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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Structural basis for the mechanisms of human presequence protease conformational switch and substrate recognition
Nature Communications Open Access 05 April 2022
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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.
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.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Tables 1–9, Supplementary Figures 1–6
Supplementary animation generated using PyMOL (1,000 frames).
Supplementary data deposited in PubMed BioAssay (numbers 1259349 and 1259348).
Supplementary reports and data provided by EuroFins (Belgium) that is summarized in Supplementary Table 6.
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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