Stanford chemists uncover new pathway for protein degradation, opening door to new therapeutics

When targeting problem proteins involved in causing or spreading disease, a drug often blocks the active site of a protein so it can’t function and cause havoc. New strategies for dealing with these proteins can send these proteins to a variety of cellular protein-degrading machinery, such as a cell’s lysosomes, which act like a protein wood chipper.

A new study published in science On October 20, Stanford chemists discovered how one of the pathways leading to this “wood chipper” protein works. In doing so, they have opened the door to new therapeutics for age-related disorders, autoimmune diseases and treatment-resistant cancers. These findings may also improve therapeutics for lysosomal storage disorders, a rare but often serious condition that mostly affects infants and children.

“Understanding how proteins are shuttled to lysosomes for breakdown may help us harness the cell’s innate power to get rid of proteins that cause so much damage to the human body,” said Carolyn Bertozzi, Anne T. and Robert M. Bess Professor in the School of Humanities and Sciences and Becker Family Director of Sarafan ChEM-H. “The work done here is a clear look at a normally opaque intracellular process, and it’s illuminating a new world of potential drug discovery.”

The ability to understand the biology of this process means we can use the inherent biology that already exists and use it to treat disease. These insights offer a unique window into a new type of biology that we haven’t really understood before.”

Steven Bonick, Assistant Professor of Chemistry, School of Humanities and Sciences

Stopping proteins from going rogue

While proteins often do the body good, such as helping us digest food or repair torn muscles, they can also be destructive. In cancer, for example, proteins can either become part of the tumor and/or allow it to grow uncontrollably, cause devastating diseases like Alzheimer’s, and build up in the heart to affect how it pumps blood to the rest of the body.

To stop the rogue protein, drugs can be deployed to block the protein’s active site and thus prevent it from interacting with a cell, which has been the standard of therapeutic research for decades. Then 20 years ago, proteolysis targeting chimeras (PROTACs) burst onto the scene, which can engage poorly-behaving proteins already inside a cell and send them to lysosomes to be broken down.

PROTACs are currently in clinical trials and have shown efficacy in the treatment of cancer. But they can only target a protein if it’s inside the cell, which is only 60% of the time. In 2020, Stanford ChEM-H researchers pioneered a way to reach the other 40% of those proteins through lysosome targeting chimeras (LYTACs), which can target and target proteins hanging around the cell or on the cell membrane for destruction. .

These findings opened up a new class of research and therapeutics, but it was not clear how the mechanism worked. The researchers also noted that it is difficult to predict when LYTACs will be highly successful or fail to work as expected.

New therapeutic targets

In this work, Green Ahn, PhD, then a Stanford graduate student and now a postdoctoral fellow at the University of Washington Institute for Protein Design and lead author of the study, used a genetic CRISPR screen to identify and identify cellular factors that modulate How LYTACs degrade proteins. Through this screening, the team identified a link between levels of neddylated cullin 3 (CUL3) – a protein that plays a housekeeping role in breaking down cellular proteins – and LYTAC effectiveness. The exact tie is not yet clear, but the more neddylated CUL3 present, the more effective LYTAC was.

Measuring levels of neddylated CUL3 may be a test to determine which patients are more likely to respond to LYTAC therapy. This was a surprising finding, Bertozzi said, because no previous studies had previously indicated this correlation.

They also identify proteins that prevent LYTAC from doing their job. LYTACs work by binding to specific receptors on the outside of cells, which they use to shuttle damaged proteins to lysosomes for degradation. However, the researchers found that proteins carrying mannose 6-phosphate (M6Ps), sugars that decorate proteins destined for lysosomes, would occupy a seat on those receptors, meaning LYTAC had no binding site. By throwing a wrench in M6P biosynthesis, resulting in an increased fraction of unexpressed receptors on the cell surface that can be hijacked by LYTACs.

New biology, new ways to treat disease

In addition to helping develop LYTACs into more effective therapeutics, these discoveries could lead to new and more effective treatments for lysosome deficiency disorders — genetic conditions in which the body does not have enough or the right enzymes in lysosomes to function properly. This can cause a toxic build-up of fats, sugars and other harmful substances, which can damage the heart, brain, skin and skeleton. A common treatment is enzyme replacement therapy, which uses the same pathway as LYTAC to get to the lysosome where they can work. Understanding how and why LYTACs work means these enzymes can be delivered more effectively.

The researchers likened the work to an important discovery of exactly how the drug thalidomide works. It was originally prescribed for morning sickness in pregnant women in the 1950s, mostly in the UK, but was taken off the market in 1961 after it was linked to serious birth defects. However, in the 1990s, it was found to be an effective treatment for multiple myeloma. In 2010, researchers realized how: through degrading proteins, an observation that significantly contributed to the growing field of PROTAC research.

“The LYTAC evolution is where the thalidomide and ProTac story was 15 years ago,” Bertozzi said. “We’re learning human biology that wasn’t known before.”