Crystal Structure Reveals Surprises

A new crystal structure of an important drug-metabolizing enzyme could lead to drugs with better metabolic profiles and fewer adverse side effects.

Scientists at Astex Technology in Cambridge, England, obtained structures of the enzyme cytochrome P450 3A4 (CYP3A4) by itself, with a substrate molecule, and with an inhibitor [Science, published online July 15, http:// www.sciencemag.org/cgi/content/abstract/1099736v1]. CYP3A4 is involved in metabolizing about half of all marketed drugs.

The structure reveals some surprises about the enzyme. The active site had been predicted to be “cavernous,” says Harren Jhoti, chief scientific officer at Astex, because the biochemistry of the enzyme is consistent with simultaneous binding of multiple substrates.

Instead, the active site was found to be relatively small, and the progesterone substrate was bound in a peripheral binding site located near an unpredicted phenylalanine cluster. “That is a pretty controversial, provocative discovery,” Jhoti says.

He suggests that the peripheral binding site may be an initial recognition site and perhaps an allosteric site, one where binding at that site affects binding elsewhere on the protein.

“Although people knew that this protein had allosteric sites, they really had no idea where they could be,” Jhoti says. “Most conventional thinking is that the allosteric site would be inside the protein and that the protein would have a really big pocket for the active site.” The peripheral site is located on the surface of the protein, albeit in a region that is embedded in the cell membrane.

Vanderbilt University biochemist F. Peter Guengerich, who also studies cytochrome P450s, says that the paper “may raise as many questions as it answers.” He suggests that the binding of the progesterone could represent an initial docking site on the way to the catalytic site. “However, this hypothesis must be considered very speculative.”

IN THE POCKET The drug-metabolizing enzyme cytochrome P450 3A4 has a smaller than expected active site. The ball-and-stick structure represents the heme group in the active site.<br > Science © 2004