Vol 6. Issue 7 / February 27, 2006
New Research Gives Scientists Powerful Tool For Drug Discovery
Researchers at Florida State University's National High Magnetic Field Laboratory and the Florida branch of The Scripps Research Institute have developed and evaluated a robust new system for analyzing how drugs bind to proteins. This work could speed the delivery of potential new drugs and improve existing ones.
The work, which appears in the journal Analytical Chemistry, is the first published paper to result from a partnership between Scripps Research and a Florida university.
The collaborative research is focused on obtaining a more accurate picture of human proteins, which are the target of most drugs. Understanding the nature of the interaction between a drug and a protein—where the drug attaches and where it doesn't—is one of the keys to drug research, because the exact placement of a drug can determine whether it enhances a natural biological function or counteracts it.
"By pairing the magnet lab's expertise in high-field research with Scripps expertise in protein dynamics and drug development, we can create a kind of map that shows where drugs bind to the surface of proteins," said Alan G. Marshall, director of the lab's Ion Cyclotron Resonance (ICR) program and the Kasha Professor of Chemistry and Biochemistry at FSU. "We can do that because our technology is the best way to generate highly accurate pictures of tiny amounts of protein molecules."
Marshall said the experiment detailed in Analytical Chemistry can best be described as "molecular spray painting." Here's how it works:
The receptor protein with a drug stuck to it is dipped into a solvent called "heavy water" (deuterium oxide, or D2O). In the portions of the receptor that can exchange with heavy water (regions not involved in hydrogen bonding), the natural hydrogen atoms are gradually replaced by deuterium atoms, which increase the mass from 1 to 2 mass units. Scientists then dissect the receptor and use the magnet to weigh pieces of it to see which segments of the receptor remain covered up by the drug.
The team saw the potential of probing human protein molecules with this spray-painting technique, but also recognized that the experiment was limited by several factors. Each test would take anywhere from one minute to several hours, and each measurement would be slow. To ensure the reliability of the experiment, the process would need to be replicated twice more to validate the results, adding additional days to the process.
The paper published in Analytical Chemistry lays out the results of research to improve the technical aspects of the experiment. By using the high-field ICR magnet and its powerful spectrometer, coupled with a sample preparation robot, the scientists were able to extract data that show how the drug alters the dynamics of the receptor upon binding. This application of the experiment can measure changes in a fraction of the time—and show those changes over time. And the results are highly reproducible.
"This research is important because it gives us a new and very powerful way to probe the interaction between drugs and proteins," said Patrick Griffin, professor of biochemistry and head of drug discovery at Scripps Florida. "Because we've now solved many of the technical problems, this technique is sure to play an even larger role in understanding the mechanism of action of many classes of drugs."
Now that the data acquisition has been automated, the next step is automating the data analysis. The amount of data generated by the magnet's high-test mass spectrometer is staggering: 1 million data points every second. To analyze the data by hand would take a month. With automated software being developed at the magnet lab, the analysis will take just a few minutes.
Send comments to: mikaono[at]scripps.edu
"Because we've now solved many of the technical problems, this technique is sure to play an even larger role in understanding the mechanism of action of many classes of drugs," says Scripps Research Professor Patrick Griffin.