Affinity Selections of DNA-Encoded Chemical Libraries on Carbonic Anhydrase IX-Expressing Tumor Cells Reveal a Dependence on Ligand Valence
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Date
2021-06-21Type
- Journal Article
Citations
Cited 8 times in
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Cited 11 times in
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Abstract
DNA-encoded chemical libraries are typically screened against purified protein targets. Recently, cell-based selections with encoded chemical libraries have been described, commonly revealing suboptimal performance due to insufficient recovery of binding molecules. We used carbonic anhydrase IX (CAIX)-expressing tumor cells as a model system to optimize selection procedures with code-specific quantitative polymerase chain reaction (qPCR) as selection readout. Salt concentration and performing PCR on cell suspension had the biggest impact on selection performance, leading to 15-fold enrichment factors for high-affinity monovalent CAIX binders (acetazolamide; KD=8.7 nM). Surprisingly, the homobivalent display of acetazolamide at the extremities of both complementary DNA strands led to a substantial improvement of both ligand recovery and enrichment factors (above 100-fold). The optimized procedures were used for selections with a DNA-encoded chemical library comprising 1 million members against tumor cell lines expressing CAIX, leading to a preferential recovery of known and new ligands against this validated tumor-associated target. This work may facilitate future affinity selections on cells against target proteins which might be difficult to express otherwise. © 2021 Wiley-VCH GmbH Show more
Publication status
publishedExternal links
Journal / series
Chemistry - A European JournalVolume
Pages / Article No.
Publisher
WileySubject
carbonic anhydrase IX; cell-based affinity selections; code-specific qPCR; DNA-encoded chemical libraries; ligand valenceOrganisational unit
03463 - Neri, Dario (ehemalig) / Neri, Dario (former)
Funding
182003 - Understanding and Exploiting the Molecular Targeting of Tumor Neo-vasculature (SNF)
670603 - Fulfilling Paul Ehrlich’s Dream: therapeutics with activation on demand (EC)
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Show all metadata
Citations
Cited 8 times in
Web of Science
Cited 11 times in
Scopus
ETH Bibliography
yes
Altmetrics