Compound 11g showed an intermittent interaction (cluster 1, Figure ) of the chromane carbonyl group with the Gly68 NH (~25%). However, in cluster 2 (Figure ), a rotation of the chromane ring led to the occupation of this moiety in the S3 pocket, and leucine at P2 position is oriented towards the S2 subsite. In the case of 11g, the S2 pocket is accommodated by a much smaller moiety in comparison with XU3 (Figures ). Both inhibitors share the nitrile warhead, but XU3 is a less potent CatL inhibitor (IC50 = 160 nM). 2.6. Glutathione stability. To determine the innate reactivity of inhibitors with electrophilic warheads towards thiols under physiological conditions, we tested the stability of three selected compounds, i.e., the peptide nitriles 11b and 11e and the peptide aldehyde 9b, in the presence of excess glutathione (GSH) as a physiological nucleophile (Figure ). These investigations demonstrated the low inherent reactivity of the inhibitors, which were stable under assay conditions (5 mM GSH, pH 7.4). Hence, the specific reactivity towards cathepsins is caused by the formation of the inhibitor-target complex and supported by tailored non-covalent interactions.