Intracellular proteins (e.g. phosphorylated through signaling pathways or misfolded) are targeted for degradation by a covalently bound ubiquitin tag [2]. Ubiquitylation is catalyzed by a multi-enzymatic system consisting of E1 (ubiquitin-activating enzyme), E2 (conjugating) and E3 (ligases). The 26S proteasome is an ATP-dependent protease complex comprised of a 20S catalytic core (organized into four stacked rings of seven subunits each, i.e. α₇β₇β₇α₇) and two 19S regulatory caps. 19S caps are responsible for recognition of ubiquitinylated proteins (lid) and also contain ATPase activity (base) required for linearization of large proteins facilitating their entry in the catalytic core. Three β-subunits (β1, β2, β5) are responsible for the different enzymatic activities of the proteasome and are differentially inhibited by small molecule inhibitors such as bortezomib and salinosporamide A. Figure adapted from reference [42].

Electrophilic functional groups are depicted in red. See text for further discussion.

Close-up view of bortezomib [33] (a) and salinosporamide A [34] (b) bound to Thr1 in the β5 active site of yeast 20S proteasome (PDB codes 2F16 and 2FAK, respectively). Hydrogen bonds are depicted as orange dashes and waters as red dots. (c, d) Surface representation showing the same view for each inhibitor as well as occupancy in specificity pockets S1, S2 and S3. (e) Reversible inhibitory mechanism of bortezomib is dictated by the boronic acid group [43]. (f) Chlorine is key for irreversible binding of salinosporamide A [34]. Figure panels a-d were generated with PyMol [44].