Since the emergence of targeted protein degraders more than 20 years ago, researchers have invested considerable time, effort, and resources specifically in developing proteolysis-targeting chimeras (PROTACs). As the first candidates approach the market, much excitement has built over the potential for PROTACs to treat conditions previously considered “undruggable.”
Interest within the pharmaceutical industry is growing fast, and each leap forward adds an extra layer of complexity to the development process. The early-stage, particularly the path from lead optimization to Investigational New Drug (IND) submission, has become a challenging bottleneck for PROTACs as they introduce intricacies not seen with traditional small molecule therapies. By addressing a few important considerations, developers can quickly bring more of these powerful, complex drugs to market.
1. Understand the Unique Structure and Mechanisms of PROTACs
PROTACs are small molecules that selectively degrade proteins, leveraging the body’s natural ubiquitin-proteasome system. They contain three elements:
- A ligand that specifically binds to the target protein
- A ligand that binds to an E3 ubiquitin ligase
- A linker to connect them
Because the molecule behaves as a catalyst, a single PROTAC can degrade multiple copies of a target protein. This creates a powerful and effective tool to eliminate disease-causing proteins, including those that lack enzymatic activity and can be difficult to target.
2. Consider the Druggability of PROTAC Molecules
PROTACs typically have a molecular weight ranging from 800 to 1000 Daltons and contain many polar groups. They also frequently break Lipinski’s Rule of Five, regarded as a good indicator for oral-drug-likeness. This means PROTACs often suffer from reduced oral bioavailability, poor membrane permeability, and restricted metabolic stability.
To address these concerns, researchers must optimize linker length, minimize polar surface area, and simplify ligand structure wherever possible. Technologies such as amorphous solid dispersion, lipid-based delivery systems, and prodrugs can enhance in vivo exposure, helping to improve the oral drug-likeness of PROTACs. Drugs suitable for oral dosage will be crucial for the development and clinical applications of PROTACs in the future, as they offer convenience for patients and support continuous treatment regimens.
3. Navigate Analytical Characterization Challenges
Due to their high molecular weight, complex structure, and the presence of multiple stereocenters, the analytical characterization of PROTACs during early development presents unique challenges. They can display assay-related measurement issues, including ion suppression, peak splitting during chromatographic separation, and in-source fragmentation, when analyzed by LC-MS/MS. PROTACs also show high non-specific binding to plasticware and glassware in the lab.
To overcome these issues, researchers must use low-binding bioanalytical techniques. Using desorbents such as Tween 20 and carefully optimizing mass spectrometry parameters helps improve signal stability and data quality.
4. Proactively Detect Metabolism and Stability
PROTACs are susceptible to metabolic degradation, especially at linker regions. Conventional in vitro assays, such as those using liver microsomes, may not be enough to understand the metabolism and stability of PROTACs. A more comprehensive approach is required, including:
- Hepatocytes: Provide a full range of metabolic enzymes and better represent in vivo metabolism.
- Liver S9 fractions: Enable detection of both oxidative and conjugative metabolism.
- Cytosolic fractions: Allow screening for non-CYP enzymes such as aldehyde oxidase (AO), which may contribute to rapid clearance and demonstrate species-specific activity.
By proactively detecting and addressing metabolic soft spots, developers can minimize the risk of late-stage failures and bolster confidence as programs advance to toxicology and first-in-human studies.
5. Appreciate the PK and PD Characteristics of PROTACs
PROTACs create unique PK and PD challenges not typically faced by traditional small molecules. They behave catalytically, so the relationship between systemic exposure and biological effect is often non-linear. The “hook effect” complicates the issue further, as high concentrations of PROTACs reduce activity due to the saturation of binary complexes.
Researchers must adopt a different approach for PROTACs. Mechanistic PK/PD models can account for catalytic and time-dependent effects. Dosing regimens need careful optimization to maintain efficacy without causing saturation or loss of selectivity. Finally, researchers must understand that efficacy correlates more closely with degradation kinetics than steady-state concentration.
A Final Word
As the promise of PROTACs translates from lab research to patient benefit, future success will rely on recognizing that this drug type is more than modified small molecules. PROTACs are a distinct modality that require their own development playbook. By addressing the unique structural, physiochemical, and DMPK characteristics of PROTACs, developers can ensure their candidates ease through early-stage development, and are ready to continue their journey towards IND submission.
