First open source all-atom models of COVID-19 'spike' protein produced

London, Jun 22: Scientists have produced the first open source all-atom models of full-length spike protein of the novel coronavirus that facilitates its entry into the host cells, an advance that may aid faster COVID-19 vaccine and antiviral drug development.

The "spike" or S protein of SARS-CoV-2 virus that causes COVID-19 facilitates viral entry into host cells, according to the researchers, including those from the University of Cambridge in the UK. This makes S protein the main target for vaccine and antiviral drug development, they said.

Described in The Journal of Physical Chemistry B, CHARMM-GUI is a programme that simulates complex biomolecular systems simply, precisely and quickly. Wonpil Im, a professor at Lehigh University in the US, describes it as a "computational microscope" that enables scientists to understand molecular-level interactions that cannot be observed any other way.

"Our models are the first fully-glycosylated full-length SARS-CoV-2 spike (S) protein models that are available to other scientists," said Im, who developed the programme. Scientists can use the models to conduct innovative and novel simulation research for the prevention and treatment of COVID-19, according to Im.

The researchers first modelled the missing amino acid residues, and then other missing domains. They also modelled all potential glycans (or carbohydrates) attached to the S protein. These glycans prevent antibody recognition, which makes it difficult to develop a vaccine. The researchers also built a viral membrane system of an S protein for molecular dynamics simulation.