Second-generation DNA-templated macrocycle libraries for the discovery of bioactive small molecules

• Published in: Nature chemistry Vol. 10; no. 7; pp. 704 - 714
• Main Authors: Usanov, Dmitry L., Chan, Alix I., Maianti, Juan Pablo, Liu, David R.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.07.2018; Nature Publishing Group
• Subjects: 631/92/2132/605; 639/638/309/507; 639/638/92/2132; Analytical Chemistry; Biochemistry; Biological activity; Chemistry; Chemistry and Materials Science; Chemistry/Food Science; Coding; Codon; Codons; Computation; Computer applications; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA biosynthesis; Enzyme inhibitors; Enzymes; Inorganic Chemistry; Insulin; Insulysin; Macrocyclic Compounds - chemistry; Molecular chains; Organic Chemistry; Physical Chemistry; Physical properties; Production methods; Purification; Small Molecule Libraries - chemistry; Software; Stereochemistry; Stereoisomerism; Templates, Genetic
• ISSN: 1755-4330; 1755-4349; 1755-4349
• DOI: 10.1038/s41557-018-0033-8

DNA-encoded libraries have emerged as a widely used resource for the discovery of bioactive small molecules, and offer substantial advantages compared with conventional small-molecule libraries. Here, we have developed and streamlined multiple fundamental aspects of DNA-encoded and DNA-templated library synthesis methodology, including computational identification and experimental validation of a 20 × 20 × 20 × 80 set of orthogonal codons, chemical and computational tools for enhancing the structural diversity and drug-likeness of library members, a highly efficient polymerase-mediated template library assembly strategy, and library isolation and purification methods. We have integrated these improved methods to produce a second-generation DNA-templated library of 256,000 small-molecule macrocycles with improved drug-like physical properties. In vitro selection of this library for insulin-degrading enzyme affinity resulted in novel insulin-degrading enzyme inhibitors, including one of unusual potency and novel macrocycle stereochemistry (IC 50  = 40 nM). Collectively, these developments enable DNA-templated small-molecule libraries to serve as more powerful, accessible, streamlined and cost-effective tools for bioactive small-molecule discovery. A second-generation DNA-templated library of 256,000 small-molecule macrocycles has been developed. The improved method was created by streamlining and integrating multiple aspects of DNA-encoded and DNA-templated library synthesis methodology. In vitro selection of the macrocycle library against insulin-degrading enzyme enabled the discovery of potent inhibitors.