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Critical Evaluation of Photo-cross-linking Parameters for the Implementation of Efficient DNA-Encoded Chemical Library Selections.
Journal article

Critical Evaluation of Photo-cross-linking Parameters for the Implementation of Efficient DNA-Encoded Chemical Library Selections.

  • Sannino A Philochem AG, 8112 Otelfingen, Switzerland.
  • Gironda-Martínez A Philochem AG, 8112 Otelfingen, Switzerland.
  • Gorre ÉMD Philochem AG, 8112 Otelfingen, Switzerland.
  • Prati L Philochem AG, 8112 Otelfingen, Switzerland.
  • Piazzi J Philochem AG, 8112 Otelfingen, Switzerland.
  • Scheuermann J Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich, Switzerland.
  • Neri D Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich, Switzerland.
  • Donckele EJ Philochem AG, 8112 Otelfingen, Switzerland.
  • Samain F Philochem AG, 8112 Otelfingen, Switzerland.
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  • 2020-02-29
Published in:
  • ACS combinatorial science. - 2020
DNA-encoded chemical libraries
ESAC
diazirine
photo-cross-linking
qPCR
English The growing importance of DNA-encoded chemical libraries (DECLs) as tools for the discovery of protein binders has sparked an interest for the development of efficient screening methodologies, capable of discriminating between high- and medium-affinity ligands. Here, we present a systematic investigation of selection methodologies, featuring a library displayed on single-stranded DNA, which could be hybridized to a complementary oligonucleotide carrying a diazirine photoreactive group. Model experiments, performed using ligands of different affinity to carbonic anhydrase IX, revealed a recovery of preferential binders up to 10%, which was mainly limited by the highly reactive nature of carbene intermediates generated during the photo-cross-linking process. Ligands featuring acetazolamide or p-phenylsulfonamide exhibited a higher recovery compared to their counterparts based on 3-sulfamoyl benzoic acid, which had a lower affinity toward the target. A systematic evaluation of experimental parameters revealed conditions that were ideally suited for library screening, which were used for the screening of a combinatorial DECL library, featuring 669 240 combinations of two sets of building blocks. Compared to conventional affinity capture procedures on protein immobilized on solid supports, photo-cross-linking provided a better discrimination of low-affinity CAIX ligands over the background signal and therefore can be used as a tandem methodology with the affinity capture procedures.
Language
  • English
Open access status
closed
Identifiers
Persistent URL
https://folia.unifr.ch/global/documents/65924
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