Network pharmacology analysis of Xinbao Pill against heart failure with preserved ejection fraction

Abstract: Background: Heart failure with preserved ejection fraction (HFpEF) accounts for approximately half of all heart failure cases and lacks effective targeted therapy. Traditional Chinese medicine formulas, such as Xinbao Pill, have shown potential cardiovascular benefits; however, their molecular mechanisms are not yet fully understood. Objectives: This study aimed to systematically explore the multi-compound, multi-target mechanism of Xinbao Pill in the treatment of HFpEF using a network pharmacology approach. Methods: Active ingredients of Xinbao Pill were identified from the TCMSP database according to predefined pharmacokinetic criteria. Three GEO datasets (GSE180065, GSE240400 and GSE269053) were analyzed to identify differentially expressed genes associated with HFpEF. Elastic Net regression was used to refine the intersecting targets. Molecular docking and 100 ns all-atom molecular dynamics simulations were used to predict and validate the structural stability of compound-target interactions. Results: A total of 32 active compounds were identified. Differential expression analysis identified 1,368 HFpEF-related genes across the three datasets, including 23 overlapping targets. Elastic Net regression further selected 11 key genes (Clk1, Comt, Drd2, Ephx2, Fgr, Hcn2, Mme, Pparg, Ptgds, Slc27a1, Vdr). Molecular docking predicted strong binding affinities for several compound-target pairs, including Withanolide D-VDR (-12.0 kcal/mol) and 12-Deoxywithastramonolide-EPHX2 (-11.5 kcal/mol). Molecular dynamics simulations confirmed the structural stability of both top-ranked complexes over 100 ns, with low RMSD values and well-defined free energy minima. Conclusions: This in-silico study identified candidate targets and bioactive compounds that may be associated with the potential effects of the Xinbao Pill in HFpEF. The identified key targets and compounds may serve as promising candidates for further experimental validation and therapeutic development.