Comprehensive Characterization and Antioxidant Function Prediction of Endogenous and Exogenous Peptides from Polygonatum kingianum

Background/Objectives: Polygonatum kingianum Collett & Hemsl. (PK) is an edible medicinal herb with tonic effects. Its natural antioxidant peptides are valuable for functional food development, while their characteristics and mechanisms are unclear. This study aimed to identify PK antioxidant peptides and explore their antioxidant molecular mechanisms to support the utilization of PK active ingredients. Methods: Three peptide fractions (P1, P2, P3) were prepared from PK via defatting, alkali–acid precipitation and enzymatic hydrolysis. Nano-liquid chromatography coupled with Q Exactive mass spectrometry was used for peptide identification. Bioinformatic tools predicted peptide antioxidant activity, and molecular docking targeting the Kelch-like ECH-associated protein 1-nuclear factor erythroid 2-related factor 2 (Keap1-Nrf2) pathway verified peptide–target-binding affinity. Results: A total of 747, 1850 and 2537 peptides were identified from P1, P2 and P3, respectively, among which 119 peptides were screened out as potential antioxidant candidates. Docking analysis revealed 10 peptides with strong binding affinity to Keap1. These active peptides were short sequences of 3–5 residues enriched in hydrophobic and aromatic amino acids, which stably bound key residues within the Keap1 binding pocket. Conclusions: This study fills the research gap in PK peptidome profiling, clarifies structural signatures of candidate antioxidant peptides, and identifies high-affinity short peptides targeting the Keap1-Nrf2 antioxidant pathway. The established screening pipeline provides technical support for bioactive peptide mining and deep processing of PK resources.