Chemists make molecular scalpels to remove unwanted proteins from cell surfaces

When scientists find a potentially dangerous protein in a cell, they can imagine themselves shrinking to become little surgeons, cutting only the problem molecule and leaving the healthy parts of the cell intact. While skilled hands and sharp instruments could never remove a single protein from a cell’s surface, a new molecular tool could make cell surgery easier, according to a study published in Nature July 29.

Stanford chemists have developed a new class of molecules that transport unwanted proteins from a cell’s surface or surrounding environment to the lysosome, the cell compartment dedicated to protein degradation. These molecules, called lysosome-targeted chimeras, or LYTACs, work by selectively labeling a protein with a tag that seals its fate for cellular debris removal. This selective degradation could help researchers study and treat diseases such as cancer and Alzheimer’s, the causes of which are related to surface proteins.

“It’s like a molecular scalpel,” said lead author Steven Banik, a postdoc in the laboratory of Carolyn Bertozzi, Professor Anne T. and Robert M. Bass at the College of Humanities and Sciences. “This tool allows you to accelerate the natural degradation of an individual protein among all the different proteins that are inside or outside of a cell.”

Proteins are vital for many biological processes like metabolism and intercellular communication, but some can also help diseases like cancer to spread and evade immune regulation. Traditional methods of hampering these bad actors involve the use of drugs that block the protein’s active site, where other cellular components can couple together while the protein works on them, usually by moving the atoms. But this blocking strategy is imperfect; sometimes the binding pocket is too shallow and the inhibitor trips too fast. Other times, the activity of a protein derives from its physical properties, such as its stiffness, and not from any active site, so blocking a small portion of the entire protein is insufficient. In these cases, draining the protein cell is the only option.

Protein degradation as a therapeutic strategy has been especially popular since the development of PROTAC, or chimeras targeting proteolysis, 20 years ago. PROTACs, which search for and label intracellular proteins for degradation, have been successful in research laboratories and in early clinical studies, but rely on a degradation pathway that is inaccessible to approximately 40 percent of all proteins. that are above or outside the cell membrane. . Bertozzi and Banik did not accept that certain proteins, and diseases, would be out of their reach.

“My lab has always been interested in what happens on the cell surface, which contains all of these proteins important for immune modulation,” said Bertozzi, who is also co-director of the Stanford ChEM-H Baker Family. “We have identified many surface and secreted proteins that we believe are playing a pathogenic role in cancer, and LYTACs could help us better understand and explore them as drug targets.”

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

This sugar serves as an accounting label for the cell. When the cell builds proteins that belong to the lysosome, it adds these sugars to ensure that they reach their destination. “Mannose phosphate 6 acts like a postal code,” said Banik. “These sugars tell the cell, ‘I’m taking this protein to the lysosome. Please send me there.'” There are receptors on the cell surface that interact with this sugar coating, and when they grab a LYTAC molecule and pull it into the cell, the tagged proteins are dragged along with it.

By attaching this tag to proteins, LYTACs hijack a natural cell transfer mechanism designed to escort newly synthesized lysosomal proteins to their new home. But while lysosomal proteins are resistant enough to survive the degrading enzymes found in the lysosome, most proteins are not, so those labeled by the LYTAC method are generally destroyed.

Stanford researchers show that, in cells, they can attack and degrade important proteins in Alzheimer’s disease and cancer. According to them, the protein binding end of LYTAC can be anything that binds to a protein, such as an antibody or an existing drug, so many other proteins and diseases could be attacked in the future.

“With protein degradation strategies, you can not only expand what is pharmacological but also improve existing therapies,” said Bertozzi. “Every cell has lysosomes. Every cell already has a way to break down protein. No matter what your goal is, if you can get a LYTAC there, you can break it down.”