Nationwide Screening Centers
The NCGC, the first component of the NIH Roadmap Molecular Libraries Screening Center Network, nationwide screening centers, will produce biomodulators to study gene, cell, and organism functions. Assays submitted to the NCGC will be screened against a diverse collection of more than 500,000 chemical compounds, including natural products, cellular metabolites, and biosynthetic intermediates.
The goal of this research tool is to maximize chances of binding a chemical compound to a target and achieving a desired therapeutic effect via this systematic screening. "Data and tools from chemical genomics efforts like ours will increase physiologically relevant information available about a prospective drug target, and will show that small molecules can be used to manipulate it. We hope these methods enable drug discovery in ways other validation techniques do not," says Dr. Inglese.
Petra Ross-MacDonald, Ph.D., senior research investigator, applied genomics, Bristol-Myers Squibb (BMS; Princeton, NJ), feels that academics will integrate and interrogate this information in different, though no less valuable, ways from industry.
"An industry scientist would say, That's a dirty compound because it hits in three diverse assays,' while an academic would ask, Why do those compounds block that set of channels and induce apoptosis?'"
Academics will also do different assays compared with industry. "The former will probably perform more cell-based pathway screens; whereas industry favors molecular target screens. Combining this information could be powerful for discovering therapeutic compounds. No matter how good the compound is at producing the desired therapeutic effect, there are strong reasons for knowing the molecular target, and few drugs make it through development without that knowledge," Dr. Ross-MacDonald says.
"Ideally, you want to know all of the potential targets a compound could hit in a cell at relevant concentrations," notes Kevin Fitzgerald, group leader, high content target validation/emerging technologies at BMS.
"Chemical genomics methods have uncovered several important mechanisms and protein targets for compounds with unique therapeutic activities in animal models, which turned out to have different molecular targets from what was originally thought.
"Each time an effort like this is successful, there is not only a new therapeutic target, but sometimes a whole new therapeutic pathway," states Fitzgerald. If the original compound shows efficacy, there is a lead compound series and the ability, with the newly discovered target, to proceed through structure activity relationship assays.
BMS is combining RNA interference (RNAi), compounds, and over-expression tools with high-content screening. Fitzgerald notes that mechanistically, RNAi and small molecules each act differently in vivo. "There is a big difference in activity and kinetics between an RNAi, which typically will result in removal, over 48 hours, of an entire protein from a cell, and a compound, which within an hour, will inactivate a single site on that protein."
An RNAi to a typical transmembrane tyrosine kinase not only removes tyrosine kinase activity of the protein, but might disrupt several protein complexes bound to other areas of the receptor, Fitzgerald explains. In contrast, the small molecule causes loss of only kinase activity, preserving the other protein complexesan important difference when interpreting a phenotypic outcome.
Fitzgerald believes that chemical genetics, genomics, high content screening, and proteomics are making it easier to find targets and may lead to a resurgence of cell-based screening techniques. "A major reason why cell-based screens fell out of fashion was because there was no easy way to find the target for compounds derived from such a screen.
"We screen millions of compounds against an isolated, purified target hoping that either inhibiting or activating that target in the complex environment of a cell will have therapeutic activity. In the past, many of the best compounds, discovered by older' cell based assays, hit multiple therapeutic targets.
"These compounds were effective primarily because they hit multiple targets, counteracting redundant networks built into living organisms. Methods used today for screening against purified individual targets would likely never find those compounds," Fitzgerald states.
"The limiting factor may be how physiologically relevant an assay can be when it's crammed into a well," he adds.