Targeting RAS via PDEδ: another protein-protein interaction

Last week we highlighted molecules that inhibit the interaction between oncogenic RAS proteins and an activator protein, SOS1. This week continues the subject of fragments and RAS, but with a different protein-protein interaction, described in a recent paper in Eur. J. Med. Chem. by Min Huang, Naixia Zhang, Bing Ciong, and colleagues at Shanghai Institute of Materia Medica.

The researchers were interested in the protein PDEδ, which binds to lipidated RAS proteins and helps shuttle them to the plasma membrane. Blocking this protein-protein interaction could interfere with RAS signaling. PDEδ was screened against just 535 fragments using two ligand-observed NMR techniques (STD and CPMG), yielding five hits. Crystallography revealed that compound 1-H9 bound at the site where RAS normally binds. Other groups had previously identified molecules that bind in this same region, and the researchers used this information to grow their fragment to compound 16, with low micromolar activity.

Interestingly, a crystal structure of compound 16 showed that the binding mode had flipped relative to the initial fragment: the isobutyl group, which had been designed to replace the isopropylthio group, was binding in a region of the protein previously unoccupied by the fragment. Further growing led to compound 40, with mid-nanomolar potency in a biochemical assay.

Unfortunately, compound 40 and other molecules in the series had at best only modest activity in a viability assay of cells dependent on PDEδ. This result is in contrast to a previously reported PDEδ inhibitor, and the researchers suggest that the difference could be due to off-target activity of that molecule. Indeed, a third group has reported that inhibition of PDEδ would need to be nearly complete to be pharmacologically useful. As the researchers conclude somewhat optimistically, “all these complexities of PDEδ-associated proteins may impose a challenge and opportunity for PDEδ-targeted anticancer drug discovery.” While it is easier to see the challenges than the opportunities, this is nonetheless a nice example of using fragments to target a protein-protein interaction.