Experimental and computational evaluation of dipeptidyl peptidase III inhibitors based on quinazolinone-Schiff’s bases

Abstract

Dipeptidyl peptidase III (DPP III) is a zinc-dependent enzyme that sequentially hydrolyzes biologically active peptides by cleaving dipeptides from their N-termini. Although its fundamental role is not been fully elucidated, human DPP III (hDPP III) has been recognized in several pathophysiological processes of interest for drug development. In this article 27 quinazolinone-Schiff’s bases were studied for their inhibitory activity against hDPP III combining an in vitro experiment with a computational approach. The biochemical assay showed that most compounds exhibited inhibitory activity at the 100 μM concentration. The best QSAR model included descriptors from the following 2D descriptor groups: information content indices, 2D autocorrelations, and edge adjacency indices. Five compounds were found to be the most potent inhibitors with IC₅₀ values below 10 µM, while molecular docking predicted that these compounds bind to the central enzyme cleft and interact with residues of the substrate binding subsites. Molecular dynamics simulations of the most potent inhibitor (IC₅₀=0.96 µM) provided valuable information explaining the role of PHE109, ARG319, GLU327, GLU329, and ILE386 in the mechanism of the inhibitor binding and stabilization. This is the first study that gives insight into quinazolinone-Schiff’s bases binding to this metalloenzyme.

Communicated by Ramaswamy H. Sarma

Keywords:

• Dipeptidyl peptidase III
• inhibitor
• molecular modeling
• quinazolinone-Schiff’s bases

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work has been supported by the Croatian Science Foundation under the projects IP-2018-01-2936, UIP-2017-05-6593 and the Isabella cluster (http://www.srce.unizg.hr/en/isabella/).