Exploring the World of Target Protein Degradation: A Look into PROTAC® Degraders and Molecular Glues

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April 20, 2023

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Colorful 3D protein structure determination by cryo-EM for targeted protein degradation | structural biology CRO | NanoImaging services

Over the past decade, targeted protein degradation (TPD) has rapidly expanded as a promising new approach in the development of therapeutics for a range of diseases, offering new hope for possible therapies for conditions that were previously considered untreatable. 

TPD involves the use of small molecules called degraders to selectively eliminate specific proteins from cells. These degraders are designed to bind to a protein of interest (POI) and recruit enzymes that are part of the two main mechanisms for native protein degradation in cells: the ubiquitin-proteasome system (UPS) and the autophagy-lysosome pathway. In this post, we will explore the ubiquitination/proteasomal degradation pathway.

The Ubiquitin-Proteasome System

The UPS is a crucial mechanism for the regulation and elimination of unwanted or damaged proteins within cells. It plays a significant role in numerous cellular processes, including immune response, DNA repair, and cell division. The UPS operates by tagging proteins with ubiquitin, a 76 amino acid protein that signals the cell's proteasome to degrade the marked protein. The process of attaching ubiquitin to a protein is known as ubiquitination, and it requires the coordinated action of three enzymes: E1, E2, and E3. The E3 ligase, or ubiquitin ligase, plays a critical role in the ubiquitination process, as it recognizes specific target proteins and brings them into contact with the ubiquitin-conjugating enzyme (E2), which facilitates the transfer of ubiquitin to the protein of interest.

Targeted Protein Degradation, Mechanisms and Subclasses

This process of targeted protein degradation is not only specific but also highly regulated. There are over 600 genes in the human genome that encode for E3 ligases, each contributing to the recognition of different target proteins or specific domains within a protein. E3 ligases are categorized into three main families: the RING (really interesting new gene) family, the HECT (homologous to the E6-AP carboxyl terminus) family, and the U-box ligases. RING E3 ligases act as scaffolds to bring the E2 and target protein into proximity; HECT E3 ligases first form a covalent bond with the ubiquitin through a conserved cysteine before transferring it to the target protein; U-box ligases have a similar mechanism to the RING E3 ligases but rely on other proteins to facilitate their interaction with the E2 enzyme.

After a POI is tagged with a polyubiquitin chain, it is recognized by the proteasome - a large complex of proteins that acts as a garbage disposal for the cell. The proteasome breaks down the tagged protein into smaller peptides and amino acids that can be recycled or used to build new proteins. The UPS is essential for maintaining proper protein levels and preventing the accumulation of misfolded or damaged proteins that can lead to cellular dysfunction and disease. Disruption of the UPS has been associated with a wide range of diseases, including cancer, neurodegenerative disorders, and autoimmune diseases.

In the TPD process small molecules, called degraders, are used to promote the interactions between the POI and UPS enzymes. The  two most studied subclasses of degraders are PROTAC® degraders and molecular glues.

Graphic depicting the ubiquitin-proteasome system, protas, and molecular glues | cryo-em services nano imaging services
Native degradation pathways: a) Substrate ubiquitination occurs via a cascade of activation and transfer reactions mediated by the E1, E2 and E3 ubiquitin enzymes. b) Polyubiquitinated proteins are recognized and degraded by the proteasome. Organelles and protein aggregates are removed via autophagy, whereas a double membrane structure encapsulates the substrate and forms the autophagosome. Upon fusion with a lysosome the autophagosome becomes an autolysosome initiating the degradation process. c) Schematic representation of different Cullin RING ubiquitin ligases (CRLs). CRLs consist of a core protein Cullin (CUL), which is regulated by neddylation, and the RING protein ligase RBX1, interacting with the E2 conjugating enzyme. Substrate specificity is achieved via adaptors and substrate receptors such as Cereblon (CRBN) or the von Hippel‐Lindau protein (VHL) as well as the E2 ligases. Ub=Ubiquitin. Adapted from 10.1002/anie.202004310.

