Citation: Qing-Xiu HE, Guang-Ping LI, Hai-Qiong GUO, Yu-Xuan WANG, Han CHU, Yong HU, Yan SHEN, Zhi-Hua LIN, Yuan-Qiang WANG. Discovery of Potential SARS-CoV-2 M Protease Inhibitors by Virtual Screening, Molecular Dynamics, and Binding Free Energy Analyses[J]. Chinese Journal of Structural Chemistry, ;2021, 40(4): 431-442. doi: 10.14102/j.cnki.0254-5861.2011-2966 shu

Discovery of Potential SARS-CoV-2 M Protease Inhibitors by Virtual Screening, Molecular Dynamics, and Binding Free Energy Analyses

Qing-Xiu HE ^{a, ②} ,
Guang-Ping LI ^{a, ②} ,
Hai-Qiong GUO ^a ,
Yu-Xuan WANG ^a ,
Han CHU ^a ,
Yong HU ^a ,
Yan SHEN ^a ,
Zhi-Hua LIN ^{a, b,,} ,
Yuan-Qiang WANG ^{a, b,,}

a.
School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
b.
Chongqing the Seventh People's Hospital, Chongqing 400054, China

Corresponding author: Zhi-Hua LIN, zhlin@cqut.edu.cn Yuan-Qiang WANG, wangyqnn@cqut.edu.cn
Received Date: 28 August 2020
Accepted Date: 29 October 2020

Fund Project: the National Natural Science Foundation of China 31400667Chongqing Municipal Education Commission Science and Technology Research Project KJZD-K201801102Chongqing Research Program of Basic Research and Frontier Technology cstc2018jcyjAX0683Opening Foundation of State Key Laboratory of Silkworm Genome Biology sklsgb1819-2

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) gained tremendous attention due to its high infectivity and pathogenicity. The 3-chymotrypsin-like hydrolase protease (Mpro) of SARS-CoV-2 has been proven to be an important target for anti-SARS-CoV-2 activity. To better identify the drugs with potential in treating coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 and according to the crystal structure of Mpro, we conducted a virtual screening of FDA-approved drugs and chemical agents that have entered clinical trials. As a result, 9 drug candidates with therapeutic potential for the treatment of COVID-19 and with good docking scores were identified to target SARS-CoV-2. Consequently, molecular dynamics (MD) simulation was performed to explore the dynamic interactions between the predicted drugs and Mpro. The binding mode during MD simulation showed that hydrogen bonding and hydrophobic interactions played an important role in the binding processes. Based on the binding free energy calculated by using MM/PBSA, Lopiravir, an inhibitor of human immunodeficiency virus (HIV) protease, is under investigation for the treatment of COVID-19 in combination with ritionavir, and it might inhibit Mpro effectively. Moreover, Ombitasvir, an inhibitor for non-structural protein 5A of hepatitis C virus (HCV), has good inhibitory potency for Mpro. It is notable that the GS-6620 has a binding free energy, with respect to binding Mpro, comparable to that of ombitasvir. Our study suggests that ombitasvir and lopinavir are good drug candidates for the treatment of COVID-19, and that GS-6620 has good anti-SARS-CoV-2 activity.
- severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2),
- virtual screening,
- molecular docking,
- molecular dynamics (MD) simulation,
- binding free energy
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