Chemical profiling of Callicarpa nudiflora and its effective compounds identification by compound-target network analysis

2020 ◽  
Vol 182 ◽  
pp. 113110 ◽  
Author(s):  
Yong-Sheng Wu ◽  
Liu Shi ◽  
Xin-Guang Liu ◽  
Wei Li ◽  
Rui Wang ◽  
...  
Keyword(s):  
Network Analysis ◽  
Chemical Profiling ◽  
Target Network ◽  
Compound Target

scholarly journals Preliminary Analysis of the Therapeutic Mechanism of Feiluoning in Convalescent Patients With COVID-19

2020 ◽  
Vol 15 (12) ◽  
pp. 1934578X2097762
Author(s):  
Zongchao Hong ◽  
Maolin Hong ◽  
Bo Liu ◽  
Ying Zhang ◽  
Yanfang Yang ◽  
...  
Keyword(s):  
Chinese Medicine ◽  
Pulmonary Fibrosis ◽  
Pulmonary Function ◽  
Target Genes ◽  
Interaction Analysis ◽  
Binding Capacity ◽  
Chemical Constituents ◽  
The Core ◽  
Target Network ◽  
Compound Target

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), is often accompanied by injury to pulmonary function and pulmonary fibrosis. Feiluoning (FLN) is a new Chinese medicine prescription which is available for the treatment of severe and critical convalescence of COVID-19 patients. FLN also has a positive effect on pulmonary function injury and pulmonary fibrosis. We explored the potential mechanism of FLN’s effect on the convalescent treatment of COVID-19. According to the pharmacodynamic activity parameters, we screened the active chemical constituents of FLN by comparing the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform. The Uniprot database was used to querying the corresponding target genes, and Cytoscape 3.6.1 was used to construct a herb-compound-target network. Protein interaction analysis, target gene function enrichment analysis, and signal pathway analysis were performed using the STRING, DAVID, and Kyoto Encyclopedia of Genes and Genomes pathway databases. Molecular docking was used to predict the binding capacity of the core compound with COVID-19 hydrolase 3 Cl and angiotensin-converting enzyme 2 (ACE2). The herb-compound-target network was successfully constructed and key targets identified, including prostaglandin G/H synthase 2, estrogen receptor 1, heat shock protein HSP 90, and androgen receptor. The major affected metabolic pathways were pathways in cancer, pancreatic cancer, nonsmall cell lung cancer, and toll-like receptor signaling. The core compounds of FLN, including quercetin, luteolin, kaempferol, and stigmasterol, could strongly bind to COVID-19 3 Cl hydrolase, and other compounds, including 7-O-methylisomucronulatol and medicocarpin, could strongly bind to ACE2. Thus, it is predicted that FLN has the characteristics of a multicomponent, multitarget, and multichannel overall control compound. FLN’s mechanism of action in the treatment of COVID-19 may be associated with the regulation of inflammation and immune-related signaling pathways, and the influence of COVID-19 3 Cl hydrolase binding ability.

scholarly journals Network Pharmacology-Based Study of the Underlying Mechanisms of Huangqi Sijunzi Decoction for Alzheimer’s Disease

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Wei Zhang ◽  
Mingti Lv ◽  
Yating Shi ◽  
Yonghui Mu ◽  
Zhaoyang Yao ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Neuroprotective Effect ◽  
Signalling Pathway ◽  
Signalling Pathways ◽  
Network Pharmacology ◽  
Neuroprotective Effects ◽  
Target Network ◽  
Compound Target

Background. Huangqi Sijunzi decoction (HQSJZD) is a commonly used conventional Chinese herbal medicine prescription for invigorating Qi, tonifying Yang, and removing dampness. Modern pharmacology and clinical applications of HQSJZD have shown that it has a certain curative effect on Alzheimer’s disease (AD). Methods. The active components and targets of HQSJZD were searched in the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). The genes corresponding to the targets were retrieved using UniProt and GeneCard database. The herb-compound-target network and protein-protein interaction (PPI) network were constructed by Cytoscape. The core targets of HQSJZD were analysed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The main active compounds of HQSJZD were docked with acetylcholinesterase (AChE). In vitro experiments were conducted to detect the inhibitory and neuroprotective effects of AChE. Results. Compound-target network mainly contained 132 compounds and 255 corresponding targets. The main compounds contained quercetin, kaempferol, formononetin, isorhamnetin, hederagenin, and calycosin. Key targets contained AChE, PTGS2, PPARG, IL-1B, GSK3B, etc. There were 1708 GO items in GO enrichment analysis and 310 signalling pathways in KEGG, mainly including the cAMP signalling pathway, the vascular endothelial growth factor (VEGF) signalling pathway, serotonergic synapses, the calcium signalling pathway, type II diabetes mellitus, arginine and proline metabolism, and the longevity regulating pathway. Molecular docking showed that hederagenin and formononetin were the top 2 compounds of HQSJZD, which had a high affinity with AChE. And formononetin has a good neuroprotective effect, which can improve the oxidative damage of nerve cells. Conclusion. HQSJZD was found to have the potential to treat AD by targeting multiple AD-related targets. Formononetin and hederagenin in HQSJZD may regulate multiple signalling pathways through AChE, which might play a therapeutic role in AD.

scholarly journals Network Pharmacology-Based Investigation into the Mechanisms of Quyushengxin Formula for the Treatment of Ulcerative Colitis

