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 Network pharmacology approach to reveals therapeutic mech-anism of traditional plants formulation used by Malaysia in-digenous ethnics in coronaviruses infection

2022 ◽  
Author(s):  
Fui Fui Lem ◽  
Dexter Jiunn Herng Lee ◽  
Fong Tyng Chee ◽  
Su Na Chin ◽  
Kai Min Lin ◽  
...  
Keyword(s):  
Bioactive Compounds ◽  
Target Genes ◽  
Interaction Network ◽  
Bioactive Compound ◽  
Functional Enrichment ◽  
Network Pharmacology ◽  
Pathway Network ◽  
Pharmacological Mechanism ◽  
Target Network ◽  
Compound Target

Network pharmacology analysis can act as a strategy to identify the pharmacological effect of plant-based bioactive compounds against coronavirus diseases. This study aimed to investigate the potential pharmacological mechanism of a local ethnomedicine (Costus speciosus, Hibiscus rosa-sinensis and Phyllanthus niruri) of Northern Borneo against coronaviruses known as CHP. Compounds in CHP were extracted from databases and screened for their oral bioavailability and drug-likeness before a compound-target network was built. Furthermore, the protein-protein interaction network and pathway enrichment were constructed and analyzed. A compound-target network consisting of 48 putative bioactive compounds targeting 587 candidate genes was identified. A total of 186 coronavirus-related genes were extracted and TP53, STAT3, HSP90AA1, STAT1, and EP300 were predicted to be the key targets. Notably, mapping of these target genes into the target-pathway network illustrated that functional enrichment was on viral infection and regulation of inflammation pathways. Urinatetralin is predicted, for the first time, as a bioactive compound that solely targets STAT3. The results from this study indicate that compounds present in CHP employ STAT3 and its connected pathways as the mechanism of action against coronaviruses. In conclusion, urinatetralin should be further investigated for its potential application against coronavirus infections.

scholarly journals Study on the Mechanism of Lianpu Drink for the Treatment of Chronic Gastritis Based on Network Pharmacology

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Shuhan Zhou ◽  
Yanjun Duan ◽  
Yu Deng ◽  
Miao Wang ◽  
Chaoqun Huang ◽  
...  
Keyword(s):  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Signaling Pathway ◽  
Chronic Gastritis ◽  
Mechanisms Of Action ◽  
Network Pharmacology ◽  
Biological Pathway ◽  
Disease Network ◽  
Target Disease ◽  
Compound Target

Chronic gastritis (CG) places a considerable burden on the healthcare system worldwide. Traditional Chinese Medicine (TCM) formulas characterized by multicompounds and multitargets have been acknowledged with striking effects in the treatment of CG in China’s history. Nevertheless, their accurate mechanisms of action are still ambiguous. In this study, we analyzed the effective compounds, potential targets, and related biological pathway of Lianpu Drink (LPD), a TCM formula which has been reported to have a therapeutic effect on CG, by contrasting a “compound-target-disease” network. According to the results, 92 compounds and 5762 putative targets of LPD were screened; among them, 8 compounds derived from different herbs in LPD and 30 common targets related to LPD and CG were selected as candidate compounds and precision targets, respectively. Meanwhile, the predicted common targets were verified by Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway analysis and pharmacological experiments. The results demonstrated that quercetin, ephedrine, trigonelline, crocetin, and β-sitosterol were major effective compounds of LPD responsible for the CG treatment by inhibiting the activation of the JAK 2-STAT 3 signaling pathway to reduce the expressions of cyclin D1 and Bcl-2 proteins. The study provides evidence for the mechanism of understanding of LPD for the treatment of CG.

scholarly journals Network Pharmacology-Based Approach to Investigate the Mechanisms of Mahai Capsules in the Treatment of Cardiovascular Diseases

2020 ◽  
Vol 2020 ◽  
pp. 1-15 ◽  
Author(s):  
Minjuan Shi ◽  
Bo Li ◽  
Qiuzhen Yuan ◽  
Xuefeng Gan ◽  
Xiao Ren ◽  
...  
Keyword(s):  
Cardiovascular Diseases ◽  
Life Quality ◽  
Enrichment Analysis ◽  
Basic Research ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Network Pharmacology ◽  
Therapeutic Effects ◽  
Target Disease ◽  
Compound Target

