USciences’ West Center Harnesses Computer Power for Drug Design
At University of the Sciences, Beowulf isn’t just an epic poem. It’s what fuels one of the University’s most powerful and collaborative research groups.
The West Center for Computational Chemistry and Drug Design brings together researchers from across USciences disciplines with the power of high-tech computer processing. Through computer science, the West Center group models and designs everything from RNA and lipids to drug molecules with the ultimate goal of drug design.
“The West Center is a collection of faculty who perform computational research across many different disciplines, from computer science to biology to chemistry to physics to math,” said Preston B. Moore, PhD, director of the West Center. “We’re a conglomeration. Each one of us has his or her own research, but we all use computational systems in one way or another to advance our knowledge.”
Dr. Moore, who is also a professor of chemistry, focuses on understanding the physical chemistry of complex chemical systems such as proteins, interfaces, and lipid bilayers. One current project explores general anesthetics and their effects on the lipid bilayers. This could help researchers design new anesthetics that are more efficient and have fewer side effects.
Additional members of the West Center faculty include a cross section of bench scientists who are tied together by technology.
These other researchers at the West Center include:
Randy J. Zauhar, PhD, associate professor of chemistry, emphasizes developing drugs that will inhibit highly mutable targets such as those in HIV protease. His research, which is funded by the National Institutes of Health, has lead him to design a computer-based drug design system called Analysis of Ligand Binding with Multiple Substitutions.
Zhijun Li, PhD, associate professor of bioinformatics, uses the processing power of the West Center to study proteins in membranes. Dr. Li is modeling the structures of membrane proteins to better understand how they work and then is using that information, in tandem with other researchers, for computer-aided drug design. Dr. Li has been supported by various agencies, including the National Institutes of Health and PhRMA.
Vojislava Pophristic, PhD, associate professor of chemistry, focuses on computer-aided foldamer design in a project funded by the National Science Foundation. Instead of trying to synthesize foldamers, which are artificial polymers that fold into stable secondary structural elements, she is modeling them at the West Center to predict what they will look like. “It’s very much like drug design,” she said. It’s not just their chemical structure she is modeling but also their 3D shape.
Michael F. Bruist, PhD, associate professor of biochemistry, focuses on nucleic acids and their dynamics, that is, how DNA and RNA wiggle and move about. One current project looks at Integration Host Factor (IHF), a protein that bends DNA for other proteins to bind to it. His computer models indicate that IHF cannot always bind and bend all of the DNA.
Zhiwei Liu, PhD, assistant professor of computational chemistry, investigates molecular mechanics force fields for both atomistic and coarse grain scale modeling of systems such as proteins and biopolymer mimetics. Force fields are fundamental to molecular simulations, and only accurate force fields lead to accurate prediction of both structures and functions of chemical systems. “I love my work at the West Center because it allows me to do two things I am passionate about at the same time: research and computers,” said Dr. Liu. She manages the powerful computer clusters for the center, from fixing broken computers to making sure every software package works at its optimal level.
In addition to this team of researchers, graduate and undergraduate students are working and learning how to do research at the West Center. They participate in weekly sessions run by their fellow graduate students and gain valuable hands-on experience while performing cutting-edge research.
“They are able to do research in this type of environment at a fairly young age and really understand what research is about as they are deciding their career paths,” said Dr. Moore.
“The West Center is a collection of faculty who perform computational research across many different disciplines, from computer science to biology to chemistry to physics to math.”
—Dr. Preston B. Moore