Exploring the Mechanisms of the Traditional Herbal Formula Sanshen Dan Against Myocardial Ischemia-Reperfusion Injury: An Integrated Strategy Combining Serum Pharmacochemistry, Network Pharmacology, and Molecular Docking

Objective: Myocardial ischemia-reperfusion injury (MIRI) is a critical clinical challenge in cardiovascular disease management. Sanshen Dan (SSD), a clinically validated traditional Chinese medicine formula, exerts therapeutic effects on MIRI, but its chemical composition and underlying mechanism remain unclear. This study aimed to systematically elucidate the cardioprotective mechanism of SSD against MIRI using an integrated strategy. Methods: An integrated approach combining serum pharmacochemistry, network pharmacology, machine learning, molecular docking, and molecular dynamics simulation was adopted. 1. Ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) was used to identify blood-absorbed components of SSD after oral administration to Sprague-Dawley rats. 2. Potential targets of these components were predicted via public databases, and overlapping targets with MIRI-related genes were screened to construct a compound-target network, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. 3. Three machine learning algorithms (random forest, SVM-RFE, LASSO regression) were applied to identify core therapeutic targets. 4. Molecular docking and 100 ns molecular dynamics simulations were performed to verify the binding affinity and stability of ligand-receptor complexes. Results: A total of 44 blood-absorbed active components of SSD were identified, including flavonoids, saponins, lignans, and phenolic acids. A total of 392 potential therapeutic targets were screened out, which were mainly enriched in apoptosis, HIF-1, TNF-α, and cAMP signaling pathways. Machine learning analysis identified Mmp14, Htr2b, and Ctnnb1 as core targets, and the constructed nomogram model showed excellent predictive performance (AUC = 1, C-index = 1). Molecular docking indicated that 6 core components (eg, Kaempferide-4′-methyl ether-3-glucoside, Licurazide) exhibited strong binding affinity to the core targets, and molecular dynamics simulations confirmed the high stability of these complexes, with mean binding free energy ranging from − 20.58 kcal/mol to − 34.31 kcal/mol. Conclusion: SSD exerts cardioprotective effects against MIRI via a “multi-component, multi-target, multi-pathway” mode. Its core blood-absorbed components may alleviate MIRI by regulating core targets including Mmp14 and Ctnnb1, and modulating key signaling pathways such as TNF-α and HIF-1. This study provides a scientific basis for the clinical application of SSD and further exploration of traditional Chinese medicine compound formulas. Keywords: myocardial ischemia-reperfusion injury, network pharmacology, molecular docking, multi-target mechanism, pharmacological basis