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Probing RNA-Small Molecule Interactions Using Biophysical and Computational Approaches.

Amiu Shino1, Maina Otsu1, Koji Imai1

  • 1Basic Research Division, Veritas In Silico Inc., Shinagawa, Tokyo 141-0031, Japan.

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|October 19, 2023
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Summary

This study optimized methods for discovering small molecules that target RNA. Fluoroquinolones were identified as binders, and fragment molecular orbital calculations aided in rational drug design for RNA-targeted therapies.

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Area of Science:

  • Biochemistry
  • Medicinal Chemistry
  • Computational Biology

Background:

  • Small molecules targeting RNA offer therapeutic potential for diseases with unmet needs.
  • Challenges exist in selecting tools and establishing workflows for RNA-targeted small molecule discovery.
  • Optimized experimental and computational approaches are crucial for advancing this field.

Purpose of the Study:

  • To demonstrate a fluorescence-based assay for screening small molecule libraries against an RNA stem-loop.
  • To validate identified binders using biophysical techniques.
  • To utilize computational methods for understanding and predicting drug-target interactions.

Main Methods:

  • Fluorescence-based assay for high-throughput screening.
  • Biolayer interferometry, isothermal titration calorimetry (ITC), and nuclear magnetic resonance (NMR) spectroscopy for biophysical validation.
  • Fragment molecular orbital (FMO) calculations for interaction analysis and rational drug design.

Main Results:

  • A fluorescence-based screen identified fluoroquinolones that bind and stabilize an RNA stem-loop.
  • Biophysical assays confirmed fluoroquinolone binding and suggested a conserved binding mode.
  • FMO calculations accurately predicted binding free energies and correlated well with ITC data.
  • Designed fluoroquinolone analogues showed predictable binding affinities via FMO analysis.

Conclusions:

  • Orthogonal assays are vital for confirming RNA-small molecule binding and selecting effective compounds.
  • Fragment molecular orbital (FMO) calculations are valuable tools for the rational design of RNA-targeted therapeutics.
  • Optimized screening and computational approaches can accelerate the discovery of novel RNA-targeting drugs.