HPC Simulations Show How Antibodies Quash SARS-CoV-2

By Oliver Peckham

May 5, 2021

Following more than a year of rapid-fire research and pharmaceutical development, nearly a billion COVID-19 vaccine doses have been administered around the world, with many of those vaccines proving remarkably effective against the dominant strains of the virus. Supercomputing, of course, was key to understanding how the virus behaved when infecting human cells, which was integral to the development of vaccines and remains integral to the development of therapeutics and vaccine boosters; now, supercomputing is showing exactly how those resulting vaccines neutralize the deadly virus.

The team, led by researchers from Los Alamos National Laboratory, simulated two variants of SARS-CoV-2. First was the dominant variant of SARS-CoV-2, known as D614G. Over the course of the last year, this variant usurped the original form of the virus, which was also simulated and which is known simply as D614 (leading the new form to be termed the “G form” of the virus). The researchers ran these multiple atomic-level simulations at the microsecond scale.

These detailed simulations were run on supercomputers at Los Alamos National Lab, which operates under the umbrella of the National Nuclear Security Administration, itself tasked with ensuring the safety and reliability of the nation’s nuclear weapons stockpile. Though Los Alamos’ resources are, accordingly, kept somewhat more clandestine than those of other national labs, it often lends access to those resources to important non-nuclear causes – like COVID-19 research.

The simulations first showed why the G form had become dominant: it had an easier time binding to human cells. “We found that the interactions among the basic building blocks of the spike protein become more symmetrical in the G form, and that gives it more opportunities to bind to the receptors in the host – in us,” explained Gnana Gnanakaran, a staff scientist at Los Alamos and corresponding author of the paper. 

That symmetry, however, is a double-edged sword for the virus, which exposes itself to “At the same time, that means antibodies can more easily neutralize it,” Gnanakaran elaborated. “In essence, the variant puts its head up to bind to the receptor, which gives antibodies the chance to attack it.” This vulnerability, the researchers say, might point at more effective targets for future vaccines.

About the research

The research discussed in this article was published in the April 2021 issue of Science Advances as “The SARS-CoV-2 Spike variant D614G favors an open conformational state.” The article, written by Rachael A. Mansbach, Srirupa Chakraborty, Kien Nguyen, David C. Montefiori, Bette Korber and S. Gnanakaran, is accessible here.

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