A novel computational approach to design has created a new compound that in laboratory studies has reduced deficits and neurodegenerative symptoms that underlie Parkinson’s disease.

In their study, the researchers describe how their compound, dubbed NPT100-18A, prevents the binding and accumulation of alpha-synuclein or α-syn in neuronal membranes, now considered a hallmark of Parkinson’s disease and a related disorder called dementia with Lewy bodies.

Parkinson’s disease, which affects more than 10 million people worldwide, is characterized by impairment or deterioration of neurons in the area of the brain known as the substantia nigra. The disease typically occurs in people over the age of 60, with symptoms of shaking, rigidity, difficulty in walking, generally developing slowly over time and sometimes followed later by impairment in behavior and thought processes.

Since most symptoms of Parkinson’s disease are triggered by a lack of dopamine in the brain, many medications are aimed at either temporarily replenishing dopamine or mimicking the action of this brain chemical. Unfortunately, current drugs have only a limited impact on long-term neurological deficits and mortality.

For that reason, scientists have begun to focus their efforts on α-syn’s role in the disease, based largely on computer modeling describing how mutant forms of this protein penetrate and coil in cell membranes, and then aggregate in a matter of nanoseconds into dangerous ring structures that open pores to toxic ions that ultimately destroy neurons. The modeling has been supported by electron microscopy showing how damaged neurons in Parkinson’s patients are riddled with these ring structures, and so the researchers homed in on “hot spots” that block the binding of two α-syn proteins, or dimers.

“Our thinking was that disrupting the formation of membrane-embedded dimers at this early intervention point could reverse the effects of α-syn on synaptic function at a stage before irreversible neurodegenerative processes have been initiated,” said Eliezer Masliah, the study’s principal investigator with the National Institutes of Health (NIH).

But the hunt proved highly complex, owing largely to the nature of the unstructured state of α-syn, sometimes referred to as a “chameleon” that constantly shifts its shape, somewhat like a slinky that’s bobbing and weaving on top of an earthquake epicenter.

“Our biggest hurdle was that α-syn doesn’t have any stable conformation,” said co-first author Igor Tsigelny, a research scientist with the San Diego Supercomputer Center (SDSC) at UC San Diego. “So long simulations were needed to define a huge set of possible conformations to find clusters of possible compounds that would work.”

Enter several supercomputers that performed molecular dynamic simulations of in silico structures that would displace α-syn from cell membranes. Based on these simulations, other members of the research team, synthesized a library of 34 potential compounds that targeted the “hot spot” where pairs of α-syn proteins bind, merge, and aggregate in the cell membrane, an early step in the formation of toxic rings and ultimate death of a neuron. Of these drug candidates, the researchers identified one compound – NPT100-18A – as the most promising.

“Essentially, this compound mimics the protein’s amino acids in the place where two α-synucleins come into contact, thus preventing the binding of the second protein,” said Wolfgang Wrasidlo, executive director of medicinal chemistry at Neuropore Therapeutics in San Diego and the study’s first author.

Subsequent electron microscopy imaging by researchers at the University of Vienna demonstrated that the new compound reduced the formation of α-syn clusters in cell membranes. Further studies with “transgenic” mouse models prone to Parkinson’s disease, both at UC San Diego and UCLA, concluded that the compound improved behavioral deficits and neurodegeneration. Within an hour after it was administered, imaging studies in these mice further showed that the compound reduced accumulation of α-syn in cortical synapses.

“Specifically targeting the α-synuclein structure that is stabilized in cell membranes also allows for a more specific molecularly targeted drug design,” added Masliah.

Though encouraging, the new compound needs to be refined before clinical trials could be launched in the future.