In Silico-Guided Identification of New Potent Inhibitors of Carbonic Anhydrases Expressed in Vibrio cholerae

Abstract

Carbonic anhydrases from Vibrio cholerae (VchCAs) play a significant role in bacterial pathophysiological processes. Therefore, their inhibition leads to a reduction of gene expression virulence and bacterial growth impairment. Herein, we report the first ligand-based pharmacophore model as a computational tool to study selective inhibitors of the β-class of VchCA. By a virtual screening on a collection of sulfonamides, we retrieved 9 compounds that were synthesized and evaluated for their inhibitory effects against VchCAβ as well as α- and γ-classes of VchCAs and selectivity over human ubiquitous isoforms hCA I and II. Notably, all tested compounds were active inhibitors of VchCAs. The N-(4-sulfamoylbenzyl)-[1,1'-biphenyl]-4-carboxamide (20e) stood out as the most exciting inhibitor toward the β-class (K _i = 95.6 nM), also showing a low affinity against the tested human isoforms. By applying docking procedures, we described the binding mode of the inhibitor 20e within the catalytic cavity of the modeled open conformation of VchCAβ.

Figure 1

Chemical structures of well-known VchCA inhibitors: acetazolamide (AAZ) and ethoxzolamide (EZA).

Figure 2

Binding site analysis of the modeled dimeric VchCAβ open cavity bound to acetazolamide (AAZ).

Figure 3

Chemical structures of compounds 1–19.

Figure 4

(A) Best pharmacophore model: one aromatic ring feature (blue) overlapped with the hydrophobic feature (yellow), three hydrogen bond acceptors (red), two hydrogen bond donors (green), one negative ionizable (red star), and 31 exclusion volumes (gray). (B) AAZ mapped into the pharmacophore model.

Figure 5

Schematic representation of structural moieties shared by sulfonamides 20a–i

Scheme 1. Synthetic Route for Desired N-(4-Sulfamoylbenzyl)amide Derivatives 20a–i

Reagents and conditions: (i) (A) RCOCl, DIPEA, DCM/DMF (2:1, v/v), MW, 25 °C, 10 min; (B) RCO₂H, HBTU, DIPEA, DCM/DMF (2:1, v/v), MW, 25 °C, 25 min.

Figure 6

Plausible binding mode of 20e into our “modeled” open conformation of VchCAβ. Dark gray dashed lines represent hydrogen bond interaction. Zinc ion is depicted as a yellow sphere. The interactions were examined by using LigandScout software. The images were created by means of PyMOL software (https://pymol.org).