Drug molecule finds way to make square peg fit round hole

BUFFALO, N.Y. — A square peg doesn’t fit a round hole. But what if the peg could change the shape of the hole?

A newly developed drug molecule can do something surprisingly similar when binding to its target protein, according to a University at Buffalo-led study published Tuesday (Sept. 15) in Angewandte Chemie International Edition.

The molecule, an inhibitor designed to block activity, initially clashed with a flexible loop in the structure of a protein implicated in cancer and known as p38 delta. This clash would normally hinder binding, but it instead caused the loop to change shape and wrap around the molecule, creating an unusually snug fit.

The molecule represented a 12,000-fold improvement in selectivity for p38 delta and was 110-fold more potent than previously available compounds.

“Typically, you design a molecule to fit the target. Here, we designed a molecule that makes the target adapt to it,” says corresponding author David Heppner, PhD, associate professor of chemistry in the UB College of Arts and Sciences.

The findings could provide a starting point for developing a new drug while also inspiring broader drug-design strategies that exploit similar structural features.

“Instead of treating a target protein’s structure as something to work around, we can think about how to make that structure work for us,” Heppner says.

The work was done in collaboration with Stefan Laufer, PhD, professor of pharmaceutical and medicinal chemistry at Tübingen University in Germany. It was supported by the National Institutes of General Medical Sciences, part of the National Institutes of Health, and the German Research Foundation. 

p38 mitogen-activated protein kinases are a family of proteins involved in regulating cellular activity. They are also notoriously difficult for drug molecules to bind to.

First author Nico J. Seidler synthesized several drug molecules to bind to these kinases as a PhD student in Laufer’s lab at the University of Tübingen. One molecule stood out for being exceptionally selective for p38 delta, but exactly why it was so selective remained unclear.

Then, as a Fulbright fellow in Heppner’s lab at UB, Seidler conducted structural studies on the molecule. X-ray crystallography revealed that the molecule was causing p38 delta to change shape around it.

“We found that the molecule accomplishes this through what we’re calling a ‘bump-kink.’” Seidler says. “Part of the molecule bumps against the flexible loop in the protein’s structure, causing the loop to kink. This kink brings the loop closer to another part of the molecule, allowing the protein to wrap, or self-encapsulate, around the molecule.”

The initial bump or clash between the molecule and the protein appears to cause a ripple effect that allows the protein to adapt to the molecule. 

“Nine times out of 10 this kind of bump would not result in binding. It would actually usually make things worse,” Seidler says. “This is an interesting example of where doing something that seems detrimental actually unlocks a whole new dimension.”

Crucially, the protein’s structural change is made possible by a distinctive amino acid located far from where the molecule actually binds. Known as histidine 30, the amino acid helps stabilize the kink in the loop. 

“It’s rare to have a region of the protein so far from the binding site influence binding,” Heppner says. “Normally we’d never even think to exploit an amino acid that far away, but here we found a way to indirectly take advantage of it.”

The molecule’s unusual binding method helps explain its increased potency and selectivity. Selectivity, which measures how much a drug binds to its target as opposed to other sites in the body, is crucial for minimizing toxic side effects. 

“We always want to isolate the place in the body where the disease is occurring and keep the rest of the body unaware that the drug is around,” Heppner says. 

The molecule could help researchers better understand p38 delta itself. The protein has been implicated in cancer and other biological processes, but researchers have lacked a highly selective way to inhibit it without affecting closely related proteins.

“Now that we have something selective for this target, we can better understand its biology and figure out where it might be best deployed therapeutically,” Laufer says.

The researchers also want to determine whether the unusual design strategy can be applied to other drug targets. In particular, they plan to investigate whether molecules can be designed to trigger similar structural changes that indirectly exploit distinctive features far from conventional binding sites.

“There may be distant features that were previously ignored because they weren’t considered druggable,” Heppner says. “Now we can start asking whether there are ways to take advantage of those features to make new drugs or improve existing ones.”