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Chemistry meets biology at screening center

February 26, 2009 By Dian Land

When University of Wisconsin–Madison bacteriologist Nancy Keller and her team managed to genetically trick fungi into making metabolic byproducts that are notoriously difficult for scientists to get at, she wondered if the substances might have any clinically useful properties. After all, most natural products used for human medicines come from fungi, bacteria and plants.

So Keller shipped the samples to the Small-Molecule Screening Facility (SMSF) tucked away in the Paul P. Carbone Comprehensive Cancer Center at the UW–Madison School of Medicine and Public Health. That’s where robot-assisted scientists mix chemistry and biology to study how human cells and proteins respond to chemicals that eventually may be developed into drugs.

Armed with tens of thousands of chemicals, or small molecules, the robots mix tiny amounts of each with a protein or cell line of interest. Like the proverbial needle in a haystack, special instruments search for the one combination that produces a “hit” indicating a relationship worthy of further examination.

Called chemical genetics, this increasingly popular way of studying cell biology complements traditional genetic approaches, says SMSF faculty supervisor Michael Hoffmann, who opened the facility six years ago. The classical strategy entails mutating genes in fruit flies or other model organisms to observe the effects, testing them later in animal and then human studies.

“The Human Genome Project has given us unprecedented access to the human proteins that are made by thousands of genes,” says Hoffmann, who switched the focus of his own lab at the McArdle Laboratory for Cancer Research to chemical genetics in 2001.

With Keller’s permission, Hoffmann added the fungal extracts to the SMSF’s new Wisconsin Discovery Library. It currently consists of some 1,000 “home-grown” natural products as well as synthetic compounds made or discovered by UW–Madison chemists who have used the facility.

“We’re screening these Wisconsin compounds to see if they may display biological effects that the scientists who made them might not have expected to occur,” says Hoffmann. He sees it as a unique way to foster interdisciplinary drug discovery on campus and to implement the Wisconsin Idea.

The growing library of locally made substances supplements the 80,000 small molecules Hoffmann and SMSF manager Noel Peters have purchased for their standard chemistry library. In the last six months alone, the chemicals have been used to screen samples from 60 UW–Madison labs.

Some 80 research teams from across campus have used the SMSF services. Several from McArdle, where Hoffmann also serves as director, are investigating specific cell receptors that bind to estrogen, hoping to find a small molecule that might produce a blocking effect in a breast cancer cell line. Other UW–Madison scientists use the screening to study proteins or cells relating to diabetes, glaucoma, infectious diseases such as West Nile virus and influenza, and neuro-degenerative and cardiovascular diseases.

Amped-up speed and capacity in a miniaturized system are hallmarks of the so-called “high-throughput” screening.

“The work would be far too demanding and time-consuming for any traditional laboratory staff to perform on its own,” says Hoffmann. “So we rely on our three robots to do the job.”

Last November, with support from the Wisconsin Alumni Research Foundation, the SMSF increased its capabilities by purchasing an RNA interference, or RNAi, library.

Instead of looking for a chemical that affects a protein, this approach uses small segments of RNA to block the synthesis, one at a time, of 18,000 different proteins in a human cell.

“Combined with the high-throughput robotic screening, this gives UW–Madison scientists the ability to efficiently identify which human proteins are most relevant to the biology they are studying,” Hoffmann says.

But the rapid screening of large numbers of chemicals or RNAi is just one aspect of the SMSF activity, says Hoffmann. He recently hired two synthetic chemists, who are based in space in the School of Pharmacy. These scientists contribute after a hit passes re-screening and counter-screening hurdles by tweaking and purifying the compounds. And later in the process, they make larger quantities for animal testing.

The synthetic chemists will soon be turning their attention to purifying some of Keller’s fungal extracts. Various strains of them are showing promising activity, warranting closer examination.