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Years Worth of the Stuff

bAP15This time last year I mentioned a particularly disturbing-looking compound, sold commercially as a so-called “selective inhibitor” of two deubiquitinase enzymes. Now, I have a fairly open mind about chemical structures, but that thing is horrible, and if it’s really selective for just those two proteins, then I’m off to truck-driving school just like Mom always wanted.
Here’s an enlightening look through the literature at this whole class of compound, which has appeared again and again. The trail seems to go back to this 2001 paper in Biochemistry. By 2003, you see similar motifs showing up as putative anticancer agents in cell assays, and in 2006 the scaffold above makes its appearance in all its terrible glory.
The problem is, as Jonathan Baell points out in that post, that this series has apparently never really had a proper look at its SAR, or at its selectivity. It wanders through a series of publications full of on-again off-again cellular readouts, with a few tenuous conclusions drawn about its structure – and those are discarded or forgotten by the time the next paper comes around. As Baell puts it:

The dispiriting thing is that with or without critical analysis, this compound is almost certainly likely to end up with vendors as a “useful tool”, as they all do. Further, there will be dozens if not hundreds of papers out there where entirely analogous critical analyses of paper trails are possible.
The bottom line: people still don’t realize how easy it is to get a biological readout. The more subversive a compound, the more likely this is. True tools and most interesting compounds usually require a lot more medicinal chemistry and are often left behind or remain undiscovered.

Amen to that. There is way too much of this sort of thing in the med-chem literature already. I’m a big proponent of phenotypic screening, but setting up a good one is harder than setting up a good HTS, and working up the data from one is much harder than working up the data from an in vitro assay. The crazier or more reactive your “hit” seems to be, the more suspicious you should be.
The usual reply to that objection is “Tool compound!” But the standards for a tool compound, one used to investigate new biology and cellular pathways, are higher than usual. How are you going to unravel a biochemical puzzle if you’re hitting nine different things, eight of which you’re totally unaware of? Or skewing your assay readouts by some other effect entirely? This sort of thing happens all the time.
I can’t help but think about such things when I read about a project like this one, where IBM’s Watson software is going to be used to look at sequences from glioblastoma patients. That’s going to be tough, but I think it’s worth a look, and the Watson program seems to be just the correlation-searcher for the job. But the first thing they did was feed in piles of biochemical pathway data from the literature, and the problem is, a not insignificant proportion of that data is wrong. Statements like these are worrisome:

Over time, Watson will develop its own sense of what sources it looks at are consistently reliable. . .if the team decides to, it can start adding the full text of articles and branch out to other information sources. Between the known pathways and the scientific literature, however, IBM seems to think that Watson has a good grip on what typically goes on inside cells.

Maybe Watson can tell the rest of us, then. Because I don’t know of anyone actually doing cell biology who feels that way, not if they’re being honest with themselves. I wish the New York Genome Center and IBM luck in this, and I still think it’s a worthwhile thing to at least try. But my guess is that it’s going to be a humbling experience. Even if all the literature were correct in every detail, I think it would be one. And the literature is not correct in every detail. It has compounds like that one at the top of the entry in it, and people seem to think that they can draw conclusions from them.

19 comments on “Years Worth of the Stuff”

  1. SP says:

    “I’m a big proponent of phenotypic screening, but setting up a good one is harder than setting up a good HTS”
    Your use of terms confuses me- isn’t phenotypic screening just a class of HTS? Or do you assume HTS = purified biochemical system?

  2. Cellbio says:

    Totally agree with the bolded emphasis in the Beall post extraction. The view that a major hurdle has been crossed when a compound is identified that perturbs a biological system is almost universal in small companies. When one begins to enumerate the other attributes required, like say not perturbing all biology, having suitable bioavailability, solubility and pharmacokinetcs, eyes can roll and hands wave off these pedestrian concerns. These things are just the “stuff” of industry, not of the importance of biology which itself is offered as the cure to maladies. The lack of appreciation for pharmacology is appalling.
    SP, I think phenotypic screening, as I have done it, is part of HTS, though we did it in a therapeutic area because of the slow uptake of traditional HT screeners. And today, most efforts I know of in the literature or company opportunities I see are done by biologists who make some of the big errors highlighted in the post. The biggest one I see is only looking at the biology that is the focus of the lab rather than making the screening itself the subject of the scientific inquiry.
    Focusing this way, outcomes almost always end with statements of tool compounds or drugs directly from the primary screen that lack any real value in my opinion. In my experience, taking a diversity library of over 25K through more than 22 biological assays (all primary human cells) shows that finding something that perturbs biology is guaranteed. Finding one that perturbs a subset of biology is possible and for me the exciting part of phenotypic screening, but not a frequent outcome to say the least.
    Just as for traditional HTS, the screen only outputs starting points whose validity as drug candidates (or tools) requires additional med chem work and much more detailed screening. Without that effort or proper insight from years of drug discovery work, one is often left with a “hit” that is in the 1-10 uM range, with apparent specificity that is likely due to playing with the compound at its solubility limit as I have seen for tools or hits that are quinoline or chromone like compounds.
    I once counted up the potential “indications” for a chromone class being touted as a great new cure that needed to be financed. It was impressive, from cancer to CV, anti-, bacterial, viral and parasite, neurological and on. I would have been interested but ED and hair loss were not on the list.

