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DNA-Encoded Solid-Phase Synthesis: Encoding Language Design and Complex Oligomer Library Synthesis.

Andrew B MacConnell1, Patrick J McEnaney1, Valerie J Cavett1

  • 1Department of Chemistry and ‡Doctoral Program in Chemical and Biological Sciences, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States.

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Summary
This summary is machine-generated.

DNA-encoded solid-phase synthesis (DESPS) overcomes the structure elucidation problem in small molecule discovery. This method enables the creation of complex compound libraries with diverse structures, facilitating drug discovery.

Keywords:
DNA-encoded librariescombinatorial synthesisone-bead-one-compoundsplit-and-pool

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Area of Science:

  • Chemical Biology
  • Organic Synthesis
  • Drug Discovery

Background:

  • Combinatorial synthesis for small molecule discovery is limited by the structure elucidation problem in mass spectrometry.
  • Isomerism and diverse scaffolds in one-bead-one-compound (OBOC) libraries lead to mass redundancy and uninterpretable MS fragmentation.
  • Key molecular features like stereochemistry and regiochemistry are often excluded from libraries due to analysis challenges.

Purpose of the Study:

  • To present DNA-encoded solid-phase synthesis (DESPS) as a solution to the structure elucidation problem in OBOC library synthesis.
  • To enable the creation of complex and diverse small molecule libraries for drug discovery.
  • To demonstrate the utility of DESPS in synthesizing compounds with stereochemical and regiochemical diversity.

Main Methods:

  • Developed DESPS combining parallel organic solvent synthesis with aqueous enzymatic ligation of DNA oligonucleotides.
  • Designed computationally optimized DNA encoding sequences for efficient sequencing and high Hamming distance.
  • Utilized split-and-pool diversification with DNA encoding for tracking compound synthesis history.

Main Results:

  • Achieved efficient (70% yield), specific, and directional DNA ligation over six encoding positions.
  • Detected high molecule counts (9 × 10^4 molecules/bead) using single-bead quantitative PCR.
  • Synthesized a 75,645-member library with high structural diversity and confirmed DNA sequence-predicted mass matched experimental MALDI-TOF MS data (<1 ppt error).

Conclusions:

  • DESPS effectively integrates solid-phase synthesis and DNA encoding, enabling single-bead structural elucidation of complex compounds.
  • The method allows synthesis using reactions incompatible with unprotected DNA, expanding accessible chemical space.
  • DESPS offers a straightforward implementation, potentially revitalizing the synthesis of complex and diverse chemical libraries.