Protein degraders are enzymes that disassemble and break down unneeded proteins. These enzymes are naturally existing in cells but can also be exploited and engineered in biotechnology to target specific proteins to degrade, thus, shedding light on a list of drug candidates.
Protein degradation pathway in cells
Eukaryotic cells have an intracellular protein degradation machinery called the ubiquitin-proteasome system. This system ensures the turnover of proteins in the cell and provides a regulated mechanism of quality control and the ability to respond to environmental stimuli.
Ubiquitin is activated by the ubiquitin-activating enzyme and is then transferred and tagged onto the N-terminus of unwanted or damaged proteins by ubiquitin ligases.
Once a protein is tagged, it serves as a signal to other ligases to attach more ubiquitin molecules. The chain of ubiquitin is then recognized by the proteasome, a protein complex that degrades proteins, and tagged proteins are degraded by peptide bond cleavage by the proteasome.
In the pharmaceutical industry, drugs are usually designed to inhibit the active site of a target protein. However, developing small-molecule inhibitors with biomedical relevance and multiple targets is still a challenge.
Targeted protein degradation with small molecule drugs could be a new therapeutic advance that allows the complete removal of a target protein and its associated functions contributing to disease onset. In particular, E3 ubiquitin ligases are unique in their role in dictating target specificity. This proposes a new set of drugs called proteolysis-targeting chimeras (PROTACs).
Proteolysis-targeting chimeras (PROTACs)
PROTACs are a group of potential drugs that artificially recruit an E3 ligase to redirect protein degradation. Nearly 20 years ago, the first PROTAC was developed. It is a chimeric molecule comprising of a ligand that binds to the target site of the protein to be degraded, linked to a ligand that binds to E3 ligase BTRC.
It acts as a “bridge” between the target protein and the E3 ligase and brings them together to proximity. This was shown to promote the degradation of the target protein. This served as a proof of principle and shortly after, various PROTACs are being developed.
PROTACs are also shown to be widely distributed to various organs and tissues, and PROTACs directed to target oncogenic proteins can induce tumor regression. Excitingly, PROTACs can also cross the blood-brain-barrier and have entered clinical trials to target the Tau protein contributing to the pathogenesis of Alzheimer's Disease.
In addition, a PROTAC named ARV-110 has entered a phase I trial in prostate cancer; one end of ARV-110 binds to an androgen receptor and the other end to an E3 ligase. The same principle can also be applied to breast cancer where the PROTAC targets the estrogen receptor.
Subtle changes in the PROTAC design can have great effects on protein degrading potency. Indeed, fewer than 10 of the more than 600 E3 ubiquitin ligases have so far been explored. The spatial co-localization of the target protein and the ligase has to be studied in detail to ensure the therapeutic efficacy of PROTACs.
Repurposing E3 ligases may also have other detrimental effects such as preventing the ligases to carry out its primary function. For example, VHL is a tumor-suppressive ubiquitin ligase of hypoxia-inducible factor 1 (HIF-1). It remains unknown if VHL-based protein degraders can function without preventing VHL from its tumor-suppressive role, and thus, triggering a series of clinical issues.
Moreover, since PROTACs competes for a ligand-binding spot with the target protein’s natural ligand, at higher ligand concentrations, PROTACs can be outcompeted, resulting in a loss of protein degradation activity.
PROTACs are a relatively new class of drugs and there are numerous potentials to target specific protein degradation. Despite the challenges and potential setbacks, protein degraders are useful tools as an alternative drug to treat diseases.
- Mullard, A. (2019). First targeted protein degrader hits the clinic. Nature Reviews. 06 March 2019.
- Schapira, M., Calabrese, M.F., Bullock, A.N., et al. (2019). Targeted protein degradation: expanding the toolbox. Nat Rev Drug Discov. 18, 949–963. https://doi.org/10.1038/s41573-019-0047-y
- Chamberlain, P.P., Hamann, L.G. (2019). Development of targeted protein degradation therapeutics. Nat Chem Biol. 15, 937–944. https://doi.org/10.1038/s41589-019-0362-y