Scientists learn how to target ‘undruggable’ Parkinson’s enzymes
Findings put GTPase enzymes on 'map for drug discovery,' per researcher
Scientists have discovered how to therapeutically target a class of molecular switches called GTPases that are involved in Parkinson’s disease and other conditions but have long been considered undruggable.
The findings of this work, led by researchers at the University of California, San Francisco (UCSF), “create a long-awaited opportunity to develop therapies for the many, diverse diseases that arise from GTPase dysfunction,” according to a university news story.
“We’ve known about the GTPases for decades but have lacked any way to reliably drug them,” said Kevan M. Shokat, PhD, the study’s senior author and a professor in the UCSF department of cellular and molecular pharmacology.
“This really puts all those GTPases on the map for drug discovery, so it’s possible to target them when they’re associated with disease,” Shokat said.
The study, “Targeting Ras-, Rho-, and Rab-family GTPases via a conserved cryptic pocket,” was published in the journal Cell.
Looking for pockets needed for a therapeutic outcome
A hallmark of Parkinson’s is the buildup of toxic clumps of the alpha-synuclein protein. These clumps, or aggregates, are thought to contribute to the progressive loss of nerve cells in the brain seen in people with the neurodegenerative disease.
Parkinson’s risk has been connected to variants in the RIT2 gene resulting in deficient production of an enzyme of the same name that has been shown to clear toxic alpha-synuclein forms from nerve cells. Thus, targeting the Rit2 enzyme could represent an effective strategy to combat nerve cell loss in Parkinson’s.
Rit2 is part of a large family of enzymes called GTPases. These enzymes function as molecular switches that govern several fundamental cellular processes, including cell growth, division, movement, and gene activity. Rab GTPase is another GTPase implicated in Parkinson’s.
Historically, however, GTPases have been challenging to target therapeutically with small molecules — making them essentially undruggable, according to the researchers. That’s because their structures have flat surfaces and appeared to lack pockets, or areas to which a molecule can bind and modify the enzyme’s function to achieve a therapeutic outcome.
“Since these GTPases switch between ‘on’ and ‘off’ states, the pocket is not usually visible, certainly not to the standard software used for drug discovery,” Shokat said.
K-Ras, a GTPase involved in cancer, was the only known exception, with a targetable region called a switch II (SII) pocket that was discovered by Shokat and colleagues in 2013. Since then, several therapies have been developed and approved to specifically target the SII pocket of a tumor-driving form of K-Ras caused by the G12C mutation.
Future work may make GTPases in Parkinson’s no longer undruggable
Now, Shokat’s team sought to determine whether other GTPases also carry a targetable SII pocket. To that end, the researchers evaluated the effects of 10 drugs designed to target the G12C mutated K-Ras enzyme on the activity of two GTPases somewhat similar to K-Ras. The two GTPases are H-Ras and N-Ras. These enzymes were also modified to carry the G12C mutation.
The results showed that, while some drugs bound selectively to K-Ras but not to the other GTPases, others bound strongly to H-Ras and N-Ras. Moreover, when the G12C mutation was reversed, many drugs were still bound to the GTPases.
Further work suggested that suppressors of GTPases beyond the Ras family could be developed. Still, drugs designed to target G12C mutated K-Ras were less effective in suppressing Rho and Rab GTPases compared with members of the Ras family.
By combining computer-based modeling and testing of new drug molecules, the team demonstrated that new molecules could be designed to selectively bind to Rab and Rho GTPases.
In the case of these enzymes, it was critical for us to first test our ideas experimentally in the laboratory, to actually see what worked. … We’re hopeful it can really accelerate drug discovery.
Through structural analysis, the researchers identified amino acids, the building blocks of proteins, that are particularly critical for SII pocket engagement, which would aid in drug design.
“In the case of these enzymes, it was critical for us to first test our ideas experimentally in the laboratory, to actually see what worked,” said Johannes Morstein, PhD, the study’s first author and a UCSF postdoctoral researcher. “We’re hopeful it can really accelerate drug discovery.”
The team noted that “the family of Ras-like GTPases consists of over 150 different members,” indicating that much more work lies ahead.
“Clinical translation of our findings to GTPases beyond K/H/N-Ras will require further compound optimization to design selective and reversible inhibitors,” they wrote.
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