Ju and colleagues identified that the combination of hepatitis C virus NS5A inhibitors Pibrentasvir and Ombitasvir effectively inhibit SARS-CoV-2 polymerase and exonuclease. Their study recently appeared in BioRxiv.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is responsible for COVID-19, is a positive-sense single-stranded RNA virus. Thus, it requires an RNA-dependent RNA polymerase (RdRp) to replicate and transcribe its genome. Because of its large genome (~30 kb) and error-prone RdRp, SARS-CoV-2 also possesses a 3’-5’ exonuclease for proofreading to maintain the integrity of the genome. The replication complex of coronaviruses consists of several viral proteins, including the RdRp itself (nonstructural protein 12; nsp12) and its two accessory proteins (nsp7 and nsp8), and the exonuclease (nsp14) with its accessory protein (nsp10).
Upto date, variety of drugs have been proposed with an aim to target various SARS-CoV-2 proteins, which are essential for its infectious cycle but, no drugs including Remdesivir, found effective in reducing viral activity of Covid-19. Why? The reason I already mentioned above. SARS-CoV-2 has an exonuclease-based proofreader, which removes nucleotide inhibitors such as Remdesivir that are incorporated into the viral RNA during replication, reducing the efficacy of these drugs for treating COVID-19. However, we could overcome this deficiency if we use the combinations of inhibitors of both the viral RNA-dependent RNA polymerase and the exonuclease.
Ju and colleagues previously demonstrated that the FDA approved HCV NS5A inhibitors, Daclatasvir and Velpatasvir, and to a lesser extent the NS5A inhibitors Elbasvir and Ledipasvir, can inhibit the SARS-CoV-2 exonuclease. Of particular interest, Daclatasvir and Velpatasvir inhibit both the SARS-CoV-2 polymerase and exonuclease. Now, they showed that two additional hepatitis C virus NS5A inhibitors, Pibrentasvir and Ombitasvir, also inhibit the exonuclease, and have the highest inhibitory activity based on their molecular assay. These compounds are predicted to interfere with the binding of the Mg++ ion with the 3’ terminus of the RNA in the active site of the exonuclease (nsp14).
“The Mg++ ion coordinates amino acid residues Asp-90, Glu-92, Glu-191 and Asp-273 and the 3’ terminus of the RNA. Because the NS5A inhibitors interfere with this coordination, they are likely to prevent nucleotide excision from the RNA.”
They also showed that, in the presence of Pibrentasvir, RNAs terminated with the active forms of the prodrugs Sofosbuvir, Remdesivir, Favipiravir, Molnupiravir, Temofovir and AT-527 were largely protected from excision by the exonuclease, while in the absence of Pibrentasvir, there was rapid excision.
Additionally, in a recent in silico modeling study it has been suggested that Ritonavir also binds to the active site of nsp14, which led the authors to the prediction that Ritonavir may inhibit exonuclease activity. Now, Ju and colleagues have experimentally shown that Ritonavir and Lopinavir, HIV protease inhibitors that make up the combination drug Kaletra, inhibit the SARS-CoV-2 exonuclease in a concentration-dependent manner, but with less potency than Pibrentasvir and Ombitasvir.
Finally, they showed that by combining Pibrentasvir or Ombitasvir with Remdesivir, Sofosbuvir, Tenofovir or Favipiravir, higher inhibitory activity for SARS-CoV-2 was achievable at lower doses, bringing the nucleotides’ pharmacological parameters more in line with their pharmacokinetic exposures.
Summing up the results, their study supports the use of combination drugs that inhibit both the SARS-CoV-2 polymerase and exonuclease for effective COVID-19 treatment.
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Reference: Xuanting Wang, Carolina Q. Sacramento, Steffen Jockusch, Otávio Augusto Chaves, Chuanjuan Tao, Natalia Fintelman-Rodrigues, Minchen Chien, Jairo R Temerozo, Xiaoxu Li, Shiv Kumar, Wei Xie, Dinshaw J Patel, Cindy Meyer, Aitor Garzia, Thomas Tuschl, Patricia T Bozza, James J Russo, Thiago Moreno L Souza, Jingyue Ju, “Combination of Antiviral Drugs to Inhibit SARS-CoV-2 Polymerase and Exonuclease as Potential COVID-19 Therapeutics”, bioRxiv 2021.07.21.453274; doi: https://doi.org/10.1101/2021.07.21.453274
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