Cell culture
The twelve types of human GC cells (AGS, SNU-484, MKN-45, MKN-28, KATO-3, SNU-5, NCI-N87, YCC-1, SNU-216, SNU-668, YCC-6, and YCC-16) and human normal lung IMR-90 cells were purchased from the American Type Culture Collection (Manassas, VA, USA), the human gastric epithelial GES-1 cells and human renal epithelial 293T cells were purchased from Saga Biotechnology Co. (Shanghai, China). The human liver THLE-2 cells were purchased from Otwo Biotech (Shenzhen, China). All types of cells were grown into DMEM medium supplemented with 10% fetal bovine serum (FBS, Gibco), 1% penicillin and streptomycin (P/S, Gibco). All types of cells were placed in an incubator at 5% CO2 and 37°C (Sanyo, Osaka, Japan).
Cell viability assay
The survival rates of twelve types of human GC cell lines and four types of human normal cell lines were determined by Cell Counting Kit-8 (CCK-8) (Solarbio, Beijing, China). All cells were seeded in 96-well plates at a density of 1 × 104 cells/well and cultured for 24 h. Cells were treated with CHR (Herbpurify, Chengdu, China) and 5-fluorouracil (5-FU) (Med Chem Express, Princeton, NJ, USA) at different concentrations (20, 40, 60, 80, and 100 µM) and at different time gradients (6, 12, 18, 24, and 30 h). Solutions of 10 µL of CCK-8 were added to each well and incubated away from the light for 3 h. Cell viability after CHR treatment were measured by a multifunctional microplate reader at 495 nm wavelength (Tecan, Mannedorf, Switzerland). Concentrations that caused 50% cell growth inhibition (IC50) values of cells treated with CHR were calculated using Sigma Plot 15.0 software.
Cell apoptosis assay
The induction of apoptosis effect of CHR on AGS cell was determined by Annexin V-FITC/PI Apoptosis Kit (4A Biotech, Beijing, China). AGS cells were seeded in 6-well plates at a density of 1 × 106 cells/well. AGS cells were treated with CHR (the IC50 values of 40.03 µM) and 5-FU (40.03 µM) at different times (3, 6, 12, and 24 h). Operate according to the instructions, the collected AGS cells were mixed with 200 µL 1× binding buffer, 5 µL Annexin V-FITC, and 3 µL Propidium Iodide (PI) successively. AGS cells were incubated in a refrigerator at 4°C for 20 min. The morphological changes of AGS cells after CHR treatment were determined by fluorescence microscopy (MSHOT, Guangzhou, China). The proportion of apoptosis was observed by flow cytometry (Sysmes Co., Kobe, Japan).
Associated targets of CHR and GC analysis
The 2D structure of CHR was determined by the PubChem database (https://pubchem.ncbi.nlm.nih.gov) and submitted to the Swiss ADME platform (http://www.swisssimilarity.ch/) for drug property prediction of CHR, and the prediction target gene of CHR was obtained using Target Prediction database (http://www.swisstargetprediction.ch/). The genetic target of GC was obtained using GeneCards database (https://www.genecards.org/).
Overlapping target protein-protein interaction networks analysis
The overlapping targets of CHR and GC were predicted on VENNY2.1 website (http://www.liuxiaoyuyuan.cn/). The target of the intersection number obtained was the common potential target of CHR and GC. Submit the resulting common targets to the STRING database (https://string-db.org/) for the protein-protein interaction (PPI) network. Visual analysis of PPI networks using Cytoscape 3.9.1 software.
GO and KEGG enrichment analysis
The PPI overlapping targets predicted import DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/) in the database for enrichment analysis. Gene Ontology (GO) enrichment was used to analyze the biological process (BP), molecular function (MF), and cellular component (CC) of the cross-linked targets, while Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment was used to analyze the involved signaling pathways. Finally, the functions were sorted according to p-value, and it is considered that the GO and KEGG channels with p-value < 0.05 is significant.
Molecular docking analysis
The PDB format of core targets was obtained through RSCB-PDB database (https://www.rcsb.org/). Water removal molecules and ligands were performed at the core target in PyMOL software. The 3D structure of CHR was obtained through PubChem database and processed in Open Babel software. The core target was hydrogenated in the AutoDocks software, the charge number was calculated, and the rigid structure of the atom was determined. The docking tool processed in the AutoDockTools-1.5.6 software perform molecular docking and selects the site with the lowest energy for subsequent operations. Next, the docking site visualization of CHR and core target was created in PyMOL software and corresponding protein residues, binding bonds, and distances were displayed.
