Network pharmacology Prediction
Active compounds Collection and Active Target Identification
In order to screen compounds ingredients of JDHXD, we searched all the herbs in the two databases (Traditional Chinese Medicine Database and Analysis Platform, TCMSP, https://tcmsp-e.com/; The Encyclopedia of Traditional Chinese Medicine, ETCM,http://www.tcmip.cn/ETCM/index.php) [13,14]. And we screened compounds by oral bioavailability (OB) value ≥30% and drug likeness (DL)≥0.18 as active compounds. Moreover, according to the content determination from Pharmacopoeia of the People's Republic of China (2020 Edition), We included principal components of the herbs that OB or DLfailedto meet the established conditions[15].
The potential targets of active compounds were collected from TCMSP and ETCM database. Next, we checked all the corresponding targets and translated to gene name via UniProt database (https://www.uniprot.org/)[16]. Duplicated, nonhuman, and nonstandard targets were eliminated.
CP/CPPS related targets collection
To assemble potential targets associated with CP/CPPS, we searched the DisGeNET database (https://www.disgenet.org/home/), Online Mendelian Inheritance in Man (OMIM,https://omim.org/) and The Human Gene Database (GeneCards,https://www.genecards.org/) databases[17–19]. We used "chronic prostatitis” and” chronic pelvic pain syndrome" as keyword searching three databases respectively. And after merging, we deleted duplicates to establish a CP/CPPS related targets dataset. Targets were normalized to the official gene symbols using UniProt database.
Herbs-compounds-targets-disease network construction and analysis
In order to illuminate and visualize the relationship between the active compounds and the targets, we constructed the herbs-compounds-targets-disease network by means of Cytoscape(version3.8.2, https://cytoscape.org)[20]. After collating drug and disease targets, these two target datasets were compared and filtered to identify common targets, which were defined as the targets of JDHXD in treating CP/CPPS. Then, those common targets, active compounds, herbs,and disease were input into Cytoscape software to construct herbs-compounds-targets-disease network. Next, we utilized Network Analyzer, a Cytoscape plugin, to perform topology analysis on nodes. We set 2-fold of the median degree as screening criteria to evaluate the essentiality of each node within the entire network and to confirm core active compounds.
Protein-protein interaction (PPI)analysis
The STRING database (Version11.5,https://string-db.org/) was used to investigate interaction and multi-targeted regulations of common targets[21]. we imported gene symbols of common targets into STRING database. The species was set as “Homo sapiens” and Confidence score more than 0.4 is defined as significant. Finally, the result was visualized and analysed in Cytoscape to establish PPI network. And, we used Network Analyzer to perform topology analysis and confirm hub targets.
GO function and KEGG pathwayenrichment analysis
Drug targets usually have specific biological functions, and it is important to analyze the cell component, molecular function, biological process, and biological pathways of target for predicting potential active compounds. Gene Ontology (GO) function enrichment elaborated the important functions of proteins from cell component (CC), molecular function (MF), and biological process (BP). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis show the network pathway of a particular set of genes. DAVID (Functional Annotation Bioinformatics Microarray Analysis, Version6.8,https://david.ncifcrf. gov/) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes[22]. Therefore, the common targets were imported into DAVID database to perform GO enrichment and KEGG pathway enrichment analysis. The species was only restricted to Homo sapiens. And the P value and the false discovery rate (FDR) were screening conditions. Finally, the main results of GO and KEGG pathway enrichment analysis were visualized as bubble plot by a free online data analysis platform— OmicShare (http://www.omicshare.com/).
