Discovery of Novel Peptides as DPP-IV Inhibitors: <i>In Silico</i> Screening, Molecular Dynamics Simulations, and Preliminary <i>In Vitro</i> Evaluation

Abstract Type 2 diabetes mellitus (T2DM) is the most common metabolic disorder characterized by impaired insulin secretion, which leads to obesity. The incretin hormone glucagon-like peptide-1 (GLP-1) has a significant role in glucose homeostasis, but its native form in the human body is highly susceptible to proteolytic degradation by dipeptidyl peptidase IV (DPP-IV). In this study, a peptide library was constructed from antimicrobial peptide databases to discover novel DPP-IV inhibitors based on structural similarity to that of native GLP-1. A total of 26 candidate peptides were shortlisted and screened using in silico analysis, including molecular docking, pharmacokinetic profiling, and molecular dynamics simulations. Particularly, two of the candidate antimicrobial peptides showed potent binding affinity to DPP-IV, with free energy scores of −15.6 and −16.5 kcal/mol, surpassing the binding affinity of native GLP-1 for DPP-IV. These peptides also exhibited lower predicted binding affinities for the GLP-1 receptor (GLP-1R) than for DPP-IV, suggesting a potential selective inhibitory effect and, consequently, a lower predicted likelihood of interfering with native GLP-1 signaling. Pharmacokinetic characteristics of the peptides were promising with an optimal absorption, distribution, metabolism, excretion, and toxicity (ADMET) profile, along with prolonged half-life and stability. Because of its better membrane permeability and more favorable predicted DPP-IV/GLP-1R binding preference, peptide 3 was further evaluated for downstream experimental validation. The biological activity test showed that peptide 3 successfully exhibited a 36.2% inhibition rate against DPP-IV in vitro. These findings indicate that both peptides 3 and 10 are promising DPP-IV inhibitor candidates.