On-DNA hit validation methodologies for ligands identified from DNA-encoded chemical libraries

Biochem Biophys Res Commun. 2020 Dec 3;533(2):235-240. doi: 10.1016/j.bbrc.2020.04.030. Epub 2020 Apr 30.

Abstract

DNA-encoded chemical libraries (DECLs) are large compound collections attached to DNA fragments, serving as amplifiable barcodes, which can be screened on target proteins of pharmaceutical interest. In DECL selections, ligands are identified by high-throughput DNA sequencing, by comparing their frequency before and after the affinity capture step. Hits identified using this procedure need to be validated by resynthesis and by performing affinity measurements. Here we report novel on-DNA hit validation strategies, which enable the facile confirmation of ligand-protein interaction as well as the determination of equilibrium and kinetic binding constants. The experimental procedures, which had been inspired by enzyme-linked immunosorbent assays (ELISA), were validated using ligands of different affinity to carbonic anhydrase II and IX.

Keywords: DNA-Encoded chemical library; ELISA; Hit validation methodology; SPR.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Carbonic Anhydrase II / metabolism
  • Carbonic Anhydrase IX / metabolism
  • Cattle
  • Combinatorial Chemistry Techniques
  • DNA / chemical synthesis
  • DNA / chemistry*
  • Drug Discovery
  • Drug Evaluation, Preclinical
  • Enzyme-Linked Immunosorbent Assay
  • Humans
  • Ligands
  • Models, Molecular
  • Protein Binding
  • Small Molecule Libraries / chemical synthesis
  • Small Molecule Libraries / chemistry*
  • Small Molecule Libraries / pharmacology

Substances

  • Ligands
  • Small Molecule Libraries
  • DNA
  • Carbonic Anhydrase II
  • Carbonic Anhydrase IX