High-Throughput Quality Control Assay for the Solid-Phase Synthesis of DNA-Encoded Libraries of Macrocycles*

Area of Science:

• Medicinal Chemistry
• Organic Synthesis
• Drug Discovery

Background:

• Macrocycles are valuable ligands for challenging drug targets, including protein-protein interaction sites.
• Synthesizing high-quality macrocyclic libraries faces challenges, as linear precursors exhibit variable cyclization efficiencies.
• Conformational preferences of linear precursors significantly impact macrocyclization success.

Purpose of the Study:

• To develop a robust quality control method for assessing macrocyclization efficiency during solid-phase synthesis.
• To distinguish between macrocyclic scaffolds that cyclize efficiently and those that do not.
• To enable rapid quality assessment of macrocyclic libraries and screening hits.

Main Methods:

• Development of a novel quality control assay for solid-phase synthesis of thioether macrocycles.
• Application of the assay to identify linear impurities in DNA-encoded macrocyclic libraries.
• Utilizing the assay for quality control during the re-synthesis of potential macrocyclic screening hits.

Main Results:

• The developed assay effectively distinguishes between efficiently and inefficiently cyclizing scaffolds.
• The method avoids the need for time-consuming liquid chromatography/mass spectrometry analysis.
• The assay successfully identified linear impurities in a DNA-encoded library.
• A practical quality control protocol for macrocyclic synthesis was established.

Conclusions:

• A powerful and efficient quality control method for macrocyclic synthesis has been established.
• This assay accelerates the development of high-quality macrocyclic libraries for drug discovery.
• The method provides a reliable protocol for validating macrocyclic screening hits.