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 Systems Pharmacological Approach of Pulsatillae Radix on Treating Crohn’s Disease

2017 ◽  
Vol 2017 ◽  
pp. 1-21 ◽  
Author(s):  
Su Yeon Suh ◽  
Won G. An
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Biological Processes ◽  
Gene Ontology Analysis ◽  
Pathway Network ◽  
Amoebic Dysentery ◽  
Study Results ◽  
Target Network ◽  
Anti Inflammatory ◽  
Antioxidant Effects

In East Asian traditional medicine, Pulsatillae Radix (PR) is widely used to treat amoebic dysentery and renowned for its anti-inflammatory effects. This study aimed to confirm evidence regarding the potential therapeutic effect of PR on Crohn’s disease using a system network level based in silico approach. Study results showed that the compounds in PR are highly connected to Crohn’s disease related pathways, biological processes, and organs, and these findings were confirmed by compound-target network, target-pathway network, and gene ontology analysis. Most compounds in PR have been reported to possess anti-inflammatory, anticancer, and antioxidant effects, and we found that these compounds interact with multiple targets in a synergetic way. Furthermore, the mRNA expressions of genes targeted by PR are elevated significantly in immunity-related organ tissues, small intestine, and colon. Our results suggest that the anti-inflammatory and repair and immune system enhancing effects of PR might have therapeutic impact on Crohn’s disease.

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 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 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 A network pharmacology-based approach to explore potential targets of Caesalpinia pulcherima: an updated prototype in drug discovery

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Nikhil S. Sakle ◽  
Shweta A. More ◽  
Santosh N. Mokale
Keyword(s):  
Breast Cancer ◽  
Target Genes ◽  
Docking Study ◽  
Network Pharmacology ◽  
Egfr Expression ◽  
Target Network ◽  
Anti Fungal ◽  
Compound Target

Abstract Caesalpinia pulcherima (CP) is a traditional herb used for the treatment of asthma, bronchitis, cancer, anti-bacterial, anti-fungal and as abortifacient. In the present study, bioactive components and potential targets in the treatment of breast cancer validated through in silico, in vitro and in vivo approach. The results for the analysis were as among 29 components, only four components were found active for further study which proved the use of CP as a multi-target herb for betterment of clinical uses. The results found by PPI states that our network has significant interactions which include the ESR-1, ESR-2, ESRRA, MET, VEGF, FGF, PI3K, PDK-1, MAPK, PLK-1, NEK-2, and GRK. Compound-target network involves 4 active compound and 150 target genes which elucidate the mechanisms of drug action in breast cancer treatment. Furthermore, on the basis of the above results the important proteins were fetched for the docking study which helps in predicting the possible interaction between components and targets. The results of the western blotting showed that CP regulates ER and EGFR expression in MCF-7 cell. In addition to this animal experimentation showed that CP significantly improved immunohistological status in MNU induced carcinoma rats. Network pharmacology approach not only helps us to confirm the study of the chosen target but also gave an idea of compound-target network as well as pathways associated to the CP for treating the complex metabolic condition as breast cancer and they importance for experimental verification.

scholarly journals Network Pharmacology Strategy to Investigate the Pharmacological Mechanism of Siwu Decoction on Primary Dysmenorrhea and Molecular Docking Verification

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Dandan Jiang ◽  
Xiaoyan Wang ◽  
Lijun Tian ◽  
Yufeng Zhang
Keyword(s):  
Molecular Docking ◽  
Target Genes ◽  
Network Pharmacology ◽  
Primary Dysmenorrhea ◽  
Ppi Network ◽  
Active Compounds ◽  
Docking Simulations ◽  
Active Target ◽  
Target Network ◽  
Compound Target

