Proteome-wide profiling for Targeted Protein Degradation (TPD) drugs

Proteome-wide Profiling for Targeted Protein Degradation (TPD) Drugs

Platform Technical Features

The Proteolysis Targeting Chimeras (PROTAC) drug is a bifunctional molecule that can bind to the targeted protein and recruit the ubiquitin E3 ligase for degradation. Therefore, novel modalities such as PROTAC and molecular glue have the ability to inadvertently alter the abundance of endogenous proteins, which provides a new therapeutic method for protein targets, especially the undruggable proteins. Comprehensively quantifying the abundance of on and off-target proteins has been one of the standard experiments for TPD drugs R&D.

Workflow

The platform follows a structured workflow, starting with cell lysate extraction, subsequently performing protease digestion, isotopic labeling, and ending with mass spectrometry detection.

Case Study

Project Aim

Two PROTAC molecules were designed and synthesized. The on and off-target proteins need to be analyzed for comparison of selectivity.

Experimental Method

TMT-based quantitative MS method was used for proteomic analysis.

A total of 5900 proteins were quantified in tumor cell lines and ON & OFF targets were identified for PROTAC1 and 2 molecules (Orbitrap Exploris 480 mass spectrometer, TMT10plex and data analysis by PD 2.5)