Longtime readers might recall that every so often I hit on the topic of the “dark matter” of drug target space. We have a lot of agents that hit G-protein coupled receptor proteins, and plenty that inhibit enzymes. Those, though, are all small-molecule binding sites, optimized by evolution to hold on to molecules roughly the size that we like to make. When you start targeting other protein surfaces (protein-protein interactions) you’re heading into the realm where small molecules are not the natural mediators, and things get more difficult.
But all of those are still proteins, and there are many other types of biomolecules. What about protein/nucleic acid interactions? Protein/carbohydrate interactions? Protein-lipid targets? Those are areas where we’ve barely even turned on the lights in drug discovery, and past them, you’d have to wonder about carbohydrate/carbohydrate systems and the like, where no proteins are involved at all. None of these are going to be straightforward, but there’s a lot to be discovered.
I’m very happy to report on this new paper from the Cravatt group at Scripps, which makes a foray into just this area. A few years ago, the group reported a series of inhibitors of monoacylglycerol lipase, as part of their chemical biology efforts on characterizing hydrolases. That seems to have led to an interest in lipid interactions in general, and this latest work is the culmination (so far) of that research path. It uses classic chemical-biology probes that mimic arachidonyl lipids and several other classes (oleoyl, palmitoyl, etc.). Exposing these to cell proteomes in labeling experiments shows hundreds and hundreds of interactions taking place, the great majority of which we have had no clue about at all. The protein targets were identified by stable-isotope labeling mass spec (comparing experiments in “light” cells versus “heavy” ones carrying the labels), and over a thousand proteins were pulled in with just the two kinds of arachidonyl probes they used (with some overlap between them, but some unique proteins to each sort of probe – you have to try these kinds of things from multiple directions to make sure you’re seeing as much as possible).
As well as including many proteins whose functions are unknown, these lists were substantially enriched in proteins that are already drug targets. That should be enough to make everyone in the drug discovery business take a look, but if you’re looking for more, try out the next part. The team went on to do the same sort of lipid interaction profiling after treatment of the cells with a range of inhibitors for enzymes involved in such pathways, and found a whole list of cross-reacting targets for these drugs that were unknown until now.
They then turned their attention to one of the proteins that was very prominent in the arachidonyl profiling experiments, NUCB1 (function unknown, but apparently playing a major role in lipid processing and signaling). Taking the arachidonyl probe structure and modifying it to make a fluorescent ligand led to a screening method for NUCB1 inhibitors. 16,000 commercial compounds were tested, and the best hit from this led to a series of indole derivatives. These were taken back around in further labeling experiments to determine the actual site of binding on NUCB1, and they seem to have narrowed it down (as well as gotten a start on the specific binding sites of many of the other protein targets they’ve discovered). There are also profiles of cellular changes induced by treatment with these new NUCB1 inhibitors, along with hypotheses about just what its real function is.
Holy cow, is this ever a good paper. I’ve just been skimming over the details; there’s a lot more to see. I strongly recommend that everyone interested in new drug targets read it closely – you can feel a whole landscape opening up in front of you (thus the title of this post). This is wonderful work, exactly the kind of thing that chemical biology is supposed to illuminate.