Coumarin Derivatives Act as Novel Inhibitors of Human Dipeptidyl Peptidase III: Combined In Vitro and In Silico Study.

Dejan Agić,Sanja Tomić,Maja Karnaš,Miroslav Lisjak,Boris M Popović,Maja Molnar,Vesna Rastija,Zrinka Karačić,Melita Lončarić,Drago Bešlo,Domagoj Šubarić

doi:10.3390/ph14060540

Abstract

Dipeptidyl peptidase III (DPP III), a zinc-dependent exopeptidase, is a member of the metalloproteinase family M49 with distribution detected in almost all forms of life. Although the physiological role of human DPP III (hDPP III) is not yet fully elucidated, its involvement in pathophysiological processes such as mammalian pain modulation, blood pressure regulation, and cancer processes, underscores the need to find new hDPP III inhibitors. In this research, five series of structurally different coumarin derivatives were studied to provide a relationship between their inhibitory profile toward hDPP III combining an in vitro assay with an in silico molecular modeling study. The experimental results showed that 26 of the 40 tested compounds exhibited hDPP III inhibitory activity at a concentration of 10 µM. Compound 12 (3-benzoyl-7-hydroxy-2H-chromen-2-one) proved to be the most potent inhibitor with IC50 value of 1.10 μM. QSAR modeling indicates that the presence of larger substituents with double and triple bonds and aromatic hydroxyl groups on coumarin derivatives increases their inhibitory activity. Docking predicts that 12 binds to the region of inter-domain cleft of hDPP III while binding mode analysis obtained by MD simulations revealed the importance of 7-OH group on the coumarin core as well as enzyme residues Ile315, Ser317, Glu329, Phe381, Pro387, and Ile390 for the mechanism of the binding pattern and compound 12 stabilization. The present investigation, for the first time, provides an insight into the inhibitory effect of coumarin derivatives on this human metalloproteinase.

Highlights

In search of new inhibitors from natural sources, we previously reported that luteolin has the best inhibitory effect against hDPP III (IC50 = 22 μM) of the 17 flavonoids tested, and that the number and exact distribution of –OH groups on the flavonoid core is important for their inhibitory properties [25]
We evaluated forty various coumarin compounds for their inhibitory potential towards hDPP III
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Summary

Introduction

As a member of the metalloproteinase family M49, DPP III distribution is detected in almost all forms of life [2]. Human DPP III is a very well-characterized member of this family in terms of biochemistry, structural biology and computational chemistry [3,4,5,6,7,8,9,10]. Due to the relative non-specificity of the peptide substrates as well as the lack of selective inhibitors of the metallopeptidases of the M49 family, the physiological substrates of DPP III have not been accurately identified, and its fundamental physiological role has not been precisely determined. It is assumed that it is involved in post-proteasomal intracellular protein catabolism [3], Pharmaceuticals 2021, 14, 540.

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Results

Conclusion