Twelfth Novalix Biophysics in Drug Discovery Conference

Last week the Twelfth Novalix Biophysics in Drug Discovery Conference was held for the first time in La Jolla, California. It’s been several years since I wrote about one of these, and I was happy to see that they’ve maintained their reputation for excellent science and convivial conversation. There’s no way to cover the two-dozen talks, but here are a few highlights.

 

One of the things I most enjoy about these meetings is learning about new and emerging methods, and these were well represented. Chris Brosey (AbbVie) discussed time-resolved high-throughput small-angle X-ray scattering (TR-HT-SAXS). As I discussed a couple years ago, the approach can be used to measure the kinetics of protein dimerization in response to fragment-sized ligands.

 

SAXS-based approaches typically require access to a synchrotron, but Takashi Sato (Rigaku) described a related approach, electron density tomography (EDT), using an in-house instrument. Using machine learning, EDT can provide more detailed structural information than standard SAXS, and Takashi provided examples for samples ranging in size from viruses to single-chain variable fragments (scFvs) smaller than 30 kD.

 

Another approach to examine protein complexes is microfluidic diffusional sizing (MDS), described by James Wilkinson of Fluidic Sciences. By assessing the amount of diffusion in disposable chip-based chambers, MDS can determine how the hydrodynamic radius changes in response to ligands. Each chip holds 24 samples, and data can be collected in less than an hour. The minimum observable size change is 5-10% so measuring small molecules directly is unlikely. Still, the technique is useful for observing induced proximity events such as those caused by molecular glues, and it is sufficiently robust that it can be run in pure serum.

 

Among solution-based methods, none have achieved such recent prominence as cryo-EM. Weiru Wang, my colleague at Frontier Medicines, described how this technique was used iteratively to design and characterize bivalent degrader molecules that covalently exploit the E3 ligase DCAF2. (We recently published this work in Structure.)

 

Cryo-EM has revolutionized the types of biological molecules that can be structurally characterized. According to Denis Zeyer (Novalix), the technique accounted for 40% of PDB entries last year. However, despite the “resolution revolution,” most structures are not as detailed as those from X-ray crystallography; Denis noted that only 20% of the new structures were solved to a resolution better than 3 Å, which may have negative implications for machine-learning methods trained on these lower resolution structures.

 

If cryo-EM is the new kid in town, NMR is the grizzled veteran. But proving that it is possible to find new applications for old methods, Matthew Eddy (University of Florida) described a clever ¹⁹F-labeling approach for GPCRs in nanodiscs to quantify the distribution of various states in response to anionic lipids and ligands. This has allowed him to distinguish between antagonists and inverse agonists, which can be difficult using cell-based assays.

 

Turning from solution-based to surface-based methods, SPR has moved into the number two slot for fragment-finding, as we noted in our recent poll. Just as there are new tricks for NMR, the same applies to SPR. Matthew Peterfreund (Bruker Biosensors) described switchSENSE, a fluorescence proximity assay built on an SPR chip that is useful for measuring the binding and kinetics of bifunctional ligands such as PROTACs to two or more proteins. He also introduced the Triceratops SPR#64 instrument, which as its name implies supports 64 sensor spots.

 

Kris Borzilleri (Pfizer) discussed SPR-microscopy (SPRm), which combines an optical microscope with an SPR instrument. This can be used to measure the affinities of ligands binding to receptors in cells grown on SPR chips, and Kris described applications to membrane proteins such as GPCRs and solute carriers. The technique is still quite slow though, at only 10-15 compounds in duplicate per week.

 

Another surface-based approach to screening cells was described by Volker Gatterdam of Lino Biotech. Focal molography relies on changes in diffraction from nanoengineered diffraction gratings, called molograms. Targets, which can include living cells, are immobilized to the molograms, and analyte is flowed over. The instrument contains 64 spots, and assays can be run in complex samples such as tissue lysates.

 

Covalent drug discovery also made an appearance, with talks by Landon Whitby (Lundbeck) and Ben Cravatt (Scripps). Landon provided an overview of chemoproteomics techniques to screen ligands in cells, such as those we wrote about in 2016. Ben continued the theme, including several success stories, and also discussed challenges for finding cryptic ligandable pockets. Despite impressive progress with machine learning, Ben noted that these methods often find only common solutions, while empirical chemoproteomics methods can find rare types of pockets.

 

Of course, as we’ve repeatedly emphasized, biophysics methods are best used in combination, as noted by Daniel Harki (University of Minnesota) and Ann Boriack-Sjodin (Takeda). Daniel presented a screen of 1056 fragments against the cancer target APOBEC3 using NMR and SPR. This yielded just a single validated hit, which interestingly turned out to be the same fragment found against KRAS in a paper we discussed in 2022. And Ann described how biophysics led to multiple clinical compounds against a variety of targets at Epizyme and Accent Therapeutics.

 

I’ll stop here, but please feel free to add your thoughts. And while the date for the next Novalix conference has not yet been scheduled, the location has, with a return to beautiful Strasbourg. Vive la biophysique!