All of the database and software which used in the present study were presented in Table 1. The details of materials and methods as following:

Table 1 Database and software which used in the study2.1 Acquisition of EM

The EM (CAS number: 518-82-1) was obtained from Wuhan Kabuda Chemical Co., Ltd with a purity of 99%. It’s molecular formula is C15H10O5, molecular weight is 270.23, melting point is between 256 ℃ and 257 ℃.

2.2 Acquisition of EM molecular targets

All target information of EM was retrieved through Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) database. The target of EM was found by Perl 5.24.1 software, and the gene names of EM target were annotated by UniProt database.

2.3 Screening the target interactions of “EM and PCa”

Using “tumor” and “cancer” as keywords, the target genes of PCa were screened by Genecards database and DisGeNET database, and the disease correlation score ≥ 1 as the reference value. Finally, utilization of R 4.0.5 software and Venny 2.1 online software, the EM target genes and PCa target genes were intersected to obtain their common target genes.

2.4 Construction of “compound-disease-target” network between EM and PCa

The common target genes screened by the above process were imported into Cytoscape 3.7.2 software to construct “EM-PCa target” network.

2.5 Protein/gene-protein/gene interaction (PPI) network analysis

Protein/gene-protein/gene interaction (PPI) network was made through the string database, and the intersection was evaluated with the plug-in “cytonca” to obtain the protein–protein interaction network core. Cytonca uses three centrality measures for data selection, which including degree centrality (DC), closeness centrality (CC), and betweenness centrality (BC). Firstly, the database is selected according to the standard of “DC ≥ 2 times the median”, and then the core target is selected according to the standard of “DC, BC, and CC ≥ the median” [6].

2.6 Gene Ontology (GO) analysis and Kyoto Encyclopedia of genes and genomes (KEGG) pathway analysis

R 4.0.5 software and LC-BIO online analysis platform were used to perform GO enrichment analysis and KEGG analysis on the targets of EM regulating PCa. “Homo sapiens” was used as the limited species, so as to obtain the results of GO enrichment analysis and KEGG pathway enrichment analysis.

2.7 Molecular docking and visualization of docking results

Download the 3D structure of emodin through PubChem database, take the core target obtained by “cytonca” plug-in as the receptor protein, find its accurate protein name through UniProt database, and then download the 3D structure of the core target molecule through PDB database. Import pymol 2.4.0 software for dehydration, ligand removal, hydrogenation and other treatments, and minimize the energy of the docking target. Then, the core gene was processed into mol2 format with the help of openbable 2.4.1 software, and then the molecular docking between EM and the core targets were carried out with the help of Discovery Studio 2019 software. The lower the energy of molecular docking, the more stable the conformation of receptor molecule in docking. Finally, openbabel 2.4.1 and paymol 2.4.0 software were used for visual analysis of docking results.

2.8 Molecular dynamics simulation

The “CHARMM” and “simulation protocols” modules of Discovery Studio 2019 software were used to add charmm36 force field to the “TP53/EM” molecular structure model constructed by precise docking, and then the model was solvated, that is, the model was placed in a 110 Å × 110 Å × 110 Å aqueous solution cubic box. The molecular dynamics simulation parameters are set as follows: the temperature increases gradually from 50 to 300 K, and the simulation time is 220 PS, including 20 ps in the equilibrium phase and 2 ns in the simulation sampling phase.

2.9 Expression of key genes and survival prognosis analysis

The gene expression profiling interactive analysis (GEPIA) is a multidimensional cancer genomics dataset that integrates a large amount of data from the Cancer Genome Atlas (TCGA) and the genotype tissue expression project (GTEX). GEPIA database was used to screen the expression differences between normal prostate cancer tissues and PCa tissues. The parameters were set as default, and P < 0.05 was considered statistically significant. According to the expression levels of 6 core genes, PCa samples were divided into two groups (low expression group and high expression group). Kaplan Meier-plotter online database can be used to evaluate the prognostic impact of different genes on different cancers. Overall survival (OS) was considered as the time to death or the last follow-up time since the initial diagnosis of PCa.

2.10 Cell level experimental verification2.10.1 Cell lines and culture

The PC-3 cells were acquired from the Stem Cell Bank of the Chinese Academy of Sciences. As a culture medium, Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS) and a combination of antibiotics, specifically 100 U/mL of penicillin and 100 μg/mL of streptomycin, was employed respectively. The cells were then maintained in an incubator set at 37 ℃ and 5% CO2 concentration.

2.10.2 Cell proliferation and inhibition experiment

Inoculate PC-3 cells at a density of 1 × 104 cells/mL into a 96 well culture plate, with 190 μL per well. Incubate overnight in a constant temperature saturated incubator containing 5% CO2 at 37 °C and divide into two groups: the experimental group is treated with 10 μL of different concentrations (0.1 ~ 1.6 μmol/L) of emodin, while the control group (Con) is treated with 10 μL of DMSO diluted in the same proportion as the corresponding emodin. Three parallel wells are set up in each group. After continuing to cultivate for 48 h, observe the cell state using an inverted optical microscope. After the cell culture is completed, centrifuge at 1000r/min for 10 min, aspirate and discard the culture medium, and add a mixture of 100 μL serum-free DMEM medium and 5 mg/mL MTT in a volume ratio of 9:1 to each well. Continue to culture for 4 h. After terminating the culture, centrifuge at 1500 r/min for 8 min, carefully remove the upper layer of liquid, add 150 μL DMSO to each well, shake at low speed for 10 min on a shaker to completely dissolve the crystals, measure the optical density (OD) of each well at a wavelength of 490 nm on an enzyme-linked immunosorbent assay (ELISA) reader, and calculate the cell proliferation inhibition rate (R) according to formula (1). A microplate reader measured the absorbance value of each well at 490 nm, and subsequently, the cell proliferation inhibition rate and half-maximal inhibitory concentration (IC50) were computed using GraphPad Prism 9 software.

