Figure 1.

Carba- and azadipeptide nitriles and their reaction with cysteine proteases. Isoelectronic CαH/N exchange in the warhead (cyan/magenta) of dipeptide nitriles (left) leads to azadipeptide nitriles (right). Two carbohydrazide nitrogens in azanitriles need to be alkylated to circumvent spontaneous heterocyclization.⁶ R¹ and R² are substituents in amino acid residues at the P1 and P2 positions (binding in the enzyme subsites S1 and S2), respectively; PG is a protecting group. The depicted azadipeptide bears an aza-alanine nitrile at the P1 position. Reactive warheads of both chemotypes form a covalent, reversible bond with the thiol of the catalytic cysteine residue (orange) of papain-family cysteine proteases (represented by SmCB1).