Discovery on Target 2023

Last week CHI’s Discovery on Target was held in Boston. This was the Twentieth Anniversary edition, though oddly last year also claimed to be the twentieth. Regardless, attendance surpassed pre-pandemic levels, with some 1200 attendees, 90% of them in person. Eight or nine concurrent tracks over the course of three days competed with one another, while a couple pre-conference symposia and a handful of short courses were held before the main event. Outside obligations kept me from seeing many talks, including plenary keynotes by Jay Bradner (Novartis), Anne Carpenter, and Shantanu Singh (both at the Broad Institute), but most of these were recorded and will be made available for a year, and I look forward to watching them. Here I’ll just touch on a few of the fragment-relevant talks I was able to attend.

 

“Protein Degraders and Molecular Glues” was a popular track during all three days of the main conference, and in a featured presentation Steve Fesik (Vanderbilt) described how he is using NMR-based FBLD to identify tissue-specific E3 ligases and β-catenin degraders. In the case of β-catenin, a difficult oncology target, a fragment screen identified a 500 µM hit that was optimized to 10-20 nM. This has no functional activity on its own, but combining it with a ligand for an E3 ligase to generate a bivalent PROTAC causes degradation of the protein. Steve is currently optimizing the pharmaceutical properties of these molecules.

 

One exciting application for PROTACs is tissue-specific targeted protein degradation, which could avoid systemic toxicity for proteins such as Bcl-x_L. Steve said that for the past five years he has been pursuing ligands against E3 ligases preferentially expressed in certain tissues, and he presented brief vignettes for three of them. These came from an initial list of 20 E3 targets, but many of them turned out to be too difficult to express.

 

Steve typically screens a library of nearly 14,000 fragments, large according to our recent poll, but this has proven fruitful as only about 10% of proteins he has screened have turned out to be “teflon.” He noted the odd little fragment hit that proved so impactful to the KRAS program we highlighted last year as being something that might have been excluded from a smaller library.

 

We wrote last week about ligands for the E3 ligase DCAF1, and Rima Al-Awar (Ontario Institute for Cancer Research) described another series. She also described ligands against the oncology target WDR5, a target Steve Fesik has pursued as well.

 

Continuing the theme of targeted protein degradation, Jing Liu described Cullgen’s discovery of fragment-sized ligands for a broadly-expressed E3 ligase which could be an alternative to CRBN-targeting ligands when resistance (inevitably) arises. Although he did not specify the E3 ligase, Cullgen has filed a patent application for ligands targeting DCAF1.

 

Rounding out targeted protein degradation, Kevin Webster, my colleague at Frontier Medicines, described the discovery of covalent ligands for the E3 ligase DCAF2 (or DTL) using chemoproteomics and a variety of other techniques including cryo-electron microscopy. Consistent with Steve’s comments, considerable effort went into successfully obtaining a soluble, well-behaved protein.

 

The late Nobel laureate Sydney Brenner said that “progress in science depends on new techniques, new discoveries, and new ideas, probably in that order.” Harvard’s Steve Gygi, one of Frontier’s Scientific Advisory Board members, described multiple new techniques in a featured presentation focused on cysteine-based profiling. These included multiplexed methods to more rapidly find covalent ligands for targets across the proteome. A just-released mass spectrometry instrument made by Thermo Fisher called the Astral further accelerates the process with order-of-magnitude improvements in both speed and sensitivity compared to existing machines.

 

The cell-based covalent screening described by Steve Gygi is very powerful, but so is investigating a single protein, as demonstrated by the discovery of sotorasib. AstraZeneca did early work on covalent screening (which Teddy noted in 2015), and they have continued to build their platform, as described by Simon Lucas. The company has around 12,000 covalent fragments, some beyond the rule of three, with molecular weights between 200 and 400 Da and logP between 0 and 4. More than 90% are acrylamides, a clinically validated warhead, and the researchers are careful to avoid particularly reactive molecules that would be non-specific.

 

In contrast to the electrophilic fragments that comprise most covalent libraries, Megan Matthews (University of Pennsylvania) is exploring nucleophilic fragments for “reverse polarity activity-based protein profiling,” as we highlighted last year. This has led to the discovery of unusual post-translational modifications. For example, the sequence of the protein SCRN3 suggests that it should be a cysteine hydrolase, but the purified protein has no cysteine hydrolase activity, and in cells the N-terminal cysteine is processed to form a glyoxylyl moiety.

 

Finally, Alex Shaginian provided an overview of DNA-encoded library screening (DEL) at HitGen. The company currently has 1.2 trillion compounds spread across more than 1500 libraries, and an obvious question is whether this is overkill. Alex noted that one protein has been screened three times over the course of several years. In the original screen, a modest (30 µM) hit was found from 4.2 billion compounds screened. A later screen of 130 billion compounds produced nothing new, but a more recent screen of 1 trillion compounds led to four mid-nanomolar series. As Steve Fesik noted, screening larger libraries, whether experimentally or computationally, really can be helpful, especially for the hardest targets.

 

Despite only attending half the conference this post is getting long, but for those of you who were there, which talks would you recommend watching?