scholarly journals A Network Pharmacology Analysis to Explore the Effect ofAstragali Radix-Radix Angelica Sinensison Traumatic Brain Injury

2018 ◽  
Vol 2018 ◽  
pp. 1-13 ◽  
Author(s):  
Genggeng Xie ◽  
Weijun Peng ◽  
Pengfei Li ◽  
Zian Xia ◽  
Yuanyuan Zhong ◽  
...  
Keyword(s):  
Traumatic Brain Injury ◽  
Brain Injury ◽  
Animal Experiment ◽  
Target Prediction ◽  
Enrichment Analysis ◽  
Neurological Deficits ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Therapeutic Effects ◽  
Go Annotation

Traumatic brain injury (TBI) is a critical public health and socioeconomic problem worldwide. The herb pairAstragali Radix(AR)-Radix Angelica Sinensis(RAS) is a common prescribed herbal formula or is added to other Chinese medicine prescriptions for traumatic brain injury (TBI) treatment. However, the underlying mechanisms are unclear. In this study, we aimed to explore the active ingredients and action targets of AR-RAS based on the combined methods of network pharmacology prediction and experimental verification. Furthermore, the corresponding potential mechanisms of “multicomponents, multitargets, and multipathways” were disclosed.Methods. A network pharmacology approach including ADME (absorption, distribution, metabolism, and excretion) filter analysis, target prediction, known therapeutic targets collection, Gene Ontology (GO), pathway enrichment analysis, and network construction was used in this study. Further verification experiments were performed to reveal the therapeutic effects of AR-RAS in a rat model of TBI.Results. The comprehensive systematic approach was to successfully identify 14 bioactive ingredients in AR-RAS, while 33 potential targets hit by these ingredients related to TBI. Based on GO annotation analysis, multiple biological processes were significantly regulated by AR-RAS. In addition, 89 novel signaling pathways (P<0.05) underlying the effects of AR-RAS for TBI treatment were identified by DAVID. The neurotrophin signaling pathway was suggested as the major related pathway targeted by AR-RAS to improve axonal growth. The animal experiment confirmed that AR-RAS significantly induced tissue recovery and improved neurological deficits on the 14th day (P<0.01). Treatment with AR-RAS markedly reduced the protein and mRNA expression level of NogoA in the hippocampus of TBI rats.Conclusion. Our work illuminates the “multicompounds, multitargets, and multipathways” curative action of AR-RAS in the treatment of TBI by network pharmacology. The animal experiment verifies the effects of AR-RAS on neurological function improvement and axonal outgrowth via downregulation of NogoA expression, providing a theoretical basis for further research on treatment of TBI.

Systematic Investigation of Quercetin for Treating Cardiovascular Disease Based on Network Pharmacology

2019 ◽  
Vol 22 (6) ◽  
pp. 411-420 ◽  
Author(s):  
Xian-Jun Wu ◽  
Xin-Bin Zhou ◽  
Chen Chen ◽  
Wei Mao
Keyword(s):  
Cardiovascular Disease ◽  
Cardiovascular Diseases ◽  
Signaling Pathway ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Therapeutic Effects ◽  
Pathway Enrichment ◽  
Compound Target

Aim and Objective: Cardiovascular disease is a serious threat to human health because of its high mortality and morbidity rates. At present, there is no effective treatment. In Southeast Asia, traditional Chinese medicine is widely used in the treatment of cardiovascular diseases. Quercetin is a flavonoid extract of Ginkgo biloba leaves. Basic experiments and clinical studies have shown that quercetin has a significant effect on the treatment of cardiovascular diseases. However, its precise mechanism is still unclear. Therefore, it is necessary to exploit the network pharmacological potential effects of quercetin on cardiovascular disease. Materials and Methods: In the present study, a novel network pharmacology strategy based on pharmacokinetic filtering, target fishing, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, compound-target-pathway network structured was performed to explore the anti- cardiovascular disease mechanism of quercetin. Results:: The outcomes showed that quercetin possesses favorable pharmacokinetic profiles, which have interactions with 47 cardiovascular disease-related targets and 12 KEGG signaling pathways to provide potential synergistic therapeutic effects. Following the construction of Compound-Target-Pathway (C-T-P) network, and the network topological feature calculation, we obtained top 10 core genes in this network which were AKT1, IL1B, TNF, IL6, JUN, CCL2, FOS, VEGFA, CXCL8, and ICAM1. KEGG pathway enrichment analysis. These indicated that quercetin produced the therapeutic effects against cardiovascular disease by systemically and holistically regulating many signaling pathways, including Fluid shear stress and atherosclerosis, AGE-RAGE signaling pathway in diabetic complications, TNF signaling pathway, MAPK signaling pathway, IL-17 signaling pathway and PI3K-Akt signaling pathway.

