Scripps Florida scientists reveal key protein interactions involved in neurodegenerative disease

A new study from the Scripps Research Institute on the structure of c-jun-N-terminal kinases 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

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JUPITER, Fla.—A new study authored by scientists at theFlorida campus of the Scripps Research Institute (TSRI) describes the structureof a class of enzymes called c-jun-N-terminal kinases (JNK) when bound to threepeptides from different protein families that play a critical role instress-induced apoptosis. According to the TSRI team, this work could presentnew drug discovery opportunities for neurodegenerative diseases in which cellsurvival could dramatically impact outcomes patients with conditions likeParkinson's disease, Alzheimer's disease and amyotrophic lateral sclerosis(ALS).
The study, "Structural Mechanisms of Allostery and Autoinhibitionin JNK Family Kinases" (which is also listed under the running title, "Allosteryand Inhibition of JNK Kinases"), was published online on Nov. 8 by the CellPress 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 andduration of JNK activation can determine whether cells proliferate or undergoprogrammed cell death, highlighting the critical importance of tight regulationof this pathway.
"We and many others have shown JNK to be very prevalent inParkinson's, Alzheimer's and ALS," says Dr. Philip LoGrasso, scientificdirector of the TSRI at Scripps Florida and a lead author on the study. "JNKinhibition protects against neurodegeneration." 
LoGrasso's lab currently focuses on drug discovery and basicresearch questions for kinases involved in neurodegeneration, inflammation,cardiovascular disease, glaucoma and oncology. Basic research studies arecentered on enzyme/substrate structure-function relationships, splice variantfunction, mitochondrial dysfunction, neurite outgrowth and smooth muscle cellcontraction. The lab also uses molecular biology, enzymology, receptorpharmacology, structure-based drug design and in-vivo pharmacology to discover potential drug leads and optimizethem leads to preclinical candidacy.
"Solving the crystal structures of these three boundpeptides gives us a clearer idea of how we can block each of these mechanismsrelated to cell death and survival," LoGrasso says. "You have to know theirstructure to know how to deal with them."
To achieve that, LoGrasso and his colleagues used anapproach called structure class analysis, which postulates that examininggroups of structures reveals subtle differences that are not apparent in anindividual structure. It allows for statistical analysis of structuraldifferences, and overcomes the difficulty in interpreting the role of crystalpacking by comparing different space groups.
"We previously used this approach to discern differencesbetween the two estrogen receptor subtypes, to identify structural mechanismsfor partial agonist activity and to define a novel role for ligand dynamics incontrolling allosteric signaling," writes LoGrasso in the study.
There are more than 40 known JNK structures, the vastmajority of which are only minimally described as part of medicinal chemistrycampaigns. From a structural point of view, these different proteins appear tobe very similar, but the biochemistry shows that the results of their bindingto JNK were very different, LoGrasso notes.
The team then used X-ray crystallography to create and solvethe crystal structure of three peptides—JIP1, SAB and ATF-2—with JNK3. Allthree peptides induced two distinct inhibitory mechanisms: one where thepeptide caused the activation loop to bind directly in the ATP pocket, and anotherwith allosteric control.
Because JNK signaling needs to be tightly controlled, evensmall changes in it can alter a cell's fate, LoGrasso points out.
"Knowing the structure of JNK bound to these proteins willallow us to make novel substrate competitive inhibitors for this enzyme witheven greater specificity and hopefully less toxicity," he says.
LoGrasso's lab is now working to use this information tomake small-molecule, drug-like compounds that bind to this pocket. These drugscould have a dramatic impact on the neurodegenerative conditions describedabove, but LoGrasso adds that knockout mice data has shown that metabolicdiseases like type 2 diabetes could be very well targeted by JNK inhibition, aswell.
"Once we have small-molecule, competitive inhibitors thatare potent enough, we will look for a commercial partner to license thesecompounds," says LoGrasso.
The study was supported by a grant from the U.S. NationalInstitutes of Health. LoGrasso's lead co-author was TSRI Associate ProfessorKendall Nettles. Also contributing to the work were John D. Laughlin, Jerome C.Nwachukwu, Mariana Figuera-Losada and Lisa Cherry.

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