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.
Crystallography
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 Approaches
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.
Success Stories
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 PLPro 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.
2 comments:
Hi Dan, was there any discussion on the use of X-ray crystallography for measuring concentration responses for ligand binding? My understanding is that it is feasible to do this (binding affinity of pyrazole for PKB was estimated using this approach as discussed in https://doi.org/10.1021/jm070091b) although I have no idea of throughput.
A goal of taking a “100 µM binder to a 10 nM lead in less than a week for less than £1000” does seem to be wildly optimistic (the COVID Moonshot approach was still iterative even though the ability to synthesize large numbers of compounds was leveraged to great effect in order to compress timelines). I would regard an affinity threshold of 10 nM as too stringent for starting lead optimization.
Did Sandor Vajda discuss estimation of the energetic cost of opening cryptic pockets? It’s certainly an issue if attempting to identify cryptic pockets by screening fragment because the affinity of a fragment for the target with an open cryptic pocket will be offset by energetic cost of opening the cryptic pocket.
Hi Pete - no discussion of affinity as a function of electron density. That paper is cool but in the past when I've discussed it with crystallographers they didn't think it would be general.
Agree that Frank's goal is more like a mars-shot than a moon-shot :)
Sandor has a paper on cryptic pockets coming out soon which I'll likely discuss here.
Post a Comment