• Journal of Physiology & Pathology in Korean Medicine
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• v.30 no.6
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• pp.419-425
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• 2016

This study analyzed research methodologies based on network pharmacology to build a new system architecture optimized for Korean Medicine research. Results form studies using network pharmacology were collected and analyzed to evaluate the strength and weakness. Finally, an improved system architecture was proposed. Whether the predicted effects of drugs or herbs from network pharmacological analyses were in agreement with those from conventioanl knowledge of Korean Medicine was evaluated. These results were used to verify the applicability of research methodologies to the modern pharmacology and Korean Medicine respectively. Eighteen papers using TCMSP were collected and analyzed. The results suggest that the research methodology based on network pharmacology is appropriate only for the modern pharmacology but not for Korean Medicine. Information about compound-compound, herb-herb and drug-compound interactions need to be considered. We propose the modified system architecture with those information.

• The Korea Journal of Herbology
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• v.38 no.1
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• pp.45-53
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• 2023

Objectives : Network pharmacology-based research is one of useful tool to predict the possible efficacy and molecular mechanisms of natural materials with multi compounds-multi targeting effects. In this study, we investigated the functional underlying mechanisms of Astragalus membranaceus Bunge (AM) on its anti-obesity effects using a network pharmacology analysis. Methods : The constituents of AM were collected from public databases and its target genes were gathered from PubChem database. The target genes of AM were compared with the gene set of obesity to find the correlation. Then, the network was constructed by Cytoscape 3.9.1. and functional enrichment analysis was conducted to predict the most relevant pathway of AM. Results : The result showed that AM network contained the 707 nodes and 6867 edges, and 525 intersecting genes were exhibited between AM and obesity gene set, indicating that high correlation with the effects of AM on obesity. Based on GO biological process and KEGG Pathway, 'Response to lipid', 'Cellular response to lipid', 'Lipid metabolic process', 'Regulation of chemokine production', 'Regulation of lipase activity', 'Chemokine signaling pathway', 'Regulation of lipolysis in adipocytes' and 'PPAR signaling pathway' were predicted as functional pathways of AM on obesity. Conclusions : AM showed high relevance with the lipid metabolism related with the chemokine production and lipolysis pathways. This study could be a basis that AM has promising effects on obesity via network pharmacology analysis.

• Herbal Formula Science
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• v.30 no.3
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• pp.205-210
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• 2022

Conventional pharmacology has followed the notion of the reductionist 'single target selective drug paradigm'. Network pharmacology has made conventional pharmacology newer while meeting the challenges of this era. Conventional pharmacological methods have not solved the problems of Korean Medicine. For this reason, Network pharmaco- logy needs urgently and desperately for Korean medicine research. However, the information on drug interactions in herbal medicines is complex and less known. There are still some hurdles before network pharmacology emerges, one factor which constitutes Korean medicine research. There is a need to look for solutions other than inheriting the network pharmacology to solve problems that Korean medicine has before. The way of 'in silico' research should be the best to meet this challenge. With the help of 'in silico' research, there might have been emerged new findings of experimental data in Korean Medicine. If 'herbalomics' has been close to foundation through the 'in silico' method, it will contribute to the formation of modern Korean medicine and, simultaneously, come to a foundation for revitalizing exchanges with orthodox Western medicine. Eventually, it ends with a significant profitable and healthy result for the patients.

• Journal of Physiology & Pathology in Korean Medicine
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• v.35 no.5
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• pp.125-131
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• 2021

The scientific understanding of Korean medicine theory remains largely unknown, since there is a lack of proper methods to investigate its complex and unique characteristics. Here, we introduce a drug-centered approach, a novel method to investigate Korean medicine theory by analyzing the mechanisms of herbal medicines. This method can be effectively conducted by employing network pharmacology that can analyze the systems-level mechanisms of herbal medicines on a large scale. Firstly, we introduce the method of network pharmacology that are applied to analyze the mechanisms of herbal medicines in a step-by-step manner. Then, we show how the drug-centered approach employing network pharmacology can be applied to investigate Korean medicine theory by describing studies that identify the biological correlates of the cold-hot nature of herbs, spleen qi deficiency syndrome, or Sasang constitution. Finally, we discuss the limitations and future directions of the proposed approach in two aspects: The methods of network pharmacology for a drug-centered approach and the process of inferring Korean medicine theory through it. We believe that a drug-centered approach employing network pharmacology will provide an advanced scientific understanding of Korean medicine theory and contribute to its development by generating biologically plausible hypothesis.

