scholarly journals Uncovering bioactive compounds and potential mechanisms of Jieduan-Niwan Formula against liver failure

2020 ◽  
Author(s):  
Chongyang Ma ◽  
Qiuyun Zhang ◽  
Yuan Gao ◽  
Lianyin Gao ◽  
Xiaoyi Wei ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Liver Failure ◽  
Signaling Pathway ◽  
Microarray Data ◽  
Fluid Shear Stress ◽  
Underlying Mechanism ◽  
Docking Study ◽  
Network Pharmacology ◽  
Data Series ◽  
Molecular Docking Study

Abstract Background Liver failure is considered as the inability of the liver to perform its normal synthetic and metabolic function. Our previous data showed that Jieduan-Niwan formula (JDNW) induced liver failure, while its underlying mechanism remains unknown. Methods In the present study, we performed a network pharmacology to analyze the bioactive ingredients and related targets. Compound and target data of JDNW formula were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database (TCMSP), and targets related to liver diseases were obtained from DisGeNET database. Information of protein protein interaction were retrieved from STRING database. Network construction and degree calculation were used Cytoscape software. Metascape web-server was used for GO and KEGG pathway enrichment. A microarray data series (GSE72081) was obtained from Gene Expression Omnibus database and analyzed using R project and Connectivity Map. Ledock was used for molecular docking. Results A total of 114 unduplicated active ingredients were identified after ADME screening. After construction of a target-liver disease network, 28 targets were identified for anti-liver failure effect. These targets were significantly enriched in fluid shear stress and atherosclerosis, pathways in cancer, IL-17 signaling pathway, HIF-1 signaling pathway, insulin resistance, toxoplasmosis, prostate cancer, microRNAs in cancer, NF-kappa B signaling pathway, Chemical carcinogenesis, VEGF signaling pathway and complement and coagulation cascades pathways. After analyzing a public microarray data of quercetin, we found biological action of some NFκB inhibitors was similar to quercetin. Molecular docking study showed that quercetin possessed a capability to bind on IKKβ and inhibited NFκB activation. Conclusions JDNW formula treated liver failure via multiple targets and multiple pathways, including NFκB signal. Quercetin was identified as a key bioactive ingredient of JDNW formula and its anti-liver failure effect may involve in NFκB inhibition.

scholarly journals Network Pharmacology Integrated Molecular Docking Reveals the Mechanism of Zhongfeng Xingnao Formula against Intracerebral Hemorrhage

2020 ◽  
Author(s):  
Can Wan ◽  
Ziyi Zhou ◽  
Yun Lu ◽  
Guangyao Zhang ◽  
Yefeng Cai ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Intracerebral Hemorrhage ◽  
Signaling Pathway ◽  
Fluid Shear Stress ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Network Pharmacology ◽  
Pathway Network ◽  
Drug Compound

Abstract Background: Previous studies have shown that Zhongfeng Xingnao Formula (ZXF) can effectively reduce the mortality of intracerebral hemorrhage (ICH), but the underlying mechanism of the treatment remained still unexplored. This study aimed to expound the potential mechanism of ZXF in the treatment of ICH through network pharmacology and molecular docking.Methods: The putative targets of ZXF were obtained from the TCMSP and Uniprot database, while the potential targets of ICH received from Drugbank, Genecards and OMIM database. Then through the Venn 2.1, the overlapping targets of disease and drug were gotten for the further study. The GO and KEGG enrichment analyses were performed by R version 4.0.2 software so that the signaling pathway was acquired to the subsequent analysis. Cytoscape was used to construct the drug-compound-target-pathway network and String was utilized for the protein-protein interaction network. What’s more, the interaction between compound and target was verified by the AutoDockTools and Autodock Vina. Results: There were a total of 166 ZXF-related targets and 1258 ICH-related targets obtained from the public databases. And 87 potential targets were both related to drug and disease. The GO enrichment analysis mainly involved receptor ligand activity, signaling receptor activator activity, and cytokine receptor binding, while the signaling pathway, such as Fluid shear stress and atherosclerosis, AGE-RAGE signaling pathway in diabetic complications, PI3K-Akt signaling pathway, were significantly enriched in the KEGG enrichment analysis. The molecular docking elucidated that the aloe-emodin, beta-sitosterol, quercetin could bound well to the top five targets sorted by degree value.Conclusions: ZXF treated ICH through multiple compounds, multiple targets, and multiple pathways. The underlying mechanism of the treatment may be promoting angiogenesis, anti-inflammatory, anti-oxidative stress, and reversing atherosclerosis, which is of great significance for the treatment of ICH.

