Structure-Based Ligand Discovery Targeting the Transmembrane Domain of Frizzled Receptor FZD7

Despite
the essential roles of Frizzled receptors (FZDs) in mediating
Wnt signaling in embryonic development and tissue homeostasis, ligands
targeting FZDs are rare. A few antibodies and peptide modulators have
been developed that mainly bind to the family-conserved extracellular
cysteine-rich domain of FZDs, while the canonical binding sites in
the transmembrane domain (TMD) are far from sufficiently addressed.
Based on the recent structures of FZDs, we explored small-molecule
ligand discovery by targeting TMD. From the ChemDiv library with ∼1.6
million compounds, we identified compound F7H as an antagonist of
FZD7 with an IC50 at 1.25 ± 0.38 μM. Focusing
on this hit, the structural dissection study, together with computing
studies such as molecular docking, molecular dynamics simulation,
and free energy perturbation calculations, defined the binding pocket
with key residue recognition. Our results revealed the structural
basis of ligand recognition and demonstrated the feasibility of structure-guided
ligand discovery for FZD7-TMD.