Introduction
Proteolysis-targeting chimeras (PROTACs) are an innovative therapeutic strategy based on Targeted Protein Degradation. Instead of merely inhibiting disease-related proteins, PROTACs are designed to eliminate them by leveraging the cell’s natural degradation machinery. A typical PROTAC comprises three parts, including a ligand that binds the protein of interest (POI), a ligand that recruits an E3 ubiquitin ligase, and a linker connecting the two parts. Once inside the cell, the PROTAC forms a ternary complex with the POI and E3 ligase, leading to ubiquitination and subsequent degradation of the target protein by the proteasome. Importantly, PROTACs act catalytically, enabling them to degrade multiple copies of the POI without being consumed.
Compared to traditional inhibitors, PROTACs offer multiple advantages:
Catalytic Action: Works at low doses by repeatedly degrading target proteins, reducing toxicity.
Bypasses Resistance: Remains effective even with target proteins mutate.
Wilder Target Range: Can degrade proteins once considered “undruggable”.
Improved Selectivity: Leverages tissue-specific E3 ligases for precise targeting.
However, several development challenges remain – such as the hook effect at high doses, off-target effects, poor pharmacokinetics due to large molecular size, and adaptive cellular responses linker rebound overexpression of the target protein.
These hurdles are driving the evolution of PROTACs beyond their original design-toward next-generation platforms with enhanced performance.
1. Activatable PROTACs: Gaining Spatial and Temporal Control
To improve selectivity and minimize off-target effects, researchers have developed activatable PROTACs, which remain inactive until triggered by external stimuli. One promising subclass is photoactivatable PRTACs, designed to be activated by light only in the desired tissue or environment. There are two major types:
Photo-caged PROTACs (pc-PROTACs): These incorporate photolabile protecting groups that block the active site of the PROTAC. Upon light exposure (e.g., UV or visible light), the cage is removed, restoring degradation activity.
Photoswitchable PROTACs: These compounds can reversibly change conformation between active and inactive states under different wavelengths of light, enabling dynamic control.
However, challenges remain. UV light has poor tissue penetration, limiting this approach to superficial tumors or hematologic cancers. Additionally, suitable modification sites on PROTACs can be scarce, which may constrain molecular design.
Beyond light-responsive strategies, researchers are also exploring alternative mechanisms to achieve conditional control over PROTAC activity including enzyme-activated PROTACs and ROS-activated PROTACs.
Enzyme-activated PROTACs: These designs utilize cleavable linkers that are recognized and processed by tumor-associated enzymes, such as cathepsins, caspases, or matrix metalloproteinases (MMPs). This strategy enhances tumor specificity and minimizes systemic toxicity.
ROS-activated PROTACs: Tumor cells often exhibit elevated levels of reactive oxygen species (ROS) compared to normal tissues. By incorporating ROS-sensitive linkers (e.g., aryl boronic esters, thioketal bonds), PROTACs can be designed to remain inert in circulation and become activated only in the oxidative milieu of cancer cells. This redox-triggered release strategy offers another layer of selectivity for targeting intracellular proteins.
These smart, activatable PROTACs systems are redefining the boundaries of targeted protein degradation, offering fine-tuned control and the potential for safer, more effective therapeutics.
2. Multitarget PROTACs: Advancing Beyond One-to One Targeting.
As targeted protein degradation evolves, PROTACs are no longer limited to one-to-one interactions. bivalent PROTACs are designed to simultaneously engage and degrade two different proteins of interest, enabling coordinated disruption of multiple disease pathways within a single molecular entity. This multitargeting strategy offers the potential for enhanced therapeutic efficacy, reduced drug resistance, and simplified treatment regimens.
Trivalent PROTACs, on the other hand, enhance degradation efficiency by incorporating two ligands for the same target protein along with one E3 ligase ligand. This multivalent architecture enables more stable and cooperative ternary complex formation, improves binding avidity, and extends cellular residence time. Such designs are especially advantageous when targeting proteins with multiple functional domains that are difficult to inhibit or degrade using traditional approaches.
