Give BACE Inhibitors a Second Chance?
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Scientists once hoped that blocking β-secretase would slow or prevent Alzheimer’s disease. Then came the rude awakening. The inhibitors caused the very thing they were supposed to prevent—cognitive decline. Enthusiasm tanked. Pharmaceutical companies canned their BACE inhibitor programs. But a few lone voices kept calling for another try, and by AAIC 2023, held July 16-20 in Amsterdam, the vibe had shifted. A small but vocal group of basic scientists had always maintained that the field gave up too quickly on these compounds, and now some clinicians have come around.
- In CSF of people who took BACE inhibitors, substrate fragments plunged.
- These reductions reflect cognitive decline caused by high doses.
- Low-dose BACE inhibition could slow plaque growth.
- It might work in primary prevention or after immunotherapy.
“BACE inhibition in primary prevention holds great potential,” said Paul Aisen, University of Southern California, San Diego, during a scientific session on the future of BACE inhibition. Even Reisa Sperling, a self-professed skeptic of BACE inhibition, said she could envision a small trial. Sperling, from Brigham and Women’s Hospital, Boston, co-chaired the session with Robert Vassar from Chicago's Northwestern University, who, with Martin Citron, had cloned BACE 24 years ago (Vassar et al., 1999).
What’s changed? For BACE inhibition itself, not much. Secretase experts had always advised low doses to avoid adverse events. That is because BACE not only catalyzes the first step in Aβ production—the cleavage of amyloid precursor protein—but also snips dozens of other substrates. Many are found in neurons; some support axon guidance and synaptogenesis.
What has changed is that scientists now have a way to identify and monitor at least some of those cleavages. In Amsterdam, Stefan Lichtenthaler, Technical University of Munich, reported analysis of cerebrospinal fluid samples taken at baseline and after treatment with three different BACE inhibitors, Merck’s verubecestat, Novartis’s umibecestat, and Shionogi’s atabecestat. The Merck samples came from a Phase 3 trial, while the others came from Phase 2s.
Stephan Muller and Pieter Giesbertz in Lichtenthaler’s lab ran mass-spectrometry-based proteomic analyses of the samples, looking for peptides snipped from cell-surface BACE substrates. “All three BACE inhibitors produced qualitatively and quantitatively similar proteome changes,” said Lichtenthaler. The three inhibitors lowered CSF concentrations of peptides cleaved from the same dozen or so substrates, including Sez6, IL6ST, CACHD1, CHL1, Sez6L, and L1CAM.
BACE Proteomes. These volcano plots show down- (blue) and upregulated (red) protein fragments in the CSF of people who had been treated in BACE inhibitor trials. The profiles for umibecestat (left) and verubecestat (right) were very similar. [Courtesy of Stefan Lichtenthaler, Technical University of Munich.]
These reductions were dose-dependent, and, in the case of the learning and memory-linked protein Sez6, the soluble fragments were almost fully suppressed at the highest inhibitor doses given in those trials. Indeed, reduction of soluble Sez6 directly correlated with reduction of Aβ40 in the CSF.
For some other substrates, however, BACE inhibition, even at the highest doses, only partially reduced their soluble fragments, suggesting other proteases help process them. This was the case for the neural cell adhesion molecules L1CAM and CHL1, for example. Whether that absolves these substrates from any part in the cognitive decline caused by BACE inhibition in the trials remains to be seen.
Nobody knows for certain which of the BACE substrates are needed for cognition. Jochen Herms, Ludwig-Maximilians University, Munich, believes Sez6 is important. At AAIC, he reported that in Sez6 knockout mice, spine density is a bit below that of control mice, but that verubecestat and other BACE inhibitors did not reduce it further. The data suggest that spines supported by this neuronal signaling molecule are vulnerable to BACE inhibition.
Importantly, Lichtenthaler noted that reductions of all these soluble fragments in the CSF reached a maximum at even the lowest doses of umibecestat and verubecestat used in the clinical trials—15mg and 12mg, respectively. Partial suppression occurred in the case of 5 mg atabecestat, which, incidentally, caused no significant cognitive decline. “Cognitive worsening only occurs at drug doses where BACE1 substrate cleavage is nearly maximally inhibited,” Lichtenthaler concluded.
He believes that low doses of BACE inhibitors would allow sufficient substrate cleavage to still occur such that cognitive decline would be avoided, while also sufficiently slowing amyloid accumulation. He said trials to test this hypothesis should collect enough CSF to correlate cleavage of these BACE substrates with any cognitive changes.
