scholarly journals Network Pharmacology Integrated Molecular Docking Reveals the Anti-COVID-19 Mechanism of Yinma Jiedu Granules

2021 ◽  
Vol 16 (2) ◽  
pp. 1934578X2199171
Author(s):  
ZiXin Yuan ◽  
Can Zeng ◽  
Bing Yu ◽  
Ying Zhang ◽  
TianShun Wang ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Signaling Pathways ◽  
Hypoxia Inducible Factor ◽  
Growth Factor Receptor ◽  
Interaction Network ◽  
Mitogen Activated Protein Kinase ◽  
Network Pharmacology ◽  
Chemical Components ◽  
Active Components ◽  
Discovery Studio

To investigate the mechanism of action of components of Yinma Jiedu granules in the treatment of coronavirus disease 2019 (COVID-19) using network pharmacology and molecular docking. The main chemical components of Yinma Jiedu granules were collected in the literature and Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform database. Using the SwissTargetPrediction database, the targets of the active component were identified and further correlated to the targets of COVID-19 through the GeneCards database. The overlapping targets of Yinma Jiedu granules components and COVID-19 were identified as the research target. Using the Database for Annotation, Visualization and Integrated Discovery database to carry out the target gene function Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway annotation and Cytoscape 3.6.1 software was used to construct a “component-target-pathway” network. The protein-protein interaction network was built using Search Tool for the Retrieval of Interacting Genes/Proteins database. Using Discovery Studio 2016 Client software to study the virtual docking of key protein and active components. One hundred active components were screened from the Yinma Jiedu Granules that involved 67 targets, including mitogen-activated protein kinase 3 (MAPK3), epidermal growth factor receptor, tumor necrosis factor, tumor protein 53, and MAPK1. These targets affected 109 signaling pathways including hypoxia-inducible factor-1, apoptosis, and Toll-like receptor signaling pathways. Molecular docking results showed that the screened active components have a strong binding ability to the key targets. In this study, through network pharmacology and molecular docking, we justified the multicomponent, multitarget, and multipathways of Yinma Jiedu Granules in the treatment of COVID-19.

scholarly journals Network Pharmacology Integrated Molecular Docking Analysis of Potential Common Mechanisms of Shu-Feng-Jie-Du Capsule in the Treatment of SARS, MERS, and COVID-19

2020 ◽  
Vol 15 (11) ◽  
pp. 1934578X2097291
Author(s):  
Ying Zhang ◽  
Yi Xie ◽  
Bing Yu ◽  
Chong Yuan ◽  
Zixin Yuan ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Protein Kinase ◽  
Signaling Pathways ◽  
Interaction Network ◽  
Mitogen Activated Protein Kinase ◽  
Network Pharmacology ◽  
Active Components ◽  
Discovery Studio ◽  
Mitogen Activated Protein ◽  
Coronavirus Infection

Shu-Feng-Jie-Du Capsules (SFJDCs) have been clinically proven to have a good therapeutic effect on COVID-19 in China. This study aimed to analyze the common mechanisms of SFJDC in the treatment of severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and COVID-19 via network pharmacology and molecular docking. We further explored the potential application value of SFJDC in the treatment of coronavirus infection. All components of SFJDC were collected from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform. The viral associated targets of the active components were forecast using the Pharmmapper database and GeneCards. The Database for Annotation, Visualization, and Integrated Discovery and KOBAS 3.0 system were used for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of SFJDC’s core targets. Further, the protein–protein interaction network was built using STRING database. The herb–component network and component–target–pathway network were constructed using Cytoscape 3.7.2. The core active components of SFJDC were docked with core targets and COVID-19 coronavirus 3 Cl hydrolase and angiotensin-converting enzyme 2 (ACE2) via Discovery Studio 2016 software. A total of 110 active components were filtered from SFJDC, with 47 core targets, including epidermal growth factor receptor, mitogen-activated protein kinase 1, mitogen-activated protein kinase 3, and interleukin 6. There were 416 GO items in the GO enrichment analysis ( P < .05) and 57 signaling pathways ( P < .05) in KEGG, mainly including pathways in cancer, pancreatic cancer, colorectal cancer, apoptosis, and neurotrophin signaling pathway, among others. The results of molecular docking showed that luteolin and rhein had a higher docking score with 3 Cl, ACE2, and core targets of SFJDC for antiviral effect. SFJDC is characterized by multicomponent, multitarget, and multisignaling pathways for the treatment of coronavirus infection. The mechanism of action of SFJDC in the treatment of MERS, SARS, and COVID-19 may be associated with the regulation of genes coexpressed with ACE2 and immune- related signaling pathways.

