Massively Parallel, Single-Molecule Assessment of Synthetic Fidelity and Drug-Like Properties in a DNA-Encoded...

Area of Science:

• Medicinal Chemistry
• Drug Discovery
• Biotechnology

Background:

• DNA-encoded libraries (DELs) are effective for hit generation against protein targets.
• Challenges include synthetic inefficiency and enrichment of poorly permeable compounds, especially macrocyclic peptides.
• Assessing individual compound quality and properties within DELs is crucial for successful drug development.

Purpose of the Study:

• To introduce LC-seq, a novel sequencing-based chromatographic strategy.
• To simultaneously evaluate synthetic fidelity and lipophilicity of individual DEL library members.
• To enable direct, per-member assessment of compound quality and permeability-relevant properties.

Main Methods:

• Development and application of LC-seq, a sequencing-based chromatographic technique.
• Analysis of a 120,000-member peptide library to map reaction efficiency and measure lipophilicity.
• Correlation of on-DNA lipophilicity with off-DNA lipophilicity and passive permeability.

Main Results:

• LC-seq successfully mapped reaction efficiency across all synthetic cycles for the peptide library.
• Lipophilicity was accurately measured for individual library members using sequencing-count-derived retention times.
• On-DNA lipophilicity strongly correlated with off-DNA lipophilicity and passive permeability, validating the method's predictive power.
• Identified building-block-specific structure-reactivity trends.

Conclusions:

• LC-seq provides a direct, per-member assessment of compound quality and lipophilicity in DELs.
• This method addresses key limitations in DEL-based drug discovery, particularly for beyond-Rule-of-5 compounds.
• LC-seq is scalable to millions of compounds, offering significant potential for future drug discovery efforts.