Final answer:
Cysteine proteases are enzymes with a nucleophilic cysteine in their active sites that cleave after aspartic acids. They are targeted by protease inhibitors like vinyl sulfones, which covalently bind the active site cysteine.
Step-by-step explanation:
Proteases in the cysteine protease family contain a nucleophilic cysteine in their active sites and they cleave after aspartic acids in the target proteins. Cysteine proteases utilize a thiol group in the side chain of cysteine to perform a nucleophilic attack on the peptide bond, leading to cleavage of the substrate protein. These enzymes are classified based on their active site constituents and mechanism of action, with cysteine proteases being one of several families, which also include serine proteases and metalloproteases. Protease inhibitors, such as peptidyl Michael acceptor inhibitors, have been designed to target these enzymes by forming covalent bonds with the nucleophilic cysteine in the active site. For example, vinyl sulfones and α,β-unsaturated carbonyl derivatives have been developed as potent inhibitors of a variety of cysteine proteases. The specificity and covalent bonding nature of these inhibitors make them attractive candidates for therapeutic applications, including for diseases like malaria, where cysteine proteases like falcipain-2 and -3 play a critical role.