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November 5, 2009

An Enzyme Reveals An Unexpected Inclusiveness

Protein Binding: Bacterial enzyme's active site welcomes both enantiomers of a chiral molecule at the same time

Sophie Rovner

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Two enantiomers nestle in the active site of a bacterial enzyme. C = gray, N = blue, Br = red, O = pink. Courtesy of Rolf Breinbauer
CLOSE QUARTERSTwo enantiomers nestle in the active site of a bacterial enzyme. C = gray, N = blue, Br = red, O = pink.

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European researchers have discovered the first enzyme that can simultaneously bind both enantiomers of a chiral molecule in its active site. They believe this behavior could have important implications for drug discovery.

Usually, an enzyme can bind only one enantiomer of a chiral molecule. Rare cases have previously been discovered in which a second enantiomer can also bind to an enzyme's active site, but never at the same time as the first. Now, in work with the bacterial enzyme PhzA/B, researchers have stumbled across an instance in which the two enantiomers of a ligand can slip into the active site together (Angew. Chem. Int. Ed., DOI: 10.1002/anie.200902997). Wulf Blankenfeldt, Rolf Breinbauer, and Matthias Mentel carried out the work at the Max Planck Institute of Molecular Physiology, in Dortmund, and the University of Leipzig, both in Germany, and Graz University of Technology, in Austria.

In bacteria, PhzA/B catalyzes the condensation of two identical amino-cyclohexenone molecules to create a phenazine precursor. Bacterial phenazines have several functions, including the production of toxic reactive oxygen species that possess antibiotic activity and the reduction of environmental iron to make it more soluble.

When the European researchers synthesized a series of ligands to study the enzyme's activity, they found that PhzA/B could host both the R and S enantiomers of 5-bromo-2-(piperidin-3-ylamino)benzoic acid, which together resemble an intermediate in the reaction normally catalyzed by the enzyme. Although these particular ligands do not affect the enzyme's activity, the researchers plan to modify the ligands so they can inhibit phenazine biosynthesis, which is associated with bacterial virulence and infectious disease.

Because the PhzA/B enzyme catalyzes a dimerization, it's reasonable that its active site could bind two molecules that mimic an intermediate in that reaction, says Romas J. Kazlauskas, a biochemistry professor who studies stereoselective enzymatic reactions at the University of Minnesota, in St. Paul. But that distinction might mean that such cases are rare.

Nevertheless, Kazlauskas says, the findings could have ramifications for drug screening studies, which are commonly performed with racemic mixtures. Results from such screens should be interpreted with an awareness that ligand-protein interactions might be more complicated than previously realized, the European researchers advise. For instance, a case might arise in which a racemic ligand is inactive but an individual enantiomer has desired drug activity.

The findings could also have an impact on fragment-based drug design, in which individual molecules that bind weakly to a protein target are connected to create a larger drug molecule that strongly binds the target. "In the context of our work, this approach can be used by linking two enantiomers with a covalent bridge," Breinbauer and Blankenfeldt note.

Chemical & Engineering News
ISSN 0009-2347
Copyright © 2011 American Chemical Society
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