Technology

Targeted protein degradation (TPD) utilizes the waste disposal system of the cell to selectively eliminate disease-causing proteins. As such, it is a promising alternative to existing therapeutic modalities in addressing high unmet medical needs.

Drug discovery concepts in TPD are based on small molecules commonly referred to as ‘degraders’. Many degrader drugs redirect E3 ubiquitin ligases to non-native substrate proteins. After forming a ternary complex, the E3 ligase modifies these ‘neosubstrates’ by attaching multiple ubiquitin molecules. The proteasome recognizes the resulting poly-ubiquitin chains and degrades the neosubstrates into amino acids that are recycled for novel protein synthesis. Unlike conventional small molecule drugs, degrader molecules don’t just inhibit their targets. Instead, they act as catalytic agents that eliminate disease-causing proteins and their associated functions.

Established degrader drugs that reprogram E3 ligases come mainly in two varieties: heterobifunctional molecules also known as PROTACs (PROteolysis TArgeting Chimeras) or molecular glue compounds. PROTACs have warheads for the E3 ligase and the target protein connected by a linker. Molecular glue degraders are smaller in size and lack discernable binding units. They reshape the substrate interaction site of E3 ligases to create complementary binding sites for non-physiological targets.

Other degrader drugs, like monovalent degraders, induce depletion by triggering conformational changes in their target proteins rather than by repurposing an E3 ligase. Another strategy is to inactivate deubiquitinases that remove poly-ubiquitin conjugates. Inhibitors of these enzymes promote ubiquitination and proteasomal degradation of substrates implicated in disease. Finally, new TPD approaches go beyond the proteasome, exploiting autophagic or lysosomal degradation pathways to eliminate extracellular targets and protein aggregates.

Discovery efforts in targeted protein degradation start either from degrader targets or from degrader chemistries. Both strategies benefit from deep proteomic screening to guide drug development.

The first case applies to heterobifunctional molecules like PROTACs, which are rationally designed to possess binding moieties for harmful proteins. Monitoring their selectivity against all cellular proteins provides crucial information for optimization efforts. In general, proteome-wide selectivity analysis should be performed for any degrader molecule under development for a known target.

In the second case, drug discovery originates from small molecules presumed or designed to be degraders. Testing such compounds against entire proteomes enables systematic identification of their targets. For example, molecular glue compounds, like those that bind to the E3 ligase cereblon, have been clinically validated to eliminate disease-causing proteins. With low-molecular weight, favorable drug-like properties, and the ability to promote target recognition in the absence of cavities or binding pockets, molecular glues can address proteins considered ‘undruggable‘ by conventional small molecule drugs. Their discovery, however, has so far relied on serendipitous observations that have led to only a few dozen potential neosubstrates. Thus, the true target scope of molecular glue degraders is largely unknown, despite their enormous therapeutic potential. Only a systematic, proteomics-based discovery approach that connects degrader compounds with targets in an unbiased manner can exploit the full targeting potential of molecular glues.

Cutting-edge technology that adds significant value to the drug discovery process
Our target and E3 ligase agnostic screening is suitable for characterizing all types of degrader libraries (e.g., PROTACs, molecular glues, monovalent degraders, DUB inhibitors). Putative degrader targets found in the proteomics screens can readily be validated using our unique proteomics-based validation pipeline. Besides identifying neosubstrates at unprecedented scale, the resulting data can be used for degrader library optimization and expansion, as well as for computational approaches such as AI-based predictive modeling of novel degrader drugs. The high-throughput and fast turnaround capabilities of our platform also support proteome-wide selectivity profiling in drug optimization cycles.

We believe that only proteomics using mass spectrometry at unprecedented scale, depth, and quality can reveal the true target scope of TPD. Proteomics will identify novel, previously undruggable targets and advance degrader drugs to develop treatments for life-threatening diseases. Our unique, integrated proteomics platform transforms today’s challenges in targeted protein degradation into tomorrow’s opportunities.

DEEP
PROTEOMIC
SCREENING

We analyze each sample in a single data-independent acquisition mass spectrometry (DIA-MS) experiment, ensuring our proteomics workflow is compatible with screening requirements. Our high-performance DIA-MS is optimized for maximum proteome detection, enabling routine quantification of 10,000 or more proteins with high sensitivity, precision, and throughput. Missing values are reduced to the absolute minimum. We perform deep proteomic screenings on a much larger scale than previously thought possible and profile libraries of 1,000s to 10,000s of degrader drugs. These high-throughput capabilities also support rapid proteome-wide selectivity profiling within drug optimization cycles, providing valuable data when needed in compound development.

FULLY AUTO-
MATED AND
SCALABLE
WORKFLOWS

Systematic and well-designed automation minimizes errors in every step of deep proteomic screening while keeping throughput flexibly scalable. We have optimized, digitized, and automated both wet lab and data analysis workflows to push our operational efficiency to new levels. That same efficiency also allows us to easily scale processes, infrastructure, and personnel to offer deep proteomic screening at any throughput level.

HIGH-QUALITY
DATA
DELIVERY

Unlike conventional screening against one or a few proteins, replicates are mandatory when examining 10,000 or more proteins. Our proteomics screens record each compound treatment in triplicate. This screen design not only filters out noise associated with highly multiplexed protein quantification, but also identifies statistically significant downregulation of candidate targets already at the screening stage.

EXPERT DATA
HANDLING AND
ANALYSIS

Our world-class team of scientists is highly experienced in processing and interpreting large-scale proteomics data. We apply effective scoring schemes to extract candidates that are likely directly downregulated by degrader molecules and not the outcome of secondary regulation. We guide our screens by monitoring candidate identification in real-time and adjust key parameters in a data-driven manner to maximize target return rates.

PROTEOMIC
VALIDATION
OF DEGRADER
TARGETS

We mechanistically validate degrader targets, such as E3 ligase neosubstrates, to establish novel starting points for drug discovery. After verifying dependence of degradation on the ubiquitin-proteasome system, we demonstrate the interaction between neosubstrates and E3 ligase and confirm drug-induced ubiquitination, both in situ. Built on world-leading ubiquitinomics expertise and MS technology, the platform reliably quantifies up to 50,000 ubiquitination sites in single MS runs.

SYSTEMATIC
MAPPING OF
NOVEL
TARGET SPACE

Our integrated proteomics platform systematically links degrader compounds to their targets, such as E3 ligase neosubstrates. Many of these reside in the previously undruggable or inadequately drugged target space and thus, represent a unique source of novel, high-value targets for future therapeutics. This expansion of target scope also enables and refines computational approaches, including structural and AI-based predictive modeling of novel degrader drugs for actionable targets. An iterative and highly synergistic interplay between computational predictions and experimental proteomics will accelerate progress in targeted protein degradation.