scholarly journals Network pharmacology and molecular docking study on the active ingredients of qidengmingmu capsule for the treatment of diabetic retinopathy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mingxu Zhang ◽  
Jiawei Yang ◽  
Xiulan Zhao ◽  
Ying Zhao ◽  
Siquan Zhu
Keyword(s):  
Diabetic Retinopathy ◽  
Molecular Docking ◽  
Molecular Mechanisms ◽  
Hypoxia Inducible Factor ◽  
Enrichment Analysis ◽  
Docking Study ◽  
Network Pharmacology ◽  
Biological Processes ◽  
Active Ingredients ◽  
Molecular Docking Study

AbstractDiabetic retinopathy (DR) is a leading cause of irreversible blindness globally. Qidengmingmu Capsule (QC) is a Chinese patent medicine used to treat DR, but the molecular mechanism of the treatment remains unknown. In this study, we identified and validated potential molecular mechanisms involved in the treatment of DR with QC via network pharmacology and molecular docking methods. The results of Ingredient-DR Target Network showed that 134 common targets and 20 active ingredients of QC were involved. According to the results of enrichment analysis, 2307 biological processes and 40 pathways were related to the treatment effects. Most of these processes and pathways were important for cell survival and were associated with many key factors in DR, such as vascular endothelial growth factor-A (VEGFA), hypoxia-inducible factor-1A (HIF-1Α), and tumor necrosis factor-α (TNFα). Based on the results of the PPI network and KEGG enrichment analyses, we selected AKT1, HIF-1α, VEGFA, TNFα and their corresponding active ingredients for molecular docking. According to the molecular docking results, several key targets of DR (including AKT1, HIF-1α, VEGFA, and TNFα) can form stable bonds with the corresponding active ingredients of QC. In conclusion, through network pharmacology methods, we found that potential biological mechanisms involved in the alleviation of DR by QC are related to multiple biological processes and signaling pathways. The molecular docking results also provide us with sound directions for further experiments.

scholarly journals The Underlying Mechanism of Chinese Herb of Regulating Marrow in the Treatment of  Osteonecrosis of the Femoral Head Based on Network Pharmacology and Molecular Docking

2021 ◽  
Author(s):  
Xiaojian Wang ◽  
Rui Wang ◽  
Ting Xu ◽  
Hongting Jin ◽  
Peijian Tong ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Chinese Medicine ◽  
Signaling Pathway ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Chinese Herbs ◽  
Network Pharmacology ◽  
Active Components ◽  
Pathway Enrichment

Abstract Background The lesion of marrow is a crucial factor in orthopedic diseases, which is recognized by orthopedics-traumatology expert from "Zhe-School of Chinese Medicine". The Chinese herbs of regulating marrow has been widely used to treat osteonecrosis of the femoral head (ONFH) in China, while the interaction mechanisms were still elucidated. Thus, we conducted this study to explore the underlying mechanism of the five highest-frequency Chinese herbs of regulating marrow(HF-CHRM) in the treatment of ONFH with the aid of network pharmacology(NP) and molecular docking(MD). Methods The active components and potential targets of HF-CHRM were obtained through several online databases, such as Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP), UniProt database. The gene targets related to ONFH were collected with the help of the OMIM and GeneCards disease-related databases. The "drug- component-target-disease" network and protein-protein interaction(PPI) network of the drug and disease intersecting targets were constructed by using Cytoscape software and the STRING database. R software was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The MD of critical components and targets was carried out using Autodock Vina and Pymol to validate the binding affinity. Results A total of 54 active components, 1074 drug targets and 195 gene targets were obtained. There were 1219 ONFH related targets. 39 drug and disease intersection targets(representative genes: IL6, TP53, VEGFA, ESR1, IL1B) were obtained and considered potential therapeutic targets. 1619 items were obtained by the GO enrichment analysis, including 1517 biological processes, 10 cellular components and 92 molecular functions, which is mainly related to angiogenesis, bone and lipid metabolism and inflammatory reaction. The KEGG pathway enrichment analysis revealed 119 pathways, including AGE-RAGE signaling pathway, PI3K-Akt signaling pathway and IL-17 signaling pathway. MD results showed that quercetin, wogonin, and kaempferol active components had good affinity with IL6, TP53, and VEGFA core proteins. Conclusion The HF-CHRM can treat ONFH by multi-component, multi-target, and multi-pathway comprehensive action.

