Molecular structures provide roadmap for targeted Parkinson’s disease therapeutics

Researchers at Weill Cornell Medicine have uncovered how a key Parkinson's protein called LRRK2 shifts between inactive and active forms, revealing the structural changes that enable certain mutations to push the protein into an overactive state.

Mutations that cause LRRK2 to become abnormally active are among the most common genetic causes of Parkinson's disease. Even without these mutations, some people with Parkinson's disease have elevated LRRK2 activity.

Understanding exactly how LRRK2 becomes overactive has become increasingly important because it is one of the leading targets for developing treatments that could slow Parkinson's disease.

Using electron microscopy and biochemistry, the team captured the structure of LRRK2 in different states, enabling them to elucidate how the protein toggles between the active and inactive forms. The findings, published Aug. 10 in Cell, point toward a new generation of targeted therapies.

"With at least four ongoing clinical trials, LRRK2 is considered one of the most promising targets for Parkinson's therapeutics," said Dr. Samara Reck-Peterson, chair and professor of biochemistry and biophysics, and Vincent and Brooke Astor Distinguished Chair in Neuroscience at Weill Cornell, who co-led the investigation. "Our work provides a platform for identifying molecules that promote the formation of one configuration or the other, which could help researchers design drugs that selectively control LRRK2 activity."

Zooming into a complex machine

A complex "machine" that regulates how materials are organized inside cells, LRRK2 comprises seven domains. Some parts act like grips, helping LRRK2 attach to other proteins and structures inside the cell, and two domains have different enzymatic activities.

One domain binds GTP, a molecule used by many proteins, such as LRRK2, that function as switches. Generally speaking, these proteins are "on" when they bind GTP, and turn "off" when they convert it to GDP. The kinase domain adds small chemical tags (phosphate groups) to target proteins, thus changing how they behave inside the cell. An increased level of these modifications is linked to Parkinson's.

LRRK2 is found throughout the body, including in the brain, immune system, lungs and kidneys. "The challenge is finding ways to selectively reduce harmful LRRK2 activity in the brain while preserving its normal functions in other tissues," said Andres Leschziner, professor of biochemistry and biophysics at Weill Cornell and the study's co-lead investigator.

Locking down the key structures

Previous evidence in the field suggested crosstalk between the enzymatic activities, which led the researchers to investigate how the two domains interact to regulate LRRK2's kinase activity.

The researchers allowed LRRK2 to take different conformations while being loaded with either GTP or GDP. Then they examined 16 different LRRK2 structures - some with GTP, some with GDP, while others held neither molecule. Capturing so many snapshots allowed the team to reconstruct the sequence of structural changes the protein undergoes as it turns on and off.

The team effort included collaborators from the University of California, San Francisco, and Goethe University in Frankfurt. Amalia Villagran Suarez, a graduate student in the Leschziner lab and Kathryn Hatch, a graduate student in the Reck-Peterson lab, are co-first authors on the paper.

Delving into the collection of structures revealed that LRRK2's activity depends largely on whether it is bound to GDP. When GDP is present, LRRK2 adopts a compact structure with key domains blocking the kinase active site and preventing it from interacting with its protein targets.

When GDP is released, LRRK2 shifts to an active conformation that exposes the kinase active site, thereby enabling its activity. This can then be stabilized by binding GTP.

"Our observations uncover the rules for how to control whether LRRK2 is active or not; and since hyperactivity is linked to Parkinson's, this provides a roadmap for new therapeutics," said Reck-Peterson, who is also an HHMI Investigator.

Understanding how PD mutations activate LRRK2

Together, the structures revealed not only how LRRK2 normally turns on and off but also how different Parkinson's mutations increase its activity through distinct mechanisms. One common mutation falls in the kinase active site, where it directly boosts kinase activity. Other common mutations are found far from the region yet still activate the kinase.

"A big question in the field was, 'how do mutations that are so far apart from each other activate the kinase?'" Reck-Peterson said.

To understand how different mutations impact kinase activity, the team used molecular tools they developed to push LRRK2 into either the on or off state. They discovered that mutations near the GTP/GDP switch increase the time LRRK2 spends in its active shape, rather than making the kinase work faster. This distinction suggests that future therapies may need to be tailored to a patient's specific genetic mutation.

"Our work gives medicinal chemists the blueprint to design drugs that target the on/off switch in LRRK2 rather than acting directly on the kinase," Leschziner said. "Such 'allosteric' drugs may offer greater precision and fewer side effects than conventional kinase inhibitors."

This research was supported by the National Institutes of Health; the National Science Foundation; the Parkinson'sFoundation; the Structural Genomics Consortium, a registered charity that received funds from Bayer AG, Boehringer Ingelheim, Bristol Myers Squibb, Genentech, Genome Canada through Ontario Genomics Institute, EU/EFPIA/OICR/McGill/KTH/Diamond Innovative Medicines Initiative 2 Joint Undertaking, Janssen, Merck KGaA, Pfizer and Takeda; the Michael J. Fox Foundation; the Howard Hughes Medical Institute; and the LRRK2 Investigative Therapeutics Exchange.

Karen Hopkin is a freelance writer for Weill Cornell Medicine.