Docking for Smoothened antagonist chemotypes not susceptible to a vismodegib-resistance mutation

The G protein-coupled receptor Smoothened (SMO) plays a pivotal role in embryonic development transducing the Hedgehog morphogen signal into the cell. Aberrant activation of the pathway is associated with various cancer types. Antagonizing SMO has been recognized as a therapeutic strategy exemplified by drugs such as vismodegib and sonidegib, but despite initial remission, cancer recurrence is frequent due to resistance mutations. Utilizing a structure-based design approach, we have identified three unprecedented chemotypes to antagonize SMO with potencies in the low micromolar range. In total, 67 compounds identified through molecular docking were assayed in four rounds with hit rates of 27% and 63% during hit identification, i.e. the first two rounds. Importantly, the potency of ligands with two of the chemotypes identified in this work is not strongly affected by the vismodegib resistance mutation D473G. The mutation affects potency and maximal inhibitory effect of these ligands only in a way similar to SANT-1, a SMO ligand unencumbered by the mutation. Our study thus shows a successful application of structure-based design for the discovery of novel SMO antagonist chemotypes.