What could such a trial look like? Julie Stone, a pharmacokineticist at Merck, has been crunching the numbers on such questions for years (e.g., May 2015 webinar). Stone modelled two scenarios discussed in Amsterdam—primary prevention among people who have tested positive for low levels of amyloid, and a post-immunotherapy “maintenance dose” to keep plaques from regrowing once they had been cleared. In both cases, Stone estimated how BACE inhibition would affect plaque load.
Regarding prevention, Stone concluded that a high dose of verubecestat, or around 27 mg daily, would be needed to halt amyloid growth at a stage where baseline levels are around 10 centiloids. Such a high dose would be needed because, in kinetic terms, plaque growth is a zero-order process, proceeding fastest early in pathogenesis. Alas, that 27 mg dose would suppress Aβ production by 80 percent, a level associated with cognitive side effects in prior trials.
What about when baseline amyloid levels are higher? Perhaps counterintuitively, Stone's model predicted that lower doses of inhibitor would suffice in that case. At a baseline of 50 or 60 centiloids, daily doses of 2.9 mg or 1.7 mg verubecestat, respectively, would prevent further plaque growth. Whether this would slow progression of the disease, including tau pathology and cognitive decline, is unknown, Stone said. The 1.7 mg dose would inhibit BACE by a third, likely low enough to avoid cognitive side effects.
Rather than stopping plaque growth, what about slowing it down? Stone modeled what 35 percent BACE inhibition at various baseline amyloid loads would achieve. At 10, 25, or even 50 centiloids, this would limit plaque growth to reach 50 to 60 centiloids after 20 years, instead of the 80 to 90 centiloids that would be reached in untreated controls.
“The big open question is, is that clinically meaningful?” Stone asked at AAIC. Many AD-related pathologies and symptoms don’t show up until plaque loads surpass 50 centiloids, suggesting this slowing could be beneficial. “Instinctively, we expect that slowing of amyloid would slow progression of the disease,” she said.
Slow Those Plaques Down. Kinetic modeling suggests that 1.7 mg verubecestat, given when amyloid burden had reached 10 (blue line), 25 (red line), or 50 centiloids (yellow line), would slow plaque growth relative to untreated controls (dashed lines). [Courtesy of Julie Stone, Merck.]
Stone predicted a similar scenario if BACE inhibitors come in after immunotherapy has removed plaques. Around 12 mg verubecestat would be able to maintain a 20 centiloid plaque load. That is in the range known to cause cognitive deficits. A dose of 1.7 mg would slow regrowth, again plateauing at about 50-60 centiloids after 20 years.
What about real-life experiments? Preclinical work makes low-dose inhibition look attractive. Elyse Watkins, a postdoc in Vassar’s lab, treated 8-month-old PDAPP mice with 109, 33, or 11 mg/Kg of MBi-10, a BACE inhibitor from Merck. Six months later, mice on the lowest dose had 40 percent less amyloid than untreated controls. The human equivalent dose would be around 0.9 mg/Kg, likely sparing cognition.
Watkins’ data suggests that this dose might even help clear plaques. She had injected the 8-month-old animals with Methoxy O4 to label existing plaques. At 14 months, she measured less of the label in treated mice than in controls, suggesting that some of the plaque present at baseline had cleared.
Going Low. At a low dose of 11 mg/Kg, the BACE inhibitor MBi-10 reduced soluble Aβ42 and plaque load in the cortices and hippocampi of PADPP mice. It even cleared some of the Methoxy O4 injected into the brain six months prior, hinting that it may help clear existing plaques. [Courtesy of Elyse Watkins, Northwestern University.]
Are trialists ready to try? “We have to be very careful,” Sperling told Alzforum. She is concerned about suppressing soluble Aβ. Like BACE inhibitors, solanezumab, a monoclonal antibody that binds monomeric Aβ, also tended to cause cognitive decline in the A4 secondary prevention trial, though without affecting BACE substrates (Mar 2023 news). Dave Morgan, Michigan State University, Grand Rapids, echoed that sentiment. Like others in the field, he thinks Aβ has some important, still-unknown function at synapses.
Even so, Sperling has warmed to the idea of testing these inhibitors once more. “I would be open to a small trial where we test for cognitive changes over a very short time, even as little as a few weeks,” she said.
Aisen is more optimistic. He pointed out that solanezumab did have a small cognitive/clinical benefit in the pooled analyses of two Phase 3 trials in LOAD, and that the solanezumab dose was subsequently increased in A4 (Oct 2012 news; Jun 2017 news). Aisen suspects A4 may have simply lowered soluble Aβ too much for synapses to function properly.
