Vildagliptin‐Derived Dipeptidyl Peptidase 9 (DPP9) Inhibitors: Identification of a DPP8/9‐Specific Lead

Abstract

Vildagliptin is a marketed DPP4 inhibitor, used in the management of type 2 diabetes. The molecule also has notable DPP8/9 affinity, with some preference for DPP9. Therefore, we aimed to use vildagliptin as a starting point for selective DPP8/9 inhibitors, and to engineer out the parent compound's DPP4affinity. In addition, we wanted to identify substructures in the obtained molecules that allow their further optimization into inhibitors with maximal DPP9 selectivity. Various 2S-cyanopyrrolidines and isoindoline were investigated as P1 residues of vildagliptin analogs. The obtained set was expanded with derivatives bearing O-substituted, N-(3-hydroxyadamantyl)glycine moieties at the P2 position. In this way, representatives were discovered with DPP8/9 potencies comparable to the parent molecule, but with overall selectivity towards DPP4, DPP2, FAP, and PREP. Furthermore, the most promising molecules in this series have a 4-to 7-fold preference for DPP9 over DPP8. Finally, a molecular dynamics study was carried out to maximize our insight into experimental selectivity data.

Novel Generation of FAP Inhibitor-Based Homodimers for Improved Application in Radiotheranostics

“…IC 50 measurements for DPP4, DPP8 and DPP9 were performed as published before, using Ala-Pro-pNA as the substrate at the respective concentrations of 25 µM (DPP4), 300 µM (DPP8) and 150 µM (DPP9) at pH 7.4 in 0.05 M HEPES-NaOH buffer with 0.1% Tween-20, 0.1 mg/mL BSA and 150 mM NaCl) [ 30 , 57 ].…”

New insights into the role of dipeptidyl peptidase 8 and dipeptidyl peptidase 9 and their inhibitors

“…Because the sequences and structures of DPP8 and DPP9 are very similar, there are no selective inhibitors for DPP8 or DPP9 respectively available now. The methylpiperazine analogs of 1G244 constructed by Van Goethem et al (2011) team and the isoindoline-derived molecules constructed by Benramdane et al (2022) have a certain selectivity, which provides a direction for selective inhibitor design. However, DPP8 and DPP9 were found to have consistent allosteric interactions with their substrates in molecular dynamics simulations, and the authors believed that it was difficult to design targeting ligands that distinguish the two ( Ross et al, 2018 ).…”

Insight into the Role of Active Site Protonation States and Water Molecules in the Catalytic Inhibition of DPP4 by Vildagliptin

“…22,23 His126 is part of the S2 recognition domain of DPP4 and has been proposed to play a structuring role by engaging in hydrogen bonding interactions with the substrate anchoring residue Glu205 (Figure 2B). 24 His126 has also been proposed as a binding site residue for noncovalent DPP4 inhibitors. 25−27 Asp663 also belongs to the S2 recognition subsite and is responsible for the differential substrate specificity and enzyme activity between DPP4 and the homologous fibroblast activation protein α (FAP).…”

“…Analysis of the crystallographic model of the covalent complex with VIL (PDB code 6B1E) with different computational tools (H++, PROPKA, , APBS, and p K a -ANI) led to inconclusive assignments for His126, Asp663, and Asp709 residues (Figure S1). These residues are within a 10 Å radius from the catalytic triad and could play a relevant role in controlling the noncovalent binding and catalytic properties of DPP4 due to differential electrostatic effects arising from their possible protonation forms (Figure A). , His126 is part of the S2 recognition domain of DPP4 and has been proposed to play a structuring role by engaging in hydrogen bonding interactions with the substrate anchoring residue Glu205 (Figure B) . His126 has also been proposed as a binding site residue for noncovalent DPP4 inhibitors. − Asp663 also belongs to the S2 recognition subsite and is responsible for the differential substrate specificity and enzyme activity between DPP4 and the homologous fibroblast activation protein α (FAP) .…”