scholarly journals Chinese Herbal Medicine Meets Biological Networks of Complex Diseases: A Computational Perspective

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Shuo Gu ◽  
Jianfeng Pei
Keyword(s):  
Herbal Medicine ◽  
Chinese Herbal Medicine ◽  
Biological Networks ◽  
Rapid Development ◽  
Regulatory Function ◽  
Network Pharmacology ◽  
Chinese Herbal ◽  
Computational Workflow ◽  
Computational Research

With the rapid development of cheminformatics, computational biology, and systems biology, great progress has been made recently in the computational research of Chinese herbal medicine with in-depth understanding towards pharmacognosy. This paper summarized these studies in the aspects of computational methods, traditional Chinese medicine (TCM) compound databases, and TCM network pharmacology. Furthermore, we chose arachidonic acid metabolic network as a case study to demonstrate the regulatory function of herbal medicine in the treatment of inflammation at network level. Finally, a computational workflow for the network-based TCM study, derived from our previous successful applications, was proposed.

scholarly journals Knowledge discovery in Chinese herbal medicine: a machine learning perspective

2021 ◽  
Vol 336 ◽  
pp. 06024
Author(s):  
Nan Liang ◽  
Qing Liang ◽  
Fenglei Ji
Keyword(s):  
Machine Learning ◽  
Herbal Medicine ◽  
Knowledge Discovery ◽  
Chinese Herbal Medicine ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Current Status ◽  
Network Pharmacology ◽  
Valuable Insight ◽  
Chinese Herbal

Traditional Chinese Medicine (TCM) has attracted more and more attention due to its remarkable effects on treating diseases, and Chinese herbal medicine (CHM) is an important partition of TCM, rich in natural active ingredients. Researchers are trying multiple analytical methods to dig out more valuable information about CHM and reveal the principle of TCM. Machine learning is playing an important role in the studies. Knowledge discovery of CHM using machine learning mainly includes quality control of CHM, network pharmacology in CHM, and medical prescriptions composed by CHM, aiming to understand TCM better, provide more efficiency methods in the production of CHM and find novel treatment of disease not curable nowadays. In this paper, we summarized the basic idea of frequently used classification and clustering machine learning algorithms, introduced pre-processing algorithms commonly used to simplify and accelerate machine learning procedure, presented current status of machine learning algorithms’ applications in knowledge discovery of CHM, discussed challenges and future trends of machine learning’s application in CHM. It is believed that the paper provides a valuable insight for the starters trying to apply machine learning in the study of CHM and catch up the recent status of related researches.

scholarly journals A Review of the Traditional Uses, Botany, Phytochemistry, Pharmacology, Pharmacokinetics, and Toxicology of Corydalis yanhusuo

2020 ◽  
Vol 15 (9) ◽  
pp. 1934578X2095775
Author(s):  
Jingxia Zhang ◽  
Surong He ◽  
Jing Wang ◽  
Changli Wang ◽  
Jianhua Wu ◽  
...  
Keyword(s):  
Herbal Medicine ◽  
Chinese Herbal Medicine ◽  
Therapeutic Potential ◽  
Gastric Ulcers ◽  
Network Pharmacology ◽  
Chemical Components ◽  
China National Knowledge Infrastructure ◽  
Traditional Chinese Herbal Medicine ◽  
Chinese Herbal ◽  
Traditional Uses

Corydalis yanhusuo W. T. Wang (Papaveraceae) is a traditional Chinese herbal medicine that has long been used to treat several conditions and is widely distributed in Asian countries. This review focuses on the traditional uses, botany, phytochemistry, pharmacology, pharmacokinetics, and toxicology of C. yanhusuo. The literature on C. yanhusuo was reviewed using several resources, including classic books on Chinese herbal medicine and scientific databases, namely, PubMed, Springer, Web of Science, Science Direct, and China National Knowledge Infrastructure. Based on information from these databases regarding the chemical components of C. yanhusuo, we evaluated the underlying interaction network between chemical components, biological targets, and associated diseases using Cytoscape software. To date, more than 160 compounds have been isolated and identified from C. yanhusuo, including alkaloids, organic acids, volatile oils, amino acids, nucleosides, alcohols, and sugars. The crude extracts and purified compounds of this plant have analgesic, antiarrhythmic, and antipeptic ulcer properties, along with hypnotic effects. However, studies on the pharmacokinetics of C. yanhusuo extracts remain limited. C. yanhusuo has therapeutic potential in diseases such as cancer and depression, probably due to glaucine and corydaline. Our network pharmacology analysis revealed interactions between 20 compounds, 54 corresponding targets, and 4 health conditions. We found that leonticine, tetrahydroberberine, and corydalmine may regulate the expression of PTGS2, PTGS1, KCNH2, SCN5A, RXRA, CAMKK2, NCOA2, and ESR1, representing a potential treatment strategy against pain, gastric ulcers, inflammation, and cardiac arrhythmias. Additionally, this article discusses the future directions of research on C. yanhusuo.

