As many of you know, Dan and I were at the CHI Drug Discovery Conference. Over the next few posts, we will be posting notes, thoughts, and some comments on what happened. First off, I live-tweeted the sessions I was at. Day 1's highlights are here , Day 2 is here, Day 3 here. Overall, I really liked the conference and thought the agenda was very high quality (one session was poor, read my tweets and guess which one). CHI had Dan and me hopping: chairing sessions, moderating round tables, and co-teaching our FBDD course. I was very lucky to moderate a breakfast roundtable on Thursday morning on PPIs and Fragments (Small Solutions for Big Problems: Fragments and PPI).
The table was a huge hit; there were more than 30 people spread over 5 or so tables. I am pretty sure it was because Rod Hubbard and Dan were there. I am going to try to capture the discussion, but I am pretty sure I am missing key points, so if people where there and remember things, add them in the comments, or email me and I will edit the post. The discussion initiated with a reference to a comment that Rod made in his talk the day before: NMR is the preferred method for screening PPIs (over SPR). He cited two main reasons: NMR is more sensitive to very weak binders and you can do QC on the protein in every samples. With SPR, once the complex is put on the chip, you have no idea if it is still intact/amenable to screening. Jan Steyaert asked a question: most of the PPIs we see targeted are stable complexes, while most of the PPIs in nature are transient, why? This led to the question of whether people are working to stabilize complexes, rather than disrupt? People agreed that you would need to have a kinetically resolved assay, like a TR-FRET. I raised the point that you would need a enzymologist to do this, and most biologists these days are pharmacologists. [As an aside, this is why we focus so strongly on IC50 without knowing really what it means. For further discussion of this, go ask Pete Kenny about this.] It was brought up that you could possibly due this by SPR if you had a a very special "group"[my handwriting sucks under the best of cases, rushing while moderating makes it even worse]. I think the idea is you could go to lower temperatures and start observing kinetics of fragment binding (vs. the normal square sensorgram).
Someone from the Broad Institute said that they use Thermal Shift for PPIs, no matter what. However, most of the people don't trust TS, no matter what. It is cheap and fast, but so full of artifacts and errors. It's a paradox, a quick, cheap assay for PPIs that everyone uses and no one trusts. Seems like a classic case of the herd mentality.
The discussion then moved on to a key concept for fragment/PPIs: how do you follow up on 3D fragments? Most people agree that fragments with higher 3D content are better for targeting PPIs. However, I think, in contrast to 2D fragments, exactly how you prosecute hits in this target class is less straight forward. I think an important distinction between 2D and 3D fragments in terms of follow up is that linking 3D fragments may actually be relevant and productive, in contrast to how most people view linking 2D fragments.
As I said above, I am sure I am missing some points, so add them in the comments or email me. Dan and I will be posting more round up notes over the next week or so, so stay tuned.
In my experience with SPR and fragments, often running at 4 degrees will not help resolve on/off rater for weak fragments. Perhaps it would be easier for stronger interaction <30 µM, but if you are expecting affinity >100 µM it may be a lot of effort for little reward. A promising technology in this area is DLS, although very much in the emerging stages: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808485/
I imagine you could play with this to derive fragment effects on complex KD, and thus derive a Ki as well as answering difficult questions and removing certain common PAINs.
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