Showing posts with label Graffinity. Show all posts
Showing posts with label Graffinity. Show all posts
29 November 2010
More techniques: NovAliX and Graffinity combine MS and SPR
We’ve written previously about Graffinity, which uses surface plasmon resonance (SPR) to find fragments, and NovAliX, which initially focused on mass spectrometry. The two companies have been collaborating since last year, and this has apparently been a fruitful partnership: this month NovAlix acquired a majority ownership stake in Graffinity (click here for press release). Earlier this year NovAlix also purchased an NMR-focused company, and they have already added crystallography expertise. Finding fragments effectively requires using a range of orthogonal technologies, and this latest move gives NovAlix a full suite of biophysical techniques.
15 February 2010
Surface Plasmon Resonance (SPR)
Fragment-based drug discovery took off with NMR in the 1990s and went mainstream with X-ray crystallography in the 2000s. Now surface plasmon resonance (SPR) is becoming increasingly popular as a primary means of identifying hits. The technique has been mentioned more than a dozen times on Practical Fragments, but we’ve never devoted an entire post to it until now.
This post follows up on two recent publications. The first is an excellent summary of SPR by our friends at FBDD-Lit. Peter Kenny gives an overview of the technique and reports on a workshop given by SPR mavens Dave Myszka and Rebecca Rich. He also covers some of the seminal papers in the field.
The second report is in the brand new journal ACS Medicinal Chemistry Letters. In it, Iva Navratilova and Andrew Hopkins of the University of Dundee provide practical advice on using SPR for fragment-screening.
The authors describe their work on using SPR to identify fragments that bind to carbonic anhydrase II, a popular target for proof-of-concept studies. They screened a library of 656 fragments with molecular weights between 94 to 341 Da, with an average of 187 Da, or about 13 non-hydrogen atoms. The entire screen, which was done at three concentrations (16.6, 50, and 150 micromolar) took 4 weeks from assay development to hit confirmation on a Biacore T100, and consumed a total of 27 micrograms of protein.
Importantly, Navratilova and Hopkins were keenly aware of the potential for false positives or nonspecific binders (of which there were 230 at the highest concentration!) One way they controlled for such artifacts was to include an unrelated reference protein; data could be corrected by subtracting the response to the reference protein from the response to the target protein. Another analytical method to reduce the number of false positives was to only consider compounds that exceeded a minimum threshold for ligand efficiency (a metric invented by Hopkins and co-workers), a decision justified here given the often high affinities observed for carbonic anhydrase inhibitors. After these filters, an examination of the stoichiometry of binding revealed a dozen specific binders and four non-specific binders, a hit rate of 1.8%.
My one reservation with this paper is that carbonic anhydrase is a particularly easy test case, unlikely to fairly represent many of targets that people screen. Indeed, the confirmed hits (all of which contain sulfonamides), have affinities from 0.13 to 14 micromolar – far better than a typical fragment screen, and comparable to many HTS screens. Still, the tools and analyses described should apply to more challenging targets.
Finally, it is worth noting that if you want access to SPR technology but don’t have the resources or expertise to do it yourself, at least a couple companies (Beactica and Graffinity) specialize in applying SPR to FBDD.
This post follows up on two recent publications. The first is an excellent summary of SPR by our friends at FBDD-Lit. Peter Kenny gives an overview of the technique and reports on a workshop given by SPR mavens Dave Myszka and Rebecca Rich. He also covers some of the seminal papers in the field.
The second report is in the brand new journal ACS Medicinal Chemistry Letters. In it, Iva Navratilova and Andrew Hopkins of the University of Dundee provide practical advice on using SPR for fragment-screening.
The authors describe their work on using SPR to identify fragments that bind to carbonic anhydrase II, a popular target for proof-of-concept studies. They screened a library of 656 fragments with molecular weights between 94 to 341 Da, with an average of 187 Da, or about 13 non-hydrogen atoms. The entire screen, which was done at three concentrations (16.6, 50, and 150 micromolar) took 4 weeks from assay development to hit confirmation on a Biacore T100, and consumed a total of 27 micrograms of protein.
Importantly, Navratilova and Hopkins were keenly aware of the potential for false positives or nonspecific binders (of which there were 230 at the highest concentration!) One way they controlled for such artifacts was to include an unrelated reference protein; data could be corrected by subtracting the response to the reference protein from the response to the target protein. Another analytical method to reduce the number of false positives was to only consider compounds that exceeded a minimum threshold for ligand efficiency (a metric invented by Hopkins and co-workers), a decision justified here given the often high affinities observed for carbonic anhydrase inhibitors. After these filters, an examination of the stoichiometry of binding revealed a dozen specific binders and four non-specific binders, a hit rate of 1.8%.
My one reservation with this paper is that carbonic anhydrase is a particularly easy test case, unlikely to fairly represent many of targets that people screen. Indeed, the confirmed hits (all of which contain sulfonamides), have affinities from 0.13 to 14 micromolar – far better than a typical fragment screen, and comparable to many HTS screens. Still, the tools and analyses described should apply to more challenging targets.
Finally, it is worth noting that if you want access to SPR technology but don’t have the resources or expertise to do it yourself, at least a couple companies (Beactica and Graffinity) specialize in applying SPR to FBDD.
15 October 2009
Genentech’s affinity for Graffinity
Heidelberg-based Graffinity today announced that they would be collaborating with the Genentech division of Roche. Graffinity will apply its surface plasmon resonance (SPR) fragment-based technology to several Genentech targets. Financial details and specific targets have not been released, though Graffinity CEO Kristina Schmidt is quoted as saying that they plan “to explore drug targets that would remain white spaces on the map of drug discovery” with conventional high-throughput screening.
SPR is rapidly becoming a workhorse in the stable of FBDD techniques. Although it provides less information than NMR or X-ray approaches, SPR is faster, and can rapidly distinguish true hits from bad-acting artifacts. Typically a protein is immobilized on a gold surface, and fragments are allowed to flow past to detect those that bind. Graffinity reverses this process: they have a collection of about 110,000 small molecules, just over a fifth of which are fragments, immobilized in microarrays which can be screened against proteins (see here for full description).
Genentech is no stranger to SPR; one of the highlights of the recent FBLD 2009 meeting was a talk by Tony Giannetti on the use of this technology at Genentech against roughly 40 target proteins. The collaboration further validates the use of SPR for FBDD, and suggests that Graffinity has an interesting – and useful – angle.
SPR is rapidly becoming a workhorse in the stable of FBDD techniques. Although it provides less information than NMR or X-ray approaches, SPR is faster, and can rapidly distinguish true hits from bad-acting artifacts. Typically a protein is immobilized on a gold surface, and fragments are allowed to flow past to detect those that bind. Graffinity reverses this process: they have a collection of about 110,000 small molecules, just over a fifth of which are fragments, immobilized in microarrays which can be screened against proteins (see here for full description).
Genentech is no stranger to SPR; one of the highlights of the recent FBLD 2009 meeting was a talk by Tony Giannetti on the use of this technology at Genentech against roughly 40 target proteins. The collaboration further validates the use of SPR for FBDD, and suggests that Graffinity has an interesting – and useful – angle.
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