scholarly journals Mechanism of Compound Houttuynia Mixture as an Anti-COVID-19 Drug Based on Network Pharmacology and Molecular Docking

2021 ◽  
Vol 16 (5) ◽  
pp. 1934578X2110167
Author(s):  
Xing-Pan Wu ◽  
Tian-Shun Wang ◽  
Zi-Xin Yuan ◽  
Yan-Fang Yang ◽  
He-Zhen Wu
Keyword(s):  
Molecular Docking ◽  
Target Prediction ◽  
Interaction Network ◽  
Scientific Basis ◽  
Network Pharmacology ◽  
Chemical Components ◽  
Active Components ◽  
Discovery Studio ◽  
The Core ◽  
Pathway Annotation

Objective To explore the anti-COVID-19 active components and mechanism of Compound Houttuynia mixture by using network pharmacology and molecular docking. Methods First, the main chemical components of Compound Houttuynia mixture were obtained by using the TCMSP database and referring to relevant chemical composition literature. The components were screened for OB ≥30% and DL ≥0.18 as the threshold values. Then Swiss Target Prediction database was used to predict the target of the active components and map the targets of COVID-19 obtained through GeneCards database to obtain the gene pool of the potential target of COVID-19 resistance of the active components of Compound Houttuynia mixture. Next, DAVID database was used for GO enrichment and KEGG pathway annotation of targets function. Cytoscape 3.8.0 software was used to construct a “components-targets-pathways” network. Then String database was used to construct a “protein-protein interaction” network. Finally, the core targets, SARS-COV-2 3 Cl, ACE2 and the core active components of Compound Houttuyna Mixture were imported into the Discovery Studio 2016 Client database for molecular docking verification. Results Eighty-two active compounds, including Xylostosidine, Arctiin, ZINC12153652 and ZINC338038, were screened from Compound Houttuyniae mixture. The key targets involved 128 targets, including MAPK1, MAPK3, MAPK8, MAPK14, TP53, TNF, and IL6. The HIF-1 signaling, VEGF signaling, TNF signaling and another 127 signaling pathways associated with COVID-19 were affected ( P < 0.05). From the results of molecular docking, the binding ability between the selected active components and the core targets was strong. Conclusion Through the combination of network pharmacology and molecular docking technology, this study revealed that the therapeutic effect of Compound Houttuynia mixture on COVID-19 was realized through multiple components, multiple targets and multiple pathways, which provided a certain scientific basis of the clinical application of Compound Houttuynia mixture.

scholarly journals A Network Pharmacology and Molecular Docking Approach to Investigate the Anticoronavirus-Induced Diseases Effect of Yinqiao Powder Combined With Modified Sangju Decoction

2021 ◽  
Vol 16 (9) ◽  
pp. 1934578X2110352
Author(s):  
Tian-Shun Wang ◽  
Xing-Pan Wu ◽  
Qiu-Yuan Jian ◽  
Yan-Fang Yang ◽  
Wu He-Zhen
Keyword(s):  
Molecular Docking ◽  
Signaling Pathway ◽  
Treatment Strategies ◽  
Interaction Network ◽  
Mitogen Activated Protein Kinase ◽  
Network Pharmacology ◽  
Common Mechanism ◽  
Active Components ◽  
Discovery Studio ◽  
The Core

