Controlled Trypsin Hydrolysis of Bovine Casein for Preferential αS1-Casein Reduction: Fraction-Specific Kinetics, αS1-Casein-Related Antigenicity and Candidate Bioactive Peptides

Cow’s milk-based infant formula aims to approximate human milk, but bovine αS1-casein remains an important allergen-related protein with a profile distinct from human milk caseins. This study controlled trypsin hydrolysis to preferentially reduce intact αS1-casein and generate candidate bioactive peptides. Under 38 °C, pH 8.0, and 5 h, the relative residual peak area of αS1-casein decreased markedly, while αS2-casein and β-casein remained detectable at 33.15% and 45.01%, respectively. Peptidomics identified 17 peptides, among which HQGLPQEVLNENLLR showed the strongest predicted binding affinity to α-amylase by molecular docking (−13.98 kcal/mol). The hydrolysate showed ABTS radical scavenging activity of 92.10% and α-amylase inhibition of 53.44%. Molecular dynamics further supported the stability of the peptide–enzyme complex. These findings provide a preliminary process window for reducing intact αS1-casein and prioritizing candidate functional peptides from casein hydrolysates.