3. Macrocyclic PROTACs: Conformational Locking for Better Properties
Macrocyclic PROTACs incorporate a rigid ring structure that constrains the overall molecular flexibility, offering several advantages over their linear counterparts. Macrocyclization can enhance selectivity by locking the molecule into a bioactive conformation, reducing entropic penalties during ternary complex formation. This conformational rigidity also contributes to improved pharmacokinetic properties, such as enhanced membrane permeability and metabolic stability. Notably, some macrocyclic PROTACs have demonstrated increasing oral bioavailability and reduced off-target degradation, addressing key limitations of traditional PROTACs. As a result, macrocyclic designs are gaining attention as a promising strategy to improve drug-like characteristics and in vivo efficacy.
4. CLIPTACs: In-Cell Click Chemistry for Smarter Assembly
Cellularly Localized In-Cell Click-formed PROTACs (CLIPACs) offer a creative solution to the size and permeability challenges of traditional PROTACs. This approach involves administering two smaller, cell-permeable precursors that undergo biorthogonal click chemistry inside the cell to form a functional PROTAC. By splitting the molecule into two fragments, each with significantly reduced molecular weight, CLIPTACs achieve better membrane permeability and pharmacokinetic profiles. This strategy adds a new level of precision to targeted protein degradation.
5. Nanotechnology-based PROTACs: Improved Delivery and Function
The integration of nanotechnology into PROTAC development (nanoPROTACs), offers significant improvements over traditional PROTACs by enhancing solubility, cellular uptake, target specificity, and controlled release. Four main strategies have emerged:
Controlled Release system: Smart nanocarriers enable precise spatiotemporal delivery of PROTACs.
Encapsulation and Delivery Platforms: Various nanostructures (e.g., peptides, lipids, polymers) improve membrane permeability and tissue targeting while reducing systemic toxicity.
Split-and-Mix (SM) PROTACs: Combinatorial nanoscale platforms generate diverse PROTAC libraries to enhance ligand exposure and targeting precision.
Carrier-Free Nano-PROTACs: Relying on self-assembly via π-π interactions, these formulations support combination therapies (e.g., photodynamic therapy) without additional delivery vectors.
Together, these approaches significantly expand the therapeutic potential and versatility of PROTACs in disease treatment.
6. Antibody-Conjugated and Antibody-based Degraders: Enhancing Specificity and Therapeutic Precision
Several antibody-based approaches have been developed to enhance the specificity and safety of targeted protein degradation”
DAC-PROTACs (Degrader-Antibody Conjugates) combine the catalytic activity of PROTACs with the tissue selectivity of antibodies, aiming to reduce off-tumor toxicity. These conjugates remain inactive until internalized by target cells, where the active PROTAC is released to induce selective protein degradation.
Trim-Away is genome-editing-free technique that uses antibodies and the endogenous E3 ligase TRIM21 to rapidly degrade intracellular proteins. Antibodies bind the target protein, and TRIM21 directs the complex to the proteasome for degradation.
PROTABs (Proteolysis-Targeting Antibodies) use bispecific antibodies: one arm binds a membrane protein of interest, and the other recruits an E3 ligase, enabling targeted degradation of membrane-bound proteins.
These strategies leverage antibody specificity to enhance the precision of targeted protein degradation therapies, offering improved safety and broader applicability.
Conclusion: Outlook
While PROTACs hold great promise, challenges remain – including high molecular weight, poor oral bioavailability, off-target effects, and limited tissue selectivity. Novel approaches – including activatable PROTACs, multitarget PROTAC, macrocyclic architectures, CLIPTACs, smart nanotechnology-based PROTAC and Antibody-conjugated degraders – are steadily overcoming traditional limitations, broadening the scope of degradable targets and enhancing therapeutic potential.
At Precise PEG, we stay at the forefront of PROTAC innovation, supporting our partners in the synthesis of these complex and cutting-edge molecules by providing high quality linkers and ligands-linker conjugates. We are excited to contribute to the future of targeted therapies across oncology, immunology, and beyond.
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