In silico discovery and in vitro validation of catechol-containing sulfonohydrazide compounds as potent inhibitors of the diguanylate cyclase PleD

Biofilm formation is responsible for increased antibiotic tolerance in pathogenic bacteria. Cyclic di-GMP (c-di-GMP) is a widely used second-messenger signal, playing a key role in bacterial biofilm formation. C-di-GMP is synthesized by diguanylate cyclases (DGC), a conserved class of enzymes absent in mammals, hence considered attractive molecular targets for the development of anti-biofilm agents.Here, the results of a virtual screening approach aimed at identifying small-molecule inhibitors of the DGC PleD from Caulobacter crescentus are described. A 3D-pharmacophore model, derived from the binding mode of GTP to the active site of PleD was exploited to screen the ZINC database of compounds. Seven virtual hits were tested in vitro for their ability to inhibit the activity of purified PleD by using circular dichroism spectroscopy. Two drug-like molecules with a cathecol moiety and a sulfonohydrazide scaffold were shown to competitively inhibit PleD at low micromolar range (IC50 ≈ 11 μM). Their predicted binding mode highlighted key structural features presumably responsible for the efficient inhibition of PleD by both hits. These molecules represent the most potent in vitro inhibitors of PleD identified so far, and could therefore result in useful leads for the development of novel classes of antimicrobials able to hamper biofilm formation.