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Integrating network pharmacology and molecular docking to explore the potential mechanism of Xinguan No. 3 in the treatment of COVID-19

  • Jiayan Peng , Kun Zhang , Lijie Wang , Fang Peng , Chuantao Zhang , Kunlan Long , Jun Chen , Xiujuan Zhou , Peiyang Gao EMAIL logo and Gang Fan EMAIL logo
Published/Copyright: July 8, 2022
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Open Chemistry
From the journal Open Chemistry Volume 20 Issue 1

Abstract

Xinguan No. 3 has been recommended for the treatment of coronavirus disease 2019 (COVID-19); however, its potential mechanisms are unclear. This study aims to explore the mechanisms of Xinguan No. 3 against COVID-19 through network pharmacology and molecular docking. We first searched the ingredients of Xinguan No. 3 in three databases (Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform, Traditional Chinese Medicines Integrated Database, and The Encyclopedia of Traditional Chinese Medicine). The active components and their potential targets were predicted through the SwissTargetPrediction website. The targets of COVID-19 can be found on the GeneCards website. Protein interaction analysis, screening of key targets, functional enrichment of key target genes, and signaling pathway analysis were performed through Search Tool for the Retrieval of Interacting Genes databases, Metascape databases, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway databases. Finally, the affinity of the key active components with the core targets was verified by molecular docking. The results showed that five core targets had been screened, including MAPK1, NF-κB1, RELA, AKT1, and MAPK14. Gene ontology enrichment analysis revealed that the key targets were associated with inflammatory responses and responses to external stimuli. KEGG enrichment analysis indicated that the main pathways were influenza A, hepatitis B, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, and TNF signaling pathway. Therefore, Xinguan No. 3 might play a role in treating COVID-19 through anti-inflammatory, immune responses, and regulatory responses to external stimuli.

Keywords: traditional Chinese medicine; Xinguan No. 3; COVID-19; network pharmacology; potential mechanism

1 Introduction

Coronavirus disease 2019 (COVID-19) is an acute respiratory infectious disease caused by a new type of coronavirus, which was named as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) [1]. The early symptoms of the disease include fever, cough, chest tightness, dyspnea, fatigue, abdominal distension and diarrhea, sore throat, and myalgia [2,3,4], which would gradually progress to severe respiratory diseases and affect other tissues and organs [5]. According to the latest data released by the World Health Organization on March 8, 2022, the confirmed cases in the world reached 445,096,612, and the confirmed deaths reached 5,998,301 [6]. Although people in some districts have already been vaccinated with vaccines against COVID-19 on a large scale, there is still a possibility for them to be infected with variants of SARS-CoV-2 [7]. In addition, some anti-COVID-19 drugs (e.g., paxlovid and molnupiravir) with good therapeutic effects seem perspective. However, they are too expensive [8]. So, it is of great significance to find safe, dependable, and inexpensive drugs to prevent COVID-19 as soon as possible.

Traditional Chinese Medicine (TCM) has played a vital role in preventing and treating COVID-19. Many TCM prescriptions have been officially recommended for the treatment of COVID-19 [9]. Studies have shown that TCM formulas could increase the cure rate and slow down the aggravation of the disease [10]. Xinguan No. 3, also known as Jing Fang Huo Pu Jie Du Mixture, is a TCM formula for treating COVID-19 in “Sichuan prevention control technology guide for novel coronavirus pneumonitis by TCM” [11]. It consists of 19 Chinese herbal medicines, including the aboveground part of Schizonepeta tenuifolia Briq., the root of Saposhnikovia divaricata (Turcz.) Schischk., the rootstock of Ligusticum chuanxiong Hort., the root of Angelica dahurica (Fisch. ex Hoffm.) Benth. et Hook. f. or A. dahurica (Fisch. ex Hoffm.) Benth. et Hook. f. var. formosana (Boiss.) Shan et Yuan, the aerial parts of Mentha haplocalyx Briq., the root of Platycodon grandiflorum (Jacq.) A. DC., the stem bark, root bark, or branch bark of Magnolia officinalis Rehd. et Wils. or M. officinalis Rehd. et Wils. var. biloba Rehd. et Wils., the tubers of Pinellia ternata (Thunb.) Breit., Medicinal Fermented Mass, the rootstock of Atractylodes macrocephala Koidz., the mature seed of Coix lacryma-jobi L. var. ma-yuen (Roman.) Stapf, the ripe seed of Dolichos lablab L., the ripe seed of Prunus armeniaca L. var. ansu Maxim., P. sibirica L., P. mandshurica (Maxim.) Koehne or P. armeniaca L., the ripe fruit of Crataegus pinnatifida Bge. var. major N. E. Br. or C. pinnatifida Bge., the sclerotia of Poria cocos (Schw.) Wolf, the aboveground part of Pogostemon cablin (Blanco) Benth., the leaves of Perilla frutescens (L.) Britt., the mature fruit of Amomum kravanh Pierre ex Gagnep. or A. compactum Soland ex Maton, and the rhizomes of Phragmites communis Trin (Table 1). The prescription of Xinguan No. 3 mainly comes from Jing Fang Bai Du Powder (JFBDP) and Huo Pu Xia Ling Decoction (HPXLD). JFBDP has a good curative effect on fever, headache, cough, and phlegm. It is often used to treat epidemic and infectious diseases, such as acute viral upper respiratory tract infections [12]. HPXLD has a therapeutic effect on diarrhea, fever, bloating, and headache. Xinguan No. 3 has the functions of relieving the exterior with the warm pungent and removing dampness with aromatic. For mild cases of COVID-19, the Xinguan No. 3 may effectively alleviate fever and cough symptoms.

