Study of screening in silico novel peptides from soy protein and deciphering their binding behavior and interaction mechanism with α -glucosidase

Abstract This study aimed to identify novel bioactive peptides with potent α-glucosidase inhibitory activity through a combination of traditional isolation, purification techniques, and computer-aided virtual screening, while exploring their interaction mechanisms. Three peptides—DAMDGWFR, PDFKNPIGW, and KDPGQDPFTF—were isolated and screened using ultrafiltration, fast protein liquid chromatography (FPLC), and computational methods, exhibiting half maximal inhibitory concentration (IC50) of (0.24 ± 0.27), (0.15 ± 0.04), and (0.17 ± 0.03) mg/mL, respectively. Peptide-glucosidase binding, evaluated using enzyme kinetics, fluorescence quenching, isothermal titration calorimetry (ITC), and atomic force microscopy (AFM), was driven by non-covalent interactions, predominantly electrostatic forces. This binding occurred through an exothermic reaction by direct interaction with the active site and effectively inhibits the intrinsic fluorescence of α-glucosidase via a static quenching mechanism. Molecular docking and pharmacophore modeling elucidated key bond types, including hydrogen bonds, electrostatic forces and hydrophobic interactions, providing a foundation for using these peptides in functional food formulations for blood glucose regulation.