Dipeptide-Derived Alkynes as Potent and Selective Irreversible Inhibitors of Cysteine Cathepsins

The potential of
designing irreversible alkyne-based inhibitors
of cysteine cathepsins by isoelectronic replacement in reversibly
acting potent peptide nitriles was explored. The synthesis of the
dipeptide alkynes was developed with special emphasis on stereochemically
homogeneous products obtained in the Gilbert–Seyferth homologation
for CC bond formation. Twenty-three dipeptide alkynes and
12 analogous nitriles were synthesized and investigated for their
inhibition of cathepsins B, L, S, and K. Numerous combinations of
residues at positions P1 and P2 as well as terminal acyl groups allowed
for the derivation of extensive structure–activity relationships,
which were rationalized by computational covalent docking for selected
examples. The determined inactivation constants of the alkynes at
the target enzymes span a range of >3 orders of magnitude (3–10 133
M–1 s–1). Notably, the selectivity
profiles of alkynes do not necessarily reflect those of the nitriles.
Inhibitory activity at the cellular level was demonstrated for selected
compounds.