思凡1)杜尚民2)高艳锋1)杜江峰1)
1)郑州大学生命科学学院 郑州 4500012)三门峡职业技术学院医护学院 河南三门峡 472143
Author(s):
YU Mingzhu1)ZHANG Pengli1)LYU Sifan1)DU Shangmin2) GAO Yanfeng1) DU Jiangfeng1)
1)School of Life Sciences,Zhengzhou University,Zhengzhou 4500012)Department of Medicine and Nursing,and nursing,College of Sanmenxia Polytechnic,Sanmenxia, Henan 472143
关键词:
指纹图谱 虚拟筛选 先导化合物 3D结构
Keywords:
fingerprint virtual screening lead compound 3D structure
分类号:
R914.2
DOI:
10.13705/j.issn.1671-6825.2018.05.113
摘要:
目的:构建小分子化合物3D结构数据库,为药物设计提供筛选平台。方法:从6个常用的小分子化合物公司的官方平台下载小分子化合物库(ChemBridge、ChemDiv、InterBioScreen、LifeChemicals、Specs和Vitas-m),同时通过整理文献获得毒理库、片段库、上市药物库以及天然产物库,用MOE软件对获得的所有化合物进行3D结构生成,通过能量最小化确定小分子化合物的最佳3D结构,并计算指纹图谱及其物理属性。结果与结论:构建了小分子化合物的3D结构数据库。对所有小分子化合物属性的分析表明6个商用数据库所包含的小分子化合物绝大多数具有类药性,但也存在具有毒性的片段; 各数据库的物理属性如氢键受体/供体数等分布图不尽相同。该平台产生的数据可以直接用于基于靶点结构的虚拟筛选和3D相似性搜索,亦有助于药物设计者选择具有针对性的数据库进行药物筛选工作。
Abstract:
Aim:To construct a 3D structural platform of small molecule compounds for drug screening and discovery.Methods:Small molecule compounds were downloaded from 6 common commercial databases such as ChemBridge,ChemDiv,InterBioScreen,LifeChemicals,Specs,and Vitas-m. At the same time,we established a toxicology library, the fragment library, FDA-approved drugs library and the natural product library by collecting data thoroughly from literatures. All obtained compounds were processed and optimized by MOE package, including the calculations of fingerprint and structural properties, and the best 3D structure determination.Results and Conclusion:A 3D structural platform of small molecule compounds was constructed and the molecular properties were analyzed.The results showed that the majority of the compounds in the 6 commercial databases were drug-like, though some toxic fragments existed in the databases as well. The results also revealed that the molecular properties such as hydrogen bond donor/acceptor had preferences in different databases, which might assist scientists to choose proper database for drug screening. The platform could be served as data resource for target-based virtual screening and 3D similarity search.

参考文献/References:

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备注/Memo

备注/Memo:
【基金项目】国家自然科学基金资助项目(31500620); 郑州大学优秀青年教师发展基金项目(F0000686) 【作者简介】杜江峰, 通信作者, 男, 1982年11月生, 博士, 副教授, 研究方向:计算机辅助药物设计,E-mail:jiangfengdu@zzu.edu.cn
更新日期/Last Update: 2019-01-20