Sixteenth Annual Fragment-Based Drug Discovery Meeting

Last week Cambridge Healthtech Institute held its Sixteenth Drug Discovery Chemistry (DDC) meeting virtually for the second year in a row. The eight tracks, four in parallel, spanned three days. There were occasional kinks, and the 6:30 morning start time was painful for those of us on the Western edge of the US, but for the most part things went smoothly. Attendance was up 25% over last year, to 750 participants. Attendees from outside the US comprised 40%, similar to last year and up from 2019, while industry representation remained steady at 70%. As always I’ll just touch on a few broad themes – please feel free to add your impressions.

 

Methods

These meetings are always great venues to learn about new techniques, and one that stood out is “mass photometry” (MP). This label-free method allows visualization of single proteins in solution. The technology, which builds on interference reflection microscopy and interferometric scattering microscopy, rapidly provides information on the molecular weight of proteins to an accuracy of about 2 kDa. Stefan Geschwindner (AstraZeneca) used the method to follow a change in the monomer-dimer equilibrium of the protein PAD4 in response to ligand-binding. He noted that the instrument, sold by Refyn, provides measurements in about 10 seconds for proteins from 35 kDa to 4 MDa in size.

 

On the opposite end of reductionism, Bryan Roth (University of North Carolina, Chapel Hill) discussed customized high-throughput cell-based screens for 320 of the 358 GPCRs in the human genome. We’ve previously described how these assays have been used to screen molecules prioritized from massive computational screens. If you’d like to profile your own molecules, you can submit compounds here for free with no IP-entanglements.

 

Cryo-EM was the subject of our April 1 post last year, but as we discussed here the technique is no joke. Pamela Williams discussed how Astex has formed a consortium with several other companies to advance the technology. She noted that of the 270 membrane protein structures released last year with resolutions better than 3.5 Å, 167 came from cryo-EM while only 103 came from crystallography. Unlike in crystallography, resolution can vary over the protein; local resolution around the region of interest may be better or worse than global resolution. And there is still much to be done to truly industrialize the approach, particularly in sample preparation (specifically making the grids).

 

Speaking of crystallography, James Fraser (University of California, San Francisco) discussed a high-throughput crystallographic screen against the SARS-CoV-2 macrodomain protein, which we covered earlier this year. A fragment-linking program called “Fragmentstein” was used to generate molecules with low micromolar affinity.

 

At the last DDC meeting Frank von Delft (Diamond Light Source) described a high-throughput crystallographic screen of the SARS-CoV-2 M^Pro protein, and this year he provided an update on how the open-source COVID Moonshot effort has advanced hits to non-covalent 30 nanomolar binders with 100 nanomolar antiviral activity in cells. Current efforts are focused on improving metabolic stability and oral bioavailability, but Frank lamented the “astonishing inertia” on the part of funding agencies to support the effort. Although the spectacular success of vaccines should contain the outbreak, there are still occasional breakthrough infections, and not everyone can be vaccinated or mount a successful immune response. Small molecule drugs will be useful, and it would be nice if more people were working on them.

 

Success Stories

I’ll never turn down a crystal structure, but it is important to remember that fragments can be advanced even in the absence of structural information. As a case in point, Paolo di Fruscia (AstraZeneca) described the discovery of allosteric binders of MEK1; we wrote about these earlier this year.

 

On the other hand, Justin Dietrich described AbbVie’s discovery of TNFα inhibitors – an effort he said would not have been possible without structural information. As we discussed here, the team struggled with the lipophilic nature of some of their initial molecules; Justin noted that “if a protein wants grease you have to find a way to get it grease.” The physicochemical properties can then be improved during optimization.

 

Rod Hubbard (Vernalis) described the discovery of LpxC inhibitors. He emphasized the importance of using biophysical methods to carefully characterize and optimize the target protein, and noted that NMR can identify fragments that crystallography might miss. Also, as we noted when we wrote about this campaign last December, fragments can provide multiple starting points, and it can be useful to optimize fragments before embarking on a fragment-to-lead effort.

 

Jus Singh (Ankaa) provided a brief history of targeted covalent drugs. Some folks are still nervous about the potential for covalent molecules to cause idiosyncratic toxicity; indeed, this was one of the reasons Frank von Delft gave for pursuing non-covalent M^Pro inhibitors. However, Jus noted that five out of seven approved covalent kinase inhibitors are not associated with liver toxicity, while some non-covalent kinases inhibitors are. Jus also noted that all three FDA-approved BTK inhibitors are covalent, despite longstanding efforts to develop non-covalent inhibitors.

 

Finally, Micah Steffek (Genentech) described the discovery of LC3 binders, the first step in making an autophagy-based version of PROTACs. An NMR screen yielded hundreds of hits, but despite obtaining multiple crystal structures the team struggled to obtain molecules with better than mM potency. However, combining fragment information with results from a DEL-screen, akin to the story we described here, led to submicromolar inhibitors. Intriguingly, these covalently modified a lysine residue.

 

Odd and ends

Micah’s talk led to some discussion in a speaker panel as to the meaning of hit rates. Do you consider the primary hit rate or the confirmed hit rate? And what level of confirmation is required? As Rod Hubbard noted, different techniques may give different answers for good reasons, and you don’t want to throw away potential hits on the basis of the worst performing or least sensitive technique.

 

Mads Clausen (Danish Technical University) described his shapely library of fluorinated fragments (see here). Hit rates seem to be similar to flatter compounds, though with only four targets screened it is perhaps too early to draw conclusions.

 

But perhaps there is a limit to shapeliness: Justin Dietrich could not recall seeing any fully unsaturated Fsp³ = 1) fragments coming up as hits, despite being present in the AbbVie libraries. Andreas Lingel said he had occasionally seen these at Novartis, but they were never pursued. Similarly, no one could recall advancing any acyclic fragments. A quick glance at the 131 fragment-to-lead success stories captured in five annual reviews revealed that all of the fragments had at least one ring and one sp²-hybridized carbon.

 

And with that I’ll close. The Seventeenth installment of DDC is scheduled for April 18-21 of next year in San Diego, and the more biology-focused Discovery on Target is scheduled to take place both online and in-person in Boston from September 27-30. Hope to see you there!