Targeted Protein Degradation Assays
Target-specific Assays

Protein Degradation Assay – PROTAC Screening

Protein degraders comprise a class of molecules that induce protein degradation of a specific disease-causing protein by the cell’s ubiquitin-proteasome pathway. In the past few years, various molecule classes have evolved, including PROTACs (Proteolysis-targeting chimeras), molecular glue, selective receptor degraders, and cerebron-binding molecules, to name a few.

All compounds to be screened in protein degradation assays have in common a drug discovery approach that is different from the classic inhibition of the function of a target. The discovery of new molecules facilitating targeted protein degradation requires a set of assays to investigate the binding of a drug to target, the structure of the drug-target complex, and the degradation of the target from the cell.

Reaction Biology works with Medinoah to accelerate the discovery of new drugs facilitating targeted protein degradation. Medinoah is a medicinal chemistry provider with expertise in drug synthesis and structural optimization and is one of the earliest CROs entering the PROTAC field. Together we offer the Rethinking PROTAC platform – a one-stop shop for the integrated discovery of new PROTAC molecules.

Protein Degradation via PROTACs

A PROTAC molecule consists of three parts – the target binding head, an E3 ligase interacting part, and the connecting linker. The PROTAC draws the target into a ternary complex with the ubiquitination complex tagging the target for degradation via proteasomes.

Because PROTACs open new possibilities to tackle difficult targets, these entities may well revolutionize conventional drug discovery.

The PROTAC draws the target into a ternary complex with the ubiquitination complex tagging the target degradation via proteasomes.

Workflow for the discovery of new targeted protein degradation molecules.

  1. The binding affinity of new compounds to the target and the ligase can be tested via microscale thermophoresis (MST), thermal shift assay, or fluorescent assays such as AlphaScreen or fluorescent polarization assays. More than 2000 assays against a variety of targets are established at Reaction Biology and readily available for screening.
  1. Cellular NanoBRET target engagement assays can determine the binding affinity of the compound to the target and the ligase in the physiologic environment of intact cells.
  1. Western blotting of lysates of treated cells is used to test whether the drug treatment actually leads to the degradation of the target in the cellular setup.
  1. SPR is used to determine the kinetics of the binding event, whereas ITC (isothermal titration calorimetry) is performed to identify the thermodynamic binding parameters. Both methods will determine the mechanism of action (MOA) of the drug.
  1. Successful lead candidates designated for treatment of oncology are then advanced to functional testing in tumor cell lines for their anti-proliferative or anti-metastatic potency and subsequently tested in mouse tumor models.

Workflow for the discovery of new targeted protein degradation molecules including PROTACs

Rethinking PROTAC

Our partnership with medicinal chemistry provider Medinoah enables access to a computational AI platform for predicting the PROTAC ternary complex structure to significantly reduce the number of compounds and screening cycles needed to generate potent and optimized PROTAC molecules. Our teams provide a one-stop-shop option to advance customers’ PROTAC program from a concept to a molecule ready for IND enabling studies.

We are currently talking to biotech and pharma companies to perform fee-for-service, shared-cost collaboration, or FTE-based work for the discovery of new targeted protein degradation drugs. Please reach out to our Business Development Team to discuss options for supporting your drug discovery program.

Validated Data for Protein Degradation Assay