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Permutational Encoding Strategy Accelerates HIT Validation from Single-Stranded DNA-Encoded Libraries.

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Summary
This summary is machine-generated.

A new DNA-encoded library (DEL) method enables precise isomer discrimination during screening. This approach enhances hit identification and streamlines drug discovery by improving enrichment factors and simplifying synthesis.

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Area of Science:

  • Medicinal Chemistry
  • Chemical Biology
  • Drug Discovery

Background:

  • DNA-encoded libraries (DELs) offer high-throughput screening of vast compound collections.
  • Current DEL construction and hit resynthesis can be challenging, particularly with stereoisomers.

Purpose of the Study:

  • To introduce a novel permutational encoding strategy for DELs that distinguishes isomers at the sequencing level.
  • To validate this method for constructing pure, single-pharmacophore DELs and assess its performance in drug discovery campaigns.

Main Methods:

  • Developed a permutational encoding strategy for single-stranded, single-pharmacophore DELs.
  • Synthesized and screened a 921,600-member 4-amino-proline DEL (DEL1) and a 24-scaffold cyclic peptide DEL (DEL2).
  • Utilized high-throughput sequencing to analyze selective enrichment and on-DNA binding affinities.

Main Results:

  • DEL1 screening demonstrated selective enrichment of potent stereoisomers, outperforming conventional methods.
  • DEL2 screening against human FAP identified five enriched cyclic peptides.
  • A direct correlation was observed between enrichment factors and on-DNA binding affinities.

Conclusions:

  • The permutational encoding strategy facilitates DEL library synthesis and hit resynthesis.
  • This method enhances enrichment factors, accelerating the identification of drug candidates.
  • The approach is versatile for various applications, including de novo discovery and affinity maturation.