Machine learning methods for unveiling the potential of antioxidant short peptides in goat milk-derived proteins during in vitro gastrointestinal digestion

Abstract

Milk serves as an important dietary source of bioactive peptides, offering notable benefits to individuals. Among the antioxidant short peptides (di- and tripeptides) generated from gastrointestinal digestion are characterized by enhanced bioavailability and bioaccessibility, while assessing them individually presents a labor-intensive and expensive challenge. Based on 4 distinct types of AA descriptors (physicochemical, 3-dimensional structural, quantum, and topological attributes) and genetic algorithms for feature selection, 1 and 4 machine learning–predicted models separately for di- and tripeptides with 2,2-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt radical scavenging capacity exhibited excellent fitting and prediction ability with random forest regression as machine learning algorithm. Intriguingly, the electronic properties of N-terminal AA were considered as only factor affecting the antioxidant capacity of dipeptides containing both tyrosine and tryptophan. Four peptides from the potential di- and tripeptides exhibited highly predicted values by the constructed predicted models. Subsequently, a total of 45 dipeptides and 52 tripeptides were screened by a customized workflow in goat milk during in vitro simulated digestion. In addition to 5 known antioxidant dipeptides, 9 peptides were quantified during digestion, exhibiting concentrations ranging from 0.04 to 1.78 mg L⁻¹. Particularly noteworthy was the promising in vivo functionality of antioxidant dipeptides with N-terminal tyrosine, supported by in silico assays. Overall, this investigation explored crucial molecular properties influencing antioxidant short peptides and high-throughput screening potential peptides with antioxidant activity from goat milk aided by machine learning, thereby facilitating the discovery of novel functional peptides from milk-derived proteins and paving the way for understanding their metabolites during digestion.