Targeted Protein Degradation (TPD) Assays and Profiling

CD Biosynsis specializes in comprehensive Targeted Protein Degradation (TPD) Assays and Profiling, crucial for the discovery and development of novel therapeutics, including PROTACs (Proteolysis Targeting Chimeras) and molecular glue degraders. TPD represents a powerful modality that leverages the ubiquitin-proteasome system (UPS) to specifically eliminate disease-causing proteins. Our platform provides a robust, quantitative pipeline covering every stage: from confirming ternary complex formation to measuring the degradation kinetics (DC50, Dmax) and assessing selectivity. We utilize advanced technologies like high-content imaging (HCI), Western blotting, and quantitative mass spectrometry (e.g., PRM/SRM). Choose from our extensive library of validated targets and E3 ligases to build a custom profiling panel tailored to your TPD program.

Get a Quote  
Overview Services Offered Service Workflow Advantages Customer Reviews FAQs Contact Us

A Comprehensive Platform for Degrader Therapeutics

The success of Targeted Protein Degradation hinges on proving the complete destruction of the target protein and elucidating the mechanism of action. Our integrated platform is designed to rigorously validate each step: target binding, E3 ligase recruitment, ubiquitination, and proteasomal degradation. We offer cellular assays to measure functional degradation (DC50 and Dmax), high-throughput methods to confirm ternary complex formation, and highly selective mass spectrometry approaches to accurately quantify target protein levels. This comprehensive and customizable approach minimizes the risk of false positives and provides the critical mechanistic evidence required for moving PROTACs and molecular glues into preclinical studies.

Customizable TPD Target and E3 Ligase Profiling

Selectable Target Proteins (POIs) Selectable E3 Ligases Selectable Assay Modules

Target Proteins of Interest (POI)

Choose Target Proteins for Degradation Analysis

Check the box next to the Target Protein you wish to profile for degradation:

BRD4 (Bromodomain-containing protein 4)

BTK (Bruton's Tyrosine Kinase)

ERα (Estrogen Receptor alpha)

KRAS (Select Mutant Alleles)

CDK9 (Cyclin-Dependent Kinase 9)

AR (Androgen Receptor)

STAT3 (Signal Transducer and Activator of Transcription 3)

Custom Target (Client-Provided)

E3 Ligase Recruitment Profiling

Choose E3 Ligases for Complex Formation Assays

Select the E3 Ligase recruitment pathways you require for mechanistic validation:

CRBN (Cereblon-dependent degradation)

VHL (Von Hippel-Lindau-dependent degradation)

MDM2 (Mouse Double Minute 2)

cIAP1 (Cellular Inhibitor of Apoptosis 1)

RNF4 (RING finger protein 4)

DCAF15 (DDB1 and CUL4-Associated Factor 15)

ARIH1 (Ariadne Homolog 1)

Other E3 Ligase (Inquire)

Available Assay Modules

Select the Quantitative and Mechanistic Services

DC50 and Dmax Determination

Quantitative measurement of degradation potency and efficacy in cellular models (via Western Blot or Quantitative MS).

Ternary Complex Formation (TCF)

Biophysical confirmation of the Target-Degrader-E3 Ligase complex using AlphaLISA, TR-FRET, or SPR assays.

Global Proteomics Selectivity

Unbiased screening using TMT/SILAC Mass Spectrometry to identify non-intended off-target protein degradation.

Targeted Protein Degradation Assay Workflow

A staged approach from binding confirmation to functional output.

Assay Development and Cell Line QC

Ternary Complex Formation (TCF) Validation

Cellular Degradation and Kinetics

Selectivity and Mechanism Reporting

Cell Line Prep: Validate endogenous or recombinant cell lines expressing the selected target protein and E3 ligase.

Baseline Quantification: Establish the optimal method (WB, MS, or HCI) and determine baseline target protein levels.

MoA Confirmation: Perform biophysical assays (e.g., AlphaLISA) to confirm that the degrader successfully bridges the target protein and selected E3 ligase.

Hook Effect Screening: Determine the compound concentration range where the ternary complex is stable and functional.

Dose-Response: Treat cells with varying degrader concentrations and measure protein levels at a fixed time point to calculate DC50 and Dmax.