Table 1

The constitution and potential targets of Xinguan No. 3

Herb Chinses name Abbreviation Dosage (g) No. of total compounds No. of compounds passing ADME filtration No. of protein targets
The aboveground part of Schizonepeta tenuifolia Jing Jie JJ 15 218 103 559
The root of Saposhnikovia divaricata Fang Feng FF 15 226 134 780
The rootstock of Ligusticum chuanxiong Chuan Xiong CX 15 342 176 860
The root of Angelica dahurica or A. dahurica var. formosana Bai Zhi BZhi 15 331 160 814
The aerial parts of Mentha haplocalyx Bo He BH 15 228 113 508
The root of Platycodon grandiflorum Jie Geng JG 30 142 21 401
The stem bark, root bark, or branch bark of Magnolia officinalis or M. officinalis var. biloba Hou Pu HP 15 235 140 884
The tubers of Pinellia ternata Ban Xia BX 15 196 83 734
The rootstock of Atractylodes macrocephala Bai Zhu BZhu 30 112 79 540
Medicinal Fermented Mass Jian Qu JQ 15 5 1 26
The mature seed of Coix lacryma-jobi var. ma-yuen Yi Yi Ren YYR 30 65 22 258
The ripe seed of Dolichos lablab Bai Bian Dou BBD 30 27 8 54
The ripe seed of Prunus armeniaca var. ansu or P. sibirica or P. mandshurica or P. armeniaca Ku Xing Ren KXR 15 118 56 544
The ripe fruit of Crataegus pinnatifida var. major or C. pinnatifida Shan Zha SZ 30 159 42 487
The sclerotia of Poria cocos Fu Ling FL 30 83 24 418
The aboveground part of Pogostemon cablin Guang Huo Xiang GHX 15 152 66 441
The leaves of Perilla frutescens Zi Su ZS 15 368 188 713
The mature fruit of Amomum kravanh or A. compactum Dou Kou DK 15 93 57 614
The rhizomes of Phragmites communis Lu Gen LG 30 46 25 243

With the development of systems biology and bioinformatics, network pharmacology has become one of the effective methods for discovering new drugs and exploring the mechanism of drug action [13,14]. Molecular docking is a computer-aided drug design method for predicting drug-target interactions. Molecular docking supports the systematic exploration of the binding modes of drug molecules to receptors [15]. Exploring the mechanism of TCM via integrating network pharmacology and molecular docking technology has been a research hotspot nowadays. In this study, we combined molecular docking and network pharmacology to reveal the underlying mechanisms and active components of the anti-COVID-19 effects of Xinguan No. 3. These studies will be beneficial for the development and clinical application of Xinguan No. 3 in the treatment of COVID-19.

2 Materials and methods

2.1 Acquiring the intersecting gene base of Xinguan No. 3 and COVID-19

All ingredients of Xinguan No. 3 were retrieved from three databases: The Encyclopedia of Traditional Chinese Medicine [16] (ETCM, http://www.tcmip.cn/ETCM/index.php/Home/Index/), Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform [17] (TCMSP, http://www.tcmspw. com/tcmsp.php), and Traditional Chinese Medicines Integrated Database [18] (TCMID, http://www. megabionet.org/tcmid/). By the way, Jian Qu is supplemented from the current literature rather than the databases mentioned above. Then, we screened each retrieved ingredient based on gastrointestinal (GI) and Drug-likeness (DL) by the SwissADME database, with the screening criteria being based on “high” GI absorption, and DL was satisfied with at least two “yes” at the same time [19]. The potential active ingredients were obtained after screening. Potential target information related to these active ingredients was predicted from the SwissTargetPrediction [20] (http://www.swisstarget prediction.ch/). The targets were sent to the UniProt database (https://www. uniprot.org/) for normalization. The targets related to COVID-19 were retrieved from the Human Gene Database [21] (GeneCards, https://www.genecards.org/) with the keyword “COVID-19.” The targets were also sent to the UniProt Database for normalization. Venny (version 2.1.0) was used to obtain Xinguan No. 3 and COVID-19-related gene set (intersection target set).

2.2 Protein–protein interaction (PPI) analysis and key targets screening

The intersecting target set was analyzed by the Search Tool for the Retrieval of Interacting Genes [22] (STRING, https://string-db.org/) to build a PPI network. Targets with confidence scores more outstanding than 0.9 were selected for analysis of protein interactions. The results were exported in TSV format and imported into Cytoscape (version 3.8.2). The network analysis in Cytoscape (version 3.8.2) [23] is used to analyze the topology parameters of the PPI network. The larger the degree value, the more likely it will become the core target in Xinguan No. 3 to treat COVID-19. In this study, the top 20 targets with the highest degree were selected as the key targets.

2.3 Functional enrichment analysis and core targets determination

To investigate the biological functions of the intersection target set, we performed gene ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis using the Metascape database [24] (http://metascape.org/gp/). GO enrichment analysis included three categories, including biological processes (BP), molecular functions (MF), and cellular components (CC). The functional categories were found and sorted by the P-value. To find the potential core targets for the treatment of COVID-19 with Xinguan No. 3, we plotted the enrichment network map of key targets in the first 15 pathways. We analyzed the importance of key targets in the pathway by degree values to obtain the core targets.

2.4 Construction of network visualization

The Drug-Component-Target-Disease network was built through Cytoscape (version 3.8.2). Among them, the core components with degree value greater than twice that of active components were selected. The establishment of visual drug–core components–key targets–pathway network reflects the complex relationships among active compounds, their potential targets, and pathways.

2.5 Molecular docking

The core components of Xinguan No. 3 were docked with the core targets (RELA, NF-κB1, AKT1, MAPK1, and MAPK14). In addition, we also docked between ACE2, Mpro, and the core components to explore the effects of Xinguan No. 3 on SARS-CoV-2 [25,26,27,28]. The crystal structure of low-resolution protein receptors was downloaded from RCSB Protein Data Bank (PDB) (https://www. rcsb.org/). The “Protein Preparation Wizard” module of Maestro 11.9 was used to optimize the structure of proteins. After optimization, the binding site of the original ligand in its crystal structure is appointed as the docking site of each protein, and the binding site of protein without the original ligand is predicted. The receptor grid file is generated by the “receptor grid generation panel.” The core components were optimized by the “Ligprep” module. Finally, the “glide docking” module is used to dock and score the treated active components and proteins.

