Identification of Drug-Target Interactions

Our YChemH screening platform is dedicated to identifying direct proteins targets of small bioactive molecules  and the understanding of their mode of action.

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Our Technology

ULTImate YChemH

The discovery of small molecule bioactives or first-in-class drugs often begins with identifying the function of possible therapeutic target(s). Our yeast three-hybrid system (Y3H) technology can support your early drug discovery program by: 

  • Elucidating Mechanism of Action of small molecule coming from a phenotypic screen, 
  • Identifying off-target interactions to anticipate side-effects of your lead compound and selection of the best clinical candidate and
  • Drug repurposing to identify new therapeutic use(s) of an existing drug.

Our Technology

ULTImate YChemH

Our ULTImate YChemH™ is a modified version of our Y2H system that enables the identification of direct protein targets (on or off-targets) of a small bioactive molecule. In the YChemH approach, a tagged probe of the molecule of interest is used as a bait to screen for protein targets from one of our 135+ domain-enriched high-complex cDNA libraries prepared from any cell type, tissue or organism.
Thanks to our complete solution, you'll be able to optimize the success rate of your drug discovery program.

Our solutions

ULTIMATE YChemH Principle

ULTIMATE YChemH Principle
Our ULTImate Libraries
ULTImate YChemH key Benefits
Deliverables
Interactions validation
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The Yeast Three-Hybrid 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 drug–target protein interaction, 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 DNA of positive clones are sequenced to reveal the interacting partners.


The YChemH technology is a three-component system

  • A hook protein fused with a DBD
  • A target protein library fragment fused to the transcriptional AD
  • A small molecule tagged with a ligand that binds to the hook protein
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We offer a large collection of cDNA and genomic libraries (135+) to accommodate your target identification 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.
New libraries are constructed upon request.

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  • Identification of direct protein targets
  • Reduced drug efflux due to the creation of a proprietary mutant yeast strain
  • Exhaustive and unbiased whole proteome screening approach
  • Uncovers multiple targets in a single screen, but only one at a time.
  • Highly sensitive transcriptional readout - Detection of weak and rare interactions
  • No competition with abundant or strong interacting partners; no washing steps
  • Technically simplistic method: Yeast used as a screening tool; no mass spectrometry equipment
  • Integrated bioinformatics: Includes assigning confidence scores & mapping of the interacting domains
  • Flagged false positives
  • Quick turnaround
circleDownload our YChemH Infographic

The results of your ULTImate YChemH screen are summarized with 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® raw data table with the sequences and the Genbank accession number
  • The ‘DomSight’ contains a graphical comparison of the experimental interacting domain for each partner and the SID®, with known functional and structural domains
    Our scientific project leaders support the interpretations of your results and help you to focus on the most relevant interactions for the best outcome of your project.
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The following in-yeast validation experiments can be performed after a YChemH screen:

  • 1-by-1 in cell validation assays with selected protein targets identified in the YChemH screen (include negative controls) to confirm binding and check specificity
  • Competition experiments using a defined concentration of chemical probe, the desired protein target and in the presence of increasing concentrations of "free" active or inactive compound
  • Interaction Domain Mapping experiments (IDM) in order to better define the interaction domain
circleContact our Experts

Our solutions

ULTIMATE YChemH Principle

+

The Yeast Three-Hybrid 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 drug–target protein interaction, 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 DNA of positive clones are sequenced to reveal the interacting partners.


The YChemH technology is a three-component system

  • A hook protein fused with a DBD
  • A target protein library fragment fused to the transcriptional AD
  • A small molecule tagged with a ligand that binds to the hook protein
circleContact our Experts
+

We offer a large collection of cDNA and genomic libraries (135+) to accommodate your target identification 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.
New libraries are constructed upon request.

circleContact our Experts
+
  • Identification of direct protein targets
  • Reduced drug efflux due to the creation of a proprietary mutant yeast strain
  • Exhaustive and unbiased whole proteome screening approach
  • Uncovers multiple targets in a single screen, but only one at a time.
  • Highly sensitive transcriptional readout - Detection of weak and rare interactions
  • No competition with abundant or strong interacting partners; no washing steps
  • Technically simplistic method: Yeast used as a screening tool; no mass spectrometry equipment
  • Integrated bioinformatics: Includes assigning confidence scores & mapping of the interacting domains
  • Flagged false positives
  • Quick turnaround
circleDownload our YChemH Infographic

