FBLD 2024

The FBLD meetings have always been calendar highlights. Starting in 2008, before Practical Fragments even existed, they have graced cities around the world in 2009, 2010, 2012, 2014, 2016, and 2018. The plan was for 2020 to be held in Cambridge, UK, but for obvious reasons that didn’t happen. Last week, Boston hosted a triumphant return of the event. With more than 30 talks and dozens of posters I’ll just touch on a few major themes.

 

High-throughput crystallography was prevalent, as befits its growing role in fragment finding. (If you haven’t yet voted in our methods poll on the right side of the page please do so!) Debanu Das (XPose Therapeutics) described how crystallographic screens of just a few hundred fragments identified hits against DNA-damage response proteins such as APE1; these have been advanced to high-nanomolar inhibitors with cell activity. And Andreas Pica described the ALPX platform that enabled screening >4000 hits from an HTS screen against PDEδ resulting in >500 structures.

 

The Diamond Light Source was a pioneer in developing high-throughput crystallography methods, and several speakers described continued progress. Blake Balcomb noted that since 2015 they have collected >240,000 datasets and identified >30,000 ligands. Of these, some 3750 have been deposited into the Protein Data Bank.

 

A crystallographic fragment hit is just the start, and Frank von Delft emphasized that “fragment progression is neither fast nor cheap.” His goal is to take a 100 µM binder to a 10 nM lead in less than a week for less than £1000. Toward this end he and his team are using rapid chemical synthesis and crude reaction screening along with various computational approaches and crowd-sourced science. The COVID Moonshot, which we wrote about here, is one model, and Diamond is trying to create a “Moonshot factory” to pursue other viral targets.

 

Computational methods are potentially the least expensive fragment-to-lead method, and these were well represented. One challenge is screening the massive chemical space represented by make-on-demand libraries, and Pat Walters (Relay) described how this can be done using Thompson Sampling, an active-learning method that traces its origins to 1933. Applied to lead discovery, the method involves breaking larger molecules into component fragments and iteratively searching for better binders. Pat showed that searching just 0.1% of a library of 335 million molecules consistently found 90% of the best hits.

 

Most computational methods rely on experimental data, and over the past 25 years Astex has generated >100 crystal structures on each of more than 40 targets, with >6600 bound fragments in total. Paul Mortenson described how these are being used to develop generative models, with chemists providing feedback on suggested molecules.

 

Artificial intelligence is the centerpiece of Isomorphic Labs, which has unfettered access to AlphaFold 3. Rebecca Paul described an example starting from a literature fragment in which the predicted affinities matched well with experiment – and the molecules were considerably more potent than those suggested by an experienced medicinal chemist.

 

Recognizing the need for experimental affinity data for fragments, Isomorphic worked with Arctoris to screen 5420 fragments against 65 kinases covering the diversity of the kinome. After carefully curating the data, including rescreening the actives at a different CRO, they found 485 fragments with an IC₅₀ of 300 µM or better. Interestingly, only about half of these fragments are known kinase binders.

 

Sandor Vajda (Boston University) suggested there may be limitations to machine learning models. He found that using AlphaFold 2 to find cryptic pockets was dependent on their representation in the PDB, with rare experimental states not being predicted. Sandor also proposed an interesting hypothesis that cryptic pockets created only by the movement of side chains are not very ligandable because the side chains move on such a rapid time scale that they effectively act as competitive inhibitors to ligands.

 

No FBLD meeting would be complete without success stories, and FBLD 2024 was no exception. Chaohong Sun noted that nearly 80% of the targets at AbbVie taken into fragment-based screening are novel. Of these, more than 80% yield actionable hits, though 44% are not pursued for a variety of reasons, including finding hits from other sources, hits at novel sites with no obvious function, and changes to the portfolio. Chaohong described a series of STING agonists that was taken forward to low nanomolar leads with in vivo activity.

 

Michelle Arkin (UCSF) described progress on creating molecular glues to link 14-3-3 proteins to the estrogen receptor, which we last wrote about here. Covalent binders to the 14-3-3 protein stabilize the interaction with ERα by more than 100-fold and show activity in cancer cell models.

 

Multiple talks focused on SARS-CoV-2 targets. Ashley Taylor (Vanderbilt) described fragment screens against the papain-like protease PL^Pro that led to both covalent and non-covalent inhibitors. James Fraser (UCSF) described how a massive crystallographic screen against the Nsp3 macrodomain Mac1 led to high nanomolar compounds, which we wrote about here. And Adam Renslo (UCSF) discussed the further optimization of Mac1 inhibitors to yield molecules that could protect mice from a fatal challenge of the virus.

 

A drawback of pursuing novel targets is that sometimes the biology proves uncooperative. Andrew Woodhead described a successful fragment screen at Astex against the oncology target elF4E that led to mid-nanomolar binders that could disrupt the protein-protein interaction with eIF4G in cells. Surprisingly, these molecules had no effect on cell viability, and a series of mutational and targeted-protein degradation experiments suggested that blocking a larger region of the protein-protein binding site might be necessary.

 

Drugs are the ultimate success stories, as David Rees reminded participants in “25 years of thinking small.” In addition to providing an overview of FBLD at Astex, David added up the sales of all seven FDA-approved fragment-derived drugs, which totals more than $3 billion. Harder to quantify—though infinitely more valuable—are the added years of life for patients with once-untreatable cancers. These numbers will only grow as the dozens of fragment-derived molecules in the clinic continue to advance.

 

I’ll close on that note. If you missed FBLD 2024, you’ll have another chance next year: FBLD 2025 is planned for Cambridge (UK) September 21-24 next year. Barring global pandemics.