Mitochondrial membrane potential analysis
The mitochondrial membrane potential (MMP) of AGS cell after CHR treatment was determined by JC-1 Detection Kit (Solarbio, Beijing, China). AGS cells were seeded in 3.5 cm cell culture dish at a density of 1 × 105 cells/well. AGS cells were treated with CHR (40.03 µM) at different times (3, 6, 12, and 24 h). 1 mL JC-1 staining solution was added to the collected AGS cells and heated in a 37°C water bath for 30 min. Then, 1 mL 1× JC-1 binding buffer and 500 µL of phosphate-buffered saline (PBS) were added to AGS cells treated with CHR. The MMP of AGS cell was measured by flow cytometry.
Western blot analysis
The expression levels of AGS cells related proteins after CHR treatment were determined by Western Blot Analysis. AGS cells were seeded in a 6 cm cell culture dish at a density of 1 × 106 cells/well. AGS cells treated with CHR (40.03 µM) at different times (3, 6, 12, and 24 h), and protein extracts were obtained with 100 µL lysis buffer. The same amount of total protein was isolated on 12% SDS-PAGE, then the gel is electrically transferred to the nitrocellulose membrane. 5% skimmed milk was added and closed at 25°C for 2 h to avoid non-specific binding. The primary antibody (Santa Cruz Biotechnology, Dallas, TX, USA) were incubated with the film in a refrigerator at 4°C away from the light. Next, the membrane was incubated with the secondary antibody (ZSBG-BIO, Beijing, China) at room temperature for 2 h. The enhanced chemiluminescence (Tanon, Shanghai, China) solution-binding proteins. Images were exposed using multifunction imager (Analytik Jena AG, Jena, Germany), and the bands were analyzed with the ImageJ version 1.42.
ROS levels analysis
The ROS levels in AGS cells treated with CHR were determined by ROS Detection Kit (Beyotime Institute Biotechnology, Shanghai, China). AGS cells were seeded in a 3.5 cm cell culture dishes at a cell density of 1 × 105 cells/well and treated with CHR (40.03 µM) at different times (3, 6, 12, and 24 h). AGS cells was combined with 10 µL 2'7'-dichlorofluorescein diacetate (DCFH-DA) and incubated at 37°C for 30 min away from the light. ROS levels were determined by flow cytometry.
Cell cycle analysis
The cell cycle arrest of AGS after CHR treatment was determined by DNA Content Detection Kit (Solarbio, Beijing, China). AGS cells were seeded in a 3.5 cm cell culture dishes at a cell density of 1 × 105 cells/well and treated with CHR (40.03 µM) at different times (3, 6, 12, and 24 h). AGS cells were collected, fixed in pre-cooled 70% ethanol and stored overnight at 4°C. 100 µL RNase was added to the cells and incubated at 37°C away from the light for 30 min. Then 400 µL PI was added to the AGS cells and incubated at 4°C for 30 min. The changes in the number of CHR treated AGS cells in G0/G1 and G2/M phases were determined by flow cytometry.
Cell invasion and migration analysis
The inhibitory effect of CHR on AGS cells invasion was determined by Transwell Assay. AGS cells suspension containing serum-free DMEM medium was added to the upper chamber, and DMEM medium containing 10% FBS and 1% P/S was added to the lower chamber. The AGS cells treated with CHR (40.03 µM) at different times (3, 6, 12, and 24 h) were stained with 1% crystal violet (Solarbio, Beijing, China). The petri dish was placed under a fluorescence microscopy to observe the number of invading cells.
In addition, the inhibitory effect of CHR on the migration of AGS cells was determined by Wound-Healing Assay. AGS cells were seeded in 6-well plates at a cell density of 1 × 106 cells/well and treated with CHR (40.03 µM) at different times (3, 6, 12, and 24 h). After the treatment time was reached, vertical labeling lines were taken. After 2 h, the culture medium was aspirated and the healing of cells was observed under fluorescence microscopy.
Statistical analysis
The data were all repeated three times and assessed by mean ± standard deviation. Sigma Plot 15.0 software was used to calculate IC50. SPSS 29.0 software was used for Tukey’s postmortem test, and p < 0.05 was statistically significant.