Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of β‑Herpesvirus Proteases

Viral
proteases, the key enzymes that regulate viral replication
and assembly, are promising targets for antiviral drug discovery.
Herpesvirus proteases are enzymes with no crystallographically confirmed
noncovalent active-site binders, owing to their shallow and polar
substrate-binding pockets. Here, we applied our previously reported
“Peptide-to-Small Molecule” strategy to generate novel
inhibitors of β-herpesvirus proteases. Rapid selection with
a display technology was used to identify macrocyclic peptide 1 bound to the active site of human cytomegalovirus protease
(HCMVPro) with high affinity, and pharmacophore queries
were defined based on the results of subsequent intermolecular interaction
analyses. Membrane-permeable small molecule 19, designed de novo according to this hypothesis, exhibited enzyme inhibitory
activity (IC50 = 10–6 to 10–7 M) against β-herpesvirus proteases, and the design concept
was proved by X-ray cocrystal analysis.