The results of your ULTImate YChemH screen are summarized with 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® raw data table with the sequences and the Genbank accession number
  • The ‘DomSight’ contains a graphical comparison of the experimental interacting domain for each partner and the SID®, with known functional and structural domains
    Our scientific project leaders support the interpretations of your results and help you to focus on the most relevant interactions for the best outcome of your project.
circleContact our Experts

The following in-yeast validation experiments can be performed after a YChemH screen:

  • 1-by-1 in cell validation assays with selected protein targets identified in the YChemH screen (include negative controls) to confirm binding and check specificity
  • Competition experiments using a defined concentration of chemical probe, the desired protein target and in the presence of increasing concentrations of "free" active or inactive compound
  • Interaction Domain Mapping experiments (IDM) in order to better define the interaction domain
circleContact our Experts

our publications

Customer Publications

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MNK2 deficiency potentiates β-cell regeneration via translational regulation

Christos Karampelias, Kathleen Watt, Charlotte L. Mattsson, Ángel Fernández Ruiz, Habib Rezanejad, Jiarui Mi, Xiaojing Liu, Lianhe Chu, Jason W. Locasale, Gregory S. Korbutt, Meritxell Rovira, Ola Larsson & Olov Andersson, Nature Chemical Biology June 2022

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PAPD5/7 Are Host Factors That Are Required for Hepatitis B Virus RNA Stabilization.

Mueller H, Lopez A, Tropberger P, Wildum S, Schmaler J, Pedersen L, Han X, Wang Y, Ottosen S, Yang S, Young JAT, Javanbakht H. Hepatology. 2019 Apr;69(4):1398-1411. doi: 10.1002/hep.30329. Epub 2019 Mar 1. PMID: 30365161.

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A fishing expedition for antidiabetic drugs : identifying new avenues to stimulate beta-cell regeneration

Karampelias, C., Thesis, Karolinska Institutet, 2021.

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Chemical Dimerizers in Three-Hybrid Systems for Small Molecule-Target Protein Profiling

De Clercq DJ, Tavernier J, Lievens S, Van Calenbergh S. ACS Chem Biol. 2016 Aug 19;11(8):2075-90. doi: 10.1021/acschembio.5b00811. Epub 2016 Jun 20. PMID: 27267544.

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FAQ

Do you have a question?

Under confidentiality agreement, we discuss together if your project is ready to move for a target ID study.


Whatever the technique, the more you know about your compound(s) and biology, the more effective the target deconvolution will be.


If structure-activity relationship hypothesis (SAR) are not yet available or not strong enough, we can help driving your medicinal chemistry efforts.


Use of complementary methods is recommended. The Y3H system is a straightforward target ID method and doesn't require specific equipment like Mass Spec.. Our integrated bioinformatics will make the analysis of the results easier.

Y3H and YchemH publications:

  • Wang P, et al.. Using the yeast three-hybrid system for the identification of small molecule-protein interactions with the example of ethinylestradiol. Biol Chem. 2022
  • Moser, S., et al. Yeast three-hybrid screening for identifying anti-tuberculosis drug targets. ChemBioChem 2013
  • Cottier S, et al. The yeast three-hybrid system as an experimental platform to identify proteins interacting with small signaling molecules in plant cells: potential and limitations. Front Plant Sci. 2011
  • Chidley C, et al. A yeast-based screen reveals that (..) inhibits tetrahydrobiopterin biosynthesis. Nat Chem Biol. 2011.

Yes, the YChemH technology can identify both functional targets as well as off-targets depending on where the small molecule compound is tagged. Our animal-free and unbiased YChemH approach is dedicated to evaluate the polypharmacology of your molecule. We can identify unexpected targets guiding you in lead optimization or clinical candidate selection.


Drug discovery and development is a risky and expensive process. Late-stage failures of drug candidates have emphasized the importance of understanding their mode of action. One drug can have multiple targets that will affect various biological processes in different ways including side-effects. “Fail fast, fail early” to eliminate risks due to off-targets and toxicity.


You may also discover opportunities for drug repositioning.

