The mRNAs expressed by SARS-CoV-2 can pass as human mRNAs without too much difficulty. All the viral mRNAs have to do is modify the cap they wear. This may seem a modest costume change, but it helps the viral mRNAs avoid being recognized by the innate immune system.

In hopes of one day preventing the costume change—and realizing a new therapeutic strategy against COVID-19—scientists based at UT Health San Antonio have been studying the cap-modifying proteins encoded by SARS-CoV-2.

Led by assistant professor of biochemistry and structural biology Yogesh K. Gupta, PhD, the scientists recently described how two cap-modifying proteins, the nonstructural proteins nsp16 and nsp10, manage to disguise viral mRNA.

After nsp16 and nsp10 form a complex with each other, they bind to an mRNA substrate and another molecule, a methyl donor. At the same time, nsp16, the catalytic subunit of the nsp16/nsp10 complex, radically changes its shape to transfer a methyl group from the methyl donor to the mRNA. Then, the disguise is complete.

The shape change, according to the scientists, is consistent with an induced-fit enzyme model. Unlike the lock-and-key enzyme model, in which an enzyme’s active site is a precise and rigid fit for a substrate, the induced-fit model relies on an active site that is dynamic and flexible. That is, the active site undergoes a conformation change after the enzyme is exposed to the substrate. The conformation change improves the fit between enzyme and substrate as catalysis proceeds.

Detailed findings, which include high-resolution structures of the nsp16/nsp10 complex, appeared July 24 in Nature Communications, in an article titled, “Structural basis of RNA cap modification by SARS-CoV-2.” The article describes how the nsp16/nsp10 complex is specifically adapted to bind and methylate the RNA cap.

“We report here the high-resolution structure of a ternary complex of SARS-CoV-2 nsp16 and nsp10 in the presence of cognate RNA substrate analog and methyl donor, S-adenosyl methionine (SAM),” the article’s authors wrote. “The nsp16/nsp10 heterodimer is captured in the act of 2′-O methylation of the ribose sugar of the first nucleotide of SARS-CoV-2 mRNA. We observe large conformational changes associated with substrate binding as the enzyme transitions from a binary to a ternary state.”

These findings provide a snapshot of precatalytic state of methyl transfer. They also reveal the nature of conformational change in nsp16.

“Another striking finding,” the authors pointed out, “includes an alternative ligand-binding site in nsp16 with distinct capability to accommodate small molecule ligands. Finally, we map the acquired mutations in SARS-CoV-2 nsp16. One of these mutation hotspots showed high frequency in COVID-19 strains associated with the New York City outbreak.”

The 3D structural details for nsp16 could guide the rational design of antiviral drugs for COVID-19 and other emerging coronavirus infections, Gupta said. The drugs, new small molecules, could inhibit nsp16 from disguising viral mRNA. The immune system would then pounce on the invading virus, recognizing it as foreign.

“Yogesh’s work revealed the 3D structure of a key enzyme of the COVID-19 virus required for its replication and found a pocket in it that can be targeted to inhibit that enzyme. This is a fundamental advance in our understanding of the virus,” said study co-author Robert Hromas, MD, professor and dean of the Long School of Medicine.

“Our work,” the article’s authors concluded, “provides a solid framework from which therapeutic modalities may be designed by targeting different ligand-binding sites of nsp16, including RNA cap and SAM pockets, for the treatment of COVID-19 and emerging coronavirus illnesses.”

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