FLC | SBU teams with Brookhaven, Argonne for COVID-19 modeling

SBU teams with Brookhaven, Argonne for COVID-19 modeling

April 14, 2020

A team of Stony Brook University (SBU) researchers is collaborating with scientists at the U.S. Department of Energy’s (DOE) Brookhaven and Argonne National Laboratories in the fight against COVID-19.

The SBU team will be leveraging those laboratories’ computational resources and expertise to develop models for a better understanding of how the "spike" protein on the surface of the COVID-19 virus interacts with the cells it infects. These spikes are the part of the virus that attaches to a cell inside an individual's respiratory system, using a specific protein on the human cell to begin the infection process. Because of this role, the spike protein is also the main target for antibodies that would provide immunity to coronavirus and for developing drugs that potentially could block infection.

But they need to know more detail in order to control it. Scientists working on the project likened the spike protein to a car door they don't yet know exactly how to unlock and open.

“You may know that your car door is the way you can get in and out of a car, but if you've only seen the door in a picture and have never watched someone actually open a door, you don't really know how it works. You also probably would not guess that the handle is the part that you need to move to get the door to open, and that perhaps there is a key that can lock it and keep it from opening," said Carlos Simmerling—the Marsha Laufer Endowed Professor of Physical and Quantitative Biology, a professor of chemistry, and Associate Director of the Laufer Center at SBU. “With our research and computer modeling, we are working to understand the process at that more detailed level. For example, what exactly leads to the spike of the virus opening the 'door’ to infection when it contacts the cell? And, are there places on the spike away from this contact point that could act like keys, where scientists might be able to make a small molecule that would bind to it and lock it closed?”

Specific components of the "door," such as its "hinges," could be undiscovered targets for treatments or vaccines, according to Kerstin Kleese van Dam, director of Brookhaven Lab’s Computational Science Initiative.

“We will be looking at 60 different target sites where a new drug may attach to the virus and 1 billion drug-like molecules that might be used to modify the ‘door handles,’ ‘hinges,’ or other components so we can identify the most promising options for neutralizing the virus to keep it from entering cells,” van Dam said.

The computer models developed in collaboration with computational scientists at Brookhaven and Argonne—soon to be scaled up to run on supercomputers at these laboratories—will help sort through the details of these virus-cell interactions to help unlock an understanding of the COVID-19 virus spike protein.

This work is being carried out with funding from Brookhaven Lab’s program development funds, Stony Brook University, and Argonne National Laboratory’s Computing, Environment and Life Sciences Directorate through DOE’s Exascale Computing Project and the National Institutes of Health.