Affinity Selections of DNA‐Encoded Chemical Libraries on Carbonic Anhydrase IX‐Expressing Tumor Cells Reveal a Dependence on Ligand Valence. Issue 35 (18th May 2021)

• Record Type: Journal Article
• Authors: Oehler, Sebastian; Catalano, Marco; Scapozza, Ilario; Bigatti, Martina; Bassi, Gabriele; Favalli, Nicholas; Mortensen, Michael R.; Samain, Florent; Scheuermann, Jörg; Neri, Dario
• Is Part Of: Chemistry. Volume 27:Issue 35(2021)
• Page Start: 8985
• Page End: 8993
• Publication Date: 2021-05-18
• Subjects: carbonic anhydrase IX -- cell-based affinity selections -- code-specific qPCR -- DNA-encoded chemical libraries -- ligand valence; Chemistry -- Periodicals; 540
• DOI: 10.1002/chem.202100816
• Languages: English
• ISSNs: 0947-6539

Abstract

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; K D =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. Abstract : DNA‐encoded chemical libraries were screened against live cells, first in a model system to apply systematically optimized conditions using a library comprising 1 million members. Both, selection conditions and bivalent ligand display had a crucial impact on the success of cell‐based selections.