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.