Hydrophobic interactions at subsite S1' of human dipeptidyl peptidase IV contribute significantly to the inhibitory effect of tripeptides

Mitsugu Araki; Norimasa Kanegawa; Hiroaki Iwata; Yukari Sagae; Keisuke Ito; Katsuyoshi Masuda; Yasushi Okuno

doi:10.1016/j.heliyon.2020.e04227

Hydrophobic interactions at subsite S1' of human dipeptidyl peptidase IV contribute significantly to the inhibitory effect of tripeptides

Heliyon. 2020 Jun 23;6(6):e04227. doi: 10.1016/j.heliyon.2020.e04227. eCollection 2020 Jun.

Authors

Mitsugu Araki¹, Norimasa Kanegawa², Hiroaki Iwata¹, Yukari Sagae¹, Keisuke Ito³, Katsuyoshi Masuda^{1

2}, Yasushi Okuno¹

Affiliations

¹ Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan.
² Suntory Global Innovation Center Limited, Suntory World Research Center, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan.
³ Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka 422-8526, Japan.

Abstract

Functional inhibitory peptides of human dipeptidyl peptidase 4 (hDPP4) have been highly anticipated as the active ingredient of functional food for type II diabetes; however, the molecular mechanism of hDPP4 inhibition remains unclear. In this study, we focused on dipeptides and tripeptides, which display structure-function correlations that are relatively easy to analyze, and examined their interactions with hDPP4 on an atomic level using a combination of docking studies and an hDPP4 inhibition assay. First, we performed comprehensive binding mode analysis of the dipeptide library and demonstrated that the formation of a tight interaction with the S1 subsite composing part of the substrate pocket is essential for dipeptides to compete with the substrate and strongly inhibit hDPP4. Next, we synthesized tripeptides by adding various amino acids to the C-terminus of Ile-Pro and Val-Pro, which have especially high inhibitory activity among compounds in the dipeptide library, and measured the hDPP4 inhibitory activity of the tripeptides. When hydrophobic amino acids (Ile, Met, Val, Trp) were added, the inhibitory activity increased several-fold. This phenomenon could be explained as follows: the C-terminal amino acid of the tripeptide formed hydrophobic interactions with Tyr547 and Trp629, which compose the S1' subsite located relatively outside the substrate pocket, thereby stabilizing the hDPP4-peptide binding. The structural information on the interaction between hDPP4 and peptide inhibitors attained in this study is anticipated to be useful in the development of a more potent hDPP4 competitive inhibitor.

Keywords: Biochemical characterization of food; Biochemistry; Bioinformatics; Biophysical chemistry; Biophysics; Computer simulation; Computer-aided drug design; Dipeptide inhibitor; Drug binding; Human dipeptidyl peptidase 4; Material science of foods; Molecular docking; Peptides; Pharmaceutical chemistry; Protein-compound binding mode; Structural biology; Structure activity relationship; Tripeptide inhibitor; Type II diabetes.