Binding site comparison for coumarin inhibitors and amine/amino acid activators of human carbonic anhydrases

The first structural analysis comparing the binding mode to the target carbonic anhydrases (CAs, EC 4.2.1.1) of two opposite classes of modulators is presented here: coumarin derivatives act as prodrug CA inhibitors (CAIs), being hydrolyzed by the enzyme esterase activity to 2-hydroxycinnamic acids that occlude the active site entrance; CA activators (CAAs) belonging of the amine and amino acid types, enhance the CA activity by increasing the efficiency of the rate-determining proton shuttling step in the CA catalytic cycle. Analysis of the crystallographic data available for the human CA isoform II in adduct with two coumarin CAIs and some CAAs showed that both types of CA modulators bind in the same region of the enzyme active site, basically interacting with superimposable amino acid residues, that are Trp5, Asn62, His64, Asn67, Gln92, Thr200. A plethora of water molecules also participate in the adducts formation. This structural analysis showed that presence of certain chemical groups in the compound structure is mandatory to produce an activating rather than inhibitory action, such as multiple nitrogen- and oxygen-based moieties capable of shuttling protons or forming extended H-bond networks nearby the proton shuttle residue. This constitutes the only known example among all enzymes of an identical binding site for inhibitors and activators, which, in addition, possess significant pharmacological applications. (C) 2021 Elsevier Masson SAS. All rights reserved.

Automated summary

This study presents the first structural analysis comparing two opposite classes of modulators binding to the target carbonic anhydrases, showing that coumarin derivatives act as prodrug CA inhibitors while CA activators belonging to the amine and amino acid types enhance CA activity by increasing the efficiency of the rate-determining proton shuttling step in the CA catalytic cycle. The analysis of crystallographic data reveals that both types of CA modulators bind in the same region of the enzyme active site, interacting with superimposable amino acid residues and involving a plethora of water molecules in the formation of adducts. Additionally, the study highlights the importance of certain chemical groups in compound structure to produce an activating rather than inhibitory action, with multiple nitrogen- and oxygen-based moieties capable of shuttling protons or forming extended H-bond networks nearby the proton shuttle residue. This unique finding showcases the significant pharmacological implications of having an identical binding site for both inhibitors and activators in enzymes.