Objective. We analyzed the efficacy and pharmacological mechanisms of action of Zhen Ren Yang Zang decoction (ZRYZD) on ulcerative colitis (UC) using meta-analysis and network pharmacology. Methods. The major databases were searched for randomized controlled trials of ZRYZD for the treatment of UC. Meta-analysis of the efficacy of ZRYZD on UC was conducted using RevMan software. Active compounds and target genes were acquired using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform. UC-related genes were searched using the GeneCards database. Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using RGUI. A compound-target network was constructed using Cytoscape software, and a protein-protein interaction network was constructed using the STRING database. Molecular docking simulations of the macromolecular protein targets and their corresponding ligand compounds were performed using the AutoDock tool and AutoDock Vina software. Results. Meta-analysis revealed that the total effective rate and recovery rate of clinical efficacy were significantly higher in the experimental group than those of the control group. The screening identified 169 active compounds and 277 active target genes for ZRYZD. The 277 active target genes were compared with the 4,798 UC-related genes. This identified 187 active target genes of ZRYZD for UC that correlated with 138 active compounds. GO functional enrichment and KEGG pathway enrichment analyses were performed, and compound-target and protein-protein interaction networks were constructed. The key compounds and key target proteins were then selected. Finally, target protein binding with the corresponding compound was analyzed using molecular docking. Conclusion. Our findings demonstrate the effectiveness and safety of ZRYZD for the treatment of UC and provide insight into the underlying pharmacological mechanisms of action. Furthermore, key compounds were identified, laying the foundation for future studies on ZRYZD for the treatment of UC.
1. Introduction
Ulcerative colitis (UC) is a common chronic intestinal disease of unknown etiology and is associated with multifactorial, multilevel, and nonspecific inflammation [1]. The clinical manifestations of UC include diarrhea, abdominal pain, and stool containing mucus, pus, and/or blood. The incidence of UC is 1.2–20.3 per 100,000 persons per year, and its prevalence is 7.6–246.0 per 100,000 per year [2].
The lesions in UC involve the rectum and sigmoid colon, sometimes throughout the whole colon, mainly invading the colorectal mucosa and submucosa and showing phased and diffuse distribution, resulting in a propensity for relapse [3]. Mesalazine, immunosuppressants, and corticosteroids are clinically used to treat UC; however, these drugs are needed chronically and can cause adverse reactions, and relapse is common after cessation [4, 5]. Traditional Chinese medicine (TCM) has a long history of treating diarrhea and dysentery and is compliant with the concept of individualized treatment [6]. Recently, TCM has been used to treat UC, with positive outcomes [7–9].
Zhen Ren Yang Zang decoction (ZRYZD), first used during the Song Dynasty as the basic prescription for the treatment of diarrhea, primarily consists of yingsuke, roudoukou, hezi, rougui, dangshen, baizhu, danggui, baishao, muxiang, and gancao (scientific names: Pericarpium Papaveris (PP), Semen Myristicae (SM), Fructus Chebulae (FC), Cortex Cinnamomi (CC), Radix Codonopsis (RC), Rhizoma Atractylodis Macrocephalae (RAM), Radix Angelicae Sinensis (RAS), Radix Paeoniae Alba (RPA), Radix Aucklandiae (RA), and Radix Glycyrrhizae (RG), respectively) [10]. According to TCM theory, PP, SM, and FC are monarch and minister herbs and are regarded as the main components of ZRYZD.
ZRYZD acts as an intestinal astringent, has antidiarrheal properties, and warms the spleen and kidney. Several clinical studies have reported that the clinical effect of ZRYZD in the treatment of UC is remarkable [10–12]. Previous basic research studies suggest that ZRYZD can ameliorate colonic mucosal dysfunction and that it has a favorable therapeutic action in trinitrobenzene sulfonic acid-induced colitis [13]. Therefore, the clinical efficacy and pharmacology of ZRYZD for the treatment of UC merit further investigation.
In this study, we analyzed the efficacy and pharmacological mechanisms of action of ZRYZD for the treatment of UC using meta-analysis and network pharmacology. First, we screened randomized controlled trials (RCTs) that investigated the clinical efficacy of ZRYZD for UC and performed a meta-analysis to assess clinical efficacy and safety. Next, we identified the active compounds in ZRYZD and its target genes and compared them with UC-related genes to identify the active target genes involved in the therapeutic action of ZRYZD for UC. Subsequently, Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed. The compound-target, key compound-target, and protein-protein interaction (PPI) networks were constructed, and the key compounds and key target proteins were selected. Finally, target protein binding with the corresponding compound was analyzed using molecular docking analysis.
2. Materials and Methods
2.1. Screening of RCTs of the Efficacy of ZRYZD in the Treatment of UC
PubMed, the Cochrane Central Register of Controlled Trials, Chinese National Knowledge Infrastructure, Wanfang Data, the Chongqing VIP database, and the Chinese Biomedical Literature database, from the establishment of each database to August 15, 2021, were searched using the terms “Zhen Ren Yang Zang decoction” and “ulcerative colitis.” These terms were searched in titles, abstracts, and the full text. We also checked references and citations in the identified studies manually to include other potentially eligible trials until no additional articles could be identified.
The inclusion criteria included the following: the study was designed as a RCT, the participants had a diagnosis of UC, ZRYZD was used in the experimental group, the control group used conventional therapy without TCM therapy, and there were clear outcome indicators. Exclusion criteria included the following: the outcome data of the study were incomplete and the ZRYZD prescription lacked the main components.
