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Biological Chemistry

The Amyloid Question

Alzheimer's researchers will soon know whether blocking amyloid-β can slow down the debilitating disease

by Lisa M. Jarvis
April 5, 2010 | A version of this story appeared in Volume 88, Issue 14

Researchers are on the verge of testing a fundamental hypothesis about how Alzheimer’s disease evolves.


The Amyloid Question

Amyloid-β, the peptide responsible for the ugly plaques coating the brains of victims of the disease, has long been considered the main culprit in triggering neuron death and subsequent mental decline. After years of complex drug discovery efforts, industry is putting that hypothesis to the test with a series of late-stage clinical trials for small molecules and antibodies that block amyloid-β.

If the trials are successful—and the amyloid hypothesis is proven true—doctors will have a slew of new drugs that could slow the progression of the disease. If the trials fail, scientists will be forced back to the drawing board to develop new hypotheses and drug targets.

The worry among some experts is that the development of amyloid-β-targeting compounds by Pfizer, Elan Pharmaceuticals, Eli Lilly & Co., Bristol-Myers Squibb, and others began long before the underlying biology of the peptide was well understood. New research suggests that amyloid-β may also play a beneficial role in the brain, whereas other studies claim the peptide is overproduced only after another neurotoxin does its dirty work. With nearly every drug in the pipeline targeting some aspect of the amyloid-β pathway, some Alzheimer’s researchers are concerned that industry has placed all its eggs in one fragile basket.

Still, many scientists in industry and academia believe that so much genetic evidence supports the amyloid-β hypothesis that at least some of the drugs will work and neurologists will soon have new weapons against Alzheimer’s. “If you have to place a bet on a pathway that’s important in Alzheimer’s disease, I’d still be betting on the amyloid cascade. There’s just too much data out there,” says Mene Pangalos, chief scientific officer of neuroscience at Pfizer.

Alzheimer’s is a form of dementia, the loss of mental function that occurs when the billions of neurons in the brain start to die in droves. Scientists still don’t know the specific trigger for that cascade, but there are telltale signs that the disease has taken hold. Afflicted brains are covered with plaques—gummy oligomers of amyloid-β fragments forming fibrils that clog the spaces between nerve cells. Clumps of the protein tau, called tangles, that accumulate inside neurons are another hallmark of the disease.

The disease is notoriously tough to catch in its earliest stages because the clues are often subtle and at times embarrassing for victims: difficulty retaining new information, confusion, mood swings, and trouble performing normal tasks, such as balancing a checkbook or driving new places.

John MacInnes first realized he was experiencing more than the usual memory loss associated with age during a board meeting to discuss a costly expansion of his local library. “I was making a PowerPoint presentation to a very sizable group,” recalls MacInnes, an 83-year-old Michigan native. He had a script, but “suddenly, I just lost it,” he says.

Although MacInnes was able to cover his confusion at the meeting fairly well, he also decided it might be time to visit a doctor. After several months of cognitive tests and neuroimaging, MacInnes, now an adviser and patient advocate for the Alzheimer’s Association, was diagnosed with the disease in 2007.

Tragically, no treatment is yet available to halt the progression of Alzheimer’s. MacInnes is one of the estimated 5.3 million Americans suffering from the disease, a figure that the Alzheimer’s Association expects to nearly quadruple by 2050. As their dementia worsens, people with Alzheimer’s eventually lose the ability to care for themselves. As a result, the disease costs the U.S. nearly $180 billion per year, according to the patient advocacy group.

Currently, patients’ only treatment options are drugs that dampen the symptoms of the disease. Pfizer’s Aricept keeps acetylcholinesterase from breaking down the neurotransmitter acetylcholine, maximizing the amount available to carry messages, and Forest Laboratories’ Namenda blocks a glutamate receptor thought to play a role in learning and memory.

For the past few years, MacInnes has been taking Aricept, but as most patients do, he experiences unpleasant side effects from the drug, such as diarrhea. Many people take both Aricept and Namenda yet see little improvement in their daily lives. Still, doctors dole out these drugs because they have nothing more to offer patients and caregivers who are desperate for help. Pfizer sold $432 million worth of Aricept last year, and Namenda brought Forest $949 million in fiscal 2009.

Between the enormous unmet need and the potential for multi-billion-dollar sales, Alzheimer’s is squarely in big pharma’s crosshairs. The goal is clear: develop drugs to treat the underlying disease, rather than simply easing the symptoms. At the minimum, companies hope that drugs that interrupt the amyloid pathway will slow the progression of Alzheimer’s.

