Virtual Screening Directly Identifies New Fragment-Sized Inhibitors of Carboxylesterase Notum with Nanomolar Activity

Notum is a negative regulator of
Wnt signaling acting through the
hydrolysis of a palmitoleoylate ester, which is required for Wnt activity.
Inhibitors of Notum could be of use in diseases where dysfunctional
Notum activity is an underlying cause. A docking-based virtual screen
(VS) of a large commercial library was used to shortlist 952 compounds
for experimental validation as inhibitors of Notum. The VS was successful
with 31 compounds having an IC50 < 500 nM. A critical
selection process was then applied with two clusters and two singletons
(1–4d) selected for hit validation.
Optimization of 4d guided by structural biology identified
potent inhibitors of Notum activity that restored Wnt/β-catenin
signaling in cell-based models. The [1,2,4]­triazolo­[4,3-b]­pyradizin-3­(2H)-one series 4 represent
a new chemical class of Notum inhibitors and the first to be discovered
by a VS campaign. These results demonstrate the value of VS with well-designed
docking models based on X-ray structures.