The world’s supercomputer identified 77 compounds to fight COVID-19

The world’s supercomputer identified 77 compounds to fight COVID-19

IBM's supercomputer Summit, equipped with the "brain of AI," identified 77 drug compounds that might effectively stop the coronavirus COVID-19 from infecting host cells.
Researchers at Oak Ridge National Laboratory published their findings in the journal ChemRxiv.


Simulations of more than 8000 compounds

The two researchers performed simulations on Summit of more than 8,000 compounds to screen for those that are most likely to bind to the main “spike” protein of the coronavirus, rendering it unable to infect host cells. They ranked compounds of interest that could have value in experimental studies of the virus.

The idea was born out of an interest in the coronavirus’ entry point into a host cell. When Chinese researchers sequenced the virus, they discovered that it infects the body by one of the same mechanisms as the Severe Acute Respiratory Syndrome, or SARS, virus that spread to 26 countries during the SARS epidemic in 2003. The similarity between the two virus structures facilitated the study of the new virus.


A 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 Angiotensin-Converting Enzyme 2, or ACE2, receptor, shown in purple. Credit: Micholas Smith/ Oak Ridge National Laboratory, U.S. Dept. of Energy



Similarity with SARS in how the viruses "dock" to  the cell


Jeremy C. Smith, Governor’s Chair at the University of Tennessee (UT) and director of the UT/ORNL Center for Molecular Biophysics, worked from the assumption that the two viruses may even “dock” to the cell in the same way.

Team member and UT/ORNL CMB postdoctoral researcher Micholas Smith built a model of the coronavirus’ spike protein, also called the S-protein, based on early studies of the structure.

We were able to design a thorough computational model based on information that has only recently been published in the literature on this virus,” Micholas Smith said, referring to a study published in Science China Life Sciences.

“Using Summit, we ranked these compounds based on a set of criteria related to how likely they were to bind to the S-protein spike,” Micholas Smith said in their statement.

The team found 77 small-molecule compounds, such as medications and natural compounds, that they suspect may be of value for experimental testing. In the simulations, the compounds bind to regions of the spike that are important for entry into the human cell, and therefore might interfere with the infection process.


Computation study again with the new version of the S-protein

After a highly accurate S-protein model was released in Science, the team plans to rapidly run the computational study again with the new version of the S-protein. This may change the ranking of the chemicals likely to be of most use. The researchers emphasized the necessity of testing of the 77 compounds experimentally before any determinations can be made about their usability.


No cure is found yet

Our results don't mean that we have found a cure or treatment for the coronavirus," said Jeremy Smith, director of the University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics.

But the findings could inform future studies. And those studies are necessary to create the most effective coronavirus vaccine.