Background. Mahai capsules (MHC) have been deemed to be an effective herb combination for treatment of cardiovascular diseases (CVD) development and improvement of the life quality of CVD patients. To systematically explore the mechanisms of MHC in CVD, a network pharmacology approach mainly comprising target prediction, network construction, biological process and pathway analysis, and related diseases was adopted in this study. Methods. We collected the bioactive compounds and potential targets of MHC through the TCMSP servers. Candidate targets related to CVD were collected from Therapeutic Targets Database and PharmGkb database and analyzed using ClueGO plugin in Cytoscape. KEGG pathway was enriched and analyzed through the EnrichR platform, and protein-protein interaction networks were calculated by STRING platform. The compound-target, target-disease, and compound-target-disease networks were constructed using Cytoscape. Results. A total of 303 targets of the 57 active ingredients in MHC were obtained. The network analysis showed that PTGS2, PTGS1, HSP90, Scn1a, estrogen receptor, calmodulin, and thrombin were identified as key targets of MHC in the treatment of CVD. The functional enrichment analysis indicated that MHC probably produced the therapeutic effects against CVD by synergistically regulating many biological pathways, such as PI3K-Akt, TNF, HIF-1, FoxO, apoptosis, calcium, T-cell receptor, VEGF, and NF-kappa B signaling pathway. Conclusions. In summary, the analysis of the complete profile of the pharmacological properties, as well as the elucidation of targets, networks, and pathways, can further illuminate that the underlying mechanisms of MHC in CVD might be strongly associated with its synergic regulation of inflammation, apoptosis, and immune function, and provide new clues for its future development of therapeutic strategies and basic research.

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 A Network Pharmacology-Based Study on Pharmacological Activities and Mechanisms of Essential Oil in Leaves of C. Grandis ‘Tomentosa’

2021 ◽  
Author(s):  
Jieshu You ◽  
Sheng-cai He ◽  
Liang Chen ◽  
Zhen-hui Guo ◽  
Fei Gao ◽  
...  
Keyword(s):  
Essential Oil ◽  
Function Analysis ◽  
Network Pharmacology ◽  
Chemical Components ◽  
Pathway Enrichment Analysis ◽  
Health Food ◽  
Disease Network ◽  
Pharmacological Activities ◽  
Integrated Network ◽  
Target Disease

Abstract Background and Objective: Citrus grandis ‘Tomentosa’, as the fruit epicarp of C. grandis ‘Tomentosa’ or C. grandis (L.) Osbeck, is widely used in health food and medicine. Actually, based on our survey results, there are also rich essential oils with bioativities in leaves, but the chemical compounds in this part and relevant pharmacological activities have never been studied systematically yet. Therefore, this study was to preliminarily decipher the pharmacological activities and mechanisms of the essential oil in leaves of C. grandis ‘Tomentosa’ by an integrated network pharmacology approach. Methods: Essential oil compositions from leaves of C. grandis ‘Tomentosa’ were identified using GC-MS/MS. And then the targets of these oil compositions were predicted and screened from TCMSP, SwissTargetPrediction, STITCH and SEA databases. STRING database was used to construct the protein-protein interaction networks, and the eligible protein targets were input into WebGestalt 2019 to carry out GO enrichment and KEGG pathway enrichment analysis. Based on the potential targets, disease enrichment information was obtained by TTD databases. Cytoscape software was used to construct the component-target-disease network diagrams. Results: Finally, 61 essential oil chemical components were identified by GC-MS/MS, which correspond to 679 potential targets. Biological function analysis showed that there were 12, 19, and 12 GO entries related to biological processes, cell components and molecular functions, respectively. 43 KEGG pathways were identified, of which the most significant categories were terpenoid backbone biosynthesis, TNF signaling pathway and leishmaniasis. The component-target-disease network diagram revealed that the essential oil compositions in leaves of C. grandis ‘Tomentosa’ could treat tumors, immune diseases, neurodegenerative diseases and respiratory diseases, which were highly related to CHRM1, PTGS2, CASP3, MAP2K1 and CDC25B.Conclusion: This study may provide a new insight into C. grandis ‘Tomentosa’ or C. grandis (L.) Osbeck and may provide useful information for future utilization and development.

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 Integrative Network Pharmacology of Moringa oleifera Combined with Gemcitabine against Pancreatic Cancer

Processes ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1742
Author(s):  
Nursaffa Alisya Sahruddin ◽  
Zhong Sun ◽  
Norsyasya Adriana Rosdi ◽  
Sudha Warrier ◽  
Karuppiah Thilakavathy
Keyword(s):  
Pancreatic Cancer ◽  
Bioactive Compounds ◽  
Moringa Oleifera ◽  
Biological Activities ◽  
Advanced Pancreatic Cancer ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Cancer Genes ◽  
Pathway Network

Gemcitabine (GEM) is the first-line chemotherapy drug for patients with advanced pancreatic cancer. Moringa oleifera (MO) exhibited various biological activities, including anticancer effects. Nevertheless, the effectiveness of their combination against pancreatic cancer has not yet been explored. This study evaluates the effect of MO and GEM against pancreatic cancer through network pharmacology. TCMSP, TCMID, and PubMed were used to identify and screen MO bioactive compounds. MO and GEM genes were predicted through DGIdb, CTD, and DrugBank. Pancreatic cancer genes were retrieved from OMIM and MalaCards. Protein–protein interaction (PPI) and compound-target-pathway network were established via STRING and Cytoscape. Gene ontology (GO) and pathway enrichment analysis were conducted using DAVID Bioinformatic Tools. Catechin, kaempferol, quercetin, and epicatechin that met the drug screening requirements, and three additional compounds, glucomoringin, glucoraphanin, and moringinine, were identified as bioactive compounds in MO. Catechin was found to be the main hub compound in MO. TP53, AKT1, VEGFA, and CCND1 from PPI network were discovered as hub genes to have biological importance in pancreatic cancer. GO and pathway analysis revealed that MO and GEM combination was mainly associated with cancer, including pancreatic cancer, through regulation of apoptosis. Combination therapy between MO and GEM might provide insight in pancreatic cancer treatment.

