Protein Degrader Building Blocks

3D model of a co-crystal structure with the PROTAC in green binding to the target in yellow and the E3 ubiquitin in pink for targeted protein degradation.

Targeted protein degradation (TPD) is a novel approach used in drug discovery to effectively infiltrate cell’s proteasomal degradation pathway and quickly eliminate the target proteins from cells. This strategy has the potential to develop new therapeutics that differ considerably from classical inhibitors and is even viable for accessing “undruggable” protein targets and difficult-to-treat diseases.

Our diverse portfolio of protein degrader building blocks allows you to easily generate libraries of protein degraders that can be screened for an effective degradation of your target proteins from the cells. Our protein degraders, such as proteolysis targeting chimeras (PROTAC® molecules), are bifunctional molecules with three primary components:

  • Ligand at one end that targets the protein of interest (POI)
  • Second ligand at the opposite end that binds an E3 ligase
  • Crosslinker in the middle that joins the two ends

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Protein Degrader Building Block Portfolio

Our protein degrader building blocks are permutations of the following components:

  • Ligands targeting the E3 ligase Cereblon (CRBN) or von Hippel–Lindau (VHL)
  • Crosslinkers with varied lengths and compositions
  • Conjugation sites with reactivity for common functional groups

All You Need for Successful Targeted Protein Degradation

The simultaneous degrader binding of two proteins brings the POI in close enough proximity for polyubiquitination to take place by the E2 enzyme associated to the E3 ligase, which flags the POI for degradation through the proteasome.

The precise design of small-molecule target degraders is crucial for successful protein degradation. Even slight alterations in ligands and crosslinkers can affect binding to the POI or E3 ligase. Thus, many analogs are synthesized, varying each structure slightly, and screened in cells to determine the optimal degrader for target degradation.

Our degrader building blocks are a collection of crosslinker-E3 ligand conjugates with a pendant functional group for covalent linkage to a target ligand to streamline synthesis. Since the same functional group is present across a series, one target ligand can be conjugated to several degrader building blocks simultaneously for facile library generation and subsequent screening.

Advantages of Our Protein Degraders

  • Compatibility: Linkers conjugate to common functional groups present on target ligands
  • Molecule design: The strategic variety of the combinations of linkers and ligands aids the design of target degraders
  • Synthetic time-saver: The E3 ligand-crosslinker conjugates decrease the amount of time spent on degrader synthesis
  • Library generation: Using degrader building blocks with the same conjugation site enables the simultaneous generation of several degraders via parallel synthesis

PROTAC® is a registered trademark of Arvinas Operations, Inc., and is used under license.

Related Webinars

An open laptop with a colorful display featuring a stylized human figure in blue on the right and a pink rectangle on the left against a yellow background.
Webinar: Targeted Protein Degradation Using Small Molecules

Learn how Protacs work for targeted protein degradation to widen the spectrum of targetable proteins.

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