With the coronavirus sweeping the globe, tech conferences and supply chains are being hit hard – but now, tech is hitting back. Oak Ridge National Laboratory (ORNL) has announced that Summit, the most powerful publicly ranked supercomputer in the world, is joining the fight to understand and mitigate the coronavirus.
Summit, which tops the most recent Top500 list, is an IBM-built system packed with 4,608 nodes (each powered by two IBM Power9 CPUs and six Nvidia Volta GPUs), delivering 148 Linpack petaflops. Now, that firepower is being turned toward the coronavirus, with Summit taking aim at a telltale “spike” protein on the virus that may be the key to developing drugs to fight it.
If a compound were able to bind to this spike protein, the virus would be rendered incapable of infection – but manually testing compounds to assess this behavior is a laborious process, especially in an urgent public health crisis. So Micholas Smith, a postdoctoral researcher at the University of Tennessee/ORNL Center for Molecular Biophysics (UT/ORNL CMB), used early studies and sequencing of the virus to build a virtual model of the spike protein.
Then, after being granted time on Summit through a discretionary allocation, Smith and his colleagues performed a series of molecular dynamics simulations on the protein, cycling through 8,000 compounds within a few days and analyzing how they bound to the spike protein, if at all.
“Using Summit, we ranked these compounds based on a set of criteria related to how likely they were to bind to the S-protein spike,” Micholas Smith said in an interview with ORNL. In total, the team identified 77 candidate “small-molecule” compounds (such as medications) that they considered worthy of further experimentation, helping to narrow the field for medical researchers.
“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, director of UT/ORNL CMB and principal researcher for the study. “Our results don’t mean that we have found a cure or treatment for the Wuhan coronavirus. We are very hopeful, though, that our computational findings will both inform future studies and provide a framework that experimentalists will use to further investigate these compounds. Only then will we know whether any of them exhibit the characteristics needed to mitigate this virus.”
Next, the researchers are planning to run the study again using a new, more accurate model of the spike protein that recently became available.
Header image: A compound (gray) binding to the spike protein (cyan). Image courtesy of Micholas Smith and ORNL.