Evidence-Based Complementary and Alternative Medicine

Evidence-Based Complementary and Alternative Medicine / 2019 / Article

Research Article | Open Access

Volume 2019 |Article ID 7870424 | 22 pages | https://doi.org/10.1155/2019/7870424

Network Pharmacology-Based Investigation into the Mechanisms of Quyushengxin Formula for the Treatment of Ulcerative Colitis

Academic Editor: Darren R. Williams
Received29 Jun 2019
Revised16 Sep 2019
Accepted09 Oct 2019
Published28 Dec 2019

Abstract

Objective. Ulcerative colitis (UC) is a chronic idiopathic inflammatory bowel disease whose treatment strategies remain unsatisfactory. This study aims to investigate the mechanisms of Quyushengxin formula acting on UC based on network pharmacology. Methods. Ingredients of the main herbs in Quyushengxin formula were retrieved from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. Absorption, distribution, metabolism, and excretion properties of all ingredients were evaluated for screening out candidate bioactive compounds in Quyushengxin formula. Weighted ensemble similarity algorithm was applied for predicting direct targets of bioactive ingredients. Functional enrichment analyses were performed for the targets. In addition, compound-target network, target-disease network, and target-pathway network were established via Cytoscape 3.6.0 software. Results. A total of 41 bioactive compounds in Quyushengxin formula were selected out from the TCMSP database. These bioactive compounds were predicted to target 94 potential proteins by weighted ensemble similarity algorithm. Functional analysis suggested these targets were closely related with inflammatory- and immune-related biological progresses. Furthermore, the results of compound-target network, target-disease network, and target-pathway network indicated that the therapeutic effects of Quyushengxin on UC may be achieved through the synergistic and additive effects. Conclusion. Quyushengxin may act on immune and inflammation-related targets to suppress UC progression in a synergistic and additive manner.

1. Introduction

Ulcerative colitis (UC) is a chronic and progressive immunologically mediated disease causing consecutive mucosal inflammation of the colon [1, 2]. The onset of UC is most often during young adulthood, which is well characterized by homogeneous and continuous lesions [3]. Although the incidence of UC is increasing in Asia, it is highly diagnosed in the developed countries, especially in Western Europe and North America. Previous reports showed that the overall incidence and prevalence of UC are nearly 1.2/20.3 cases and 7.6/245 per 100,000 persons per year, respectively [4, 5].

UC therapy is aimed to reduce the recurrent rate, as well as improve the life quality and minimize drug-related adverse events. Basic therapies for UC are determined based on the severity of symptoms, which are often thought as step-up approaches. To date, 5-aminosalycilates (5-ASAs) have been the mainstay for treatment of mild-to-moderate UC [6]. Though 5-ASAs are safe and have no dose-related toxicity in short-term use with a dose-response efficacy, long-term use of them might induces adverse events, such as headache, diarrhea, nausea, interstitial nephritis, and hepatitis. In addition, patients with more moderate-to-severe UC after 5-ASAs therapy are typically treated with corticosteroids, and these patients are often followed by transition to a steroid-sparing agent with a thiopurine, adhesion molecule inhibitor, or anti-tumor necrosis factor (TNF) agent [6]. However, these corticosteroid-based therapies also accompany with side effects, such as cataracts, osteopenia, avascular necrosis, insomnia, mood changes, delirium, glaucoma, and adrenal insufficiency [7, 8]. Besides, despite improved medical therapies, it is estimated that about 15% of UC patients still require proctocolectomy [9]. Therefore, it is of great significance to develop more optimized and integrated therapies for UC patients.

To date, an increasing number of traditional Chinese herbal compounds are successfully used for treating UC with less side effects, such as Gegen Qinlian decoction [10], Jianpi Qingchang decoction [11, 12], Zhikang capsule [13], Huangkui Lianchang decoction [14], and Qingchang Wenzhong decoction [15, 16]. Quyushengxin formula is mainly composed of four herbs, Panax ginseng C.A. Mey. (Araliaceae), Astragalus membranaceus (Fisch) Bunge, Pulsatilla chinensis (Bge.) Regel, and Coptis chinensis Franch. Our clinical practice demonstrated Quyushengxin formula could relieve the clinical symptoms in active stage and suppress the inflammatory reaction of UC patients and could be used for treating mild-to-moderate UC [17]. Although the therapeutic effects of Quyushengxin on UC are attractive, molecular mechanisms of its action remain to be further elucidated.