Credit: Elan
β-Secretase is an attractive but challenging drug target.
Credit: Elan
β-Secretase is an attractive but challenging drug target.

Right now, most drug development efforts are focused on amyloid-β. Although the peptide is clearly implicated in the disease, researchers have no proof that it is the cause. The hypothesis is that deposition of amyloid-β in the form of “plaques triggers a neurodegenerative process that causes neuronal cells to die,” says Eric Siemers, medical director of Lilly’s global Alzheimer’s research team.

Scientists have much genetic evidence implicating the peptide in the earliest stages of the disease. For example, members of some families with a history of mutation in the amyloid precursor protein (APP) gene have amped-up production of amyloid-β and a much higher risk of developing Alzheimer’s. “What the amyloid story has on its side is six genes on four different chromosomes that all point to amyloid metabolism in some way,” says Samuel E. Gandy, associate director of the Mount Sinai Alzheimer’s Disease Research Center, in New York City.

The emergence of amyloid-β begins when APP, a long protein, becomes embedded in the neuron cell membrane as it is being made. In the absence of disease, an enzyme called α-secretase snips APP to release a fragment that aids neuron growth. In the disease pathway, β-secretase cleaves a different protein fragment from APP and exposes one end of amyloid-β. Then, with part of APP still stuck in the cell membrane, γ-secretase swoops in to make a cut at the other end of amyloid-β.

Upon release, amyloid-β molecules start sticking together. Although some amyloid oligomers are swept out of the cell, others grow to form insoluble fibers that become the plaques gumming up the brain of someone with Alzheimer’s.

The good news is that production of amyloid-β has multiple points in which small and large molecules can stop it cold. Since the late 1980s, companies have taken three main tacks: sequestering amyloid-β after it is formed, blocking γ-secretase, and blocking β-secretase.

Arguably, the most clinical data to date have been from clearing already-formed amyloid from the brain. Elan scientists struck on the idea after trying to directly inoculate mice with the errant peptide in hopes of prompting an immune response.

“We were pretty surprised and happy when we vaccinated mice with amyloid-β and saw in our animal model—a prevention model—that there were no plaques,” recalls Dale Schenk, chief scientific officer at Elan. “So surprised, we thought we had the mice mixed up. I think the entire field had the same reaction.”

Elan scientists published the results in 1999 and were quickly able to move into human tests. They first tried vaccinating patients with a synthetic amyloid-β, AN1792. But they halted a Phase II study of the drug after 6% of patients developed a serious brain infection.

The scientists switched tacks and turned to bapineuzumab, an antibody that binds to amyloid-β. Although many industry observers considered the results of Phase II trials of this antibody weak at best, Elan’s development partners, Pfizer and Johnson & Johnson, are conducting multiple Phase III trials to see whether long-term treatment with bapineuzumab can improve cognition and function in patients with mild to moderate Alzheimer’s.

The industry’s new-drug pipeline holds several other drugs aimed at sequestering amyloid-β. Lilly’s solanezumab, which binds only to soluble amyloid-β monomers, is also in Phase III trials. Elan has another vaccine in Phase II trials, Schenk notes, and it is also trying to prevent plaque deposits with ELND005, a small molecule that keeps amyloid-β from aggregating. Elan and partner Transition Therapeutics are bringing ELND005 to Phase II trials.

Credit: Bristol-Myers Squibb
Bristol-Myers is working on both γ- and β-secretase blockers.
Credit: Bristol-Myers Squibb
Bristol-Myers is working on both γ- and β-secretase blockers.

Rather than directly blocking amyloid-β aggregation, most other companies are working on small molecules that can keep it from forming in the first place. The most advanced drug candidates target γ-secretase, the enzyme that makes the second snip that releases amyloid-β from the cell membrane.

Pharmaceutical companies have been working on γ-secretase blockers for decades, slowly clearing a series of hurdles on the road to safe and potent compounds. In the earliest efforts, chemists worked in the dark, without knowing the exact identity of γ-secretase. James Audia, a distinguished Lilly scholar, recalls being challenged by a manager in the early 1990s to find a molecule capable of testing the amyloid-β hypothesis. “At that time, we didn’t have a lot of the discrete molecular targets that are now known to cleave APP,” Audia says. “γ-Secretase hadn’t been identified, nor had β-secretase.”

Lilly scientists screened for compounds that would block the release of amyloid-β from cells transfected with human APP. Similar screens were going on at Elan and DuPont, and all the scientists working on the problem remember that it was easy to find molecules to inhibit what was later discovered to be γ-secretase.

