D3Targets-2019-nCoV: a webserver for predicting drug targets and for multi-target and multi-site based virtual screening against COVID-19.
10.1016/j.apsb.2020.04.006
- Author:
Yulong SHI
1
;
Xinben ZHANG
1
;
Kaijie MU
1
;
Cheng PENG
1
;
Zhengdan ZHU
1
;
Xiaoyu WANG
1
;
Yanqing YANG
1
;
Zhijian XU
1
;
Weiliang ZHU
1
Author Information
1. CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
- Publication Type:Journal Article
- Keywords:
COVID-19;
D3Targets-2019-nCoV;
Docking;
Multi-conformation;
Multi-site;
SARS-CoV-2;
Target prediction
- From:
Acta Pharmaceutica Sinica B
2020;10(7):1239-1248
- CountryChina
- Language:English
-
Abstract:
A highly effective medicine is urgently required to cure coronavirus disease 2019 (COVID-19). For the purpose, we developed a molecular docking based webserver, namely D3Targets-2019-nCoV, with two functions, one is for predicting drug targets for drugs or active compounds observed from clinic or / studies, the other is for identifying lead compounds against potential drug targets docking. This server has its unique features, (1) the potential target proteins and their different conformations involving in the whole process from virus infection to replication and release were included as many as possible; (2) all the potential ligand-binding sites with volume larger than 200 Å on a protein structure were identified for docking; (3) correlation information among some conformations or binding sites was annotated; (4) it is easy to be updated, and is accessible freely to public (https://www.d3pharma.com/D3Targets-2019-nCoV/index.php). Currently, the webserver contains 42 proteins [20 severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) encoded proteins and 22 human proteins involved in virus infection, replication and release] with 69 different conformations/structures and 557 potential ligand-binding pockets in total. With 6 examples, we demonstrated that the webserver should be useful to medicinal chemists, pharmacologists and clinicians for efficiently discovering or developing effective drugs against the SARS-CoV-2 to cure COVID-19.
