Science Editor

In the Oct. 17, 2008, issue of Cell, researchers from Rutgers University and the German Helmholtz Centre for Infection Research reported structural and mechanistic data on three antibiotics that kill bacteria by the same mechanism: through interfering with the so-called switch region of RNA polymerase.

The compounds used by the researchers - myxopyronin, corallopyronin and ripostatin - are themselves not new. But the researchers hope that the new information on how they work will help them to develop additional drugs that target RNA polymerase. "This information puts us in a position to design outstanding analogues," senior author Richard Ebright told BioWorld Today.

In their Cell paper, the scientists used structural approaches to get a detailed picture of how and where the three compounds bind to RNA polmerase. The enzyme "has a shape reminiscent of a crab claw, with two prominent pincer-like projections," Ebright said. "Just as with a real crab claw, one pincer stays fixed and one pincer moves . . . by rotating about a hinge. Our studies show that the three antibiotics bind to and jam this hinge."

RNA polymerase is one of the many proteins that is shared between bacteria and their hosts. But the polymerase is much more conserved between different bacterial species than between bacteria and humans, allowing the potential development of targeting agents that are specific to bacteria, but nevertheless a broad-spectrum agent within the bacterial world.

Ebright said that RNA polymerase could have "special importance" for targeting tuberculosis - a bacterium, which has been bedeviling humans for 9,000 years, affects a third of the world's population, and is now going from multidrug resistant to extremely drug resistant, making new weapons an urgent public health need.

Tuberculosis bacteria divide slowly during what's known as latent infection, and a subset also divide slowly or not at all during active infection. "In this effectively dormant state, very few biochemical processes are occurring within those cells, and as a result, there are very few ways to kill those cells," Ebright said.

But RNA polymerase is one of the enzymes that is critical even for dormant bacteria. The current first-line treatment for tuberculosis is a combination treatment that includes the RNA polymerase inhibitor rifamycin, which binds to the RNA polymerase at a site that is distant from the switch region. But rifamycin only can be given at comparatively low doses, which means a long treatment course.

The standard treatment lasts six months to get the relapse rate down to 5 percent, and as with most other antibiotics, resistance to rifamycins is a rapidly growing problem.

One of the reasons that Ebright and his colleagues are optimistic about the switch region's prospects as a drug target is that it has similarities to the site that is targeted by non-nucleoside reverse transcriptase inhibtiors, or NNRTIs, a major class of anti-HIV agents.

First off, despite the fact that they have no structural or sequence similarities, the two work by an analogous mechanism. In both cases, the targeted region "serves as the hinge around which the pincer opens and closes," Ebright explained.

A second, and "probably more important," similarity is that "in both cases, the binding site is a nearly completely enclosed, predominantly hydrophobic pocket," Ebright explained. And such a structure is "highly druggable, and druggable by multiple chemotypes." There are a number of structurally unrelated NNRTIs, and Ebright pointed out that while two of the compounds his team used in its study were structurally related, the third one was not.

Ebright and his colleagues currently are looking for promising analogues of the three compounds they used in their paper, but also are hoping to identify additional chemotypes that will target the switch region.

"We are currently doing all of this in house," Ebright said. "But we are definitely interested in making contacts with industry."

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