World's Fastest Supercomputer Joins The Battle Against COVID-19 - Physics-Astronomy.org

World's Fastest Supercomputer Joins The Battle Against COVID-19

COVID-19 has got a fearsome new enemy: the fastest supercomputer in the world.Biophysicists at the University of Tennessee have used the IBM-built supercomputer SUMMIT to sift through thousands of molecules and find potential compounds that could be used as a new drug against SARS-CoV-2, the coronavirus responsible for the current COVID-19 pandemic




After a couple of days of calculations, the supercomputer managed to find at least 77 compounds that indicate they could potentially help to prevent SARS-CoV-2 from invading human cells. 
The findings were recently published in a paper available on the preprint server ChemRxiv. This means the paper is awaiting peer-review, so the research should be considered a "work in progress".  
The surfaces of coronaviruses are covered in spikey crown-like proteins (hence the name) that allow the viruses to bind to and infect human cells, a bit like a lock and key. By understanding the viruses’ proteins and the human cell host receptors, as well as the way other chemical compounds interact with them, it’s possible to work out how drugs might be effective against the pathogen. 


SUMMIT was used to deeply analyze a database of over 8,000 compounds that are known from existing drugs, chemicals, herbal medicines, and natural products. Its job was to sniff out compounds that appear to be capable of binding to the SARS-CoV-2 protein spikes, thereby blocking the virus’s key and theoretically stopping it from invading the body's cells.
“It took us a day or two whereas it would have taken months on a normal computer,” study author Jeremy Smith, director of the University of Tennessee Center for Molecular Biophysics, said in a statement.


The compound, shown in gray, was calculated to bind to the SARS-CoV-2 spike protein, shown in cyan, to prevent it from docking to the human cell receptor, shown in purple. Micholas Smith/Oak Ridge National Laboratory, U.S. Dept. of Energy

Of course, there’s no guarantee any of the compounds found by the supercomputer will be effective in practice. Furthermore, just like any drug, it will require extensive testing and clinical trials before we see it as a viable treatment. However, the supercomputer’s work has helped to identify some promising candidates for researchers to follow up on.


“Our results don’t mean that we have found a cure or treatment for COVID-19," said Smith. "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.” 
SUMMIT is described as the “Formula One of supercomputers”. Found at Oak Ridge National Laboratory in Tennessee, the supercomputer is the size of two tennis courts and is capable of processing over 200 quadrillion calculations per second. It’s used by a variety of different researchers for a variety of noble missions, from modeling supernovas and the environment to crunching data about cancer and genetics.
This research is not the first to use computers to find new drugs. Just last month, researchers used a novel computer algorithm to sift through a vast digital archive of over 100 million chemical compounds and found a molecule that appeared to possess some truly remarkable antibiotic properties.

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