  3. bhip says:

    “I’m a big proponent of phenotypic screening, but setting up a good one is harder than setting up a good HTS”
    I don’t think I agree. Setting up phenotypic screens can be relatively straight forward (compound kills tumor cells, allosteric compound increases insulin secretion, compound decreases TNF-alpha, etc.) but they aren’t magic. If you have crappy, reactive compounds in your screening collection, you are going find more of them in a phenotypic screen (for example, there are lot of nasty ways to kill a cell). That said, I would be willing to sift through a bunch of junk (false positives). It’s the knowledge/certainty of false negatives that keep you up at night.

  4. David Borhani says:

    Make that “Baell”, Derek.

  5. Cellbio says:

    I think the key here is the simple qualifier, ‘good one’. Was part of program that set up a technically good assay, screened 700K for TNF inhibitor, produced 1500 confirmed hits, all crap. I share the idea that shifting is not too big a problem, but better, imo, to construct the phenotypic paradigm to not be single biology focused for the reason that the bulk of the hits have nothing to do with the biology of interest, like inhibition of TNF production, but rather just muck up biology in general. None of the 1500 compounds inhibited TNF production when migrated to primary human cells. The common signature was inhibition of T cell proliferation.
    This last point also indicates that phenotypic screening is best done in relevant tissue and cells. Cell lines are almost pure garbage in my experience as they are totally rewired and sensitive to inhibitors of pathways irrelevant for the biology of focus. These screens may, however, be a way of screening large collections for biologically active compounds whose utility can be further probed by assessing impacts in relevant phenotypes. But, a long way to go to get there and enriching for broadly active compounds.

  6. Puff the Mutant Dragon says:

    How could anybody look at a structure like that and believe it was a “selective inhibitor”? come on, folks. the kind of people who believe that’s a selective inhibitor probably believe everything they read on the Internet too…

  7. barry says:

    promiscuous inhibitors show up in any small molecule collection when screened against many targets. prof. Brian Shoichet has shown how some of these “work” in cell-free assays by aggregation. The mechanisms by which these “work” in cell-based or whole-organism assays will be different, but the med. chemist should treat them the same. The problem arises in academic group (or the small company) that isn’t running enough assays to notice that these things are promiscuous. If you are married to one target and therefore run only that assay, you’re blind to promiscuity

  8. annonie says:

    Can you explain why you continue to post on this? It’s been done before, so what’s the point, except as a place for you to rant.

  9. normal scientist says:

    Annonie, the reason it is important to post on this topic is because of papers like the ones published in Cancer Cell, a high-impact journal. Lots of people read In the Pipeline, and some of these people may not be familiar with earlier posts.
    As long as the literature continues to be filled with garbage it is important to call it out, both to educate people about potential problems and to shame people who knowingly publish shoddy research. There is an important difference between ranting, which serves no purpose other than to make the ranter feel good, and ascerbic commentary, which hopefully informs as well as amuses.

  10. a. nonymaus says:

    If that’s selective, what does it take to have a nonselective electrophile, phosgene?

  11. pgwu says:

    If they think Watson is so good, I wonder why they do not use Watson to analyze if their statements are bs. That could be the first validation.

  12. anon the II says:

    @ annonie
    I think Dr. Lowe’s point was to address a more recent piece of news, that Watson was going to tell us how to cure cancer. He used an older piece of news and Dr. Baell’s commentary on its ubiquity to illustrate why he is a little skeptical of IBM’s PR piece. Does that help?

  13. anon says:

    definition of a tool compound – a compound for tools, not as a tool as is commonly thought. (mostly by tools)

  14. Hap says:

    @8: People keep believing that it’s easy to find selective inhibitors for biological functions, and keep funding drug research accordingly. They then end up wasting lots of money which leads them to do counterproductive things to make money now so that maybe they can find drugs. Since the belief is wrong and counterproductive, it seems like a good target for impalement. If it isn’t impaled soon, then there won’t be too many more rants, because there won’t a pharma to complain at.

  15. Anonymous says:

    @13: LOL, must remember that one! 🙂

  16. Zetson says:

    What is the colour of this compound?

  17. Maks says:

    @16: What is the colour of this compound?
    I’d bet yellow.

  18. sepisp says:

    That thing looks like pure concentrated evil. Someone has stapled thorny bits into every corner of the molecule. An evil Batman, composed of a sheet of axle grease with potential Michael acceptors and with nitros at ends, plus a bonus hanging Michael acceptor. It’s probably intensely yellow and can be used as a desinfectant.
    Probably, you’re just kidding us and this is actually a pesticide banned already in 1974.

  19. Mark says:

    Basically, I agree with everything on here, and am well aware of the need to screen for off-target effects. Problem is, in academia, we simply don’t have the money because the cost of running appropriate off-target screens will likely run into thousands.
    I would like to think others have better experiences, but in mine, nobody will fund such in-depth profiling. Even if it is wholly necessary scientifically (and it is), it isn’t “translational” or part of an “exploitation plan”, so forget it. It falls under those two very dirty words in the academic funding environment right now: “basic research”.

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