scholarly journals Investigation of Active Ingredients and Mechanism of Sanao Decoction in the Treatment of Chronic Cough by Network Pharmacology

2020 ◽  
Author(s):  
Mengke Sheng ◽  
Xing Liu ◽  
Qingsong Qu ◽  
Xiaowen Wu ◽  
Yuyao Liao ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Signaling Pathway ◽  
Chronic Cough ◽  
Fluid Shear Stress ◽  
Oxidant Stress ◽  
Network Pharmacology ◽  
Ppi Network ◽  
Active Ingredients ◽  
Active Components ◽  
Pathway Network

Abstract Background: Chronic cough significantly affects human health and quality of life. Studies have shown that Sanao Decoction（SAD）can clinically treat chronic cough. To investigate its mechanisms, we used the method of network pharmacology to conduct research at the molecular level.Methods: The active ingredients and their targets were screened by pharmacokinetics parameters from the traditional Chinese medicine system pharmacology analysis platform (TCMSP). The relevant targets of chronic cough were obtained from two databases: GeneCards and DrugBank. Take the intersection to get potential targets of SAD to treat chronic cough and establish the component-target regulatory network by CytoScape3.7.2 and protein-protein interaction (PPI) network by STRING 1.0. The function of the target gene and related pathways were analyzed by the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) in the Database for Annotation, Visualization, and Integrated Discovery (DAVID). The significant pathways and their relevant targets were obtained and the target-pathway network was established by CytoScape3.7.2. Finally, molecular docking of the core active components and relevant targets was performed.Results: A total of 98 active components, 113 targets were identified. The component-target and target-pathway network of SAD and PPI network were established. Enrichment analysis of DAVID indicated that 2062 terms were in biological processes, 77 in cellular components, 142 in molecular functions and 20 significant pathways. In addition, the molecular docking showed that quercetin and luteolin had a good combination with the corresponding targets.Conclusions: It indicates that the active compounds of SAD, such as quercetin, luteolin, may act on AKT1, MAPK1, RELA, EGFR, BCL2 and regulate PI3K-Akt signaling pathway, AGE-RAGE signaling pathway in diabetic complications and Fluid shear stress and atherosclerosis pathway to exert the effects of anti-inflammatory, anti-airway remodeling, anti-oxidant stress and repair airway damage to treat chronic cough.

Design Graph Theoretical Analysis and In Silico Modeling of Dunaliella Bardawil Biomass Encapsulated N-Succinyl Chitosan Nanoparticles for Enhanced Anticancer Activity

2019 ◽  
Vol 18 (13) ◽  
pp. 1900-1918 ◽  
Author(s):  
Selvaraj Kunjiappan ◽  
Theivendren Panneerselvam ◽  
Balasubramanian Somasundaram ◽  
Murugesan Sankaranarayanan ◽  
Pavadai Parasuraman ◽  
...  
Keyword(s):  
Particle Size ◽  
Molecular Docking ◽  
Anticancer Activity ◽  
Signaling Pathway ◽  
Pathway Analysis ◽  
Chitosan Nanoparticles ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Dunaliella Bardawil ◽  
Ras P21

Purpose: To investigate N-succinyl chitosan nanoparticles (NSC NPs) encapsulation with Dunaliella bardawil (D. bardawil) biomass for high utilization enhanced effectiveness and least side effects for anticancer activity. Methods: The potential bioactive compounds from D. bardawil biomass were encapsulated NSC NPs by ionotropic gelation method and to characterize its molecular shape, particle size, stability and polydispersity index using FTIR, XRD, SEM, TEM and Zetasize Nano analyzer. Signaling pathway analysis, molecular docking study and in vitro anticancer screening were performed on chosen H-Ras P21, 721P and liver cancer cell lines (HepG2), respectively. Results: The D. bardawil biomass majorly contains 6 bioactive compounds such as β-carotene, lutein, zeaxanthin, phytoene, canthaxanthin, and phytofluene were identified by LC-MS. The D. bardawil biomass encapsulated NSC NPs showed an average particle size of 80±5.6 nm in spherical shape, crystalline nature, zeta potential of -32±2.7 mV and polydispersity index of 0.51±0.02. Interestingly, the identified target using graph theoretical signaling pathway analysis and molecular docking study showed strong interaction of NSC NPs in binding pockets of H-Ras P21 protooncogene. At 50μg/mL, NPs displayed 95.60% cytotoxicity in HepG2 cell line. The apoptotic cell cycle analysis showed cell death for 24 h and 48 h representing 13.13% and 47.04%, respectively. Conclusion: The highly cross-linked, biocompatible, biodegradable, nontoxic NSC NPs promising carrier for delivery of bioactive molecules present in the D. bardawil biomass was found to be actively involved in deregulation of cellular growth in targeted cancer cells. Thus active NPs serve as a novel nanodrug to enhance the controlled; site specific drug delivery in the management of cancer.

