PROTACs, full name is Proteolysis-Targeting Chimeras. This technology is a new drug development direction that has emerged in recent years. To put it simply, PROTAC is a heterozygous bi-functional small molecule compound containing two different ligands: one is the ligand of E3 ubiquitin ligase and the other is the ligand that binds to the target protein in the cell. The two ligands are connected by linker to form a "trisome" polymer-the target protein ligand-Linker-E3 ligand.
The development history of PROTAC
In 2001, the team of Professor Craig M. Crews of Yale University and Professor Raymond J. Deshaies of California Institute of Technology first proposed the concept of PROTAC and reported the first PROTAC molecule-Protac-1 after a series of proof of concept.
The structure of Protac-1
In 2004, the polypeptide PROTAC based on Von Hippel Lindau (VHL) E3 ubiquitin ligase was reported for the first time.
In 2008, the team of Professor Craig M. Crews of Yale University synthesized the small molecule PROTAC containing nutlins for the first time and successfully recruited AR onto mouse double minute 2 (MDM2). And acts as an E3 ubiquitin ligase to trigger its ubiquitination and proteasome degradation.
In 2010, the first cIAP-based small molecule PROTAC was reported.
In 2013, Crews founded the first pharmaceutical company focused on PROTAC.
In 2015, PROTAC with nanomolar degradation activity based on VHL and CRBN was discovered.
In March 2019, Arvinas announced that its first AR degradant ARV-110 for the treatment of prostate cancer entered phase I clinical trials (NCT03888612). ARV-110 is the first PROTAC molecule publicly reported to enter Phase I clinical trials, marking a new stage in the research of PROTAC technology.
The structure of ARV-110
On October 23, 2019, Arvinas announced the initial results of phase I clinical trials of ARV-110 and ARV-471: Oral PROTAC is safe and tolerated in cancer patients.
The structure of ARV-471
The advantages of PROTAC
As Arivinas announced the positive initial phase 1 clinical results of two oral PROTAC molecules, ARV-110 (AR) and ARV-471 (ER), the prospects for PROTAC are very good. Compared with small molecule inhibitors, it shows great potential in the following aspects.
PROTAC is expected to slow down the occurrence of resistance to small molecule inhibitors. PROATC can quickly bind to the target protein and induce its degradation at a lower concentration, which is of positive significance for overcoming the drug resistance caused by the target protein itself.
PROATC is expected to degrade the target protein that was not druggable, and then develop corresponding drugs. For example, signal transducer and activator of transcription 3 (STAT3) is a key factor in cell survival, proliferation, angiogenesis, metastasis and chemotherapy resistance. However, there is no obvious direct action pocket in the structure of STAT3, which directly blocks the development of STAT3 inhibitors, and no effective drugs have appeared yet. However, professor Wang Shaomeng’s team has developed a STAT3 degrading agent, and it has shown good effects both in vivo and in vitro.
PROTAC can affect protease activity and non-enzymatic activity by degrading the entire kinase. For example, focal adhesion kinase (FAK) provides a scaffold for a variety of signal proteins and plays a vital role in the process of tumor invasion and metastasis.
The challenges of PROTAC technology
What appears to be a straightforward mechanism of action is not so simple in practice. Like all emerging technologies, PROTAC technology also has some challenges. This article "The PROTAC gold rush" published on Nature-Biotechnology pointed out that being able to "pull" E3 ligase to the vicinity of the target protein does not guarantee that the latter can be degraded. In practice, a stable ternary structure needs to be formed between the different molecules and ubiquitin can be carried out smoothly. In addition, even if proteins are successfully ubiquitinated, it does not mean that they will be degraded smoothly.
The mechanism of PROTAC Technology (Image source: Reference )
Another challenge in the development of PROTAC molecules is to ensure the orally bioavailable of this class of drugs. Professor Wang Shaomeng, a protein degradation expert at the University of Michigan in the United States, pointed out in the article that the molecular weight of PROTAC molecules is about 0.7 to 1.1 kDa, which has a larger surface polar area than traditional small molecules. These will affect the penetration of molecules. And compared with mouse models, the oral bioavailability of these molecules in humans is lower. The mouse model cannot be used to predict the results in humans, which further increases the complexity of new drug discovery.
In addition, it is also pointed out in the article that a bottleneck in the development of PROTAC molecules is the selection of E3 ligase. In humans, there are about 600 different E3 ligases. But most companies that are developing oral protein degrading agent focus on the Cereblon-based E3 ligase system. On the one hand, this is because the relevant research has been relatively proficient, and the related molecules are smaller, more flexible, and more medicable; on the other hand, it is also because some of the other options are collectively more complex and prone to unintended consequences. This is certainly a viable pioneering strategy at the moment. But in the long term, we need to find targets beyond Cereblon -- in certain tissues, other E3 ligases may be more active.
The article also mentioned some other challenges of PROTAC technology. For example, the types of proteins that can be degraded are relatively limited. For membrane proteins that are less exposed to the cytoplasm, it may be difficult to find binding sites, and it is also difficult to add the ubiquitin label. In addition, if a protein has many repetitive sequences or polymerizes, it will also make drug design difficult. Of course, like other drug molecules, new drug developers also need to limit its potential toxicity and off-target effects.
PROTAC and other protein degradation technology
Of course, drug developers are well aware of these challenges and are trying to find solutions. If these bottlenecks can be overcome, PROTAC will undoubtedly unleash greater potential. Compared with traditional protein inhibitors, the protein degradation technology represented by PROTAC does not just inactivate the target protein. In many cases, proteins act as structural scaffolds in addition to their own biochemical functions. In this regard, protein degradation therapy has a unique advantage. And theoretically, molecules such as PROTAC can detach from the target protein after it has been degraded, binding to more targets. As a result, the doses used are expected to be lower. Of course, this advantage of the PROTAC molecule has not been fully demonstrated in some clinical trials so far, but it is expected to become a reality in the future.
We also need to understand that PROTAC is not the only technology for protein degradation. As mentioned in that article, many companies are currently developing a type of protein degradation technology called "molecular glue". Unlike PROTAC molecules, molecular glue only binds E3 ligase to change the shape of its surface, thereby recruiting target proteins and completing protein degradation. Lenalidomide developed by Celgene can be regarded as the prototype of molecular glue, which can activate cereblon protein, degrade Ikaros and Aiolos transcription factors, and treat multiple myeloma.
Unlike traditional new drug development, the development of molecular glues is a bit upstream-it is difficult to select a disease-related target first, and then proceed with drug development. On the contrary, it often screens molecules that can bind to E3 ligase until it obtains the desired properties, and then uses it for large-scale screening of protein databases to find protein targets that can be degraded.
As an emerging technology, PROTAC greatly expands the possibility of target selection for human drug development in the future. We also look forward to the progress of science and the development of technology, protein degradation therapy can achieve more breakthrough achievements, and benefit the patients as soon as possible!
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 Garber, K. The PROTAC gold rush. Nat Biotechnol (2021).
 PROTACs VS. Tranditional Small Molecule Inhibitors
 Focus On PROTAC: Summary Of Targets From 2001 To 2019
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 PROTACs and Targeted Protein Degradation