Network pharmacology and molecular docking study on the active ingredients of qidengmingmu capsule for the treatment of diabetic retinopathy

Abstract

Diabetic retinopathy (DR) is a leading cause of irreversible blindness globally. Qidengmingmu Capsule (QC) is a Chinese patent medicine used to treat DR, but the molecular mechanism of the treatment remains unknown. In this study, we identified and validated potential molecular mechanisms involved in the treatment of DR with QC via network pharmacology and molecular docking methods. The results of Ingredient-DR Target Network showed that 134 common targets and 20 active ingredients of QC were involved. According to the results of enrichment analysis, 2307 biological processes and 40 pathways were related to the treatment effects. Most of these processes and pathways were important for cell survival and were associated with many key factors in DR, such as vascular endothelial growth factor-A (VEGFA), hypoxia-inducible factor-1A (HIF-1Α), and tumor necrosis factor-α (TNFα). Based on the results of the PPI network and KEGG enrichment analyses, we selected AKT1, HIF-1α, VEGFA, TNFα and their corresponding active ingredients for molecular docking. According to the molecular docking results, several key targets of DR (including AKT1, HIF-1α, VEGFA, and TNFα) can form stable bonds with the corresponding active ingredients of QC. In conclusion, through network pharmacology methods, we found that potential biological mechanisms involved in the alleviation of DR by QC are related to multiple biological processes and signaling pathways. The molecular docking results also provide us with sound directions for further experiments.

Molecular Mechanism of Food-Derived Polyphenols on PD-L1 Dimerization: A Molecular Dynamics Simulation Study

“…The 3D structures of food-derived compounds and initial complex structures for MD simulations are displayed in Figures 1 and 2. Molecular docking was conducted to provide initial models of the complex systems for subsequent MD simulation studies [34]. The X-ray crystal structure of the PD-L1 dimer (PDB ID 5N2F) was used as the receptor for this study.…”

“…Molecular docking is a tool for predicting ligands' binding affinities to target proteins and exploring their possible binding modes [34]. The crystal structures of the PD-L1 dimer (PDB ID: 5N2F), CC (PDB ID: 4K58), RSV (PDB ID: 1CGZ) and EGCG (PDB ID: 3NG5) were acquired from the Protein Data Bank (PDB) database.…”

Celastrol Alleviates Autoimmune Hepatitis Through the PI3K/AKT Signaling Pathway Based on Network Pharmacology and Experiments

“…It is worth mentioning that, celastrol plays a role in inhibiting PI3K/AKT signaling pathway in the treatment of various diseases, such as glioblastoma and prostate cancer ( Pang et al, 2010 ; Kannaiyan et al, 2011 ). Besides, it is thought to be correlated with the cell cycle ( Zhang M. et al, 2021 ). Li H et al reported that PTEN, a negative regulating factor, may suppress the PI3K/AKT pathway and maintain moderate T cell proliferation in healthy individuals ( Li et al, 2019 ).…”

Network Pharmacology and Molecular Docking Elucidate the Underlying Pharmacological Mechanisms of the Herb Houttuynia cordata in Treating Pneumonia Caused by SARS-CoV-2

“…The species was then set to Homo sapience and the minimum required interaction score to the highest confidence of 0.9 in order to retrieve the concise protein–protein interaction (PPI) information for the next step of the analysis. The PPI network was also visualized with Cytoscape software [ 28 ].…”

“…The results of the KEGG enrichment analysis were used to construct a KEGG pathway network to determine the proteins involved in the treatment effects of HC. Based on the STRING results, the gene–pathway of HC against pneumonia was constructed to delineate the various pathways and key targets in order to explore the potential mechanisms underlying the effect of HC on the treatment of pneumonia [ 28 ].…”