Kinetics: Conduct time-course experiments to determine the rate of degradation and monitor target re-synthesis post-washout.

  • Specificity Checks: Test degradation in E3 knockout cells or perform parallel cellular profiling for key off-targets.
  • Proteomics Analysis: Run quantitative proteomics on top hits for global off-target assessment (if selected).
  • Reporting: Deliver quantitative DC50/Dmax values, TCF data, kinetic curves, and full mechanistic validation.

Leading-Edge Expertise in PROTAC and Molecular Glue Discovery

Quantitative MS for DC50

           

Superior accuracy using PRM/SRM or TMT-based mass spectrometry for highly precise protein quantification.

Ternary Complex Validation

           

Biophysical assays (AlphaLISA, TR-FRET) to confirm the direct engagement and bridging of the E3 ligase and target protein.

Global Selectivity Profiling

           

TMT-based quantitative proteomics for unbiased screening of all cellular proteins for off-target degradation.

Challenging Target Expertise

           

Specialized methods for targets with low natural expression or those requiring specific cellular contexts for degradation.

Client Testimonials on TPD Assays

"The TCF assay validation was critical for our PROTAC design. The TR-FRET data definitively proved complex formation, saving us months of empirical testing."

Dr. Lena Olin, PROTAC Chemistry Lead

"The quantitative proteomics profiling was indispensable. It confirmed our target was selectively degraded and identified two minor off-targets, which guided our next synthetic steps."

Mr. Kenji Sato, Molecular Glue Development

"The DC50/Dmax determination using their PRM mass spectrometry approach provided superior precision compared to our standard Western blot, leading to a much clearer rank-ordering of our leads."

Ms. Clara Davis, Translational Biology Manager

FAQs about Targeted Protein Degradation (TPD) Assays

Still have questions?

Contact Us

What is the difference between IC50 and DC50 in TPD?

IC50 measures the concentration required for 50 percent inhibition of enzyme activity. DC50 measures the concentration required for 50 percent degradation of the target protein level in a cell, which is the functional measure of a degrader.

Why is the Hook Effect important to analyze?

The Hook Effect occurs at high degrader concentrations where the degrader saturates the binding sites on either the E3 ligase or the target protein, preventing the necessary trimerization (bridging) and leading to a loss of degradation efficacy.

How do you confirm that the degradation is proteasome-dependent?

We confirm proteasome dependence by co-treating cells with the degrader and a known proteasome inhibitor (e.g., MG132 or Bortezomib). If the degradation is successfully blocked by the inhibitor, it confirms the proteasome-mediated mechanism.

What is the advantage of using quantitative MS (PRM/SRM) over Western Blot?

Quantitative MS offers superior precision, a wider dynamic range, and the ability to multiplex many targets simultaneously, making it ideal for accurate DC50 determination and global off-target screening where antibody validation may be challenging.

How much does Metabolic Engineering services cost?

The cost of Metabolic Engineering services depends on the project scope, complexity of the target compound, the host organism chosen, and the required yield optimization. We provide customized quotes after a detailed discussion of your specific research objectives.

Do your engineered strains meet regulatory standards?

We adhere to high quality control standards in all strain construction and optimization processes. While we do not handle final regulatory approval, our detailed documentation and compliance with best laboratory practices ensure your engineered strains are prepared for necessary regulatory filings (e.g., GRAS, FDA).

What to look for when selecting the best gene editing service?

We provide various gene editing services such as CRISPR-sgRNA library generation, stable transformation cell line generation, gene knockout cell line generation, and gene point mutation cell line generation. Users are free to select the type of service that suits their research.

Does gene editing allow customisability?

Yes, we offer very customised gene editing solutions such as AAV vector capsid directed evolution, mRNA vector gene delivery, library creation, promoter evolution and screening, etc.

What is the process for keeping data private and confidential?

We adhere to the data privacy policy completely, and all customer data and experimental data are kept confidential.

Get a free quote

If your question is not addressed through these resources, you can fill out the online form below and we will answer your question as soon as possible.

CD Biosynsis

Copyright © 2025 CD Biosynsis. All rights reserved.