Deep Learning Based Drug Screening for Novel Coronavirus 2019-nCov

doi:10.1007/s12539-020-00376-6

	Deep Learning Based Drug Screening for Novel Coronavirus 2019-nCov
	Zhang, Haiping 1; Saravanan, Konda Mani 1; Yang, Yang 2; Hossain, Md Tofazzal 1,6; Li, Junxin 3; Ren, Xiaohu 4; Pan, Yi 5; Wei, Yanjie 1
	2020-06-01
发表期刊	INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES
ISSN	1913-2751
页码	9
摘要	A novel coronavirus, called 2019-nCoV, was recently found in Wuhan, Hubei Province of China, and now is spreading across China and other parts of the world. Although there are some drugs to treat 2019-nCoV, there is no proper scientific evidence about its activity on the virus. It is of high significance to develop a drug that can combat the virus effectively to save valuable human lives. It usually takes a much longer time to develop a drug using traditional methods. For 2019-nCoV, it is now better to rely on some alternative methods such as deep learning to develop drugs that can combat such a disease effectively since 2019-nCoV is highly homologous to SARS-CoV. In the present work, we first collected virus RNA sequences of 18 patients reported to have 2019-nCoV from the public domain database, translated the RNA into protein sequences, and performed multiple sequence alignment. After a careful literature survey and sequence analysis, 3C-like protease is considered to be a major therapeutic target and we built a protein 3D model of 3C-like protease using homology modeling. Relying on the structural model, we used a pipeline to perform large scale virtual screening by using a deep learning based method to accurately rank/identify protein-ligand interacting pairs developed recently in our group. Our model identified potential drugs for 2019-nCoV 3C-like protease by performing drug screening against four chemical compound databases (Chimdiv, Targetmol-Approved_Drug_Library, Targetmol-Natural_Compound_Library, and Targetmol-Bioactive_Compound_Library) and a database of tripeptides. Through this paper, we provided the list of possible chemical ligands (Meglumine, Vidarabine, Adenosine, d-Sorbitol, d-Mannitol, Sodium_gluconate, Ganciclovir and Chlorobutanol) and peptide drugs (combination of isoleucine, lysine and proline) from the databases to guide the experimental scientists and validate the molecules which can combat the virus in a shorter time.
关键词	Coronavirus Deep learning Drug screening Homology modeling 3C-like protease
DOI	10.1007/s12539-020-00376-6
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2018YFB0204403] ; National Key Research and Development Program of China[2016YFB0201305] ; National Science Foundation of China[U1813203] ; National Science Foundation of China[61433012] ; National Natural Youth Science Foundation of China[31601028] ; Shenzhen Basic Research Fund[JCYJ20180507182818013] ; Shenzhen Basic Research Fund[GGFW2017073114031767] ; Shenzhen Basic Research Fund[JCYJ20170413093358429] ; China Postdoctoral Science Foundation[2019M653132] ; CAS Key Lab[2011DP173015] ; Shenzhen Discipline Construction Project for Urban Computing and Data Intelligence, Youth Innovation Promotion Association, CAS
WOS研究方向	Mathematical & Computational Biology
WOS类目	Mathematical & Computational Biology
WOS记录号	WOS:000537395500001
出版者	SPRINGER HEIDELBERG
引用统计	被引频次：118[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/15353
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Wei, Yanjie
作者单位	1.Chinese Acad Sci, Ctr High Performance Comp, Joint Engn Res Ctr Hlth Big Data Intelligent Anal, Shenzhen Inst Adv Technol, Shenzhen 518055, Guangdong, Peoples R China 2.Southern Univ Sci & Technol, Shenzhen Peoples Hosp 3, Hosp 2,State Key Discipline Infect Dis, Shenzhen Key Lab Pathogen & Immun,Guangdong Key L, Shenzhen 518112, Peoples R China 3.Univ City Shenzhen, Chinese Acad Sci, Inst Biomed & Biotechnol, Shenzhen Lab Human Antibody Engn,Shenzhen Inst Ad, 1068 Xueyuan Blvd, Shenzhen 518055, Peoples R China 4.Shenzhen Ctr Dis Control & Prevent, Inst Toxicol, 8 Longyuan Rd, Shenzhen 518055, Peoples R China 5.Georgia State Univ, Dept Comp Sci, Atlanta, GA 30302 USA 6.Univ Chinese Acad Sci, 19 A Yuquan Rd, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Haiping,Saravanan, Konda Mani,Yang, Yang,et al. Deep Learning Based Drug Screening for Novel Coronavirus 2019-nCov[J]. INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES,2020:9.
APA	Zhang, Haiping.,Saravanan, Konda Mani.,Yang, Yang.,Hossain, Md Tofazzal.,Li, Junxin.,...&Wei, Yanjie.(2020).Deep Learning Based Drug Screening for Novel Coronavirus 2019-nCov.INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES,9.
MLA	Zhang, Haiping,et al."Deep Learning Based Drug Screening for Novel Coronavirus 2019-nCov".INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES (2020):9.