scholarly journals Network-based modeling of herb combinations in Traditional Chinese Medicine

2021 ◽  
Author(s):  
Yinyin Wang ◽  
Hongbin Yang ◽  
Linxiao Chen ◽  
Mohieddin Jafari ◽  
Jing Tang
Keyword(s):  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Interaction Network ◽  
Modern Medicine ◽  
Network Pharmacology ◽  
Therapeutic Effects ◽  
Human Interactome ◽  
Protein Targets ◽  
Protein Protein Interaction ◽  
Multiple Network

AbstractTraditional Chinese Medicine (TCM) has been practiced for thousands of years for treating human diseases. In comparison to modern medicine, one of the advantages of TCM is the principle of herb compatibility, known as TCM formulae. A TCM formula usually consists of multiple herbs to achieve the maximum treatment effects, where their interactions are believed to elicit the therapeutic effects. Despite being a fundamental component of TCM, the rationale of combining specific herb combinations remains unclear. In this study, we proposed a network-based method to quantify the interactions in herb pairs. We constructed a protein-protein interaction network for a given herb pair by retrieving the associated ingredients and protein targets, and determined multiple network-based distances including the closest, shortest, center, kernel, and separation, both at the ingredient and at the target levels. We found that the frequently used herb pairs tend to have shorter distances compared to random herb pairs, suggesting that a therapeutic herb pair is more likely to affect neighboring proteins in the human interactome. Furthermore, we found that the center distance determined at the ingredient level improves the discrimination of top-frequent herb pairs from random herb pairs, suggesting the rationale of considering the topologically important ingredients for inferring the mechanisms of action of TCM. Taken together, we have provided a network pharmacology framework to quantify the degree of herb interactions, which shall help explore the space of herb combinations more effectively to identify the synergistic compound interactions based on network topology.

scholarly journals A Network Pharmacology-Based Study on the Anti-Lung Cancer Effect of Dipsaci Radix

2020 ◽  
Vol 2020 ◽  
pp. 1-9 ◽  
Author(s):  
Jiayan Wu ◽  
Shengkun Hong ◽  
Xiankuan Xie ◽  
Wangmi Liu
Keyword(s):  
Lung Cancer ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Interaction Network ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Hub Genes ◽  
Active Compounds

Objective. Dipsaci Radix (DR) has been used to treat fracture and osteoporosis. Recent reports have shown that myeloid cells from bone marrow can promote the proliferation of lung cancer. However, the action and mechanism of DR has not been well defined in lung cancer. The aim of the present study was to define molecular mechanisms of DR as a potential therapeutic approach to treat lung cancer. Methods. Active compounds of DR with oral bioavailability ≥30% and drug-likeness index ≥0.18 were obtained from the traditional Chinese medicine systems pharmacology database and analysis platform. The potential target genes of the active compounds and bone were identified by PharmMapper and GeneCards, respectively. The compound-target network and protein-protein interaction network were built by Cytoscape software and Search Tool for the Retrieval of Interacting Genes webserver, respectively. GO analysis and pathway enrichment analysis were performed using R software. Results. Our study demonstrated that DR had 6 active compounds, including gentisin, sitosterol, Sylvestroside III, 3,5-Di-O-caffeoylquinic acid, cauloside A, and japonine. There were 254 target genes related to these active compounds as well as to bone. SRC, AKT1, and GRB2 were the top 3 hub genes. Metabolisms and signaling pathways associated with these hub genes were significantly enriched. Conclusions. This study indicated that DR could exhibit the anti-lung cancer effect by affecting multiple targets and multiple pathways. It reflects the traditional Chinese medicine characterized by multicomponents and multitargets. DR could be considered as a candidate for clinical anticancer therapy by regulating bone physiological functions.

scholarly journals Investigation of the Potential Mechanism Governing the Effect of the Shen Zhu San on COVID-19 by Network Pharmacology

2020 ◽  
Vol 2020 ◽  
pp. 1-23 ◽  
Author(s):  
Yuxuan Wang ◽  
Yuhua Ru ◽  
Guowei Zhuo ◽  
Maozheng Sheng ◽  
Shuangqiu Wang ◽  
...  
Keyword(s):  
Combined Therapy ◽  
Target Prediction ◽  
Interaction Network ◽  
Modern Medicine ◽  
Network Pharmacology ◽  
Target Tissue ◽  
Protein Protein Interaction ◽  
Compound Screening ◽  
Therapeutic Mechanisms ◽  
Microarray Analyses

