Molecular Glues and Targeted Protein Degradation

Identify protein-protein interactions (PPI)  induced by small molecules with our versatile Y2HChem screening platform, a Y2H-based technology.

Your Applications

Chemically induced proximity

Molecular glues or bifunctional molecules like PROTACs® are promising chemical modalities to expand the druggable proteome in drug discovery. They promote the formation of ternary complexes, bringing proteins with low or no affinity together. These complexes trigger downstream signaling.

  • Targeted Protein Degradation (TPD): Degraders target the disease-causing protein for destruction, utilizing the ubiquitin associated cellular machinery to induce degradation.
  • Targeted Protein Stabilization (TPS): Stabilizers protect proteins from their degradation.

Our Technology

A versatile screening platform

In our Y2HChem system, a protein used as bait (Protein of Interest POI or E3 ligase) and a small molecule (mono or bivalent) are screened together against our highly complex cDNA domain libraries (the targets).
Our versatile screening platform identifies:

  • Protein-protein interactions induced by a small bioactive molecule (deconvolution)
  • E3 ligases that bring your POI to degradation
  • New molecules stabilizing protein-protein interactions
  • Potential off-targets of protein degraders

Our solutions

 Y2HChem Principle

Y2HChem Principle
Unbiased proteome wide or E3 ligases focused libraries
Key-benefits of our Y2HChem screening technology
Deliverables
Interactions validation
PPIs modulated by small molecules
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The Y2HChem relies on the reconstitution of a functional transcription factor (TF) followed by the expression of a reporter gene in genetically modified yeast cells. Upon a small molecule-induced PPI (mono or bivalent molecule), the DNA Binding Domain (DBD) of the TF is brought in close proximity to its Activation Domain (AD). This activates the transcription of the HIS3 reporter gene, allowing yeast cells to grow on selective medium lacking histidine.

The technique involves 3 components:

  • Your protein of interest fused to the DBD
  • Target proteins (fragment) fused to the transcriptional AD (the library)
  • A small molecule
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We offer a large collection of cDNA and genomic libraries (135+) to accommodate your screening project. The libaries are constructed from tissues, cell lines, primary cells or whole organisms derived from various species including human, rodents, plants, bacteria, etc. Using a patent cell-to-cell mating assay, libraries are screened to saturation, averaging an 8-fold in library coverage. Go to Our Libaries


We can construct new libraries on demand to meet your needs.

For Y2HChem projects dedicated to Protein Degradation with Molecular Glues or bifunctional molecules, we can construct focused E3 ligase libraries (full-length or domain-enriched).

Key-benefits of our technology

  • Identification of direct interactions
  • Enhanced drug intake thanks to proprietary permeable yeast strain
  • Exhaustive and unbiased in vivo screening of highly complex domain libraries
  • Putative partners are screened individually in a different yeast colony
  • No competition with abundant or strong interacting partners
  • High sensitivity transcriptional readout and no washing steps
  • Integrated bioinformatics: Includes assigning confidence scores & mapping of the interacting domains
  • Flagged false positives
  • Flexible screening platform

The results of each Y2HChem screen are summarized in three complementary user-friendly deliverables:

  • A Results summary with the identified protein partners, the detailed fragments and our confidence score- Predicted Biological Score, PBS®.
  • An Excel® table with the sequences and the Genbank accession number and relevant IDs from e.g. Flybase, Wormbase, TAIR.
  • The ‘DomSight’ contains a graphical comparison of the experimental interacting domain for each partner and the Smalles Interacting Domain SID®, with known functional and structural domains


Our scientific project leaders support the interpretation of your results and help you to focus on the most relevant interactions for the best outcome of your project.

After results delivery, we can perform different validation experiments using the same technology:

  • 1-by-1 in cell validation assays with selected protein targets identified in the Y2HChem screen to confirm binding induced by the small molecule and check specificity.
  • Test side-by-side interactions with active and inactive compounds
  • Interaction Domain Mapping (IDM) experiments can be performed to further delineate the minimal domain of interaction.
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We have developed complementary high-throughput assays to either stabilize or inhibit PPIs with small molecules.

  • Y2HChem cell-based assays in 96- or 384-well plates format using HIS3, LacZ or luciferase reporters (1-to-1 format or focused library of protein preys).
  • in vitro HTRF® assays in 96- or 384-well plates format for a given protein-protein interaction.
  • Chemical libraries available: FDA approved compounds and PPIChem
  • Expertise in ubiquitin and deubiquitin enzymes.

Our Publications

Customer Publications

An Academic Compound Library Dedicated to Protein-Protein Interactions.

Bosc N, Muller C, Hoffer L, Lagorce D, Bourg S, Derviaux C, Gourdel ME, Rain JC, Miller TW, Villoutreix BO, Miteva MA, Bonnet P, Morelli X, Sperandio O, Roche P. Fr-PPIChem. ACS Chem Biol. 2020 Jun 19;15(6):1566-1574. doi: 10.1021/acschembio.0c00179. Epub 2020 May 5. PMID: 32320205; PMCID: PMC7399473.

Discovery of specific inhibitors of human USP7/HAUSP deubiquitinating enzyme.

Reverdy C, Conrath S, Lopez R, Planquette C, Atmanene C, Collura V, Harpon J, Battaglia V, Vivat V, Sippl W, Colland F. Chem Biol. 2012 Apr 20;19(4):467-77. doi: 10.1016/j.chembiol.2012.02.007. PMID: 22520753.

FAQ

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