Peptidomics and Computational Docking Prioritize Candidate Peptide–Protein Associations Relevant to Upper-Gastrointestinal Biology in a Fermented Soy-Derived Postbiotic

Abstract

Highlights What are the main findings? GAD contains multiple families of overlapping soy-derived peptides characterized by extensive truncation ladders. A diversity-sampling peptide panel was linked computationally to candidate interactors spanning mucosal immune regulation, extracellular-matrix remodeling, epithelial turnover, and tissue restitution. What are the implications of the main findings? The findings support a multi-component model in which several peptide families may contribute to the biological properties of GAD, with mucosal integrity, injury responses, and tissue restitution emerging as priorities for future investigation. The integrated peptidomics and computational workflow provides a systems-oriented framework for investigating complex fermented peptide mixtures. Abstract Background/Objectives: Gastro-AD® (GAD) is a fermented soy-derived postbiotic supported by clinical and preclinical evidence related to gastric comfort and mucosal injury. Although fermentation-derived metabolites have been characterized, the peptide fraction remains poorly defined. This study characterized GAD peptides and explored their potential biological contexts. Methods: Untargeted peptidomics was used to identify soy-derived peptides in GAD and map them to source proteins. A diversity-sampling panel of ten peptides was selected using sequence, physicochemical, and predicted structural features. These peptides were screened against a human protein-structure library by computational docking, followed by GO enrichment and context-based prioritization of candidate interactors. Results: A total of 219 peptides, originating predominantly from soybean storage proteins, were identified. The GAD peptide fraction contained extensive overlapping sequence families and truncation ladders, consistent with extensive proteolytic processing. Three literature-reported antioxidant peptide sequences were identified as exact contiguous regions within longer GAD peptides. Large-scale docking against the screened human protein-structure library combined with GO-enrichment recurrence analysis and an independent review of top-ranked docking-derived candidates identified 180 candidate protein targets spanning innate immune and inflammatory defense, protease activity and peptide processing, extracellular-matrix remodeling, tissue repair and wound healing, and apoptotic signaling and epithelial turnover. Repeated randomized-affinity controls yielded substantially fewer FDR-significant GO terms than the observed docking-derived rankings, supporting non-random functional structure in the docking-derived protein rankings without establishing the accuracy of individual peptide–protein interactions. Context-based prioritization identified 43 unique Tier 1 and Tier 2 candidates with direct or context-dependent extracellular accessibility. The prioritized biological contexts included mucosal immune regulation, extracellular-matrix remodeling, epithelial turnover, and tissue restitution. Conclusions: The GAD peptide fraction described herein comprises multiple overlapping peptide families whose prioritized biological contexts center on mucosal defense, remodeling, and tissue restitution. These findings support further investigation of peptides as potential contributors to the multi-component biological properties of GAD.