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Area of Science:

  • RNA structural biology
  • Antiviral drug discovery
  • Molecular virology

Background:

  • The SARS-CoV-2 frameshift stimulation element (FSE) is crucial for viral replication and a potential antiviral target.
  • Understanding RNA-ligand interactions is key for developing effective antiviral therapies.

Purpose of the Study:

  • To identify small-molecule binding pockets within the SARS-CoV-2 FSE.
  • To develop a ligandability map for the FSE.
  • To design and synthesize novel bioactive compounds with antiviral activity.

Main Methods:

  • Chemical Cross-Linking and Isolation by Pull-down (Chem-CLIP) for covalent target validation and binding site mapping.
  • Dimethyl sulfate (DMS) probing combined with Deconvolution of RNA Alternative Conformations (DRACO) to assess ligand-induced structural changes.
  • Structure-based design, synthesis, and competitive displacement assays.
  • In silico pocket analysis of cryo-EM derived FSE structures.

Main Results:

  • Chem-CLIP precisely mapped the binding pocket of the fluoroquinolone merafloxacin at nucleotide resolution.
  • Development of bioactive compounds with antiviral activity through structure-based design and synthesis.
  • DMS-DRACO revealed ligand-induced alterations in local RNA folding, distinguishing direct binding from structural changes.
  • In silico analysis identified recurring cavities in the FSE, corroborating experimental findings.

Conclusions:

  • Combining Chem-CLIP and DMS profiling is essential for accurate RNA-ligand interaction studies.
  • The study provides a strategy for designing small molecules that target RNA structures.
  • Findings advance the understanding of RNA-ligand interactions and support FSE as an antiviral target.