Traditional Chinese medicine- (TCM-) oriented network pharmacology provides us a novel way to unveil the molecular mechanisms of TCM through pharmacokinetic evaluation, network/pathway analysis, and target prediction [18, 19]. In this study, we tried to unveil the molecular mechanisms of Quyushengxin formula acting on UC based on network pharmacology.

2. Materials and Methods

2.1. Screening of Potential Bioactive Compounds in Quyushengxin Formula

Traditional Chinese Medicine Systems Pharmacology Database (TCMSP, http://lsp.nwu.edu.cn) is a systems pharmacology platform of Chinese herbal medicines that captures the relationships between drugs, targets, and diseases [20]. Ingredients along with their molecular weight (MW), water partition coefficient (AlogP), number of hydrogen bond donors (Hodn), number of hydrogen acceptors (Hacc), oral bioavailability (OB), Caco-2 permeability (Caco-2), blood-brain barrier (BBB), drug-likeness (DL), fractional negative accessible surface area (FASA) ,and half-life (HL), of all four herbs in Quyushengxin formula were retrieved from TCMSP. Then, absorption, distribution, metabolism, and excretion (ADME) properties, including OB, DL, and HL, were evaluated for screening out bioactive compounds. The potential bioactive compounds in Quyushengxin were predicted and sifted out via an integrated model including PreOB (for prediction of OL), PreDL (for prediction of DL), and PreHL (for prediction of HL) [21, 22]. In detail, OB value was obtained by OBioavail 1.1, and the compounds with OB ≥ 30% were selected out for further analysis [20, 23]. PreDL was utilized to calculate the DL index of compounds, and compounds with DL ≥ 0.18 were included for further research. The DL evaluation approach was constructed via both Tanimoto coefficient and molecular descriptors, and the formula is listed as follows:where X was the molecular descriptors of herbal ingredients and Y showed the average molecular properties of all molecules in the DrugBank database (http://www.drugbank.ca/).

Besides, PreHL was estimated by combining multivariable linear regression model and MLR (mixed logistic regression) algorithm [22], as follows:where R2 was the correlation coefficient of training set and Q2 was the correlation coefficient of external test sets of the model. SEE was the estimated standard deviation of training set. F was the mean square ratio. Besides, Ntraining indicated the number of chemical compounds in the training set, and Ntest indicated the number of chemical compounds in the test set. It was evidenced that there were eight descriptors satisfying the linear regression as follows: nArCO, H7m, D/Dr09, N-070, C-032, JGI6, nRC=N, and Mor02e. Finally, 4 ≤ HL ≤ 8 was defined as appropriate selection criteria for drug HL evaluation.

2.2. Prediction of the Candidate Targets of Bioactive Compounds

Weighted ensemble similarity (WES) algorithm was applied for predicting direct targets of the bioactive compounds via a large scale of drug target relationships [24]. Those targets with likelihood score ≥7 were deemed as direct targets in this study. Thereafter, candidate targets were mapped to Uniprot (http://www.uniprot.org/) for annotation and normalization.

2.3. Functional Enrichment Analyses

Gene Ontology- (GO-) biological processes (BPs) and Kyoto Encyclopedia of Genes and Genomes (KEGG, http://www.genome.jp/kegg/) pathways of the candidate targets of bioactive compounds were predicted via the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database [25] with as the criterion for significance.

2.4. Prediction of Target-Related Disease

Target-related diseases were predicted by integrating multisource databases, including Comparative Toxicogenomics Database (CTD, http://ctdbase.org/) [26], Therapeutic Target Database (TTD, http://bidd.nus.edu.sg/group/cjttd/) [27], and PharmGKB database (https://www.pharmgkb.org/) [28].

