Huntsville scientists are using a supercomputer to search for natural compounds that can fight the COVID-19 virus on a mission they liken to a Moon shot.
“We are looking at molecules that can block the so-called ‘spike proteins’ that look like a crown around the virus under a microscope,” University of Alabama in Huntsville researcher Dr. Jerome Baudry said this week. “The spike proteins are why the virus is called a ‘corona virus’ or ‘crown virus.’”
“If these spike proteins cannot attach themselves to some other proteins on the surface of our cells,” Beaudry said, “the virus will not be able to enter the cell and will hence not be able to infect the cell.”
The project has “a very ambitious goal, not a lot of time to achieve it, a lot of pressure to do so and the need for very powerful new technology to do it,” Beaudry said.
In this case, the technology is Hewlett Packard Enterprise’s Cray supercomputer in Texas. The analogy is that it is “as fast as the Earth’s entire population doing 20,000 calculations every second” with storage capacity for 45 years of high-definition videos. Machines this special are given names, and this one is Sentinel.
“A fantastic machine,” Beaudry called Sentinel, and using it for this mission is “very Huntsvillian in a way, like being given the Saturn V and a crew for our own Moon trip.”
“Huntsville’s scientific and technological psyche was built on the need to go to the Moon in a few short years, and to develop a rocket large enough to take us there,” Baudry said. “Today, we need to address a terrible health crisis, we have a very short time to do it…. We have done it before; we will do it again.”
Looking at natural compounds also links modern science with the “oldest shared knowledge of humankind,” Beaudry said. What plants can we eat to survive? What plants can heal?
“Artificial intelligence meets ancient knowledge,” he said.
Three months ago, Beaudry said scientists knew “almost nothing” about the coronavirus and the proteins that might affect it. Their goal still isn’t “finding needles, but reducing the size of the haystacks” to speed up a treatment.
Several hundred candidate compounds have been found already and are named in the scientific paper published this week. Some are from plants found in Alabama with chemicals developed over millions of years of evolution to have “biochemical friendliness,” Beaudry said.
“If we can identify computationally such a natural product,” Baudry said, “then we have colleagues who will test it in specialized labs.”
The work in Huntsville isn’t the only scientific attack on COVID-19, and Beaudry said the virus has “the scientific community coming together around the world in a kind of synergy of effort and good will.”
Baudry holds the Mrs. Pei-Ling Chan Chair in the UAH Department of Biological Sciences. At UAH, the Baudry Lab collaborates on machine learning and big data in drug discovery with the laboratory of Dr. Vineetha Menon, an assistant professor of computer science.
UAH graduate student Anna Petroff is also involved at the Baudry Lab, and undergraduate Corinne Peacher is working with Baudry and Menon.
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