#Cytoscape viral Activator#
#Cytoscape viral software#

The active ingredients of XBJ regulated different genes, acted on different pathways, and synergistically produced anti-inflammatory and immune-regulatory effects, which fully demonstrated the synergistic effects of different components on multiple targets and pathways. The molecular docking results showed that the core 18 effective ingredients had a docking score of less than − 4.0 with those top 10 targets.

XBJ exerted its therapeutic effects through the renin-angiotensin system (RAS), nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB), MAPK, phosphatidylinositol-4, 5-bisphosphate 3-kinase ( PI3K)-protein kinase B ( Akt)-vascular endothelial growth factor (VEGF), toll-like receptor (TLR), TNF, and inflammatory-mediator regulation of transient receptor potential (TRP) signaling pathways to ultimately construct a “drug-ingredient-target-pathway” effector network. They participated in extracellular signal–regulated kinase 1 and 2 ( ERK1, ERK2) cascade, the T-cell receptor signaling pathway, activation of MAPK activity, cellular response to lipopolysaccharide, and other inflammation- and immune-related BPs.

#Cytoscape viral Activator#

Fourteen of these targets-glyceraldehyde 3-phosphate dehydrogenase ( GAPDH), albumin ( ALB), tumor necrosis factor ( TNF), epidermal growth factor receptor ( EGFR), mitogen-activated protein kinase 1 ( MAPK1), Caspase-3 ( CASP3), signal transducer and activator of transcription 3 ( STAT3), MAPK8, prostaglandin-endoperoxide synthase 2 ( PTGS2), JUN, interleukin-2 ( IL-2), estrogen receptor 1 ( ESR1), and MAPK14 had degree values > 40 and therefore could be considered key targets. We obtained 144 potential COVID-19 effector targets of XBJ.

#Cytoscape viral software#

We used AutoDock vina and PyMOL software for molecular docking. We used the ClueGO and CluePedia plugins in Cytoscape to conduct gene ontology (GO) biological process (BP) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway enrichment analysis of XBJ’s effector targets. Cytoscape software version 3.7.0 was used to construct a “XBJ active-compound-potential-effector target” network and protein-protein interaction (PPI) network, and then to carry out network topology analysis of potential targets. Next, we used the SwissTargetPrediction database to predict XBJ’s effector targets and map them to the abovementioned COVID-19 disease targets in order to obtain potential therapeutic targets of XBJ. Then, we compiled COVID-19 disease targets from the GeneCards gene database and via literature searches. We searched Chinese and international papers to obtain the active ingredients of XBJ. This study aimed to examine the potential effector mechanisms of XBJ on COVID-19 based on network pharmacology. But the bioactive compounds and potential mechanisms of XBJ for COVID-19 prevention and treatment are unclear. Chinese medicine Xuebijing (XBJ) has proven to be effective in the treatment of mild coronavirus disease 2019 (COVID-19) cases.