2.5. Network Construction

Three kinds of networks in this study were established using Cytoscape 3.6.0 software [29]: compound-target network (C-T network), target-disease network (T-D network), and target-pathway network (T-P network). C-T network was composed of bioactive compounds and their potential targets, which was built to reveal the drug-target interactions. T-D network was built based on the potential targets and their related diseases. The pathway information of targets was selected from the results for KEGG pathway enrichment analysis by excluding those pathways with no relevance to UC based the latest pathological information of UC. T-P network was generated based on potential targets and UC-related pathways. In the networks, the nodes represented compounds, targets, diseases, and pathways, and the edges displayed the interactions between two nodes. Furthermore, the significance of each node in the networks was assessed via one crucial topological parameter, namely, “degree,” which was defined as the total of edges related with a node [30, 31]. Degree of all nodes was analyzed using plugin NetworkAnalyzer of Cytoscape 3.6.0.

3. Results

3.1. Screening of Potential Bioactive Compounds from Four Herbs in Quyushengxin Formula

Quyushengxin formula consists of 4 main herbs: Panax ginseng C.A. Mey. (Araliaceae), Astragalus membranaceus (Fisch) Bunge, Pulsatilla chinensis (Bge.) Regel, and Coptis chinensis Franch. After retrieving from TCMSP, 190, 87, 57, and 48 ingredients were obtained for these four herbs, respectively. Based on the criteria of OB ≥ 30%, DL ≥ 0.18, and 4 ≤ HL ≤ 8, 41 potential bioactive compounds, including quercetin, ursolic acid, kaempferol, β-sitosterol, and rutin, were sifted out (Table 1), which accounted for 10.73% of all 382 ingredients in Quyushengxin.


IDCompoundsStructureOB (%)DLHLDegreeHerb

mol01Quercetin46.430.2814.4073Coptis chinensis Franch
Astragalus membranaceus (Fisch) Bunge

mol02Ferulic acid39.560.062.387Coptis chinensis Franch

mol03Palmatine64.600.652.259Coptis chinensis Franch

mol04Jatrorrizine19.650.594.219Coptis chinensis Franch

mol05Berberine36.860.786.578Coptis chinensis Franch
mol06Columbamine26.940.595.219Coptis chinensis Franch

mol07Coptisine30.670.869.338Coptis chinensis Franch

mol08Worenine45.830.878.416Coptis chinensis Franch

mol09Magnoflorine0.480.556.228Coptis chinensis Franch

mol10Berberrubine35.740.736.468Coptis chinensis Franch
mol11Epiberberine43.090.786.107Coptis chinensis Franch

mol12(R)-Canadine55.370.776.419Coptis chinensis Franch

mol13Berlambine36.680.827.339Coptis chinensis Franch

mol14Corchoroside A_qt104.950.786.682Coptis chinensis Franch
mol15Tetrandrine26.640.104.779Coptis chinensis Franch

mol16β-Sitosterol36.910.755.3615Panax ginseng C.A. Mey. (Araliaceae)
Pulsatilla chinensis (Bge.) Regel

mol17Kaempferol41.880.2414.7426Panax ginseng C.A. Mey. (Araliaceae)

mol18Stigmasterol43.830.765.5710Panax ginseng C.A. Mey. (Araliaceae)G
Pulsatilla chinensis (Bge.) Regel

mol19β-Elemene25.630.066.328Panax ginseng C.A. Mey. (Araliaceae)
mol20Ginsenoside Ro_qt17.620.767.501Panax ginseng C.A. Mey. (Araliaceae)

mol21Dianthramine40.450.205.143Panax ginseng C.A. Mey. (Araliaceae)

mol22Arachidonate45.570.207.565Panax ginseng C.A. Mey. (Araliaceae)

mol23Ginsenoside La_qt15.700.785.201Panax ginseng C.A. Mey. (Araliaceae)
mol24Ginsenoside rh236.320.5611.089Panax ginseng C.A. Mey. (Araliaceae)

