15 February 2021

Fragments vs Notum, three ways

The Wnt signaling pathway has been implicated in multiple diseases, from Alzheimer’s to cancer to osteoporosis. To be able to bind receptors, Wnt proteins must be post-translationally modified with a palmitoleate group. The carboxylesterase Notum removes this group, shutting of signaling. Thus, inhibitors of Notum could maintain Wnt activity. In two J. Med. Chem. papers, E. Yvonne Jones (University of Oxford), Paul Fish (University College London), and collaborators describe three series of inhibitors derived from fragments.
The palmitoleoyl group is highly lipophilic, and previous work with Notum had revealed a predilection for hydrophobic carboxylic acids. Thus, in the first paper, the researchers assembled a library of 250 diverse carboxylic acids, all rule-of-three compliant. Each was tested (10-point dose-response) in a biochemical screen up to 100 µM. Twenty compounds had IC50 < 25 µM, and all of these were soaked into crystals of Notum, resulting in 14 structures. Two series were pursued.
Compound 5 was one of three pyrroles with low micromolar potency. Fragment growing led to compound 20, and further SAR ultimately led to compound 20z, with high nanomolar activity. Unfortunately, this is a fairly lipophilic molecule, with clogP = 5.5. Indeed, despite best efforts, including paying close attention to lipophilic ligand efficiency (LLE), potency tracked closely with clogP for this series.
The second series, as represented by compound 8, was less potent but also less lipophilic. Walking various substituents around the phenyl increased both properties (compound 25n) and further tweaking led to compound 26. Although this molecule had promising in vitro ADME properties, it was deprioritized in favor of another series described in the second paper

In addition to the biochemical screen, the researchers also conducted a crystallographic fragment screen at the Diamond Light Source XChem platform. This yielded a whopping 60 hits of the 768 fragments screened, with compound 7 being notable for its high potency, ligand efficiency, and LLE. Iterative structure-based design led ultimately to low nanomolar compound 23dd.
Compound 23dd was active in cell-based assays and had acceptable pharmacokinetic properties in mice. The researchers were particularly interested in modulating Wnt signaling in the brain, and in vitro studies suggested that compound 23dd would have good blood-brain permeability. Unfortunately, this turned out not to be the case, for reasons that are still not clear. However, another molecule derived from compound 7 was superior – hopefully the subject of a future paper.

These are nice structurally-enabled fragment to lead stories, and the medicinal chemistry strategies are particularly well described. Notably, the researchers were able to optimize fragment hits to nanomolar binders while maintaining low molecular weights and (in the second and third cases) reasonable lipophilicity. In addition to clear examples of property-driven medicinal chemistry, these papers illustrate that fragment-based methods can yield a variety of starting points, which can be useful when one lead series runs into trouble.


david rees said...

Dan, PF is such a great summary of the literature. I always learn something new from your comments and perspectives. Yours are very wise words, please keep going! I always to promote PF on my slides when lecturing.

david rees said...

Your three February blogs illustrate: comparison of biochemical vs Xray fragment screening (Notum); the application of X-ray structure analysis and parallel synthesis in tandem (PF-06835919); and fragment-to-lead can be successful even without X-ray structures (NPBWR1). Although, as you say, structures are highly preferable, so roll on CryoEM.

Dan Erlanson said...

Thanks David for the kinds words, and for reading!