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

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Abstract

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 (IC50 = 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.

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Fig. 1: DNA-templated macrocycle library synthesis scheme.
Fig. 2: Identification of an orthogonal codon set for second-generation DNA-templated libraries.
Fig. 3: Building blocks for the second-generation DNA-templated macrocycle library.
Fig. 4: Distribution of physical parameters among library members from the second-generation macrocycle library and first-generation library.
Fig. 5: Approaches to the assembly of DNA template libraries.
Fig. 6: In vitro selection of the 256,000-membered DNA-templated macrocycle library for binding to IDE.

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  • 01 October 2019

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Acknowledgements

This paper is dedicated to Hisashi Yamamoto on the occasion of his 75th birthday. This work was supported by US National Institutes of Health (NIH) R35 GM118062, DARPA HR0011-17-2-0049, the Howard Hughes Medical Institute, and the F-Prime Biomedical Research Initiative.

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D.L.U. and D.R.L. designed the research and wrote the manuscript. D.L.U. conducted all the experimental, analytical and computational work for the development and synthesis of the library. Selections and library regeneration were optimized and conducted by D.L.U. and A.I.C. Macrocyclic hits were synthesized and purified by A.I.C. and IDE inhibition assays were conducted by J.P.M. All authors edited the manuscript.

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Correspondence to David R. Liu.

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Usanov, D.L., Chan, A.I., Maianti, J.P. et al. Second-generation DNA-templated macrocycle libraries for the discovery of bioactive small molecules. Nature Chem 10, 704–714 (2018). https://doi.org/10.1038/s41557-018-0033-8

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