3 Results

3.1 Main chemical compounds and protein targets of Xinguan No. 3

It is generally believed that the therapeutic effect of Chinese herbal medicines is achieved through the interaction of multiple active components/targets. Therefore, we searched for the chemical compounds and protein targets of the 19 herbal medicines used to formulate Xinguan No. 3. We first collected the chemical components of each plant in three Chinese herbal medicine databases. We then screened them by ADME to determine the chemical components that can be absorbed orally because Xinguan No. 3 is administered orally. After identifying those components that can be absorbed orally, we predicted the corresponding targets for each chemical component. Each herbal ingredient, the total number of its compounds, the number of orally absorbable compounds, and the number of their protein targets are listed in Table 1. The GeneCards database was used to screen for targets related to COVID-19. A total of 682 COVID-19 targets were retrieved using a filter set to score greater than or equal to the median. These 682 targets were combined with targets of Xinguan No. 3 to obtain a total of 153 intersection targets.

3.2 Construction and analysis of the Herb–Compound–Target network

To visualize the network topology status of Xinguan No. 3 treatment of COVID-19, we built a Drug–Component–Target–Disease network that reflects the complex relationships between drugs, active components, targets, and disease through Cytoscape (version 3.8.2). There were 19 drug nodes, 1,049 component nodes, 113 gene nodes, and 7,680 kinds of edges, as shown in Figure 3. In the network, the degree value represents the number of threads connected to one node and other nodes in the network. For components, the larger the degree value, the more targets it corresponds to, and the more likely it is component that plays a significant role in Xinguan No. 3. Therefore, we screened 241 components as core components using the 2-fold degree value as the screening criterion.

3.3 Construction and analysis of the PPI network

PPIs are essential for most BPs [29]. In this study, we constructed a PPI network to analyze the interaction of the intersection targets. The confidence score of PPI networks can be seen as an indicator of protein sequence pairs [30]. The confidence score of protein sequence pairs is related to the probability of the protein participating in biological regulation. Therefore, we selected the core targets with a confidence score greater than 0.9, of which 112 targets were enriched. As shown in Figure 1, the PPI network finally holds 112 nodes and 419 edges. The shape and color of the nodes represent the magnitude of the degree value, indicating the importance of the targets. Therefore, we chose the top 20 targets as the key targets which have a higher degree value than other targets, for example, RELA, JUN, STAT3, MAPK14, TNF, NFKB1, PIK3R1, STAT1, MAPK3, MAPK1, IL6, EGFR, and NFKBIA. They may be the most important potential targets in Xinguan No. 3 treatment for COVID-19 (Figure 2).

Figure 1 The Herb–Compound–Target–Disease network. Yellow circles are drugs of Xinguan No. 3. Green circles are the active components. Light green circles are the duplicate components. Orange circles are intersection targets.
Figure 1

The Herb–Compound–Target–Disease network. Yellow circles are drugs of Xinguan No. 3. Green circles are the active components. Light green circles are the duplicate components. Orange circles are intersection targets.

Figure 2 The PPI network of 113 targets. The size and brightness of the nodes indicate the importance of the targets.
Figure 2

The PPI network of 113 targets. The size and brightness of the nodes indicate the importance of the targets.

3.4 GO enrichment and KEGG pathway analysis

To further understand the mechanism of Xinguan No. 3 in treating COVID-19, the intersection targets were imported into Metascape for analysis. With P < 0.05 as the screening condition, a total of 368 BPs, 106 MFs, and 73 CCs were obtained. The top 15 GO items of each category were selected to draw cell component enrichment map, MF enrichment map, and BP enrichment map (Figure 3). Among them, BPs are the most important. The enrichment results of BPs show that the intersection targets are connected to the regulation of cytokine production, positive regulation of cytokine production, MAPK cascade, response to bacterium, regulation of defense response, positive regulation of response to external stimulus, and so on. For MFs, these targets are associated with kinase activity, cytokine receptor binding, transcription factor binding, etc. For the analysis of CC, these targets are mainly on the side of the membrane, lytic vacuole, and the lysosome.

Figure 3 GO and KEGG enrichment analysis of 113 core targets.
Figure 3

GO and KEGG enrichment analysis of 113 core targets.

KEGG pathway enrichment analyses (2D) of the 113 intersecting targets showed that the main signaling pathways involved Influenza A, Hepatitis B, Hepatitis C, Epstein–Barr virus infection, Toll-like receptor signaling pathway, Chagas disease (American trypanosomiasis), NOD-like receptor signaling pathway, Measles, TNF signaling pathway, Th17 cell differentiation, and so on.

Then, we have constructed a clearer network diagram of the relationship between drugs, core active ingredients, key targets, and pathways to express the role of Xinguan No. 3 more concisely and intuitively in the fight against COVID-19, as shown in Figure 4. After that, we further constructed a network map of key targets and pathways, as shown in Figure 5. The results showed that the five genes (MAPK1, NFKB1, RELA, AKT1, and MAPK14) could be considered as core targets and may be potential therapeutic targets for the treatment of Xinguan No. 3, according to the degree value. These networks reveal that Xinguan 3 exerted its anti-coronavirus effect through multiple components, targets, and pathways.

Figure 4 Drug–Core active component–Key target–pathway network. The dark green squares are the medicinal herbs, the light green squares are the core active ingredients, the yellow octagons are the key targets, and the purple V shapes are the pathways.
Figure 4

Drug–Core active component–Key target–pathway network. The dark green squares are the medicinal herbs, the light green squares are the core active ingredients, the yellow octagons are the key targets, and the purple V shapes are the pathways.

Figure 5 Key target–pathway network. The yellow octagons are the key targets, and the red V shapes are the pathways.
Figure 5

Key target–pathway network. The yellow octagons are the key targets, and the red V shapes are the pathways.

