Development of a Genetically Encoded and Potent PDE6D Inhibitor

PDE6D is a trafficking chaperone of prenylated proteins, such as small GTPases. Several small molecule inhibitors have been developed against it, given that the oncogene K-Ras is one of the cargo proteins. Inhibitor development suffers from the fact that inhibitors against the hydrophobic pocket of PDE6D are typically poorly water-soluble. Herein, the development of genetically encoded inhibitors that are inspired by high-affinity natural cargo of PDE6D is described. The most potent inhibitor, SNAP-STI, encodes merely a farnesylated tetra-peptide, which efficiently blocks PDE6D binding of farnesylated cargo. Direct comparison with small molecule PDE6D inhibitors suggests its higher potency. It is shown that inhibition of K-Ras membrane anchorage and K-RasG12C-dependent MAPK signaling by SNAP-STI is weak, consistent with what is observed after PDE6D knockdown. The data therefore further support that PDE6D is not a suitable surrogate target for efficient inhibition of K-Ras membrane anchorage and MAPK-activity. Nonetheless, by exploiting contacts at the pocket entry, a generalizable strategy to design high-affinity PDE6D inhibitors is established, providing powerful tools for PDE6D biology and target validation.