scholarly journals Network Pharmacology: A New Approach for Chinese Herbal Medicine Research

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Gui-biao Zhang ◽  
Qing-ya Li ◽  
Qi-long Chen ◽  
Shi-bing Su
Keyword(s):  
Herbal Medicine ◽  
Chinese Herbal Medicine ◽  
Target Prediction ◽  
Network Pharmacology ◽  
Multiple Targets ◽  
Medicine Research ◽  
Chinese Herbal ◽  
Long Time ◽  
Effective Drugs

The dominant paradigm of “one gene, one target, one disease” has influenced many aspects of drug discovery strategy. However, in recent years, it has been appreciated that many effective drugs act on multiple targets rather than a single one. As an integrated multidisciplinary concept, network pharmacology, which is based on system biology and polypharmacology, affords a novel network mode of “multiple targets, multiple effects, complex diseases” and replaces the “magic bullets” by “magic shotguns.” Chinese herbal medicine (CHM) has been recognized as one of the most important strategies in complementary and alternative medicine. Though CHM has been practiced for a very long time, its effectiveness and beneficial contribution to public health has not been fully recognized. Also, the knowledge on the mechanisms of CHM formulas is scarce. In the present review, the concept and significance of network pharmacology is briefly introduced. The application and potential role of network pharmacology in the CHM fields is also discussed, such as data collection, target prediction, network visualization, multicomponent interaction, and network toxicology. Furthermore, the developing tendency of network pharmacology is also summarized, and its role in CHM research is discussed.

scholarly journals Untargeted Metabolomics Profiling and Global Semi-quantitation of a Prescription Chinese Herbal Medicine Formula Yinqiaosan Using UPLC-QTOF-MS with a Single Exogenous Reference Internal Standard

2020 ◽  
Vol 07 (02) ◽  
pp. e45-e57
Author(s):  
Yachun Shu ◽  
Chandana Mannem ◽  
Gang Xu ◽  
Shashank Gorityala ◽  
Xiao Liu ◽  
...  
Keyword(s):  
Herbal Medicine ◽  
Chinese Herbal Medicine ◽  
Viral Infections ◽  
Chemical Constituents ◽  
Internal Standard ◽  
Untargeted Metabolomics ◽  
Network Pharmacology ◽  
Qualitative And Quantitative ◽  
Chinese Herbal ◽  
Chinese Herbal Medicine Formula

Abstract Yinqiaosan is a classic Chinese herbal medicine formula that has been used to treat various bacterial and viral infections by Chinese medicine doctors for over two centuries. In this work, we developed a comprehensive qualitative and quantitative method for identification, quantitation, and quality assessment of chemical constituents of Yinqiaosan formula in four different preparation forms (i.e., decoction, granule, pill, and tablet), which employed ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry with a single exogenous reference internal standard for untargeted metabolomics profiling and global semiquantitative analysis. The use of a single exogenous reference internal standard permitted not only qualitative and quantitative analyses of multiple herbal components in a single instrument run, but also cross-comparison of chemical contents in between all four Yinqiaosan preparation forms. The acquired mass chromatograms were analyzed, quantitated, and compared using multivariate data analysis for similarities and differences of chemical constituents in four Yinqiaosan preparation forms. For the first time, we were able to identify over 100 chemical constituents from each preparation form using the available database. Among the 49 commonly identified compounds in the 4 Yinqiaosan preparation forms, 16 have been reported to have pharmacological activities, which may be used in a network pharmacology study of Yinqiaosan for exploring the underlying mechanism of the herbal formula.