Our YChemH screening platform can accomodate different tag systems: DHFR with  TMP or MTX ligand, Halo-tag or Snap-tag technologies. We have optimized the screening conditions for the E. coli DHFR and TMP pair for the best signal/noise ratio. (E. coli DHFR Ki 0.17 nM (Cammarata M, et al. Chem Sci. 2017)).


Tagging strategy for the YChemH with a TMP ligand is similar to affinity pull-down + MS that uses a biotin ligand. You can carry out the tagging yourself or ask us to take care of it for you.

Yes, it's a straightforward and technically simple method. You will benefit from the most comprehensive Y2H technology, our highly complex libraries and a quick turnaround time. False positive rate is reduced thanks to the dependency assay and the confidence scores ofr each interaction.

 

Please find additional publications with more information:

  • Wang P, et al.. Using the yeast three-hybrid system for the identification of small molecule-protein interactions with the example of ethinylestradiol. Biol Chem. 2022
  • Moser, S., et al. Yeast three-hybrid screening for identifying anti-tuberculosis drug targets. ChemBioChem 2013
  • Cottier S, et al. The yeast three-hybrid system as an experimental platform to identify proteins interacting with small signaling molecules in plant cells: potential and limitations. Front Plant Sci. 2011
  • Chidley C, et al. A yeast-based screen reveals that S inhibits tetrahydrobiopterin biosynthesis. Nat Chem Biol. 2011.

Yes, we can provide you with our mutual confidentiality agreement (CDA) template. We can also work with your CDA template.

Yes, you own the IP of the results. Our drug-target identification platform is available on a fee-for-service basis.

My lab has previously used Hybrigenics services to perform Yeast two-hybrid screens. The data that they provided initiated a new direction in our research. They also used Y2H screening to select..

Dr. Emilia Galperin
University of Kentucky

We asked Hybrigenics to select intrabodies against four different proteins involved in vesicular trafficking. They quickly provided us with several candidates per protein, in the form of ready-to-use..

Dr. Thierry Galli
Jacques Monod Institute

My group has been using the services provided by Hybrigenics to perform Y2H screens from Arabidopsis thaliana libraries using viral proteins as baits at several occasions, and has been very satisfied.

Dr. Isabelle Jupin
Jacques Monod Institute
×

My lab has previously used Hybrigenics services to perform Yeast two-hybrid screens. The data that they provided initiated a new direction in our research. They also used Y2H screening to select nanobodies working as intrabodies against our protein of interest. Hybrigenics team have put a large effort to provide us with several candidate clones. All the clones were provided as plasmids for mammalian expression and went through the initial validation. After a more in-depth validation, we now have reagents that work in several different assays. I am very impressed with the customer service and dedication of the scientific team at Hybrigenics.

Dr. Emilia Galperin
University of Kentucky
×

We asked Hybrigenics to select intrabodies against four different proteins involved in vesicular trafficking. They quickly provided us with several candidates per protein, in the form of ready-to-use plasmids for mammalian expression. We already validated some of these intrabodies. Fused to a red fluorescent protein, they will be extremely valuable tools to block our target proteins in live cells.

Dr. Thierry Galli
Jacques Monod Institute
×

My group has been using the services provided by Hybrigenics to perform Y2H screens from Arabidopsis thaliana libraries using viral proteins as baits at several occasions, and has been very satisfied.
Not only Hybrigenics teams have a great expertise in bait design, in performing high-coverage screens, and most importantly in scoring the candidates obtained and pinpointing the technical false-positives - which are invaluable assets, but I also found very enjoyable to work with them.
They are friendly, supportive, and highly competent, and I always appreciated the discussions we had together.
I will for sure never ever perform a yeast two-hybrid screen myself again and I strongly recommend their high-quality services, which are really worth the price.

Moreover, following a very successful yeast two-hybrid screen using one of our viral protein as a bait, our group also got the chance to make use of their newly developed Hybribody service, i.e. synthetic single chains nanobodies. Hybrigenics selected several VHH intrabodies, which they further validated in mammalian cells using fluorescence microscopy. Our lab is now currently validating them in plant cells and the preliminary data we obtained appear very promising. In addition to their use as basic research tools to detect our proteins in living cells, the intrabodies obtained may as well turn useful to inhibit key steps in the viral multiplication process, thus opening new possibilities for designing antiviral strategies.

Dr. Isabelle Jupin
Jacques Monod Institute

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