$$} = \left( - }_}}} /}_}}} } \right) \, \times 00\%$$

(1)

2.10.3 RT-PCR validation of mRNA expression of signaling pathway related genes

Cells were seeded in 6-well cell culture plates at 2 × 105 cells/mL, with 2 mL per well. After complete cell adhesion, the experimental group was treated with 100 μL of active compound/active extract to achieve a final concentration of 20 μg/L. The control group was treated with DMSO diluted in the same proportion as the active compound which named EM. Three wells were set up in each group. After 48 h of cultivation, collect the cells, centrifuge at 1000 r/min for 8 min, discard the supernatant culture medium, wash three times with 3 mL of pre-cooled PBS, add 1 × binding buffer to suspend the cells, and make the cell concentration 1 × 106 cells/mL.

After collecting cells, total RNA was extracted from each group of cells using the Trizol method, and the content and purity of RNA were measured using an ultra micro spectrophotometer. Take 1 μg of total RNA and synthesize cDNA according to the instructions of the first strand cDNA synthesis kit. Use this as a template for reverse transcription-polymerase chain reaction (RT-PCR) amplification, with beta(β)-actin as the internal reference. The primer sequences used for the RT-PCR reaction are shown in Table 2. Amplification procedure: Pre-denaturation at 95 ℃ for 2 min, denaturation at 94 ℃ for 30 s, refolding at 60 ℃ for 1 min, extension at 72 ℃ for 60 s, and total extension at 72 ℃ for 10 min after 32 cycles. After the reaction, the PCR product is electrophoretic by 1% agarose gel, scanned and photographed by digital gel imaging, and analyzed the band.

Table 2 Primers used for RT-PCR2.10.4 Western blotting validation of protein expression of signaling pathway related genes

The Western blotting method was employed to assess the expression levels of proteins associated with anti-PCa. In the control group, 20 μL of DMSO was administered to PC-3 cells. Conversely, PC-3 cells in the drug intervention group received 15 μL of EM, with final concentrations varying at 10, 20, 40, 80, and 160 µmol/L respectively. Following a 48 h incubation period, the cells were harvested on ice, and total protein extraction was conducted using the radio immuno precipitation assay (RIPA) lysis buffer assay kit for each group. Protein quantification was then performed using the bicinchoninic acid assay (BCA) assay, sourced from Wuhan Servicebio Technology Co., Ltd., China. Each protein sample, weighing 20 μg, was denatured by heating at 100 ℃ for 12 min, separated via 10% sodium dodecyl sulfate -polyacrylamide gel electrophoresis (SDS-PAGE), and transferred onto polyvinylidene fluoride (PVDF) immobilon membranes.

For the Western blotting process, primary antibodies targeting rabbit/mouse/rat/human cysteine-aspartate protease 3 (CASP3, CAT. NO: YM8058), tumor necrosis factor (TNF, CAT. NO: YM3477), interleukin 1 beta (IL1B, CAT. NO: GB-122059), peroxisome proliferator-activated teceptor gamma (PPARG, CAT. NO: GB11164), human recombinant protein (MYC, CAT. NO: YM-8143), tumor protein 53 (TP53, CAT. NO: 10442-1-AP), and beta-actin (β-actin, CAT. NO: 66009-1-Ig) were used, each at a 1:5000 dilution. The secondary antibody utilized was goat anti-rabbit IgG (H + L) (CAT. NO: SA00001-2) and goat anti-mouse IgG (H + L) (CAT. NO: SA00001-1), at a 1:2000 dilution, sourced from Proteintech Group, Inc, China, Immunoway Co., Ltd, China, and Servicebio Tecnology Co., Ltd, China, respectively. The membranes were incubated with the corresponding primary antibody at room temperature for 1 h, followed by overnight incubation at 4℃. After washing the membranes, the secondary antibody was added, and the membranes were incubated on a shaking table for 2 h. Subsequently, the membranes were washed with TBST three times, with each wash lasting 10 min. The ECL imaging system was used for luminescent development. After replacing the membrane with a full one, the laboratory's costs increased substantially. As well as there are some labor costs need to be considered. When film cutting was the norm, a single film could be used to its maximum capacity, allowing for the detection of multiple indicators. Based on the above reasons, we generally use trimmed membranes to reduce labor and time costs. Therefore, trimmed membranes were finally used in the manuscript.

The experiment was repeated a minimum of three times, and the values obtained were measured and analyzed. The gray values of the bands were quantified using Image J 2.0 software (National Institutes of Health, https://imagej.net/software/fiji/downloads).

2.11 Statistical analysis

Statistical analysis was performed on all data using SPSS 21.0 software and GraphPad Prism 9.0, and the results were expressed as mean ± standard deviation. Single factor analysis of variance was used for comparison between multiple groups, with P < 0.05 indicating statistically significant differences.