In silico analysis of SARS-CoV-2 spike glycoprotein and insights into antibody binding (original) (raw)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China in December 2019. Since then, COVID-19, the disease caused by SARS-CoV-2, has become a rapidly spreading pandemic that has reached most countries in the world. So far, there are no vaccines or therapeutics to fight this virus. Here, I present an in silico analysis of the virus spike glycoprotein (recently determined at atomic resolution) and provide insights into how antibodies against the 2002 virus SARS-CoV might be modified to neutralize SARS-CoV-2. I ran docking experiments with Rosetta Dock to determine which substitutions in the 80R and m396 antibodies might improve the binding of these to SARS-CoV-2 and used molecular visualization and analysis software, including UCSF Chimera and Rosetta Dock, as well as other bioinformatics tools, including SWISS-MODEL. Supercomputers, including Bridges Large, Stampede and Frontera, were used for macromolecular assemblies and large scale analysis and visual...