ArticleNature chemical biology2026
Designing small molecules targeting a cryptic RNA binding site through base displacement.
Article in Nature chemical biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Accurate RNA-Ligand Binding Site Prediction Based on a Multi-Channel Graph Neural Network.Interdisciplinary sciences, computational life sciences · 2026Article
- Geometric Deep Learning Reveals Ligandable and Cryptic RNA Binding Small Molecule Pockets (SMARTPocket).bioRxiv : the preprint server for biology · 2026Article
- Seeing the hidden pocket.Nature chemical biology · 2026Article
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Therapeutic rewiring of ceRNA networks: a computational pipeline for drug repurposing in acute kidney injury via circRNA-miRNA-mRNA axis disruption.Human genomics · 2026Review
- MicroRNA-phytochemical interactome targeting thioredoxin-interacting protein: a narrative review at the nexus of RNA therapeutics, cancer biology, and metabolic regulation.Frontiers in oncology · 2026Review
- AI-Integrated QSAR Modeling for Enhanced Drug Discovery: From Classical Approaches to Deep Learning and Structural Insight.International journal of molecular sciences · 2025Review
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4 authors.
Funding
Abstract
Most RNA-binding small molecules have limited solubility, weak affinity and/or lack of specificity, restricting the medicinal chemistry often required for lead compound discovery. We reasoned that conjugation of these unfavorable ligands to a suitable 'host' molecule can solubilize the 'guest' and deliver it site-specifically to an RNA of interest to resolve these issues. Using this framework, we designed a small-molecule library that was hosted by cobalamin (Cbl) to interact with the Cbl riboswitch through a common base displacement mechanism. Combining in vitro binding, cell-based assays, chemoinformatic modeling and structure-based design, we unmasked a cryptic binding site within the riboswitch that was exploited to discover compounds that have affinity exceeding the native ligand, antagonize riboswitch function or bear no resemblance to Cbl. These data demonstrate how a privileged biphenyl-like scaffold effectively targets RNA by optimizing π-stacking interactions within the binding pocket.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.