Background. Since December 2019, coronavirus disease 2019 (COVID-19) due to SARS-CoV-2 infection has emerged in Wuhan and rapidly spread throughout China and even to other countries. Combined therapy with modern medicine and traditional Chinese medicine has been proposed, in which Shen Zhu San (SZS) was regarded as one of the basic prescriptions. Methods. Network pharmacological approaches along with candidate compound screening, target prediction, target tissue location, protein-protein interaction network, gene ontology (GO), KEGG enrichment analyses, and gene microarray analyses were applied. Results. A total of 627 targets of the 116 active ingredients of SZS were identified. Targets in immune cells and tissues were much more abundant than those in other tissues. A total of 597 targets were enriched in the GO biological cellular process, while 153 signaling pathways were enriched according to the KEGG analysis. A total of 450 SARS-related targets were integrated and intersected with the targets of SZS to identify 40 common targets that were significantly enriched in five immune function aspects of the immune system process during GO analysis. Several inflammation-related pathways were found to be significantly enriched throughout the study. Conclusions. The therapeutic mechanisms of the effects of SZS on COVID-19 potentially involve four effects: suppressing cytokine storms, protecting the pulmonary alveolar-capillary barrier, regulating the immune response, and mediating cell death and survival.

scholarly journals Navigating Traditional Chinese Medicine Network Pharmacology and Computational Tools

2013 ◽  
Vol 2013 ◽  
pp. 1-23 ◽  
Author(s):  
Ming Yang ◽  
Jia-Lei Chen ◽  
Li-Wen Xu ◽  
Guang Ji
Keyword(s):  
Systems Biology ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Network Models ◽  
Research Process ◽  
Modern Medicine ◽  
Machine Learning Algorithms ◽  
Network Pharmacology ◽  
Research Approach ◽  
Computational Tools

The concept of “network target” has ushered in a new era in the field of traditional Chinese medicine (TCM). As a new research approach, network pharmacology is based on the analysis of network models and systems biology. Taking advantage of advancements in systems biology, a high degree of integration data analysis strategy and interpretable visualization provides deeper insights into the underlying mechanisms of TCM theories, including the principles of herb combination, biological foundations of herb or herbal formulae action, and molecular basis of TCM syndromes. In this study, we review several recent developments in TCM network pharmacology research and discuss their potential for bridging the gap between traditional and modern medicine. We briefly summarize the two main functional applications of TCM network models: understanding/uncovering and predicting/discovering. In particular, we focus on how TCM network pharmacology research is conducted and highlight different computational tools, such as network-based and machine learning algorithms, and sources that have been proposed and applied to the different steps involved in the research process. To make network pharmacology research commonplace, some basic network definitions and analysis methods are presented.

scholarly journals Systems Pharmacology Dissection of Traditional Chinese Medicine Wen-Dan Decoction for Treatment of Cardiovascular Diseases

2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
Tao-Hua Lan ◽  
Lu-Lu Zhang ◽  
Yong-Hua Wang ◽  
Huan-Lin Wu ◽  
Dan-Ping Xu
Keyword(s):  
Chinese Medicine ◽  
Cardiovascular Diseases ◽  
Traditional Chinese Medicine ◽  
Molecular Mechanisms ◽  
Modern Medicine ◽  
System Level ◽  
Therapeutic Effects ◽  
Active Compounds ◽  
System Pharmacology ◽  
Underlying Mechanisms

Cardiovascular diseases (CVDs) have been recognized as first killer of human health. The underlying mechanisms of CVDs are extremely complicated and not fully revealed, leading to a challenge for CVDs treatment in modern medicine. Traditional Chinese medicine (TCM) characterized by multiple compounds and targets has shown its marked effects on CVDs therapy. However, system-level understanding of the molecular mechanisms is still ambiguous. In this study, a system pharmacology approach was developed to reveal the underlying molecular mechanisms of a clinically effective herb formula (Wen-Dan Decoction) in treating CVDs. 127 potential active compounds and their corresponding 283 direct targets were identified in Wen-Dan Decoction. The networks among active compounds, targets, and diseases were built to reveal the pharmacological mechanisms of Wen-Dan Decoction. A “CVDs pathway” consisted of several regulatory modules participating in therapeutic effects of Wen-Dan Decoction in CVDs. All the data demonstrates that Wen-Dan Decoction has multiscale beneficial activity in CVDs treatment, which provides a new way for uncovering the molecular mechanisms and new evidence for clinical application of Wen-Dan Decoction in cardiovascular disease.

scholarly journals Network Pharmacology-Based Strategy for Predicting Active Ingredients and Potential Targets of Coptis chinensis Franchin Polycystic Ovary Syndrome

