FBLD, of course, starts with
small libraries of small fragments. DNA-encoded chemical libraries (DEL) usually
start from the opposite extreme. Massive numbers of molecules are combinatorially
synthesized attached to DNA, screened against a target using affinity selection,
and hits identified by sequencing the DNA. A recent paper in J. Med. Chem.
by Christopher Wellaway and colleagues at GlaxoSmithKline uses information from
both approaches to generate a high-quality candidate.
The researchers were interested in
bromodomain and extraterminal (BET) family proteins – the same targets we discussed
last week. GlaxoSmithKline had already put molecules into the clinic, but they
were looking for structurally different backup candidates, so they performed a
DEL screen on the BD1 domain of BRD4. A library of 117 million compounds yielded
potent compound 10, and crystallography revealed that the 2,6-dimethylphenol
moiety bound in the acetyl-lysine-binding pocket.
Phenols are often metabolic
liabilities, and indeed compound 10 was rapidly cleared in mice. However, GlaxoSmithKline
has a long and successful history of fragment screening against bromodomains;
Teddy first described some of their seminal work back in 2012, when the world didn’t end. Compound 16 had been found in a previous screen as a hit against
BRD4, and crystallography revealed that the pyridone binds in a similar fashion
to the phenol moiety. (Similar pyridones had been reported by others, for example this one.) Merging the molecules led – after a bit of tweaking – to compound
20a. In addition to BRD4, this molecule binds another bromodomain, BAZ2A, which
the researchers wanted to avoid. Structure-based design led them to the more selective
compound 20i.
Although compound 20i is potent
in cells, it still has moderate clearance in rats. Unsubstituted benzimidazole rings
have been reported to be unstable, so the researchers systematically explored a
series of substitutions, ultimately arriving at compound 24 (I-BET469). Not only is this compound
potent and soluble, it is remarkably stable, with “no detectable turnover in
rat, dog, and human microsomal and hepatocyte preparations.” Oral bioavailabilities
approach 100%, and the compound proved to be effective in acute and chronic
mouse inflammation models. Although selectivity against non-BET family bromodomains
members is good, compound 24 does strongly bind to both BD1 and BD2 domains of
all four BET family members, and as we saw last week this may lead to toxicity.
Nonetheless, this is a lovely example
of using a fragment to replace a problematic moiety in a larger molecule, as we’ve
seen previously for chymase, Factor VIIa, and Factor XIa. Throughout the
optimization the researchers paid close attention to molecular properties such
as lipohilicity and molecular weight, and this resulted in a molecule with
excellent pharmacokinetics despite the presence of potentially unstable
moieties such as the morpholine. If nothing else, this will be a useful in vivo chemical probe.
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