3.5 Molecular docking simulation for core components

The genetic names of the docking targets were imported into the UniPort database to determine the protein identifier, and the structures of the proteins were downloaded in the PDB database, including MAPK1 (PDB ID: 4QP9), NFKB1 (PDB ID: 2O61), RELA (PDB ID: 6NV2), AKT1 (PDB ID: 4EKL), MAPK14 (PDB ID: 6SFI), ACE2 (PDB ID: 1R42), and Mpro (PDB ID: 6LU7). This study docked the core active ingredients with the target proteins. Figure 6 shows the binding pattern of the core active ingredients and the target proteins. The docking results show that magnolignan B and isolariciresino can be well bound to dock with seven target proteins, and the score of docking pairs was less than 5.5 kcal/mol, as shown in Table 2. When ligands bind to receptors, it is generally believed that the lower the binding energy, the higher the binding affinity of the ligand to the target protein.

Figure 6 Binding mode of molecular docking, taking magnolignan B as an example. (a) MAPK1, (b) NFKB1, (c) RELA, (d) AKT1, (e) MAPK14, (f) ACE2, and (g) Mpro.
Figure 6

Binding mode of molecular docking, taking magnolignan B as an example. (a) MAPK1, (b) NFKB1, (c) RELA, (d) AKT1, (e) MAPK14, (f) ACE2, and (g) Mpro.

Table 2

Molecular docking results (docking score greater than 5.5 kcal/mol)

No. Compounds Docking score Source
RELA NF-KB1 AKT1 MAKP1 MAKP14 Mpro ACE2
HP46 Magnolignan B –6.20 –6.79 –6.93 –8.52 –6.90 –8.48 –5.66 HP
BX17 Isolariciresino –5.65 –6.61 –6.33 –8.18 –7.45 –6.94 –5.55 BX
GHX8 Apigenin-7-olate –6.26 –7.45 –7.39 –8.10 –8.35 –7.50 — GHX
CF49 Apigenin –6.28 –7.44 –7.34 –7.94 –8.34 –7.51 — JJ, BH, ZS, and GHX
CF207 Genkwanin –5.83 –7.79 –6.53 –8.35 –8.47 –6.79 — BH and GHX
CF70 Quercetin –5.82 –7.26 –7.03 –7.89 –8.09 –6.15 — JJ, GHX, and ZZ
CF23 Luteolin –6.50 –6.99 –7.12 –7.86 –7.26 –6.44 — JJ, BH, ZS, GK, and JG
JJ33 2-(3,4-Dihydroxyphenyl)-5-hydroxy-4-oxo-4H-chromen-7-olateluteolin-7-olate (1-) –6.5 –6.98 –7.12 –7.86 –7.26 –6.44 — JJ
DK19 1,7-Diphenyl-3,5-dihydroxy-1-heptene –5.51 –7.65 –5.91 –8.14 –8.44 –6.65 — DK
JJ37 Schizonepetoside –5.64 –6.43 –7.66 –8.28 –7.3 –7.25 — JJ
CF185 Rhamnocitrin –5.62 –7.87 –5.72 –7.69 –8.34 –6.68 — DK and GXH
HP73 Reticulin –6.08 –7.42 –6.45 –7.65 –7.63 –6.84 — HP
FF61 Primetin –5.87 –6.61 –6.78 –8.31 –7.35 –7.19 FF
CF208 Acacetin –5.63 –6.36 –6.15 –7.14 –8.71 –6.59 — BH and JG
BH28 5-hydroxy-2-(4-methoxyphenyl)-4-oxo-4H-chromen-7-olate –5.63 –6.16 –6.15 –7.18 –8.72 –6.61 — BH
CX29 Senkyunolide-L –6.03 –7.15 –5.97 –7.38 –6.89 –6.51 — CX
CF32 Carvacrol –6.02 –6.20 –6.96 –7.73 –6.4 –5.84 — BZHI, BH, ZS, and DK
CF144 Diosmetin –5.86 –5.93 –6.76 –6.80 –7.65 –6.05 — JJ and BH
CX28 Senkyunolide-F –5.58 –7.5 –5.99 –7.21 –6.59 –5.58 — CX
CX23 Perlolyrine –5.65 –6.28 –5.79 –7.18 –7.58 –5.90 — CX
CX75 Senkyunolide K –6.07 –6.75 –6.64 –6.23 –6.68 –6.23 — CX
CX84 Butylidenephthalide –5.75 –6.3 –7.04 –6.44 –6.75 –5.76 — CX
CX85 3-Butyl-4,7-dihydroxy-3H-2-benzofuran-1-one –6.03 –6.78 –6.54 –5.89 –6.84 –5.94 — CX
CX46 4,7-Dihydroxy-3-butylphthalide –6.03 –6.75 –6.56 –5.89 –6.84 –6.01 — CX
BZHU19 Ethyl 2-hydroxyquinoline-4-carboxylate –6.21 –5.54 –5.94 –7.52 –6.63 –6.27 — BZHU
CX114 3-Butylidene-4,5-dihydrophthalide –5.63 –6.28 –6.73 –6.55 –6.62 –5.57 — CX
CX92 cnidium lactone –5.84 –6.29 –6.41 –6.20 –6.55 –5.60 — CX
CX83 3-Butyl-4,5,6,7-tetrahydro-3H-2-benzofuran-1-one –5.64 –6.20 –5.63 –6.06 –6.09 –5.53 — CX
CX43 (3S)-3-Butyl-4,5,6,7-tetrahydro-3H-2-benzofuran-1-one –5.64 –6.20 –5.63 –5.98 –6.09 –5.53 — CX

4 Discussion

Although SARS-CoV-2 has been effectively controlled in China, the number of confirmed cases of COVID-19 abroad is still increasing rapidly. In addition, the virus has produced a new variant called Omicron, with higher transmissibility, infectivity, and vaccine breakthrough properties [31]. Due to the lack of clinical studies of drugs against COVID-19 and the common presence of side effects, analyzing the exact components and ingredients of TCM is increasingly urgent [32]. There have been several TCM playing a significant role in fighting against epidemics since ancient times. Since the outbreak of COVID-19, some TCMs have been used in clinical practice, and their safety and efficacy have been demonstrated [33,34,35]. However, the active ingredients and molecular mechanisms of these drugs in the treatment of COVID-19 are still unclear.

