Supercomputing Technology Creates Opportunities for Drug Discovery

Jerome Baudry of the University of Tennessee and the US Department of Energy's Oak Ridge National Laboratory (ORNL) Center for Molecular Biophysics (Oak Ridge, USA) adapted a widely used existing software to allow supercomputers such as ORNL's Jaguar to filter through massive molecular databases and pinpoint chemical compounds as potential drug candidates.

The research was published online December 2010 online ahead of print in the Journal of Computational Chemistry. "Our research is the missing link between supercomputers and the huge data available in molecular databases like the Human Genome Project,” Dr. Baudry said. "We have an avalanche of data available to us, and now we need to translate that data into knowledge.”

Such translation is vital for the first stages of drug development, in which researchers look for applicable chemicals that interact with a target in the body, typically a protein. If the chemical is suitable, it attaches onto the protein and produces a desirable effect in the cell. However, with thousands of known proteins and millions of chemicals as potential drugs, the number of possible combinations is enormous. "It is very expensive and time-consuming to measure these interactions experimentally,” Dr. Baudry stated. "But with supercomputers, we can process millions of molecules a day.”

The fast and efficient processing of molecules gives scientists an opportunity to take risks on previously unexamined drug candidates, which could lead to diverse and novel classes of drugs. "Before, we threw away a lot of information because molecules did not have a preferred profile,” Dr. Baudry noted. "Now, every molecule can be examined without worrying about wasting resources.”

The scientists have already begun work to launch the research into reality through a new collaboration supported by the US National Institutes of Health (Bethesda, MD, USA). The project team plans to put the computational development to work on ORNL supercomputers to search for chemicals that could treat prostate cancer.

"Our development work is the computational equivalent of building the Saturn V rocket,” Dr. Baudry concluded. "Now we want to fly it to the moon.”

Related Links:
Oak Ridge National Laboratory Center for Molecular Biophysics