2. Academic Validation
  3. Programming inactive RNA-binding small molecules into bioactive degraders

Programming inactive RNA-binding small molecules into bioactive degraders

  • Nature. 2023 May 24. doi: 10.1038/s41586-023-06091-8.
Yuquan Tong # 1,  Yeongju Lee # 1,  Xiaohui Liu # 1,  Jessica L Childs-Disney # 1,  Blessy M Suresh 1,  Raphael I Benhamou 1,  Chunying Yang 2,  Weimin Li 2,  Matthew G Costales 1,  Hafeez S Haniff 1,  Sonja Sievers 3 4,  Daniel Abegg 1,  Tristan Wegner 5,  Tiffany O Paulisch 5,  Elizabeth Lekah 1,  Maison Grefe 1,  Gogce Crynen 6,  Montina Van Meter 7,  Tenghui Wang 1,  Quentin M R Gibaut 1,  John L Cleveland 2,  Alexander Adibekian 1,  Frank Glorius 8,  Herbert Waldmann 9 10 11,  Matthew D Disney 12
Affiliations

Affiliations

  • 1 Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA.
  • 2 Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
  • 3 Max Planck Institute of Molecular Physiology, Dortmund, Germany.
  • 4 Compound Management and Screening Center, Dortmund, Germany.
  • 5 Organisch-Chemisches Institut, University of Münster, Münster, Germany.
  • 6 Bioinformatics and Statistics Core, The Scripps Research Institute and The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA.
  • 7 Histology Core, The Scripps Research Institute and The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA.
  • 8 Organisch-Chemisches Institut, University of Münster, Münster, Germany. glorius@uni-muenster.de.
  • 9 Max Planck Institute of Molecular Physiology, Dortmund, Germany. herbert.waldmann@mpi-dortmund.mpg.de.
  • 10 Compound Management and Screening Center, Dortmund, Germany. herbert.waldmann@mpi-dortmund.mpg.de.
  • 11 Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany. herbert.waldmann@mpi-dortmund.mpg.de.
  • 12 Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA. disney@scripps.edu.
  • # Contributed equally.
PMID: 37225982 DOI: 10.1038/s41586-023-06091-8
Abstract

Target occupancy is often insufficient to elicit biological activity, particularly for RNA, compounded by the longstanding challenges surrounding the molecular recognition of RNA structures by small molecules. Here we studied molecular recognition patterns between a natural-product-inspired small-molecule collection and three-dimensionally folded RNA structures. Mapping these interaction landscapes across the human transcriptome defined structure-activity relationships. Although RNA-binding compounds that bind to functional sites were expected to elicit a biological response, most identified interactions were predicted to be biologically inert as they bind elsewhere. We reasoned that, for such cases, an alternative strategy to modulate RNA biology is to cleave the target through a ribonuclease-targeting chimera, where an RNA-binding molecule is appended to a heterocycle that binds to and locally activates RNase L1. Overlay of the substrate specificity for RNase L with the binding landscape of small molecules revealed many favourable candidate Binders that might be bioactive when converted into degraders. We provide a proof of concept, designing selective degraders for the precursor to the disease-associated microRNA-155 (pre-miR-155), JUN mRNA and MYC mRNA. Thus, small-molecule RNA-targeted degradation can be leveraged to convert strong, yet inactive, binding interactions into potent and specific modulators of RNA function.

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