Screening of DPP-4 inhibitory peptides derived from the skin of Takifugu bimaculatus and analysis of their inhibitory mechanisms

Introduction To address the growing global type 2 diabetes mellitus burden, dietary intervention via dipeptidyl peptidase‐4 (DPP‐4) inhibition provides a viable approach for glycemic control. Takifugu bimaculatus skin hydrolysates exhibit favorable hypoglycemic efficacy; however, the core active components remain uncharacterized. Methods An integrated workflow was established sequentially coupling gel filtration chromatography, liquid chromatography‐tandem mass spectrometry (LC-MS/MS) sequencing, virtual screening, and molecular dynamics (MD) simulations. A <1 kDa fraction (TBP) with potent DPP‐4 inhibitory activity was isolated and sequenced to construct an experimental peptide library. Candidate peptides were screened, chemically synthesized, and validated via in vitro enzymatic assays, ADMET prediction, and MM-GBSA binding free energy calculations. Results Three potent peptides –PPGFPGGA (PA8), APGYVGPA (AA8), and GPSVLAF (GF7) –were identified, displaying in vitro IC 50 values of 34.60 μM, 61.90 μM, and 73.26 μM, respectively. ADMET profiling computationally predicted acceptable oral absorption and in silico safety profiles. MD simulations and MM-GBSA calculations demonstrated that the most potent peptide, PA8 (binding free energy: −32.52 kcal/mol, counteracted desolvation penalties via favorable electrostatic and van der Waals interactions to maintain complex stability. Conversely, AA8 (−28.70 kcal/mol) and GF7 (−16.30 kcal/mol) exhibited lower potencies due to insufficient complex stability or fewer specific contacts. Discussion These findings substantiate that T. bimaculatus skin-derived DPP-4 inhibitory peptides hold promise as functional factors for blood glucose management, providing lead sequences for future in vivo translational validation while advancing the high-value utilization of marine processing by-products.