“I think if we embed sufficient cognitive monitoring, we would be comfortable in planning a significant [BACE inhibitor] trial,” he told Alzforum. “Clearly there are cognitive effects, but these are dose-related, reversible, and we can monitor them,” he said.
Aisen believes that in preclinical AD, the A4 trial validated the PACC and RBANS as being sensitive enough to quantify cognitive decline, and would pick up decline caused by BACE inhibition, as well (Mar 2023 news). “I believe we can develop BACE inhibitor trials at lower than 50 percent inhibition, and do it now,” he claimed.
Others welcomed the idea. Ralph Nixon, New York University, noted that BACE inhibition would not only reduce Aβ, but also APP's β-C-terminal fragments. Nixon and others have reported that β-CTFs scupper the endolysosomal system, disrupting proteostasis and exacerbating amyloid pathology (Jun 2010 news; Jun 2022 news; Jul 2023 news).
Lichtenthaler agreed that tempering β-CTF could be an important benefit—as could an increase in sAPPα, a fragment generated by α-secretase, which completes with BACE to cleave APP (Jan 2019 news). “We could have a triple-positive effect of BACE inhibition,” he suggested. Low-dose BACE inhibition might even correct lysosomal dysfunction in AD, he predicted (see Lichtenthaler’s recent comment).
Injecting a cautionary note, Bart De Strooper, University College, London, said that in addition to suppressing cleavage of BACE's other substrates, inhibitors would also lead to more of the shorter, more hydrophobic Aβ peptides generated by α-cleavage of APP between amino acids 16 and 17 of the Aβ peptide sequence. Also called p3 fragments, these Aβ17-x peptides tend to be neglected, but can insinuate themselves into plaques (Iwatsubo et al., 1996). “These are difficult to detect, but I would not overlook them,” said De Strooper.
De Strooper wants to see γ-secretase modulators (GSMs) reconsidered. “Mechanism-based side effects that are difficult to circumvent are always a struggle with BACE inhibitors,” he said. “With GSMs, you aim to lower the toxic Aβ fragments instead of lowering total Aβ. This is a better rationale, because you keep all other biology intact.”
Lichtenthaler countered that the protective Icelandic A673T mutation in APP, which slows its cleavage by BACE and reduces Aβ production by a third, supports the rationale for BACE inhibition, as do mice having only one copy of the BACE1 gene (Maloney et al., 2014). The latter lack the neurological dysfunction of the full knockouts.
BACE inhibitors have been tested up to Phase 3 and could be retested without delay. “I’m pretty convinced low-dose BACE inhibition will work,” said Lichtenthaler.
What would such a trial look like? Aisen is enthusiastic about both types of trial Stone modeled, one for primary prevention and one to augment immunotherapy. Whether pharmaceutical companies would be willing to restart their BACE programs remains to be seen.
“I’m not confident we’ll get that kind of support, but am optimistic that pharma will be willing to supply the drugs,” Aisen said. One pharma scientist told Alzforum her company would likely sell its BACE inhibitor for $1 to a group able to fund and run new trials.
One possibility is an A2 trial akin to the A3 and A45 trials of lecanemab targeting people with amyloid levels between 20 and 40 centiloids, and above 40 centiloids, respectively. Aisen and Sperling are investigators on both. Indeed, the A3 trial was initially slated to test a BACE inhibitor until the cognitive side effects put the kibosh on that. “It seemed plausible then, and it seems plausible now, that BACE inhibition will have a clinically meaningful effect,” said Aisen.
As for A2, Aisen said the goal was always to go lower, to 20 or 10 centiloids. He believes it may be possible to treat people before they test positive for amyloid, using plasma tests for various p-taus or Aβ42/40 as indicators of imminent amyloid deposition. “We are discussing A2,” noted Aisen. “Our intention is to continue to move earlier, toward primary prevention, but we are not ready to pin down a trial design,” he told Alzforum.
“Our goal is to devise a path forward for new clinical trials to test low-level BACE inhibition,” said Vassar, “because we are going to need an oral disease-modifying therapy for Alzheimer’s disease.” De Strooper agreed. "It is extremely important to emphasize that anti-amyloid antibodies cannot be the primary prevention we are all looking for.” —Tom Fagan
References
Therapeutics Citations
Webinar Citations
News Citations
- Legacy of A4 Secondary Prevention Study Goes Beyond Negative Result
- The Solanezumab Benefit: Oh, So Small, But Probably Real
- A4 Researchers Raise Solanezumab Dosage, Lengthen the Trial
- Death of the Neatnik: Neurons Perish When Trash Clutters Their Space?
