Coronavirus Drugs: Studies Show Remdesivir’s Activity against Viral Enzyme

By Ruchi Jhonsa, Ph.D.

Just over a month ago, a research group from the University of Alberta reported the mechanism of action of Remdesivir against the RNA dependent RNA polymerase (RdRp) of MERS coronavirus. RdRp catalyzes the synthesis of viral RNA, and is, therefore, a primary target for antiviral drugs like remdesivir to suppress viral replication. A collaborative study has now reported the high-resolution structure of the SARS-CoV-2 RNA dependent RNA polymerase (RdRp) and performed an analysis to investigate how Remdesivir binds to it. Besides, the study provides a basic design of the enzyme with which researchers and pharma companies can develop more potent drugs.

In this study, the researchers determined the cryo-EM structure of the full-length RdRp protein also known as nsp12 in complex with cofactors nsp7 and nsp8 at 2.9 Angstrom resolution revealing previously undetermined beta-hairpin domain at its N terminus. Based on the structure, the authors also briefly analyzed the possible binding and inhibition mechanisms of Remdesivir to RdRp. The study published in the journal Science is the result of a collaboration between researchers from universities in China and Australia. Meanwhile, the group from the University of Alberta also published a follow-up study in the Journal of Biochemistry reporting Remdesivir’s efficacy against the RdRp of COVID-19 causing virus.

Through the Eyes of Cryo-EM: A Finer Look into the SARS-CoV-2 RdRp Structure

Like any other electron microscope, cryo-EM works by bombarding the sample with high-speed electrons that resolves tiny structures and gives a molecular landscape of the sample. But unlike conventional EM’s, cryo-EM requires samples to be frozen. Since proteins are mostly dissolved in solution, cryo-EM works best for determining their structure. Using this technique, the authors determined the finer chemical details along with conserved and distinct structural features of the RdRp enzyme. The domain that catalyzes viral RNA replication in SARS-CoV-2 RdRp was mostly found similar to the polymerase in other RNA viruses comprising of finger, palm, and thumb subdomains analogous to a human hand. Even the finer details of the enzyme, like the active site, nucleoside entry point, and final product exit paths, were found similar to those described for SARS-CoV and other RNA polymerases such as HCV and PV polymerase.

Interaction of Remdesivir with RdRp of MERS and SARS-CoV-2

When animal studies showed that Remdesivir could inhibit coronaviruses, SARS and MERS, it was immediately picked up by scientists for further analysis. On February 24, researchers from the University of Alberta published detailed research on the actions of Remdesivir on the replication of MERS coronavirus. They found identical results with SARS-CoV-2 RdRp too, which they published on April 13^th. The group determined that the drug is an analog inhibitor, meaning that it resembles the natural base nucleotides found in our cells and halts the entire machinery when incorporated in a normal RNA or DNA chain. Specifically, when the drug gets incorporated in the genetic material, the polymerase incorporates three more nucleotide bases and stops working, thereby stalling RNA production. When the virus fails to copy its genome, it immediately stops multiplying.

If this was the case, the drug should also have worked for treating Ebola for which it was initially developed. However, it didn’t. It turns out that the genome copying polymerase in Ebola and coronavirus are slightly different when it comes to incorporating the drug. It was observed that the MERS polymerase incorporated the drug in the genetic material at a greater frequency than the natural nucleotide while Ebola polymerase incorporated the natural nucleotide adenosine triphosphate at greater frequency leaving the drug unincorporated.

Taking a step further, the authors of the Science publication indirectly determined how the drug might interact with the enzyme at the amino acid level before it gets incorporated into the genetic material. Based on the prior knowledge on another nucleotide mimic, sofosbuvir that binds to Hepatitis C ns5b polymerase, the authors modeled the interaction of remdesivir with the nsp12 enzyme by superimposing the 3D structure of the two proteins. On analysis, nsp12 was found most similar to ns5b in its most natural state i.e. devoid of any natural nucleotide or drug. When looked further, it was observed that while sofosbuvir’s interaction with the ns5b destabilizes the machinery and stalls the viral RNA replication right away, the interaction of remdesivir with the nsp12 might stabilize the incoming nucleotide and stall the viral chain only after addition of three nucleotides to it. All of this is still model-based and direct interaction of the drug with the enzyme will be needed to understand the actual mechanism. Nevertheless, it is something that researchers can use to start working on new antiviral drugs.

Editor: Rajaneesh K. Gopinath, Ph.D.

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References

1. https://science.sciencemag.org/content/early/2020/04/09/science.abb7498
2. https://www.jbc.org/content/295/15/4773.long
3. https://www.jbc.org/content/early/2020/04/13/jbc.RA120.013679.abstract
4. https://science.sciencemag.org/content/347/6223/771?ijkey=512547b2d57f385b8e0f20fa87ff4b7b8873eba1&keytype2=tf_ipsecsha

Author

Ruchi Jhonsa