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Gene & Protein in Disease Drugs and immune infiltration in IPF

Figure 5. Construction of the miRNA–TF–mRNA regulatory network related to hub genes. Red nodes (circles) represent predicted mRNA, blue nodes
(triangles) represent miRNA, and green nodes (squares) represent TFs
Abbreviations: mRNA: Messenger RNA; miRNA: MicroRNA; TFs: Transcription factors.

were identified: collagenase clostridium histolyticum were downloaded from PDB. Molecular docking was
(targeting COL15A1 and COL6A3), ocriplasmin (targeting performed using CB-Dock2, and the best ligand–receptor
COL15A1 and COL6A3), cyclosporine (targeting VCAN), binding modes were selected based on “Vina score”
bevacizumab (targeting THBS2), and talabostat (targeting and “cavity size.” The results showed that cyclosporine
FAP). In addition, CTD screening revealed more drugs was bound tightly to the COL15A1 protein receptor
or compounds, with each of them targeting ≥5 hub (Figure 8A) with a Vina score of −7.2 Furthermore,
genes. Finally, drugs or compounds that could reduce the cyclosporine also exhibited high binding affinity toward
expression levels of hub genes were identified: aristolochic the COL6A3 protein receptor (Figure 8B). Respectively,
acid I, (+)-JQ1 compound, triclosan, sodium arsenite, dexamethasone (Figure 8C) and (+)-JQ1 compound
doxorubicin, dexamethasone, valproic acid, tobacco smoke (Figure 8D) also displayed notable binding affinities.
pollution, and cyclosporine (Figure 7 and Supplementary The detailed results are presented in Table 2. Further
File: Table S9). visualization was performed for binding results with a
Vina score of <−7.0.
3.8. Molecular docking
The 3D structures of aristolochic acid I, (+)-JQ1 4. Discussion
compound, triclosan, doxorubicin, dexamethasone, IPF is a chronic progressive interstitial lung disease
valproic acid, and cyclosporine were obtained from the characterized by fibrosis, primarily affecting middle-aged
PubChem Compound Database (2D structures were and older individuals. Its etiology and pathogenesis remain
converted to 3D structures using Chem3D if needed). The unclear. Owing to small sample sizes in previous studies,
3D structures of COL15A1 (PDB ID: 3N3F; resolution: limited research has been conducted on gene expression
2.005 Å) and COL6A3 (PDB ID: 6SNK; resolution: 2.2 Å) in IPF. This study integrated three IPF datasets to examine

Volume 3 Issue 4 (2024) 8 doi: 10.36922/gpd.4101