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A full simulation of H1N1 flu virus

160-million-atom simulation reveals potential drug targets

by Sam Lemonick
March 7, 2020 | A version of this story appeared in Volume 98, Issue 9


Computer-generated image of H1N1 virus.
Credit: Rommie Amaro
Researchers modeled all 160 million atoms of the H1N1 virus and its surroundings.

The flu virus kills hundreds of thousands of people each year, but few effective drugs exist to treat it. Computational chemists have now modeled the entire virus and its surroundings in one of the largest molecular dynamics simulations published to date and have observed activity that could lead to new treatments (ACS Cent. Sci. 2020, DOI: 10.1021/acscentsci.9b01071). Rommie Amaro of the University of California San Diego and colleagues’ supercomputer simulation included about 160 million atoms, including water molecules and ions in addition to the influenza A H1N1 2009 virus itself and its outer envelope. Neuraminidase, a glycoprotein on the envelope, helps the virus enter and leave host cells. The researchers confirmed previous suggestions that one of neuraminidase’s binding sites helps locate host-cell sugar receptors and guide them to a second site on the protein, which acts like a pair of scissors, cleaving the virus so it can go infect a new host. They also identified a movable loop in neuraminidase. Both the locator and the moving loop could prove useful to drug designers. Amaro says the size of the simulation allowed them to draw more statistically rigorous conclusions about the virus, and her group plans to apply the modeling techniques to other viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).


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