A team of Mount Sinai researchers has produced a high-resolution crystal structure of an enzyme essential to the survival of SARS-CoV-2, the virus that causes COVID-19. The invention could lead on to the design of critically needed latest antivirals to combat current and future coronaviruses.

The enzyme, often called nsp14, has a crucially necessary region often called the RNA methyltransferase domain, which has eluded previous attempts by the scientific community to characterize its three-dimensional crystal structure. A paper describing the progressive process was published within the September 8 online edition of Nature Structural & Molecular Biology [DOI: 10.1038/s41594-022-00828-1].

Having the ability to visualize the form of the methyltransferase domain of nsp14 at high resolution gives us insights into how one can design small molecules that fit into its lively site, and thus inhibit its essential chemistry. With this structural information, and in collaboration with medicinal chemists and virologists, we will now design small molecule inhibitors so as to add to the family of antivirals that go hand-in-hand with vaccines to combat SARS-CoV-2.”

Aneel Aggarwal, PhD, Senior Creator, Professor of Pharmacological Sciences on the Icahn School of Medicine at Mount Sinai

Prescription antivirals that concentrate on key enzymes of SARS-CoV-2 include nirmatrelvir for the principal protease (MPro) enzyme, and molnupiravir and remdesivir for the RNA polymerase (nsp12) enzyme. Research to develop latest antivirals targeting different enzymatic activities has been accelerating in laboratories all over the world, and Mount Sinai’s discovery has added significantly to that effort.

“A part of what drives our work,” says Dr. Aggarwal, “is the knowledge gained from treating HIV-;that you usually need a cocktail of inhibitors for optimum impact against the virus.”

The Mount Sinai team actually developed three crystal structures of nsp14, each with different cofactors, from which they identified the very best scaffold for the design of antivirals for inhibiting the RNA methyltransferase activity that the enzyme enables and the virus must survive. In keeping with their scheme, the antiviral would take the place of the natural cofactor S-adenosylmethionine, thus stopping the methyltransferase chemistry from occurring. The crystal structures that the team has elucidated have been made available to the general public and can now function guides for biochemists and virologists globally to engineer these compounds.

Making the invention possible was the power of researchers to clear a hurdle that had prevented others previously from creating three-dimensional crystals of the nsp14 methytransferase domain. “We employed an approach often called fusion-assisted crystallization,” explains lead creator Jithesh Kottur, PhD, a postdoctoral fellow at Icahn Mount Sinai, and a crystallographer and biochemist. “It involves fusing the enzyme with one other small protein that helps it to crystalize.”

Dr. Aggarwal, an internationally recognized structural biologist, underscores the importance of ongoing investigative work by researchers in his field against a virus that has led to thousands and thousands of deaths globally. “The virus evolves so quickly that it may well develop resistance to the antivirals now available, which is why we’d like to proceed developing latest ones,” he observes. “Due to the high sequence conservation of nsp14 across coronaviruses and their variants (meaning it doesn’t mutate much), our study will aid within the design of broad-spectrum antivirals for each present and future coronavirus outbreaks.”

Source:

Mount Sinai Health System

Journal reference:

Kottur, J., et al. (2022) High resolution structures of the SARS-CoV-2 N7-methyltransferase inform therapeutic development. Nature Structural & Molecular Biology. doi.org/10.1038/s41594-022-00828-1.