About this Author
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: Twitter: Dereklowe

Chemistry and Drug Data: Drugbank
Chempedia Lab
Synthetic Pages
Organic Chemistry Portal
Not Voodoo

Chemistry and Pharma Blogs:
Org Prep Daily
The Haystack
A New Merck, Reviewed
Liberal Arts Chemistry
Electron Pusher
All Things Metathesis
C&E News Blogs
Chemiotics II
Chemical Space
Noel O'Blog
In Vivo Blog
Terra Sigilatta
BBSRC/Douglas Kell
Realizations in Biostatistics
ChemSpider Blog
Organic Chem - Education & Industry
Pharma Strategy Blog
No Name No Slogan
Practical Fragments
The Curious Wavefunction
Natural Product Man
Fragment Literature
Chemistry World Blog
Synthetic Nature
Chemistry Blog
Synthesizing Ideas
Eye on FDA
Chemical Forums
Symyx Blog
Sceptical Chymist
Lamentations on Chemistry
Computational Organic Chemistry
Mining Drugs
Henry Rzepa

Science Blogs and News:
Bad Science
The Loom
Uncertain Principles
Fierce Biotech
Blogs for Industry
Omics! Omics!
Young Female Scientist
Notional Slurry
Nobel Intent
SciTech Daily
Science Blog
Gene Expression (I)
Gene Expression (II)
Adventures in Ethics and Science
Transterrestrial Musings
Slashdot Science
Cosmic Variance
Biology News Net

Medical Blogs
DB's Medical Rants
Science-Based Medicine
Respectful Insolence
Diabetes Mine

Economics and Business
Marginal Revolution
The Volokh Conspiracy
Knowledge Problem

Politics / Current Events
Virginia Postrel
Belmont Club
Mickey Kaus

Belles Lettres
Uncouth Reflections
Arts and Letters Daily
In the Pipeline: Don't miss Derek Lowe's excellent commentary on drug discovery and the pharma industry in general at In the Pipeline

In the Pipeline

« Pursuing Other Interests, As They Say | Main | Scientific Posters, Heads on Platters, and Lawsuits »

April 8, 2013

The Basics of Phenotypic Screening

Email This Entry

Posted by Derek

I wanted to mention another paper from Nature Chemical Biology's recent special issue, this one on the best ways to run phenotypic screens. This area has been making a comeback in recent years (as discussed around here before), so articles like this are very useful to help people get up to speed - similar to that article on fragment-based screening pitfalls I mentioned last week.

The author, Ulrike Eggert at King's College (London), has this observation about the cultural factors at work here:

Although my degrees are in chemistry, I have worked mostly in academic biology environments and have been immersed in the cultures of both disciplines. In my experience, biologists are very happy to use chemical tools if they are available (even if they are not optimal) but are less enthusiastic about engaging in small-molecule discovery. One of the reasons for this is that the academic funding culture in biology has focused almost entirely on hypothesis-driven research and has traditionally been dismissive of screening programs, which were considered to be nonintellectual fishing expeditions. With a growing appreciation for the value of interdisciplinary science and the serious need for new tools and approaches, this culture is slowly changing. Another reason is that some early phenotypic screens were perceived to have been only partial successes, resulting in 'low-quality' (for example, low-potency and nonselective) chemical probes.

These observations are right on target. The reaction of some academic biologists to screening programs reminds me of the reaction of some chemists to the "reaction discovery" schemes that have emerged in recent years: "Well, if you're just going to stagger around in circles until you trip over something, then sure. . ." But this, to me, just means that you should be careful to set up your discovery programs in the right places. One of my favorite quotes comes from Francis Crick, talking about the discovery of the double helix structure: "It's true that by blundering about we stumbled on gold, but the fact remains that we were looking for gold."

Eggert goes on to lay out the basic principles for success in this field. First, you'd better have clear, well-defined phenotypes as your readout, or you're sunk right from the start. Cell death is a pretty poor choice, for example, given the number of ways that you can kill a cell, and unfortunately, the same goes for inhibiting proliferation of cancer cells in vtiro. There really are an awful lot of compounds that will do that, in one cell line or another, and most of them are of no use at all. It's important to remember, though, that "well-defined" doesn't mean setting the boundaries so tight that you'll miss something interesting and unusual if it shows up - what it means is understanding your system well enough so that you'll recognize something unusual if it happens.

Assay design is, of course, critical. What's your signal-to-noise? How high is the throughput? How good are the positive and negative controls? What are the secondary assays that could be used to characterize your hits? And the point is also emphasized that the usual problem in these systems is not that you don't get any hits, but that you get so many that following them up is a problem all by itself. You're probably not going to find some compound that just lights up the assay perfectly all by itself - the more typical situation is a whole pile of different-looking things that might have worked, sort of. Sorting those out is a painful but essential part of the screen.