scholarly journals Ganghuo Kanggan Decoction in Influenza: Integrating Network Pharmacology and In Vivo Pharmacological Evaluation

2020 ◽  
Vol 11 ◽  
Author(s):  
Yanni Lai ◽  
Qiong Zhang ◽  
Haishan Long ◽  
Tiantian Han ◽  
Geng Li ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Influenza A ◽  
Target Prediction ◽  
Enrichment Analysis ◽  
New Drugs ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Active Components ◽  
Compound Screening

Background: Ganghuo Kanggan decoction (GHKGD) is a clinical experience prescription used for the treatment of viral pneumonia in the Lingnan area of China, and its clinical effect is remarkable. However, the mechanism of GHKGD in influenza is still unclear.Objective: To predict the active components and signaling pathway of GHKGD and to explore its therapeutic mechanism in influenza and to verified it in vivo using network pharmacology.Methods: The potential active components and therapeutic targets of GHKGD in the treatment of influenza were hypothesized through a series of network pharmacological strategies, including compound screening, target prediction and pathway enrichment analysis. Based on the target network and enrichment results, a mouse model of influenza A virus (IAV) infection was established to evaluate the therapeutic effect of GHKGD on influenza and to verify the possible molecular mechanism predicted by network pharmacology.Results: A total of 116 candidate active compounds and 17 potential targets were identified. The results of the potential target enrichment analysis suggested GHKGD may involve the RLR signaling pathway to reduce inflammation in the lungs. In vivo experiments showed that GHKGD had a protective effect on pneumonia caused by IAV-infected mice. Compared with the untreated group, the weight loss in the GHKGD group in the BALB/c mice decreased, and the inflammatory pathological changes in lung tissue were reduced (p &lt; 0.05). The expression of NP protein and the virus titers in lung were significantly decreased (p &lt; 0.05). The protein expression of RIG-I, NF-kB, and STAT1 and the level of MAVS and IRF3/7 mRNA were remarkably inhibited in GHKGD group (p &lt; 0.05). After the treatment with GHKGD, the level of Th1 cytokines (IFN-γ, TNF-α, IL-2) was increased, while the expression of Th2 (IL-5, IL4) cytokines was reduced (p &lt; 0.05).Conclusion: Through a network pharmacology strategy and in vivo experiments, the multi-target and multi-component pharmacological characteristics of GHKGD in the treatment of influenza were revealed, and regulation of the RLR signaling pathway during the anti-influenza process was confirmed. This study provides a theoretical basis for the research and development of new drugs from GHKGD.

A Network Pharmacology Analysis of the Systems-Perspective Anticancer Mechanisms of the Herbal Drug FDY2004 for Breast Cancer

2021 ◽  
Vol 16 (10) ◽  
pp. 1934578X2110491
Author(s):  
Ho-Sung Lee ◽  
In-Hee Lee ◽  
Kyungrae Kang ◽  
Sang-In Park ◽  
Tae-Wook Kwon ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Therapeutic Effects ◽  
Herbal Drugs ◽  
Apoptosis Pathway ◽  
Anticancer Properties ◽  
Systems Perspective

Breast cancer is a malignant tumor with high incidence, prevalence, and mortality rates in women. In recent years, herbal drugs have been assessed as anticancer therapy against breast cancer, owing to their promising therapeutic effects and reduced toxicity. However, their pharmacological mechanisms have not been fully explored at the systemic level. Here, we conducted a network pharmacology analysis of the systems-perspective molecular mechanisms of FDY2004, an anticancer herbal formula that consists of Moutan Radicis Cortex, Persicae Semen , and Rhei Radix et Rhizoma, against breast cancer. We determined that FDY2004 may contain 28 active compounds that exert pharmacological effects by targeting 113 breast cancer-related human genes/proteins. Based on the gene ontology terms, the FDY2004 targets were involved in modulating biological processes such as cell growth, cell proliferation, and apoptosis. Pathway enrichment analysis identified various breast cancer-associated pathways that may mediate the anticancer activity of FDY2004, including the PI3K-Akt, MAPK, TNF, HIF-1, focal adhesion, estrogen, ErbB, NF-kappa B, p53, and VEGF signaling pathways. Thus, our analysis offers novel insights into the anticancer properties of herbal drugs for breast cancer treatment from a systemic perspective.

