Special Chemical Biology Seminar
Enzymes that act on multiple substrates pose unique challenges as therapeutic targets. The zinc-metalloprotease IDE modulates blood glucose levels by cleaving insulin. However, IDE also degrades glucagon, a peptide hormone that undesirably elevates blood glucose and opposes the effects of insulin. In prior work, we uncovered the opposing phenotypes of IDE's hormone substrates in lean and diet-induced obese mice using the first physiologically active IDE inhibitor derived from a DNA-encoded library of macrocycles. Therefore, to unlock the therapeutic benefits of IDE inhibition will require preferentially blocking insulin degradation, but not glucagon, in contrast to the conventional mode of inhibition of the vast majority of enzyme ligands discovered to-date. We performed a high-throughput screen for non-active-site IDE ligands and we report the discovery of the first potent (EC50 < 1 nM) and highly specific substrate-selective inhibitors (SSI), which alter IDE's substrate-binding preference without blocking its zinc-dependent catalytic mechanism. X‑ray co-crystallography elucidated the molecular basis of substrate-selective inhibition and the exquisite specificity for IDE inhibition over >25 metalloproteases tested. The X-ray structure of the ternary complex IDE:glucagon:SSI reveals the ligands bind in a substrate-engagement site (exosite) distal to the catalytic core of IDE without inducing allosteric conformational changes on the protein structure. The SSI exosite ligands generate steric clashes that exclude insulin from the substrate-binding cavity, but allow the binding and proteolytic cleavage of glucagon even at saturating SSI concentrations. These findings provide a path forward for developing IDE-targeting therapeutics, and offer a blueprint to unlock the therapeutic potential of other challenging biomedically relevant enzymes by targeting distal exosite pockets.