Deciphering the antiviral mechanisms of Fangqin Qinggan decoction against influenza A virus: a multi-omics and machine learning approach

BACKGROUND: Influenza A virus (IAV) infection poses a significant global health burden, contributing to high morbidity and mortality in both humans and animals through rapid viral transmission and dysregulated inflammatory responses. Fangqin Qinggan Decoction (FQ-01), a traditional Chinese medicine (TCM) formula, has demonstrated clinical efficacy in treating viral upper respiratory infections, however, its underlying therapeutic mechanisms remain poorly understood. METHODS: The therapeutic efficacy and mechanisms of FQ-01 against IAV infection were comprehensively investigated using a multidisciplinary approach, including in vivo murine models, histopathological (H&E staining), RT-qPCR, immunohistochemistry (IHC), network pharmacology, weighted gene co-expression network analysis (WGCNA), machine learning (LASSO), transcriptomics, metabolomics, molecular docking and molecular dynamics (MD) simulation. RESULTS: FQ-01 significantly improved survival rates, reduced clinical mortality, and mitigated pulmonary inflammation in an IAV-infected mice while suppressing viral replication. Integrated bioinformatics and LASSO regression analyses identified 20 genes associated with FQ-01's antiviral effects, with Myd88 and Ccl5 emerging as key targets. Transcriptomic profiling of murine lung tissues further validated these genes as critical mediators of FQ-01's therapeutic action. Spearman correlation analysis revealed strong associations between Myd88/Ccl5 expression and serum/lung metabolites, particularly 3-indolyl sulfate and inosine. Subsequent in vivo RT-qPCR and IHC validation, molecular docking, and MD simulations confirmed that FQ-01 exerts its anti-IAV effects by inhibiting Myd88 and Ccl5 expression. CONCLUSIONS: Our findings elucidate the molecular mechanisms underlying FQ-01's therapeutic potential against IAV infection, highlighting Myd88 and Ccl5 as promising targets for antiviral and anti-inflammatory interventions. This study provides a foundation for further exploration of TCM-based strategies in combating influenza and related respiratory infections.