scholarly journals Analysis of Molecular Mechanism of Erxian Decoction in Treating Osteoporosis Based on Formula Optimization Model

2021 ◽  
Vol 2021 ◽  
pp. 1-20
Author(s):  
Lang Yang ◽  
Liuyi Fan ◽  
Kexin Wang ◽  
Yupeng Chen ◽  
Lan Liang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Osteoclast Differentiation ◽  
Antibody Therapy ◽  
Enrichment Analysis ◽  
Estrogen Signaling ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Therapeutic Effects ◽  
Mechanism Analysis ◽  
Erxian Decoction

Osteoporosis (OP) is a highly prevalent orthopedic condition in postmenopausal women and the elderly. Currently, OP treatments mainly include bisphosphonates, receptor activator of nuclear factor kappa-B ligand (RANKL) antibody therapy, selective estrogen receptor modulators, teriparatide (PTH1-34), and menopausal hormone therapy. However, increasing evidence has indicated these treatments may exert serious side effects. In recent years, Traditional Chinese Medicine (TCM) has become popular for treating orthopedic disorders. Erxian Decoction (EXD) is widely used for the clinical treatment of OP, but its underlying molecular mechanisms are unclear thanks to its multiple components and multiple target features. In this research, we designed a network pharmacology method, which used a novel node importance calculation model to identify critical response networks (CRNs) and effective proteins. Based on these proteins, a target coverage contribution (TCC) model was designed to infer a core active component group (CACG). This approach decoded the mechanisms underpinning EXD’s role in OP therapy. Our data indicated that the drug response network mediated by the CACG effectively retained information of the component-target (C-T) network of pathogenic genes. Functional pathway enrichment analysis showed that EXD exerted therapeutic effects toward OP by targeting PI3K-Akt signaling (hsa04151), calcium signaling (hsa04020), apoptosis (hsa04210), estrogen signaling (hsa04915), and osteoclast differentiation (hsa04380) via JNK, AKT, and ERK. Our method furnishes a feasible methodological strategy for formula optimization and mechanism analysis and also supplies a reference scheme for the secondary development of the TCM formula.

scholarly journals Network Pharmacology-Based Prediction of Mechanism of Shenzhuo Formula for Application to DKD

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Xinmiao Wang ◽  
Haoyu Yang ◽  
Lili Zhang ◽  
Lin Han ◽  
Sha Di ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Signaling Pathway ◽  
Topological Analysis ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Regulation Of Transcription ◽  
Therapeutic Effects ◽  
Active Ingredients ◽  
Go Analysis

Background. Shenzhuo formula (SZF) is a traditional Chinese medicine (TCM) prescription which has significant therapeutic effects on diabetic kidney disease (DKD). However, its mechanism remains unknown. Therefore, this study aimed to explore the underlying anti-DKD mechanism of SZF. Methods. The active ingredients and targets of SZF were obtained by searching TCMSP, TCMID, SwissTargetPrediction, HIT, and literature. The DKD target was identified from TTD, DrugBank, and DisGeNet. The potential targets were obtained and PPI network were built after mapping SZF targets and DKD targets. The key targets were screened out by network topology and the “SZF-key targets-DKD” network was constructed by Cytoscape. GO analysis and KEGG pathway enrichment analysis were performed by using DAVID, and the results were visualized by Omicshare Tools. Results. We obtained 182 potential targets and 30 key targets. Furthermore, a “SZF-key targets-DKD” network topological analysis showed that active ingredients like M51, M21, M5, M71, and M28 and targets like EGFR, MMP9, MAPK8, PIK3CA, and STAT3 might play important roles in the process of SZF treating in DKD. GO analysis results showed that targets were mainly involved in positive regulation of transcription from RNA polymerase II promoter, inflammatory response, lipopolysaccharide-mediated signaling pathway, and other biological processes. KEGG showed that DKD-related pathways like TNF signaling pathway and PI3K-Akt signaling pathway were at the top of the list. Conclusion. This research reveals the potential pharmacological targets of SZF in the treatment of DKD through network pharmacology and lays a foundation for further studies.

