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Ligand-based approach for predicting drug targets and for virtual screening against COVID-19

文献类型：期刊论文

作者Yang, Yanqing1,2,3; Zhu, Zhengdan1,2,3; Wang, Xiaoyu4; Zhang, Xinben1,2; Mu, Kaijie5; Shi, Yulong1,2,3; Peng, Cheng1,2,3; Xu, Zhijian1,2,3; Zhu, Weiliang1,2,3
刊名BRIEFINGS IN BIOINFORMATICS
出版日期2021-03-01
卷号22期号:2页码:1053-1064
ISSN号1467-5463
关键词D3Similarity COVID-19 target prediction database virtual screening
DOI10.1093/bib/bbaa422
通讯作者Xu, Zhijian(zjxu@simm.ac.cn) ; Zhu, Weiliang(wlzhu@simm.ac.cn)
英文摘要Discovering efficient drugs and identifying target proteins are still an unmet but urgent need for curing coronavirus disease 2019 (COVID-19). Protein structure-based docking is a widely applied approach for discovering active compounds against drug targets and for predicting potential targets of active compounds. However, this approach has its inherent deficiency caused by e.g. various different conformations with largely varied binding pockets adopted by proteins, or the lack of true target proteins in the database. This deficiency may result in false negative results. As a complementary approach to the protein structure-based platform for COVID-19, termed as D3Docking in our previous work, we developed in this study a ligand-based method, named D3Similarity, which is based on the molecular similarity evaluation between the submitted molecule(s) and those in an active compound database. The database is constituted by all the reported bioactive molecules against the coronaviruses, viz., severe acute respiratory syndrome coronavirus (SARS), Middle East respiratory syndrome coronavirus (MERS), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), human betacoronavirus 2c EMC/2012 (HCoV-EMC), human CoV 229E (HCoV-229E) and feline infectious peritonitis virus (FIPV), some of which have target or mechanism information but some do not. Based on the two-dimensional (2D) and three-dimensional (3D) similarity evaluation of molecular structures, virtual screening and target prediction could be performed according to similarity ranking results. With two examples, we demonstrated the reliability and efficiency of D3Similarity by using 2Dx3D value as score for drug discovery and target prediction against COVID-19. The database, which will be updated regularly, is available free of charge at https://www.d3pharma.com/D3Targets-2019-nCoV/D3Similarity/index.php.
WOS关键词PROTEASE INHIBITORS ; MAIN PROTEASE ; CORONAVIRUS ; REPLICATION
资助项目National Key Research and Development Program of China[2016YFA0502800] ; National Key Research and Development Program of China[2016YFA0502301]
WOS研究方向Biochemistry & Molecular Biology ; Mathematical & Computational Biology
语种英语
出版者OXFORD UNIV PRESS
WOS记录号WOS:000642298000034
源URL[http://119.78.100.183/handle/2S10ELR8/297017]  
专题中国科学院上海药物研究所
通讯作者Xu, Zhijian; Zhu, Weiliang
作者单位1.Chinese Acad Sci, CAS Key Lab Receptor Res, Shanghai 201203, Peoples R China
2.Chinese Acad Sci, Drug Discovery & Design Ctr, Shanghai Inst Mat Med, Shanghai 201203, Peoples R China
3.Univ Chinese Acad Sci, Sch Pharm, 19A Yuquan Rd, Beijing 100049, Peoples R China
4.Shanghai Univ Elect Power, Coll Math & Phys, Shanghai 200090, Peoples R China
5.Univ Sci & Technol China, Nano Sci & Technol Inst, Suzhou 215123, Jiangsu, Peoples R China
推荐引用方式
GB/T 7714		 Yang, Yanqing,Zhu, Zhengdan,Wang, Xiaoyu,et al. Ligand-based approach for predicting drug targets and for virtual screening against COVID-19[J]. BRIEFINGS IN BIOINFORMATICS,2021,22(2):1053-1064.
APA Yang, Yanqing.,Zhu, Zhengdan.,Wang, Xiaoyu.,Zhang, Xinben.,Mu, Kaijie.,...&Zhu, Weiliang.(2021).Ligand-based approach for predicting drug targets and for virtual screening against COVID-19.BRIEFINGS IN BIOINFORMATICS,22(2),1053-1064.
MLA Yang, Yanqing,et al."Ligand-based approach for predicting drug targets and for virtual screening against COVID-19".BRIEFINGS IN BIOINFORMATICS 22.2(2021):1053-1064.

入库方式： OAI收割

来源：上海药物研究所

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