In this study, 1,049 active components and 1,378 targets were found in total. Among them, 153 targets were related to the COVID-19, called intersection targets. And 112 highly expressed targets were obtained by analyzing the intersection targets of the PPI network, and the PPI network map was imported into Cytoscape (version 3.8.2), the higher the degree value, the stronger the Xinguan No. 3 effects on the core genes. The most important core targets were indicated, including RELA, IKBKG, JAK1, IL1B, IL2, AKT1, NFKBIA, IL6, MAPK1, MAPK3, STAT1, PIK3R1, NFKB1, TNF, MAPK14, STAT3, etc. It has been indicated that they played important roles in the PPI network. These genes of Xinguan No. 3, related to inflammatory responses [36,37], immuno-modulation [38], and cellular stress processes [39], may play a key role in treating COVID-19.

Then, KEGG enrichment analysis showed that the intersection targets of COVID-19 and Xinguan No. 3 were mainly concentrated in pathways with virus-induced diseases, such as Influenza A, Hepatitis B, Hepatitis C, Epstein–Barr virus infection, and Measles. In addition, Xinguan No. 3 participates in regulating immune and inflammatory pathways, such as Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, and TNF signaling pathway. Parasites, such as chagas disease, and toxoplasmosis, might also be involved in the disease. Five key targets, such as MAPK1, NFKB1, RELA, AKT1, and MAPK14 appeared more often in the top 15 pathways. Therefore, we assumed that these five genes can also be relative to the treatment of COVID-19 by Xinguan No. 3. For example, RELA and NF-KB1 are members of the NF-KB family, and the activation of NF-kB signals helps inhibit SARS-CoV-2 infection, delay induction of interferon signals, and ultimately inhibit viral replication [40]. MAPKs regulate a variety of cellular processes, including gene expression, immune responses, cell proliferation and apoptosis, and responses to oxidative stress [41]. AKT1 is one of the human AKT serine-threonine protein kinase families, and it has been documented that overexpressed AKT1 can enhance the transcription of viral genes and the synthesis of viral proteins [42]. The downregulation of the expression of the AKT1 gene promotes macrophage M1 polarization, leading to the occurrence of inflammation [43]. Overall, MAPK1, NFKB1, RELA, AKT1, and MAPK14 might be ideal targets for treating COVID-19.

Eventually, we screened the core active ingredients via molecular docking and obtained 29 active components which can have good binding energy with at least 6 target proteins. Among them, magnolignan B and isolariciresino had good binding energy with all target proteins, playing a therapeutic effect of Xinguan No. 3. Isolariciresino has only antioxidant activity [44], while the pharmacological effects of magnolignan B cannot be found in the literature so far. Therefore, the two components might possess the potential as antivirals for future research. Moreover, quercetin and luteolin in the 29 components obtained by docking have been confirmed to have therapeutic effects on COVID-19. Quercetin effectively reduces serum levels of ALP, q-CRP, and LDH, increases viral clearance, and helps improve early symptoms of SARS-CoV-2 infection [45,46]. The combination of supplementation with luteolin and palmitoylethanolamide can effectively improve the recovery of olfactory function in COVID-19, most notably in patients with long-term olfactory dysfunction [47].

5 Conclusion

In this study, we used network pharmacology and molecular docking technology to explore the potential mechanism of Chinese medicine Xinguan No. 3 in the treatment of COVID-19. The results have shown that Xinguan No. 3 might play a vital role in treating COVID-19 by inhibiting viral replication and improving inflammatory response. Two potential active components (magnolignan B and isolariciresino) have been found, providing a reference for the development of new drugs for the treatment of COVID-19. However, due to the limitations of network pharmacology and molecular docking, further experiments are needed to validate our results in the future.

# These authors contributed equally to this work.

Acknowledgments

The author is highly grateful to Yunsen Zhang from Chengdu University of Traditional Chinese Medicine for selflessly teaching us to use molecular docking software.

  1. Funding information: The studies were financed by the Sichuan Provincial Administration of Traditional Chinese Medicine (No. 2020yj019) and the Science and Technology Department of Sichuan Province (No. 2021YFS0410).

  2. Author contributions: Jiayan Peng and Kun Zhang conducted the experiments, performed data analysis, and wrote the article; Lijie Wang and Fang Peng collected the ingredients and revised the article; Chuantao Zhang, Kunlan Long, Jun Chen, and Xiujuan Zhou supported the study and provided the prescription information; Peiyang Gao and Gang Fan conceived and designed the study.

  3. Conflict of interest: The authors declare no conflict of interest.

  4. Ethical approval: The conducted research is not related to either human or animal use.

  5. Data availability statement: The data presented in this study are available on request from the corresponding author.

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Received: 2022-04-06
Revised: 2022-05-16
Accepted: 2022-06-03
Published Online: 2022-07-08

© 2022 Jiayan Peng et al., published by De Gruyter

This work is licensed under the Creative Commons Attribution 4.0 International License.

