A fragment-sized chemical probe for Notum

Practical Fragments has written previously (here and here) about the enzyme Notum, which shuts down Wnt signaling by removing a palmitoyl group. Aberrant Wnt signaling is implicated in maladies from cancer to osteoporosis, but Paul Fish has been particularly focused on neurological conditions such as Alzheimer’s disease. In a paper just published in J. Med. Chem., Fish and collaborators at University College London, University of Oxford, and The Francis Crick Institute describe their discovery of a chemical probe for this target.

 

As we discussed last year, the researchers conducted a crystallographic screen of the 768-member Diamond-SGC Poised Library, which resulted in 59 hits. Biochemical confirmation studies revealed that fragment 6b, a close analog of a fragment described earlier, is remarkably potent. The substituted phenyl ring nicely fills the lipophilic active site, and the triazole forms a hydrogen bond with a backbone amide of the protein. Structure-based design subsequently led to compound 7y, with low nanomolar potency.

 

The previous fragment-based efforts against Notum also yielded potent molecules, but they had poor brain-penetration. In contrast, compound 7y has a high brain-to-plasma ratio, though the compound also has high clearance, which was attributed to phase 2 metabolism at the hydroxyl. The researchers explored a variety of replacements and substitutions, all of which led to loss in potency, but interestingly removing the hydroxymethyl substituent altogether was tolerated.

 

The resulting molecule, ARUK3001185, is a potent inhibitor of Notum both in biochemical and cell assays. It has good oral bioavailability and pharmacokinetics in mouse and rat. Importantly, it also has excellent brain penetration in both species. The molecule showed virtually no inhibition of 39 other serine hydrolases or 485 kinases and was fairly clean in a safety panel of some four-dozen human targets, including hERG. In other words, ARUK3001185 appears to be an excellent chemical probe.

 

This is a nice example of how a fragment-sized molecule can nonetheless achieve high affinity and selectivity. As we’ve seen repeatedly, potency is not enough; one often needs to spend considerable effort to optimize other properties such as brain penetration. It will be fun to see what this new probe can teach us about Wnt signaling in the brain.