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Affinity Selections of DNA‐Encoded Chemical Libraries on Carbonic Anhydrase IX‐Expressing Tumor Cells Reveal a Dependence on Ligand Valence
Author(s) -
Oehler Sebastian,
Catalano Marco,
Scapozza Ilario,
Bigatti Martina,
Bassi Gabriele,
Favalli Nicholas,
Mortensen Michael R.,
Samain Florent,
Scheuermann Jörg,
Neri Dario
Publication year - 2021
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.202100816
Subject(s) - carbonic anhydrase , dna , acetazolamide , chemical library , chemistry , ligand (biochemistry) , carbonic anhydrase ii , computational biology , tumor cells , biochemistry , microbiology and biotechnology , combinatorial chemistry , biology , small molecule , enzyme , cancer research , physiology , receptor
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.