scholarly journals Elucidation of the mechanism of action of the anticholecystitis effect of the Tibetan medicine “Dida” using network pharmacology

2020 ◽  
Vol 19 (7) ◽  
pp. 1449-1457
Author(s):  
Chuan Liu ◽  
Fang-Fang Fan ◽  
Xuan-Hao Li ◽  
Wen-Xiang Wang ◽  
Ya Tu ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Bioactive Compounds ◽  
Kegg Pathway ◽  
Docking Simulation ◽  
Cell Receptor ◽  
Mapk Signaling ◽  
Tibetan Medicine ◽  
Network Pharmacology ◽  
Molecular Docking Simulation ◽  
Pathway Network

Purpose: To study the mechanism involved in the anti-cholecystitis effect the Tibetan medicine “Dida”, using network pharmacology-integrated molecular docking simulationsMethods: In this investigation, the bioactive compounds of Dida were collected, network pharmacology methods to predict their targets, and networks were constructed through GO and KEGG pathway analyses. The potential binding between the bioactive compounds and the targets were demonstrated using molecular docking simulations.Results: A total of 12 bioactive compounds and 50 key targets of Dida were identified. Two networks, namely, protein–protein interaction (PPI) network of cholecystitis targets, and compound–target– pathway network, were established. Network analysis showed that 10 targets (GAPDH, AKT1, CASP3, EGFR, TNF, MAPK3, MAPK1, HSP90AA1, STAT3, and BCL2L1) may be the therapeutic targets of Dida in cholecystitis. Analysis of the KEGG pathway indicated that the anti-cholecystitis effect of Dida may its regulation of a few crucial pathways, such as apoptosis, as well as toll-like  receptor, T cell receptor, NOD-like receptor, and MAPK signaling pathways. Furthermore, molecular docking simulation revealed that CASP3, CAPDH, HSP90AA1, MAPK3, MAPK1, and STAT3 had well-characterized interactions with the corresponding compounds.Conclusion: The mechanism underlying the anti-cholecystitis effect of Dida has been successfully predicted and verified using a combination of network pharmacology and molecular docking simulation. This provides a firm basis for the experimental verification of the use of Dida in the treatment of cholecystitis, and enhances its rational application in clinical practice. Keywords: Tibetan medicine, Dida, Cholecystitis, Mechanism, Network pharmacology, Molecular docking simulation

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.

Virtual Screening of Potential Anti-fatigue Mechanism of Polygonati Rhizoma Based on Network Pharmacology

2020 ◽  
Vol 22 (9) ◽  
pp. 612-624 ◽  
Author(s):  
Ze-Feng Wang ◽  
Ye-Qing Hu ◽  
Qi-Guo Wu ◽  
Rui Zhang
Keyword(s):  
Virtual Screening ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Vital Role ◽  
Network Pharmacology ◽  
Pathway Network ◽  
Protein Protein Interaction ◽  
Target Network ◽  
Protein Protein Interaction Network ◽  
Fatigue Mechanism

Background and Objective: A large number of people are facing the danger of fatigue due to the fast-paced lifestyle. Fatigue is common in some diseases, such as cancer. The mechanism of fatigue is not definite. Traditional Chinese medicine is often used for fatigue, but the potential mechanism of Polygonati Rhizoma (PR) is still not clear. This study attempts to explore the potential anti-fatigue mechanism of Polygonati Rhizoma through virtual screening based on network pharmacology. Methods: The candidate compounds of PR and the known targets of fatigue are obtained from multiple professional databases. PharmMapper Server is designed to identify potential targets for the candidate compounds. We developed a Herbal medicine-Compound-Disease-Target network and analyzed the interactions. Protein-protein interaction network is developed through the Cytoscape software and analyzed by topological methods. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment are carried out by DAVID Database. Finally, we develop Compound-Target-Pathway network to illustrate the anti-fatigue mechanism of PR. Results: This approach identified 12 active compounds and 156 candidate targets of PR. The top 10 annotation terms for GO and KEGG were obtained by enrichment analysis with 35 key targets. The interaction between E2F1 and PI3K-AKT plays a vital role in the anti-fatigue effect of PR due to this study. Conclusions: This study demonstrates that PR has multi-component, multi-target and multipathway effects.

Sign in / Sign up

Export Citation Format

Share Document