Like all viruses, SARS-CoV-2 must subvert the synthesis of host proteins while simultaneously favoring the production of its own proteins, although both processes require the same molecular machinery. How the virus accomplishes this feat has posed a conundrum.

A new study shows how the virus takes over the cell’s protein factory to synthesize viral proteins while preventing the production of host proteins and disrupting the host cell’s immune response. The findings were published in the journal RNA, in at article titled “The key features of SARS-CoV-2 leader and NSP1 required for viral escape of NSP1-mediated repression.”

Mechanistic insights on how the virus claims control over the host’s protein factory uncovered in this study could help identify new approaches to treat SARS-CoV-2 infection, beyond vaccine-based preventative strategies that are unable to completely stop transmission of the virus and are subject to decreased efficacy with continued viral evolution.

Marina Chekulaeva, PhD, a scientist at the Berlin Institute for Medical Systems Biology is senior author of the study.

A team of researchers led by Marina Chekulaeva, PhD, a scientist at the Berlin Institute for Medical Systems Biology (BIMSB) that is part of the Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), working with colleagues at the Leibniz-Institut für Analytische Wissenschaften in Dortmund, has pinpointed a crucial mechanism involved in the process.

“NSP1 suppresses protein production in the cell without impairing the synthesis of viral proteins,” said Chekulaeva. “Until now, there had been very contradictory hypotheses about how this worked. We decided to explore this mechanism with Lucija Buinic, the first author of the manuscript who joined the lab during the lockdown to do her master thesis.”

The viral nonstructural protein 1 (NSP1) is the first viral protein expressed in a host cell.  NSP1 inhibits host protein synthesis by blocking the ribosomal tunnel through which mRNA enters the molecular complex.

Surprisingly, the presence of NSP1 at the gate of the ribosomal protein synthesis factory interferes with the binding of host cellular mRNA to the ribosome but viral mRNAs overcome this blockade. Blocking the synthesis of important cellular proteins suppresses the host’s immune response. Chekulaeva’s team demonstrates how this is accomplished.

“We show that NSP1 enhances expression of mRNAs containing the SARS-CoV-2 leader. The first stem-loop (SL1) in viral leader is both necessary and sufficient for this enhancement mechanism,“ the authors note.

Chekulaeva and her team shows that residues within the first stem-loop structure (SL1) of the leader sequence in viral mRNAs act as an entry ticket to the ribosome. These viral-specific structural elements interact with NSP1 that stands guard at the ribosomal entry, granting permission to viral mRNAs to enter the ribosome and resulting in the synthesis of viral proteins.

“This analysis helps reconcile conflicting reports in the literature regarding the mechanisms by which the virus avoids NSP1 silencing,” the authors note. “Our analysis pinpoints specific residues within SL1 (three cytosine residues at the positions 15, 19 and 20) and another within NSP1 (R124) which are required for viral evasion, and thus might present promising drug targets.”

Chekulaeva explains that this mechanistic feature uncovers three possible antiviral treatment approaches. First, to target NSP1 to prevent it from interacting with the ribosome; second, to prevent the interaction between NSP1 and the viral mRNA, for instance its stem loop structure, and third to target the ticketing structures that give viral mRNA preferential right-of-way through the ribosome and specifically eliminate viral mRNA.

“We target SL1 with the anti-sense oligo to efficiently and specifically downregulate SARS-CoV-2 mRNA,” the authors note.

The researchers produced antisense oligonucleotides (ASO), stabilized through chemical modification. The ASOs bind to the stem loop of viral mRNAs, creating an RNA-DNA hybrid that is discarded by the cell. Since the stem loop is only present in viral mRNA, this intervention is very specific. It does not affect host cellular mRNA or protein synthesis.

“It’s also a very important structure, which we can assume with a fair degree of confidence undergoes very little mutation,” said Chekulaeva. “So it’s unlikely that any resistance would develop.”

Further research will establish which of the possibilities uncovered in this work provide clinically effective treatments.

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