mol25Ginsenoside-Rh3_qt13.090.766.221Panax ginseng C.A. Mey. (Araliaceae)

mol26Ginsenoside-Rh4_qt31.110.786.971Panax ginseng C.A. Mey. (Araliaceae)

mol27Malkangunin57.710.634.091Panax ginseng C.A. Mey. (Araliaceae)
mol28Alexandrin_qt36.910.755.531Panax ginseng C.A. Mey. (Araliaceae)

mol29Ginsenoside rf17.740.244.665Panax ginseng C.A. Mey. (Araliaceae)

mol30Hederagenin36.910.755.356Astragalus membranaceus (Fisch) Bunge

mol31Isorhamnetin49.600.3114.3410Astragalus membranaceus (Fisch) Bunge
Pulsatilla chinensis (Bge.) Regel
mol327-O-methylisomucronulatol74.690.302.9811Astragalus membranaceus (Fisch) Bunge

mol33Rutin3.200.686.2215Astragalus membranaceus (Fisch) Bunge

mol341,7-Dihydroxy-3,9-dimethoxy pterocarpene39.050.487.955Astragalus membranaceus (Fisch) Bunge

mol35Isoferulic acid50.830.062.457Astragalus membranaceus (Fisch) Bunge
mol36Betulinic acid55.380.788.871Pulsatilla chinensis (Bge.) Regel

mol37Oleanolic acid29.020.765.566Pulsatilla chinensis (Bge.) Regel

mol38Sitosteryl acetate40.390.856.341Pulsatilla chinensis (Bge.) Regel

mol39Lanosterol42.120.755.841Pulsatilla chinensis (Bge.) Regel
mol403-beta,23-Dihydroxy-lup-20(29)-ene-28-O-alpha-L-rhamnopyranosyl-(1-4)-beta-D-glucopyranosyl(1-6)-beta-D-glucopyranoside_qt37.590.796.701Pulsatilla chinensis (Bge.) Regel

mol41Ursolic acid16.770.755.2835Pulsatilla chinensis (Bge.) Regel

3.2. Establishment of C-T Network

Candidate targets of the 41 bioactive compounds were predicted via WES algorithm. A total of 367 potential targets for these 41 bioactive compounds were obtained. After removing the overlapping targets, 94 candidate proteins were reserved. Then, C-T network was built by Cytoscape 3.6.0 which contains 367 connections between 41 compounds and corresponding 94 candidate targets (Figure 1). The degrees of the 41 bioactive compounds in the C-T network were calculated and are displayed in Table 1. The average degree of targets per compound was 4.7, indicating multitarget functions of Quyushengxin formula. Among the 41 bioactive compounds, 8 of them showed a high degree (degree > 10). Quercetin possessed the highest degree of targets (degree = 73), followed by ursolic acid (degree = 35), kaempferol (degree = 26), β-sitosterol (degree = 15), rutin (degree = 15), 7-O-methylisomucronulatol (degree = 11), stigmasterol (degree = 10), and isorhamnetin (degree = 10).

The degree of the candidate targets was also calculated and displayed in Table 2. Eight out of the 94 compounds possessed a degree larger than 10, including ESR1 (estrogen receptor 1, degree = 34), PTGS2 (prostaglandin-endoperoxide synthase 2, degree = 27), NOS2 (nitric oxide synthase 2, degree = 25), PTGS1 (degree = 23), PPARG (peroxisome proliferator-activated receptor gamma, degree = 21), NOS3 (degree = 21), ESR2 (degree = 17), and KCNH2 (Potassium Voltage-Gated Channel Subfamily H Member 2, degree = 13).


