R-BIND

R-BIND catalogs bioactive small-molecule ligands that target non-rRNA to support discovery and development of RNA-targeted chemical probes.

Key Features:

• Curated ligands: A curated collection of bioactive ligands reported to have activity in cell culture and/or animal models against non-rRNA targets.
• Cheminformatics annotations: Cheminformatics-derived annotations include physicochemical, structural, and spatial properties, functional groups, substructures, and experimental details.
• Nearest neighbor algorithm: A nearest neighbor algorithm enables assessment of molecular similarity between query molecules and R-BIND ligands.
• RNA-privileged property identification: Cheminformatics analyses identify RNA-privileged physicochemical and structural features across the dataset.
• Consistent property distributions: Distinguishing physicochemical, structural, and spatial property distributions are retained despite database expansion.

Scientific Applications:

• Small-molecule library design: Use cheminformatics annotations and substructure filters to design focused libraries for RNA-targeted screening.
• Lead optimization: Leverage physicochemical and structural data and nearest neighbor similarity to optimize lead ligands for RNA targeting.
• Target and probe selection: Prioritize RNA targets and select chemical probes and appropriate control experiments based on curated activity data.
• Functional RNA studies: Provide ligands with reported activity in cell culture and animal models to support interrogation of RNA function.

Methodology:

Manual curation of literature-reported chemical probes targeting non-rRNA with activity in cell culture and/or animal models; cheminformatics analyses to compute physicochemical, structural, and spatial properties and to identify RNA-privileged features; implementation of a nearest neighbor algorithm for ligand similarity assessment.