Exploring Urease Inhibition by Coumarin Derivatives through in silico and in vitro Methods

In this report, we designed and synthesized ten N-(R-phenyl)-3-carboxamide-coumarin derivatives (2a-2j), exploring the coumarin nucleus, and an R-phenyl group as a structural scaffold and a peptide bond as a linker between them. The structure-activity relationships were investigated with different R-substituents (H, Br, NO₂, Cl) in ortho, meta, or para positions from the phenyl group. Coumarins were obtained in good yields (72-95%), and in vitro screening against Canavalia ensiformis urease showed potential inhibitory percentages ranging from 42 to 65%. Half-maximal inhibitory concentration (IC₅₀) values were determined for the best compounds 2b (R = 2-Br) and 2d (R = 4-Br). After conducting molecular docking and molecular dynamics on urease from C. ensiformis and Helicobacter pylori, potential binding modes for the most effective compounds 2b and 2d showed that these derivatives are able to interact with the crucial residue Cys592, thereby blocking the access of the urea substrate to the active site. According to density functional theory (DFT) calculations, 4-Br substitution on H. pylori urease was necessary for interacting with catalytic amino acids on the active site.

Keywords:
Canavalia ensiformis ; Helicobacter pylori ; molecular docking; DFT; molecular dynamics