Proteolysis targeting chimeras (PROTACs) represent a groundbreaking approach in drug discovery and development. These innovative molecules offer a promising strategy to modulate protein levels within cells by harnessing the cell's natural protein degradation machinery. The concept of PROTACs has evolved rapidly, leading to the approval of several drugs that utilize this technology.
What are PROTACs?
PROTACs are bifunctional molecules designed to exploit the ubiquitin-proteasome system (UPS) for targeted protein degradation. A typical PROTAC consists of three key components: a ligand that binds to a target protein of interest (POI), a ligand that binds to an E3 ubiquitin ligase enzyme, and a linker joining these two ligands. Once inside the cell, the PROTAC recruits the target protein and the E3 ligase into close proximity, leading to ubiquitination of the target protein. This ubiquitinated protein is then recognized and degraded by the proteasome, resulting in its elimination from the cell.
Fig. 1 PROTACs hijack the UPS to induce targeted protein degradation. (Li, K. 2022)
Approved PROTAC drugs
Up to the current time (2024), there is no direct public information indicating that specific PROTAC drugs have been approved for marketing by FDA. However, in the research and development stage, many PROTAC molecules have been designed and tested to target proteins of various diseases. There are at least 20 PROTACs in the clinical trials by the end of 2022, with more expected to follow and eventually get FDA approval.
In the 20 years since the first small-molecule PROTAC was reported in the literature, the technology has moved from academia to industry, where several biotech and pharmaceutical companies have disclosed programmes in preclinical and early clinical development. The era of rationally designed targeted protein degraders as potential human therapeutics began in 2019 with the entry of two heterobifunctional degraders into first-in-human trials: the PROTACs ARV-110 (NCT03888612) and ARV-471 (NCT04072952), targeting the AR and the ER, respectively. Both of these degraders have now moved on to phase II trials, and have been followed into the clinic by degraders from Bristol Myers Squibb (BMS), Nurix Therapeutics, Kymera Therapeutics, Dialectic Therapeutics, Foghorn Therapeutics and others. By far, the PROTACs have proved effective in degrading a variety of proteins, such as representative AR, ER nuclear receptors, various kinases, transcription factors, and abnormal protein aggregates.
Fig. 2 Milestones in the development of PROTAC technology. (Liu, Z., 2022)
ARV-110
This PROTAC targets the androgen receptor (AR), a pivotal protein in prostate cancer progression. By inducing degradation of AR, ARV-110 disrupts the signaling pathways that drive tumor growth. The research data indicate that ARV-110 is safe as an oral bioavailable degradation agent. Phase I trials have shown that ARV-110 reduced prostate-specific antigen (PSA) levels by more than 50% in 40% of patients with mCRPC in a population with a specific gene mutation. In addition, in the initial clinical study, the biopsy data of one patient showed a 70%~90% decrease in AR. Clinical trials have demonstrated promising results, with significant anti-tumor activity observed in patients with metastatic castration-resistant prostate cancer (mCRPC).
ARV-471
Another notable PROTAC developed by Arvinas, ARV-471, targets the estrogen receptor (ER) in breast cancer. ER-positive breast cancer is a prevalent subtype characterized by the dependence on estrogen signaling for tumor growth. ARV-471 effectively degrades the ER protein, leading to the inhibition of cancer cell proliferation. A Phase I clinical study of ER+ and HER2- breast cancer patients who had received an average of five continuous treatments showed that ARV-471 could significantly reduce the expression level of ER in tumor tissue of patients, reducing the ER. level by 62% on average, up to 90% at most. In addition, the phase I clinical data of ARV-471 also showed that a high level of ER degradation (89%) was observed at all dose levels of 30-700 mg, and it was well tolerated. ARV-471 exhibited certain degradation effects on both wild type ER and ER mutants. ARV-471 is undergoing a phase II dose expansion clinical trial to evaluate the efficacy of ARV-471 in the treatment of ER+/HER2- patients with locally advanced or metastatic breast cancer.
Related products at BOC Sciences
The advantages of PROTACs
PROTACs offer several advantages over traditional small molecule inhibitors in drug discovery and development.
Potency and efficacy: PROTACs can achieve potent and effective target degradation at lower doses compared to traditional inhibitors. By harnessing the cell's own ubiquitin-proteasome system, PROTACs can induce degradation of the target protein, leading to a more profound and sustained pharmacological effect.
Broader target range: PROTACs can target proteins that were previously considered "undruggable" by conventional small molecule inhibitors. This includes proteins lacking suitable binding pockets or those involved in protein-protein interactions that are difficult to disrupt with traditional approaches.
Specificity: PROTACs can achieve highly specific degradation of the intended target protein while sparing closely related proteins. This selectivity is beneficial in reducing off-target effects and potential toxicity associated with broad inhibition.
Longer duration of action: PROTAC-induced protein degradation often leads to a longer duration of action compared to reversible binding inhibitors. This sustained effect can be advantageous in treating diseases where continuous target suppression is required.
Overcoming resistance: PROTACs may offer a strategy to overcome drug resistance mechanisms observed with traditional inhibitors. By targeting proteins for degradation rather than inhibition, PROTACs can circumvent certain resistance mechanisms, such as mutations that interfere with inhibitor binding.
Flexible design: PROTACs are designed as chimeric molecules that consist of a ligand for the target protein, a linker, and a ligand for an E3 ubiquitin ligase. This modular design allows for flexibility in optimizing selectivity, potency, and pharmacokinetic properties.
Potential for novel therapeutics: The unique mechanism of action of PROTACs opens up new opportunities for therapeutic interventions in diseases where conventional small molecule inhibitors have limitations.