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Jian Xiong Ma ◽  
Miaoyong Ye ◽  
Ke Ma ◽  
Kang Zhou ◽  
Yingying Zhang ◽  
...  
Keyword(s):  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Polycystic Ovary Syndrome ◽  
Signaling Pathways ◽  
Polycystic Ovary ◽  
Interaction Network ◽  
Network Pharmacology ◽  
Bioactive Components ◽  
Coptis Chinensis ◽  
Ovary Syndrome

Background. Polycystic ovary syndrome (PCOS) causes low fertility in females. Coptis chinensis (C. chinensis) is used to clear heat and dampness, purify fire, and detoxify in traditional Chinese medicine (TCM). Although C. chinensis has demonstrated efficacy against PCOS in clinical practice, there are no available data regarding the bioactive components of C. chinensis, their targets, and molecular mechanisms underlying their effects. Methods and Results. Network pharmacology was used to analyze the bioactive components of C. chinensis, their targets, and signaling pathways underlying their effects. The TCM systems pharmacology database and analysis platform (TCMSP) was used to screen 14 effective active ingredients and 218 targets of C. chinensis. The GeneCards, OMIM, and PharmGkb databases were used to screen 3517 disease targets for PCOS, and 102 common targets of drugs and diseases were screened using R Cytoscape that was utilized to build a drug-active ingredient-disease target interaction network, and the STRING platform was utilized to construct a common target protein-protein interaction network, including 102 nodes and 221 edges. Key targets of C. chinensis for the treatment of PCOS included JUN, MAPK, IL6, CXCL8, FOS, and IL1B. A total of 123 gene ontology (GO) terms and 129 pathways were acquired by GO and KEGG enrichment analyses. The AGEs/RAGE, TNF, IL-17, MAPK, and HIF-1 signaling pathways were closely related to PCOS and may be the core pathways involved in PCOS. Schrodinger software was used to evaluate the interaction between active components and their targets and explore binding modes. Furthermore, based on the prediction of network pharmacology study, a mouse model of PCOS was established to evaluate the curative role and underlying mechanisms of C. chinensis. The results showed that C. chinensis treatment reversed histopathological damage of the ovary and also ameliorated the mRNA and protein expression levels of the predicted hub targets (MAPK1, CXCL8, IL-6, and IL-1β). These results indicated that WZYZP has a protective effect on spermatogenesis disorder, suggesting that it could be an alternative choice for male infertility therapy. Conclusions. This preliminary study verified the basic pharmacological effects and mechanisms of C. chinensis, a TCM, in the treatment of PCOS. These results indicate that the therapeutic effects of C. chinensis on PCOS may be achieved by regulating the expression of inflammatory factors. This study provides new insights for the systematic exploration of the mechanism of traditional Chinese medicine.

scholarly journals Uncovering the Pharmacological Mechanism of Chaibei Zhixian Decoction on Epilepsy by Network Pharmacology Analysis

2019 ◽  
Vol 2019 ◽  
pp. 1-7 ◽  
Author(s):  
Jian Zhang ◽  
Chenglong Zheng ◽  
Siyuan Yuan ◽  
Xiaoke Dong ◽  
Le Wang ◽  
...  
Keyword(s):  
Chinese Medicine ◽  
Protein Kinase ◽  
Traditional Chinese Medicine ◽  
Protein Kinase B ◽  
Interleukin 1 ◽  
Negative Regulation ◽  
Network Pharmacology ◽  
Protein Targets ◽  
Treatment Of Epilepsy ◽  
Go Terms

Objective. Epilepsy is a neuronal disorder that is characterized by epileptic seizures and linked with abnormal neural functioning in the brain. Traditional Chinese medicine (TCM) formula Chaibei Zhixian decoction (CZD) has been widely used for epilepsy in China while the pharmacological mechanisms are still unclear. In the present study, systematic and comprehensive network pharmacology was utilized for the first time to reveal the potential pharmacological mechanisms of CZD on epilepsy. Methods. Traditional Chinese Medicine Systems Pharmacology (TCMSP) database and analysis platform was utilized for the development of an ingredients-targets database. After identifying epileptic targets of CZD, their interaction with other proteins was estimated based on protein-protein interaction network created from STITCH and gene ontology (GO) enrichment analysis utilizing Cytoscape-ClueGO plugin. Results. CZD formula was found to have 643 chemical ingredients, and the potential protein targets of these ingredients were 5230, as retrieved from TCMSP database. Twenty-six protein targets were found to be associated with epilepsy. Thirteen hub genes were regulated by CZD in epilepsy, including estradiol, ESR1, ESR2, SRC, CTNNB1, EP300, MAPK1, MAPK3, SP1, BRCA1, NCOA3, CHRM1, and GSK3B. The results of GO terms analysis showed that 8 GO terms were recovered in the form of 3 clusters, including negative regulation of protein kinase B signaling, positive regulation of interleukin-1 production, and microvillus assembly. Conclusions. Network pharmacology approach provides better understanding of the underlying pharmacological mechanisms of CZD on epilepsy. Estradiol, ESR1, ESR2, CTNNB1, EP300, MAPK1, MAPK3, BRCA1, and GSK3B are likely to be important molecules regulated by CZD in treatment of epilepsy. Negative regulation of protein kinase B signaling may play vital roles in the treatment of epilepsy by CZD.

