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.
3 comments:
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.
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.
Thanks David for the kinds words, and for reading!
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