SUMMIT Supercomputer Used to Test Possible Treatments for COVID-19
Andrew Wheeler posted on March 20, 2020 |
77 promising small molecules found during simulation from a library of 8,000.
 The SUMMIT supercomputer. (Image courtesy of IBM, US Department of Energy and Oak Ridge National Laboratory.)
The SUMMIT supercomputer. (Image courtesy of IBM, US Department of Energy and Oak Ridge National Laboratory.)

Scientists at Oak Ridge National Laboratory are leveraging the awesome computing power of IBM’s SUMMIT supercomputer to find drugs to combat the ongoing coronavirus pandemic. SUMMIT, the fastest supercomputer in the world, allowed researchers to simulate the effects that 8,000 molecules would have on the novel coronavirus. These molecules are already known, approved, and readily-available. The small molecules used for testing included drug compounds, natural products, and metabolites. Seventy-seven such molecules were identified based on gene-sequencing data of the coronavirus.

Using virtual high-throughput screening, the 8,000 different small-molecules were tested to see if they bind to either the Viral S-protein at the host receptor region or to the S protein-human interface. The scientists at Oak Ridge Laboratory hypothesized that some of the small molecules could be used to “limit viral recognition of host cells and/or disrupt host-virus interactions,” according to a paper entitled Repurposing Therapeutics for COVID-19: Supercomputer-Based Docking to the SARS-CoV-2 Viral Spike Protein and Viral Spike Protein-Human ACE2 Interface.

The SUMMIT supercomputer occupies approximately 5600 square feet at the U.S Department of Energy’s Oak Ridge National Laboratory in Tennessee. Its computing power is off the charts: it can compute 200 quadrillion calculations per second. This is about one million times more computing power your average laptop. The virtual high-throughput screening used by the scientists at Oak Ridge is described as “an approximate early-stage drug discovery technique with a high failure rate.” The hit rate for this technique is about 10 percent.

Bottom Line

The compounds identified as promising by the SUMMIT simulation include pemirolast, which is an anti-allergy medicine used to treat chronic asthma, two antibiotics (one used to treat urinary tract infections and one used to treat tuberculosis), and a flavanone found in Herba Santa (a traditional herbal remedy for colds and asthma). A few small molecules found by SUMMIT are known for their efficacy as anti-viral medications used to treat other forms of coronavirus, including Cepharanthine and Hypericin.

The calculations performed on SUMMIT only took about two days, whereas an average computer would have taken months to perform the same calculations and computations. While the research is preliminary, it’s a hopeful look at how the novel coronavirus may be tackled in the months to come.

“The results presented are a first step towards the identification of small-molecule treatments against COVID-19,” concludes the paper.

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