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https://doi.org/10.1515/chem-2022-0178
Keywords for this article
traditional Chinese medicine; Xinguan No. 3; COVID-19; network pharmacology; potential mechanism
Creative Commons
BY 4.0

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  2. Photocatalytic degradation of Rhodamine B in aqueous phase by bimetallic metal-organic framework M/Fe-MOF (M = Co, Cu, and Mg)
  3. Assessment of using electronic portal imaging device for analysing bolus material utilised in radiation therapy
  4. A detailed investigation on highly dense CuZr bulk metallic glasses for shielding purposes
  5. Simulation of gamma-ray shielding properties for materials of medical interest
  6. Environmental impact assesment regulation applications and their analysis in Turkey
  7. Sample age effect on parameters of dynamic nuclear polarization in certain difluorobenzen isomers/MC800 asphaltene suspensions
  8. Passenger demand forecasting for railway systems
  9. Design of a Robust sliding mode controller for bioreactor cultures in overflow metabolism via an interdisciplinary approach
  10. Gamma, neutron, and heavy charged ion shielding properties of Er3+-doped and Sm3+-doped zinc borate glasses
  11. Bridging chiral de-tert-butylcalix[4]arenes: Optical resolution based on column chromatography and structural characterization
  12. Petrology and geochemistry of multiphase post-granitic dikes: A case study from the Gabal Serbal area, Southwestern Sinai, Egypt
  13. Comparison of the yield and purity of plasma exosomes extracted by ultracentrifugation, precipitation, and membrane-based approaches
  14. Bioactive triterpenoids from Indonesian medicinal plant Syzygium aqueum
  15. Investigation of the effects of machining parameters on surface integrity in micromachining
  16. The mesoporous aluminosilicate application as support for bifunctional catalysts for n-hexadecane hydroconversion
  17. Gamma-ray shielding properties of Nd2O3-added iron–boron–phosphate-based composites
  18. Numerical investigation on perforated sheet metals under tension loading
  19. Statistical analysis on the radiological assessment and geochemical studies of granite rocks in the north of Um Taghir area, Eastern Desert, Egypt
  20. Two new polypodane-type bicyclic triterpenoids from mastic
  21. Structural, physical, and mechanical properties of the TiO2 added hydroxyapatite composites
  22. Tribological properties and characterization of borided Co–Mg alloys
  23. Studies on Anemone nemorosa L. extracts; polyphenols profile, antioxidant activity, and effects on Caco-2 cells by in vitro and in silico studies
  24. Mechanical properties, elastic moduli, transmission factors, and gamma-ray-shielding performances of Bi2O3–P2O5–B2O3–V2O5 quaternary glass system
  25. Cyclic connectivity index of bipolar fuzzy incidence graph
  26. The role of passage numbers of donor cells in the development of Arabian Oryx – Cow interspecific somatic cell nuclear transfer embryos
  27. Mechanical property evaluation of tellurite–germanate glasses and comparison of their radiation-shielding characteristics using EPICS2017 to other glass systems
  28. Molecular screening of ionic liquids for CO2 absorption and molecular dynamic simulation
  29. Microwave-assisted preparation of Ag/Fe magnetic biochar from clivia leaves for adsorbing daptomycin antibiotics
  30. Iminodisuccinic acid enhances antioxidant and mineral element accumulation in young leaves of Ziziphus jujuba
  31. Cytotoxic activity of guaiane-type sesquiterpene lactone (deoxycynaropicrin) isolated from the leaves of Centaurothamnus maximus
  32. Effects of welding parameters on the angular distortion of welded steel plates
  33. Simulation of a reactor considering the Stamicarbon, Snamprogetti, and Toyo patents for obtaining urea
  34. Effect of different ramie (Boehmeria nivea L. Gaud) cultivars on the adsorption of heavy metal ions cadmium and lead in the remediation of contaminated farmland soils
  35. Impact of a live bacterial-based direct-fed microbial (DFM) postpartum and weaning system on performance, mortality, and health of Najdi lambs
  36. Anti-tumor effect of liposomes containing extracted Murrayafoline A against liver cancer cells in 2D and 3D cultured models
  37. Physicochemical properties and some mineral concentration of milk samples from different animals and altitudes
  38. Copper(ii) complexes supported by modified azo-based ligands: Nucleic acid binding and molecular docking studies
  39. Diagnostic and therapeutic radioisotopes in nuclear medicine: Determination of gamma-ray transmission factors and safety competencies of high-dense and transparent glassy shields
  40. Calculation of NaI(Tl) detector efficiency using 226Ra, 232Th, and 40K radioisotopes: Three-phase Monte Carlo simulation study
  41. Isolation and identification of unstable components from Caesalpinia sappan by high-speed counter-current chromatography combined with preparative high-performance liquid chromatography
  42. Quantification of biomarkers and evaluation of antioxidant, anti-inflammatory, and cytotoxicity properties of Dodonaea viscosa grown in Saudi Arabia using HPTLC technique
  43. Characterization of the elastic modulus of ceramic–metal composites with physical and mechanical properties by ultrasonic technique
  44. GC-MS analysis of Vespa velutina auraria Smith and its anti-inflammatory and antioxidant activities in vitro
  45. Texturing of nanocoatings for surface acoustic wave-based sensors for volatile organic compounds
  46. Insights into the molecular basis of some chalcone analogues as potential inhibitors of Leishmania donovani: An integrated in silico and in vitro study
  47. (1R,2S,5R)-5-Methyl-2-(propan-2-yl)cyclohexyl 4-amino-3-phenylbutanoate hydrochloride: Synthesis and anticonvulsant activity
  48. On the relative extraction rates of colour compounds and caffeine during brewing, an investigation of tea over time and temperature
  49. Characterization of egg shell powder-doped ceramic–metal composites
  50. Rapeseed oil-based hippurate amide nanocomposite coating material for anticorrosive and antibacterial applications
  51. Chemically modified Teucrium polium (Lamiaceae) plant act as an effective adsorbent tool for potassium permanganate (KMnO4) in wastewater remediation
  52. Efficiency analysis of photovoltaic systems installed in different geographical locations
  53. Risk prioritization model driven by success factor in the light of multicriteria decision making
  54. Theoretical investigations on the excited-state intramolecular proton transfer in the solvated 2-hydroxy-1-naphthaldehyde carbohydrazone