Severe acute respiratory syndrome (SARS) once caused great harm in China, but now it is the coronavirus disease 2019 (COVID-19) pandemic that has become a huge threat to global health, which raises urgent demand for developing effective treatment strategies to avoid the recurrence of tragedies. Yinqiao powder, combined with modified Sangju decoction (YPCMSD), has been clinically proven to have a good therapeutic effect on COVID-19 in China. This study aimed to analyze the common mechanism of YPCMSD in the treatment of SARS and COVID-19 through network pharmacology and molecular docking and further explore the potential application value of YPCMSD in the treatment of coronavirus infections. Firstly, the active components were collected from the literature and Traditional Chinese Medicine Systems Pharmacology database platform. The COVID-19 and SARS associated targets of the active components were forecasted by the SwissTargetPrediction database and GeneCards. A protein–protein-interaction network was drawn and the core targets were obtained by selecting the targets larger than the average degree. By importing the core targets into database for annotation, visualization, and integrated discovery, enrichment analysis of gene ontology, and construction of a Kyoto Encyclopedia of genes and genomes pathway was conducted. Cytoscape 3.6.1 software was used to construct a “components–targets–pathways” network. Active components were selected to dock with acute respiratory syndrome coronavirus type 2 (SARS-COV-2) 3CL and angiotensin-converting enzyme 2 (ACE2) through Discovery Studio 2016 software. A network of “components–targets–pathways” was successfully constructed, with key targets involving mitogen-activated protein kinase 1, caspase-3 (CASP3), tumor necrosis factor (TNF), and interleukin 6. Major metabolic pathways affected were those in cancer, the hypoxia-inducible factor 1 signaling pathway, the TNF signaling pathway, the Toll-like receptor signaling pathway, and the PI3K-Akt signaling pathway. The core components, such as arctiin, scopolin, linarin, and isovitexin, showed a strong binding ability with SARS-COV-2 3CL and ACE2. We predicted that the mechanism of action of this prescription in the treatment of COVID-19 and SARS might be associated with multicomponents that bind to SARS-COV-2 3CL and ACE2, thereby regulating targets that coexpressed with them and pathways related to inflammation and the immune system.

scholarly journals Network Pharmacology Integrated Molecular Docking Reveals the Anti-COVID-19 Mechanism of Xingnaojing Injection

2020 ◽  
Vol 15 (12) ◽  
pp. 1934578X2097802
Author(s):  
Bing Yu ◽  
Xin-Ge Ke ◽  
Chong Yuan ◽  
Peng-Yu Chen ◽  
Ying Zhang ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Signaling Pathway ◽  
Growth Factor Receptor ◽  
Docking Studies ◽  
Mitogen Activated Protein Kinase ◽  
Network Pharmacology ◽  
Active Components ◽  
Molecular Docking Studies ◽  
Discovery Studio ◽  
Xingnaojing Injection

In the process of fighting against COVID-19 in China, Xingnaojing injection has been recommended for its clinical treatment, but the information about its active components and mechanism is still lacking. Therefore, in this work, using network pharmacology and molecular docking, we studied the active components of Xingnaojing injection having anti-COVID-19 properties. Using the DL parameter, TCMSP and CNKI databases were used to screen the active components of the Xingnaojing injection. Then, the SwissTargetPrediction webserver was used to collect the corresponding gene targets, and the gene targets related to COVID-19 were searched in the Genecards database. The DAVID database was used to enrich the function of gene targets, and the KOBAS3.0 database for the annotation of related KEGG pathways. The “components–targets–pathways” network of Xingnaojing injection was constructed with Cytoscape 3.6.1 software. The protein–protein interaction networks were analyzed using the String database. Specific proteins, SARS-COV-2 3 Cl, ACE2, and the active components were imported into Discovery Studio 2016 Client for molecular docking studies. From the Xingnaojing injection, a total of 58 active components, including Divanillalaceton and Q27139023, were screened. These were linked to 53 gene targets including mitogen-activated protein kinase 1 (MAPK1), tumor necrosis factorTNF, epidermal growth factor receptor, MAPK3, and 196 signaling pathways related to COVID-19, such as apoptosis, C-type lectin receptor signaling pathway, and hypoxia-inducible factor 1 signaling pathway. Furthermore, molecular docking studies were performed to study potential binding between the key targets and selected active components. Xingnaojing injection exhibits anti-COVID-19 effects via multiple components, multiple targets, and multiple pathways. These results set a scientific basis for further elucidation of the anti-COVID-19 mechanism of Xingnaojing injection.

