An Overview of Targeted Protein Degradation by PROTAC (Part One)

 

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An Overview of Targeted Protein Degradation by PROTAC (Part One)

The background

Traditional drug development has focused on regulating the activity of proteins or enzymes directly to treat diseases. The development and application of protein activity regulators, especially inhibitors, has been the mainstream of drug development. Nucleic acid-based strategies to control protein function by affecting protein expression have recently made a breakthrough, have begun to enter the clinic and have gained attention. However, poor metabolic stability and low bioavailability limit the wider application of small molecule nucleic acid technology.

PROTAC is invented in 2001. It uses the ubiquitin-proteasome system, the "cleaner" in cells. The normal physiological functions of the ubiquitin-proteasome system are responsible for cleaning up denatured, mutated, or harmful proteins in cells. PROTAC uses the cell's own protein destruction mechanism to remove specific oncogenic proteins from cells and is an alternative method of targeted therapy.

In recent years, PROTAC has become the focus of the entire pharmaceutical industry because it has successfully obtained high cell activity and good pharmacokinetic properties in several proteins, especially the BET family of proteins and hormone receptors.

Different from the principle of traditional protein inhibitors, PROTAC platform technology is a bifunctional hybrid compound. One side is used to bind the target protein and the other is used to bind an E3 ligase and ubiquitinate and degrade the proteome. In theory, PROTAC only provides binding activity and is event-driven. It is different from traditional occupancy-driven. It does not need to directly inhibit the functional activity of the target protein and can be reused.

In 2017, the platform matured greatly.

The development process and target selection of PROTAC

PROTAC technology is often classified as a so-called undruggable target, such as transcription factors, protein backbone, and regulatory functions. As a research tool, it is significant for exploring difficult and incomprehensible targets, but for the development of clinical drugs, the breakthrough targets should still be selected for proven targets, reducing variables, and first proving the feasibility of PROTAC. This is also the key research direction of PROTAC in the past few years.

PROTAC is an improved and universal platform technology for inducing protein degradation technology. Prior to this, there have been some similar technologies and its prototypes, such as some of the earliest selective hormone receptor inhibitors with their own degradation function, HyT technology, etc.

Hormone receptor inhibitor

Selective estrogen receptor modulator (SERM), such as tamoxifen, were first approved by the FDA in 1977 for the treatment of ER + breast cancer patients, with significant curative effects. And the improved version of SERM fulvestrant (ICI82780, Faslodex; AstraZeneca) accidentally and fortunately found its own function to degrade the estrogen receptor. This is also the earliest prototype of the induced degradation protein technology reported. Although fulvestrant has no oral activity and PK is also poor, it can degrade the estrogen receptor, making it the only breast cancer patient approved so far for second-line resistance to Tamoxifen (FDA approval in 2002). It is presumably that Tamoxifen overcome drug resistance due to contribution from its ability to induce degradation of the estrogen receptor. Attempts to improve the drugability of fulvestrant have not made significant progress.

Similarly, attempts to find fulvestrant analogs that target prostate cancer have continued, that is, selective androgen receptor degraders (SARDs).

At present, small molecule degradation agents based on SARDs and SERDs are limited to estrogen and androgen receptors, which is difficult to develop into a universal technology platform.

Hydrophobic tagging, HyT

In order to extend the concept of induced protein instability to a wider range of protein targets, some laboratories developed hydrophobic tagging (HyT).

Similar to fulvestrant-induced surface hydrophobicity, this method attaches a hydrophobic portion (ie, adamantane or Boc3-Arg) to the surface of the target protein, which attempts to mimic a partially unfolded protein state, and responds with cytoplasmic unfolded proteins to degrade targets.

The ability of Boc3-Arg to induce protein degradation was demonstrated in 2012, and the covalent inhibitor etacrynic acid was linked to Boc3-Arg to target degradation of glutathione-S-transferase α1 (GST-α1). Similarly, dihydrofolate reductase can be degraded using micromolar concentrations of trimethoprim, a non-covalent inhibitor coupled to Boc3-Arg.

Although the mechanism of action of detailed chaperones or other control pathways is still unknown, the known pathway that induced targeted protein degradation occurs independently of the proteasome ubiquitin and ATP.

Peptide-based PROTAC

In the first proof-of-concept experiments published in 2001, Crews Lab and collaborator Ray Deshaies reported on the first batch of PROTACs bifunctional molecules: the ubiquitin-proteasome system, which recruited E3 ligase to the target protein, leading to ubiquitination and subsequent protein degradation. The original technology was based on the short peptide PROTAC technology. Successful targets include MetAP2, androgen receptor, aromatic hydrocarbon receptor, PI3K, etc.

However, the activity of these peptides PROTAC is low, and they still stay in the micromolar range. The main obstacle may be the poor cell penetration of the peptide technology platform. Fortunately, continuous improvement attempts have promoted the development of the PROTAC small molecule technology platform with in vivo stability.

To be continued in Part Two…

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