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Scripps Florida scientists reveal key protein interactions involved in neurodegenerative disease
JUPITER, Fla.—A new study authored by scientists at the Florida campus of the Scripps Research Institute (TSRI) describes the structure of a class of enzymes called c-jun-N-terminal kinases (JNK) when bound to three peptides from different protein families that play a critical role in stress- induced apoptosis. According to the TSRI team, this work could present new drug discovery opportunities for neurodegenerative diseases in which cell survival could dramatically impact outcomes patients with conditions like Parkinson's disease, Alzheimer's disease and amyotrophic lateral sclerosis (ALS).
The study, "Structural Mechanisms of Allostery and Autoinhibition in JNK Family Kinases" (which is also listed under the running title, "Allostery and Inhibition of JNK Kinases"), was published online on Nov. 8 by the Cell Press journal Structure.
JNKs are members of the mitogen activated protein kinases (MAPKs), acting as primary mediators of the stress response to regulate insulin signaling, cell fate, DNA repair and T cell differentiation. Differences in the timing and duration of JNK activation can determine whether cells proliferate or undergo programmed cell death, highlighting the critical importance of tight regulation of this pathway.
"We and many others have shown JNK to be very prevalent in Parkinson's, Alzheimer's and ALS," says Dr. Philip LoGrasso, scientific director of the TSRI at Scripps Florida and a lead author on the study. "JNK inhibition protects against neurodegeneration."
LoGrasso's lab currently focuses on drug discovery and basic research questions for kinases involved in neurodegeneration, inflammation, cardiovascular disease, glaucoma and oncology. Basic research studies are centered on enzyme/substrate structure- function relationships, splice variant function, mitochondrial dysfunction, neurite outgrowth and smooth muscle cell contraction. The lab also uses molecular biology, enzymology, receptor pharmacology, structure-based drug design and in-vivo pharmacology to discover potential drug leads and optimize them leads to preclinical candidacy.
"Solving the crystal structures of these three bound peptides gives us a clearer idea of how we can block each of these mechanisms related to cell death and survival," LoGrasso says. "You have to know their structure to know how to deal with them."
To achieve that, LoGrasso and his colleagues used an approach called structure class analysis, which postulates that examining groups of structures reveals subtle differences that are not apparent in an individual structure. It allows for statistical analysis of structural differences, and overcomes the difficulty in interpreting the role of crystal packing by comparing different space groups.
"We previously used this approach to discern differences between the two estrogen receptor subtypes, to identify structural mechanisms for partial agonist activity and to define a novel role for ligand dynamics in controlling allosteric signaling," writes LoGrasso in the study.
There are more than 40 known JNK structures, the vast majority of which are only minimally described as part of medicinal chemistry campaigns. From a structural point of view, these different proteins appear to be very similar, but the biochemistry shows that the results of their binding to JNK were very different, LoGrasso notes.
The team then used X-ray crystallography to create and solve the crystal structure of three peptides—JIP1, SAB and ATF-2—with JNK3. All three peptides induced two distinct inhibitory mechanisms: one where the peptide caused the activation loop to bind directly in the ATP pocket, and another with allosteric control.
Because JNK signaling needs to be tightly controlled, even small changes in it can alter a cell's fate, LoGrasso points out.
"Knowing the structure of JNK bound to these proteins will allow us to make novel substrate competitive inhibitors for this enzyme with even greater specificity and hopefully less toxicity," he says.
LoGrasso's lab is now working to use this information to make small-molecule, drug-like compounds that bind to this pocket. These drugs could have a dramatic impact on the neurodegenerative conditions described above, but LoGrasso adds that knockout mice data has shown that metabolic diseases like type 2 diabetes could be very well targeted by JNK inhibition, as well.
"Once we have small-molecule, competitive inhibitors that are potent enough, we will look for a commercial partner to license these compounds," says LoGrasso.
The study was supported by a grant from the U.S. National Institutes of Health. LoGrasso's lead co-author was TSRI Associate Professor Kendall Nettles. Also contributing to the work were John D. Laughlin, Jerome C. Nwachukwu, Mariana Figuera-Losada and Lisa Cherry.