Combination of antiviral drugs inhibits SARS-CoV-2 polymerase and exonuclease and demonstrates COVID-19 therapeutic potential in viral cell culture

Xuanting Wang,Natalia Fintelman-Rodrigues,Thiago Moreno L Souza,Shiv Kumar,James J Russo,Wei Xie,Jairo R Temerozo,Otávio Augusto Chaves,Xiaoxu Li,Dinshaw J Patel,Aitor Garzia,Thomas Tuschl,Patrícia T Bozza,Cindy Meyer,Chuanjuan Tao,Carolina Q Sacramento,Steffen Jockusch,Minchen Chien,Jingyue Ju

doi:10.1038/s42003-022-03101-9

Abstract

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. Combinations of inhibitors of both the viral RNA-dependent RNA polymerase and the exonuclease could overcome this deficiency. Here we report the identification of hepatitis C virus NS5A inhibitors Pibrentasvir and Ombitasvir as SARS-CoV-2 exonuclease inhibitors. In the presence of Pibrentasvir, RNAs terminated with the active forms of the prodrugs Sofosbuvir, Remdesivir, Favipiravir, Molnupiravir and AT-527 were largely protected from excision by the exonuclease, while in the absence of Pibrentasvir, there was rapid excision. Due to its unique structure, Tenofovir-terminated RNA was highly resistant to exonuclease excision even in the absence of Pibrentasvir. Viral cell culture studies also demonstrate significant synergy using this combination strategy. This study supports the use of combination drugs that inhibit both the SARS-CoV-2 polymerase and exonuclease for effective COVID-19 treatment.

Highlights

1234567890():,; Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2), which is responsible for COVID-19, is a positivesense single-stranded RNA virus[1,2]
We previously demonstrated that the FDA-approved Hepatitis C virus (HCV) NS5A inhibitors, Daclatasvir and Velpatasvir, and to a lesser extent the NS5A inhibitors Elbasvir and Ledipasvir, can inhibit the SARS-CoV-2 exonuclease[30]
We showed that two additional NS5A inhibitors, Pibrentasvir and Ombitasvir, inhibit the exonuclease, and have the highest inhibitory activity based on our molecular assay

Summary

Introduction

1234567890():,; Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2), which is responsible for COVID-19, is a positivesense single-stranded RNA virus[1,2]. We have investigated a library of nucleotide analogues targeting the SARS-CoV-2 RdRp, several of which have been FDA approved for other viral infections including HIV/AIDS and hepatitis B and C8–11. Of particular interest are those that are able to be incorporated into the replicated RNA by the viral RdRp where they halt or slow further replication These include, among several others, nucleotide analogues such as Sofosbuvir (Fig. 1a), an immediate terminator of the polymerase reaction which has since entered COVID-19 clinical trials[12,13], Remdesivir (Fig. 1b), a delayed terminator[14,15], and Tenofovir, an obligate terminator (Fig. 1d)[10,11]. Three other prodrugs related to nucleotides, Favipiravir (Fig. 1c), Molnupiravir, and AT-527 (Fig. 1e, f), are undergoing clinical trials for COVID-19

Methods

Results

Conclusion