RAPID: Biophysical characterization of the native SARS-CoV-2 virion by atomistic simulations

Biological Sciences - Since December 2019, a novel coronavirus (SARS-CoV-2) that emerged in China has become a global pandemic. Research into the molecular basis of SARS-CoV-2 is now essential to provide understanding of viral entry and infection of human cells, a first step in developing novel drugs and vaccines to combat SARS-CoV-2. The research supported through this RAPID award will enable the development of an all-atom molecular dynamic simulation of the virus that includes realistic predictions of the envelope, membrane and spike proteins of the virus, as well as simulations of the complex surfaces of the human cells that the virus infects. This research could have immediate impact on steps taken to halt the spread of SARS-CoV-2. Simulation results will be broadly and quickly disseminated to ensure impact of the research. In addition, the investigators will use this as a training opportunity for students at all levels.

This project will use to state of the art tools of computational virology to provide bio-physical characterization of the SARS-CoV-2 virion, revealing information relevant to the function and potential targeting and disruption of the virus. The PI proposes a study of the full-size viral envelope which can establish the effects of specific components of the virus, including its bilayer lipid composition, shedding light on the need for coronaviruses to remodel the host cell membrane for successful infection. Additionally the characterization of the native SARS-CoV-2 viral surface proteins, which represent key functional and antigenic sites, will form a good basis for development of an infectious SARS-CoV-2 virion and a platform to investigate a mechanism of host cell entry, in which coronaviruses bind to CD13 receptors in lipid rafts. Study of glycosylated S protein, proposed as one of the aspects of the work, will reveal details of epitope masking by the glycan shield, relevant to vaccine and antibody design, as well as the role of viral glycans in host cell adhesion in a second mechanism of cell entry mediated by S binding to ACE2 receptors. The work could have immediate impact of the current pandemic.

This RAPID award is cofounded by the Molecular Biophysics Program in the Division of Molecular and Cellular Biosciences and the EPSCoR Program.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.