In silico study to predict potential precursors of human dipeptidyl peptidase-IV inhibitors from hazelnut

Abstract

Chinese hazelnut was chosen to become a probable precursor of biological active peptides via computer simulations in this article. There were a large number of bioactive peptides in Chinese hazelnut sequences according to analytical results from the BIOPEP database. The most prominent of these was the inhibitory peptide for dipeptidyl peptidase-IV (DPP-IV; EC 3.4.14.5), which can be used to treat type 2 diabetes, so the theoretical method to obtain DPP-IV inhibitory peptides by hydrolysis with a single or combination of enzymes was studied. Cytotoxicity analysis performed by ToxinPred showed that all of the DPP-IV inhibitory peptides generated from protein hydrolysis were not cytotoxic. Structural interaction fingerprint analysis revealed that Asp663 and Phe357 may be important residues for ligand binding. In order to further understand the inhibitory mechanism of peptide, VR with lowest half maximum inhibitory concentration (IC50) and IPI (inhibitors have been reported) were selected as ligand of DPP-IV to perform steered molecular dynamics simulations and PMF calculations. The results showed that P1 is the preferred (un)binding tunnel for the inhibitors obtained. Our findings help in the development of new DPP-IV inhibitors which were derived from common food.

Communicated by Ramaswamy H. Sarma

Keywords:

• Chinese hazelnut
• dipeptidyl peptidase-IV inhibitory peptides
• structural interaction fingerprint (SIFt) analysis
• steered molecular dynamics simulations
• PMF calculations

Acknowledgements

This work was conducted at the High-Performance Computing Center of Jilin University.

Disclosure statement

The authors declare no competing financial interests.

Additional information

Funding

This work was supported by the Overseas Cooperation Project of Jilin Province under Grant [20200801069GH].