Inclusion bodies - sequestered clumps of misfolded proteins - might be the misunderstood heroes, rather than the villains, of neurodegenerative disease. Or, they might just be irrelevant altogether.

That’s the logical conclusion from data published this week in the early online edition of the Proceedings of the National Academy of Sciences by researchers from the Massachusetts Institute of Technology and Massachusetts General Hospital, located in Cambridge and Charlestown, Mass, respectively. The authors found that in models of both Huntington’s and Parkinson’s disease, a compound they studied increased the number of inclusion bodies, while reducing the cellular havoc those diseases cause.

"What is unique here is that there has been a real focus on finding aggregation inhibitors and breaking up these inclusions, at the same time that the field is moving in the direction that maybe inclusions aren’t so bad," Ruth Bodner told BioWorld Today, adding that "it’s certainly still a controversial notion" that inclusion bodies might be harmless, or even protective. Bodner is a postdoctoral fellow at MIT’s Center for Cancer Research and the paper’s first author.

Based on recent research showing that inclusion bodies might be a helpful part of the response to mutant proteins, the researchers first investigated a series of small molecules for their effect on the signal of mutant huntingtin. Five compounds raised the level of mutant huntingtin; two of those, termed B2 and B5, were chosen for further study. Both compounds were derivatives of the same chemical scaffold, and in cell culture, both increased the level of mutant huntingtin and the number and size of inclusion bodies.

Working in cell culture, the scientists found that B2 was able to prevent one cellular hallmark of Huntington’s disease: the toxicity caused by the fact that the proteasome, which has been described variously as the cell’s trash disposal or inventory control system, is unable to digest mutant huntingtin protein. The finding that chemicals that increased mutant huntingtin also had beneficial effects "was initially a surprise," Bodner said. "But it could be consistent with the idea that what matters is the level of oligomers rather than inclusions."

Bodner and her colleagues tested the effect of changing B2’s chemical structure on its effectiveness and found that when they made minor changes to its chemical structure, its activity was greatly reduced in both assays. The structural specificity suggested that B2 had a specific molecular target, but that target could be either mutant huntingtin or another protein.

The scientists next tested whether B2’s effects were specific to huntingtin, which they were not. When the researchers tested it in a model of Parkinson’s rather that Huntington’s disease, they found that there, too, inclusion body formation was increased while cellular toxicity was reduced. Huntingtin and alpha-synuclein have different structures, though Bodner said "it is still possible that B2 is binding to related conformations of disease proteins, such as oligomers."

B2 did not affect the level of several chaperone proteins, which are something like the stylists of the neurodegeneration world, helping the major players fold correctly. But the combination of high structural specificity and effectiveness across different diseases makes it the more likely scenario that it is binding "to some quality control protein in the cell," Bodner said.

The researchers currently are working on developing more potent analogues of B2. Asked about commercial prospects for extension of this work, Bodner said: "It is gratifying that there is significant interest on the part of both pharmaceutical and biotechnology companies in treatments for Huntington’s disease. Although this segment of the neurodegenerative market is small, relative to a disease like Alzheimer’s, our interactions with industry reflect an increased appreciation of the potential for a truly efficacious product in this market. I believe that the work we have carried out to date brings us a step closer to such a product."