Synergistic Effects of Chinese Herbal Medicine and Biological Networks

2020 ◽  
pp. 393-436
Author(s):  
Deep Jyoti Bhuyan ◽  
Saumya Perera ◽  
Kirandeep Kaur ◽  
Muhammad A. Alsherbiny ◽  
Mitchell Low ◽  
...  
Keyword(s):  
Herbal Medicine ◽  
Chinese Herbal Medicine ◽  
Biological Networks ◽  
Synergistic Effects ◽  
Chinese Herbal

scholarly journals Application of Molecular Methods in the Identification of Ingredients in Chinese Herbal Medicines

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2728 ◽  
Author(s):  
Ke Han ◽  
Miao Wang ◽  
Lei Zhang ◽  
Chunyu Wang
Keyword(s):  
Herbal Medicine ◽  
Chinese Herbal Medicine ◽  
Future Development ◽  
Rapid Development ◽  
Herbal Medicines ◽  
Taxonomic Identification ◽  
Traditional Methods ◽  
Chinese Herbal Medicines ◽  
Chinese Herbal ◽  
Speed And Accuracy

There are several kinds of Chinese herbal medicines originating from diverse sources. However, the rapid taxonomic identification of large quantities of Chinese herbal medicines is difficult using traditional methods, and the process of identification itself is prone to error. Therefore, the traditional methods of Chinese herbal medicine identification must meet higher standards of accuracy. With the rapid development of bioinformatics, methods relying on bioinformatics strategies offer advantages with respect to the speed and accuracy of the identification of Chinese herbal medicine ingredients. This article reviews the applicability and limitations of biochip and DNA barcoding technology in the identification of Chinese herbal medicines. Furthermore, the future development of the two technologies of interest is discussed.

scholarly journals The Strategy of Studying the Herb-Pair Inter-Reinforcement Mechanism Mapping on Chemical Space Between Sparganii Rhizoma and Curcumae Rhizoma

2021 ◽  
Author(s):  
Zhao Chen ◽  
Shiqi Sun ◽  
Xingde Ren ◽  
Yankun Chen
Keyword(s):  
Cardiovascular Diseases ◽  
Herbal Medicine ◽  
Chinese Herbal Medicine ◽  
Molecular Mechanisms ◽  
Chemical Space ◽  
Chinese Herb ◽  
Global Perspective ◽  
Network Pharmacology ◽  
Reinforcement Mechanism ◽  
Chinese Herbal

Abstract BackgroundWith the ever-increasing acceptance of combination therapy and the use of traditional Chinese medicine (TCM) has become an emerging trend. The multi-herb formulae therapy is one of the most important characteristics of TCM, but the modernization drive of this conventional wisdom has faced many obstacles due to its unimaginable complexity. Herb pairs, the most fundamental and the simplest form of multi-herb formulae, are a centralized representative of Chinese herbal compatibility. A systematic search of herb pair related research was carried out using multiple online literature databases, books and monographs published in the past 20 years. The herb-pair has an important characteristics---inter-reinforcement (Xiangxu in TCM terms) in TCM basic theory. The inter-reinforcement mechanisms of herb pairs are extremely complicated and their exact molecular mechanisms are also still not well elucidated. MethodsThis research integrated the cheminformatics’ and network pharmacology approach to elucidate the inter-reinforcement mechanisms in treating cardiovascular diseases (CVDs) with the herb-pair (Sparganii Rhizoma and Curcumae Rhizoma) at the scale of chemical space. Chemical space is a term often used for ‘multi-dimensional descriptor space’, geographical map to illustrate the distribution of molecules and their properties. It also encompasses all possible small organic molecules in Chinese herbal medicine (CHM). The concept of chemical space was proposed for the first time to study the herb-pair inter-reinforcement mechanism. ResultsThose compounds from Sparganii Rhizoma and Curcumae Rhizoma with the HIA<=2 were as candidate compounds. The herb-pair shared 2 common compounds with 6 common targets and they have 24 targets from four public databases. The compound-target-pathway-disease networks were constructed to obtain a global perspective of the interactions between Sparganii Rhizoma and Curcumae Rhizoma in chemical space. On this basis, a series of pathway guided compound combinations were found. Screen with HIA<2 (Human intestinal Absorption), which were derived from Sparganii Rhizoma and Curcumae Rhizoma (Chinese herb pair). The CTPAs network embodied 327 nodes (100 compounds, 104 targets, and 128 pathways). After setting compounds similarity to 0.7 in each compound combinations, 497 pairs of compound combinations associated 128 pathways were obtained in Target-Pathway Association Interactions (TPAs). Five, three and thirty-six compound combinations were screened which their targets were in platelet activation pathway, vascular smooth muscle contraction and calcium signaling pathway.ConclusionsMapping the chemical compounds of Chinese herbal medicine into chemical space is helpful to explain herb-pair inter-reinforcement mechanism at molecular level. Several combination compounds were mapped into cardiovascular diseases pathways, and the results showed that the strategy of studying the herb-pair inter-reinforcement mechanism mapping on chemical space is a certain scientific and rational method to illustrate material basis of Chinese herbal medicine at multi-dimension.

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