scholarly journals Exploring Pharmacological Mechanisms of Xuefu Zhuyu Decoction in the Treatment of Traumatic Brain Injury via a Network Pharmacology Approach

2018 ◽  
Vol 2018 ◽  
pp. 1-20 ◽  
Author(s):  
Yuanyuan Zhong ◽  
Jiekun Luo ◽  
Tao Tang ◽  
Pengfei Li ◽  
Tao Liu ◽  
...  
Keyword(s):  
Traumatic Brain Injury ◽  
Brain Injury ◽  
Target Prediction ◽  
Docking Simulation ◽  
Network Pharmacology ◽  
Chemical Components ◽  
Combination Principle ◽  
Bioactive Ingredients ◽  
Molecule Docking ◽  
Xuefu Zhuyu Decoction

Objectives. Xuefu Zhuyu decoction (XFZYD), a traditional Chinese medicine (TCM) formula, has been demonstrated to be effective for the treatment of traumatic brain injury (TBI). However, the underlying pharmacological mechanisms remain unclear. This study aims to explore the potential action mechanisms of XFZYD in the treatment of TBI and to elucidate the combination principle of this herbal formula. Methods. A network pharmacology approach including ADME (absorption, distribution, metabolism, and excretion) evaluation, target prediction, known therapeutic targets collection, network construction, and molecule docking was used in this study. Results. A total of 119 bioactive ingredients from XFZYD were predicted to act on 47 TBI associated specific proteins which intervened in several crucial pathological processes including apoptosis, inflammation, antioxidant, and axon genesis. Almost each of the bioactive ingredients targeted more than one protein. The molecular docking simulation showed that 91 pairs of chemical components and candidate targets had strong binding efficiencies. The “Jun”, “Chen”, and “Zuo-Shi” herbs from XFZYD triggered their specific targets regulation, respectively. Conclusion. Our work successfully illuminates the “multicompounds, multitargets” therapeutic action of XFZYD in the treatment of TBI by network pharmacology with molecule docking method. The present work may provide valuable evidence for further clinical application of XFZYD as therapeutic strategy for TBI treatment.

scholarly journals Network Pharmacology and Molecular Docking Reveal the Mechanism of Isodon Ternifolius (D. Don) Kudo Against Liver Fibrosis

2021 ◽  
Author(s):  
Le Qin ◽  
Zhipin Zhou ◽  
Hui Huang ◽  
Jingjing Wang ◽  
Yong Chen ◽  
...  
Keyword(s):  
Liver Fibrosis ◽  
Umbilical Vein ◽  
Target Prediction ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Active Ingredients ◽  
Chemical Structures

Abstract BackgroundIsodon ternifolius (SanYe Xiang ChaCai, SYXCC) is a traditional Chinses medicine commonly used in the treatment of chronic hepatitis B in China. Many studies have demonstrated the hepatoprotective or anti-fibrotic effects of SYXCC, but its pharmacological basis and mechanism remain unclear. In this study, we used in vitro models to validate the predicted results and reveal the potential mechanism of action and active ingredients with the help of network pharmacology methods and molecular docking.MethodsWe obtained the chemical structures of SYXCC by literatures. Potential targets of SYXCC were predicted by Swiss Target Prediction. The disease targets were collected through the databases of Gene Card. PPI protein interaction network was obtained using STRING database. Signaling pathway enrichment analysis was performed on drug-disease targets with of DAVID database. In vitro, human umbilical vein endothelial cell was used to validate the results predicted by network pharmacology.Results90 pathways related to liver fibrosis were obtained by KEGG enrichment. We were interested in the top 25 core target proteins involved in the TLR4, MAPK and PI3K-Akt signaling pathways associated with liver fibrosis. RT-PCR result showed that SYXCC could reduce EGFR, ERK1, Akt1, VEFGR-2, ERK2 mRNA expression. ConclusionIn the study, our results suggest that a multitude of active ingredients of Isodon ternifouis play an important role in the liver fibrosis disease network. Inhibition of angiogenesis was a new potential pharmacological mechanism for the anti-hepatic fibrosis activity of Isodon ternifoius.

scholarly journals Network Pharmacology-based Prediction of Mechanism of Shenzhuo Formula for Application to DN

