Reprogramming of Protein-Targeted Small-Molecule Medicines to RNA by Ribonuclease Recruitment

J Am Chem Soc. 2021 Aug 25;143(33):13044-13055. doi: 10.1021/jacs.1c02248. Epub 2021 Aug 13.

Abstract

Reprogramming known medicines for a novel target with activity and selectivity over the canonical target is challenging. By studying the binding interactions between RNA folds and known small-molecule medicines and mining the resultant dataset across human RNAs, we identified that Dovitinib, a receptor tyrosine kinase (RTK) inhibitor, binds the precursor to microRNA-21 (pre-miR-21). Dovitinib was rationally reprogrammed for pre-miR-21 by using it as an RNA recognition element in a chimeric compound that also recruits RNase L to induce the RNA's catalytic degradation. By enhancing the inherent RNA-targeting activity and decreasing potency against canonical RTK protein targets in cells, the chimera shifted selectivity for pre-miR-21 by 2500-fold, alleviating disease progression in mouse models of triple-negative breast cancer and Alport Syndrome, both caused by miR-21 overexpression. Thus, targeted degradation can dramatically improve selectivity even across different biomolecules, i.e., protein versus RNA.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Benzimidazoles / chemistry
  • Benzimidazoles / pharmacology*
  • Humans
  • MicroRNAs / antagonists & inhibitors*
  • MicroRNAs / metabolism
  • Molecular Structure
  • Nephritis, Hereditary / drug therapy
  • Nephritis, Hereditary / metabolism
  • Protein Kinase Inhibitors / chemistry
  • Protein Kinase Inhibitors / pharmacology*
  • Quinolones / chemistry
  • Quinolones / pharmacology*
  • Receptor Protein-Tyrosine Kinases / antagonists & inhibitors
  • Receptor Protein-Tyrosine Kinases / metabolism
  • Ribonucleases / antagonists & inhibitors*
  • Ribonucleases / metabolism
  • Small Molecule Libraries / chemistry
  • Small Molecule Libraries / pharmacology*
  • Triple Negative Breast Neoplasms / drug therapy*
  • Triple Negative Breast Neoplasms / metabolism

Substances

  • 4-amino-5-fluoro-3-(5-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl)quinolin-2(1H)-one
  • Benzimidazoles
  • MIRN21 microRNA, human
  • MicroRNAs
  • Protein Kinase Inhibitors
  • Quinolones
  • Small Molecule Libraries
  • Receptor Protein-Tyrosine Kinases
  • Ribonucleases