Targeted protein degradation (TPD) has emerged as a revolutionary approach in drug discovery, offering new ways to target disease-causing proteins. Of the various TPD technologies, molecular glue degraders and proteolysis-targeting chimeras (PROTACs) stand out for their unique mechanisms and potential therapeutic applications. We provide a comprehensive overview of both, comparing their mechanisms of action, advantages, disadvantages, and broader implications in drug development.   

What are Molecular Glue Degraders?

Molecular glue degraders are small molecules that enhance or stabilize interactions between proteins that do not typically bind to each other. In the context of TPD, they facilitate the formation of a complex between an E3 ubiquitin ligase and a target protein, leading to the degradation of the target protein. Thalidomide and its analogs, lenalidomide and pomalidomide, are FDA-approved molecular glue degraders used in multiple myeloma and other conditions. These drugs recruit the cereblon (CRBN) unit of the ubiquitin E3 ligase complex to degrade transcription factors IKZF1/3. For a more indepth discussion on molecular glue degraders, head to our dedicated blog.

What are PROTACs?

PROTACs are heterobifunctional molecules composed of two ligands connected by a linker. One ligand binds to the target protein, while the other recruits an E3 ubiquitin ligase. This mechanism brings the target protein and the E3 ligase into close proximity, leading to the ubiquitination and subsequent degradation of the target protein by the proteasome. For a broader understanding of TPDs and PROTACs, try our TPD blog.

Advantages and Disadvantages

Advantages of Molecular Glue Degraders

· Favorable drug-like properties: Molecular glue degraders typically adhere to Lipinski's rule of five, making them more likely to have good membrane permeability and oral bioavailability.   

· Potential for CNS indications: Their smaller size may enable them to cross the blood-brain barrier, opening possibilities for treating neurological conditions.   

· Synthetic tractability: Molecular glue degraders are often simpler to synthesize and have more straightforward structure-activity relationships (SAR) compared to PROTACs.   

Disadvantages of Molecular Glue Degraders

· Serendipitous discovery: Historically, the identification of molecular glue degraders has been largely serendipitous, making targeted discovery challenging.   

· Limited design principles: The rational design of molecular glue degraders is still an emerging field, with limited understanding of the complex interactions involved.   

Advantages of PROTACs

· Rational design: PROTACs can be rationally designed based on the knowledge of target protein and E3 ligase ligands.   

· Broad targeting potential: PROTACs can potentially target a wide range of proteins, including those that are difficult to drug with traditional inhibitors.   

· Catalytic activity: PROTACs function in a catalytic manner, meaning that one PROTAC molecule can degrade multiple target protein molecules.   

Disadvantages of PROTACs

· Drug-like properties: PROTACs often have high molecular weight and complex structures, which can lead to poor membrane permeability and oral bioavailability.   

· Hook effect: At high concentrations, PROTACs can experience the hook effect, where the formation of ternary complexes is disrupted, reducing efficacy.   

· Synthetic complexity: The synthesis of PROTACs can be complex and challenging, requiring careful optimization of linker length and composition.

Key Techniques in TPD Discovery and Development

Several techniques are used in the discovery and development of molecular glue degraders and PROTACs:

· High Throughput Screening (HTS) and Fragment-Based Screening (FBS): HTS and FBS are used to identify compounds that bind to a protein and promote interactions between a ubiquitin ligase and a target protein. For example, a phenotypic screen against a panel of AML cell lines using a CRBN modulator library was used to identify the starting point for the molecular glue degrader CC-9009.   

· HTRF and Other Protein-Protein Interaction Assays: HTRF and other protein-protein interaction assays are used to identify compounds that promote interactions between proteins, such as a ubiquitin ligase and a target protein.

· Structure-Guided Design: Structure-guided design is used to optimize the interactions between a molecular glue degrader or PROTAC and its target proteins. For example, C4 Therapeutics used structure-guided design to optimize the tricyclic imide core of their molecular glue degrader CFT7455.   

· Chemical Optimization: Chemical optimization is used to improve the drug-like properties of molecular glue degraders and PROTACs, such as membrane permeability, oral bioavailability, and stability. For example, Novartis used SAR optimization to develop the molecular glue degrader DKY709.   