scholarly journals Mechanisms of indigo naturalis on treating ulcerative colitis explored by GEO gene chips combined with network pharmacology and molecular docking

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sizhen Gu ◽  
Yan Xue ◽  
Yang Gao ◽  
Shuyang Shen ◽  
Yuli Zhang ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Molecular Docking ◽  
Signaling Pathways ◽  
Interaction Network ◽  
Oxygen Metabolism ◽  
Network Pharmacology ◽  
Signal Pathways ◽  
Active Components ◽  
Gene Chips ◽  
Indigo Naturalis

Abstract Oral administration of indigo naturalis (IN) can induce remission in ulcerative colitis (UC); however, the underlying mechanism remains unknown. The main active components and targets of IN were obtained by searching three traditional Chinese medicine network databases such as TCMSP and five Targets fishing databases such as PharmMapper. UC disease targets were obtained from three disease databases such as DrugBank,combined with four GEO gene chips. IN-UC targets were identified by matching the two. A protein–protein interaction network was constructed, and the core targets were screened according to the topological structure. GO and KEGG enrichment analysis and bioGPS localization were performed,and an Herbs-Components-Targets network, a Compound Targets-Organs location network, and a Core Targets-Signal Pathways network were established. Molecular docking technology was used to verify the main compounds-targets. Ten core active components and 184 compound targets of IN-UC, of which 43 were core targets, were enriched and analyzed by bioGPS, GO, and KEGG. The therapeutic effect of IN on UC may involve activation of systemic immunity, which is involved in the regulation of nuclear transcription, protein phosphorylation, cytokine activity, reactive oxygen metabolism, epithelial cell proliferation, and cell apoptosis through Th17 cell differentiation, the Jak-STAT and IL-17 signaling pathways, toll-like and NOD-like receptors, and other cellular and innate immune signaling pathways. The molecular mechanism underlying the effect of IN on inducing UC remission was predicted using a network pharmacology method, thereby providing a theoretical basis for further study of the effective components and mechanism of IN in the treatment of UC.

scholarly journals Network Pharmacology Approach to Uncover the Mechanism Governing the Effect of Simiao Powder on Knee Osteoarthritis

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Zhengquan Huang ◽  
Xiaoqing Shi ◽  
Xiaochen Li ◽  
Li Zhang ◽  
Peng Wu ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Knee Osteoarthritis ◽  
Signaling Pathway ◽  
Protein Interaction ◽  
Cell Metabolism ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Active Components ◽  
Discovery Studio

Objective. To explore the molecular mechanism of Simiao powder in the treatment of knee osteoarthritis. Methods. Based on oral bioavailability and drug-likeness, the main active components of Simiao powder were screened using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). GeneCard, OMIM, DisGeNET, DrugBank, PharmGkb, and the Therapeutic Target Database were used to establish target databases for knee osteoarthritis. Cytoscape software was used to construct a visual interactive network diagram of “active ingredient - action target – disease.” The STRING database was used to construct a protein interaction network and analyze related protein interaction relationships. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) biological process enrichment analysis were performed on the core targets. Additionally, Discovery Studio software was used for molecular docking verification of active pharmaceutical ingredients and disease targets. Results. Thirty-seven active components of Simiao powder were screened, including 106 common targets. The results of network analysis showed that the targets were mainly involved in regulating biological processes such as cell metabolism and apoptosis. Simiao powder components were predicted to exert their therapeutic effect on the AGE-RAGE signaling pathway in diabetic complications, IL-17 signaling pathway, TNF signaling pathway, Toll-like receptor signaling pathway, and HIF-1 signaling pathway. The molecular docking results showed that the active components of Simiao powder had a good match with the targets of IL1B, MMP9, CXCL8, MAPK8, JUN, IL6, MAPK1, EGF, VEGFA, AKT1, and PTGS2. Conclusion. Simiao powder has multisystem, multicomponent, and multitarget characteristics in treating knee osteoarthritis. Its possible mechanism of action includes inhibiting the inflammatory response, regulating immune function, and resisting oxidative stress to control the occurrence and development of the disease. Quercetin, wogonin, kaempferol, beta-sitosterol, and other active ingredients may be the material basis for the treatment of knee osteoarthritis.