Objective. To study the pharmacological mechanisms of Siwu decoction (SWD) on primary dysmenorrhea (PDM) and verify with molecular docking. Methods. The  Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was utilized to acquire the active compounds and their corresponding target genes. The GeneCards database was utilized in the search for target genes that were associated with PDM. The intersection genes from the active target genes of SWD and those associated with PDM represented the active target genes of SWD that act on PDM. The Gene Ontology (GO) function enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were both carried out by RGUI 3.6.1 and Cytoscape 3.6.0 software. Cytoscape was also utilized for creating a compound-target network, and a protein-protein interaction (PPI) network was created through the STRING database. Molecular docking simulations of the macromolecular protein target receptors and their corresponding compounds were performed using AutoDockTool 1.5.6 and AutoDock Vina software. Results. We identified 14 active compounds as well as 97 active target genes of SWD by using the TCMSP. We compared the 97 active target genes of SWD to the 299 target genes related to PDM, and 23 active target genes for SWD that act on PDM which correlated with 11 active compounds were detected. The compound-target network as well as the PPI network were created, in addition to selecting the most essential compounds and their targets in order to create a key compound-target network. The most essential compounds were kaempferol, beta-sitosterol, stigmasterol, and myricanone. The key targets were AKT1, PTGS2, ESR1, AHR, CASP3, and PGR. Lastly, molecular docking was used to confirm binding of the target with its corresponding compound. Conclusion. The pharmacological mechanisms of SWD that act on PDM were investigated, and the active compounds in the SWD for treating PDM were further verified.

scholarly journals Exploring the Pharmacological Mechanism of Quercetin-Resveratrol Combination for Polycystic Ovary Syndrome: A Systematic Pharmacological Strategy-Based Research

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kailin Yang ◽  
Liuting Zeng ◽  
Tingting Bao ◽  
Zhiyong Long ◽  
Bing Jin
Keyword(s):  
Polycystic Ovary Syndrome ◽  
Molecular Mechanism ◽  
Polycystic Ovary ◽  
Pathway Enrichment Analysis ◽  
Biological Processes ◽  
Ppi Network ◽  
Ovary Syndrome ◽  
Potential Target ◽  
Target Network ◽  
Compound Target

AbstractResveratrol and quercetin have effects on polycystic ovary syndrome (PCOS). Hence, resveratrol combined with quercetin may have better effects on it. However, because of the limitations in animal and human experiments, the pharmacological and molecular mechanism of quercetin-resveratrol combination (QRC) remains to be clarified. In this research, a systematic pharmacological approach comprising multiple compound target collection, multiple potential target prediction, and network analysis was used for comparing the characteristic of resveratrol, quercetin and QRC, and exploring the mechanism of QRC. After that, four networks were constructed and analyzed: (1) compound-compound target network; (2) compound-potential target network; (3) QRC-PCOS PPI network; (4) QRC-PCOS-other human proteins (protein-protein interaction) PPI network. Through GO and pathway enrichment analysis, it can be found that three compounds focus on different biological processes and pathways; and it seems that QRC combines the characteristics of resveratrol and quercetin. The in-depth study of QRC further showed  more PCOS-related biological processes and pathways. Hence, this research not only offers clues to the researcher who is interested in comparing the differences among resveratrol, quercetin and QRC, but also provides hints for the researcher who wants to explore QRC’s various synergies and its pharmacological and molecular mechanism.

scholarly journals Investigating the Biomarkers of the Sasang Constitution via Network Pharmacology Approach

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Won-Yung Lee ◽  
Choong-Yeol Lee ◽  
Chang-Eop Kim ◽  
Ji-Hwan Kim
Keyword(s):  
Target Genes ◽  
Metabolic Diseases ◽  
Chromosomal Abnormalities ◽  
Network Pharmacology ◽  
Biological Processes ◽  
Sasang Constitution ◽  
Target Network ◽  
Physical Traits ◽  
Nutritional And Metabolic Diseases ◽  
Constitutional Medicine

Sasang constitutional (SC) medicine classifies people into Soeum (SE), Soyang (SY), Taeeum (TE), and Taeyang (TY) types based on psychological and physical traits. However, biomarkers of these types are still unclear. We aimed to identify biomarkers among the SC types using network pharmacology methods. Target genes associated with the SC types were identified by grouping herb targets that preserve and strengthen the requisite energy (Bomyeongjiju). The herb targets were obtained by constructing an herb-compound-target network. We identified 371, 185, 146, and 89 target genes and their unique biological processes related to SE, SY, TE, and TY types, respectively. While the targets of SE and SY types were the most similar among the target pairs of the SC types, those of TY type overlapped with only a few other SC-type targets. Moreover, SE, SY, TE, and TY were related to “diseases of the digestive system,” “diseases of the nervous system,” “endocrine, nutritional, and metabolic diseases,” and “congenital malformations, deformations, and chromosomal abnormalities,” respectively. We successfully identified the target genes, biological processes, and diseases related to each SC type. We also demonstrated that a drug-centric approach using network pharmacology analysis provides a deeper understanding of the concept of Sasang constitutional medicine at a phenotypic level.

