SCAN--a high-throughput assay for detecting small molecule binding to RNA targets

Area of Science:

• Biochemistry
• Molecular Biology
• Drug Discovery

Background:

• RNA targets represent a largely untapped area for therapeutic intervention.
• Existing high-throughput screening (HTS) methods are not optimized for RNA targets.
• A need exists for efficient technologies to discover small molecules that bind RNA.

Purpose of the Study:

• To develop and validate a novel optical-based HTS technology for RNA targets.
• To demonstrate the utility of the SCAN assay for identifying RNA-binding small molecules.
• To establish SCAN as a robust and cost-effective platform for RNA-centric drug discovery.

Main Methods:

• Developed the Screen for Compounds with Affinity for Nucleic Acids (SCAN) assay, an affinity-based, homogeneous format.
• Applied SCAN to screen a compound library against the Hepatitis C Virus (HCV) IRES Loop IIId RNA domain.
• Validated assay robustness using Z' values and assessed correlation between assay potency (EC50) and binding affinity (KD).

Main Results:

• Successfully developed a SCAN assay for the HCV IRES Loop IIId RNA domain.
• Identified small molecule ligands that specifically bind to the target RNA structure.
• Achieved Z' values greater than 0.8, confirming the assay's robustness for HTS.
• Demonstrated a correlation between SCAN EC50 and KD values, indicating suitability for compound optimization.

Conclusions:

• The SCAN technology is a novel, efficient, and robust method for HTS of RNA targets.
• SCAN facilitates the discovery of small molecules with affinity for structured RNA elements.
• This platform opens new avenues for developing therapeutics targeting RNA.