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Chemical Biology

Lipids, Proteins, and Chapman’s Homer

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.

9 comments on “Lipids, Proteins, and Chapman’s Homer”

  1. luysii says:

    This is particularly true when you think by just how much lipid molecules outnumber proteins. Assume that the average cross sectional area taken up by a phospholipid is 5 x 5 Angstroms (probably less), and a square micron of plasma membrane has 4 x 10^6 x 2 (lipid bilayer). That’s just the outside — inside we have the endoplasmic reticulum, the nuclear envelope, mitochondria, peroxisomes, endocytic vesicles, the lysosome, all rich in membranes which are mostly lipid.

  2. Wavefunction says:

    Chapman’s Homer:
    Much have I travell’d in the realms of drugs,
    And many goodly states and targets seen;
    Round many lipid bilayers have I been
    Which bends in fealty to van der Waals’s hold.
    Oft of one wide expanse had I been told
    That deep-pocketed ion channel ruled as his demesne;
    Yet did I never solvate its pure ligand
    Till I heard Pauling speak out loud and bold:
    Then felt I like some watcher of the skies
    When a new target swims into his ken;
    Or like stout Woodward when with eagle eyes
    He star’d at the polyketide — and all his postdocs
    Look’d at each other with a wild surmise —
    Silent, upon a peak in Cambridge, MA.

  3. liberalartschemistry says:

    I was edified in at least three dimensions in reading this post. Thanks!

  4. scarodactyl says:

    @Wavefunction: D’oh!

  5. Anonymous says:

    Excellent work – thanks Derek for bringing this up.
    This humbling research shows us how little we know about the way *life* happens, and the levels of molecular complexity we don’t understand.
    For sure, it brings a whole new meaning to the concept of SAR…
    But, what does this tell us about the chances of affecting complex diseases with one small molecule? What would it take for one to conclude this exercise is just not feasible?

  6. Mark Thorson says:

    Aw, crap, it’s in Cell. That’s part of the dark matter of the publication space. I’m fortunate that most of the papers I’m interested in are published in journals like Circulation and Journal of Biological Chemistry which can be downloaded freely on the net.

  7. Anonymous says:

    Glycobiology was described by one MIT review as one of the top 10 sciences that will transform medicine and health within the next century for reasons such as this. The glycome is believed to be orders of magnitude more complex that the proteome. A single change in a dissacharide linkage from alpha to beta, or between different positions between monosaccharides within a glycan can completely alter biology. For example, the presence of alpha 2,6 linked sialic acids (as opposed to alpha 2,3 linked) are quite often associated with poorer clinical outcomes in cancer. Is it possible to target sugars for therapeutic benefits? Well, for one thing, I know that off the top of my head there is active research going on with analoging tons of boronic acid containing molecules to create almost an artificial type of lectin (boronic acids are known to bind to carbohydrates on the surfaces of cells). Could this type of approach provide tremendous benefit through disrupting something like the galectin lattice, which essentially cross-links, regulates, and organizes the proteome on the surfaces of cells? See:
    Metabolism, cell surface organization, and disease.
    Dennis JW, Nabi IR, Demetriou M.
    Cell. 2009 Dec 24;139(7):1229-41
    There’s a massive world of unexplored biology outside the realm of DNA and proteins.

  8. Curt F. says:

    I had the good fortune to see Dr. Cravatt speak just this morning, on the same topic as mentioned here. I’d never heard him speak before, and am not an expert in the area, but I was amazed by his work. I hope even more people start doing this ABPP stuff, especially with compounds that are permeable to/uptaken by microbes.

  9. Pedantic Spaker says:

    What about protein/nucleic acid interactions? Protein/carbohydrate interactions? Protein-lipid targets?
    If I recall correctly, general anesthetics are thought to alter protein-lipid interactions. There are also be drugs that work on lipid membranes (the gramicidins come to mind), and I think that there may be drugs that bind directly to cholesterol.

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