2019 ◽  
Vol 2019 ◽  
pp. 1-22
Author(s):  
Haojie Yang ◽  
Ying Li ◽  
Sichen Shen ◽  
Dan Gan ◽  
Changpeng Han ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Bioactive Compounds ◽  
Functional Enrichment ◽  
Network Pharmacology ◽  
Disease Network ◽  
Pathway Network ◽  
Similarity Algorithm ◽  
Target Network ◽  
Target Disease ◽  
Compound Target

Objective. Ulcerative colitis (UC) is a chronic idiopathic inflammatory bowel disease whose treatment strategies remain unsatisfactory. This study aims to investigate the mechanisms of Quyushengxin formula acting on UC based on network pharmacology. Methods. Ingredients of the main herbs in Quyushengxin formula were retrieved from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. Absorption, distribution, metabolism, and excretion properties of all ingredients were evaluated for screening out candidate bioactive compounds in Quyushengxin formula. Weighted ensemble similarity algorithm was applied for predicting direct targets of bioactive ingredients. Functional enrichment analyses were performed for the targets. In addition, compound-target network, target-disease network, and target-pathway network were established via Cytoscape 3.6.0 software. Results. A total of 41 bioactive compounds in Quyushengxin formula were selected out from the TCMSP database. These bioactive compounds were predicted to target 94 potential proteins by weighted ensemble similarity algorithm. Functional analysis suggested these targets were closely related with inflammatory- and immune-related biological progresses. Furthermore, the results of compound-target network, target-disease network, and target-pathway network indicated that the therapeutic effects of Quyushengxin on UC may be achieved through the synergistic and additive effects. Conclusion. Quyushengxin may act on immune and inflammation-related targets to suppress UC progression in a synergistic and additive manner.

scholarly journals Systems Pharmacological Approach to the Effect of Bulsu-san Promoting Parturition

2017 ◽  
Vol 2017 ◽  
pp. 1-15 ◽  
Author(s):  
Su Yeon Suh ◽  
Won G. An
Keyword(s):  
Analytical Approach ◽  
Target Genes ◽  
Clinical Applications ◽  
Oriental Medicine ◽  
Biological Processes ◽  
Gene Ontology Analysis ◽  
Multiple Target ◽  
Pathway Network ◽  
Target Network ◽  
Compound Target

Bulsu-san (BSS) has been commonly used in oriental medicine for pregnant women in East Asia. The purpose of this research was to elucidate the effect of BSS on ease of parturition using a systems-level in silico analytic approach. Research results show that BSS is highly connected to the parturition related pathways, biological processes, and organs. There were numerous interactions between most compounds of BSS and multiple target genes, and this was confirmed using herb-compound-target network, target-pathway network, and gene ontology analysis. Furthermore, the mRNA expression of relevant target genes of BSS was elevated significantly in related organ tissues, such as those of the uterus, placenta, fetus, hypothalamus, and pituitary gland. This study used a network analytical approach to demonstrate that Bulsu-san (BSS) is closely related to the parturition related pathways, biological processes, and organs. It is meaningful that this systems-level network analysis result strengthens the basis of clinical applications of BSS on ease of parturition.

scholarly journals In silico target network analysis of de novo-discovered, tick saliva-specific microRNAs reveals important combinatorial effects in their interference with vertebrate host physiology

RNA ◽  
2017 ◽  
Vol 23 (8) ◽  
pp. 1259-1269 ◽  
Author(s):  
Michael Hackenberg ◽  
David Langenberger ◽  
Alexandra Schwarz ◽  
Jan Erhart ◽  
Michail Kotsyfakis
Keyword(s):  
Network Analysis ◽  
In Silico ◽  
De Novo ◽  
Vertebrate Host ◽  
Tick Saliva ◽  
Target Network ◽  
Host Physiology

scholarly journals The Methodological Trends of Traditional Herbal Medicine Employing Network Pharmacology

Biomolecules ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 362 ◽  
Author(s):  
Won-Yung Lee ◽  
Choong-Yeol Lee ◽  
Youn-Sub Kim ◽  
Chang-Eop Kim
Keyword(s):  
Herbal Medicine ◽  
Network Pharmacology ◽  
Therapeutic Effects ◽  
Systems Pharmacology ◽  
Traditional Herbal Medicine ◽  
Affiliation Networks ◽  
Target Network ◽  
Analysis Platform ◽  
Combining Methods ◽  
Compound Target

Natural products, including traditional herbal medicine (THM), are known to exert their therapeutic effects by acting on multiple targets, so researchers have employed network pharmacology methods to decipher the potential mechanisms of THM. To conduct THM-network pharmacology (THM-NP) studies, researchers have employed different tools and databases for constructing and analyzing herb–compound–target networks. In this study, we attempted to capture the methodological trends in THM-NP research. We identified the tools and databases employed to conduct THM-NP studies and visualized their combinatorial patterns. We also constructed co-author and affiliation networks to further understand how the methodologies are employed among researchers. The results showed that the number of THM-NP studies and employed databases/tools have been dramatically increased in the last decade, and there are characteristic patterns in combining methods of each analysis step in THM-NP studies. Overall, the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was the most frequently employed network pharmacology database in THM-NP studies. Among the processes involved in THM-NP research, the methodology for constructing a compound–target network has shown the greatest change over time. In summary, our analysis describes comprehensive methodological trends and current ideas in research design for network pharmacology researchers.

scholarly journals Confirming an integrated pathology of diabetes and its complications by molecular biomarker-target network analysis

2016 ◽  
Vol 14 (3) ◽  
pp. 2213-2221 ◽  
Author(s):  
Zide Zhao ◽  
Yingying Zhang ◽  
Fengchun Gai ◽  
Ying Wang
Keyword(s):  
Network Analysis ◽  
Molecular Biomarker ◽  
Target Network
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