Dual-display of small molecules enables the discovery of ligand pairs and facilitates affinity maturation

• Published in: Nature chemistry Vol. 7; no. 3; pp. 241 - 249
• Main Authors: Wichert, Moreno, Krall, Nikolaus, Decurtins, Willy, Franzini, Raphael M., Pretto, Francesca, Schneider, Petra, Neri, Dario, Scheuermann, Jörg
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.03.2015; Nature Publishing Group
• Subjects: 639/638/309/2132; 639/638/309/2144; 639/638/403/932; 639/638/92/605; Analytical Chemistry; Animals; Biochemistry; Carbonic Anhydrases - chemistry; Chemistry; Chemistry/Food Science; Deoxyribonucleic acid; DNA; DNA - chemistry; Drug Discovery; Horseradish Peroxidase - chemistry; Inorganic Chemistry; Ligands; Mice; Mice, Inbred BALB C; Mice, Nude; Nucleic Acid Hybridization; Organic Chemistry; Orosomucoid - chemistry; Physical Chemistry; Small Molecule Libraries; Streptavidin - chemistry
• ISSN: 1755-4330; 1755-4349
• DOI: 10.1038/nchem.2158

In contrast to standard fragment-based drug discovery approaches, dual-display DNA-encoded chemical libraries have the potential to identify fragment pairs that bind simultaneously and benefit from the chelate effect. However, the technology has been limited by the difficulty in unambiguously decoding the ligand pairs from large combinatorial libraries. Here we report a strategy that overcomes this limitation and enables the efficient identification of ligand pairs that bind to a target protein. Small organic molecules were conjugated to the 5′ and 3′ ends of complementary DNA strands that contain a unique identifying code. DNA hybridization followed by an inter-strand code-transfer created a stable dual-display DNA-encoded chemical library of 111,100 members. Using this approach we report the discovery of a low micromolar binder to alpha-1-acid glycoprotein and the affinity maturation of a ligand to carbonic anhydrase IX, an established marker of renal cell carcinoma. The newly discovered subnanomolar carbonic anhydrase IX binder dramatically improved tumour targeting performance in vivo . A method to identify pairs of ligands that simultaneously bind to a target protein has been developed. The method uses two DNA-encoded chemical sub-libraries that self-assemble to form stable dual-display structures, and an encoding system that can be decoded by DNA sequencing and enables both ligands to be identified.