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X-rays Pinpoint Drug Target for Stomach Ulcers

Mon, 12/10/2012 - 1:08pm
SLAC National Accelerator Laboratory

This diagram shows the first-ever glimpse of the six-molecule ring of urea channels embedded in the membrane of a type of bacteria called Helicobacter pylori. Understanding the structure of the urea channels will allow researchers to design future drugs to target this bacteria, which harm hundreds of millions of people worldwide. Image: Hartmut Luecke, UC IrvineExperiments at the U.S. Department of Energy's (DOE) SLAC National Accelerator Laboratory have revealed a potential new way to attack common stomach bacteria that cause ulcers and significantly increase the odds of developing stomach cancer.

The breakthrough, made using powerful X-rays from SLAC's Stanford Synchrotron Radiation Lightsource (SSRL), was the culmination of five years of research into the bacterium Helicobacter pylori, which is so tough it can live in strong stomach acid. At least half the world's population carries H. pylori and hundreds of millions suffer health problems as a result; current treatments require a complicated regimen of stomach-acid inhibitors and antibiotics.

"We were looking for a means to disrupt H. pylori's own mechanism for protecting itself against stomach acid," says Hartmut "Hudel" Luecke, a researcher at the Univ. of California, Irvine, and principal investigator on the paper, published online in Nature. With this study, he says, "We have deciphered the three-dimensional molecular structure of a very promising drug target."

Luecke and his team zeroed in on tiny channels that H. pylori uses to allow in urea from gastric juice in the stomach; it then breaks this compound into ammonia, which neutralizes stomach acid. Blocking the channels would disable this protective system, leading to a new treatment for people with the infection.

Solving the structure of the protein to find the specific area to target wasn't easy. The channels are formed by the protein embedded in the bacterium's cell membrane, and membrane proteins are notoriously difficult to crystallize, which is a prerequisite for using protein crystallography, the main technique for determining protein structures. This technique bounces X-rays off of the electrons in the crystallized protein to generate the experimental data used to build a 3D map showing how the protein's atoms are arranged.

The challenge with membrane proteins is that they are especially hard to grow good quality crystals of, and for this experiment, says Luecke, "We needed to grow and screen thousands of crystals."

"We collected over 100 separate data sets and tried numerous structural determination techniques," says Mike Soltis, head of SSRL's Structural Molecular Biology division, who worked with Luecke and his team to create the 3D map of the atomic structure. The final data set was measured at SSRL's highest brightness beam line (12-2), which produced the critical data that met the challenge.

"This is the hardest structure I've ever deciphered, and I've been doing this since 1984," Luecke says. "You have to try all kinds of tricks, and these crystals fought us every step of the way. But now that we have the structure, we've reached the exciting part—the prospect of creating specific, safe and effective ways to target this pathogen and wipe it out."

This work was supported by the National Institutes of Health, the National Cancer Institute, the UC Irvine Center for Biomembrane Systems and the US Veterans Administration. SSRL is supported by DOE's Office of Science, and the SSRL Structural Molecular Biology Program by DOE and NIH. The research team also included scientists from the Univ. of California, Los Angeles (Greater West Los Angeles Health Care System).

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