Stalling the Enemy: Targeting Nsp13 for Next-Generation SARS-CoV-2 Antivirals

TL;DR

This paper explores targeting the SARS-CoV-2 protein nsp13 to develop new antiviral drugs, identifying compounds that inhibit viral replication.

Contribution

The study introduces nsp13 as a novel drug target and screens FDA-approved drugs to find potential inhibitors.

Findings

Forty inhibitors of nsp13 were identified with IC50 values between 1.4 and 10 μM.

Four compounds bind to nsp13 without affecting its ATPase activity or nucleic acid substrate.

Some compounds show antiviral activity against SARS-CoV-2 in cell lines.

Abstract

The SARS-CoV-2 public health challenges have highlighted the urgent need for coronavirus-targeting life-saving therapeutics. Given the emergence of drug-resistant strains, the development of antivirals against viral proteins beyond the commonly targeted main protease or RNA-dependent RNA polymerase is critical. The SARS-CoV-2 nonstructural protein 13 (nsp13) is a highly conserved RNA helicase and an essential component of the viral replication–transcription complex (RTC). It unwinds double-stranded RNA to facilitate viral transcription and replication, making it a strong target for drug development. To identify nsp13 inhibitors, we used an ultra-high-throughput nucleic acid unwinding assay to screen a library of FDA-approved drugs and bioactive compounds. We identified forty inhibitors with IC50 values ranging from 1.4 to 10 μM. Ten were further selected for biochemical and biophysical characterization. Four of these are bound to nsp13 without interacting with the nucleic acid substrate and without inhibiting the ATPase activity of nsp13. Hydrogen–deuterium exchange coupled with Mass Spectrometry (HDX-MS) studies show compound binding causes differential exchange in two regions of nsp13. Furthermore, these compounds have antiviral activity against infectious SARS-CoV-2 in multiple cell lines, with cytotoxicity affecting, in some cases, the apparent antiviral effect. Future optimization efforts could help develop therapeutics against SARS-CoV-2 and other potential coronavirus threats.

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