IDUniProtProtein namesGene namesDegreeOrganism

1P35228Nitric oxide synthase, inducibleNOS225Homosapiens
2P23219Prostaglandin G/H synthase 1PTGS123Homosapiens
3P03372Estrogen receptorESR134Homosapiens
4P37231Peroxisome proliferator-activated receptor gammaPPARG21Homosapiens
5P35354Prostaglandin G/H synthase 2PTGS227Homosapiens
6Q92731Estrogen receptor betaESR217Homosapiens
7P11388DNA topoisomerase 2-alphaTOP2A5Homosapiens
8P16389Potassium voltage-gated channel subfamily H member 2KCNH213Homosapiens
9P08709Coagulation factor VIIF76Homosapiens
10P29474Nitric-oxide synthase, endothelialNOS321Homosapiens
11P27338Amine oxidase [flavin-containing] BMAOB5Homosapiens
12Q04206Transcription factor p65RELA6Homosapiens
13P00533Epidermal growth factor receptorEGFR1Homosapiens
14P31749RAC-alpha serine/threonine-protein kinaseAKT12Homosapiens
15P15692Vascular endothelial growth factor AVEGFA2Homosapiens
16P24385G1/S-specific cyclin-D1CCND13Homosapiens
17P10415Apoptosis regulator Bcl-2BCL25Homosapiens
18P01100Proto-oncogene c-FosFOS3Homosapiens
19P38936Cyclin-dependent kinase inhibitor 1CDKN1A4Homosapiens
20P55211Caspase-9CASP94Homosapiens
21P00749Urokinase-type plasminogen activatorPLAU4Homosapiens
22P0825372 kDa type IV collagenaseMMP22Homosapiens
23P14780Matrix metalloproteinase-9MMP92Homosapiens
24P22301Interleukin-10IL101Homosapiens
25P01133Proepidermal growth factorEGF1Homosapiens
26P06400Retinoblastoma-associated proteinRB12Homosapiens
27P01375Tumor necrosis factorTNF6Homosapiens
28P05412Transcription factor AP-1JUN4Homosapiens
29P05231Interleukin-6IL-63Homosapiens
30P42574Caspase-3CASP37Homosapiens
31P04637Cellular tumor antigen p53TP534Homosapiens
32P11926Ornithine decarboxylaseODC11Homosapiens
33Q14790Caspase-8CASP83Homosapiens
34P00441Superoxide dismutase [Cu-Zn]SOD12Homosapiens
35P17252Protein kinase C alpha typePRKCA2Homosapiens
36P03956Interstitial collagenaseMMP13Homosapiens
37P42224Signal transducer and activator of transcription 1-alpha/betaSTAT12Homosapiens
38P04626Receptor tyrosine-protein kinase erbB-2ERBB21Homosapiens
39P09601Heme oxygenase 1HMOX13Homosapiens
40P05177Cytochrome P450 1A2CYP1A22Homosapiens
41P01106Myc proto-oncogene proteinMYC1Homosapiens
42P05362Intercellular adhesion molecule 1ICAM14Homosapiens
43P01584Interleukin-1 betaIL1B5Homosapiens
44P13500C-C motif chemokine 2CCL21Homosapiens
45P19320Vascular cell adhesion protein 1VCAM12Homosapiens
46P10145Interleukin-8CXCL82Homosapiens
47P05771Protein kinase C beta typePRKCB2Homosapiens
48O15392Baculoviral IAP repeat-containing protein 5BIRC52Homosapiens
49P04792Heat shock protein beta-1HSPB11Homosapiens
50P01137Transforming growth factor beta-1TGFB13Homosapiens
51P60568Interleukin-2IL22Homosapiens
52Q16678Cytochrome P450 1B1CYP1B12Homosapiens
53P00750Tissue-type plasminogen activatorPLAT1Homosapiens
54P01579Interferon gammaIFNG4Homosapiens
55P09917Arachidonate 5-lipoxygenaseALOX53Homosapiens
56P60484Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTENPTEN1Homosapiens
57P05164MyeloperoxidaseMPO1Homosapiens
58Q9UNQ0ATP-binding cassette subfamily G member 2ABCG21Homosapiens
59P09211Glutathione S-transferase PGSTP13Homosapiens
60Q16236Nuclear factor erythroid 2-related factor 2NFE2L21Homosapiens
61P15559NAD(P)H dehydrogenase [quinone] 1NQO12Homosapiens
62P09874Poly [ADP-ribose] polymerase 1PARP11Homosapiens
63P35869Aryl hydrocarbon receptorAHR2Homosapiens
64P19875C-X-C motif chemokine 2CXCL21Homosapiens
65O96017Serine/threonine-protein kinase Chk2CHEK21Homosapiens
66Q07869Peroxisome proliferator-activated receptor alphaPPARA1Homosapiens
67P02741C-reactive proteinCRP1Homosapiens
68P02778C-X-C motif chemokine 10CXCL101Homosapiens
69Q9NS23Ras association domain-containing protein 1RASSF11Homosapiens
70P17936Insulin-like growth factor-binding protein 3IGFBP31Homosapiens
71P01344Insulin-like growth factor IIIGF21Homosapiens
72P21860Receptor tyrosine-protein kinase erbB-3ERBB31Homosapiens
73P09488Glutathione S-transferase Mu 1GSTM12Homosapiens
74P282235-Hydroxytryptamine 2A receptorHTR2A4Homosapiens
75P84022Mothers against decapentaplegic homolog 3SMAD31Homosapiens
76P08588Beta-1 adrenergic receptorADRB13Homosapiens
77P29466Caspase-1CASP12Homosapiens
78P18509Pituitary adenylate cyclase-activating polypeptideADCYAP11Homosapiens
79O95456Proteasome assembly chaperone 1PSMG11Homosapiens
80P05112Interleukin-4IL-41Homosapiens
81P00325Alcohol dehydrogenase 1BADH1B1Homosapiens
82P28702Retinoic acid receptor RXR-betaRXRB1Homosapiens
83P04040CatalaseCAT1Homosapiens
84P01308InsulinINS1Homosapiens
85P21731Thromboxane A2 receptorTBXA2R1Homosapiens
86P07858Cathepsin BCTSB1Homosapiens
87P40763Signal transducer and activator of transcription 3STAT31Homosapiens
88Q00534Cell division protein kinase 6CDK61Homosapiens
89P09038Heparin-binding growth factor 2FGF21Homosapiens
90P15336Cyclic AMP-dependent transcription factor ATF-2ATF21Homosapiens
91P04141Granulocyte-macrophage colony-stimulating factorCSF21Homosapiens
92P17677NeuromodulinGAP431Homosapiens
93P18031Tyrosine-protein phosphatase nonreceptor type 1PTPN11Homosapiens
94P30279G1/S-specific cyclin-D2CCND21Homosapiens