  55. Mechanical and gamma-ray shielding examinations of Bi2O3–PbO–CdO–B2O3 glass system
  56. Machine learning-based forecasting of potability of drinking water through adaptive boosting model
  57. The potential effect of the Rumex vesicarius water seeds extract treatment on mice before and during pregnancy on the serum enzymes and the histology of kidney and liver
  58. Impact of benzimidazole functional groups on the n-doping properties of benzimidazole derivatives
  59. Extraction of red pigment from Chinese jujube peel and the antioxidant activity of the pigment extracts
  60. Flexural strength and thermal properties of carbon black nanoparticle reinforced epoxy composites obtained from waste tires
  61. A focusing study on radioprotective and antioxidant effects of Annona muricata leaf extract in the circulation and liver tissue: Clinical and experimental studies
  62. Clinical comprehensive and experimental assessment of the radioprotective effect of Annona muricata leaf extract to prevent cellular damage in the ileum tissue
  63. Effect of WC content on ultrasonic properties, thermal and electrical conductivity of WC–Co–Ni–Cr composites
  64. Influence of various class cleaning agents for prosthesis on Co–Cr alloy surface
  65. The synthesis of nanocellulose-based nanocomposites for the effective removal of hexavalent chromium ions from aqueous solution
  66. Study on the influence of physical interlayers on the remaining oil production under different development modes
  67. Optimized linear regression control of DC motor under various disturbances
  68. Influence of different sample preparation strategies on hypothesis-driven shotgun proteomic analysis of human saliva
  69. Determination of flow distance of the fluid metal due to fluidity in ductile iron casting by artificial neural networks approach
  70. Investigation of mechanical activation effect on high-volume natural pozzolanic cements
  71. In vitro: Anti-coccidia activity of Calotropis procera leaf extract on Eimeria papillata oocysts sporulation and sporozoite
  72. Determination of oil composition of cowpea (Vigna unguiculata L.) seeds under influence of organic fertilizer forms
  73. Activated partial thromboplastin time maybe associated with the prognosis of papillary thyroid carcinoma
  74. Treatment of rat brain ischemia model by NSCs-polymer scaffold transplantation
  75. Lead and cadmium removal with native yeast from coastal wetlands
  76. Characterization of electroless Ni-coated Fe–Co composite using powder metallurgy
  77. Ferrate synthesis using NaOCl and its application for dye removal
  78. Antioxidant, antidiabetic, and anticholinesterase potential of Chenopodium murale L. extracts using in vitro and in vivo approaches
  79. Study on essential oil, antioxidant activity, anti-human prostate cancer effects, and induction of apoptosis by Equisetum arvense
  80. Experimental study on turning machine with permanent magnetic cutting tool
  81. Numerical simulation and mathematical modeling of the casting process for pearlitic spheroidal graphite cast iron
  82. Design, synthesis, and cytotoxicity evaluation of novel thiophene, pyrimidine, pyridazine, and pyridine: Griseofulvin heterocyclic extension derivatives
  83. Isolation and identification of promising antibiotic-producing bacteria
  84. Ultrasonic-induced reversible blood–brain barrier opening: Safety evaluation into the cellular level
  85. Evaluation of phytochemical and antioxidant potential of various extracts from traditionally used medicinal plants of Pakistan
  86. Effect of calcium lactate in standard diet on selected markers of oxidative stress and inflammation in ovariectomized rats
  87. Identification of crucial salivary proteins/genes and pathways involved in pathogenesis of temporomandibular disorders
  88. Zirconium-modified attapulgite was used for removing of Cr(vi) in aqueous solution
  89. The stress distribution of different types of restorative materials in primary molar
  90. Reducing surface heat loss in steam boilers
  91. Deformation behavior and formability of friction stir processed DP600 steel
  92. Synthesis and characterization of bismuth oxide/commercial activated carbon composite for battery anode
  93. Phytochemical analysis of Ziziphus jujube leaf at different foliar ages based on widely targeted metabolomics
  94. Effects of in ovo injection of black cumin (Nigella sativa) extract on hatching performance of broiler eggs
  95. Separation and evaluation of potential antioxidant, analgesic, and anti-inflammatory activities of limonene-rich essential oils from Citrus sinensis (L.)
  96. Bioactivity of a polyhydroxy gorgostane steroid from Xenia umbellata
  97. BiCAM-based automated scoring system for digital logic circuit diagrams
  98. Analysis of standard systems with solar monitoring systems
  99. Structural and spectroscopic properties of voriconazole and fluconazole – Experimental and theoretical studies
  100. New plant resistance inducers based on polyamines
  101. Experimental investigation of single-lap bolted and bolted/bonded (hybrid) joints of polymeric plates
  102. Investigation of inlet air pressure and evaporative cooling of four different cogeneration cycles
  103. Review Articles
  104. Comprehensive review on synthesis, physicochemical properties, and application of activated carbon from the Arecaceae plants for enhanced wastewater treatment
  105. Research progress on speciation analysis of arsenic in traditional Chinese medicine
  106. Recent modified air-assisted liquid–liquid microextraction applications for medicines and organic compounds in various samples: A review
  107. An insight on Vietnamese bio-waste materials as activated carbon precursors for multiple applications in environmental protection
  108. Antimicrobial activities of the extracts and secondary metabolites from Clausena genus – A review
  109. Bioremediation of organic/heavy metal contaminants by mixed cultures of microorganisms: A review
  110. Sonodynamic therapy for breast cancer: A literature review
  111. Recent progress of amino acid transporters as a novel antitumor target
  112. Aconitum coreanum Rapaics: Botany, traditional uses, phytochemistry, pharmacology, and toxicology
  113. Corrigendum
  114. Corrigendum to “Petrology and geochemistry of multiphase post-granitic dikes: A case study from the Gabal Serbal area, Southwestern Sinai, Egypt”
  115. Corrigendum to “Design of a Robust sliding mode controller for bioreactor cultures in overflow metabolism via an interdisciplinary approach”
