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Substrate-selective inhibitors that reprogram the activity of insulin-degrading enzyme

Nature Chemical Biology volume 15, pages 565–574 (2019)Cite this article

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Abstract

Enzymes that act on multiple substrates are common in biology but pose unique challenges as therapeutic targets. The metalloprotease insulin-degrading enzyme (IDE) modulates blood glucose levels by cleaving insulin, a hormone that promotes glucose clearance. However, IDE also degrades glucagon, a hormone that elevates glucose levels and opposes the effect of insulin. IDE inhibitors to treat diabetes, therefore, should prevent IDE-mediated insulin degradation, but not glucagon degradation, in contrast with traditional modes of enzyme inhibition. Using a high-throughput screen for non-active-site ligands, we discovered potent and highly specific small-molecule inhibitors that alter IDE’s substrate selectivity. X-ray co-crystal structures, including an IDE-ligand-glucagon ternary complex, revealed substrate-dependent interactions that enable these inhibitors to potently block insulin binding while allowing glucagon cleavage, even at saturating inhibitor concentrations. These findings suggest a path for developing IDE-targeting therapeutics, and offer a blueprint for modulating other enzymes in a substrate-selective manner to unlock their therapeutic potential.

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Fig. 1: High-throughput screen for IDE exo-site ligands and discovery of substrate-selective IDE inhibitors.
Fig. 2: Structure-activity relationships and potency optimization of substrate-selective IDE inhibitors.
Fig. 3: Concentration-dependent substrate discrimination and metalloprotease specificity of potent substrate-selective IDE inhibitors.
Fig. 4: Structural basis for substrate-selective small-molecule inhibition of IDE.
Fig. 5: SSIs reprogram IDE’s substrate binding without inducing conformational changes or allosteric effects on the catalytic site.

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Data availability

Complete results of the IDE high-throughput screens and the IDE inhibition counter-screen are available in the PubChem BioAssay database (1259348, 1259349), the IDE–37, IDE–63 and the IDE–63–glucagon X-ray structures are available in the PDB (PDB IDs 6BYZ, 6MQ3 and 6EDS, respectively).

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Acknowledgements

We thank A. Saghatelian, S. Schreiber and M. Morningstar for helpful discussions. We are grateful to S. Trauger and J. Wang for mass spectrometry assistance. We thank J. Bittker, M. Wawer and V. Dancik for assistance with library management and analysis. We thank Z. Foda and A. Lyczek for ligand docking studies and D. Dobrovolsky for assistance with assays. We thank S.-L. Zheng for small-molecule structural determination. IDE X-ray diffraction data were collected at ALS (operated by LBNL) and NSLS2 (operated by BNL) on behalf of DOE and this is supported by DOE Office of Biological and Environmental Research (KP1605010) and NIH (R01GM105404, S10OD018483, P41GM111244). This research was supported by the NIH grant nos. R35 GM118062 (to D.R.L.), R01 EB022376 (to D.R.L.), R35 GM119437 (to M.A.S.), R56 DK106200 (to M.A.S.) and the Howard Hughes Medical Institute (to D.R.L.). The Fonds de Recherche en Santé du Québec and Alfred Bader Fund provided fellowship support to J.P.M.

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Author notes

  1. These authors contributed equally: Juan Pablo Maianti, Grace A. Tan.

Authors and Affiliations

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

    Juan Pablo Maianti & David R. Liu

  2. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA

    Juan Pablo Maianti & David R. Liu

  3. Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA

    Juan Pablo Maianti & David R. Liu

  4. Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Juan Pablo Maianti, Amedeo Vetere, Bridget K. Wagner & David R. Liu

  5. Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA

    Grace A. Tan, Amie J. Welsh & Markus A. Seeliger

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Contributions

J.P.M. designed the exo-site screen, expressed proteins, synthesized the SSIs and ran biochemistry assays. G.A.T. co-crystallized and solved the IDE X-ray structures with A.J.W.’s assistance. A.V. optimized screen analysis. B.K.W. supervised the screen. M.A.S. and D.R.L. supervised the research program. All authors contributed to the writing of the manuscript.

Corresponding authors

Correspondence to Markus A. Seeliger or David R. Liu.

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Competing interests

J.P.M. and D.R.L. are co-inventors on patents and patent applications based on this work, and are co-founders of Exo Therapeutics, a small-molecule drug discovery company.

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Supplementary information

Supplementary Information

Supplementary Tables 1–9, Supplementary Figures 1–6

Reporting Summary

Supplementary Note

Synthetic protocols

Supplementary Video

Supplementary animation generated using PyMOL (1,000 frames).

Supplementary Data Set 1

Supplementary data deposited in PubMed BioAssay (numbers 1259349 and 1259348).

Supplementary Data Set 2

Supplementary reports and data provided by EuroFins (Belgium) that is summarized in Supplementary Table 6.

Supplementary Data Set 3

Nuclear Magnetic Resonance spectra (1H-, 13C-, and 19F-NMR).

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Maianti, J.P., Tan, G.A., Vetere, A. et al. Substrate-selective inhibitors that reprogram the activity of insulin-degrading enzyme. Nat Chem Biol 15, 565–574 (2019). https://doi.org/10.1038/s41589-019-0271-0

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