scholarly journals Exploring the Antiglioma Mechanisms of Luteolin Based on Network Pharmacology and Experimental Verification

2021 ◽  
Vol 2021 ◽  
pp. 1-18
Author(s):  
Renxuan Huang ◽  
Rui Dong ◽  
Nan Wang ◽  
Beiwu Lan ◽  
Hongyang Zhao ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Signaling Pathway ◽  
Fruits And Vegetables ◽  
Docking Simulation ◽  
Underlying Mechanism ◽  
Venn Diagram ◽  
Network Pharmacology ◽  
Discovery Studio ◽  
Inorganic Substances

Luteolin, a natural flavone compound, exists in a variety of fruits and vegetables, and its anticancer effect has been shown in many studies. However, its use in glioma treatment is hampered due to the fact that the underlying mechanism of action has not been fully explored. Therefore, we elucidated the potential antiglioma targets and pathways of luteolin systematically with the help of network pharmacology and molecular docking technology. The druggability of luteolin, including absorption, excretion, distribution, and metabolism, was assessed via the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). The potential targets of luteolin and glioma were extracted from public databases, and the intersecting targets between luteolin and glioma were integrated and visualized by a Venn diagram. In addition, GO and KEGG pathway analysis was engaged in Metascape. The network of the luteolin-target-pathway was visualized by Cytoscape. Ultimately, the interactions between luteolin and predicted key targets were confirmed by Discovery studio software. According to the ADME results, luteolin shows great potential for development into a drug. 4860 glioma-associated targets and 280 targets of luteolin were identified, of which 205 were intersection targets. 6 core targets of luteolin against glioma, including AKT1, JUN, ALB, MAPK3, MAPK1, and TNF, were identified via PPI network analysis of which AKT1, JUN, ALB, MAPK1, and TNF harbor diagnostic value. The biological processes of luteolin are mainly involved in the response to inorganic substances, response to oxidative stress, and apoptotic signaling pathway. The essential pathways of luteolin against glioma involve pathways in cancer, the PI3K-Akt signaling pathway, the TNF signaling pathway, and more. Meanwhile, luteolin’s interaction with six core targets was verified by molecular docking simulation and its antiglioma effect was verified by in vitro experiments. This study suggests that luteolin has a promising potential for development into a drug and, moreover, it displays preventive effects against glioma by targeting various genes and pathways.

scholarly journals Ping Feng Qingfei mixture treats airway hyperresponsiveness: a network pharmacology and molecular docking study

2021 ◽  
Vol 10 (4) ◽  
pp. 4747-4759
Author(s):  
Min Wang ◽  
Min Peng ◽  
Hongshuo Shi ◽  
Chengda Dong ◽  
Lujie Cui ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Airway Hyperresponsiveness ◽  
Docking Study ◽  
Network Pharmacology ◽  
Molecular Docking Study

Study on the Mechanism of Bushen Jianpi Decoction in the Treatment of T2DM Based on Network Pharmacology

2021 ◽  
Author(s):  
Dongqiang Luo ◽  
Ying Shao ◽  
Yong Sun ◽  
Shuntang Du ◽  
Feng Liu
Keyword(s):  
Molecular Docking ◽  
Signaling Pathway ◽  
Target Genes ◽  
Fluid Shear Stress ◽  
Interaction Network ◽  
Binding Potential ◽  
Network Pharmacology ◽  
Signal Pathways ◽  
Protein Protein Interaction ◽  
Target Disease

