Computation-Based Discovery of Potential Targets for Rheumatoid Arthritis and Related Molecular Screening and Mechanism Analysis of Traditional Chinese Medicine

Abstract

This study is aimed at screening potential therapeutic ingredients in traditional Chinese medicine (TCM) and identifying the key rheumatoid arthritis (RA) targets using computational simulations. Data for TCM-active ingredients with clear pharmacological effects were collected. Absorption, distribution, metabolism, excretion, and toxicity were evaluated. Potential RA targets were identified using the Gene Expression Omnibus (GEO) database, protein-protein interaction network, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses and potential TCM ingredients using AutoDock Vina. To examine the mechanisms underlying small molecules, target prediction, Gene Ontology, KEGG, and network modeling analyses were conducted; the effects were verified in rat synovial cells using cell proliferation assay. The activities of tumor necrosis factor TNF-α and IL-1β and alterations in cellular target protein levels were detected by ELISA and Western blotting, respectively. In total, data for 432 TCM active ingredients with clear pharmacological effects were obtained. Five critical RA-related genes were identified; CCL5 and CXCL10 were selected for molecular docking. Target prediction and network-based proximity analysis showed that dioscin could modulate 22 known RA clinical targets. Dioscin, asiaticoside, and ginsenoside Re could effectively inhibit in vitro cell proliferation and secretion of TNF-α and IL-1β in RA rat synovial cells. Using bioinformatics and computer-aided drug design, the potential small anti-RA molecules and their mechanisms of action were comprehensively identified. Dioscin could significantly inhibit proliferation and induce apoptosis in RA rat synovial cells by reducing TNF-α and IL-1β secretion and inhibiting abnormal CCL5, CXCL10, CXCR2, and IL2 expression.