FragNet: The next generation

The first fragment event of 2018 was held in Barcelona last week. This was part of FragNet, established “to train a new generation of researchers in all aspects of FBLD.” Fifteen graduate students from 13 European countries are participating over the course of three years. This meeting marked the midway point for them. I was privileged to serve as a scientific advisor, and was impressed at how much they’ve been able to accomplish in just 16 months. They’ll be on the market next year, so you’ll definitely want to prioritize them if they apply to your institution.

One interesting feature of the program is that, in addition to their primary research, each student completes two “secondments” in other labs – one in academia and one in industry. This is unusual (in the US), and gives them a much broader range of experiences than is typical in graduate school.

The projects themselves are diverse, ranging from synthetic chemistry through computational approaches and biophysics. Fragment library design is a major theme: David Hamilton is building substituted cyclobutanes, Hanna Klein is focusing on pyrrolidines and piperidines, and Aaron Keely is exploring covalent fragments. Darius Vagrys, Sebastien Keiffer, Edward FitzGerald, Pierre Boronat, Lorena Zara, Eleni Makraki, Bas Lamoree, and Lena Muenzker are applying multiple (mostly) biophysical techniques against a variety of different targets. Andrea Scarpino, Moira Rachman, and Maciej Majewski are focusing on computational approaches. Finally, Angelo Romasanta is exploring the diffusion of FBLD techniques through industry. Often multiple students work on one problem from different angles: for example, Andrea is using modeling to explain some of the experimental results produced by Aaron. Plenty of interesting data are being generated in the projects, and I look forward to seeing the eventual publications.

In addition to the student presentations, there was a one day workshop open to the public, with a strong focus on computational approaches. Chris Murray (Astex) discussed how these play a role in all aspects of FBLD, from library design to finding related compounds using the Fragment Network (discussed here). Having a good set of validated experimental data is essential for benchmarking computational methods, and Astex has contributed one of these. But not every computational approach is applicable to every problem. Free energy perturbation (FEP), a rigorous method for predicting SAR, worked well retrospectively for the target XIAP but was not useful prospectively for a target in which the researchers were trying to find a less lipophilic replacement for a phenyl ring. Chris also pointed out that computational methods have a high hurdle – not just to make predictions but to do so better than experienced scientists.

Jenny Sandmark (AstraZeneca) discussed structure-guided design, with a heavy focus on crystallography. She emphasized the importance of quality control: resolution better than ~2.4 Å, with good electron density and low B factors. (Computation can help: Maciej gave an example where dynamic undocking was able to clarify an ambiguous crystal structure.) Jenny also highlighted a set of 52 crystal structures of fragments bound to the capacious binding site of soluble epoxide hydrolase that has been made publicly available for the benefit of modelers.

Chun-wa Chung (GlaxoSmithKline) discussed the importance of understanding your screening technologies and all their limitations. How to establish a cascade assay depends on the needs: if crystallography is challenging, you may want to limit the hits to those that confirm in multiple methods, as these are more likely to confirm crystallographically. If, on the other hand, you have the capacity to do lots of structures you should examine hits from all screens, as those that don’t repeat may be false negatives. Chun-wa also discussed the importance of biophysics for HTS (though this may require different protein constructs for different methods). An HTS screen of 1.7 million molecules against ATAD2 produced a 1% hit rate, of which 444 were studied using a variety of methods including fluorescence polarization, SPR, and NMR. Ultimately only 16 compounds turned out to be useful – all in a single series. (See here for their fragment efforts.)

John Overington (Medicines Discovery Catapult) gave an overview of the open-access database ChEMBL, which holds data from publications and patents on more than 11,000 targets and 14.5 million molecules, including 13,000 clinical candidates and 1500 drugs. Of course, the entries are only as good as the underlying publications: biochemical assays can vary by about 10-fold, cell-based assays can differ by about 100-fold, and in vivo results can vary by 1000-fold. Still, studying these data can produce interesting insights. For example, the observation that antibacterial compounds tend to be larger and more polar appears to be due to the fact that many antibiotics bind to bacterial RNA – those that just bind to bacterial proteins have more standard properties.

Finally, Anthony Bradley described the computational resources at XChem. We’ve recently discussed some of these, including their open-access version of Fragment Network for analog searching. XChem uses extremely high concentrations of fragments for soaking – DMSO stocks are 500 mM and are soaked at 30-50%, so the final concentration can be as high as 250 mM! This often results in multiple fragments binding to a crystal, many of which are of uncertain functional relevance; Anthony used the term “putosteric” for putative allosteric site. Achieving functional activity can be challenging, but it is encouraging that of 16 targets initiated in the past 12 months, 7 have produced compounds with IC₅₀ values better than 100 µM.

All in all a great start to the year – and lots of good events ahead – hope to see you at some!