Molecular docking verification
To validate the binding ability of between the hub targets and core active compounds, AutoDock Vina software (version 4.2, http://vina.scripps.edu/) was used to perform the molecular docking program[23]. We got the structure of the hub targes from RCSB PDB (http://www.rcsb.org/)[24]. 3D structure files of core active compounds were downloaded from TCMSP or PubChem (https://pubchem.ncbi.nlm.nih.gov/)[25]. Then, we used the PyMOL Molecular Graphics System (version 2.5.0, http://www.pymol. org/) to remove the original ligands and water, and add hydrogens to the proteins[26]. The proteins and ligands were converted into “PDBQT” format, which were imput to AutoDock Vina to conduct molecular docking. The results were imported into PyMOL for visualization and analysis of the interaction and binding mode of the active compounds.
Experimental Validation
Main reagents and instruments
Main reagents and instrumentslisted in Supporting Information Table S1.
Animals and Housing
48 Sprague Dawley (SD) healthy male rats (4-6 month-old, weighted 190 ± 20 g) were purchased from (license number: scxk (Zhe) 2019–0002). Then the rats freely ingested food and water and were allowed 1 week to acclimate to the standard laboratory conditions (12h light-dark cycle,23 ± 1°C and 60 ± 5% humidity).
JDHXD Preparation
The JDHXD contains 10 herbs obtained from the Affiliated Hospital of Jiangxi University of traditional medicine and were fully validated by Medical Products Administration of Jiangxi Province. The JDHXD was prepared according to the traditional Chinese decoction method. 10 herbs were kept in the arenaceous boiler and soaked for 40 min in 8 volumes of cold water before boiling. The mixture was then boiled for 40 min and filtered. The first filter liquor was kept, and the herbal materials were resuspended in 6 volumes of cold water, boiled for further 30 min and filtered. The two filter solutions were mixed together and concentrated 0.75 g/ml for the JDHXD group. In addition,Positive control drug(Qianliekang Tablets, NMPA approval No. Z33020303, 0.57g) was ground and added to the same amount of therapist for Qianliekang-treated group.
CP/CPPS Model Induction
SD male rats was castrated and injected estradiol benzoate (EB) (0.25 mg/ kg/ day, s.c.) for 30 days to establish EB-inducted CP/CPPS model accordance with literatures[27–29]. The detailed steps are as follows: firstly, rats were anaesthetized with 2.5% pentobarbital sodium (0.3ml/100g, i.p.), fixed in a supine position on a heating pad, and the skin of the lower abdomen and scrotum was shaved and disinfected before the surgery. Anesthetized rat was sterilized with iodophor in lower abdomen and cut with a longitudinal incision about 0.5 cm in length along medioventral line. The testicle was extruded from the scrotum on both sides, and the spermatic cord was cut after ligation. Then, sutured skin, disinfected and bandaged wound. The awakened rats were routinely fed. The wounds were wiped with iodophor every day and penicillin 200,000 U /kg was injected intramuscularly for one week. After castrating, estradiol benzoate (0.25 mg/ kg/ day, s.c.) were multipoint hypodermic injected into the back on day 2 for 30 days.
Experimental Design and Test Protocol
After the castration surgery,all rats were adaptive feeding 7 days. Then, those rats were randomly divided into six groups with 8 rats in each group:
Normal group (Normal): the rats were given subcutaneous injection of 0.25 mg/kg distilled water on the back, continuously for 30 day, then given distilled water at a dose of 100mg/kg/d by oral gavage for 30 days;
Model group (Model): the rats were induced into CP/CPPS model and daily given distilled water at a dose of 1g/kg/d by oral gavage for 30 days;
Qianliekang table-treated group (QLKT): CP/CPPS rats were given Qianliekang table at a dose of 0.45g/kg/d by oral gavage for 30 days;
Low-dose JDHXD group (JDHXD-L):CP/CPPS rats were given JDHXD at a dose of 5g/kg/d by oral gavage for 30 days;
Middle-dose JDHXD group (JDHXD-M): CP/CPPS rats were given JDHXD at a dose of 10g/kg/d by oral gavage for 30 days;
High-dose JDHXD group (JDHXD-H): CP/CPPS rats were given JDHXD at a dose of 20g/kg/d by oral gavage for 30 days.
