High-Throughput Tracking Ribosome Technique May Revolutionize Drug Discovery

The ribosome is like a factory for protein production in the cell, and as such, has long been a key target for drug discovery. Now, a technologic development is set to revolutionize research in this field.

For the first time, scientists from Weill Cornell University Medical College (New York, NY, USA) have developed a way to observe at the molecular level, real-time movies of significant structural processes within the ribosome underpinning the synthesis of protein. They were able to do it in a manner that should someday allow for screening of novel drugs that inhibit the ribosome or for the improvement of existing antibiotics that are sometimes toxic.

"This is really a proof-of-principle of what we hoped we could achieve--that we can make these types of measurements in a very robust and high-throughput manner,” reported study senior author Dr. Scott Blanchard, assistant professor of physiology and biophysics at Weill Cornell Medical College. His team published their findings in the March 23, 2007, issue of the journal Molecular Cell.

The ribosome is comprised of approximately 60 different molecules. These molecules work together in complicated ways, using instructions found in RNA to produce the proteins that cells need to live and grow. In the field of drug development, it is hard to overestimate the importance of the ribosome--for example, more than 50% of current antibiotics target this major cellular machine.

"Genetic instructions are presented to the ribosome in the form of messenger RNA,” explained Dr. Blanchard. "The process of translating those mRNA instructions into proteins involves the selection by the ribosome of RNA molecules called transfer RNA [tRNA].”

This selection process is the determining factor linking gene sequences with their end-product proteins. However, for years, much of what scientists know about ribosomal activity--and how drugs might affect it--has been conjecture, since it has been virtually impossible to view molecular activity within this tiny structure firsthand.

However, Dr. Blanchard's research has yielded a breakthrough: an advanced technology in microscopy called single-molecule fluorescence resonance energy transfer (smFRET) that uses long-established technologies in a whole new way.

"Using this technique, we're able to collect photons of light coming from many single molecules simultaneously,” Dr. Blanchard explained. "This information reports on a biomolecule's location, its interaction with other molecules, and tiny motions within the molecule itself. Before this technology, investigations of molecular processes were like trying to figure out how cars worked by watching traffic on the freeway from a satellite high up in space. Now, it's as if we're able to able to inspect the individual cars directly. In fact, both are important but having this new perspective should go a long way towards improving our understanding of how these machines operate.”

Observing one molecule at a time is fine, but effective drug discovery requires the rapid analysis of hundreds or even thousands of compounds in a high-throughput manner. In their latest research, Dr. Blanchard's team used smFRET to track sub-nanometer movements in tRNA positions deep within the ribosome (that is a distance change of approximately one hundred millionths of an inch).

"We observed three discrete configurations of tRNA within the ribosome that interconvert on the 100 millisecond timescale, including an intermediate hybrid configuration that no one had ever had evidence of before,” the researcher stated. The ability of scientists to make nearly real time measurements of how the ribosome's structure changes during function may be the study's biggest achievement. "Not only can you make exquisitely sensitive measurements on ribosome structure over time, you can also detect how the system changes in response to ligands, including antibiotics,” Dr. Blanchard said. "Those measurements should be able to be performed in a high-throughput manner,” he noted.

"Our next step is to watch how specific drugs affect the dynamic processes within the ribosome,” added Dr. Blanchard. "We hypothesize that drugs activities that block normal ribosomal functions can be detected by measuring how they change the cadence of structural events in the molecule. As my graduate advisor coined it, it's like a molecular EKG [electrocardiogram]. This new, close-up look at how molecular machines work, and how they are affected by therapeutic agents should open the door to better opportunities in drug discovery.”


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