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Investigation of the Mechanism of Traditional Chinese Medicines in Angiogenesis Through Network Pharmacology and Data Mining

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Investigation of the Mechanism of Traditional Chinese Medicines in Angiogenesis Through Network Pharmacology and Data Mining Investigation of the Mechanism of Traditional Chinese Medicines in Angiogenesis Through Network Pharmacology and Data Mining WingYan Yun China Academy of Chinese Medical Sciences Guanganmen Hospital Wenchao Dan China Academy of Chinese Medical Sciences Guanganmen Hospital Jinlei Liu China Academy of Chinese Medical Sciences Guanganmen Hospital Xinyuan Guo Cancer Hospital Chinese Academy of Medical Sciences Min Li China Academy of Chinese Medical Sciences Guanganmen Hospital Qingyong He ( [email protected] ) University of Chinese Medicine https://orcid.org/0000-0002-5885-8005 Research Keywords: angiogenesis, mechanism research, network pharmacology Posted Date: November 12th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-104137/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License 1 Investigation of the Mechanism of Traditional Chinese 2 Medicines in Angiogenesis through Network Pharmacology and 3 Data Mining 4 Wingyan Yun 1,2, Wenchao Dan 1,2, Jinlei Liu 1, Xinyuan Guo 3, Min Li 1, Qingyong He 1* 5 1. Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, 6 China 7 2. Graduate School of Beijing University of Chinese Medicine, Beijing 100029, China 8 3. Cancer Hospital Chinese Academy of Medical Sciences, Beijing 100021, China 9 10 Abstract 11 Background: Although traditional Chinese medicine is safe for the clinical treatment of 12 angiogenesis, the in vivo intervention mechanism is diverse, complex, and largely unknown. 13 Therefore, we aimed to explore the active ingredients of traditional Chinese medicine and their 14 mechanisms for the treatment of angiogenesis. 15 Methods: Data on angiogenesis-related targets were collected from the GeneCards, Therapeutic 16 Target Database, Online Mendelian Inheritance in Man, DrugBank, and DisGeNET databases. 17 These were matched to related molecular compounds and ingredients in the traditional Chinese 18 medicine system pharmacology platform. The data were integrated; based on the condition of 19 Degree >1 and relevant literature, a target-compound network as well as compound-medicine and 20 target-compound-medicine networks were constructed using Cytoscape. Molecular docking was 21 used to predict the predominant binding combination of core targets and components. 22 Results: We obtained a total of 79 targets for angiogenesis, and 41 targets were matched to 3839 1 23 compounds. Then, 110 compounds were selected owing to their high correlation with 24 angiogenesis. Fifty-five combinations in the network were obtained by molecular docking, among 25 which PTGS2-Astragalin (-9.18 kcal/mol), KDR-Astragalin (-7.94 kcal/mol), PTGS2-quercetin (- 26 7.41 kcal/mol), and PTGS2-myricetin (-7.21 kcal/mol) were the top combinations. These results 27 indicated that the selected potential core compounds may have good binding activity with the core 28 targets. Eighty new combinations were obtained from the network, and the top combinations 29 based on affinity were KDR-beta-carotene (-10.13 kcal/mol), MMP9-beta-Sitosterol (-8.04 30 kcal/mol), MMP9-Astragalin (-7.82 kcal/mol), and MMP9-Diosgenin (-7.51 kcal/mol). The core 31 targets included PTGS2, KDR, VEGFA, and MMP9. The essential components identified were 32 astragalin, kaempferol, myricetin, quercetin, and β-sitosterol. The crucial Chinese medicines 33 identified included Polygoni Cuspidati Rhizoma et Radix, Morus alba Root Bark, and Forsythia 34 Fructus. 35 Conclusions: By systematically analysing the essential ingredients of traditional Chinese 36 medicine and their targets, it is possible to determine their potential mechanism of action in the 37 treatment of pathological angiogenesis. Our study provides a basis for further research and 38 development of new therapeutics for angiogenesis. 39 40 Keywords: angiogenesis; mechanism research; network pharmacology 41 42 Background 43 John Hunter provided the first recorded scientific insights into the field of angiogenesis and 44 coined the term angiogenesis in 17871. Folkman2-6 proposed the role of angiogenesis in tumour 2 45 growth in 1971. He hypothesised that tumour growth depends on angiogenesis to increase blood 46 supply and proposed stopping the blood supply to inhibit tumour growth, which subsequently 47 initiated the field of research on the relationship between angiogenesis and diseases. Angiogenesis 48 is the process of capillary sprouting from pre-existing vasculature, and it is highly induced by 49 hypoxia and other biological processes5, 7. The mechanism of angiogenesis can be divided into 50 two types. The first is sprouting angiogenesis, wherein vascular endothelial cell growth factor 51 (VEGF) can stimulate tip cells in the original blood vessel network to induce vascular sprouting8, 52 9. The second is intussusceptive angiogenesis, which proceeds through transluminal tissue pillar 53 formation and subsequent vascular splitting to expansion and remodelling of microvascular 54 networks9-11. 