At the end of model establishment, a mouse was randomly selected from normal group and model group, which used to confirm the successful establishment of prostatitis model by Histological analysis. At the end of the experiment, all rats were sacrificed, and the prostate and serum samples were collected for subsequent analysis.
Histological analysis
Rat’s prostate tissues were soaked and fixed in 10% neutral formalin for 24h,then eluted with PBS solution 3 times, 4 minutes each time. The fixed tissues were dehydrated and embedded in paraffin, which were sliced into 3μm paraffin sections and stored at 4℃ for later use. After that, Hematoxylin and eosin (HE) stain was performed to observe the tissue and cytological changes such as inflammatory cell infiltration level, necrotic tissue retention and shedding, and interstitial edema in the prostate tissue under an optical microscope.
Quantitative Real-time PCR detect MAPKs signaling pathway related mRNA (JNK, ERK1/2 and P38) expression level
According to manufacture's instructions, we used Trizol reagent to extract total RNA of 100 mg rat’s prostate tissues stored at -80℃. And reverse transcription was performed to synthesize cDNA, which was then amplified target gene JNK, ERK1/2 and P38 mRNA by PCR. The information of primers sequence listed in Table 2. Then, the amplified products were subjected to 1.5% agarose gel electrophoresis. The gray value of each band was analyzed by MIAS-2000 image analysis system, and the relative content of mRNA was expressed as semi-quantitative RT-PCR results by the ratio of sample targets gene to the Internal Control (GAPDH). The 2-ΔΔCt (Livak) Method is used to perform relative gene expression analysis[30].
Table 2. The information of primers sequence
Gene
|
Sequence(5’-3’) (F:Forward;R:Reverse)
|
GAPDH
|
F:ATCAACGGGAAACCCATC
|
R:GAAGACGCCAGTAGACTCCA
|
JNK
|
F:CGCCATTCTTAGTTCGCTCC
|
R:CTCTCCAGCACCCGTACATC
|
ERK1/2
|
F:TCATAGGCATCCGAGACAT
|
R:GCTCAGGGTCAGCAATCC
|
p38
|
F:TTGGACTCGGATAAGAGGATCAC
|
R:TAGGTCAGGCTCTTCCATTCG
|
Protein expression of p-JNK, p-ERK1/2 and p-P38 detected with Western Blot
The total protein concentration in the tissue homogenates was determined using a BCA protein assay kit. The first step of the sample preparation is disruption of the sample's cellular structure by grinding and cell lysis reagents (SDS). After centrifugation, the supernatant was transferred to a new 1.5 mL centrifuge tube and stored in -80℃. In addition, a 200 ul centrifuge tube was divided into a small amount of supernatant for protein concentration determination to avoid repeated freeze-thaw. Based on the Protein assay technical handbook, we prepare a set of protein standards for determining the concentration of proteins in solution to calculate the concentration of read the value at 570 nm. Calculated the protein volume required for detection according to the protein concentration determined by BCA, which were boil at 100℃ for 5 min to reduce and denature protein. Then, the proteins were separated by electrophoresis with 10% SDS polyacrylamide. After electrophoretic, transferring the proteins from the gel to the membrane (PVDF), overnight at 4℃ using 5% blocking solution. Shake and wash 3 times in PBST (PBS, 0.05% Tween 20, pH 7.4) at room temperature, rabbit anti-rat p-JNK, p-ERK1/2, p-P38 and GAPDH (1:1000,TBS), incubate at room temperature for 2 h, HRP-linked secondary antibody (1: 2000)Incubate at room temperature for 2 h, add developing liquid to photograph. The gel analysis system imaging was used to quantitatively analyze the Western blot results.
Statistical Analysis
The GraphPad Prism 8.0 was used for data analysis. The results were expressed in the form of mean ± standard deviation (SD). Student’s t-test, one-way ANOVA or two-way ANOVA methods were used. Statistically significant differences were defined as p<0.05.