2.5. Molecular modeling of potent inhibitors with cathepsin L. Using molecular modeling, we proposed a binding mode for 9b and 11g as representatives of the peptide aldehydes and peptide nitriles investigated in this study. For this purpose, covalent docking was applied to generate the inhibitor-protein complex with the initial conformation of the inhibitor, followed by molecular dynamics simulations to corroborate the proposed interactions. We also performed simulations to compare the binding mode of our CatL inhibitors with that of the cocrystallized inhibitor XU3 (PDB ID: 2XU3). Peptide aldehydes form reversible-covalent complexes with cysteine proteases with a tetrahedral geometry of the resulting hemithioacetals with an sp 3 hybridization. Hence, they act as transition state analogs. Peptide nitriles generate a covalent linkage with cysteine proteases adopting a trigonal geometry of the thioimidate moiety possessing an sp 2 hybridization, which rather resembles the acyl enzyme intermediate. The XU3 inhibitor is a peptide nitrile that forms a covalent thioimidate connection with the active site cysteine of CatL. Simulations of the CatL-XU3 complex (Figure ) recapitulated the hydrogen bond interactions of the inhibitor with the backbone CO of Asp162 (in the S1 subsite, 95% of the analyzed trajectory) and the backbone NH of Gly68 (in the S3 subsite, with a frequency of ~80%), as well as multiple hydrophobic contacts with the S2 and S3 pockets. The new inhibitors 9b and 11g were also proposed to covalently bind to the catalytic Cys25 residue (Figure ) in the S1 pocket. The hemithioacetal and thioimidate adducts, respectively, were stabilized by the oxyanion hole of the protease. The inhibitors also formed hydrogen bonds to the backbone carbonyl oxygen of Asp162 (>85% of the analyzed trajectory). Figure illustrates the major representative cluster of 9b-CatL complexes. The indole-2-carbonyl moiety of 9b was engaged in hydrogen bonding to both the CO and NH moiety of Gly68 (~80% of the analyzed trajectory). Additional hydrogen bond interactions are predicted to take place between the two NH groups of the ligand and the Asp162 backbone CO (>85%). We hypothesize that this binding mode enables 9b to be in a position that allows the covalent bond to be formed.