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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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« Think Your Drug Is Strange-Looking? Beat This. | Main | Every Tiny Detail »

November 28, 2012

Advice For Those Trying High-Throughput Screening

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Posted by Derek

So here's a question that a lot of people around here will have strong opinions on. I've heard from someone in an academic group that's looking into doing some high-throughput screening. As they put it, they don't want to end up as "one of those groups", so they're looking for advice on how to get into this sensibly.

I applaud that; I think it's an excellent idea to look over the potential pitfalls before you hop into an area like this. My first advice would be to think carefully about why you're doing the screening. Are you looking for tool compounds? Do they need to get into cells? Are you thinking of following up with in vivo experiments? Are you (God help you) looking for potential drug candidates? Each of these require somewhat different views of the world.

No matter what, I'd say that you should curate the sorts of structures that you're letting in. Consider the literature on frequent-hitter structures (here's a good starting point, blogged here), and decide how much you want to get hits versus being able to follow up on them. I'd also say to keep in mind the Shoichet work on aggregators (most recently blogged here), especially the lesson that these have to be dealt with assay-by-assay. Compounds that behave normally in one system can be trouble in others - make no assumptions.

But there's a lot more to say about this. What would all of you recommend?

Comments (13) + TrackBacks (0) | Category: Academia (vs. Industry) | Drug Assays


COMMENTS

1. Regrets on November 28, 2012 10:32 AM writes...

Derek's spot on WRT starting first with the goal in mind of the compound you eventually want. Additionally, think through carefully what counterscreens (confirmatory and off-target) you need to prove that what you have is what you want.

If chemistry is your strength and you have access to X-ray or very good modeling, try fragments as an academic lab. They're cheaper to run, you may be more likely to get something (after a lot of tough med chem) with tractable properties to do all kinds of experiments in living systems. Pay attention to phys chem properties along the way and appropriate efficiency metrics to measure progress and not just raw potency.

If biology is your strength and you plan to do only a little chemistry, God help you with any approach to setting up a screen/screening set! You will wind up with an academic curiosity that will haunt future programs.

Permalink to Comment

2. barry on November 28, 2012 11:27 AM writes...

if your goal is to "find a drug" go back and read more. Small-molecule space is too big to be well represented in any library that we can screen in 2012 at that level.
Make sure that your library is "diverse and lead-like". Get back to me when you actually know what those terms mean. Good luck.

Permalink to Comment

3. student on November 28, 2012 1:04 PM writes...

A major reason to choose academia over industry is the ability to work on whatever you want (provided you can get your ideas funded). If, given this freedom, what you choose to do is grunt high-throughput screening, you need to seriously reconsider your life choices.

Permalink to Comment

4. chris on November 28, 2012 1:27 PM writes...

What do they mean by "doing some high-throughput screening"?
Unless they are planning to provide HTS as a service I can't believe it is cost effective to invest in the robotics and build a sample collection for HTS for just a couple of screens.

There are a couple of ongoing collaborations to provide screening collections it might be worth investigating them.

Permalink to Comment

5. Chris on November 28, 2012 1:41 PM writes...

I would back Derek’s suggestion to seriously think about “why” running a screen, but I would also recommend to ask the question: “then what?”.

In my experience, there is very often a disconnect between PIs expectations and the actual outcome of a screen. What you end up with is a long list of compounds or genes, and what HTS does not tell you is ”go with that one first”. I blame the literature for this disconnect, with many misleading high profile publications that make it seem like there were one or two hits that stood out from the rest. It’s rarely the case, and the outcome of HTS really is a starting point, not an end point.

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6. A. Postdoc on November 28, 2012 1:49 PM writes...

Just don't. High throughput screening in academia is a joke. It is too costly and not a scientific or intellectual pursuit. Like #3 said, you should reconsider your life choices if this is what your life has come to. With all the millions of experiments to do, why become one of those labs that does high throughput screening only to find complete nonsense and spends years chasing artifacts and aggregators?

Seriously, just don't. I would recommend against funding any grant that involves high-throughput screening.

Permalink to Comment

7. HTSguy on November 28, 2012 2:21 PM writes...

Wise comments about thinking about your goal before you dive into the experimental details. I second the comments about thinking clearly about your followup and counterscreens. As for fragment screening, many academics have access to high-field NMR and/or Biacore instruments, either of which can be used for fragment screening.

@6 - why find small molecules (even probe molecules)? For proteins with moderate to long half-lives, siRNA doesn't work. You can do complicated drug-regulated knockouts or anti-sense expression, but these are anything but straightforward and may take many years of work. Finding small molecule inhibitors fits that description as well, but at least provides a different approach and is transportable to other strains or species.

