Development of Specific and Potent α-Helical Inhibitors and Probes of Cysteine Proteases

Cysteine proteases are of great scientific and pharmaceutical interest due to their diverse roles in cellular processes and diseases. However, it has been difficult to design inhibitors for use in determining their individual roles due to the conserved active site. Interestingly, each protease has an endogenous inhibitor that forms an α-helix at the prime side of the active site. We developed a new method for stabilizing α-helices using natural amino acids that allowed us to make small peptides into α-helical inhibitors. We were then able to use structure based design to turn these α-helices into specific inhibitors and probes for use in understanding the proteases\u27 roles in various diseases and cell processes. The use of α-helices has further implications as a new method of creating investigative tools for understanding proteases. new method of creating investigative tools for understanding proteases

Thioamide-Based Fluorescent Protease Sensors

Thioamide quenchers can be paired with compact fluorophores to design “turn-on” fluorescent protease substrates. We have used this method to study a variety of serine-, cysteine-, carboxyl-, and metallo-proteases, including trypsin, chymotrypsin, pepsin, thermolysin, papain, and calpain. Since thioamides quench some fluorophores red-shifted from those naturally occurring in proteins, this technique can be used for real time monitoring of protease activity in crude preparations of virtually any protease. We demonstrate the value of this method in three model applications: (1) characterization of papain enzyme kinetics using rapid-mixing experiments, (2) selective monitoring of cleavage at a single site in a peptide with multiple proteolytic sites, and (3) analysis of the specificity of an inhibitor of calpain in cell lysates

Development of α‑Helical Calpain Probes by Mimicking a Natural Protein–Protein Interaction

We have designed a highly specific inhibitor of calpain by mimicking a natural protein–protein interaction between calpain and its endogenous inhibitor calpastatin. To enable this goal we established a new method of stabilizing an α-helix in a small peptide by screening 24 commercially available cross-linkers for successful cysteine alkylation in a model peptide sequence. The effects of cross-linking on the α-helicity of selected peptides were examined by CD and NMR spectroscopy, and revealed structurally rigid cross-linkers to be the best at stabilizing α-helices. We applied this strategy to the design of inhibitors of calpain that are based on calpastatin, an intrinsically unstable polypeptide that becomes structured upon binding to the enzyme. A two-turn α-helix that binds proximal to the active site cleft was stabilized, resulting in a potent and selective inhibitor for calpain. We further expanded the utility of this inhibitor by developing irreversible calpain family activity-based probes (ABPs), which retained the specificity of the stabilized helical inhibitor. We believe the inhibitor and ABPs will be useful for future investigation of calpains, while the cross-linking technique will enable exploration of other protein–protein interactions

Development of α-Helical Calpain Probes by Mimicking a Natural Protein–Protein Interaction

We have designed a highly specific inhibitor of calpain by mimicking a natural protein-protein interaction between calpain and its endogenous inhibitor calpastatin. To enable this goal we established a new method of stabilizing an α-helix in a small peptide by screening twenty-four commercially available crosslinkers for successful cysteine alkylation in a model peptide sequence. The effects of crosslinking on the α-helicity of selected peptides were examined by CD and NMR spectroscopy, and revealed structurally rigid crosslinkers to be the best at stabilizing α-helices. We applied this strategy to the design of inhibitors of calpain that are based on calpastatin, an intrinsically unstable polypeptide that becomes structured upon binding to the enzyme. A two-turn α-helix that binds proximal to the active site cleft was stabilized, resulting in a potent and selective inhibitor for calpain. We further expanded the utility of this inhibitor by developing irreversible calpain family activity-based probes (ABPs), which retained the specificity of the stabilized helical inhibitor. We believe the inhibitor and ABPs and will be useful for future investigation of calpains, while the crosslinking technique will enable exploration of other protein-protein interactions