Revolutionizing drug discovery with RNA in the spotlight

January 25, 2018, Ohio Supercomputer Center
Jennifer Hines, Ph.D., professor of chemistry and biochemistry at Ohio University, is studying RNA riboswitches as a possible new approach to kiling harmful bacteria. Credit: Ohio University

The rise of antibiotic resistance among common infectious bacteria is a worrisome health threat that has many scientists looking for a solution. Jennifer Hines, Ph.D., professor of chemistry and biochemistry at Ohio University, is one of the few looking to ribonucleic acid (RNA) structures for new drug discovery. Her research group is studying a key regulator for bacterial gene expression made up of RNA, called a riboswitch, that could be crucial in designing new drugs to kill bacteria.

"Just like a light switch you flick with your finger and turn on or off the light, the global fold of the RNA changes in response to interactions with the signaling molecule," Hines said. "My research group is working toward designing small that can disrupt that key RNA signaling molecule interaction in order to permanently turn off the switch and kill the bacteria specifically."

To determine the structure of these potential new antibiotics, Hines' group tests how different small molecules interact with the RNA riboswitch. Since Hines has to test the docking of entire libraries of small molecules on the riboswitch, she uses the power of the Ohio Supercomputer Center's Oakley Cluster to speed up the calculation process. This allows her to test multiple RNA sites against many different small molecules to identify the best pairing.

While performing a single calculation with one molecule may take Hines two minutes on her lab computer, the same calculation is done almost as soon as she enters it by using the Oakley Cluster. She also realizes cost savings through using MacroModel and Glide shared software licenses through OSC.

"Bottom line, I cannot afford more than one computer in my lab to be working on it," Hines said. "If I have multiple students with different projects, they have to line up after one another whereas with the Ohio Supercomputer Center, they can all be working on it at the same time. It allows more people to investigate simultaneously and the calculations just run a lot faster."

Antibiotics are not the only pharmaceutical area where RNA holds promise. Traditionally, significant advances in drug discovery have occurred through targeting specific proteins or DNA. RNA is present in every living cell also, but in the past was overlooked as a potential therapeutic target. Because it is involved in nearly every biological chemical process, yet has a relatively simple structure, it makes for an enticing target in the world of discovery. Hines said it is only within recent years that RNA has become a major player for structural and molecular biologists who are looking for novel therapies.

"It is just mind-blowing what RNA does in bacteria, in humans and in viruses," Hines said. "We're just at the dawn of targeting RNA for purposes and so with RNA being so elegantly involved in all sorts of regulatory processes, if you get more information about the best ways to target RNA with , you could potentially open up new areas for anticancer research, antiviral research, in addition to the antibacterial research that I'm doing."

Explore further: How molecular riboswitches work in bacteria

Related Stories

How molecular riboswitches work in bacteria

October 13, 2017

Many bacteria have molecular control elements via which they can switch genes on and off. These riboswitches also open up new options in the development of antibiotics or the detection and decomposition of environmental toxins. ...

Researchers flip riboswitch to kill bacteria

October 1, 2015

(Phys.org)—A team of researchers working for pharmaceutical company Merck has found an instance of a molecule that is able to flip a switch in a bacterium that prevents it from synthesizing a needed nutrient, and thus kills ...

Recommended for you

Plug-and-play technology automates chemical synthesis

September 20, 2018

Designing a new chemical synthesis can be a laborious process with a fair amount of drudgery involved—mixing chemicals, measuring temperatures, analyzing the results, then starting over again if it doesn't work out.

Commercially relevant bismuth-based thin film processing

September 20, 2018

Developing materials suitable for use in optoelectronic devices is currently a very active area of research. The search for materials for use in photoelectric conversion elements has to be carried out in parallel with developing ...

A game of pool in the live cell

September 20, 2018

Cells need to react to environmental changes and maintain a balanced system of signaling cascades within the cell. Proteins outside of the cell, on the cellular surface, inside the cellular membrane, and within the cell orchestrate ...

Nucleation a boon to sustainable nanomanufacturing

September 19, 2018

Calcium carbonate is found nearly everywhere, in sidewalk cement, wall paint, antacid tablets and deep underground. Engineers at Washington University in St. Louis have used a unique set of state-of-the-art imaging techniques ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.