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Updated: Jun 12, 2025

Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
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Stapled Peptides as Inhibitors of mRNA Deadenylation

Sunit Pal1, Ilja Gordijenko1, Stefan Schmeing1

  • 1Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.

Angewandte Chemie (International Ed. in English)
|September 25, 2024
PubMed

Insights

Researchers developed a novel peptide, NIP-2, to inhibit messenger RNA (mRNA) degradation by targeting the CCR4-NOT complex. This approach stabilizes beneficial mRNA, offering a new therapeutic strategy to increase mRNA levels.

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Drug Discovery

Background:

  • Therapeutic strategies often focus on reducing disease-causing mRNA.
  • Stabilizing beneficial mRNA by preventing its degradation is an underexplored area.
  • mRNA degradation, initiated by poly(A) tail removal, is regulated by the CCR4-NOT complex.

Purpose of the Study:

  • To explore methods for blocking the destruction of beneficial mRNA.
  • To develop a peptide-based inhibitor targeting the CCR4-NOT complex's deadenylation activity.
  • To investigate the potential of stabilizing mRNA for therapeutic benefit.

Main Methods:

  • Identified the NOT9 binding motif in the CCR4-NOT complex as a target.
  • Designed and synthesized hydrocarbon stapled peptides, starting with NIP-2.
  • Utilized co-crystallography for peptide optimization and in vitro/cell-based assays to assess inhibition and cell permeability.

Main Results:

  • Developed NIP-2 peptide with nanomolar affinity for NOT9 and potent inhibition of RNA binding and deadenylation in vitro.
  • Demonstrated cell permeability of NIP-2 (EC50 = 2.44 μM).
  • Optimized peptide NIP-2-H27A-N3 showed improved affinity and significantly enhanced cell permeability (EC50 = 0.34 μM), inhibiting mRNA deadenylation in HeLa cells.

Conclusions:

  • Peptide-based inhibition of the CCR4-NOT complex is feasible.
  • The developed peptides can effectively inhibit mRNA deadenylation and increase mRNA stability.
  • This strategy presents a novel therapeutic avenue for conditions requiring increased levels of specific beneficial mRNAs.
Keywords:
RNA-binding proteinscell-permeabilitydeadenylationmRNA stabilizationstapled peptides

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