3.3. GO-BP Analysis

To further validate whether biological processes enriched by candidate targets as mentioned above were correlated with UC, GO-BP enrichment analysis was performed via DAVID. The top 20 significant GO-BP terms are shown in Figure 2. Most of them were strongly associated with inflammatory- and immune-related BPs such as “positive regulation of interleukin-6 biosynthetic process,” “regulation of inflammatory response,” “immune response,” and “positive regulation of T-cell proliferation.” In short, the 41 bioactive compounds in Quyushengxin formula may act on 94 candidate targets with inflammatory- and immune-related effects to affect UC pathogenesis.

3.4. Establishment of T-D Network

Target-related diseases were predicted by mapping them to integrating multisource databases, including CTD, TTD, and PharmGKB. A T-D network consisting of 90 targets and 4 kinds of diseases was built (Figure 3). The four diseases were digestive system disease (degree = 60), pathology (degree = 49), cancer (degree = 23), and signs and symptoms (degree = 14).

3.5. T-P Network Evaluation

KEGG pathway enrichment analysis was performed for the 94 targets, and T-P network was built. Results displayed that 79 targets could be further mapped to 78 pathways, including “mTOR signaling pathway,” “T-cell receptor signaling pathway,” “JAK-STAT signaling pathway,” and “FOXO signaling pathway” (Figure 4). The average degree of targets was 6.85, and the average degree of pathway was 2.8. In addition, 71 candidate targets could be mapped to several pathways (≥5), suggesting that these targets might mediate the cross-talk and interactions between different pathways. Besides, those pathways (70/78) mapped by multiple targets (≥8) might be the main factors for UC development and progression. These pathways were further divided into five function modules, including inflammatory regulation, immune regulation, metabolic regulation, bacterial infection or mycosis and other function.