But there was a problem: Time and again the molecules that block γ-secretase also cause the kind of toxic side effects that make chemists want to run for the hills. “At DuPont, we took literally hundreds, even thousands, of compounds, and they all had this problem,” says Charles Albright, group director of neuroscience biology at Bristol-Myers, which bought DuPont’s pharmaceutical division in 2001.

It turned out that in addition to clipping APP, γ-secretase also cleaves Notch, a protein that spans the cell membrane and is involved in a laundry list of cell-signaling processes. “Back then, we didn’t even know Notch existed,” recalls Elan’s Schenk, who with his colleagues did groundbreaking work to identify the enzymes involved in amyloid-β production.

Working empirically, medicinal chemists were able to move toward compounds that blocked γ-secretase but had less of an impact on Notch. Eventually, academics’ understanding of Notch caught up with the molecular screens and optimization going on at big pharma. When Notch was identified as a substrate for γ-secretase, some companies abandoned the enzyme as a target. Many competitors “turned pale and looked at alternatives,” Lilly’s Audia says.

Even today, finding compounds with a big enough gap between hitting γ-secretase and avoiding Notch is a challenge. No crystal structure is available for γ-secretase, so researchers don’t know where on the enzyme their compounds are actually binding. “The enzyme is composed of four different proteins and cleaves within a lipid bilayer. It has made characterization very difficult,” Albright explains.

Today, a handful of small-molecule γ-secretase inhibitors are on their way to commercialization. Lilly completed enrollment for one of two Phase III trials of semagacestat last fall and is now close to wrapping up recruitment for the second one, Siemers notes. Elan is a partner on semagacestat but also has two of its own γ-secretase inhibitors in preclinical and Phase I studies. Bristol-Myers expects to move its most advanced γ-secretase inhibitor, BMS-708163, into Phase III trials by the end of the year.

Researchers are also using small molecules to inhibit β-secretase, also known as BACE, because in principle it is an ideal target: Its activity seems limited to cleaving APP, meaning it can be blocked without fear of toxic side effects.

But BACE is a much harder nut to crack than γ-secretase. The enzyme has a huge catalytic pocket, making it tough for researchers to find molecules to bind to it that have the right mix of potency, bioavailability, and ability to enter the central nervous system, Elan’s Schenk explains.

“Many of the pharmas have worked long and hard to make potent inhibitors,” Schenk says, but nobody has been successful in developing molecules with the right characteristics, partially due to the molecules’ size. “A lot of big programs were launched,” he adds, and many of them were abandoned.


One particular stumbling block is that even when researchers find BACE inhibitors that can cross the blood-brain barrier, the molecules “get chucked out faster than they go in,” Schenk adds.

Although BACE has clear challenges as a target, “it does have the huge advantage over γ-secretase in that we have a very strong fundamental understanding of the target at a molecular level,” Lilly’s Audia notes. “Ultimately, I think that will prevail.”

Many researchers point to BACE inhibitors discovered at Schering-Plough, now part of Merck & Co., as evidence that chemists can overcome the challenges. Although Merck has yet to put its lead molecule into advanced trials, scientists are confident that they can surmount the chemistry challenge.

With a handful of antibodies and small molecules in late-stage trials and many more generations of γ- and β-secretase inhibitors waiting in the wings, the next set of data is critical. Results from studies of γ-secretase inhibitors should provide insight into whether chemists can sufficiently raise the potency of the molecules without also turning up harmful side effects. And the trials will help determine how much amyloid-β needs to be sequestered to have an impact on disease.

Even if a trial fails, it could tell neurologists more about whether a point exists in the disease’s progression after which it is too late for treatment to have a marked impact on a patient’s life. To that end, Bristol-Myers will soon start a large trial to test its γ-secretase inhibitor in patients with an early form of the disease.

In the past, clinical trials involving people with predementia, known in academia as MCI for “mild cognitive impairment,” have largely failed. In addition to being saddled with questionable drug candidates, clinicians had no good way to predict which patients with memory loss would develop full-blown dementia, says Howard Feldman, head of neuroscience global clinical research at Bristol-Myers.

But industry is now in a much better position to design early-stage trials, thanks to the Alzheimer’s Disease Neuroimaging Initiative, a public-private partnership that has been instrumental in identifying biomarkers and in imaging how an Alzheimer’s brain develops.

Bristol-Myers scientists believe they have come up with the right battery of tests to determine whether a patient with predementia will develop Alzheimer’s. The company plans to recruit people suffering from memory decline who also have low levels of amyloid-β and the protein tau in their cerebrospinal fluid, as well as a pattern of brain atrophy unique to Alzheimer’s, as revealed by magnetic resonance imaging.

