Page 33 - FCW, July 2020

SCIENTISTS
ENLIST SUPERCOMPUTERS IN FIGHT
AGAINST CORONAVIRUS
High-performance computing has been critical in powering drug discoveries, and Oak Ridge National Lab is pushing that work further and faster to tackle the COVID-19 pandemic
BY JEREMY SMITH
In “The Hitchhiker’s Guide to the Galaxy” by Douglas Adams, the haughty supercomputer Deep Thought is asked whether he can find the answer to the ultimate question concerning life, the universe and everything. He replies that, yes, he can do it, but it’s tricky and he’ll have to think about it. When asked how long it will take him, he replies, “Seven-and-a-half million years. I told you I’d have to think about it.”
Real-life supercomputers are being asked somewhat less expansive questions but tricky ones nonetheless about how to tackle the COVID-19 pandemic. They’re being used in many facets of responding to the disease, including to predict the spread of the virus, to optimize contact tracing, to allocate resources and provide decisions for physicians, to design vaccines and rapid testing tools, and to understand sneezes. And the answers are needed in a rather shorter time frame than Deep Thought was proposing.
The largest number of COVID-19 supercomputing projects involves designing drugs. It’s likely to take several effective drugs to treat the disease. Supercomputers allow researchers to take a rational
approach and aim to selectively muzzle proteins that SARS-CoV-2, the virus that causes COVID-19, needs for its life cycle.
The viral genome encodes proteins needed by the virus to infect humans and to replicate. Among them is the infamous spike protein that sniffs out and penetrates its human cellular target, but there are also enzymes and molecular machines that the virus forces its human subjects to produce for it. Finding drugs that can bind to these proteins and stop them from working is a logical way to go.
I am a molecular biophysicist. My lab, at the Center for Molecular Biophysics at the University of Tennessee and Oak Ridge National Laboratory, uses a supercomputer to discover drugs. We build three- dimensional virtual models of biological molecules like the proteins used by cells and viruses and simulate how various chemical compounds interact with those proteins. We test thousands of compounds to find the ones that “dock” with a target protein. The compounds that fit, lock-and- key style, with the protein are potential therapies.
The top-ranked candidates are then
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