Small molecule screening of RNA aptamers using native mass spectrometry

Area of Science:

• Biochemistry
• Drug Discovery
• Molecular Biology

Background:

• Targeting RNA with small molecules offers a promising therapeutic strategy to expand the druggable chemical space.
• Developing efficient methods for identifying small molecule binders for RNA targets remains a key challenge in drug discovery.
• Native mass spectrometry (nMS) is a proven biophysical technique for screening protein-ligand interactions but is less explored for RNA targets.

Purpose of the Study:

• To evaluate the application of native mass spectrometry (nMS) for the biophysical screening of RNA aptamers.
• To assess nMS for identifying small molecule binders, including FDA-approved drugs, for RNA aptamers.
• To determine the potential of nMS as an orthogonal screening technology in RNA-targeting drug discovery.

Main Methods:

• Applied native mass spectrometry (nMS) to analyze the binding of aminoglycoside RNA aptamers with their cognate ligands.
• Tested related aminoglycoside ligands and a diverse library of FDA-approved drugs for binding to RNA aptamers using nMS.
• Utilized nMS for library screening to identify novel RNA-binding small molecules.

Main Results:

• nMS successfully confirmed cognate ligand binding to RNA aptamers.
• The technique allowed for semi-quantitation of binding strength and selectivity across tested compounds.
• nMS library screening identified previously unknown small molecule binders for RNA aptamers.

Conclusions:

• Native mass spectrometry (nMS) is a viable method for the biophysical screening of RNA aptamers.
• nMS demonstrates potential as an orthogonal screening technology for RNA-targeting drug discovery.
• Challenges related to the physicochemical properties of RNA present limitations for nMS application in this context.