UNC study: Drugs throw a wrench into the molecular works of enzymes

Abstract

Drugs that work by blocking the function of a protein from the outside also disrupt the protein’s internal workings, according to new research from the University of North Carolina at Chapel Hill.

The discovery, made by scientists at the UNC Eshelman School of Pharmacy and published in the March 11, 2009 issue of the journal Structure, opens the door to the possibility of targeting proteins with drugs in new ways. The study is the first to take a comprehensive look at the changes that take place within the molecular machinery of a protein when it binds with a drug.

“Previous studies have looked at the movement within proteins, and they’ve looked at how the structure of proteins change when drugs bind to them,” said Andrew Lee, Ph.D., an associate professor in the pharmacy school and senior author of the study. “However no one has looked to see how actual movement is affected when drugs bind until now.” Lee is a member of UNC Lineberger Comprehensive Cancer Center.

Using sophisticated spectroscopic technology, Lee and his colleagues studied how two drugs, the cancer drug methotrexate and the antibiotic trimethoprim, affected the internal mechanics of a particular protein – an enzyme called DHFR - in a strain of E. coli bacteria.

Only in the past decade have scientists become convinced of the importance of movement in the function of protein enzymes, Lee said. Those movements give proteins the energy needed to complete the biological processes for which they are responsible. The motions are very quick; some of them are so fast they are measured in picoseconds, or trillionths of a second, and appear as vibrations rather than large movements. “The proteins almost appear to be breathing,” Lee said.

“We found that when we bound a drug to the protein in our study, parts of the protein away from the receptor site stop moving,” Lee said. “The drug decoupled the global motion that was occurring throughout the enzyme.”

The study raises some interesting possibilities. Instead of trying to design a drug to plug one specific receptor site on a protein, scientists could target alternative sites or even multiple sites to disrupt the protein’s functional movements. In any case, learning more about the composition and movement of proteins is crucial to future drug development, Lee said.

“We’re still not that good at predicting a drug molecule’s affinity for binding to a particular site,” he said. “I think that is partially due to the flexible nature of proteins. To have a complete picture of a protein’s behavior and be able to predict its interaction with other molecules, you need to know not just its structure but its dynamic properties.”

The lead author of the study is Randall Mauldin, a graduate student in the UNC School of Medicine’s biochemistry and biophysics department. Mary Carroll, a graduate student in the pharmacy school, is the other author. The study was funded by a grant from the National Institutes of Health.