To help respond to the COVID-19 coronavirus outbreak, researchers at the Oak Ridge National Laboratory (ORNL) are using the world’s fastest supercomputer to identify compounds that may effectively combat the virus.
Using Summit, which is powered by 9,216 IBM Power9 CPUs and over 27,000 NVIDIA V100 Tensor Core GPUs, the researchers identified 77 small-molecule drug compounds that are likely to bind to the glycosylated spike (S) protein, which is how the virus gains entry into host cells.
“We were able to design a thorough computational model based on information that has only recently been published in the literature on this virus,” Micholas Smith said, referring to a study published in Science China Life Sciences, Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission.
With the help of the NVIDIA V100 GPUs, and GROMACS, a GPU-accelerated simulation package for biomolecular systems, the team ran their experiments on over 8,000 compounds. Their results were published last month on ChemRxiv, a preprint server for chemistry research. The supercomputer’s involvement was noted in the paper’s title, Repurposing Therapeutics for the Wuhan Coronavirus nCov-2019 Supercomputer-Based Docking to the Viral S Protein and Human ACE2 Interface.
“We ranked these compounds based on a set of criteria related to how likely they were to bind to the S-protein spike,” Smith stated in a Department of Energy/ORNL press release.
In parallel to this research, another group of scientists at the University of Texas at Austin and the National Institutes of Health released a more accurate model of the S protein. The ORNL team plans to run their study again with the new data, which may affect how the 77 compounds rank.
“Summit was needed to rapidly get the simulation results we needed. It took us a day or two whereas it would have taken months on a normal computer,” said Jeremy Smith, Governor’s Chair at the University of Tennessee and director of the UT/ORNL Center for Molecular Biophysics.
Smith doesn’t believe that the work will cure or treat COVID-19. However, he and the team are hopeful that their findings can be used to inform future research and provide a framework for scientists to further investigate these compounds.