Molecule of the Month: PROTACs and Molecular Glue Degraders

In our cells, proteins are constantly being synthesized in order to carry out the multitude of tasks needed to maintain life. When proteins are damaged, misfolded, or no longer needed, they are degraded and their amino acids recycled. Protein degradation is largely carried out by the ubiquitin-proteasome system, in which proteins are tagged for destruction with a covalently attached chain of ubiquitin molecules. The proteasome recognizes the ubiquitin chain and breaks down the tagged protein into short peptide fragments.

Protein ubiquitination is a carefully regulated multistep process. First, E1 enzymes activate ubiquitin and pass them to E2 enzymes. E3 ubiquitin ligases then bring together the ubiquitin-loaded E2 enzyme and the target protein, enabling the target protein to be ubiquitinated and marked for destruction by the proteasome. Discovery of this pathway, which was awarded the 2004 Nobel Prize in Chemistry, has given rise to a new class of therapeutics that aim to selectively destroy disease-causing proteins.

One of the most significant breakthroughs in this field began with a tragedy. In the late 1950s and early 1960s, a drug called thalidomide was widely prescribed to treat morning sickness in pregnant women. It was only after thousands of children globally were born with birth defects, particularly in limb development, that thalidomide was recognized as a potent human teratogen. Despite its notoriety, thalidomide continued to be prescribed in limited cases as a sedative, leading researchers to find that thalidomide and its derivatives were remarkably effective at treating specific diseases, including leprosy and multiple myeloma. It wasn't until 2010, however, that thalidomide's mechanism of action was understood.

Thalidomide works by binding to a protein called cereblon, which is part of an E3 ubiquitin ligase complex. In normal cells, the cereblon E3 ligase (CRBN) targets proteins with C-terminal cyclic imide modifications that result from protein damage or enzymatic processing. When bound to thalidomide, however, CRBN is redirected to ubiquitinate a completely different subset of proteins, including the zinc finger transcription factors Ikaros (IKZF1) and Aiolos (IKZF3). The destruction of these new targets is responsible for both the teratogenic and therapeutic activities of thalidomide.

Thalidomide and its analogs, including lenalidomide and pomalidomide, are the first members of a class of drugs now known as molecular glue degraders. Generally, these drugs act by binding tightly to the substrate-binding domain of an E3 ligase, which both blocks binding of the normal substrates and presents an altered binding interface that can recognize new substrates. On the right, the cereblon E3 ligase (blue) is shown bound to the thalidomide analog pomalidomide (orange) and the transcription factor Ikaros, shown in pink (pdb_00006h0f and pdb_00004a0k).

The finding that a small molecule could effectively “reprogram” the cell’s disposal system has opened new horizons for drug discovery. Today, more than 20 molecular glue degraders are in clinical trials, with several reaching Stage III for the treatment of cancers including multiple myeloma and B-cell lymphoma.

While molecular glue degraders can be effective drugs, it has proven difficult to rationally design these small molecules to target a specific protein of interest. First proposed in 2001, PROTACs (short for PROteolysis TArgeting Chimeras) utilize a far more design-friendly approach. PROTACs are created as two-headed molecules, with one end binding specifically to a target protein of interest, and the other end binding to an E3 ubiquitin ligase. A short linker connecting the two. By tethering a target protein to an E3 ligase, PROTACs can direct its ubiquitination and subsequent degradation.

Early versions of PROTACs were protein-based, using short peptide sequences to recruit both the E3 ligases and target protein. Currently, PROTACs are largely designed using small molecule ligands connected by a chemical linker. For example, the PROTAC MZ1 (shown in yellow In the illustration on the left) targets both BRD4, a transcriptional regulator that plays a role in some cancers and immune-mediated diseases (shown in pink), and the Von Hippel-Lindau E3 ligase (shown in blue; pdb_00005t35 and pdb_00005n4w).

The “plug-and-play” design makes PROTACs highly adaptable to a large range of potential therapeutic targets. There are currently over 50 PROTACs currently in clinical trials worldwide, including several in phase III trials targeting breast and prostate cancers.