Mass Spectrometry Proteomics is Key to Realizing the Potential of Targeted Protein Degraders

Mass Spectrometry Proteomics is Key to Realizing the Potential of Targeted Protein Degraders

Targeted protein degradation is an exciting new strategy in drug development with applications in a wide range of diseases, from cancer to neurodegeneration to autoimmune conditions (Mullard, 2021).


Rather than using conventional small molecules or antibodies that bind to a target and inhibit its function, targeted protein degradation directs harmful proteins for destruction by the cell’s own degradation machinery. A detailed understanding of protein interactions and dynamics is therefore an essential component of research into these potentially game-changing therapeutics.


Mass spectrometry proteomics is the perfect tool for this task, providing detailed data about target binding, degradation selectivity and mechanism of action in the early stages of drug development, as well as information about efficacy and safety in preclinical and clinical phases (Zhang et al., 2021).


At Biognosys, we are always pushing the boundaries of mass spectrometry to develop new and exciting applications that support the latest advances in drug discovery and development.


Targeted protein degradation is one of our key therapeutic focus areas, and our three next-generation mass spectrometry (MS) proteomics research service platforms – TrueDiscovery™, TrueTarget™ and TrueSignature™ – all have something to offer biopharma companies working in this fast-growing field. Let’s take a closer look.



TrueDiscovery: Supercharging the search for novel targeted protein degraders


The quest for novel targeted protein degraders starts with discovery – finding and evaluating molecules that interact with both the target protein and the cellular degradation machinery, such as the E3 ligase pathway (Lee et al., 2022). This requires a technology with sufficient sensitivity and specificity to evaluate the effects of compounds on protein levels, with the speed and scale to carry out high-throughput screening.


TrueDiscovery, our ultra-deep mass spectrometry platform, is the ideal companion for this phase of drug development. Identifying and quantifying thousands of proteins and proteoforms, TrueDiscovery enables the deepest profiling of tissue and biofluid proteomes with unbeatable specificity.


By taking an unbiased proteome-wide approach, we not only measure changes in the level of the target and turnover rates but can reveal alterations in downstream pathways resulting from its removal. TrueDiscovery can uncover off-target effects, flagging up potential safety signals that could cause issues later down the line. And it can also identify novel components of the degradation machinery and mechanisms to target in the future.


Ultimately, this aids a deeper understanding and prioritization of leads, helping to progress the most effective and safe compounds towards the clinic faster and more efficiently.



TrueTarget: In-depth lead characterization to de-risk targeted protein degraders


Once a potential lead compound has been identified, it is important to fully characterize its interactions with the target to ensure that it is binding and behaving as expected. Ensuring selectivity is one of the most important aspects of targeted protein degrader development, as unanticipated off-target activity can cause serious side effects (Zhang et al., 2021).


Powered by limited proteolysis mass spectrometry (LiP-MS) and available exclusively from Biognosys, our TrueTarget platform maps drug-target interactions with peptide-level resolution to support target validation and lead optimization.


LiP-MS works by digesting treated and untreated cell extracts proteins with proteases, creating distinctive peptide fingerprints based on where and how the drug is bound. These peptides are then identified and quantified with high-precision mass spectrometry, revealing detailed information about on- and off-target binding events and generating a ranked list of predicted drug targets across the proteome.


A high-resolution version of the technology, HR-LiP, takes a more in-depth look at specific drug-target interactions and can identify with peptide-level resolution where a drug is binding to its target. HR-LiP provides profound structural and mechanistic insights, such as conformational changes or allosteric effects induced by binding.


Recently, we applied TrueTarget in collaboration with researchers at the University of Cambridge to study the binding of novel activators of VCP/p97, a key component of the proteasomal protein degradation pathway and an exciting emerging target in a number of neurodegenerative diseases.


Publishing our findings in Nature Communications, we confirmed VCP/p97 as a target for the novel activator SMER28 and showed where it binds within the protein (figure 1). In turn, this helped the research team delineate the mechanism of action involving the clearance of toxic proteins via the ubiquitin-proteasome pathway and autophagy (Wrobel et al., 2022).



Figure 1: HR-LiP peptides (red, orange) predict the likely binding site of SMER28 (yellow) to be between the substrate binding domain (green) and the ATPase domain (purple, blue) of VCP.



TrueSignature: Turning up the sensitivity on targeted protein degradation pharmacodynamics


Accurate protein quantification is essential when it comes to preclinical and clinical pharmacodynamic assessments of novel targeted protein degraders, which are critical to confirm efficacy and safety. TrueSignature, our fully quantitative, targeted proteomics platform, generates highly accurate measurements of protein dynamics in tissues or blood plasma to measure target and degradation pathway engagement.


Unlike affinity-based proteomics methods, which rely on having antibodies against the biomarkers of interested, TrueSignature is able to accurately measure any protein or proteoform, including mutated variants and post-translational modifications that may be highly relevant for targeted protein degradation.


Underpinned by the latest precision mass spectrometry technology, FAIMS-PRM, and our exacting internal standards, we can achieve unprecedented attomole levels of sensitivity, as highlighted in results presented at the 2022 Keystone Symposium for Targeted Protein Degradation.


Our custom TrueSignature panels can robustly and reproducibly measure up to 70 different proteins in a single multiplexed assay, covering all aspects of the target biology and protein degradation pathways. Panels can be applied across a wide range of sample types, including blood plasma and serum, and fresh frozen or formalin-fixed tissue. And we can deliver regulatory-grade data through our GCP certified and GLP compliant facility if required.



Taking targeted protein degraders from the lab to the clinic


The ultimate success of the emerging field of targeted protein degradation requires a deep understanding of what’s going on at the level of the proteome. Mass spectrometry proteomics is the only technique that can reliably offer this detailed information required to develop targeted protein degraders from the early discovery stages through to clinical testing.


At Biognosys we have the proteomics tools you need to support the development of targeted protein degraders, from high-throughput proteome-wide assays in early discovery to lead optimization and clinical biomarkers. As an example, we’re delighted to be partnering with leading targeted protein degradation specialists Kymera Therapeutics to apply our precision TrueSignature proteomics panels in their preclinical and clinical studies.


We are now stepping up our high-throughput capabilities thanks to a strategic partnership with leading MS instrumentation manufacturer Bruker. We’ll be opening an advanced proteomics facility in the US, offering an even faster service and breaking through the bottleneck for high-throughput discovery and clinical research.


If you are developing targeted protein degrader therapeutics, contact us today to find out how our next generation proteomics platforms could help take your leads from the lab to the clinic.




  1. Mullard, A (2021). Targeted protein degraders crowd into the clinic. Nature Reviews Drug Discovery 20(4), pp.247–250. doi:10.1038/d41573-021-00052-4.
  2. Zhang, AX et al. (2021) The Vital Role of Proteomics in Characterizing Novel Protein Degraders. SLAS Discovery 26(4):518-523. doi: 10.1177/2472555220985776.
  3. Lee, J et al. Discovery of E3 Ligase Ligands for Target Protein Degradation. Molecules. 2022 Oct 2;27(19):6515. doi: 10.3390/molecules27196515. PMID: 36235052; PMCID: PMC9573645.
  4. Wrobel, L et al. (2022). Compounds activating VCP D1 ATPase enhance both autophagic and proteasomal neurotoxic protein clearance. Nature Communications 13(1). doi:10.1038/s41467-022-31905-0.
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