A Smaller Approach to HTS

Millions of wells, thousands of hits. All of this implied big budgets, which meant that the smaller labs, and the smaller companies, began to think that HTS, as practiced by big pharma, was out of their league.

But, along the way, the big HTS highway began to run into a few unexpected curves. A recent large-scale survey of the HTS industry tells of some signposts. For instance, throughput from even the largest HTS labs, as measured in wells read per week, went down from 2003 to 2004. Also, in all labs, on average, HTS budgets went down from 2001 to 2004.

Part of the story here is industry consolidation, as the number of large HTS labs has ceased to grow. In addition, cost containment has constricted HTS . where capital budgets and equipment entrenchment play a large role. Having made large investments in 384-well gear, the labs are slow to commit to the additional expense of newer, smaller formats. In fact, the use of the 384 well format is projected to grow to over two thirds of all HTS work in 2006.

It would seem that HTS is somewhat stuck where it is, in terms of cost and format. One cost-saving innovation has been the use of focused libraries for some screens, and smaller diverse sets for others, avoiding the “million compound” screen scenario. Another innovation has largely consisted of more high content screening assays, rather than finding new ways to use HTS. One company, Reaction Biology Corporation (RBC), is seeking to change that. Using proprietary protocols, RBC has combined 384 well liquid handling techniques and genomics microarray printing to create new options for HTS. RBC has pioneered a miniaturized microarray format called DiscoveryDot™ that features printing 6600 one-nanoliter reaction drops on a single one by three inch glass slide.

The use of true HTS is first limited by cost. An individual pharma lab or a small pharma company is loathe to order a HTS screen until absolutely necessary. RBC found this to be the case with one client whose in-house kinase assay was costing $2.45 per well. A screen of even a small compound library at this price would be a significant expense for a small company. Using its DiscoveryDot™ platform, RBC was able to quote an all-in price of $0.60 per well for the same assay, which translated to a 75% reduction in cost. Screening a 20,000 compound focused library at this price now becomes only $12,000, an amount small enough that it can fit in a lab budget, as opposed to getting caught in a larger corporate allocation.

Using the RBC method, a drug discovery lab can use HTS in ways it had been avoiding, and can order screens that otherwise would have been avoided. Being able to run more screens at a lower price is a big advantage. However, reduced size and cost also open up new ways of using HTS. Consider profiling: It is essential to profile candidate compounds against a range of subsidiary targets as part of preclinical discovery. However, due to the cost of this step, most labs wait until other secondary assays have reduced the number of candidates to profile. At that point, a large amount of time and money has been invested in a group of candidates that may not pass profiling tests.

What if compounds could be profiled earlier? A reasonable SAR program that generates analogs of hit compounds will create dozens or even hundreds of compounds to test. Being able to profile all of them, immediately after they are created, means some expensive dead ends will be avoided. And when the ultimate goal is hundreds of millions of dollars a year in revenue from an approved drug, the time=money equation is very powerful.

Often, academic or small pharma lab will agonize over which compounds to profile. At some budget levels, with conventional profiling prices, profiling only ten or twenty compounds is a decision which may leave other compounds of interest on the benchtop. RBC’s goal is to make larger scale profiling available at lower cost.

Another area of current HTS practice that creates delays and dead ends is the multiplicity of assay detection technologies. Over 30 major detection technologies are currently in use. One problem with this is that different detection technologies do not correlate very well. One recent study quoted a correlation of only r = 0.12 to 0.17 correlation between two major detection formats in standardized tests. Fluorescent detection technologies each have different issues with assay artifacts – false positive and negatives. As a result, more and more HTS lab managers are asking for detection modes that do not need fluorescent detection labeling. Again, the DiscoveryDot™ microarray system can help as shown below.

A recent survey commissioned by RBC of eight large pharma HTS managers yielded the following results: 100% of them consider radioisotope screening to be the “gold standard” of HTS kinase screening. However, 75% of them cited cost and hazards as reasons why the assays are not deployed at large scale. And yet, radioisotope assays are free of extraneous labeling mechanisms, which is the goal they seek.

Using microarray techniques, RBC can print only one nanoliter of radioisotopes, buffers, targets and substrate mixture on an array. Reading one small glass slide is then equivalent to reading seventeen 384 well plates. RBC Chief Technology Officer Haiching Ma said, “Using our microarray technology, many aspects of radioisotope screening actually get easier than in well plates. Disposal and storage issues are greatly minimized. But also, it actually is much easier to read an array of 6,600 reactions in a scanner than to read seventeen 384-well plates one plate at a time. We expect to have this new product available to the market in the first half of 2007.”

Ma expects to offer customers one final advantage: Cost. Although the pricing of this product is not yet final, RBC does expect to bring the cost of radioisotope based HTS down to earth from its current “golden” levels.

A big pharma with a large existing investment in 384 well technology will doubtless want to continue extracting maximum value and performance out of that platform. But the DiscoveryDot™ service from RBC can create budget flexibility for individual labs that need smaller screens fast, without disrupting the flow of the larger HTS lab. A smaller pharma company with no HTS facilities at all will find that DiscoveryDot™ puts them in the HTS game with no upfront investment and minimal ongoing cost. And finally, after RBC introduces its radioisotope based screens, the goal of large-scale label free detection may be in reach. Clearly, microarrays have a role to play in advancing HTS to the next level.