A new type of molecule can take out misbehaving target proteins while leaving others unaffected. Photo: U.S. Army / Spc. Gregory Gieske

A new type of molecule can take out misbehaving target proteins while leaving others unaffected. Photo: U.S. Army / Spc. Gregory Gieske

By Shelly Fan

Sometimes, good proteins go bad.

Normally, when a protein has served out its useful life, cellular mechanisms break it down. In Huntington’s disease, however, a mutation affecting a protein called Hungtintin causes the protein to aggregate into harmful clumps that the cell cannot clear. In certain types of Parkinson’s disease, the number of an otherwise normal protein skyrockets, disrupting the delicate balance of the cell’s protein ecology and eventually causing the cell to die.

In other cases, it’s all about set and setting: death-associated protein kinase 1 (Dapk1) tells cancerous cells to commit suicide, but during a stroke Dapk1 mistargets, turning its death command on damaged neurons. (When scientists learned to blocked the protein’s activity, they gave rats that had strokes a better chance of their brain cells surviving.)

For decades, researchers have been working on clever ways of reducing or eliminating disease-causing proteins without affecting their non-mutated counterparts. Many highly sophisticated methods go after the mutated or “overactive” gene by knocking it out or killing off its messenger, blocking its production. These methods work, but the medications often need to be injected directly into the patient’s brain—multiple times—to sustain the knockdown, limiting their use.

But what if, instead of going after the gene that makes a mutated protein, doctors could directly wipe out the disease-causing protein itself? In a recent study, a team of neuroscience researchers from the University of British Columbia, of which I am a part, showed how we could harness the power of the cell’s internal protein-chopping machinery to target disease-causing mutated proteins. We did this by hijacking a process called chaperone-mediated autophagy.

Certain proteins have a short stretch of amino acids (a “motif”) that makes them recognizable by a family of protein chaperones. During chaperone-mediated autophagy, chaperones grab onto the protein’s motif and direct it to the cell’s execution chamber—the lysosome, a highly acidic sac filled with over 50 types of enzymes that ensures the complete disintegration of any protein that enters it.

My team and I took this motif and added another short stretch of amino acids to it. This added stretch is fully customizable—it binds to whichever protein you want to target—meaning that we can use it to send the cell’s executioners after whichever protein we choose.

Say you want to degrade α-synuclein, the over-expressed protein in Parkinson’s disease. One way to go about it is to find existing proteins that are already built to grab onto α-synuclein. Although proteins are intricately structured molecules, they often interact with each other through short amino acid sequences, like two human bodies only touching through a brush of their fingertips. Once you find a protein already built to target α-synuclein, you can chop it up into tiny chunks. Bathing this mix of protein bits in a soup of your target protein (α-synuclein), lets you figure out which part, specifically, is the part that binds to α-synuclein. This is the part you’ll need to target the protein.

By designing a molecule that carries both a chaperone-attracting motif and the protein chunk that targets α-synuclein, you can build a homing beacon that causes the body’s executioner to fight Parkinson’s disease.

In our study, rather than targeting α-synuclein, we set our sights on Dapk1, one of the proteins that commands neurons to die after a stroke. Building on previous research, we designed our Dapk1-targeting molecule with the condition that it only binds to the death-inducing protein after the latter’s “death message” is activated—this generally happens in areas of the brain that succumb to stroke damage.

Testing our molecule on rats that had had strokes, we found that a single abdominal injection of our molecule decreased the level of Dapk1 in areas that normally would have sustained damage from the stroke. Yet, our molecule also didn’t hinder the normal functioning of Dapk1 in other parts of the body. This means that Dapk1 was able to go on doing its job fighting cancer, but we were also able to shut it down in a targeted way and help mitigate damage from stroke. Eliminating this cellular death-inducing protein protected neurons from their fate, almost completely rescuing the rats’ brains from stroke-induced damage.

This is the first time that scientists have been able to snipe down a disease-causing mutated protein in such a targeted way.

This isn’t to say, however, that we’ll soon have a vaccine for stroke. Although theoretically the concept can be applied clinically, researchers have not yet completely mapped out its potential side effects: will the immune system attack the foreign molecule? Will it only go to its desired destination, like a homing torpedo, or is there a threat of it going rogue? What if the protein targeting system isn’t as specific as we’ve hoped, and instead of a sniper rifle you make a machine gun? Finally, remember that the chaperone-attracting motif is part of the molecule; this means that, in essence, it has an activated self-destruct signal. What if the weapon disintegrates before it reaches its target?

Nevertheless, scientists now have a new tool to help interrogate the function of proteins, and a new way to develop therapeutics. Even a small step down this path may mean a big leap in scientific discover.


Fan X. et al., Rapid and reversible knockdown of endogenous proteins by peptide-directed lysosomal degradation. Nat Neurosci published online 26 January 2014; doi: 10.1038/nn.3637

Shelly Fan is a neuroscience graduate student at the University of British Columbia, and a science writer who blogs at neurorexia.com. You can find her on twitter @ShellyFan

One Response to Custom Targeting Beacons Harness Cellular Executioners to Fight Disease

  1. […] over at the Canadian Science Writers’ Association today, talking about a new way to wipe out undesirable proteins with custom-designed molecules. “Undesirable” can mean […]

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