Ending the Coronavirus outbreak might start with a computer

Before today, epidemiologists were reluctant to submit antiviral treatment as an immediate solution to the worsening Covid-19 pandemic. Medical experts haven’t underestimated the importance of coronavirus therapeutics,  the outbreak is simply outpacing research.

Vaccination development is a notoriously complex and lengthy discipline. To expedite the process, researchers at Oak Ridge National Laboratory enlisted the help of Summit; the fastest computer in the world. 

The super-machine can process 200 quadrillion calculations per second-which makes it one million times more powerful than the fastest laptop.

“The researchers were able to solve a problem on Summit in one hour that would take 30 years on a desktop computer,” Morgan McCorkle, the media manager for Oak Ridge, told CNN.

In the recent past, Summit successfully identified predictors in cellular systems associated with the development of Alzheimer’s disease. With an understanding of the genetic mechanisms at play, physicians are now better equipped to counteract them. 

Similarly, Covid-19 vaccinations were made a distant reality after Summit identified 77 drug compounds that can potentially disturb the novel coronavirus’s infection process.  

In order for a virus to infect a host, it needs to inject cells with an S-protein spike of genetic material.

After running molecular dynamics simulations of more than 8,000 different small-molecule drug compounds, the advanced computer was able to isolate the ones that could curb the virus’s ability to spread throughout the body. Summit was even able to rank these agents based on a set of criteria related to how likely they were to bind to the S-protein spike,” Micholas Smith said.

 “Knowing the atomic-level structure of the 2019-nCoV spike will allow for additional protein-engineering efforts that could improve antigenicity and protein expression for vaccine development,” the authors wrote in the new paper. “We were able to design a thorough computational model based on information that has only recently been published in the literature on this virus,” 

Covid-19 shares a lot of similarities with Severe Acute Respiratory Syndrome, (SARS). Most notably, both Coronaviruses evidence similar entry point behaviors in host cells. Before any vaccines can be administered to the public, the most promising compounds must be surveyed by a computational screening process.

“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, in a statement. But the findings could inform future studies. Studies are necessary to create the most effective coronavirus vaccine. Only then will we know whether any of them exhibit the characteristics needed to mitigate this virus.”

This research was funded by the Laboratory Directed Research and Development program and used resources of the OLCF, a DOE Office of Science User Facility located at ORNL.

The new study was co-authored by Micholas Smith and Jeremy C. Smith, and can be read in full in The Journal ChemRxiv.