The blood coagulation cascade involves several serine
proteases, many with an appetite for arginine-containing peptides. The polar,
basic guanidine moiety of arginine tends to wreak havoc on the pharmacokinetic
properties of small molecules, sparking an intensive search for replacements. A
few months ago we described how researchers were able to use fragment screening
to find an alternative moiety for one member of the blood coagulation cascade.
In a recent paper in J. Med. Chem.,
Daniel Cheney and colleagues at Bristol-Myers Squibb report their work on
another, factor VIIa.
The researchers started by filtering commercially available
small molecules to look for those with ≤ 17 non-hydrogen atoms, ≤ 3 rotatable
bonds, and without anything nasty. This computational work left them with
18,000 fragments. These were then clustered based on similarity, and 200
compounds were chosen by chemists as having the potential to bind in the deep
S1 pocket, where the guanidine normally binds.
At the same time, the 18,000 fragments were computationally
docked (using Glide) against several different crystal structures of factor VIIa;
this “ensemble docking” was used to account for the protein flexibility
observed in various structures. This led to a further 250 fragments being
chosen.
The 450 fragments were then assessed in biochemical and STD
NMR-based assays, and 41 were soaked into crystals of factor VIIa, resulting in
27 structures with fragments bound in the S1 pocket. Happily, 12 of these
fragments were – unlike guanidine – neutral. All of them were quite weak (even
by fragment standards), with Ki values ranging from 8-19 mM, though searching
for related fragments led to some with slightly improved affinities. However,
when examining the binding mode of fragment 7, the researchers realized they
could use it to replace a more basic moiety in their existing lead series (17),
yielding compound 18. Although this reduced the potency, it dramatically
improved the permeability. Also, the researchers stated that they were able to
subsequently improve the potency, with details to come in a subsequent paper.
This is another nice example of using fragments to fix part
of a larger molecule, though it is not necessarily easy. The researchers note
that other attempts to append new fragments onto their existing scaffold were
unsuccessful, likely due to geometric incompatibilities. This paper is also an
illustration of how long it can take to get things published. One of the
authors gave a nice presentation on some of this work at an ACS meeting in 2012, and there’s a line in the paper referring to a publication that came out
“shortly after completion of this work” – in 2006! Still, late or not, it is
nice to see the story in print, with a promise of more to come.
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