Cyclic peptides targeting the SARS-CoV-2 programmed ribosomal frameshifting RNA from a multiplexed phage display...

Area of Science:

• Chemical Biology
• Molecular Biology
• Drug Discovery

Background:

• RNA's tertiary structures offer binding sites for drug-like molecules.
• Targeting RNA with high-affinity, specific molecules is a significant challenge.
• SARS-CoV-2, like other viruses, relies on RNA as its genetic material.

Purpose of the Study:

• To develop a novel strategy for discovering and selecting RNA-targeted macrocyclic peptides.
• To create large, structurally diverse libraries of genetically encoded peptide macrocycles.
• To identify specific macrocyclic peptides that bind the SARS-CoV-2 FSS RNA pseudoknot with high affinity and selectivity.

Main Methods:

• Utilized a phage display platform for macrocyclic organo-peptide hybrids (MOrPH-PhD).
• Employed diverse non-canonical amino acid-based cyclization modules to generate libraries of 10^7 peptide macrocycles.
• Panned libraries against the SARS-CoV-2 FSS RNA pseudoknot.

Main Results:

• Identified specific macrocyclic peptide sequences with high affinity and selectivity for the target RNA.
• Determined that peptide binding localizes to the FSS dimerization loop.
• Demonstrated specificity of cyclic peptides for the target RNA over unrelated RNA pseudoknots.

Conclusions:

• Introduced a novel system (multiplexed MOrPH-PhD) for generating and screening topologically diverse cyclopeptide scaffolds.
• Provided a blueprint for evolving genetically encoded macrocyclic peptides against specific RNA targets.
• Highlighted the potential of macrocyclic peptides as therapeutic agents against RNA viruses like SARS-CoV-2.