2.2. Data Extraction, Quality Assessment, and Meta-Analysis
Two reviewers independently extracted the information from the included studies. The main information included the first author, year of publication, number of patients in each group, methods of intervention in the experimental and control groups, and outcome data.
The Cochrane Reviewers’ Handbook of guidelines was used to assess the risk of bias. The following seven criteria were used: random sequence generation; allocation concealment; patient blinding; assessor blinding; incomplete outcome data; selective outcome reporting; other risks of bias [14].
These main data were input into the Cochrane Collaboration’s RevMan 5.3 software for meta-analysis to analyze the efficacy of ZRYZD on UC.
2.3. Screening of Active Compounds in ZRYZD
The compounds in the ten component herbs (PP, SM, FC, CC, RC, RAM, RAS, RPA, RA, and RG) were obtained using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) (https://tcmspw.com/tcmsp.php) [15]. TCMSP is a unique systems pharmacology platform of Chinese herbal medicines that captures the relationships between drugs, targets and diseases. Oral bioavailability (OB) and drug-likeness (DL) are commonly used in network pharmacology to define active compounds. OB represents the rate the compound is absorbed into the body, and DL represents the degree to which a compound contains specific functional groups or has physical characteristics similar to existing drugs [16]. We used OB ≥ 30% and DL ≥ 0.18 to screen for the active compounds (the DLs of compounds in CC are generally low, and we, therefore, set DL ≥ 0.10 as the filter criteria) [17].
2.4. Screening of the Target Genes of Active Compounds
The corresponding target genes of the active compounds were also retrieved from the TCMSP. Setting the search format as “homo sapiens,” the target genes were imported into the UniProt Knowledgebase, a comprehensive resource for protein sequences and annotation data (https://www.uniprot.org/) [18]. Then, the human official gene symbols were identified and were considered the active target genes of ZRYZD.
2.5. Acquisition of UC-Related Genes and Identification of Active Target Genes of ZRYZD Acting on UC
“Ulcerative colitis” was used as the keyword in the GeneCards database (https://www.genecards.org/). The GeneCards database is a searchable, integrative database providing comprehensive, user-friendly information on all annotated and predicted human genes [19], from which the UC-related genes were searched and acquired. Then, the active target genes of ZRYZD were compared with the UC-related genes, and the intersecting genes were defined as the active target genes of ZRYZD acting on UC.
2.6. GO Functional Enrichment and KEGG Pathway Enrichment Analyses
The RGUI 3.6.1 and org.Hs.eg.db packages were used to obtain the entrezIDs of the active target genes. Then, RGUI and the clusterProfiler package were used to perform the GO functional enrichment analyses, which included the biological process (BP), molecular function (MF), cellular component (CC) analysis, and the KEGG pathway enrichment analysis [20].
2.7. Construction of the Compound-Target Network
Cytoscape 3.6.0 software and its NetworkAnalyzer tool function were used to construct and analyze the compound-target network. Nodes represent compounds and target genes, and edges represent the relationships between them. According to the degree of connection between the compound and the target gene (the more the connections, the higher the degree value), the compounds and target genes in the network were subject to further analysis [21].
2.8. Construction of the PPI Network
A PPI network was constructed after introducing the active target genes into the STRING database. The STRING database supports functional discovery in genome-wide experimental datasets (https://string-db.org/) [22]. Defining the research species as “homo sapiens” and the lowest interaction score of 0.4, a PPI network was obtained. Then, the PPI network data were used to perform topology analysis, and the key target proteins of ZRYZD acting on UC were selected according to the degree values of each target protein (the more the connections, the higher the degree value) using Cytoscape 3.6.0 software and its NetworkAnalyzer tool [21].
2.9. Verification of Molecular Docking
The binding of the target protein with its corresponding compound was analyzed using molecular docking. The structures of the target proteins were obtained from the RCSB PDB database (https://www.rcsb.org/), and the compounds were obtained from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/). Molecular docking simulations of target proteins with their corresponding compounds were performed using AutoDockTool 1.5.6 and AutoDock Vina software [23, 24].
2.10. Statistical Analysis
RevMan 5.3 software was used for meta-analysis, and dichotomous data were expressed as the odds ratio (OR) with 95% confidence interval (CI), and continuous data were expressed as mean difference (MD) with 95% CI. Heterogeneity was assessed with the Q-test (-value and I²), and indicated heterogeneity across studies. Studies with I² < 50% were considered to have no heterogeneity, and those with I² ≥ 50% were considered to have heterogeneity. If no heterogeneity was detected, the fixed effects model was used as the pooling method; otherwise, the random effects model was used [25, 26]. was considered statistically significant.
Using the bioinformatics tools of the platforms and software mentioned above, some statistical analyses for network pharmacology were performed automatically. In the GO functional enrichment and KEGG pathway enrichment analyses, an adjusted (q-value) < 0.05 was considered statistically significant.
3. Results
3.1. Screened RCTs Investigating the Efficacy of ZRYZD for the Treatment of UC
A total of 118 studies were retrieved through database searching, and 36 studies were retained after removing duplication. According to the inclusion and exclusion criteria, a total of 31 studies were excluded after reading the title, abstract, and full text. Five RCTs [11, 12, 27–29] were included for further evaluation. The literature screening process is shown in Figure 1.