I'm a fan of phenotypic screening, personally, mainly because I don't think that we're smart enough to always realize what it is we're looking for, or exactly how to find it. But done suboptimally, this sort of screen is capable of wasting more time and effort than almost any other method. Eggert's article (and the references in it) are essential reading for anyone trying to get into the field. Medicinal chemists who find themselves working in this area for the first time should make sure to get caught up on these issues, because good med-chem followup is essential to any successful phenotypic campaign, and you want to make sure (as usual) that you're marching under the right flag.

Comments (7) + TrackBacks (0) | Category: Drug Assays


1. John Wayne on April 8, 2013 8:36 AM writes...

I've got to agree with Derek on this one. I've worked up several phenotypic screens performed with cell or parasite death as the primary readout; you pick up a lot of mechanism-based inhibitors. It takes a diligent medicinal chemist to weed out all the noise. You will also need a good relationship with your biologists. Since the chemistry team is probably not going to work on most of the really active hits; setting the expectations of the biology team is really important.

Permalink to Comment

2. SP on April 8, 2013 12:28 PM writes...

On the flip side, cell death is probably the most extensively run phenotypic screen, so it's easy to remove promiscuous compound informatically and narrow down pretty quickly to the mechanism/context of interest.

Permalink to Comment

3. lynn on April 8, 2013 12:37 PM writes...

@#1 - It takes a diligent biologist to weed out noise as well. To sift through the output of phenotypic screens, whether kill-the-organism or turn-on of a mechanism-based-reporter, etc., takes biologists and chemists working together.

Permalink to Comment

4. Doug Steinman on April 8, 2013 12:37 PM writes...

I once had a senior biologist tell me that using a positive control in an assay was a waste of time since "you know that it is always going to be active". Of course, the same individual was always very reluctant to put the names of the bench chemists on his publications because "all they did was supply the compounds that were tested". Go figure.

Permalink to Comment

5. Ethan Perlstein (@eperlste) on April 8, 2013 12:53 PM writes...

I side with @#3 on this one. Cell death is a perfectly fine readout for a phenotypic screen in the right hands. Obviously, it's all about specificity, so I wouldn't recommend doing growth/no growth assays with a random mammalian cell line just because there's a kit available to measure cellular ATP levels.

But if you overlay genetic specificity, by looking for synthetic lethality or focusing on specific mutants of simple model organisms, then cytotoxicity can be an extremely informative and incredibly cheap readout.

Permalink to Comment

6. Krupp on April 8, 2013 8:20 PM writes...

I haven't had a phenotypic screening still I want to thank you for posting such a great review on this type of screening. Somehow, I have an idea on what to do with this and if I'm going to consider doing this.

Permalink to Comment

7. Cellbio on April 10, 2013 9:12 AM writes...

My experiences with large scale phenotypic screens (now 10 years age, yikes!), was that chemists saw the value right away, with SAR driven by biology. Biologists were slower to come to the party, but those with a molecular background were pretty quick, one such fellow pausing to reflect..'I guess we operated in solely a hypothesis driven matter because we could measure so few things'. Paradigm driven biologists, like Immunologists, were either slow to warm to the idea or failed to come aboard, as their manner of thinking is more a reduction of a complex system to digestible concepts which limit the complexity. Phenotypic screening showed me that our signal transduction diagrams and understanding of cellular systems are influenced by our wiring favoring adoption of simple schema.

To this point, I think the authors miss one point when they mention enzyme inhibition, allostery and protein:protein interactions. After screening whole target based med chem campaigns in a phenotype broad biology measure with multiple cell types and multiple read-outs, the diversity of pharmacology is, well, unsettling to the mind that wants clean buckets of mechanisms. Though only a theory, I surmised that the only way for this level of diversity to exists was a contribution from active site inhibitors having variable allosteric impacts that had additional, context dependent pharmacological effects.

Last point, the missing part of biologists skill set to both see the value of phenotypic screening and makes sense of the output, at least for the slice of the research world I saw, was a pharmacology background. Understanding simple concepts like dose response, curve shape and 'dose makes the poison' enables folks to rapidly see the value. If someone uses a nano-molar inhibitor at 50 uM because they, to paraphrase an oft heard justification of dose, "wanted to be sure to see something", then they are not testing compound pharmacology but playing in their biological system. In drug discovery, we need fewer biologists dedicated to their biology, and more pharmacologists dedicated to testing the value of compounds.

Permalink to Comment


Remember Me?


Email this entry to:

Your email address:

Message (optional):

The Last Post
The GSK Layoffs Continue, By Proxy
The Move is Nigh
Another Alzheimer's IPO
Cutbacks at C&E News
Sanofi Pays to Get Back Into Oncology
An Irresponsible Statement About Curing Cancer
Oliver Sacks on Turning Back to Chemistry