The purpose of this research was to examine the interaction between metabolites of Lactobacillus plantarum YW11, characterized through GC–mass spectra (MS) analysis, and the FN1 protein in cases of familial pulmonary fibrosis, found from hub genes analysis. GC–MS analysis was performed to identify metabolites in L. plantarum. Then, gene expression analysis and functional annotations were conducted to investigate the hub genes. A network of hub genes and transcription factors (TFs) was constructed, highlighting the significance of FN1 in the disease’s etiology. Molecular docking was employed to explore the interaction between the characterized metabolites and the FN1 protein. Toxicity analysis was also carried out. Thirty-two active compounds of L. plantarum YW11 were characterized by GC–MS. The gene expression analysis identified 295 differentially expressed genes, including 10 hub genes and 6 TFs, providing further support for the involvement of FN1 protein in the disease. The results of the molecular docking studies suggest the therapeutic potential of targeting FN1, with the best docking result observed for the interaction between FN1 and the 2,4-di-tert-butylphenol metabolite (energy of −6.9 kcal/mol). The toxicity analysis and molecular dynamic simulations support the suitability of 2,4-di-tert-butylphenol as a candidate for targeting FN1.
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