Permalink to Comment

8. HTSguy on November 28, 2012 2:43 PM writes...

Wise comments about thinking about your goal before you dive into the experimental details. I second the comments about thinking clearly about your followup and counterscreens. As for fragment screening, many academics have access to high-field NMR and/or Biacore instruments, either of which can be used for fragment screening.

@6 - why find small molecules (even probe molecules)? For proteins with moderate to long half-lives, siRNA doesn't work. You can do complicated drug-regulated knockouts or anti-sense expression, but these are anything but straightforward and may take many years of work. Finding small molecule inhibitors fits that description as well, but at least provides a different approach and is transportable to other strains or species.

Permalink to Comment

9. Anon Academic on November 28, 2012 3:05 PM writes...

There are some good reasons to do HTS in academic. For example, if you are working on a neglected target, it makes sense. If you are working on a pharma target, however, it's crazy to think you will find something that pharma has missed.

Like "Regrets" said, if you have chemistry capabilities, FBDD makes the most sense in an academic lab. Because: (1) your chance of finding a hit is high and (2) you don't need to worry about buying hundreds of thousands of compounds (and the equipment to screen them). A FBDD screen can realistically be performed using multi-channel pipettors and a plate reader with no robotics.

Permalink to Comment

10. Helical_Investor on November 28, 2012 4:04 PM writes...

To remember that only the 'screening' is high throughput. Effective assay development is not. Given this, educating on effective assay development is a good reason to do HTS in the academic setting where the output is the lessons more so than the hits.

Zz

Permalink to Comment

11. JB on November 28, 2012 5:00 PM writes...

It should be also checked what the HTS for that group means, some people think 1000 compounds is HTS.

HTS without a previous enrichment makes not much sense, but that is easier said than done of course. If they know what they want to target e.g. a particular protein then virtual library screening could be applied and then cherry pick say 2000 compounds from that 400000 compound library and run an assay on it.

SPR with fragments and then building on those results is feasible assuming it's a protein they can produce.

Permalink to Comment

12. Academic111 on November 28, 2012 5:11 PM writes...

Hi,

A number of notable drug discovery CROs have been offering academic HTS services by lauding their "industry-grade" chemical libraries. The academic collaborator would have identified a novel target and MOI for a disease process and is seeking a tool compound or potentially a hit compound that (if shows promise in follow on in cellular & animal models) may be good starting point for med chem optimization. Any thoughts on these CROs and their "libraries for hire"?

Permalink to Comment

13. Virgil on November 29, 2012 12:04 PM writes...

As an academic who has dabbled in HTS (well, medium TS really), I would suggest the following caveats...

1) Invest in decent software/statistics. For many life-science academics, the volumes of data (particularly for multi-parameter data sets) are much bigger than anything we've dealt with in the past, and you'd be shocked at the lack of statistical understanding many of us have.

2) Read the literature on multiplexing. You can save yourself a LOT of work by running multiple compounds per well, but ONLY if you do it right (e.g., an orthogonal pooling approach).

3) Never, ever assume that what the library company claims is in the well, is actually in the well. MS and NMR are absolute requirements once you start to narrow down your hits. Being able to purchase more of said hits, for in-vivo work-up, is also advantageous, and you'd be surprised how many compounds in commercial libraries are actually not available for individual purchase.

4) Avoid the colored wells, they will screw with your assay.

5) Be very aware of edge effects, what causes them, and how to correct for them. This can save you a lot of false positives or negatives. Same goes for things like passage number, plating density, media batches, and all those other little variables that creep into cell based experiments. You have to nail that stuff down really well so your plate-to-plate noise is as low as possible.

6) Don't expect to find any freinds at NIH study sections. They will not fund a screen, but if you already did a screen and found an interesting hit, they will fund the follow up investigation. Thus, it's almost a requirement to do a screen "off the books", in the 3rd or 4th year of a grant, so you have a hit to write about when you submit the renewal grant application.

7) Same goes for journals - although editors will often send things out for review, there is a dearth of qualified reviewers out there to assess many HTS papers, so you will get some real dumb-ass comments back, and likely be rejected several times before it finds a home (although in this respect, HTS is like every other field!) We have found it useful in such situations to cite the HTS-methods literature extensively, referring to things mentioned above (edge effects, pooling strategies). Paper reviewers will often be marginally familiar with this stuff - just enough to be dangerous - and you can stop many of these silly comments by appearing to be "on top of things" right off the bat.

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