• The Journal of Korean Medicine
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• v.44 no.2
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• pp.106-118
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• 2023

Objectives: Network pharmacology is a method of constructing and analyzing a drug-compound-target network to predict potential efficacy and mechanisms related to drug targets. In that large-scale analysis can be performed in a short time, it is considered a suitable tool to explore the function and role of herbal medicine. Thus, we investigated the potential functions and pathways of Chongmyunggongjin-dan (CMGJD) on Alzheimer's disease (AD) via network pharmacology analysis. Methods: Using public databases and PubChem database, compounds of CMGJD and their target genes were collected. The putative target genes of CMGJD and known target genes of AD were compared and found the correlation. Then, the network was constructed using Cytoscape 3.9.1. and functional enrichment analysis was conducted based on the Gene Ontology (GO) Biological process and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways to predict the mechanisms. Results: The result showed that total 104 compounds and 1157 related genes were gathered from CMGJD. The network consisted of 1157nodes and 10034 edges. 859 genes were interacted with AD gene set, suggesting that the effects of CMGJD are closely related to AD. Target genes of CMGJD are considerably associated with various pathways including 'Positive regulation of chemokine production', 'Cellular response to toxic substance', 'Arachidonic acid metabolic process', 'PI3K-Akt signaling pathway', 'Metabolic pathways', 'IL-17 signaling pathway' and 'Neuroactive ligand-receptor interaction'. Conclusion: Through a network pharmacological method, CMGJD was predicted to have high relevance with AD by regulating inflammation. This study could be used as a basis for effects of CMGJD on AD.

• Journal of Physiology & Pathology in Korean Medicine
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• v.29 no.6
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• pp.443-450
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• 2015

The purpose of this study was is to understand how the network pharmacology databases of traditional medicine in China are established and provide suggestion for successful implementation in Traditional Korean Medicine. We searched for network-pharmacology-related TCM Databases provided on the internet, and analysed their contents. Then, we compared herbs related to Sasang with herbs of the TCM Databases. We chose 8 network-pharmacology-related TCM Databases. They shared information about compounds, herbs, formulae, drugs, targets and diseases, and provided interaction networks between these components. In comparison with herbs related to Sasang, TCMSP Database did not have information about 99 herbs in total, and 25 herbs included in major Sasang formulae. The implications and recommendations for Traditional Korean Medicine researches were discussed. Based on the results of this primary study, more related studies should be carried out in the future.

• Herbal Formula Science
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• v.28 no.3
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• pp.243-254
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• 2020

Objectives : Network pharmacology analysis is commonly used to investigate the synergies and potential mechanisms of multiple compounds by analyzing complex, multi-layered networks. We used TCMSP and BATMAN-TCM databases to compare results of network pharmacological analysis between White Ginseng(WG) and Red Ginseng(RG). Methods : WG and RG were compared with components and their target molecules using TCMSP database, and compound-target-pathway/disease networks were compared using BATMAN-TCM database. Results : Through TCMSP, 104 kinds of target molecules were derived from WG and 38 kinds were derived from RG. Using the BATMAN-TCM database, target pathways and diseases were screened, and more target pathways and diseases were screened compared to RG due to the high composition of WG ingredients. Analysis of component-target-pathway/disease network using network analysis tools provided by BATMAN-TCM showed that WG formed more networks than RG. Conclusions : Network pharmacology analysis can be effectively performed using various databases used in system biology research, and although the materials that have been reported in the past can be used efficiently for research on diseases related to targets, the results are unreliable if prior studies are focused on limited or narrow research areas.

