Lysosomal targeted chimeras degrade extracellular proteins

When scientists discover potentially dangerous proteins on cells, they may imagine shrinking themselves as small surgeons, removing only problematic protein molecules and leaving the healthy cells. In a new study, researchers from Stanford University point out that although dexterous hands and sharp devices can never remove a single protein from the cell surface, a new molecular tool can make cell surgery easier. The relevant findings were published online July 29, 2020 in the journal Nature under the title "Lysosome-targeting chimaeras for degradation of extracellular proteins".

These authors developed a new class of molecules that can shuttle unwanted proteins from the cell surface or surrounding environment into lysosomes, which are cellular compartments specialized for protein degradation. These molecules are called lysosome targeting chimera (LYTAC), and their working mechanism is to selectively label proteins with tags, which determine the fate of proteins and allow them to be degraded as cellular waste. This selective degradation can help scientists study and treat diseases such as cancer and Alzheimer's disease. The causes of which are related to surface proteins.

Steven Banik, lead author of the paper and a postdoctoral researcher in the laboratory of Professor Carolyn Bertozzi at Stanford University School of Humanities, said, "This is like a molecular scalpel. This tool allows you to accelerate the natural degradation of a protein from all proteins on or outside the cell."

Proteins are essential for many biological processes, such as metabolism and cell-cell communication, but some proteins can also help diseases such as cancer spread and evade immune regulation. When a protein functions, other cellular components can dock to its active site. The traditional approach to hinder these bad proteins involves the use of drugs that block the active site of the protein, which is usually achieved by moving the atom. But this blocking strategy is not perfect, sometimes the binding pocket is too shallow and the inhibitor is ejected too quickly. At other times, the activity of a protein comes from its physical properties, such as its rigidity, rather than from any active site, so blocking a small part of the entire protein is not enough. In these cases, expulsion of the protein from the cell is the only option.

Since the development of proteolysis targeting chimera (PROTAC) 20 years ago, protein degradation has been particularly popular as a therapeutic strategy. PROTAC has been successful in research laboratories and early clinical studies in finding and labeling intracellular proteins for subsequent degradation, but they rely on a degradation pathway that is inaccessible to approximately 40% of proteins located on or outside the cell membrane. Bertozzi and Banik do not accept that certain proteins, as well as diseases, are out of reach.

Bertozzi said, "My laboratory has been interested in what happens on the cell surface, which includes proteins that are important for immune regulation. We have identified many cell surface proteins and secreted proteins that we believe play a pathogenic role in cancer, and LYTAC can help us better understand them and explore them as drug targets."

The key to making this tool work lies in its dual-function design. One side of the LYTAC molecule can be customized to bind to any protein of interest. On the other side is a short amino acid sequence, or peptide, embedded with a sugar called mannose-6-phosphate.

This sugar serves as a bookkeeping label for the cell. When cells contain proteins that are sent to lysosomes for degradation, it adds this sugar to ensure that they reach their destination. "Mannose-6-phosphate acts like a zip code," says Banik. “This sugar tells the cell, ‘I’ll bring this protein to lysosomes. Please send me there.’ There are receptors on the cell surface that interact with this sugar, and when they grasp the LYTAC molecule and pull it into the cell, the labeled protein is also dragged in with it.”

In attaching this tag to the protein, LYTAC hijacks a natural cell shuttling mechanism designed to escort newly synthesized lysosomal proteins to their new home. However, lysosomal proteins are tough enough to survive in the presence of degradative enzymes encountered in lysosomes, while most proteins do not, so those labeled by the LYTAC method are usually destroyed.

These researchers confirmed that in cells, they can target and degrade proteins that play an important role in Alzheimer's disease and cancer. According to them, the protein tethering ends of LYTAC can be anything that binds to proteins, such as antibodies or existing drugs, so in the future, many other proteins and diseases can be attacked.

"With protein degradation strategies, you can not only expand the number of druggable target cells, but also improve existing therapies," Bertozzi said. Each cell has lysosomes. Each cell already has a way to degrade proteins. Whatever your target is, if you can get LYTAC there, you can degrade it."