Just as April
brings CHI’s Drug Discovery Chemistry in San Diego, September brings CHI’s
Discovery on Target in Boston, and last week saw more than 1100 attendees
attend 14 tracks over three days, along with associated training seminars and
short courses. Fragments made appearances throughout.
Perhaps the
most notable new development was an entire session devoted to covalent
fragments. We spent three blog posts in June covering five papers on this
topic, so this was a timely addition.
Eranthie
Weerapana (Boston College) described proteomics methods for analyzing cysteine modification
in cells. (Some of this is similar to Ben Cravatt’s work, which we discussed
here.) She noted that many mitochondrial proteins have low abundance and are thus
hard to detect, but by isolating the mitochondria she has been able to observe
about 1500 cysteines on 500 proteins. Selenocysteine-containing proteins are even less common
and can thus be lost in the noise, but by lowering the pH these rare beasts can
be labeled selectively.
Alexander Statsyuk
(University of Houston) gave two wide-ranging talks, and he noted that
(beyond acrylamides) there are about 50 warheads that have not been widely
explored. We’ve previously covered his work with fragments containing the 4-aminobut-2-enoate
methyl ester, and Katrin Rittinger (Francis Crick Institute) discussed her recent use
of a small library of just 104 of these to find a covalent inhibitor of LUBAC. And on the subject of very recent
papers, I presented work from Carmot and Amgen on the discovery of covalent KRASG12C
inhibitors.
You know a
field is becoming popular when suppliers start selling reagents, and this is certainly
the case for covalent fragments: Enamine and Life Chemicals both sell covalent
fragment libraries. If you’ve had experience with them or others, please leave
comments!
Natalia
Kozlyuk (Vanderbilt) gave a nice presentation that emphasized some of the
challenges that can arise in FBLD. Screening 14,000 fragments against the
protein RAGE by NMR resulted in a number of hits, and crystallography revealed
that a couple of these bind just 4 Å apart. Linking these together with variable-length
linkers led to one molecule that bound as expected, while in another one of the linked
fragments bound in a third site. Unfortunately,
even the best dimeric molecules are quite weak, and they also cause the protein to
precipitate. This appears to be a different mechanism from “classic” small
molecule aggregation, in which the small molecules first form aggregates that block protein activity, though it is not unprecedented.
In a similar
vein, Stijn Gremmen and Jan Schultz (ZoBio) described work done with Gotham Therapeutics
to discover inhibitors of the methyltransferase complex METTL3/METTL14.
HTS-derived compounds caused aggregation
of protein as assessed by size exclusion chromatography and multiangle light
scattering, but a fragment screen followed by optimization led to potent,
well-characterized molecules.
Continuing the
theme, Beth Knapp-Reed (GSK) described an HTS assay against the anti-cancer
target LDHA in which 1.9 million compounds yielded 560 hits, almost all of
which turned out to be false positives due to oxalic acid contamination.
Fragment screening was more productive, yielding 16 crystallographically validated
hits, and the researchers were able to improve the affinity more than 10,000-fold.
And Puja Pathuri discussed successful efforts at Astex to discover ERK1/2
inhibitors (see here for more details).
Finally, last year
we noted the increasing number of talks on PROTACs and targeted protein degradation.
This year for the first time the conference held a full day and a half long
program on the topic. PROTACs typically consist of two-component molecules
in which one piece binds to a target of interest and the other piece binds to
a protein called an E3 ligase which ultimately causes proteolytic degradation
of the target. For example, Michael Plewe described how he and his colleagues
at Cullgen have modified the fragment-derived vemurafenib to target an oncolytic
mutant form of BRAF.
One of the
interesting features of targeted protein degradation is that a high affinity
ligand is not always necessary: Craig Crews (Yale) described how an 11 µM p38α
ligand was sufficient to degrade 99% of the protein in cells. And fragments can
help not just with target proteins, but in identifying new E3 ligase ligands as
well. Carles Galdeano (University of Barcelona) described how fragment
screening has yielded a couple sub-micromolar affinity ligands of an E3 ligase called
Fbw7.
In the interest
of time I’ll stop here, but if you were particularly struck by anything please
mention it in the comments. And if you missed the meeting, be sure to mark
September 15-18 on your calendar for next year!
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