Treating COVID-19 by inhibiting viral replication

When SARS-CoV-2, the virus that causes COVID-19, enters a person’s cells, it hijacks those cells to make more viruses. First SARS-CoV-2 releases its RNA into the host cell. Then the host ribosomes translate the viral RNA into two giant protein chains (polyproteins). One protein in the giant chain, called MPro, cleaves the chain into smaller proteins, which help create more viruses and, therefore, more infection. Because of MPro’s role in initiating the viral replication process, the protein has become a target for antiviral drug developers. Recently, a team of scientists using high-brightness x-rays at the U.S. Department of Energy’s Advanced Photon Source (APS) has determined x-ray crystallographic structures of MPro cleaving the polyprotein at ten cleavage sites. Their findings, published in the journal Nature Communications, provide information about the mechanistic steps and molecular interactions that initiate viral replication, which can be used to inform antiviral therapeutic development for COVID-19, as well as other conditions for which MPro may be responsible.

Viruses can’t reproduce on their own; they need a human or animal cell to make other viruses and continue their infectious rampage. The SARS-CoV-2 virus, which causes COVID-19, employs its spike protein to enter a human cell. Once inside, the virus’s protective coating dissolves, and it dumps its genetic material—RNA—into the host cell. This RNA contains all the instructions the virus needs to replicate. What’s more, it comes in a handy form that is ready for a human cell to translate into proteins that will compose the next generation of viruses.

The SARS-CoV-2 RNA includes instructions for four proteins that make up the virus’s structure—its spike protein, protective coating, and the like—and sixteen proteins that replicate the virus. The replication process begins when the host’s ribosomes translate the replication genes into two gigantic protein chains called polyproteins.

Before replication can continue, however, these gigantic chains must be chopped up into their constituent proteins. Remarkably, the molecule that does the chopping is itself contained in the polyprotein and must hack its way out of the chain before attending to its neighbors.

Read more on the APS website

Image: Fig. 1. The amino acid residues preceding the SARS-CoV-2 polyprotein cleavage site between non-structural proteins nsp10 and nsp11 are shown in yellow. These residues are bound within the Mpro acceptor active site groove (grey semitransparent molecular surface).