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!