Open Access Tools for CDCL Informatics

several publications have reported the value of a systems pharmacological approach to studying TCM recipes and formulations starting with a detailed network or pathway analysis.35-42 Wang et al.42 reviewed TCM network pharmacological research highlighting a process involving (1) retrieval of interaction information from various databases, (2) network construction, and (3) knowledge discovery based on network models. The authors present a summary of all relevant databases for systems/network pharmacology and present detailed network frameworks. Zhang et al.35 used a TCM network pharmacology platform to analyze Qing Luo Yin and its use in rheumatoid arthritis, while Ding et al.40 used detailed network pharmacology approaches to study herbal formulations used for cardiovascular diseases. Li et al.36 applied an addition and subtraction theory to herb combinations (as in recipes) to create new formulations based on systems pharmacology analyses using several tools including the TCMsp platform. they applied these methods to two classical prescriptions, Xiao Choihu and Da Chaihu decoctions. the findings included 63 bioactive compounds with 65 potential targets and a proposal of dividing the formulations into two aspects: the fundamental formula that is primarily responsible for the basic pharmacological effect, and the additive herbs that exhibit reinforcement functions, thereby achieving a complementary synergistic effect. this can be envisioned as a process to establish new formulations with enhanced synergistic effects. Liu et al.41 used a pathway-based strategy by combining pathway integration, target selection, reverse drug targeting, and network analysis to analyze Reduning injection, a widely used herbal medicine for combating inflammation. ten key chemical constituents were identified and used for in silico assessment and the predicted results were experimentally validated in lipo- polysaccharide-stimulated raw 265.7 cells. the results provide a systemic understanding of the mechanisms of herbal medicines that act on specific disease-related pathways. In a study that illustrates the wide use of several databases and tools, Wang et al.42 used a network-based pharmacological identification of active compounds of Erxian decoction used for the alleviation of menopause-related symptoms. of the total 721 compounds in the medicine, 20 compounds related to 34 significant pathways or genes associated with menopause. the researchers used TCMsp,16 TCM Database® Taiwan,9 the Comparative Toxicogenomics Database (CTD),43 Stitch,29 and DAVID 6.7 44 for the analyses. This study represents a good example of the use of open access tools for TCM analyses.

Chu et al.45 studied the potential of alleviating side effects of chemotherapy drugs (taxol as an example) with herbal medications in the treatment of breast cancer. Several resources were used including the TCM Database® Taiwan9 and DrugBank.18 Five herbs were identified as being used in breast cancer and these are listed with therapeutic functions, primary active phyto- chemical(s), and potential interactive effects:

  • Dian Huang Qin: clears heat; baicalein, baicalin; (inhibition of VEGF, cMyc)
  • Dan Shen: improves blood circulation; baiclin, tanshinones; (inhibition of cyclin D)
  • Shan Ci Gu: resolves abscesses and masses; colchicine; (tubulin)
  • Bai Zhu: improves spleen function and appetite; atractydolin; (induction of ghrelin)
  • Dang Gui: improves blood circulation; ferulic acid; (possible antagonistic effects with taxol involving VEGFA, ERa)
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