Despite all the headway, some Alzheimer’s experts are concerned that scientists’ years of effort could be for naught. The amyloid hypothesis “rests on a number of assumptions that were never sorted through,” says Robert Moir, assistant professor of neurology at Harvard Medical School. The primary assumption has been that amyloid-β “is a piece of junk,” he says. “But if you look at the basic biology, it seems pretty bizarre that such a thing would evolve as junk.”

Moir and his colleague, renowned Alzheimer’s researcher Rudolph E. Tanzi, recently published a paper suggesting that amyloid-β could in fact play a protective role in the brain (PLoS One 2010, 5, e9505). They found that the culprit behind those ugly plaques in Alzheimer’s also acts as an antimicrobial peptide.

The implications of the findings are still unclear. But if amyloid-β is being overproduced for a reason—say, to control a low-level infection—dampening its effect could prove dangerous.

Other researchers suggest that a calcium imbalance is killing neurons and prompting amyloid-β accumulation, which would mean that blocking the amyloid won’t stop the disease. Other hypotheses finger various oxidation agents as culprits.

Adding to the uncertainty, the industry has already seen several high-profile failures of drugs that target the amyloid-β pathway. Earlier this year, Myriad Pharmaceuticals stopped development of tarenflurbil, an anti-inflammatory drug billed as a γ-secretase inhibitor, after it flopped in a Phase III trial.

And ongoing trials suggest that clearing amyloid-β isn’t enough to slow disease progression. Patients from the trial of Elan’s AN1792, the synthetic amyloid-β, were followed for up to five years after the study ended. The vaccine elicited an antibody response in some patients, but autopsies performed on eight of them showed that neurons kept dying despite lower amyloid-β levels.

A recent paper in Lancet Neurology showed that in a Phase II study, bapineuzumab, the drug candidate developed by Pfizer and J&J, elicited a 25% reduction in amyloid plaques in the brains of patients with Alzheimer’s disease (Lancet Neurol. 2010, 9, 363). At the same time, patients did not show improvement in cognitive measures.

Scientists working on drugs that interrupt the amyloid pathway acknowledge lingering questions about the approach. “It’s a controversial area,” Pfizer’s Pangalos concedes.

But they also point to flaws in earlier studies of small molecules that block amyloid-β production. In particular, many researchers question whether Myriad’s tarenflurbil even hits its target. A 2007 study by University of California, San Diego, researcher Douglas R. Galasko showed no change in amyloid-β levels in the spinal fluid of patients dosed with tarenflurbil, indicating that it wasn’t actually blocking γ-secretase (Alzheimer Dis. Assoc. Disord. 2007, 21, 292).

“Some of the studies have purportedly been studies of the amyloid hypothesis,” but the compound was having no effect on the pathway or was having a minimal effect on the pathway, says David Michelson, vice president of clinical neuroscience and ophthalmology at Merck.

Michelson warns against drawing conclusions about the role of amyloid-β until better compounds are in the clinic. “I don’t feel like any of the studies yet have given us really definitive information about the amyloid hypothesis,” he adds.

Until more and better data are available, academic researchers will remain cautious about the prospects for the drugs that are currently in the clinic. “I don’t think there’s going to be a magic bullet from any of the compounds being studied,” Steven H. Ferris, a professor at New York University’s Alzheimer’s Disease Center, said at a panel on Alzheimer’s drugs at the BIO CEO & Investor Conference earlier this year. Ferris believes that blunting the disease’s progress will most likely require a combination of drugs against several targets.

Yet most researchers say the amyloid hypothesis still deserves a fair test. “I think the genetic argument is so compelling that we are obliged to find a way to prevent amyloid formation and see if those brains still dement,” Mount Sinai’s Gandy says.

Meanwhile, researchers are already looking ahead to the next wave of drug targets. The most obvious is tau, the protein that makes up the tangles within neurons. Experimental data have shown that the behavior of mice with dementia, amyloid plaque, and tangles improves when tau levels are knocked down, Gandy points out. However, tau is such a ubiquitous protein with many functions that developing a safe drug “is going to be very difficult,” he cautions.

Despite myriad challenges, researchers in academia and industry alike expect that the next five to 10 years will yield an arsenal of new drugs that could be mixed and matched to start modifying the disease.

Indeed, scientists who have spent their careers trying to understand Alzheimer’s are optimistic. “The field is undergoing a revolution right now,” Elan’s Schenk says. He is encouraged by the ability to test drugs more rationally and the growing knowledge of the disease’s basic biology. Although obstacles to curing Alzheimer’s abound, he says he is confident that “we’re going to look back at this as the most exciting time in drug development.”


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