Targeted protein degradation is a therapeutic strategy that leverages the ubiquitin–proteasome system to eliminate disease-associated proteins—including those that have traditionally been considered undruggable.
Protein degraders remove unwanted proteins from inside a cell by disposing of them using the cell’s built-in recycling system. Specifically, a molecular glue degrader binds an E3 ligase and redirects it to tag a disease-related protein for disposal.
Now, investigators at Dana-Farber Cancer Institute have developed a platform for systematically discovering molecular glues that could become protein degradation drug candidates. The platform could help drug developers expand the range of disease-related proteins that can be therapeutically targeted for elimination via protein degradation. The platform also enabled their discovery of the first molecular glue degrader that is metabolically activated, suggesting that molecular glues could be more context dependent and potentially tunable than previously thought.
The study was published in Nature in the paper, “DCAF11-dependent molecular glue degrader activated by glutathionylation.”
“This novel platform is an exciting scalable approach to the discovery of molecular glues that could help drive the significant expansion of molecular glue applications for the treatment of cancer and other diseases,” says Eric Fischer, PhD, professor of Biological Chemistry and Molecular Pharmacology at Harvard Medical School.
In 2014, Benjamin Ebert, MD, PhD, president and CEO of Dana-Farber, found the mechanism of action behind the multiple myeloma drug lenalidomide to be a molecular glue degrader of a transcription factor. Because transcription factors tend to have few pockets for inhibitor drugs to bind to, they were thought to be “undruggable.” Degrading transcription factors opened a new way of thinking about the treatment of cancer.
Today, several protein degraders have entered clinical testing. However, these degraders only leverage a small handful of the 600 E3 ligases in the human genome.
“There is an incredible range of opportunity for discovering new molecular glue degraders,” says Ebert. “This systematic approach could help accelerate the discovery of novel degraders that could change the way we think about the treatment of cancer.”
The screen in the new research fixes a subset of E3 ligases to magnetic beads in a well and bathes them in cellular lysate and a library of drug compounds. A hit occurs when a drug binds to one of the E3 ligases and increases its affinity for a given protein. The team used mass spectrometry to determine which cellular proteins have affinity for the drug-bound E3 ligase and would be likely to be tagged for disposal inside a cell.
They tested the system by screening seven E3 ligases and found the DDX18 protein was drawn to the E3 ligase DCAF11 and that the compound M12 enabled the connection. Using cryo-EM, the team found that M12 had been altered by glutathionylation; it would only act as a molecular glue inside cells with elevated levels of metabolites related to oxidative stress in the cell—something common in cancer cells.
“This was a huge surprise, and it is the first observation of a molecular glue that has been activated metabolically by glutathionylation,” says Franziska Wachter, MD, pediatric oncologist and instructor in pediatrics at Dana-Farber Cancer Institute.
Further exploration of activated M12 revealed that it functions as a prodrug that is activated through glutathione S-transferase-mediated glutathionylation and reprograms the E3 ligase DCAF11 to degrade DDX18. More specifically, the authors write that it “the glutathione moiety binds to an evolutionary conserved glutathione-binding site on DCAF11, and the exposed M12 moiety facilitates neo-substrate recruitment.”
By binding additional proteins to the complex, the team was able to tune the system to degrade multiple other proteins, including cancer-related protein targets such as SMARCA2, WEE1 and CDK7. “This systematic approach to discovering novel molecular glue degraders opens up the possibility for expanding the number of proteins that can be targeted for degradation as a treatment for cancer,” says Ebert.
