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

Nature Chemistryvolume 10pages704714 (2018) | Download Citation

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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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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Affiliations

  1. Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    • Dmitry L. Usanov
    • , Alix I. Chan
    • , Juan Pablo Maianti
    •  & David R. Liu
  2. Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA

    • Dmitry L. Usanov
    • , Alix I. Chan
    • , Juan Pablo Maianti
    •  & David R. Liu
  3. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA

    • Dmitry L. Usanov
    • , Alix I. Chan
    • , Juan Pablo Maianti
    •  & David R. Liu

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Contributions

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.

Competing interests

The authors are inventors on patents and patent applications describing DTS methods and applications.

Corresponding author

Correspondence to David R. Liu.

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https://doi.org/10.1038/s41557-018-0033-8