• The Korean Journal of Physiology and Pharmacology
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• v.17 no.4
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• pp.315-320
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• 2013

Here, we show that radicicol, a fungal antibiotic, resulted in marked inhibition of inducible nitric oxide synthase (iNOS) transcription by the pancreatic beta cell line MIN6N8a in response to cytokine mixture (CM: TNF-${\alpha}$, IFN-${\gamma}$, and IL-$1{\beta}$). Treatment of MIN6N8a cells with radicicol inhibited CM-stimulated activation of NF-${\kappa}B$/Rel, which plays a critical role in iNOS transcription, in a dose-related manner. Nitrite production in the presence of PD98059, a specific inhibitor of the extracellular signal-regulated protein kinase-1 and 2 (ERK1/2) pathway, was dramatically diminished, suggesting that the ERK1/2 pathway is involved in CM-induced iNOS expression. In contrast, SB203580, a specific inhibitor of p38, had no effect on nitrite generation. Collectively, this series of experiments indicates that radicicol inhibits iNOS gene expression by blocking ERK1/2 signaling. Due to the critical role that NO release plays in mediating destruction of pancreatic beta cells, the inhibitory effects of radicicol on iNOS expression suggest that radicicol may represent a useful anti-diabetic activity.

• The Korea Journal of Herbology
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• v.38 no.6
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• pp.73-91
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• 2023

Objectives : This study used a network pharmacology approach to elucidate the efficacy and molecular mechanisms of Daehwangmokdanpitang (DHMDPT) on Psoriasis. Methods : Using OASIS databases and PubChem database, compounds of DHMDPT and their target genes were collected. The putative target genes of DHMDPT and known target genes of psoriasis were compared and found the correlation. Then, the network was constructed using Cytoscape 3.10.1. The key target genes were screened by Analyzer network and their functional enrichment analysis was conducted based on the Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways to predict the mechanisms. Results : The result showed that total 30 compounds and 439 related genes were gathered from DHMDPT. 264 genes were interacted with psoriasis gene set, suggesting that the effects of DHMDPT are closely related to psoriasis. Based on GO enrichment analysis and KEGG pathways, 'Binding', 'Cytokine Activity', 'Receptor Ligand Activity' 'HIF-1 signaling pathway', 'IL-17 signaling pathway', 'Toll-like receptor signaling pathway', and 'TNF signaling pathway' were predicted as functional pathways of 16 key target genes of DHMDPT on psoriasis. Among the target genes, IL6, IL1B, TNF, AKT1 showed high correlation with the results of KEGG pathways. Additionally, Emodin, Acetovanillone, Gallic acid, and Ferulic acid showed a high relevance with key genes and their mechanisms. Conclusion : Through a network pharmacological method, DHMDPT was predicted to have high relevance with psoriasis. This study could be used as a basis for studying therapeutic effects of DHMDPT on psoriasis.

• Journal of Pharmacopuncture
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• v.18 no.3
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• pp.11-18
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• 2015

Objectives: Systems biology is a novel subject in the field of life science that aims at a systems' level understanding of biological systems. Because of the significant progress in high-throughput technologies and molecular biology, systems biology occupies an important place in research during the post-genome era. Methods: The characteristics of systems biology and its applicability to traditional medicine research have been discussed from three points of view: data and databases, network analysis and inference, and modeling and systems prediction. Results: The existing databases are mostly associated with medicinal herbs and their activities, but new databases reflecting clinical situations and platforms to extract, visualize and analyze data easily need to be constructed. Network pharmacology is a key element of systems biology, so addressing the multi-component, multi-target aspect of pharmacology is important. Studies of network pharmacology highlight the drug target network and network target. Mathematical modeling and simulation are just in their infancy, but mathematical modeling of dynamic biological processes is a central aspect of systems biology. Computational simulations allow structured systems and their functional properties to be understood and the effects of herbal medicines in clinical situations to be predicted. Conclusion: Systems biology based on a holistic approach is a pivotal research methodology for understanding the mechanisms of traditional medicine. If systems biology is to be incorporated into traditional medicine, computational technologies and holistic insights need to be integrated.