Mechanisms of indigo naturalis on treating ulcerative colitis explored by GEO gene chips combined with network pharmacology and molecular docking

Abstract

Oral administration of indigo naturalis (IN) can induce remission in ulcerative colitis (UC); however, the underlying mechanism remains unknown. The main active components and targets of IN were obtained by searching three traditional Chinese medicine network databases such as TCMSP and five Targets fishing databases such as PharmMapper. UC disease targets were obtained from three disease databases such as DrugBank,combined with four GEO gene chips. IN-UC targets were identified by matching the two. A protein-protein interaction network was constructed, and the core targets were screened according to the topological structure. GO and KEGG enrichment analysis and bioGPS localization were performed,and an Herbs-Components-Targets network, a Compound Targets-Organs location network, and a Core Targets-Signal Pathways network were established. Molecular docking technology was used to verify the main compounds-targets. Ten core active components and 184 compound targets of IN-UC, of which 43 were core targets, were enriched and analyzed by bioGPS, GO, and KEGG. The therapeutic effect of IN on UC may involve activation of systemic immunity, which is involved in the regulation of nuclear transcription, protein phosphorylation, cytokine activity, reactive oxygen metabolism, epithelial cell proliferation, and cell apoptosis through Th17 cell differentiation, the Jak-STAT and IL-17 signaling pathways, toll-like and NOD-like receptors, and other cellular and innate immune signaling pathways. The molecular mechanism underlying the effect of IN on inducing UC remission was predicted using a network pharmacology method, thereby providing a theoretical basis for further study of the effective components and mechanism of IN in the treatment of UC.

Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1

Framework based on an integration strategy of network pharmacology.

Figure 2

Differential genes volcano map jointly analyzed by four GEO chips. mRNA of intestinal mucosal biopsies from normal group and UC group.

Figure 3

Venn diagram of the targets in UC and IN.

Figure 4

Herb-ingredients-targets (H-I-T) network. Red node represents IN, green nodes represent core active compounds of IN, purple nodes represent targets of IN.

Figure 5

The process of topological screening for the PPI network. The PPI network diagram of 43 core targets was obtained by screening 182 IN-UC composite targets through DC,BC,CC.

Figure 6

The PPI network of 182 nodes. The node size is proportional to the target degree in the network. The Blue nodes are the core targets of IN-UC.

Figure 7

Gene expression data were based on gene expression microarray analysis results in BioGPS. Targets-organs location network (H–O): Nodes represent targets and organ locations. Node size is relative to degree.

Figure 8

The GO enrichment analysis of core nodes. Including cellular components, molecular functions, biological processes and GO secondary classification.

Figure 9

Targets-pathways network (T-P network). The green Rhombus nodes represent the targets of IN-UC. The red triangles represent the related pathways. Node size is relative to degree.

Figure 10

The protein–ligand of the docking simulation. The three core compounds (indigo, indirubin, tryptamethrin) of IN are docked with three targets.