Virtual screening of active ingredients of traditional Chinese medicine in treating COVID-19 based on molecular docking and molecular dynamic simulation.
10.7507/1001-5515.202205021
- Author:
Minghao LIU
1
;
Iqbal Khan FAEZ
2
;
Yuqing XIAO
3
;
Xu WANG
4
;
Ziran HU
5
;
Dakun LAI
1
Author Information
1. School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, P. R. China.
2. Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215000, P. R. China.
3. School of Medicine, University of Electronic Science and Technology of China, Chengdu 610054, P. R. China.
4. School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, P. R. China.
5. First Clinical Medical College, Heilongjiang University of Chinese Medicine, Harbin 150006, P. R. China.
- Publication Type:Journal Article
- Keywords:
COVID-19;
Molecular docking;
Molecular dynamics simulations;
Traditional Chinese medicines;
Virtual screening;
Xambioona
- MeSH:
Humans;
SARS-CoV-2;
Molecular Docking Simulation;
Medicine, Chinese Traditional;
Molecular Dynamics Simulation;
Nucleocapsid Proteins;
Antiviral Agents/pharmacology*;
COVID-19 Drug Treatment
- From:
Journal of Biomedical Engineering
2022;39(5):1005-1014
- CountryChina
- Language:Chinese
-
Abstract:
We aim to screen out the active components that may have therapeutic effect on coronavirus disease 2019 (COVID-19) from the severe and critical cases' prescriptions in the "Coronavirus Disease 2019 Diagnosis and Treatment Plan (Trial Ninth Edition)" issued by the National Health Commission of the People's Republic of China and explain its mechanism through the interactions with proteins. The ETCM database and SwissADME database were used to screen the active components contained in 25 traditional Chinese medicines in 3 prescriptions, and the PDB database was used to obtain the crystal structures of 4 proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Molecular docking was performed using Autodock Vina and molecular dynamics simulations were performed using GROMACS. Binding energy results showed that 44 active ingredients including xambioona, gancaonin L, cynaroside, and baicalin showed good binding affinity with multiple targets of SARS-CoV-2, while molecular dynamics simulations analysis showed that xambioona bound more tightly to the nucleocapsid protein of SARS-CoV-2 and exerted a potent inhibitory effect. Modern technical methods are used to study the active components of traditional Chinese medicine and show that xambioona is an effective inhibitor of SARS-CoV-2 nucleocapsid protein, which provides a theoretical basis for the development of new anti-SARS-CoV-2 drugs and their treatment methods.