3.6. Establishment of Compound-Target-Function Module Network

By combing the networks above, a compound-target-function module network was built, which included 140 nodes (5 function modules, 41 compounds and 95 targets) and 653 edges (Figure 5).

3.7. Details of 4 UC-Related Pathways from T-P Network Analysis

To further unveil the multi-targets mechanisms of Quyushengxin formula in the treatment of UC, an integrated “UC-related pathway” was established according to the key pathways from the T-P network analysis. UC-related pathways as shown in Figure 6 were composed of four pathways, including “T cell receptor signaling pathway” (hsa04660), “FOXO signaling pathway” (hsa04068), “JAK-STAT signaling pathway” (hsa04630) and “mTOR signaling pathway” (hsa04150). Those targets of the integrated “UC-related pathways” displayed the functional relationship with the UC-related proteins. UC-related pathways can be divided into three modules: immunology module, metabolism module and cell apoptosis-related module. Immunology module consisted of “T cell receptor signaling pathway” (hsa04660), and metabolism module consisted of “FOXO signaling pathway” (hsa04068). Cell apoptosis-related module was comprised of “JAK-STAT signaling pathway” (hsa04630) and “mTOR signaling pathway” (hsa04150). Taken together, Quyushengxin formula may well regulate immunology progress, metabolism progress and cell apoptosis progress to suppress UC progression.

4. Discussion

TCM has the advantages of high treatment efficacy and low treatment cost and side effect in the treatment of several diseases, including UC in China for several thousands of years [3234]. After preliminary screening based on ADME properties, 41 potential bioactive compounds of Quyushengxin were screened out. Thereafter, 94 candidate targets of these 41 bioactive compounds were predicted for further analysis. Functional enrichment analyses suggested that these targets were closely related with inflammatory- and immune-related biological processes. Besides, a C-T network, a T-D network, a T-P network, and a compound-target-function module network were built. These networks indicated that the therapeutic effects of Quyushengxin on UC may be achieved through the synergistic and additive effects on multiple molecules and multiple pathways with immune and inflammatory effects to treat UC.

Previous reports showed that the TCMSP-based method was reliable for screening out bioactive compounds of TCM for treatment of thrombosis [35], gastric precancerous lesions [36], cardiocerebrovascular disease [37], and rheumatoid arthritis [38]. In this study, 41 bioactive compounds of Quyushengxin formula were selected out by using TCMSP database in combination with ADME properties. Most of the 41 compounds have been reported to have anti-inflammatory and immune-regulatory effects. For example, quercetin (mol01, OB = 46.43%, DL = 0.28, HL = 14.40) could inhibit lipopolysaccharide- (LPS-) induced interleukin- (IL-) 6 production [39], TNF-α production, and IL-8 production [40, 41] to exert anti-inflammatory effect. Besides, ursolic acid (mol17, OB = 16.77%, DL = 0.75, HL = 5.28) was reported to have human neutrophil elastase inhibitory effect both in vitro and in vivo [42]. Kaempferol (mol17, OB = 41.88%, DL = 0.24, HL = 14.74) was reported to significantly reduce the overproduction of TNF-α, IL-1β, IL-6, intercellular adhesion molecule- (ICAM-) 1, and vascular cell adhesion molecule- (VCAM-) 1 induced by LPS [43]. In addition, β-sitosterol (mol16, OB = 36.91%, DL = 0.75, HL = 5.36) and rutin (mol33, OB = 3.2%, DL = 0.68, HL = 6.22) were shared with significant anti-inflammatory activity [44, 45]. Above all, TCMSP-based systems pharmacology sifted out 41 potential bioactive compounds in Quyushengxin formula for treatment of UC.

