Exploring the Mechanism of Yi-Jing Decoction in Treating Polycystic Ovary Syndrome by Using Network Pharmacology.

BACKGROUND: Yi-Jing decoction (YJD), a traditional Chinese medicine prescription, has been reported to be effective in the treatment of polycystic ovary syndrome (PCOS). However, the underlying mechanisms of YJD in treating PCOS are still unclear. OBJECTIVE: In the present work, the effective ingredients of YJD and their treatment mechanisms on PCOS were systematically analyzed. METHODS: The effective ingredients of YJD and targets of PCOS were selected from public databases. The network pharmacology method was used to analyze the ingredients, potential targets, and pathways of YJD for the treatment of PCOS. RESULTS: One hundred and three active ingredients were identified from YJD, of which 82 were hit by 65 targets associated with PCOS. By constructing the disease-common targetcompound network, five ingredients (quercetin, arachidonate, beta-sitosterol, betacarotene, and cholesterol) were selected out as the key ingredients of YJD, which can interact with the 10 hub genes (VEGFA, AKT1, TP53, ALB, TNF, PIK3CA, IGF1, INS, IL1B, PTEN) against PCOS. These genes are mainly involved in prostate cancer, steroid hormone biosynthesis, and EGFR tyrosine kinase inhibitor resistance pathways. In addition, the results of molecular docking showed that the ingredients of YJD have a good binding affinity with the hub genes. CONCLUSION: These results demonstrate that the treatment of PCOS by YJD is through regulating the levels of androgen and insulin and improving the inflammatory microenvironment.

TCMPG: an integrative database for traditional Chinese medicine plant genomes.

Because of their great therapeutic and economic value, medicinal plants have attracted increasing scientific attention. With the rapid development of high-throughput sequencing technology, the genomes of many medicinal plants have been sequenced. Storing and analyzing the increasing volume of genomic data has become an urgent task. To solve this challenge, we have proposed the Traditional Chinese Medicine Plant Genome database (TCMPG, http://cbcb.cdutcm.edu.cn/TCMPG/), an integrative database for storing the scattered genomes of medicinal plants. TCMPG currently includes 160 medicinal plants, 195 corresponding genomes, and 255 herbal medicines. Detailed information on plant species, genomes, and herbal medicines is also integrated into TCMPG. Popular genomic analysis tools are embedded in TCMPG to facilitate the systematic analysis of medicinal plants. These include BLAST for identifying orthologs from different plants, SSR Finder for identifying simple sequence repeats, JBrowse for browsing genomes, Synteny Viewer for displaying syntenic blocks between two genomes, and HmmSearch for identifying protein domains. TCMPG will be continuously updated by integrating new data and tools for comparative and functional genomic analysis.

INPUT: An intelligent network pharmacology platform unique for traditional Chinese medicine.

The application of network pharmacology has greatly promoted the scientific interpretation of disease treatment mechanism of traditional Chinese medicine (TCM). However, the data required by network pharmacology analysis were scattered in different resources. In the present work, by integrating and reorganizing the data from multiple resources, we developed the intelligent network pharmacology platform unique for traditional Chinese medicine, called INPUT (http://cbcb.cdutcm.edu.cn/INPUT/), for automatically performing network pharmacology analysis. Besides the curated data collected from multiple resources, a series of bioinformatics tools for network pharmacology analysis were also embedded in INPUT, which makes it become the first automatic platform able to explore the disease treatment mechanisms of TCM. With the built-in tools, researchers can also analyze their own in-house data and obtain the results of pivotal ingredients, GO and KEGG pathway, protein-protein interactions, etc. In addition, as a proof-of-principle, INPUT was applied to decipher the antidepressant mechanism of a commonly used prescription. In summary, INPUT is a powerful platform for network pharmacology analysis and will facilitate the researches on drug discovery.

Computational Analysis Illustrates the Mechanism of Qingfei Paidu Decoction in Blocking the Transition of COVID-19 Patients from Mild to Severe Stage.

BACKGROUND: The epidemic of SARS-CoV-2 has made COVID-19 a serious threat to human health around the world. The severe infections of SARS-CoV-2 are usually accompanied by higher mortality. Although the Qingfei Paidu Decoction (QFPDD) has been proved to be effective in blocking the transition of COVID-19 patients from mild to severe stage, its mechanism remains unclear. OBJECTIVE: This study aims to explore the mechanism of QFPDD in blocking the transition of COVID- 19 patients from mild to severe stage. MATERIALS AND METHODS: In the process of screening active ingredients, oral bioavailability (OB) and drug likeness (DL) are key indicators, which can help to screen out pivotal compounds. Therefore, with the criteria of OB≥30% and DL≥0.18, we searched active ingredients of QFPDD in the Traditional Chinese Medicine Systems Pharmacology (TCMSP, https://tcmspw.com/) by using its 21 herbs as keywords. RESULTS: We filtered out 6 pivotal ingredients from QFPDD by using the bioinformatics method, namely quercetin, luteolin, berberine, hederagenin, shionone and kaempferol, which can inhibit the highly expressed genes (i.e. CXCR4, ICAM1, CXCL8, CXCL10, IL6, IL2, CCL2, IL1B, IL4, IFNG) in severe COVID-19 patients. By performing KEGG enrichment analysis, we found seven pathways, namely TNF signaling pathway, IL-17 signaling pathway, Toll-like receptor signaling pathway, NFkappa B signaling pathway, HIF-1 signaling pathway, JAK-STAT signaling pathway, and Th17 cell differentiation, by which QFPDD could block the transition of COVID-19 patients from mild to severe stage. CONCLUSION: QFPDD can prevent the deterioration of COVID-19 in the following mechanisms, i.e. inhibiting SARS-CoV-2 invasion and replication, anti-inflammatory and immune regulation, and repairing body damage. These results will be helpful for the prevention and treatment of COVID-19.