Enabling Protein Degradation Drug Discovery

The ubiquitin–proteasome system (UPS) targets selected proteins for degradation by the 26S proteasome. The initial steps in this pathway generate proteins that are covalently tagged with a polyubiquitin chain that is then recognized by ubiquitin receptors of the 26S proteasome. This is a large complex composed of a 20S catalytic core particle and two 19S regulatory particles (Kok et al., 1993) that catalyse the final step in the pathway. While the 20S particle comprises a catalytic chamber for protein degradation, collectively the proteins that compose the 19S particle perform several functions that include recognition of ubiquitylated substrates, cleavage of the polyubiquitin chain for ubiquitin recycling, control of access to the 20S proteolytic chamber, and substrate unfolding and subsequent translocation into the 20S core particle for degradation (Boehringer et al., 2012). S5a (Rpn10) is a major ubiquitin binding protein that binds preferentially to polyubiquitin chains. It is found as a subunit of the 26S proteasome, but unlike other proteasome subunits, S5a also exists predominantly as a free protein in the cytosol. S5a contains two stretches of approximately 15 amino acids called the ubiquitin interacting motifs (UIMs), which are responsible for its high affinity for ubiquitin chains (Kim and Goldberg, 2012). One essential feature of the UPS is that the proteasome must have the ability to capture substrates by recognizing their covalently linked polyubiquitin chains. S5a and Rpn13 are two major such subunits of the 19S regulatory particle (RP). The polyubiquitin on a substrate can bind with S5a through its C-terminal UIMs, or with Rpn13 through its N-terminal pleckstrin- like receptor for Ub (Pru) domain. Recently it was proposed that polyubiquitin can bind with S5a and Rpn13 simultaneously (Elangovan et al., 2010). S5a is also itself regulated by ubiquitylation. Monoubiquitylation of S5a has been shown to strongly inhibit the capacity of S5a to interact with substrates, thus decreasing proteasome activity (Isasa et al., 2010). S5a is commonly used as a control substrate because unlike typical substrates of E3 ligases, S5a can be ubiquitylated by all types of E3s tested including the multimeric and monomeric Ring finger E3s (MuRF1, Siah2, Parkin, APC, and SCFTRCP1), the U-box E3, CHIP, and HECT domain E3s (E6AP and Nedd4) when assayed with the Ube2D family of E2 conjugating enzymes (Kim et al., 2009; Uchiki et al., 2009).

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