Targeted protein degradation (TPD)
goes beyond merely inhibiting a protein; it takes a protein out of commission
entirely. This is frequently done using a bivalent ligand: one part binds to the protein
of interest, while the other part binds to an E3 ligase, which ubiquitinates
the protein of interest, targeting it for destruction in the proteasome. Human
cells have hundreds of E3 ligase proteins, some of which may work better in
certain situations, such as specific cell compartments or tissues. In a recent
ACS Med. Chem. Lett. paper, Anna Vulpetti and colleagues at Novartis describe
progress against DCAF1.
DCAF1 is one component of the
Cullin4-RING E3 ubiquitin ligase complex. The C-terminus of the protein
contains a WD40 repeat (WDR) domain, which in this case consists of seven “blades”
arranged around a central cavity, or “donut hole”. WDR domains are relatively common,
and indeed we wrote about a previous Novartis effort that identified chemical
probes against another WDR domain in the protein EED. In the new work, the
researchers took 21 EED binders and screened them using both protein-detected
and ligand-detected NMR against DCAF1, identifying two hits. Crystallography
revealed that compound 1 binds in the central cavity, which previous computational
screening had suggested would be ligandable.
Next, the researchers screened 30
related compounds from within Novartis. Two of them, including compound 4, had improved affinity (as
assessed both by NMR and SPR) and could be characterized crystallographically.
In addition to binding in the central cavity, these compounds also bound to a
site in the blade region, which the researchers wanted to avoid. Adding a piperazine to compound 4 both improved affinity and disrupted
binding to the blade region; further optimization and growing to better fill
the central cavity led to compound 13, the most potent molecule in the paper.
A crystal structure of a closely
related molecule reveals that the acetyl group is near the entrance to the
donut hole, providing an easy synthetic attachment point to construct bivalent
degraders. A separately published preprint revealed this to be successful, with
degraders of BRD9, multiple tyrosine kinases, and BTK.
There are several takeaways from
this nice fragment to lead story. First, despite the fact that compound 1 is
clearly fragment-sized (albeit a bit too lipophilic to be fully rule-of-three
compliant), the word fragment never appears in the article. FBLD has become so routine
that researchers may not even mention it, which does mean that our list of
fragment-derived drugs is destined to be incomplete.
Second, although DCAF1 and EED
share less than 25% sequence similarity, screening EED hits turned out to be
successful, which could argue for screening specific subsets of fragments (for example
kinase-focused or, in this case, WDR-focused). On the other hand, compound 1 binds
in a different manner to DCAF1 than it does to EED. Indeed, compound 1 actually
binds in two different orientations to DCAF1, consistent with its low
affinity. The researchers mention a paper published earlier this year that
reports a successful DEL screen against the target. Perhaps DCAF1 is just very
ligandable, and a naïve fragment screen would have worked just as well as
the pre-selected set.
Finally, the fact that this
program yielded bivalent degraders suggests that many E3 ligases might be
coopted for drug discovery. The field of targeted protein degradation is just
getting started.
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