Exploiting a Cryptic Pocket in DsbA through Structure-Guided Parallel Synthesis and Direct-to-Biology Screening

Antibacterial
resistance is a major global health problem,
causing
an increasing number of deaths worldwide. DsbA, a bacterial oxidoreductase
enzyme, is pivotal for the correct folding and activity of virulence
factors in bacteria. Inhibiting DsbA presents a promising avenue for
developing antivirulence compounds and combating bacterial resistance.
The enzyme’s structure features two ligand-binding sites: a
hydrophobic groove that is the binding site for natural peptide substrates
and a “cryptic pocket” enclosed within the protein,
which has recently been identified as a target for ligand design.
In this study, we report the elaboration of a fragment from within
the enclosed cryptic pocket into the hydrophobic groove of Escherichia coli DsbA, using X-ray crystallography-guided
structure-based design and parallel synthesis coupled with crude reaction
mixture screening (direct-to-biology). This effort yielded the most
potent small-molecule EcDsbA inhibitors reported
to date and exemplifies a productive strategy for exploiting a cryptic
pocket for drug development.