· Computational Modeling: Computational modeling is used to predict the interactions between a molecular glue degrader or PROTAC and its target proteins, as well as to optimize the linker length and composition of PROTACs.   

· In vitro and in vivo Studies: In vitro and in vivo studies are used to evaluate the efficacy and safety of molecular glue degraders and PROTACs. For example, the molecular glue degrader BI-3802 was found to promote the degradation of BCL6 in vitro and in vivo.

Clinical Trials: A Glimpse into the Future of TPD

While both molecular glue degraders and PROTACs are still in the early stages of development, several clinical trials are underway, showcasing their potential therapeutic applications.   

Approved Molecular Glue Degraders:

· Thalidomide and its analogs, lenalidomide, and pomalidomide, are FDA-approved molecular glue degraders used in treating multiple myeloma and other conditions.   

· These drugs recruit the cereblon (CRBN) unit of the ubiquitin E3 ligase complex to degrade transcription factors IKZF1/3.   

Clinical Trials of Molecular Glue Degraders:

· C4 Therapeutics' CFT7455 is a potent molecular glue degrader that recruits CRBN for IKZF1/3 degradation and is being investigated for treating multiple myeloma and non-Hodgkin's lymphoma (NCT04756726).   

· Eisai Therapeutics' E7820 is an aryl sulfonamide molecular glue degrader that recruits DCAF15 for the targeted degradation of RNA binding protein RBM39 and is being studied in a Phase II trial (NCT05024994) for treating patients with relapsed or refractory AML, MDS, or CMML.   

Clinical Trials of PROTACs:

· Arvinas' ARV-471, a PROTAC molecule targeting the estrogen receptor, has entered Phase III clinical trials for breast cancer.   

· Other PROTACs in clinical trials include ARV-110 for prostate cancer, KT-474 for immunological diseases, and several others targeting various proteins and conditions.

Biosynth's Products and Services: Tailored Solutions for TPD Development and Manufacturing

Biosynth offers a comprehensive suite of products and services that are highly relevant to the development and manufacture of molecular glue degraders and PROTACs. These include:

· Custom Synthesis to support PROTACs and LYTACs development: Biosynth can design and synthesize custom products for PROTACs and LYTACs projects based on the client's desired target protein and E3 ligase.   

· Peptide Discovery with Biosynth's CLIPS™ Technology: Biosynth's proprietary CLIPS™ technology allows for the discovery and optimization of constrained peptides that bind to the target protein of interest.   

· Antibody Development for TPD: Biosynth can develop custom antibodies that specifically bind to target proteins, enabling targeted protein degradation upon antibody binding.   

· Plasma for In Vitro TPD Diagnostics: Biosynth provides high-quality plasma samples for in vitro testing and validation of TPD therapies.   

· Peptide Synthesis for TPD: Biosynth can synthesize custom peptides for various TPD applications, such as peptide-based PROTACs, peptide linkers for bifunctional molecules, or peptides for target validation and screening.   

· Hit Validation and Lead Identification: Biosynth provides services for screening, in vitro validation, and assessment of in vivo proteolytic stability of hits and leads.   

· Lead Optimization: Biosynth offers lead optimization services, including the incorporation of non-natural amino acids for enhanced binding and activity.   

· Large-Scale GMP Manufacturing: Biosynth can provide purified R&D and GMP-compliant peptides at various scales for use in clinical trials.   

· On-Cell Screening: Biosynth's on-cell screening services enable the identification of high-affinity peptide binders for challenging targets.   

Visit our Dedicated TPD Services Page

By offering this comprehensive suite of products and services, Biosynth can effectively support researchers throughout the entire TPD drug discovery and development process, from target validation and lead optimization to preclinical and clinical testing.

Both molecular glue degraders and PROTACs hold significant promise for drug development. Molecular glue degraders offer advantages in terms of drug-like properties and potential for CNS indications, while PROTACs allow for rational design and broad targeting potential. Overcoming the challenges associated with each approach, such as the serendipitous discovery of molecular glue degraders and the drug-like properties of PROTACs, will be crucial for their successful clinical application. As the field of TPD continues to evolve, we can expect to see the development of even more effective and targeted protein degraders for a wide range of therapeutic applications.