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

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.

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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.

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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.