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. 2022 Nov 24:12:1044770.
doi: 10.3389/fcimb.2022.1044770. eCollection 2022.

Molecular docking and molecular dynamics study Lianhua Qingwen granules (LHQW) treats COVID-19 by inhibiting inflammatory response and regulating cell survival

Jun-Feng Cao  1   2 , Yunli Gong  1 , Mei Wu  1 , Li Xiong  1 , Shengyan Chen  1 , Haonan Huang  1 , Xinge Zhou  1 , Ying-Chun Peng  1   3 , Xue-Fang Shen  1   3 , Jinyu Qu  1   3 , Yi-Li Wang  1   3 , Xiao Zhang  1   2
Affiliations

Molecular docking and molecular dynamics study Lianhua Qingwen granules (LHQW) treats COVID-19 by inhibiting inflammatory response and regulating cell survival

Jun-Feng Cao et al. Front Cell Infect Microbiol. .

Abstract

Purpose: 2019 Coronavirus disease (COVID-19) is endangering health of populations worldwide. Latest research has proved that Lianhua Qingwen granules (LHQW) can reduce tissue damage caused by inflammatory reactions and relieve patients' clinical symptoms. However, the mechanism of LHQW treats COVID-19 is currently lacking. Therefore, we employed computer simulations to investigate the mechanism of LHQW treats COVID-19 by modulating inflammatory response.

Methods: We employed bioinformatics to screen active ingredients in LHQW and intersection gene targets. PPI, GO and KEGG was used to analyze relationship of intersection gene targets. Molecular dynamics simulations validated the binding stability of active ingredients and target proteins. Binding free energy, radius of gyration and the solvent accessible surface area were analyzed by supercomputer platform.

Results: COVID-19 had 4628 gene targets, LHQW had 1409 gene targets, intersection gene targets were 415. Bioinformatics analysis showed that intersection targets were closely related to inflammation and immunomodulatory. Molecular docking suggested that active ingredients (including: licopyranocoumarin, Glycyrol and 3-3-Oxopropanoic acid) in LHQW played a role in treating COVID-19 by acting on CSF2, CXCL8, CCR5, NLRP3, IFNG and TNF. Molecular dynamics was used to prove the binding stability of active ingredients and protein targets.

Conclusion: The mechanism of active ingredients in LHQW treats COVID-19 was investigated by computer simulations. We found that active ingredients in LHQW not only reduce cell damage and tissue destruction by inhibiting the inflammatory response through CSF2, CXCL8, CCR5 and IFNG, but also regulate cell survival and growth through NLRP3 and TNF thereby reducing apoptosis.

Keywords: COVID-19; bioinformatics analysis; lianhua qingwen granules (LHQW); molecular docking; molecular dynamics.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
The venny of intersection gene targets. Targets of the intersection of Lianhua Qingwen granules (LHQW) and COVID-19.
Figure 2
Figure 2
Protein-protein interaction (PPI) network. (A) PPI network of protein targets, (B) PPI network of core protein targets (confidence>0.95).
Figure 3
Figure 3
Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of related genes. (A) The top 10 terms in biological processes (BP) were greatly enriched. (B) The subnetwork displayed the top 10 BP terms and related genes. (C) The top 10 terms in cellular components (CC) were greatly enriched. (D) The subnetwork displayed the first 10 CC terms and related genes. (E) The top 10 terms in molecular function (MF) were greatly enriched. (F) The subnetwork displayed the top 10 MF terms and related genes. (G) The top 20 KEGG pathways were showed. (H) The subnetworks displayed the top 20 KEGG pathways and related.
Figure 4
Figure 4
The result of molecular docking.
Figure 5
Figure 5
Binding conformation of active ingredients and protein targets. (A) CCR5/Licopyranocoumarin, (B) CSF2/3-3-Oxopropanoic acid, (C) CXCL8/Glycyrol, (D) IFNG/Glycyrol, (E) NLRP3/Licopyranocoumarin, (F) TNF/Glycyrol.
Figure 6
Figure 6
The result of root mean square deviation (RMSD).
Figure 7
Figure 7
The result of root mean square fluctuations (RMSF). (A) CCR5/Licopyranocoumarin, (B) CSF2/3-3-Oxopropanoic acid, (C) CXCL8/Glycyrol, (D) IFNG/Glycyrol, (E) NLRP3/Licopyranocoumarin, (F) TNF/Glycyrol.
Figure 8
Figure 8
Analysis of hydrogen bonds. (A) CCR5/Licopyranocoumarin, (B) CSF2/3-3-Oxopropanoic acid, (C) CXCL8/Glycyrol, (D) IFNG/Glycyrol, (E) NLRP3/Licopyranocoumarin, (F) TNF/Glycyrol.
Figure 9
Figure 9
Analysis of radius of rotation (Rog).
Figure 10
Figure 10
Analysis of solvent accessible surface area (SASA).
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