Combination therapies: PROTACs can be used in combination with other drugs to achieve synergistic effects or to target multiple nodes in a disease pathway, potentially enhancing therapeutic outcomes.
Application of PROTACs in diseases
Over the last two decades, PROTACs have demonstrated unique advantages in addressing disease associated proteins. Currently, some representative PROTACs have reached clinical trials for the treatment of cancers. Except for cancer, PROTACs also offer great advantages in the treatment of other diseases, such as neurodegenerative diseases, immune system diseases or viral infection.
PROTACs targeting cancer-related targets
The indispensability of oncogenic proteins in the progression of cancer makes PROTAC particularly suitable for the treatment of cancer. Most of the current research on PROTACs focused on cancer-related targets. In the reported studies, researchers preferred kinases as degradation targets. Statistically, kinases account for 45% of the total targets degraded by PROTAC, of which, more than half of PROTACs targeted RTK and CMGC kinase group (CMGCs). BTK PROTACs have entered clinical trials and several compounds have shown good clinical benefits. PROTACs targeting kinases such as ALK, MEK and CDK have also been studied and investigated extensively in the literature. Besides the kinase-based PROTACs, there are still a large number of PROTACs focused on targeting nuclear receptors and epigenetic protein.
PROTACs for treating neurodegenerative diseases
The most common neurodegenerative disorders include Alzheimer's disease, Huntington's disease, and Parkinson's disease. They often occur in the elderly population and, are a class of diseases that cause cognitive impairment. Aggregation of misfolded proteins is one of the leading causes of neurodegenerative diseases, and the commonly misfolded proteins are β-amyloid, Tau, alpha-synuclein, and polyglutamates. Tau is an important microtubule-associated pathological protein of Alzheimer's disease, minimizing Tau aggregation is considered as a potential way to treat AD. Lu's group designed and synthesized a peptide-based PROTAC bearing Keap1 E3 ligase ligand for the degradation of intracellular Tau, it showed high affinity with tau and keap1 in vitro and induced moderate degradation of Tau.
Huntington's disease (HD) is caused by the variation of Huntington gene, and the abnormal mutant huntingtin (mHtt) produced by the variation that accumulates in the brain will affect neural and nerve cell function. Consequently, inhibition or clearance of toxic mHtt aggregation is considered as a potential treatment modality. Tomoshige et al. designed two small molecule PROTACs, conjugating probes for mHtt aggregates with a ligand for ubiquitin ligase cIAP1. Experimental data showed that the two compounds are capable of inducing the degradation of mHtt in living cells. The effect is particularly pronounced in HD patients and mHtt with a much longer polyglutamine repeat sequence (145Q).
PROTACs for treating immune-related diseases
IRAK4: Interleukin-1 receptor-associated kinase 4 (IRAK4) plays an important role in toll-like receptors (TLRs) and interleukin1 receptors (1L-1R) signaling pathways. Overactivation or dysfunction of IRAK4 can lead to different problems accordingly. In addition to its kinase activity, IRAK4 also has scaffolding signaling. Therefore, traditional small-molecule inhibitors are unable to block all the functions of IRAK4. As a promising technology, PROTACs can eliminate all the functions of protein.
HDAC3: The histone deacetylases (HDACs) family is a class of chromatin-modifying enzymes that silence transcription via the modification of histones. HDAC1-3 and 8 belong to class I HDACs that play a key role in cell motility, immunoregulation, and proliferation. However, the structure of HDAC3 contains a well-conserved catalytic structural domain that makes selective targeting of HDAC3 challenging. In 2022, Liao et al. unraveled VHL-based PROTAC XZ9002 (Fig. 2k) that could specifically degrade HDAC3 and inhibit tumor cell activity.
PROTACs targeting virus-related targets
It has been thought that PROTACs also can be applied in the antivirus field to reduce susceptibility to resistance mutations. With the drug resistance of conventional antiviral drugs, the effect of clinical treatment began to gradually deteriorate. Recent study leveraged PROTACs to develop a chemical knock-down antiviral to induce degradation of viral proteins. Wispelaere et al. designed a PROTAC which consists of a reversible-covalent inhibitor telaprevir that binds to the hepatitis C virus (HCV) protease active site and a ligand for CRBN ligase. The compound DGY-08-097, not only inhibits but also degrades the HCV NS3/4A protease, exhibiting efficiency in a cellular infection model.
Other PROTACs
In 2020, Rao et al. reported the first PROTAC of HMGCoA reductase (HMGCR), which is the rate-limiting enzyme in the cholesterol biosynthetic pathway. They synthesized a series of PROTACs by tethering Atorvastatin and CRBN ligands. After optimization and screening, they ultimately found the most potent degrader P22A. This PROTAC stressed the potential application for the treatment of hypercholesterolemia and cardiovascular disease.
Li et al. reported the first PROTAC that induced degradation of α1A-adrenergic receptor (α1A-AR) and is also the first PROTAC for G protein-coupled receptors (GPCRs). They connected α1A-AR inhibitor prazosin with pomalidomide by different linkers and finally found the potent compound. The compound could inhibit the proliferation of PC-3 cells and cause tumor growth slowdown, which provided a new strategy for the treatment of prostate cancer. PROTAC technology is so widespread in the field of disease treatment, making it a powerful tool for drug discovery.
References:
- Li, K.; Crews, C. M. PROTACs: past, present and future. Chemical Society Reviews. 2022, 51(12): 5214-5236.
- Békés, M., et al. PROTAC targeted protein degraders: the past is prologue. Nature Reviews Drug Discovery. 2022, 21(3): 181-200.
- Liu, Z., et al. An overview of PROTACs: a promising drug discovery paradigm. Chem Soc Rev. 2022, 51(12): 5214-5236.