scholarly journals Investigating the pharmacological mechanisms of SheXiang XinTongNing against coronary heart disease based on network pharmacology

2020 ◽  
Author(s):  
Li-ying Jia ◽  
Jia Li ◽  
Gui-yun Cao ◽  
Zhao-qing Meng ◽  
Lu Gan ◽  
...  
Keyword(s):  
Coronary Heart Disease ◽  
Heart Disease ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Signaling Pathway ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Network Pharmacology

Abstract Background SheXiang XinTongNing, a commercially available Chinese patent medicine, has been widely used in the treatment of coronary heart disease. However, the mechanisms of SheXiang XinTongNing are still unclear. The aim of this study was to investigate the pharmacological mechanisms of SheXiang XinTongNing against coronary heart disease via network analysis. Method The traditional Chinese medicine system pharmacology analysis platform was used to screen the potential active constituents of the six traditional Chinese medicines in SheXiang XinTongNing, and the potential targets were obtained from PharmMapper. The genome annotation database platform was used to screen the candidate targets related to coronary heart disease. Then the drug-components-targets network and protein interaction network were built by Cytoscape 3.6.0 software. Further, GO bio-functional enrichment analysis and KEGG pathway enrichment analysis were performed through annotation, visualization and integrated discovery database. Results Results showed that the drugs-components-targets network contains 104 targets and 62 key components. The protein interaction network consisted of 107 nodes; key targets included Bcl2l1, IGF1, SRC, CASP3, et al. Functionally, the candidate targets were significantly associated with multiple pathways such as PI3K-Akt signaling pathway, MAPK signaling pathway, Ras signaling pathway, FoxO signaling pathway, Endocrine resistance. Given the above, the pharmacological activities of SheXiang XinTongNing may be predominantly related to several factors such as cell apoptosis, inflammation and angiogenesis. Conclusion XTN can effectively attenuate the symptoms of coronary heart disease through diverse pathways. The research proves that network pharmacology can successfully reveal the mechanisms of traditional Chinese medicine in a holistic view. Our systematic analysis lays a foundation for further studying.

scholarly journals Network Pharmacology-Based Prediction of Bioactive Compounds and Potential Targets of Wenjing Decoction for Treatment of Endometriosis

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Yu-nan Liu ◽  
Xiao-jing Hu ◽  
Bei Liu ◽  
Yu-jie Shang ◽  
Wen-ting Xu ◽  
...  
Keyword(s):  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Signaling Pathways ◽  
Signaling Pathway ◽  
Bioactive Compounds ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Estrogen Signaling ◽  
Network Pharmacology ◽  
Inflammatory Disorder

Endometriosis is a chronic estrogen-dependent inflammatory disorder that negatively affects the quality of life in women. The Wenjing decoction (WJD) is a traditional Chinese medicine that has been shown to have a therapeutic effect on endometriosis. Our study systematically explored the mechanism of WJD against endometriosis using a network pharmacology approach. Potentially bioactive compounds of WJD and their possible targets were retrieved from the Traditional Chinese Medicine System Pharmacology Database and Analysis Platform. The protein-protein interaction network and herbs-compounds-genes multinetwork were constructed using Cytoscape for visualization. Subsequently, the signaling pathways of common targets were retrieved from the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and molecular docking was performed using PyRx software. In total, 48 common targets were screened, such as IL6 and ESR1, which were related to inflammation and the endocrine system. The top five bioactive compounds were quercetin, kaempferol, wogonin, beta-sitosterol, and stigmasterol. KEGG enrichment analysis revealed 65 pathways containing inflammatory- and endocrine-related signaling pathways, such as the “TNF signaling pathway” and the “estrogen signaling pathway.” Taken together, the results of our network pharmacology analysis predicted that certain active ingredients of WJD might treat endometriosis by regulating inflammation and/or endocrine, which provided references for further understanding and exploration of WJD on endometriosis.