2020 ◽  
Author(s):  
Xin-miao Wang ◽  
Lin Han ◽  
Li-li Zhang ◽  
Sha Di ◽  
Xiu-xiu Wei ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Signaling Pathway ◽  
Drug Targets ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Regulation Of Transcription ◽  
Therapeutic Effects ◽  
Go Analysis ◽  
Pathway Enrichment

Abstract Background: Shenzhuo formula is a traditional Chinese medicine (TCM) prescription which has significant therapeutic effects on diabetic nephropathy (DN). However, its mechanism remains unknown. Therefore, this study aimed to explore the underlying anti-DN mechanism of shenzhuo formula.Methods: The active ingredients and targets of shenzhuo formula were obtained by searching TCMSP, TCMID, SwissTargetPrediction and HIT. The DN target was identified from TTD, DrugBank and DisGeNet. The potential targets were obtained and PPI network were built after mapping the disease and drug targets. The key targets were screened out by network topology and the “drugs - DN - key targets” network was constructed by Cytoscape. GO analysis and KEGG pathway enrichment analysis were performed using DAVID, and the results were visualized using the Omicshare Tools.Results: We obtained 182 potential targets and 30 key targets. Ulteriorly, “drugs - DN - key targets” network were constructed, and results showed that nodes like M51, M21, M5, M71, M28, EGFR, MMP9, MAPK8, PIK3CA and STAT3 had a higher degree. GO analysis results mainly involved in positive regulation of transcription from RNA polymerase II promoter, inflammatory response, lipopolysaccharide-mediated signalingpathway and other biological processes. The results of KEGG showed that DN-related pathways like TNF signaling pathway, PI3K-Akt signaling pathway were at the top of the list.Conclusion: This article reveals the possible mechanism of shenzhuo formula in the treatment of DN through network pharmacology research, and lays a foundation for further studies.

scholarly journals Mechanisms Underlying the Action of Ziziphi Spinosae Semen in the Treatment of Insomnia: A Study Involving Network Pharmacology and Experimental Validation

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhenhua Bian ◽  
Wenming Zhang ◽  
Jingyue Tang ◽  
Qianqian Fei ◽  
Minmin Hu ◽  
...  
Keyword(s):  
Enrichment Analysis ◽  
Immunohistochemical Analysis ◽  
Functional Enrichment ◽  
Morphological Observation ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Therapeutic Effects ◽  
Gabaergic Synapse ◽  
Pentobarbital Sodium

Purpose: This study aimed to investigate the potential mechanisms and related bioactive components of ZSS for the treatment of insomnia.Method: The insomnia model of rat induced by PCPA was established. After oral administration of ZSS extract, the general morphological observation, pentobarbital sodium-induced sleep test and histopathological evaluation were carried out. Network pharmacology, assisted by UHPLC-Q-Exactive-MS/MS analysis, was developed to identify the targets of ZSS in the treatment of insomnia, as well as the corresponding signaling pathways. In addition, we validated the identified targets and pathways by RT-qPCR and immunohistochemical analysis.Results: The pentobarbital sodium-induced sleep test, determination of 5-HT and GABA levles in hypothalamic tissues and HE staining showed that ZSS extract was an effective treatment for insomnia. Network pharmacology analysis identified a total of 19 candidate bioactive ingredients in ZSS extract, along with 433 potentially related targets. Next, we performed protein-protein interaction (PPI), MCODE clustering analysis, GO functional enrichment analysis, KEGG pathway enrichment analysis, and ingredient-target-pathway (I-T-P) sub-networks analysis. These methods allowed us to investigate the synergistic therapeutic effects of crucial pathways, including the serotonergic and GABAergic synapse pathways. Our analyses revealed that palmitic acid, coclaurine, jujuboside A, N-nornuciferine, caaverine, magnoflorine, jujuboside B, and betulinic acid, all played key roles in the regulation of these crucial pathways. Finally, we used the PCPA-induced insomnia in rats to validate the data generated by network pharmacology; these in vivo experiments clearly showed that pathways associated with the serotonergic and GABAergic system were activated in the rats model. Furthermore, ZSS treatment significantly suppressed high levels of HTR1A, GABRA1, and GABRG2 expression in the hypothalamus and reduced the expression levels of HTR2A.Conclusion: Based on the combination of comprehensive network pharmacology and in vivo experiments, we successfully identified the potential pharmacological mechanisms underlying the action of ZSS in the treatment of insomnia. The results provide a theoretical basis for further development and utilization of ZSS, and also provide support for the development of innovative drugs for the treatment of insomnia.

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