A Discovery Funnel for Nucleic Acid Binding Drug Candidates

Area of Science:

• Drug discovery and computational chemistry
• Structural biology and biophysics
• Medicinal chemistry

Background:

• Proteins are common drug targets, but DNA targets, especially non-canonical structures like G-quadruplexes, are underexplored in virtual screening.
• The functional importance of G-quadruplex DNA structures necessitates the discovery of selective small molecule binders.
• Current virtual screening methods are not optimized for DNA targets.

Purpose of the Study:

• To develop an integrated in silico and in vitro platform for discovering selective small molecule binders for DNA targets.
• To validate the platform using G-quadruplex DNA as a target.
• To identify and characterize novel compounds with potential therapeutic applications.

Main Methods:

• In silico screening of millions of compounds against a specific DNA structure, including competing structures.
• High-throughput 96-well thermal denaturation assays for experimental validation of top computational hits.
• Rigorous biophysical characterization of promising candidates using isothermal titration calorimetry, differential scanning calorimetry, spectroscopy, and competition dialysis.

Main Results:

• The integrated platform successfully screened millions of compounds in silico, identifying several hundred potential binders.
• Experimental validation yielded the top ten candidates, with one novel G-quadruplex binding compound discovered.
• The identified compound shows potential anti-cancer activity.

Conclusions:

• The developed integrated platform is effective for discovering selective small molecule binders for DNA targets, including G-quadruplexes.
• This approach expands virtual screening capabilities beyond protein targets.
• The newly discovered compound warrants further investigation for its anti-cancer potential.