Abstract Through the preliminary clinical observation, we had found that Bushen Jianpi decoction (BJD) combined with had better efficacy and less side effects, but its mechanism was not clear. The purpose of this study was to determine its molecular targets and mechanism in T2DM therapy by means of network pharmacology and molecular docking.Results: A total of 144 candidate compounds and 1103 differentially expressed genes were screened, and 43 common targets related to T2DM in BJD were identified. The "TCM-compound-target-disease" network suggested that quercetin, luteolin and kaempferol were the top three compounds. Through protein-protein interaction network, 45 core target genes were identified, including ITGA4, TP53, MYC and so on. GO enrichment showed that genes were significantly enriched in biological processes such as response to oxidative stress, response to lipopolysaccharide, response to molecule of bacterial origin and response to reactive oxygen species. KEGG enrichment showed that there was significant gene enrichment in Fluid shear stress and atherosclerosis, TNF signaling pathway, P13K-Akt signaling pathway, IL-17 signaling pathway and AGE-RAGE signaling pathway in diabetic complications signal pathways. The results of molecular docking showed that the key components of BJD had good binding potential with target genes. Conclusions: BJD may play a role in the treatment of T2DM through anti-inflammation, antioxidation and regulating metabolism, but it still needs to be further confirmed by experiments.Keywords: Network pharmacology, GEO database, Molecular docking, Bushen Jianpi decoction; T2DM

scholarly journals A Hub Signaling Pathway of Antimicrobial-Antifungal-Anticancer Peptides Axis With Cationic Residue Amino Acids on N, C- Terminals Under 500 Dalton Rule Via Network Pharmacology

2021 ◽  
Author(s):  
Ki Kwang Oh ◽  
Md. Adnan ◽  
Dong Ha Cho
Keyword(s):  
Signaling Pathway ◽  
Host Defense ◽  
Docking Study ◽  
Notch Signaling Pathway ◽  
Network Pharmacology ◽  
Amino Acid Residues ◽  
Defense System ◽  
Molecular Docking Study ◽  
Anticancer Peptides ◽  
Host Defense System

Abstract Background: Short cationic peptides (SCPs) with therapeutic efficacy of Antimicrobial peptides (AMPs), Antifungal peptides (AFPs), and Anticancer peptides (ACPs) are known as enhancement of host defense system. Here, we investigated the uppermost peptide(s), hub signaling pathway(s), and its associated target(s) through network pharmacology. Method: Firstly, we selected SCPs with positive amino acid residues on N-, C- terminals under 500 Dalton via RStudio. Secondly, EMBOSS pepstats, PASTA 2.0 and Aggrescan were used to remove non- AMPs, after that, ADAM, dbAMP, DBAASP v3.0, and MLAMP were utilized for AMPs selection. AMPs-targets were identified from both SEA and STP databases. The overlapping targets between the bacteria-responsive targets (TTD and OMIM) and AMPs-targets were visualized by VENNY 2.1. Thirdly, AFPs were filtered through Antifp tool, and TTD and OMIM selected fungal responsive targets. The overlapping targets between AFPs-targets and fungal-responsive targets were visualized by VENNY 2.1. Fourthly, the overlapping targets between cancer-related targets (TTD and OMIM) and fungal-responsive targets were visualized by VENNY 2.1. Fifthly, signaling pathway analysis of overlapping targets was performed via RStudio. Finally, molecular docking study (MDS) was carried out to discover the most potent peptides on a hub signaling pathway. Results: A total of 1,833 SCPs were identified, and AMPs, AFPs, and ACPs filtration suggested that 197 peptides-30 targets, 81 peptides-6 targets, and 59 peptides-4 targets are connected, respectively. The AMPs-AFPs-ACPs axis indicated that 27 peptides-2 targets are associated. Each hub signaling pathway for enhancement of host defense system was "Inactivation of Rap1 signaling pathway on AMPs", "Activation of Notch signaling pathway on AMPs-AFPs axis", and "Inactivation of HIF-1 signaling pathway on AMPs-AFPs-ACPs axis". The most potent peptides were assessed via MDS; finally, HPIK on STAT3, HVTK on NOS2 manifested the HIF-1 signaling pathway's highest affinity. Furthermore, the two peptides have better affinity scores than standard selective inhibitors (Stattic, 1400W). Conclusion: Overall, the most potent SCPs for the host defense system were HPIK on STAT3 and HVTK on NOS2, which might inactivate the HIF-1 signaling pathway.

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