DNA-Encoded Combinatorial Library of Macrocyclic Peptoids

Bioconjug Chem. 2019 Nov 20;30(11):2931-2938. doi: 10.1021/acs.bioconjchem.9b00628. Epub 2019 Nov 8.

Abstract

We report the design and synthesis of a DNA-encoded one-bead one-compound library of cyclic peptoids composed of more than 11 million molecules. We show that affinity-based screening of this large library can identify cyclic peptoid ligands for a target protein. In this work, we developed a simple method for amplifying the PCR product from DNA tags on a single bead, thereby enabling determination of the structures of hit cyclic peptoids with no need for high-throughput sequencing and complicated data analysis. We also developed a sublibrary screening strategy to minimize false positives caused by the interference of coding DNA tags before starting laborious and impractical hit confirmation. Given the simplicity and robustness of the synthesis and screening, along with the desirable features of macrocyclic peptoids including improved conformational rigidity, our method will be highly useful for discovering biologically active molecules modulating challenging targets such as protein-protein interactions that are not easily targeted by typical peptidomimetics and small-molecules.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Combinatorial Chemistry Techniques / methods*
  • Cyclization
  • DNA / analysis
  • DNA / chemistry*
  • DNA / metabolism
  • Humans
  • Ligands
  • Macrocyclic Compounds / chemistry*
  • Peptidomimetics
  • Peptoids / chemistry*
  • Peptoids / metabolism
  • Small Molecule Libraries / chemistry*
  • Small Molecule Libraries / metabolism

Substances

  • Ligands
  • Macrocyclic Compounds
  • Peptidomimetics
  • Peptoids
  • Small Molecule Libraries
  • DNA