Among the various epigenetic “writers,”
only one is capable of trimethylating lysine 36 of histone H3. SET
domain-containing protein 2 (SETD2) is thought to be a tumor suppressor, but some
evidence suggests it may have the opposite effect in certain cancers. A
chemical probe would be useful to resolve these conflicting ideas, and in an (open
access) ACS Med. Chem. Lett. paper Neil Farrow and colleagues at Epizyme
describe one.
Epizyme has been pursuing epigenetic
targets for years and has built a methyltransfersase-biased compound collection.
A radiometric screen of this library yielded compound 1 and a related molecule.
Both were weak inhibitors, but a co-crystal structure with the enzyme revealed
the indole buried deep in the substrate binding pocket. Tweaking this led to compound
4, with low micromolar activity.
Substitution off the indole and
phenyl moieties ultimately led to compound 25, with low nanomolar biochemical
and cell activity. However, this molecule also had low aqueous solubility and poor
pharmacokinetics in mice. Recognizing that the lipophilic and aromatic nature
of the molecule were likely responsible, the researchers returned to the
initial hit. Replacing the phenyl with a cyclohexyl moiety and making a few
more modifications ultimately led to EPX-719.
The pharmacokinetics of EPX-719
in mice are reasonable, and the molecule is >8000-fold selective against a
panel of 14 other histone methyltransferases. It is also fairly clean against a
panel of 47 off-targets and 45 kinases. EPX-719 showed antiproliferative
activity in two multiple myeloma cell lines, and more detailed biological studies
are promised in a future paper.
This is a nice hit to lead story.
As the researchers note, “close attention to the physical chemical properties of
the inhibitors, in particular basicity, lipophilicity, and aromatic character,
led to compounds with attractive cellular activities and in vivo exposures.”
Interestingly though, the word “fragment” does not appear once in the paper. Although
compounds 1 and 4 venture a bit beyond the rule of three, I would argue that
starting with small, low affinity binders and focusing closely on molecular
properties is the very definition of fragment-based lead discovery.
A quarter-century of FBLD has influenced
the scientific zeitgeist, and a fragment by any other name is still as sweet.
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