Design, synthesis and evaluation of cysteine protease inhibitors

Cysteine proteases are important drug targets due to their involvement in many biological processes such as protein turnover, digestion, blood coagulation, apoptosis, cell differentiation, cell signaling, and the immune response. In this thesis, we have reported the design, synthesis and evaluation of clan CA and clan CD cysteine protease inhibitors.;In the first project, we focused on the design, synthesis and evaluation of aza-peptidyl Michael acceptor and epoxide inhibitors for asparaginyl endopeptidases (legumains) from the bloodfluke, Schistosoma mansoni (SmAE) and the hard tick, Ixodes ricinus (IrAE). Structure activity relationships (SARs) were determined for a set of forty one aza-peptide Michael acceptors and eight aza-peptide epoxides. For both enzymes, SARs were similar, but with some notable exceptions. Both enzymes prefer disubstituted amides to monosubstituted amides in the P1' position and potency increased as we increased the hydrophobicity of the inhibitor in this position. Extending the inhibitor to P5 resulted in increased inhibitory potency, especially against IrAE, and both enzymes prefer small over large hydrophobic residues in the P2 position. Aza-peptide Michael acceptor inhibitors are more potent than aza-peptide epoxide inhibitors and, for some of these compounds, second order inhibition rate constants are the fastest yet discovered.;For the second project, we synthesized seventeen aza-peptidyl Michael acceptor and epoxide inhibitors for the parasitic cysteine proteases; cruzain, rhodesain and TbCatB. We have found that monosubstituted amides were favored over disubstituted amides indicating the involvement of the amide hydrogen in a H-bond network. We have shown that aza-peptide epoxides were as potent as Michael acceptors and we have obtained compounds with IC50 values as low as 20 nM.;In the third project, we worked on the synthesis of heterocyclic peptidyl alpha-ketoamides, peptidyl ketones and aza-peptidyl ketones as calpain inhibitors. We have synthesized peptidyl alpha-ketoamides with nucleotide bases in the primed region to create compounds that can cross the blood-brain barrier. Based on the crystal structure obtained with previous heterocyclic peptidyl alpha-ketoamides synthesized by our group, we have improved the potency by introducing a hydrophobic group on the adenine ring. We have obtained compounds with Ki values in the nanomolar range. We have also designed two new classes of inhibitors for calpain; peptidyl aminoketones and aza-peptidyl ketones. Peptidyl aminoketones were less potent than peptidyl alpha-ketoamides but still reasonable inhibitors of calpain that have the potential to cross the BBB. Aza-peptidyl ketones, on the other hand, did not inhibit calpain and cathepsin B.