- Behold PANTHOS, a Toxic Wreath of Perinuclear Aβ That Kills Neurons
- Too Basic: APP β-CTF's YENTPY Motif Binds Proton Pump, Thwarts Lysosomes
- Secreted APP Binds GABA-B Receptors, Blocks Neurotransmitter Release
Mutations Citations
Paper Citations
- Vassar R, Bennett BD, Babu-Khan S, Kahn S, Mendiaz EA, Denis P, Teplow DB, Ross S, Amarante P, Loeloff R, Luo Y, Fisher S, Fuller J, Edenson S, Lile J, Jarosinski MA, Biere AL, Curran E, Burgess T, Louis JC, Collins F, Treanor J, Rogers G, Citron M. Beta-secretase cleavage of Alzheimer's amyloid precursor protein by the transmembrane aspartic protease BACE. Science. 1999 Oct 22;286(5440):735-41. PubMed.
- Iwatsubo T, Saido TC, Mann DM, Lee VM, Trojanowski JQ. Full-length amyloid-beta (1-42(43)) and amino-terminally modified and truncated amyloid-beta 42(43) deposit in diffuse plaques. Am J Pathol. 1996 Dec;149(6):1823-30. PubMed.
- Maloney JA, Bainbridge T, Gustafson A, Zhang S, Kyauk R, Steiner P, van der Brug M, Liu Y, Ernst JA, Watts RJ, Atwal JK. Molecular mechanisms of Alzheimer disease protection by the A673T allele of amyloid precursor protein. J Biol Chem. 2014 Nov 7;289(45):30990-1000. Epub 2014 Sep 24 PubMed.
Further Reading
Papers
- Nash A, Aumann TD, Pigoni M, Lichtenthaler SF, Takeshima H, Munro KM, Gunnersen JM. Lack of Sez6 Family Proteins Impairs Motor Functions, Short-Term Memory, and Cognitive Flexibility and Alters Dendritic Spine Properties. Cereb Cortex. 2020 Apr 14;30(4):2167-2184. PubMed.
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Comments
Tel Aviv University
We developed a novel approach to inhibit β-secretase cleavage site of APP by blocking the substrate rather than by inhibiting the total enzymatic activity. This approach overcomes some of the limitations presented by BACE1 inhibition methodologies, as BACE1 shares the processing of other non-APP substrates (Arbel and Solomon, 2008).
Several studies suggest that the amyloidogenic cleavage of APP occurs through the endocytic pathway, while BACE1 cleavage of other vital substrates are independent of endocytosis. Prominent alterations of the endocytic pathway and lysosomal system have been identified in AD, including the upregulated expression of endocytic genes with increased endocytic activity and enhanced amyloidogenic processing of APP.
The amyloidogenic pathway generates, besides the Aβ peptide, the intracellular β- AICD, which has a number of important cellular functions. β-AICD may contribute to cellular dysfunction via an increase in p53 expression and in tau phosphorylation. The antibodies developed by us are directed to the β-secretase cleavage site of APP (BBS1). They interfere with the endocytic pathway of BACE1, block the cleavage site of BACE1, and interfere with APP-BACE interaction, exploiting APP's presence at the cell surface prior to internalization into early endosomes.
Treatment of 3xTg-AD mice with BBS1 not only improves the cognitive functions and lowers the levels of total Aβ as expected, but induces a considerable effect on TAU pathology, i.e., 80 percent reduction in phosphorylated tau levels and 56 percent reduction in tangles. In addition, the treatment moderates the inflammatory response in mice and reduce the expression levels of p53 and pGSK3β involved in neuronal apoptosis.
This is the first attempt to inhibit β-secretase activity by blocking the cleavage site on APP. It overcomes some of the limitations presented by BACE1 inhibitors regarding non-specific inhibition of BACE1 and BACE2 activities, as well as the mechanism-based toxicity arising from inhibition of BACE1 as well as other proteases that were shown to cleave APP at the β-site.
References:
Arbel M, Solomon B. Immunotherapy for Alzheimer's disease: attacking amyloid-beta from the inside. Trends Immunol. 2007 Dec;28(12):511-3. PubMed.
Amyloid beta oligomers are the accepted neurotoxic agents, while plaque seems to be a protection mechanism. That all of the effective monoclonal antibodies target the oligomers supports the latter's cytotoxic role. Aβ oligomers are cytotoxic at a nanomolar scale. Thus, the question will be, what are the concentrations of these oligomers in patients being treated with the BACE inhibitors? If BACE inhibitors can reduce those toxic oligomers' concentrations below the nanomalor scale, then it would be possible to expect some benefits.
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