scholarly journals Investigation of Anti-SARS, MERS, and COVID-19 Effect of Jinhua Qinggan Granules Based on a Network Pharmacology and Molecular Docking Approach

2021 ◽  
Vol 16 (5) ◽  
pp. 1934578X2110206
Author(s):  
Ying Zhang ◽  
Yunfeng Yao ◽  
Yanfang Yang ◽  
Hezhen Wu
Keyword(s):  
Molecular Docking ◽  
Signaling Pathways ◽  
Interaction Network ◽  
Antiviral Effect ◽  
Network Pharmacology ◽  
Active Compounds ◽  
Discovery Studio ◽  
Pathway Network ◽  
Protein Protein Interaction ◽  
The Common

Objective Jinhua Qinggan Granules (JQGs) have achieved certain results in the prevention and treatment of COVID-19 in China during this coronavirus storm. In this study, we aimed to analyze the common mechanisms of JQG in the treatment of coronavirus-induced diseases, such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and COVID-19 via network pharmacology and molecular docking. Methods The active compounds of JQG were collected through Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform. The common targets associated with these 3 diseases were screened from GeneCards database. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of JQG’s core targets were analyzed using The Database for Annotation, Visualization, and Integrated Discovery and KOBAS 3.0 system. Further, the protein-protein interaction network was built using STRING database. The compound-target- signaling pathway network was constructed using Cytoscape 3.7.2. The core components of JQG were docked with core targets, COVID-19 coronavirus 3 Cl hydrolase, and angiotensin-converting enzyme 2 (ACE2) via Discovery Studio 2016 software. Results A total of 139 active compounds, 50 core targets, and 122 signaling pathways were screened out. The results of molecular docking showed that arctiin and linarin had a higher docking score with 3 Cl, ACE2, and core targets of JQH for antiviral effect. Conclusion The potential mechanism of action of JHQ in the treatment of MERS, SARS, and COVID-19 may be associated with the regulation of genes co-expressed with ACE2 and immune- related signaling pathways.

scholarly journals The important herbal pair for the treatment of COVID-19 and its possible mechanisms

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Shujie Xia ◽  
Zhangfeng Zhong ◽  
Bizhen Gao ◽  
Chi Teng Vong ◽  
Xuejuan Lin ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Association Rules ◽  
Hypoxia Inducible Factor ◽  
Mitogen Activated Protein Kinase ◽  
Network Pharmacology ◽  
Therapeutic Effects ◽  
Active Ingredients ◽  
Active Components ◽  
Ephedra Sinica ◽  
Rule Approach

Abstract Background Coronavirus Disease 2019 (COVID-19) is an unprecedented disaster for people around the world. Many studies have shown that traditional Chinese medicine (TCM) are effective in treating COVID-19. However, it is difficult to find the most effective combination herbal pair among numerous herbs, as well as identifying its potential mechanisms. Herbal pair is the main form of a combination of TCM herbs, which is widely used for the treatment of diseases. It can also help us to better understand the compatibility of TCM prescriptions, thus improving the curative effects. The purpose of this article is to explore the compatibility of TCM prescriptions and identify the most important herbal pair for the treatment of COVID-19, and then analyze the active components and potential mechanisms of this herbal pair. Methods We first systematically sorted the TCM prescriptions recommended by the leading experts for treating COVID-19, and the specific herbs contained in these prescriptions across different stages of the disease. Next, the association rule approach was employed to examine the distribution and compatibility among these TCM prescriptions, and then identify the most important herbal pair. On this basis, we further investigated the active ingredients and potential targets in the selected herbal pair by a network pharmacology approach, and analyzed the potential mechanisms against COVID-19. Finally, the main active compounds in the herbal pair were selected for molecular docking with severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) 3CLpro and angiotensin converting enzyme II (ACE2) for further verification. Result We obtained 32 association rules for the herbal combinations in the selection of TCM treatment for COVID-19. The results showed that the combination of Amygdalus Communis Vas (ACV) and Ephedra sinica Stapf (ESS) had the highest confidence degree and lift value, as well as high support degree, which can be used in almost all the stages of COVID-19, so ACV and ESS (AE) were selected as the most important herbal pair. There were 26 active ingredients and 44 potential targets, which might be related to the herbal pair of AE against COVID-19. The main active ingredients of AE against COVID-19 were quercetin, kaempferol, luteolin, while the potential targets were Interleukin 6 (IL-6), Mitogen-activated Protein Kinase 1 (MAPK)1, MAPK8, Interleukin-1β (IL-1β), and Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB) p65 subunit (RELA). The protein-protein interaction (PPI) cluster demonstrated that IL-6 was the seed in the cluster, which plays an important role in connecting other nodes in the PPI network. The potential pathways mainly involved tumor necrosis factor (TNF), Toll-like receptor (TLR), hypoxia-inducible factor-1 (HIF-1), and nucleotide-binding oligomerization domain (NOD)-like receptor (NLRs). The molecular docking results showed that the main active ingredients of AE have good affinity with SARS-COV-2 3CLpro and ACE2, which are consistent with the above analysis. Conclusions There were 32 association rules in the TCM prescriptions recommended by experts for COVID-19. The combination of ACV and EAS was the most important herbal pair for the treatment of COVID-19. AE might have therapeutic effects against COVID-19 by affecting the inflammatory and immune responses, cell apoptosis, hypoxia damage and other pathological processes through multiple components, targets and pathways.

