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June 26, 2013
Protein-Protein Compounds - The Flip Side
The topic of protein-protein inhibitor compounds has come up around here several times. It's the classic "undruggable" target, although that adjective isn't quite accurate. Let's leave it at "definitely harder than the usual stuff"; no one could argue with that.
But there's a flip side to this area that people don't think about so much. What about a compound that would make two proteins interact more tightly? A conversation with a reader of the site got me to thinking about this, and it turns out that there's a good review of the concept here, from 2012. The compounds that are known to really do this sort of thing all seem to be natural products, which I don't suppose should come as a surprise. The most well-worked-out of the group is (as some readers will have guessed) FK506 (tacrolimus). Very few drug research organizations have been brave enough to tackle a mechanism like this, so you're not going to see many examples of synthetic compounds. How small (and drug-like) a compound can be and still work through a mechanism like this is an open question.
In principle, it shouldn't be that hard a screen to run - you could imagine an assay where you watch a FRET signal hang around instead of disappearing (once you're sure that hanging all the FRET thingies off the protein partners didn't mess with the binding event, of course). You'd probably be able to see this effect by biophysical techniques as well - NMR, SPR (if you could recapitulate the protein-protein interaction with an immobilized partner on a chip), etc. You'd want a lot of structural information - seeing some sort of plausible binding surface that spans the two proteins would help to settle the nerves a bit.
You'd also want some targets, but there are probably more of them than we're used to thinking about. That's because we're don't tend to think about this mode of action at all, and if you're not keeping it in mind, you won't spot opportunities for it. The whole gain-of-function side of the business is hard to work in, for good reasons. I'm not aware of endogenous small molecules that work this way, so it's not like there are a lot of highly evolved binding pockets waiting for us to fill them. Come to think of it, I'm not aware of endogenous small molecules that work as protein-protein inhibitors, either - those processes seem to get regulated by modifications on the proteins themselves, by local concentration, or by intervention of still other proteins to rearrange binding surfaces. The scarce evolutionary record of this sort of thing might be an accident, or it might be telling us (believably) that this isn't an easy thing to do.
So I would not necessarily pin all my hopes for next year's new targets portfolio on one of these, but it would be interesting to screen and see what might turn up. Who wants to be first?
Update: here's an example from the recent literature for you!
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