It took nearly 20 years for PROTAC technology to transform from academia to preclinical and clinical drug development projects. In 2019, PROTAC obtained the clinical proof of concept in oncology for the first time, which has become the focus of researchers.
Recently, Professor Craig M. Crews of Yale University and his partners jointly published an in-depth review on Nature Reviews Drug Discovery, looking forward to four development directions of PROTAC targeted protein degradation technology in the next 20 years. They believe that the field of targeted protein degradation is “ready to go”.
Identify the most suitable target types for protein degradation
The targets of the first clinical phase protein degradants are mature targets that have been clinically proven, such as androgens and estrogen receptors. In view of the success of these targets, protein degradants have been established as a mode of treatment. However, the real potential of this treatment model is to reach the target that are currently difficult to drug or haven’t been drugged at all. Several common features of PROTAC targets include:
- Overexpression, mutation, aggregation, isomer expression or intracellular localization of proteins leading to disease-causing gain of function.
- A binding surface that can be reached by E3 ligase.
- An unstructured region that can enter the proteasome.
Because gene mutations are resistant to conventional targeted therapy, proteins with skeleton function and proteins that are “unavailable” with other treatment modes may also be suitable targets for the use of PROTAC technology.
Although targets suitable for PROTAC protein degradation do not require an enzyme active site, they need a small molecular binding site that can be reached by E3 ligase. The affinity of this site does not need to be particularly high, usually in the range of 1 to 500 nM, and the recruited E3 ligase must be able to reach the surface of the target.
For skeletal proteins, the selection of binding sites is particularly critical, because only part of the surface of the target proteins present in the complex is exposed. For those targets whose surfaces are mostly hidden in the complex, targeting adjacent proteins in the complex is a strategy.
Although the affinity of the ligand that binds to the target protein does not need to be very high, the ligand that binds to E3 ligase should have strong binding force and slow dissociation rate. PROTAC molecules that can covalently bind to E3 ligase can simplify the dynamic changes of assembly of three parts (target, PROTAC molecule and E3 ligase) into two parts (target, PROTAC/E3 ligase complex), which may enhance the catalytic efficiency.
Expand available E3 ligases
At present, most of the first targeted proteolytic drugs in the clinical development stage tend to recruit an E3 ligase named CRBN. A noteworthy exception is DT2216, a BCL-XL degrader developed by Dialectic Therapeutics, which recruited an E3 ligase named VHL. However, the potential to target protein degradation has led to the exploration of new E3 ligases in both academia and medicine. There are more than 600 E3 ligases in the human body, and the review points out that the current question is when targeted proteolysis therapy based on the new E3 ligase will benefit patients and for what diseases they will be used, rather than whether they will appear.
Treatment of diseases other than oncology
At present, the approved protein degradation drugs (doxamine drugs) and most of the newly developed clinical PROTAC molecules and molecular glue compounds are used to treat different types of cancer. However, the scope of targeted protein degradation is expanding beyond oncology.
- Inflammation, immunity and immune oncology
Among the first degradants to enter the clinical development phase, Nurix’s Bruton tyrosine kinase (BTK) inhibitor NX-5948 and Kymera’s IRAK4 degradant (KT-474) will test the application of the PROTAC treatment model in non-cancer diseases. They can be used to treat a variety of immune inflammatory diseases, such as rheumatoid arthritis.
After the success of immune checkpoint inhibitors, the development of small molecular drugs that can stimulate anti-cancer immune response is an important field of drug development. PROTAC molecules can activate immune cells in the mode of small molecular drugs, simulate the effect of PD-1/PD-L1 targeted therapy, and have the potential to become “first-in-class” therapy. Recently, PROTAC molecules targeting MAP4K1 have shown gratifying preclinical activity.
Although small molecular inhibitors may achieve the same goal in this respect, PROTAC molecules may have better tolerance and lower toxicity.
- Neurology and neurodegenerative diseases
One of the key characteristics of PROTAC molecules is its ability to degrade proteins that are not targeted by traditional small molecule inhibitors because there are no active sites. This feature makes proteins accumulated in a variety of neurodegenerative diseases (such as Tau protein, alpha synuclein, Huntington protein mutants). become a potential target.
Tau protein disease (Tauopathies) is a disease field in which small molecular drugs are difficult to target, but PROTAC molecules can make a difference. They include neurological diseases such as Alzheimer’s disease and frontotemporal dementia (FTD). The pathology of these diseases is related to the accumulation of abnormal Tau proteins, and the resulting neurofibrillary tangles can lead to neuronal death.
Alpha synuclein accumulated in patients with Parkinson’s disease is similar to Tau protein and is also a natural disordered protein. Previous studies have reported a peptide-based alpha synuclein degrader that protects neurons from neurotoxicity caused by overexpression of alpha synuclein in experiments.
Antiviral PROTACs
The feasibility of antiviral PROTAC molecule was initially established in the study of degradation of hepatitis C virus (HCV) NS3/4A protease. With the emergence of novel coronavirus, this strategy was also used to target novel coronavirus. Novel coronavirus’s main proteases (Mpro and PLpro) and RNA-dependent RNA polymerase (RdRP) are currently targeted by small molecular inhibitors. They may be potential targets for PROTAC molecules.
Develop and innovate PROTAC model
Innovative PROTAC strategies, including PROTACs based on biological products (bioPROTACs) and heterozygous PROTACs (hybrid PROTACs), may further expand the range of targets that PROTAC can target. PROTACs, a biological product, uses peptides, fusion proteins, and oligonucleotides as ligands for recognition targets. PROTACs based on fusion proteins or peptides has successfully degraded HER2, MYC, KRAS and other cancer-related targets in the study. PROTAC based on oligonucleotides can be used to target transcription factors and RNA binding proteins. In the short term, biological product PROTACs can be used as a tool molecule to drive the development of small molecule PROTACs, and they can be used to confirm whether the complete inhibition caused by degraded protein is better than the partial inhibition caused by small molecule inhibitor, or to compare the biological difference between protein degradation after protein expression and inhibition of protein expression by RNAi. It can also be used to determine which surface of the target protein can be reached by E3 ligase.