scholarly journals The Important Herbal Pair for the Treatment of COVID-19 and Its Possible Mechanisms

2020 ◽  
Author(s):  
Shujie Xia ◽  
Zhangfeng Zhong ◽  
Bizhen Gao ◽  
Chi Teng Vong ◽  
Xuejuan Lin ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Hypoxia Inducible Factor ◽  
Mitogen Activated Protein Kinase ◽  
Network Pharmacology ◽  
Therapeutic Effects ◽  
Active Ingredients ◽  
Active Components ◽  
Ephedra Sinica ◽  
Rule Approach ◽  
Confidence Degree

Abstract Background: Coronavirus Disease 2019 (COVID-19) is an unprecedented disaster for people around the world. Many studies have shown that traditional Chinese medicine (TCM) are effective in treating COVID-19. However, it is difficult to find the most effective combination herbal pair among numerous herbs, as well as identifying its potential mechanisms. Herbal pair is the main form of a combination of TCM herbs, which is widely used for the treatment of diseases. It can also help us to better understand the compatibility of TCM prescriptions, thus improving the curative effects. The purpose of this article is to explore the compatibility of TCM prescriptions and identify the most important herbal pair for the treatment of COVID-19, and then analyze the active components and potential mechanisms of this herbal pair.Methods: We first systematically sorted the TCM prescriptions recommended by the leading experts for treating COVID-19, and the specific herbs contained in these prescriptions across different stages of the disease. Next, the association rule approach was employed to examine the distribution and compatibility among these TCM prescriptions, and then identify the most important herbal pair. On this basis, we further investigated the active ingredients and potential targets in the selected herbal pair by a network pharmacology approach, and analyzed the potential mechanisms against COVID-19. Finally, the main active compounds in AE were selected for molecular docking with severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) 3CLpro and angiotensin converting enzyme II (ACE2).Result: We obtained 32 association rules for the herbal combinations in the selection of TCM treatment for COVID-19. The results showed that the combination of Amygdalus Communis Vas (ACV) and Ephedra sinica Stapf (ESS) had the highest confidence degree and lift value, as well as high support degree, which can be used in almost all the stages of COVID-19, so ACV and ESS (AE) were selected as the most important herbal pair. There were 26 active ingredients and 44 potential targets, which might be related to the herbal pair of AE against COVID-19. The main active ingredients of AE against COVID-19 were quercetin, kaempferol, luteolin, while the potential targets were Interleukin 6 (IL-6), Mitogen-activated Protein Kinase 1 (MAPK)1, MAPK8, Interleukin-1β (IL-1β), and Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB) p65 subunit (RELA). The protein-protein interaction (PPI) cluster demonstrated that IL-6 was the seed in the cluster, which plays an important role in connecting other nodes in the PPI network. The potential pathways mainly involved tumor necrosis factor (TNF), Toll-like receptor (TLR), hypoxia-inducible factor-1 (HIF-1), and nucleotide-binding oligomerization domain (NOD)-like receptor (NLRs). The molecular docking results showed that the main active ingredients of AE had good affinity with SARS-COV-2 3CLpro and ACE2.Conclusion: The combination of ACV and EAS was the most important herbal pair for the treatment of COVID-19. AE with multicomponents might have therapeutic effects against COVID-19 by affecting the inflammatory and immune responses, cell apoptosis, hypoxia damage and other pathological processes through multiple components, targets and pathways.

