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

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. [Display omitted] •Novel on-DNA hit validation ELISA and SPR methodology.•Single on-DNA conjugate designed for a plurality of hit validation assays.•Validation performed measuring CAII and CAIX protein-ligands affinities.