Potency of Antioxidant Peptides Encrypted in Commercially Important Marine Invertebrates: A Bioinformatics Approach

Abstract

Efficient and beneficial food utilization calls for sustainable and innovative practices that add value at every stage of production. In this study, we conducted a computational analysis of protein sequences from the bivalve Mytilus galloprovincialis, the crustacean Penaeus vannamei (whiteleg shrimp), the purple sea urchin Paracentrotus lividus, and the echinoderm Holothuria leucospilota, utilizing bioinformatic tools to estimate their antioxidant bioactive potential. This potential is indicated by the presence of small bioactive peptides encrypted within their sequences, which can be released by proteolytic enzymes. The peptides of interest from a total of 47 proteins were matched with known antioxidant peptides (APs) from the BIOPEP database. We studied the properties of 236 different peptides out of a total of 995 peptides encrypted in the proteins. To evaluate the bioactivity of peptides, we sorted them based on the predicted free radical scavenging (FRS) and ion-chelating (CHEL) scores. Furthermore, to investigate protein–peptide interactions, molecular docking of selected peptides was performed with two protein models. Penaeus vannamei and Paracentrotus lividus exhibited the highest average antioxidant FRS potency. The most potent FRS peptides for each organism are encrypted in the kinesin-like Boursin protein of Paracentrotus lividus, the Chitinase protein of Penaeus vannamei, the Myosin-16 protein of Holothuria leucospilota, and the Perlucin-like protein of Mytilus galloprovincialis. We demonstrate a correlation between the potency of APs, based on the FRS score, and their calculated binding affinity to serine/threonine protein kinase D1 and glutathione peroxidase. Our results highlight an effective approach to utilizing by-products of primary production for mining high-value ingredients.