scholarly journals Study on the Mechanism of Salvia miltiorrhiza in the Treatment of Traumatic Bone Defects

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Qian Tan ◽  
Yaoxi Liu ◽  
Ting Lei ◽  
Weihua Ye ◽  
Xin Hu ◽  
...  
Keyword(s):  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Salvia Miltiorrhiza ◽  
Interaction Network ◽  
Bone Defects ◽  
Biological Properties ◽  
Bone Diseases ◽  
Network Pharmacology ◽  
Active Components ◽  
Compound Target

Traumatic bone defect is one of the major orthopedic diseases in clinics, and its incidence is increasing year by year. And repairing traumatic bone defects is a very difficult problem in clinics at present. The surface of medical titanium-based alloy has good biological properties, and its implant has a certain role in promoting bone in bone tissue. However, titanium-based materials are biologically inert and have no biological activity. As a traditional Chinese medicine, Salvia miltiorrhiza has the efficacy of treating bone diseases and promoting bone healing. The curative effect can be better exerted by loading the traditional Chinese medicine active compound Salvia miltiorrhiza on the surface of the titanium implant in a certain way. At present, due to the complex chemical composition of Salvia miltiorrhiza, the mechanism of its use for the treatment of traumatic bone defects is still unclear. Therefore, in this study, we mainly discussed the potential target and mechanism of Salvia miltiorrhiza in the treatment of traumatic bone defects through network pharmacology, which may provide a scientific basis for the treatment of traumatic bone defects with Salvia miltiorrhiza loaded on the surface of medical titanium-based alloy. We screened out effective compounds and targets of Salvia miltiorrhiza and targets related to traumatic bone defects with the help of relevant databases. The targets of Salvia miltiorrhiza for traumatic bone defects were analyzed by STRING and GeneCards databases, and the results were visualized by constructing a compound-target network, protein-protein interaction network, and compound-target-disease network with Cytoscape 3.7.1 analysis software. Finally, the selected core targets carried out GO and KEGG enrichment. The results showed that 60 main active components were screened from Salvia miltiorrhiza Bunge, which could act on 149 targets. There were 33 active components and 70 targets related to traumatic bone defects, respectively. The core targets of Salvia miltiorrhiza in the treatment of traumatic bone defects were MAPK1, MAPK10, MAPK14, TGFB1, and TNF. The results of enrichment analysis showed that Salvia miltiorrhiza might treat traumatic bone defects through an osteogenic differentiation pathway.

scholarly journals A network pharmacology study on the Cervix Prescription for treatment of Cervical Cancer

2021 ◽  
Author(s):  
Pian Ying ◽  
Yingping Zhu
Keyword(s):  
Cervical Cancer ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Therapeutic Targets ◽  
Interaction Network ◽  
Research Direction ◽  
Network Pharmacology ◽  
Jiangxi Province ◽  
Signal Pathways ◽  
Active Ingredients

Abstract Purpose: Based on the method of network pharmacology to explore the mechanism of the Cervical Prescription(CP) in the treatment of cervical cancer(CC) . Methods: To obtain the active ingredients and potential targets of CP from the Traditional Chinese Medicine Systems Pharmacology database and analysis platform (TCMSP) ; To search for targets related to cervical cancer through the database, and map the CP and the targets; Screen the core Targets, a Chinese medicine compoundtarget network and STRING database was used to construct a protein-protein interaction network (PPI). The DAVID 6.8 online tool was used to perform gene ontology (GO) and kyoto encyclopedia of genes and genome (KEGG) pathway enrichment analyses of overlapping targets. Results: The CP contains 2 active ingredients, corresponding to 301 non-reactive targets; 10 GO biological process related items and 73 signal pathways were obtained. Conclusion: By constructing a network diagram of "components-targets-pathways", 1Project fund: Zhejiang Provincial Natural Science Foundation Project(CN) (LQ20H270016); Zhejiang Traditional Chinese Medicine Administration (CN) (2020ZB087). *Profile of the author: Zhu Yingping, (1987-), female, attending physician, from Ganzhou, Jiangxi Province, master's degree student, research direction: Chinese medicine prevention and treatment of gynecological malignancies; E-mail: [email protected] this study revealed that CP can exert its efficacy through multiple components, multiple targets, and multiple pathways to achieve the purpose of preventing and treating CC.The network pharmacology-based approach in the present study showed promising potential for identifying the main therapeutic targets from TCM formulas. This study provides valuable information for TCM researchers and clinicians to better understand the main therapeutic targets and therapeutic roles of herbal decoctions in clinical settings.

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