While studies suggested that Huangqi Guizhi Wuwu Decoction (HGWD) can mitigate doxorubicin-induced cardiotoxicity (DIC), the specific mechanism of action remains unclear. GSE106297, GSE157282, and GSE206803 were downloaded to screen for differentially expressed genes (DEGs), followed by gene set enrichment analysis and immune infiltration analysis. DIC-related genes were obtained by the intersection of weighted gene co-expression network analysis and DEGs. The active ingredients and target genes of HGWD were obtained from the Traditional Chinese Medicine System Pharmacology Database and Analysis Platform database, and HGWD-DIC common targets were identified by intersecting them with DIC-related genes. A drug-active ingredient-target network was constructed to select the core components of HGWD. Mitophagy-related genes were obtained from GeneCards, PHARMGKB, and OMIM databases, and intersecting them with common targets yielded the core genes, which were then subjected to enrichment analyses. A protein-protein interaction network was constructed to identify key genes, further assessing their diagnostic value. The effect of HGWD on the expression of key genes was further validated using prepared medicated serum. The interactions between the core components and key genes were validated through molecular docking and molecular dynamics simulation. A total of 2344 DEGs were identified, with gene set enrichment analysis results primarily enriched in categories such as apoptosis, p53 signaling pathway, cell cycle, PLK1 pathway, mitochondrial translation, and metabolism of RNA. Immune infiltration analysis suggested that the immune response may also be involved in the pathogenesis of DIC. We identified 2969 key modular genes by weighted gene co-expression network analysis, and intersecting these with DEGs yielded 1569 DIC-related genes. Network pharmacology analysis revealed 74 active ingredients and 692 target genes of HGWD, resulting in 64 common targets when intersected with DIC-related genes. The core components of HGWD were identified as quercetin and kaempferol. By intersecting the obtained mitophagy-related genes with common targets, 13 core genes were identified, with enrichment analyses indicating significant associations with cellular response to mitophagy and autophagy. Further analysis showed that 5 key genes: AKT1, TP53, BCL2L1, FASN, and HRAS, all demonstrated good diagnostic value, and their DOX-induced expression alterations were reversed by HGWD. Molecular docking and molecular dynamics simulation showed a strong binding affinity between the core components and key genes. HGWD may alleviate DIC by regulating mitophagy.
