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College of Science and Mathematics

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Chemistry Students Compute Ways to Stop Viruses

Zach Petrek and his research poster
Zach Petrek presents his research on viruses at the American Chemical Society Meeting.


"Computational characterization of molecular interactions" isn't a phrase you hear every day, but someday, it might keep you from getting sick. Chemistry Professor Ashley McDonald and her students are using computers to study HIV in hopes of learning how to stop the virus from reproducing.

All viruses — HIV, flu, ebola — work by taking over their host's cells and forcing those cells to reproduce the virus. Some viruses start the process by using short pieces of DNA or RNA, called aptamers, that bind to small molecules, called ligands. That interaction triggers another event, in this case the reproduction of the virus.

Each aptamer has an opening of a certain shape for the ligand to bond to. The challenge is, scientists don't know much about what happens when the ligand approaches that opening. That's what McDonald and her students are hoping to find out. If they can change the interaction between the molecules, the virus won't be able to reproduce.

"Does aptamer geometry matter? Does it change? What is the binding mechanism? These are all unknowns," McDonald said.

What is known is the molecular structure of the HIV aptamer and an attached ligand. The students plugged this information into the computer and then wrote a program that virtually takes the two molecules apart and puts them back together again looking at different pieces of the aptamer each time.

They had guessed that only the part of the aptamer near the ligand mattered in the binding process, but it turns out that most of the aptamer changes its geometry when the two molecules interact.

"This result was completely unexpected," McDonald said. "That's what students really gain from any kind of research experience — they understand science is about things that we don't know."

"In doing real world research, I learned that failing to find a solution is a natural part of the learning process," said Zack Petrek, a chemistry major who is part of McDonald's group. "No time is truly wasted when you are challenging your mind to think in a different way."

The students' results raise the possibility of approaching the aptamer-ligand interaction in ways no one had considered before. Because the entire aptamer changes shape, it might be possible to develop anti-viral drugs that interact with the molecule at other points than where it binds to the ligand.

"They really are finding out something that no one knows," McDonald said. "That's what science really is."

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