April 11, 2012
How do you like to screen for fragments?
The relatively new field of Fragment Based Drug Discovery received a much-needed boost late last year when the FDA approved the first drug whose genesis was screening of a fragment library (see reference below). The BRAF inhibitor Zelboraf (vemurafenib) grew out of biochemical screening of a panel of kinases at Plexxikon, followed by intensive X-ray crystallographic analysis of hits from the primary screen.
There are, however, many different methods that FBDD practitioners can employ in screening. If an amenable crystal system is available, soaking of crystals and XRD analysis can be performed. Ligand-observe NMR methods such as saturation transfer difference (STD-NMR) are also often used. SPR, thermal shift, and a variety of biochemical methods are likewise well-documented.
What methods should you use? The answer is usually complex, and depends on the nature and abundance of your target macromolecule, as well as the size of the fragment library you wish to screen. At Emerald, we currently rely heavily on X-ray, STD-NMR, SPR and thermal shift techniques, and we prefer to use more than one technique at a time to aid with prioritization and characterization of hits. There are a couple of upcoming opportunities to have this discussion in real time…
We are looking forward to meeting lots of our past and future collaborators at the Drug Discovery Chemistry (DDC) conference in San Diego April 16-19. Alex Burgin, CSO of Emerald BioStructures, will be giving a workshop as part of the FBDD session on April 16. He will be co-teaching a short course with Daniel Erlanson (author of the excellent blog practical fragments) entitled “Advanced Tools and Technologies for Fragment-Based Design." If you would like to speak personally with Alex, he will be available for the remainder of the week in San Diego. Additionally, Emerald is holding an informal MeetUp at the conference on April 17, from 6;30-8:30 PM. Interested parties should contact Diana Wetmore for location details.
New fragment screening methods are constantly evolving. One technology we find particularly intriguing is the “CEfrag” Capillary Electrophoresis technique of Selcia, Inc. This approach monitors the mobility shift of a probe ligand as both target and a cocktail of fragments move through a gel-filled capillary. The image below is a schematic of the technology from the Selcia Discovery website.
In addition to presentations at DDC, a scientist from Selcia will give a full description of their fragment screening method as a guest presenter in the Emerald BioStructures Webinar series. The webinar, titled "Complementing Biophysical and Structural Methods for Drug Discovery with Capillary Electrophoresis," can be watched live on April 17 at 11 am Pacific Time, or as an archived presentation any time after that. If you watch live there’ll be opportunities to send in questions for discussion at the end of the webinar.
References 
Tsai J, Lee JT, Wang W, Zhang J, Cho H, Mamo S, Bremer R, Gillette S, Kong J, Haass NK, Sproesser K, Li L, Smalley KS, Fong D, Zhu YL, Marimuthu A, Nguyen H, Lam B, Liu J, Cheung I, Rice J, Suzuki Y, Luu C, Settachatgul C, Shellooe R, Cantwell J, Kim SH, Schlessinger J, Zhang KY, West BL, Powell B, Habets G, Zhang C, Ibrahim PN, Hirth P, Artis DR, Herlyn M, & Bollag G (2008). Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity. Proceedings of the National Academy of Sciences of the United States of America, 105 (8), 3041-6 PMID: 18287029