55 56 Under normal circumstances, angiogenesis is the balance between the inhibiting factor and 57 growth factor. If the functions of either the inhibiting or growth factors are abnormal, it presents 58 as overgrowth, defect, or malformation. Angiogenesis is essential for nutrition and oxygen for the 59 growth and development of tumour cells. Under hypoxic conditions, tumours stimulate 60 neovascularization via the expression of growth factors such as VEGF12. Thus, exploring the 61 inhibition of angiogenesis for the treatment of tumours has gained increasing attention. However, 62 some studies have shown that using anti-angiogenic agents can induce potential resistance 63 mechanisms such as autophagy, VEGF-dependent alterations, non-VEGF pathways, and stromal 64 cell interactions13-17. Tumour cells may become accustomed to hypoxia or nutrient deprivation, or 65 they may induce angiogenesis via other growth factors18, 19. Such events can lead to higher 66 survival levels of the tumour cells. Moreover, some anti-angiogenic agents can cause side effects 3 67 such as acne-like rash, hypertension, and diarrhoea20, 21. 68 69 Traditional Chinese medicine is valuable for the treatment of various diseases, especially 70 refractory diseases. Previously, we found that many herbal extracts such as Epimedium brevicornu 71 Maxim, Dalbergia odorifera T. Chen, and Trichosanthes kirilowii Maxim can regulate 72 angiogenesis22. Cucurbitacin E, a compound in herbal extracts, can inhibit tumour angiogenesis by 73 inhibiting vascular endothelial growth factor receptor 2 (KDR/VEGFR2)-mediated Jak-STAT3 74 and mitogen-activated protein kinase (MAPK) signalling pathways23. Astragaloside IV and 75 curcumin can suppress the expression of fibroblast growth factor-2, matrix metalloproteinase 2, 76 VEGF, hepatocyte growth factor, thrombosis-related factor tissue factor, and coagulation factor 77 VII, thereby reducing the microvessel count24. The above herbal studies focused on single or 78 several compounds related to angiogenesis. Nevertheless, during treatment, multiple herbal 79 compounds interact or cross-react to regulate different targets and pathways. Thus, even though 80 traditional Chinese medicine is safe for clinical treatment, the in vivo intervention mechanism is 81 diverse, complex, and largely unknown. 82 83 In this study, the targets of angiogenesis were explored through network pharmacology, and 84 the corresponding compound and herbs were matched. Furthermore, the effect of herbal 85 compounds on angiogenesis and the intervention mechanism were demonstrated. The findings of 86 this study are expected to provide insights for the development of novel therapeutics for 87 angiogenesis. The detailed workflow of investigation is shown in Figure 1. 4 Angiogenesis Molecular docking Molecular docking mode Target-compound Target-compound-traditional Potential core network Chinese medicine network compounds 88 89 Figure 1. The workflow of the investigation 90 Methods 91 Collection of data regarding angiogenesis-related targets 92 93 Data were collected from GeneCards (https://www.genecards.org/)25, Therapeutic Target 94 Database (TTD; http://db.idrblab.net/ttd/)26, Online Mendelian Inheritance in Man (OMIM, 95 omim.org)27, DrugBank (www.drugbank.ca)28, and DisGeNET (www.disgenet.org)29. The 96 keyword used to search these databases was ‘angiogenesis’. After sorting and removing repeated 97 targets, the full name of the matching targets was established using the UniProt database 98 (https://www.uniprot.org/)30. 99 5 100 Screening of related herbal compounds 101 102 The targets were used to match the compounds related to angiogenesis in the Traditional 103 Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP; 104 http://tcmspw.com/)31 and Encyclopedia of Traditional Chinese Medicine (ETCM; 105 http://www.tcmip.cn/ETCM/index.php/Home/Index/)32. The compounds and targets were 106 imported to Cytoscape version 3.8.1 (Institute for Systems Biology, Seattle, WA, USA)33 to 107 construct a ‘target-compound’ network. After preliminary screening, the related compounds were 108 verified through a literature review, and the compounds closely related to diseases under the 109 current generation research were screened as related compounds. 110 111 Collection of related traditional Chinese medicines and construction of a target-compound- 112 traditional Chinese medicine network 113 114 By collecting the traditional Chinese medicines related to compounds and constructing the 115 ‘compound-traditional Chinese medicine’
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