Enabling Protein Degradation Drug Discovery

The Ubiquitin System

The critical role that the ubiquitin cascade plays in cellular signalling, coupled with increasing validation of the therapeutic potential of targets in this pathway, is accelerating interest in this field among both academic and industry researchers.  Ubiquigent is helping to lead the way with cutting edge Drug Discovery Screening  PlatformResearch Toolsand Chemistry that enable investigators to advance their understanding of ubiquitin’s fundamental and underlying biochemistry, as well as accelerating drug discovery in this arena.

Ubiquitin System Diagram


Ubiquitylation, like phosphorylation, describes a reversible post-translational protein modification. Ubiquitylation or ‘ubiquitination’ may control the protein substrate’s destiny – in respect of its turnover – or its signalling functionality.  It is a process that refers to the covalent attachment of a small, 76 amino acid protein called ubiquitin to the epsilon-amino group of a lysine residue residing within a substrate protein – which may also be another ubiquitin molecule.  This results in either mono- or poly-ubiquitylation of the substrate; the latter being where chains of ubiquitin are attached to the substrate protein.  The structure of the chain determines whether a protein modulates a specific signalling cascade or becomes degraded in a proteasomal or lysosomal dependent manner.  Mono-ubiquitylated proteins may be further ubiquitylated to form polyubiquitin chains, and deubiquitylases may act on either mono-ubiquitylated or poly-ubiquitylated substrates to remove the ubiquitin monomers or chains, respectively.

The enzymes of the ubiquitylation pathway play a pivotal role in a number of cellular processes including, but not exclusively, the targeted proteasome-dependent degradation of substrate proteins.  Three classes of enzymes are involved in the process of substrate ubiquitylation; activating enzymes (E1s)conjugating enzymes (E2s) and ligases (E3s).  Ubiquitylation of substrate proteins depends on the sequential action of these three enzymes.  In an ATP-dependent first step, an E1 enzyme forms a thioester linkage with ubiquitin which is then transferred to the sulphydryl group of the active-site cysteine on an E2 enzyme forming a ubiquitin-thioester intermediate.  An E3 then acts as an adaptor to bind both substrate protein and E2 ‘loaded’ with ubiquitin.  The E3 facilitates isopeptide bond formation between ubiquitin and the substrate protein.

Although still a post-translational modification, albeit involving a functional protein rather than a functional group, ubiquitylation is a much more complex process than phosphorylation.  This is mainly due to the ability of ubiquitin to form polyubiquitin chains of a variety of different linkage types and complexity, but also because there are further related ubiquitin-like (Ubl) proteins (including SUMO, NEDD8, ISG15, and FAT10) that despite following a similar specific enzymatic cascade, may result in different outcomes for the Ubl-modified target substrate.  In a further level of system complexity, modifications of either the E3 ligase or the substrate may alter their ability to modify substrates or themselves be modified; for example by NEDDylation (NEDD8 being a further Ubl) in the case of E3 ligases or phosphorylation in the case of both E3 ligases and substrates.