  116. Corrigendum to “Statistical analysis on the radiological assessment and geochemical studies of granite rocks in the north of Um Taghir area, Eastern Desert, Egypt”
  117. Corrigendum to “Aroma components of tobacco powder from different producing areas based on gas chromatography ion mobility spectrometry”
  118. Corrigendum to “Mechanical properties, elastic moduli, transmission factors, and gamma-ray-shielding performances of Bi2O3–P2O5–B2O3–V2O5 quaternary glass system”
  119. Erratum
  120. Erratum to “Copper(ii) complexes supported by modified azo-based ligands: Nucleic acid binding and molecular docking studies”
  121. Special Issue on Applied Biochemistry and Biotechnology (ABB 2021)
  122. Study of solidification and stabilization of heavy metals by passivators in heavy metal-contaminated soil
  123. Human health risk assessment and distribution of VOCs in a chemical site, Weinan, China
  124. Preparation and characterization of Sparassis latifolia β-glucan microcapsules
  125. Special Issue on the Conference of Energy, Fuels, Environment 2020
  126. Improving the thermal performance of existing buildings in light of the requirements of the EU directive 2010/31/EU in Poland
  127. Special Issue on Ethnobotanical, Phytochemical and Biological Investigation of Medicinal Plants
  128. Study of plant resources with ethnomedicinal relevance from district Bagh, Azad Jammu and Kashmir, Pakistan
  129. Studies on the chemical composition of plants used in traditional medicine in Congo
  130. Special Issue on Applied Chemistry in Agriculture and Food Science
  131. Strip spraying technology for precise herbicide application in carrot fields
  132. Special Issue on Pharmacology and Metabolomics of Ethnobotanical and Herbal Medicine
  133. Phytochemical profiling, antibacterial and antioxidant properties of Crocus sativus flower: A comparison between tepals and stigmas
  134. Antioxidant and antimicrobial properties of polyphenolics from Withania adpressa (Coss.) Batt. against selected drug-resistant bacterial strains
  135. Integrating network pharmacology and molecular docking to explore the potential mechanism of Xinguan No. 3 in the treatment of COVID-19
  136. Chemical composition and in vitro and in vivo biological assortment of fixed oil extracted from Ficus benghalensis L.
  137. A review of the pharmacological activities and protective effects of Inonotus obliquus triterpenoids in kidney diseases
  138. Ethnopharmacological study of medicinal plants in Kastamonu province (Türkiye)
  139. Protective effects of asperuloside against cyclophosphamide-induced urotoxicity and hematotoxicity in rats
  140. Special Issue on Essential Oil, Extraction, Phytochemistry, Advances, and Application
  141. Identification of volatile compounds and antioxidant, antibacterial, and antifungal properties against drug-resistant microbes of essential oils from the leaves of Mentha rotundifolia var. apodysa Briq. (Lamiaceae)
  142. Phenolic contents, anticancer, antioxidant, and antimicrobial capacities of MeOH extract from the aerial parts of Trema orientalis plant
  143. Chemical composition and antimicrobial activity of essential oils from Mentha pulegium and Rosmarinus officinalis against multidrug-resistant microbes and their acute toxicity study
  144. Special Issue on Marine Environmental Sciences and Significance of the Multidisciplinary Approaches
  145. An insightful overview of the distribution pattern of polycyclic aromatic hydrocarbon in the marine sediments of the Red Sea
  146. Antifungal–antiproliferative norcycloartane-type triterpenes from the Red Sea green alga Tydemania expeditionis
  147. Solvent effect, dipole moment, and DFT studies of multi donor–acceptor type pyridine derivative
  148. An extensive assessment on the distribution pattern of organic contaminants in the aerosols samples in the Middle East
  149. Special Issue on 4th IC3PE
  150. Energetics of carboxylic acid–pyridine heterosynthon revisited: A computational study of intermolecular hydrogen bond domination on phenylacetic acid–nicotinamide cocrystals
  151. A review: Silver–zinc oxide nanoparticles – organoclay-reinforced chitosan bionanocomposites for food packaging
  152. Green synthesis of magnetic activated carbon from peanut shells functionalized with TiO2 photocatalyst for Batik liquid waste treatment
  153. Coagulation activity of liquid extraction of Leucaena leucocephala and Sesbania grandiflora on the removal of turbidity
  154. Hydrocracking optimization of palm oil over NiMoO4/activated carbon catalyst to produce biogasoline and kerosine
  155. Special Issue on Pharmacology and metabolomics of ethnobotanical and herbal medicine
  156. Cynarin inhibits PDGF-BB-induced proliferation and activation in hepatic stellate cells through PPARγ
  157. Special Issue on The 1st Malaysia International Conference on Nanotechnology & Catalysis (MICNC2021)
  158. Surfactant evaluation for enhanced oil recovery: Phase behavior and interfacial tension
  159. Topical Issue on phytochemicals, biological and toxicological analysis of aromatic medicinal plants
  160. Phytochemical analysis of leaves and stems of Physalis alkekengi L. (Solanaceae)
  161. Phytochemical and pharmacological profiling of Trewia nudiflora Linn. leaf extract deciphers therapeutic potentials against thrombosis, arthritis, helminths, and insects
  162. Pergularia tomentosa coupled with selenium nanoparticles salvaged lead acetate-induced redox imbalance, inflammation, apoptosis, and disruption of neurotransmission in rats’ brain
  163. Protective effect of Allium atroviolaceum-synthesized SeNPs on aluminum-induced brain damage in mice
  164. Mechanism study of Cordyceps sinensis alleviates renal ischemia–reperfusion injury
  165. Plant-derived bisbenzylisoquinoline alkaloid tetrandrine prevents human podocyte injury by regulating the miR-150-5p/NPHS1 axis
  166. Network pharmacology combined with molecular docking to explore the anti-osteoporosis mechanisms of β-ecdysone derived from medicinal plants
  167. Chinese medicinal plant Polygonum cuspidatum ameliorates silicosis via suppressing the Wnt/β-catenin pathway
  168. Special Issue on Advanced Nanomaterials for Energy, Environmental and Biological Applications - Part I
  169. Investigation of improved optical and conductivity properties of poly(methyl methacrylate)–MXenes (PMMA–MXenes) nanocomposite thin films for optoelectronic applications
  170. Special Issue on Applied Biochemistry and Biotechnology (ABB 2022)
  171. Model predictive control for precision irrigation of a Quinoa crop
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