Compounding ingredients of Folium Artemisiae argyi
Compounds from Folium Artemisiae argyi were determined using the public databases Traditional Chinese Medicines for Systems Pharmacology Database and Analysis Platform (TCMSP, https://tcmspw.com/tcmsp.php)[11] and Integrative Pharmacology-based Research Platform of Traditional Chinese Medicine (TCMIP, http://www.tcmip.cn/TCMIP)[12].
Pharmacokinetic absorption, distribution, metabolism, and excretion (ADME) screen
The ADME criteria of Folium Artemisiae argyi were extracted from the TCMSP database. Drug-likeness (DL) and oral bioavailability (OB) were selected to identify the bioactive ingredients of Folium Artemisiae argyi. OB is the percentage of an oral dose capable of producing pharmacological activity[13]. DL is an indicator for determining the similarity or likeness of a compound that can help in determining whether a compound has a therapeutic effect or not[14].
Targets of Compounds searching
Information on the compounded ingredient target genes was obtained from the TCMSP database, and the Drug Bank (https://go.drugbank.com/) database was also used for determining the comprehensive drug targets of all ingredients. The related target genes of atherosclerosis were searched from the Mala Cards (https://www.malacards.org/) and OMIM (https://omim.org/) databases. The target genes of compounds were collected according to the Similarity ensemble approach (SEA) online database (http://sea.bkslab.org/).
Protein-protein interaction (PPI) network
The overlapping genes of AS and the compounds were selected as the hub genes and analyzed using the database STRING (https://string-db.org), which could provide the PPI network results. The Cytoscape (https://cytoscape.org/) software is widely applied to pharmacology studies in network construct and visualization.
KEGG analysis and enrichment
KEGG database was established by the Kanehisa Laboratory in 1995 and is typically used in pathway analysis and annotation in network pharmacology. We used WebGestalt[15] (WEB-based Gene Set Analysis Toolkit, http://www.webgestalt.org/) for KEGG pathway analysis, which is a functional enrichment analysis web tool. Then, the interactions between genes and pathways were validated by ClueGo and Pedia apps in Cytoscape.
GEO Validation
Candidate target genes were identified in the GEO database (GSE9128, GSE71226). GEO2R was used to identify the differentially expressed genes (DEGs), p £ 0.05, and ½log FC½ > 1 were the screening limitations.
Molecular Docking
Molecular docking is a crucial technology of network pharmacology analysis in proteins and small compounds. It is performed using the Molecular Operating Environment (MOE, v2019.0102) software to validate interactions between compounds and target proteins. The 3D structure of target proteins were obtained from the Protein Data Bank (PDB, http://www.rcsb.org) and imported into MOE to perform molecular docking after protein structure preparation. The structure of participant compounds was obtained from PubChem (https://pubchem.ncbi.nlm.nih.gov).
Cell culture and treatment
Raw264.7 was provided by Tianjin University of Traditional Chinese Medicine, and cultured by Dulbecco's modified Eagle medium (DMEM) containing 10% fetal bovine serum and 1% penicillin/streptomycin in an incubator (5% CO2, 37oC). The cells were stimulated with lipopolysaccharide (LPS) (10 mg/ml) in the presence or absence of quercetin (10, 20, 50 mM), naringenin (10, 20, 50 mM)
Real-Time Quantitative Reverse Transcription PCR and Western blot analysis
The total RNA of Raw264.7 was isolated using an RNA extraction kit (Vazyme Biotech Co., Ltd), according to the manufacturer's instructions. The concentration of extracted RNA was detected using NanoDrop (Thermo), and complementary DNA (cDNA) was synthesized according to the manufacturer's instructions of RNA reverse transcription kit (Thermo). The messenger RNA (mRNA) expression levels of Interleukin-6 (IL-6), Interleukin-1 beta (IL-1B), matrix metallopeptidase 9 (MMP9) were analyzed using quantitative real-time polymerase chain reaction (qRT-PCR) on the LightCycler 96 (Roche) with SYBR Green (Thermo). Relative expression was calculated as 2-△△Ct using glyceraldehyde 3-phosphate dehydrogenase (GAPDH) as a reference gene. Primers were purchased from Sangon Biotech (Shanghai, China), sequences were listed in Table 4. Protein expression of IL-6/ IL-1β/ MMP9 were determined by Western blot. Rabbit anti-IL-6 (21865-1-AP) Polyclonal antibody was purchased from Proteintech; Mouse anti- IL-1 β (SC-52012), MMP-9 (SC-393859) monoclonal antibody were purchased from Santa Cruz Biotechnology, Inc. (Santa Cruz, CA); Mouse anti-β-actin monoclonal antibody were purchased from Cell Signaling Technology, Inc. (Danvers, MA, USA). Quercetin and naringenin were purchased from Yuanye (Shanghai, China).
Data analysis
All data analysis were proceeding according online database (https://tcmspw.com/tcmsp.php, https://go.drugbank.com/, https://www.malacards.org/, https://omim.org/, http://sea.bkslab.org/, https://string-db.org, http://www.webgestalt.org/, https://www.ncbi.nlm.nih.gov/geo/geo2r/) and MOE software (v2019.0102). Statistical analysis was performed by GraphPad (PRISM 7.0.a), statistical significance was considered as p < 0.05, the differences among groups were analyzed with one-way ANVOA .