scholarly journals Systematic elucidation of the pharmacological mechanisms of Rhynchophylline for treating epilepsy via network pharmacology

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Hua Geng ◽  
Xuqin Chen ◽  
Chengzhong Wang
Keyword(s):  
Gene Ontology ◽  
Oral Bioavailability ◽  
Target Genes ◽  
Interaction Analysis ◽  
Network Pharmacology ◽  
Receptor Interaction ◽  
Biological Processes ◽  
Pathway Network ◽  
Protein Protein Interaction ◽  
Network Analyses

Abstact Background Epilepsy, one of the most common neurological disorders, affects over 70 million people worldwide. Rhynchophylline displays a wide variety of pharmacologic actives. However, the pharmacologic effects of rhynchophylline and its mechanisms against epilepsy have not been systematically elucidated. Methods The oral bioavailability and druglikeness of rhynchophylline were evaluated using the Traditional Chinese Medicine Systems Pharmacology Database. Rhynchophylline target genes to treat epilepsy were identified using PharmMapper, SwissTargetPrediction and DrugBank databases integration. Protein-protein interaction analysis was carried out by utilizing the GeneMANIA database. WebGestalt was employed to perform Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. The drug-disease-target-Gene Ontology-pathway network was constructed using Cytoscape. Results The oral bioavailability and druglikeness of rhynchophylline were calculated to be 41.82% and 0.57, respectively. A total of 20 rhynchophylline target genes related to epilepsy were chosen. Among the 20 genes and their interacting genes, 54.00% shared protein domains and 16.61% displayed co-expression characteristics. Gene ontology, Kyoto Encyclopedia of Genes and Genomes and network analyses illustrate that these targets were significantly enriched in regulation of sensory perception, morphine addiction, neuroactive ligand-receptor interaction and other pathways or biological processes. Conclusion In short, rhynchophylline targets multiple genes or proteins, biological processes and pathways. It shapes a multiple-layer network that exerts systematic pharmacologic activities on epilepsy.

Abiotic Stress Tolerance in Soybean : Regulated by ncRNA

2016 ◽  
Vol 3 (1) ◽  
Author(s):  
YASIN JESHIMA KHAN ◽  
HUSNARA Tyagi ◽  
Anil kumar Singh ◽  
Santosh kumar. Magadum
Keyword(s):  
Abiotic Stresses ◽  
Target Genes ◽  
Abiotic Stress Tolerance ◽  
Crop Improvement ◽  
Vital Role ◽  
Grain Legume ◽  
Biological Processes ◽  
Small Interfering Rnas ◽  
Cellular Environment ◽  
Non Coding Rnas

Plants respond through a cascade of reactions resulting in varied cellular environment leading to alterations in the patterns of protein expression resulting in phonotypic changes. Single cell genomics and global proteomics came out to be powerful tools and efficient techniques in studying stress tolerant plants. Non-coding RNAs are a distinct class of regulatory RNAs in plants and animals that control a variety of biological processes. Small ncRNAs play a vital role in post transcriptional gene regulation by either translational repression or by inducing mRNA cleavage. The major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis. miRNAs control the expression of cognate target genes by binding to complementary sequences, resulting in cleavage or translational inhibition of the target RNAs. siRNAs too have a similar structure, function, and biogenesis like miRNAs but are derived from long double-stranded RNAs and can often direct DNA methylation at target sequences.In this review, we focus on the involvement of ncRNAs in comabting abiotic stresses of soybean. This review emphasis on previously known miRNAs as they play important role in several abiotic stresses like drought, salinity, chilling and heat stress by their diverse roles in mediating biological processes like gene expression, chromatin formation, defense of genome against invading viruses. This review attempts to elucidate the various kinds of non-coding RNAs explored, their discovery, biogenesis, functions, and response for different type of abiotic stresses and future aspects for crop improvement in the context of soybean, a representative grain legume.

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