Novel Antioxidant Self-Assembled Peptides Extracted from Azumapecten farreri Meat: In Vitro- and In Silico-Assisted Identification

Previous studies have found that the self-assembled supramolecules of Azumapecten farreri meat peptides have antioxidant effects. Therefore, this study aims to isolate and identify novel antioxidant peptides with self-assembly characteristics and analyze their structure–activity relationship through molecular docking and molecular dynamics simulation. The in vitro results show that as the purification steps increased, the antioxidant activity of peptides became stronger. Additionally, the purification step did not affect its pH-responsive self-assembly. Using LC-MS/MS, 298 peptide sequences were identified from the purified fraction PF1, and 12 safe and antioxidant-active peptides were acquired through in silico screening. The molecular docking results show that they had good binding interactions with key antioxidant-related protein ligands (KEAP1 (Kelch-like ECH-associated protein 1) and MPO (myeloperoxidase)). The peptide QPPALNDSYLYGPQ, with the lowest docking energy, was selected for a 100 ns molecular dynamics simulation. The results show that the peptide QPPALNDSYLYGPQ exhibited excellent stability when docked with KEAP1 and MPO, thus exerting antioxidant effects by regulating the KEAP1-NRF2 pathway and inhibiting MPO activity. This study further validates the antioxidant and self-assembling properties of the self-assembled supramolecules of Azumapecten farreri meat peptide and shows its potential for developing new, effective, and stable antioxidants.