The development of new antivirals can benefit from an understanding of their targets. To this end, a new study that unravels an enzyme essential to the survival of SARS-CoV-2 paves the way for new antivirals to treat COVID-19.

The work produced a high-resolution crystal structure of nsp14. The enzyme has a crucially important region known as the RNA methyltransferase domain, which has eluded previous attempts by the scientific community to characterize its 3D crystal structure.

This work is published in Nature Structural & Molecular Biology in the paper, “High-resolution structures of the SARS-CoV-2 N7-methyltransferase inform therapeutic development.

“Being able to visualize the shape of the methyltransferase domain of nsp14 at high resolution gives us insights into how to design small molecules that fit into its active site, and thus inhibit its essential chemistry,” said Aneel Aggarwal, PhD, professor of pharmacological sciences at the Icahn School of Medicine at Mount Sinai. “With this structural information, and in collaboration with medicinal chemists and virologists, we can now design small molecule inhibitors to add to the family of antivirals that go hand-in-hand with vaccines to combat SARS-CoV-2.”

Prescription antivirals that target key enzymes of SARS-CoV-2 include nirmatrelvir for the main protease (MPro) enzyme, and molnupiravir and remdesivir for the RNA polymerase (nsp12) enzyme.

The team developed three crystal structures of nsp14, each with different cofactors, from which they identified the best scaffold for the design of antivirals for inhibiting the RNA methyltransferase activity that the enzyme enables and the virus needs to survive.

Specifically, they present three “high-resolution crystal structures of the SARS-CoV-2 nsp14 N7-methyltransferase core bound to S-adenosylmethionine (1.62 Å), S-adenosylhomocysteine (1.55 Å), and sinefungin (1.41 Å).”

The authors wrote, “We identify features of the methyltransferase core that are crucial for the development of antivirals and show SAH as the best scaffold for the design of antivirals against SARS-CoV-2 and other pathogenic coronaviruses.”

According to their scheme, the antiviral would take the place of the natural cofactor S-adenosylmethionine, thus preventing the methyltransferase chemistry from occurring.

Making the discovery possible was the ability of researchers to clear a hurdle that had prevented others in the past from creating three-dimensional crystals of the nsp14 methytransferase domain. “We employed an approach known as fusion-assisted crystallization,” explained Jithesh Kottur, PhD, a postdoctoral fellow at Icahn Mount Sinai, and a crystallographer and biochemist. “It involves fusing the enzyme with another small protein that helps it to crystalize.”

“Part of what drives our work,” said Aggarwal, “is the knowledge gained from treating HIV—that you typically need a cocktail of inhibitors for maximum impact against the virus.”

Aggarwal underscores the importance of ongoing investigative work by researchers in his field against a virus that has led to millions of deaths globally. “The virus evolves so quickly that it can develop resistance to the antivirals now available, which is why we need to continue developing new ones,” he observed. “Because of the high sequence conservation of nsp14 across coronaviruses and their variants, our study will aid in the design of broad-spectrum antivirals for both present and future coronavirus outbreaks.”

The crystal structures that the team has elucidated have been made available to the public and will now serve as guides for biochemists and virologists globally to engineer these compounds.

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