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A faster way to find drugs to target some of the body’s key catalysts

dartsFor more than a decade, some medical researchers have been eyeing an enzyme that ratchets up damage to the heart during a heart attack. They’ve been thinking how nice it would be to develop a drug to put that enzyme out of commission.

So they’ve tried to find a molecule that cleanly knocks out the enzyme. But their work was to no avail — until now. Stanford postdoctoral researcher Nir Qvit, PhD, and colleagues in the lab of Daria Mochly-Rosen, PhD, professor of chemical and systems biology, reported the details in the recent print edition of the Journal of the American Chemical Society.

The troublesome enzyme does its work by grabbing a nearby phosphate group -- a cluster of one oxygen and four phosphorous atoms -- and then transferring it to another molecule. When the enzyme, called delta-PKC (short for delta protein kinase C), transfers the phosphate group to its partner in crime, PDK, mayhem ensues.

Since the enzyme has a special site where it carries out the transfer, why not simply plug it up? That would stop it from working with PDK and causing heart damage, right?

The problem is that plugging the transfer site would interfere with a lot of other phosphate group transfers, many of them to molecules that carry out crucial business in our cells. So a drug that completely blocks delta-PKC’s phosphate group transfer site would lead to nasty side effects.

Even more troubling, delta-PKC has lots of cousins -- researchers estimate about 500 different members of the protein kinase family -- and their transfer sites are all very similar. So if you block the transfer site on one member, you’ll probably block the transfer sites on all. That would be bad. These proteins are catalysts that make possible thousands of chemical reactions that keep us alive.

But now there’s good news. Qvit and colleagues have found a way to stop delta-PKC from transferring phosphate groups to PDK that doesn’t interfere with delta-PKC’s ability to make other phosphate group transfers. They did this by moving their focus from the transfer site to another important locale on the enzyme’s surface: its docking site for PDK. This is where delta-PKC and PDK hook up and set the stage for a phosphate group transfer to PDK.

The key was an algorithm Qvit developed to locate the docking site. Once he found it, he and the rest of the team -- Mochly-Rosen and colleagues Marie-Helene Disatnik, PhD, and Jie Sho -- created a molecule to block it and ran experiments in rats and mice to see if it reduced the harm from heart attacks. It did.

Even better, this same technology could be used to create molecules to block other protein kinase docking sites - which would be very useful for lab research and for drug development. “We think it’s a great technology,” said Qvit.

“It’s fast and inexpensive compared to screening big chemical libraries to identify an inhibitor,” a primary approach others have used in the past, he said. It’s also faster and easier than the other standard method: mutating each transfer site and doing further experiments to discover the mutation’s impact.

“To identify an inhibitor using our approach, it takes a couple of hours to design, a week -- at most -- to make and a week to test,” said Mochly-Rosen. The other approaches require several months at a minimum. Stanford has patented the technology and it's available for licensing.

“We hope other labs and companies will adopt this. Hopefully we will be able to transfer it successfully,” Qvit said

Previously: Are your cells stressed out? One Stanford researcher is helping them relax and An inside look at drug development.
Photo by Richard Matthews

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