scholarly journals The Important Herbal Pair for the Treatment of COVID-19 and Its Possible Mechanisms

2021 ◽  
Author(s):  
Shujie Xia ◽  
Zhangfeng Zhong ◽  
Bizhen Gao ◽  
Chi Teng Vong ◽  
Xuejuan Lin ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Association Rules ◽  
Hypoxia Inducible Factor ◽  
Mitogen Activated Protein Kinase ◽  
Network Pharmacology ◽  
Therapeutic Effects ◽  
Active Ingredients ◽  
Active Components ◽  
Ephedra Sinica ◽  
Rule Approach

Abstract Background: Coronavirus Disease 2019 (COVID-19) is an unprecedented disaster for people around the world. Many studies have shown that traditional Chinese medicine (TCM) are effective in treating COVID-19. However, it is difficult to find the most effective combination herbal pair among numerous herbs, as well as identifying its potential mechanisms. Herbal pair is the main form of a combination of TCM herbs, which is widely used for the treatment of diseases. It can also help us to better understand the compatibility of TCM prescriptions, thus improving the curative effects. The purpose of this article is to explore the compatibility of TCM prescriptions and identify the most important herbal pair for the treatment of COVID-19, and then analyze the active components and potential mechanisms of this herbal pair. Methods: We first systematically sorted the TCM prescriptions recommended by the leading experts for treating COVID-19, and the specific herbs contained in these prescriptions across different stages of the disease. Next, the association rule approach was employed to examine the distribution and compatibility among these TCM prescriptions, and then identify the most important herbal pair. On this basis, we further investigated the active ingredients and potential targets in the selected herbal pair by a network pharmacology approach, and analyzed the potential mechanisms against COVID-19. Finally, the main active compounds in AE were selected for molecular docking with severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) 3CLpro and angiotensin converting enzyme II (ACE2) for further verification. Result: We obtained 32 association rules for the herbal combinations in the selection of TCM treatment for COVID-19. The results showed that the combination of Amygdalus Communis Vas (ACV) and Ephedra sinica Stapf (ESS) had the highest confidence degree and lift value, as well as high support degree, which can be used in almost all the stages of COVID-19, so ACV and ESS (AE) were selected as the most important herbal pair. There were 26 active ingredients and 44 potential targets, which might be related to the herbal pair of AE against COVID-19. The main active ingredients of AE against COVID-19 were quercetin, kaempferol, luteolin, while the potential targets were Interleukin 6 (IL-6), Mitogen-activated Protein Kinase 1 (MAPK)1, MAPK8, Interleukin-1β (IL-1β), and Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB) p65 subunit (RELA). The protein-protein interaction (PPI) cluster demonstrated that IL-6 was the seed in the cluster, which plays an important role in connecting other nodes in the PPI network. The potential pathways mainly involved tumor necrosis factor (TNF), Toll-like receptor (TLR), hypoxia-inducible factor-1 (HIF-1), and nucleotide-binding oligomerization domain (NOD)-like receptor (NLRs). The molecular docking results showed that the main active ingredients of AE had good affinity with SARS-COV-2 3CLpro and ACE2, which was consistent with the above analysis. Conclusion: There were 32 association rules in the TCM prescriptions recommended by experts for COVID-19. The combination of ACV and EAS was the most important herbal pair for the treatment of COVID-19. AE might have therapeutic effects against COVID-19 by affecting the inflammatory and immune responses, cell apoptosis, hypoxia damage and other pathological processes through multiple components, targets and pathways.

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