Mining and Validation of Novel Hemp Seed-Derived DPP-IV-Inhibiting Peptides Using a Combination of Multi-omics and Molecular Docking

Abstract

Hemp seed-derived inhibitors of dipeptidyl peptidase IV (DPP-IV) demonstrate potential as novel therapeutics for diabetes; however, their proteome and genome remain uncharacterized. We used multi-omics technology to mine peptides capable of inhibiting DPP-IV. First, 1261 and 1184 proteins were identified in fresh and dry hemp seeds, respectively. Simulated protease cleavage of dry seed proteins yielded 185,446 peptides for virtual screening to select the potential DPP-IV-inhibiting peptides. Sixteen novel peptides were selected according to their DPP-IV-binding affinity determined via molecular docking. In vitro DPP-IV inhibition assays identified the peptides LPQNIPPL, YPYY, YPW, LPYPY, WWW, YPY, YPF, and WS with half-maximal inhibitory concentration (IC 50 ) values lower than 0.5 mM, which were 0.08 ± 0.01, 0.18 ± 0.03, 0.18 ± 0.01, 0.20 ± 0.03, 0.22 ± 0.03, 0.29 ± 0.02, 0.42 ± 0.03, and 0.44 ± 0.09 mM, respectively. The dissociation constants (K D ) of the 16 peptides ranged from 1.50 × 10 −4 to 1.82 × 10 −7 M. Furthermore, Caco2 and INS-1 cell assays showed that all 16 peptides could efficiently inhibit DPP-IV activity and increase insulin and glucagon-like peptide-1 concentrations. These results demonstrate a well-established and efficient method to isolate food-derived therapeutic DPP-IV-inhibiting peptides.

A novel bifunctional peptide VAMP mined from hemp seed protein hydrolysates improves glucose homeostasis by inhibiting intestinal DPP-IV and increasing the abundance ofAkkermansia muciniphila

“…The affinity between DPP-IV and the selected peptides was evaluated by using a Biacore 8K high-throughput intermolecular interaction analysis system (GE Healthcare, Chicago, IL) with CM5 chips (Cytiva, Marlborough, MA) at 25 °C. The specific experimental processes were performed according to our previous study (3).…”

“…The disturbance of glucose homeostasis has become a substantial medical problem due to its increasing global prevalence and because disordered glucose metabolism is closely linked with diabetes, obesity, liver disease and several cardiovascular diseases (1, 2). Accordingly, exploration of effective approaches to alleviate glucose metabolic disorders has therefore gained increasing attention (3,4).…”

“…Hemp seeds are rich in proteins (20-25%), which contain various essential amino acids in a desirable ratio (29). Hemp seed protein (HSP) hydrolysates exhibit a variety of bioactivities (3,29), our previous study predicted the potential biological activities of HSP-derived peptides by using the BIOPEP-UWM web server and revealed that HSP-derived peptides are rich in DPP-IV inhibitory peptides (3). However, the composition of peptides in HSP hydrolysates and their mechanism of action on DPP-IV and glucose reduction have not yet been explored, especially the efficient mining methods of DPP-IV-inhibiting peptides from HSP-derived peptide libraries and the discovery of key target peptides for glucose metabolism regulation.…”

Identification of a Novel Peptide with Alcohol Dehydrogenase Activating Ability from Ethanol-Induced Lactococcus lactis: A Combined In Silico Prediction and In Vivo Validation

“…Moreover, conventional activity-based purification methods may overlook small BAPs in the hydrolysate. In contrast, the in silico approach is notably more expedient and efficient, facilitating the discovery of novel BAPs through virtual screening. , Currently, some studies have employed a combination of multiomics and molecular docking techniques to rapidly mine novel functional peptides, and experimentally in vitro and in vivo validated their activity. − For example, several novel peptides with high angiotensin-I-converting enzyme inhibitory activity were successfully screened and identified from Salmo salar and sericin hydrolysate via coupling in silico simulation and in vitro verification. Similarly, two novel α-glucosidase inhibitory peptides from Ginkgo biloba seed cake were screened based on molecular docking combined with molecular dynamics simulation .…”

Molecular Mechanistic Insights into Dipeptidyl Peptidase-IV Inhibitory Peptides to Decipher the Structural Basis of Activity

“…DPP-IV inhibitory peptides, usually encrypted in food proteins, can exert their biological activities after enzymatic release . A better understanding of peptide structural requirements for bioactivity may facilitate the discovery and targeted release of the biopeptides from food proteins. , To date, Nongonierma et al have evaluated the DPP-IV inhibitory effects of 20 amino acids, and 3 amino acids (Met, Leu, and Trp) could inhibit the DPP-IV activity . The DPP-IV inhibitory activities of the dipeptides were also systematically analyzed using a dipeptide library.…”