Natural Compounds, Identified via HPC, Move Forward in COVID-19 Therapeutic Testing

By Oliver Peckham

December 2, 2020

Nearly six months ago, HPCwire reported on efforts by researchers at the University of Alabama in Huntsville (UAH) to identify natural compounds that could be useful in the fight against COVID-19. At the time, the researchers – led by Jerome Baudry, a molecular biophysicist at UAH – managed to identify over a hundred natural compounds (or close derivatives) with promising characteristics. Now, the UAH researchers have provided a major update: a subset of those compounds are now undergoing experimental testing.

Back in June, the researchers assessed 50,000 natural products to see how they interacted with key proteins on SARS-CoV-2. To do this, they leveraged supercomputing power – specifically, Sentinel, a Microsoft Azure-accessible Cray XC50 supercomputer with around 2,000 cores, with access provided via HPE.

After running through those 50,000 compounds, the researchers identified “125 natural products or close derivatives across plants, fungi, the sea and microbes” that possess chemical elements which bind to key proteins on the novel coronavirus, including compounds found in traditional medicines from around the world.

Now, 35 of those 125 compounds have progressed past the computational analysis stage. Those 35 compounds – as-yet unenumerated – are now undergoing first-batch testing at the University of Tennessee Health Science Center’s Regional Biocontainment Laboratory (UTHSC RBL). 

The lab is testing the candidate compounds for their ability to either kill the virus or prevent the virus from infection cells – the next stage in the compounds’ pathway to potentially becoming viable pharmaceuticals. “They use live virus infections of living cells grown in the equivalent of Petri dishes,” Baudry said. “The chemicals that will have a good profile can then be tested in animal models using mice.”

The news on the compounds comes amid a flurry of promising results from phase three vaccine trials. Baudry clarified, however, that the vaccine news does not eliminate the need for effective therapeutics.

“There is very good news on vaccine developments, and it is great, but it is important that we continue working on other pharmaceuticals,” Baudry said. “It’s a bit like for the flu, where there are vaccines and there are pharmaceuticals, and they work together, not against each other. And what we learned here will be priceless to respond to other similar crises, if and when they show up in the future.”

“As terrible as this COVID-19 crisis is,” he continued, “how we all came together in research has been incredible. In my nearly 25 years of performing and leading scientific research, I have never experienced anything like that.”

Baudry’s team was recently awarded a 2020 Hyperion HPC Innovation Excellence Award for their important work.

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