Development of RNA Aptamers That Inhibit the RNA-Dependent RNA Polymerase Activity of SARS-CoV-2 Strains In Vitro

Area of Science:

• Virology
• Molecular Biology
• Drug Discovery

Background:

• Emerging SARS-CoV-2 variants necessitate mutation-independent antiviral strategies.
• The viral RNA-dependent RNA polymerase (NSP12) is a conserved and essential target for therapeutic intervention.

Purpose of the Study:

• To develop RNA aptamers targeting the highly conserved SARS-CoV-2 NSP12.
• To evaluate the efficacy of these aptamers as broad-spectrum inhibitors against various SARS-CoV-2 strains.

Main Methods:

• Systematic Evolution of Ligands by EXponential enrichment (SELEX) was employed to identify aptamers targeting NSP12.
• RNA-protein pull-down and competition assays confirmed aptamer binding affinity and specificity.
• In vitro primer extension assays assessed the inhibitory activity of aptamers against NSP12 RNA-dependent RNA polymerase (RdRp) activity.

Main Results:

• High-affinity RNA aptamers targeting NSP12 were successfully identified.
• The selected aptamers demonstrated effective inhibition of NSP12 RdRp activity in vitro.
• Aptamers showed consistent binding and inhibition across wild-type, Alpha, Delta, and Omicron SARS-CoV-2 variants.

Conclusions:

• The developed RNA aptamers show potential as broad-spectrum inhibitors of SARS-CoV-2.
• These aptamers target a conserved region of NSP12, making them effective against current and emerging variants.
• The findings suggest a promising platform for developing novel antiviral agents against SARS-CoV-2 and other RNA viruses.