Supercomputer Identifies 125 Natural Compounds To Potentially Beat Coronavirus

In a first of its kind research methodology, scientists at the University of Alabama in Huntsville (UAH) used computational technology directly from a supercomputer to identify natural compounds to block coronavirus proteins. These proteins are nothing but enzymes in SARS-CoV-2’s virus genome that help the virus replicate in infected cells. Hence, targeting the proteins stops COVID-19 in its tracks.  

Led by molecular biophysicist Dr. Jerome Baudry, the Mrs. Pei-Ling Chan Chair, Department of Biological Sciences at UAH, the project was conducted at the Baudry Lab located at UAH’s Shelby Center for Science and Technology. Hewlett Packard Enterprise and the National Center for Natural Products Research at the University of Mississippi School of Pharmacy were collaborators on the extensive study.

The HPE Cray Sentinel supercomputer was used to rapidly assess 50,000 natural compounds at an accelerated pace to source chemicals from nature. So far, they have narrowed down 125 naturally occurring compounds to combat coronavirus proteins and prevent them from multiplying. This experiment only tested one batch of compounds, but there are more than 400,000 compounds they could potentially test.

“Many are from relatively common medicinal plants that can be found in the U.S., and many are from more distant plants from Southeast Asia and South America, as well as from some ground and oceanic bacteria strains and fungi,” Dr Buadry explained in the news release

From this first batch, the researchers found 60 compounds that could successfully interact with the protein in SARS-CoV-2 called papain-like protease (PLpro) and 41 molecules that responded to the main protease (Mpro). They also found 24 compounds that gelled with the crown-like spike protein that binds to ACE2 on cells to spread infection. 

Applying a computational technique called pharmacophore analysis, the common chemical features among these compounds that are suitable to manufacture pharmaceuticals will be identified. This is to provide information for further research into medication that can treat COVID-19. 

“We can then have a good idea of what the natural products exhibit that makes them successful in these different proteins, and that is the starting point for screening larger databases of millions of chemicals much faster, helping chemists to synthesize novel molecules down the road, maybe more potent and more selective than the original natural products against these proteins,” Dr. Baudry said.

The next step the researchers plan to take is using live viruses and cells in another laboratory environment, to figure out the chemical modifications the potential drugs need. This experiment is meant to serve as a reference for future trials on efficacy and tolerance. 

Time is of the essence in finding treatment as the pandemic continues to grow and may be even in usher in a second wave. “Sentinel helps to cut compound testing time from months or even years to weeks,” Dr. Baudry says. How is this possible? 

The Cray XC50 supercomputer is equipped with a high performance computing system (HPC) that can deal with 147 trillion floating point operations every single second. The speed of the computer’s calculation is equivalent to the current human population’s attempt at performing 20,000 calculations per second. It comes with 830,000 gigabytes of data and storage capacity for 45 years of video in high definition format. 

“The fight to prevent COVID-19’s sometimes devastating health consequences has created a new meeting of modern high-capacity artificial intelligence with humankind’s most ancient healing knowledge,” Dr. Baudry said. 


A representational image of spike proteins produced by SARS-CoV-2. Credit: Thomas Splettstoesser, CC BY-ND