# In Search of the Most Significant Potential G-Quadruplexes in SARS-CoV-2 RNA: Genomic Analysis

## TL;DR

This paper identifies potential G-quadruplex structures in SARS-CoV-2 RNA and explores their roles in viral replication and possible antiviral drug targets.

## Contribution

The study systematically analyzes and identifies the most significant potential G-quadruplexes in SARS-CoV-2 RNA and evaluates their structural and functional roles.

## Key findings

- SARS-CoV-2 RNA contains 42 putative G-quadruplex-forming sequences, many stabilized by U·A-U triads or 3′ U-tetrads.
- Most G-quadruplex-forming sequences are highly conserved, with only a few showing transient destabilizing mutations.
- Compound EKM showed specific binding to G4 3467 and emerged as a promising antiviral candidate.

## Abstract

G-quadruplexes (G4s) are emerging as potential antiviral targets. SARS-CoV-2 genomic RNA contains 42 G-rich regions harboring putative G-quadruplex-forming sequences (PQSs). Here, we performed a systematic genomic and structural analysis of SARS-CoV-2 PQSs. It was proposed that non-G-tetrads or different triads may stabilize most G4s in this RNA. Many G4s may include the most stable U·A-U triad. Several G-quadruplexes may be significantly stabilized by 3′ U-tetrad. Large-scale mutational analysis of RNA structural elements containing PQSs showed that most PQSs are highly conserved, while persistent G4-destroying mutations were observed only for one PQS and were transient for two others. Based on G4 position and structural context, we propose that: (i) G4 370 in nsp1 may contribute to cap-independent translation initiation; (ii) certain putative G4s in different genes may assist in co-translational folding of viral proteins; (iii) G4 13385, located upstream of the frameshift stimulation element, may promote formation of a pseudoknot competent for −1 frameshifting. For putative G4s at positions 3467, 13385 and 28903, we analyzed binding to 13 compounds by molecular docking and selected four candidates for molecular dynamics simulations. The ligand EKM emerged as a promising antiviral candidate due to its specific binding to G4 3467.