Eight of the 94 targets have degree larger than 10 in the C-T network, including ESR1, PTGS2, NOS2, PTGS1, PPARG, NOS3, ESR2, and KCNH2. ESR1 was targeted by 34 compounds, which contributed to T-cell-mediated autoimmune inflammation by promoting T-cell activation and proliferation [46]. Besides, PTGS2 with the second highest degree played a critical role in the pathogenesis of gut inflammation [47, 48]. Moreover, PPARG was demonstrated to be able to downregulate proinflammatory cytokines production, such as IL-4, -5, and -6. In addition, PPARG could also enable to interfere with profibrotic molecules, such as platelet-derived growth factor (PDGF), IL-1, and transforming growth factor beta (TGF-β) [49]. These results suggested that Quyushengxin formula could probably treat UC by regulating anti-inflammatory action and the immune system.

In this study, 94 targets were utilized to perform T-P network analysis, and the results showed that 79 targets could be further mapped to 78 pathways. Meanwhile, numerous pathways mapped by multiple targets might be the main factors for UC progression. Four pathways including “T-cell receptor signaling pathway,” “FOXO signaling pathway,” “JAK-STAT signaling pathway,” and “mTOR signaling pathway” were closely associated with immune and inflammatory effects. T-cell receptors play significant role in function of T cells and formation of the immunological synapse, and they connected T cells and the antigen-presenting cells [50]. T-cell receptor pathway was reported to be important in regulation of UC [51, 52]. FOXO pathway plays a key role in regulating the expression of genes related to cell function such as apoptosis, cell cycle, oxidative stress, and differentiation [5355]. FOXO3a was shown to control the inflammatory response and help maintain the homeostasis of the intestinal mucosa, which may also be a protective factor in the gut, and maintain a balance between the mucosal immune hemostasis against intravascular bacteria and inflammatory cytokines [56]. Besides, JAK-STAT pathway is the fulcrum for many important cellular processes, including cell survival, differentiation, proliferation, and regulation of immune function [57]. The mTOR pathway plays an important role in regulation of cell metabolism, proliferation, and autophagy. It is reported that mTOR signaling pathway was activated in bacteria-induced colitis in mice [58]. Inhibitors of mTOR signaling pathway are effective as anti-inflammatory drugs in treating colitis [5961]. Therefore, Quyushengxin might suppress UC progression through targeting these anti-inflammation, autophagy, and immunoregulation pathways.

Nevertheless, limitations in this study could never be neglected. First, results in this study were mainly based on known chemical components in Quyushengxin, related targets, and pathways in UC. With the development of science and technology, new components in Quyushengxin, as well as new targets and pathways in UC will be further discovered, which will supply us with more theoretical evidences for further elucidation of underlying mechanisms of UC pathology. Second, the interaction relationships of the nodes in the networks, such as the action type, e.g., activation, inhibition, binding, and catalysis, and the action effect, e.g., positive, negative, and unspecified, are not investigated due to lack of these data. Third, due to the complex interaction between TCM and the human body, many of its acting mechanisms still needed to be further elucidated via pharmacokinetic test and other experiments.

5. Conclusion

In short, network pharmacology analysis of Quyushengxin showed that 41 bioactive components of Quyushengxin may act on 94 immune and inflammation-related targets to suppress UC progression in a synergistic and additive manner, which may provide us with a new starting point for a more detailed knowledge of mechanisms of UC pathogenesis.

Data Availability

The datasets used and analyzed during the current study are available by sending email to the corresponding author.

Conflicts of Interest

The authors declare that they have no conflicts of interest.

Authors’ Contributions

Haojie Yang, Ying Li, and Sichen Shen contributed equally to this study.

Acknowledgments

The authors would like to thank Ms. Huaping Liu in assistance with data analysis. This work was supported by the National Natural Science Foundation of China project (nos. 81603633, 81874468, and 81403399), Shanghai Committee of Science and Technology project (no. 16401971400), and Peak Research Team Project in Shanghai University of Traditional Chinese Medicine.

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