Understanding Proteolysis-Targeting Chimeras

graphic depicting PROTAC targeted protein degradation TPD with cryo-em | cryo em cro nanoimaging services

PROTAC® degraders, or Proteolysis-Targeting Chimeras, are small molecules designed to selectively degrade specific proteins within cells. The basic idea behind a PROTAC® degrader is to use a bifunctional molecule that contains two different binding domains - one that binds to the target protein and another that binds to an E3 ubiquitin ligase. When the PROTAC® degrader binds to both the target protein and the E3 ligase, the E3 ligase marks the target protein with ubiquitin molecules, signaling the cell's proteasome to degrade the target protein. PROTAC® degraders allow for selective degradation of target proteins that are difficult or impossible to inhibit by traditional methods. By promoting the natural process of protein degradation within the cell, PROTAC® degraders offer a highly specific way to eliminate target proteins. They have shown promise in preclinical studies as a potential therapeutic approach for a range of diseases, including cancer, neurodegenerative disorders, and viral infections.

Molecular Glues and Their Uses

graphic depicting molecul r gluetargeted protein degradation TPD with cryo-em | cryo em cro nanoimaging services

A molecular glue is a type of small molecule that binds two proteins together, leading to changes in the structure or function of the proteins. This is a promising approach in drug discovery for diseases caused by protein-protein interactions that are difficult to target using traditional small molecule drugs. The basic idea behind molecular glues is to use a small molecule that binds to a specific site on one protein and another site on a second protein, bringing the two together and potentially altering their activity. This can be useful for activating or inhibiting protein interactions that are important for various biological processes such as gene expression and cell signaling.

The Applications of PROTAC® degraders and Molecular Glues in Drug Discovery

A great example of this is the serendipitous discovery of thalidomide and its analogs, which bind to CRBN, an E3 ubiquitin ligase that is part of the CUL4 complex (Cullin4-RBX1-DDB1-CRBN). This ligand binding promotes and stabilizes the protein-protein interactions between the CUL4 complex and the transcription factors IKZF1 or IKZF3, leading to the latter's ubiquitination and subsequent degradation by the proteasome. This is reflected in the antitumor and immunomodulatory effects of the thalidomide family. Although still in the early stages of development, molecular glues have shown potential for a range of applications in drug discovery and biological research.

PROTAC® degraders tend to be rationally designed by modifying the linker between the warhead binding the E3 ligase and the ligand binding the POI, making their mechanism almost predictable. On the other hand, most molecular glues were discovered serendipitously, and the interactions that they can mediate are difficult to predict. Naturally, molecular glues can be used as a warhead in the design of PROTAC® degraders. Despite their potential, PROTAC® degraders have limitations such as high molecular weight, poor pharmacokinetic profiles, and limited cell permeability. In contrast, molecular glues are more drug-like, with low molecular weight, improved pharmacokinetics, and increased oral availability. However, they are limited by their serendipitous discovery and lack of systematic evaluations.

As the field of targeted protein degradation continues to advance, we can expect to see even more breakthroughs in the development of novel therapeutics. Structure-based drug design can aid this evolution: X-ray crystallography and cryo-electron microscopy (cryo-EM) can be used to gain insight into the ternary complex structure and protein-protein interactions and provide guidance for further development.  At NIS, our Structural Biology team has successfully resolved the structures of several PROTAC® degraders and molecular glues, and we are proud to be contributing to the growth of the TPD field by With our expertise and imaging capabilities, we are excited to continue supporting drug discovery efforts and pushing the boundaries of what is possible with TPD. The future of targeted protein degradation looks bright, and we are eager to be a part of it.

Get in touch to talk about how cryo-EM can can assist in solving your PROTAC or Molecular Glue.

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Targeted protein degradation (TPD) is integral in developing new therapeutics, NanoImaging Services uses cryo-EM to solve PROTACs and Molecular Glues.

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