Small Molecule Microarrays Enable the Discovery of Compounds
That Bind the Alzheimer’s A? Peptide and Reduce its Cytotoxicity
Jermont Chen,†,‡Anne H. Armstrong,†Angela N. Koehler,§and Michael H. Hecht*,†
Department of Chemistry, Princeton UniVersity, Princeton, New Jersey 08544, United States,
and Broad Institute of HarVard and MIT, Cambridge, Massachusetts 02142, United States
Received August 20, 2010; E-mail: firstname.lastname@example.org
Abstract: The amyloid-? (A?) aggregation pathway is a key target in efforts to discover therapeutics that
prevent or delay the onset of Alzheimer’s disease. Efforts at rational drug design, however, are hampered
by uncertainties about the precise nature of the toxic aggregate. In contrast, high-throughput screening of
compound libraries does not require a detailed understanding of the structure of the toxic species, and can
provide an unbiased method for the discovery of small molecules that may lead to effective therapeutics.
Here, we show that small molecule microarrays (SMMs) represent a particularly promising tool for identifying
compounds that bind the A? peptide. Microarray slides with thousands of compounds immobilized on their
surface were screened for binding to fluorescently labeled A?. Seventy-nine compounds were identified by
the SMM screen, and then assayed for their ability to inhibit the A?-induced killing of PC12 cells. Further
experiments focused on exploring the mechanism of rescue for one of these compounds: Electron
microscopy and Congo red binding showed that the compound enhances fibril formation, and suggest that
it may rescue cells by accelerating A? aggregation past an early toxic oligomer. These findings demonstrate
that the SMM screen for binding to A? is effective at identifying compounds that reduce A? toxicity, and
can reveal potential therapeutic leads without the biases inherent in methods that focus on inhibitors of
Considerable genetic and biochemical evidence indicates that
aggregation of the amyloid-? peptide (A?) plays a causative
role in the neurodegeneration, memory loss, and dementia
associated with Alzheimer’s disease (AD).1-5Although the
precise structure of the toxic aggregate is still under investiga-
tion, the major features of the “amyloid cascade” pathway are
understood: Proteolytic processing of the amyloid precursor
protein (APP) results in the extracellular release of the 4 kDa
A? peptide. Differential cleavage by secretase enzymes leads
to the formation of A? variants ranging in size from 39 to 43
amino acids, with the 40-residue A?40 and 42-residue A?42
peptides being the most prevalent.6-8Compared to A?40, A?42
is more prone to aggregation,9more neurotoxic,10and more
closely correlated with symptomatic disease.2,11
A?42 is also the predominant component of the extracellular
plaque that has long been viewed as the pathological hallmark
of AD.12,13While this insoluble plaque provides posthumous
evidence of the disease, numerous findings over the past decade
implicate earlier soluble intermediates as the neurotoxic agents.
A?-derived diffusible ligands (ADDLs) have been observed to
induce neuronal death in cell culture,14and soluble A? oligo-
meric species are more closely associated with cognitive decline
in AD patients and synapse loss in transgenic mice than fibril
or plaque load.15-17Most recently, a murine model in which
ADDLs were endogenously expressed with sequence mutations
‡Current Address: Propulsion Directorate, Air Force Research Labora-
tory, Wright-Patterson AFB, OH 45433.
§Broad Institute of Harvard and MIT.
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Published on Web 11/09/2010
10.1021/ja107552s 2010 American Chemical Society
J. AM. CHEM. SOC. 2010, 132, 17015–17022 9 17015
that prevented subsequent plaque formation showed that cogni-
tive deficits depend on soluble A? oligomers rather than end-
With the prevalence of Alzheimer’s disease projected to rise
dramatically in the coming decades,19there is increasing urgency
to develop novel therapeutics to prevent and/or treat this
debilitating disease. The pharmaceuticals currently used to treat
AD include cholinesterase inhibitors and memantine, a modula-
tor of glutamate receptors.20,21These drugs provide symptomatic
relief and may slow cognitive decline; however, they do not
target the underlying molecular cause of AD. Therefore,
currently approved drugs neither halt nor reverse progression
of the disease. In contrast to these existing drugs, novel
compounds that interfere with A? aggregation, and thereby
block the molecular events that cause AD, represent a promising
approach to the prevention and/or cure of Alzheimer’s disease.
In principle, compounds that interfere with A? aggregation
could be discovered by either of two approaches: structure-based
rational drug design or high-throughput screening. Since a range
of intermediates along the A? aggregation pathway have been
implicated as potential toxic species,22-25and none of their
precise structures are known, structure-based drug design is not
yet possible. For the time being, high-throughput screening
remains a more promising approach.
A number of high-throughput methods have been developed
to screen for compounds that interfere with A? aggregation.
Most screens use synthetic A? peptide and monitor aggregation
by following the fluorescence of thioflavin-T or another dye
that binds to fibrillar aggregates.26-28Although relatively
convenient to perform, these screens have limitations. First, they
are hampered by the need for substantial quantities of synthetic
peptide, which is expensive and difficult to produce in a form
that is free of preaggregated seeds. A second and more
significant drawback of dye-binding assays is their reliance on
a reporter that detects amyloid fibrils or protofibrils, rather than
the early intermediates that are now thought to be the neurotoxic
agent. The limitations of assays that screen for inhibitors of
fibrillization are highlighted by recent reports that accelerating
fibril formation may, in fact, be advantageous as a way to
decrease the presence of toxic soluble A? oligomers.29,30
As an alternative to traditional assays using synthetic A?
peptide, our lab previously reported the development of a high-
throughput screen using an A?42-GFP fusion protein expressed
in Escherichia coli.31,32In that system, aggregation of the A?42
sequence drags the entire fusion protein into misfolded insoluble
aggregates, thereby preventing the folding and fluorescence of
GFP. Compounds that inhibit the aggregation of A?42 enable
the GFP part of the fusion to fold into its native structure, and
thereby give rise to green fluorescent colonies (or liquid cultures)
of E. coli. The A?42-GFP screen overcame two of the
limitations of the dye binding assays: (i) synthetic A? peptide
was not required, and (ii) the assay reported A? misfolding and
aggregation without requiring the formation of amyloid fibrils.
Application of the GFP-based screen enabled the identification
of several aggregation inhibitors from a library of triazine
derivatives,32and from other libraries screened subsequently.
Some of these compounds look promising and are being
evaluated in a Drosophila model of AD. Nonetheless, the GFP-
based screen also has several limitations. (i) Because the A?42-
GFP fusion protein was expressed in E. coli, compounds that
fail to cross the cell wall and membrane of E. coli, or which
were toxic to E. coli, may have been missed. (ii) Because the
folding and fluorescence of the GFP reporter is based on the
solubility of the upstream sequence,33the screen may not
distinguish between compounds that block all aggregation (by
favoring monomeric A?) and those that block fibrillization by
favoring the toxic soluble oligomers. Thus, compounds that
allow the A?42-GFP fusion protein to fold and fluoresce by
enhancing the stability of soluble oligomers would be mistakenly
identified as inhibitors of aggregation (hits) rather than as
enhancers of the toxic species. (iii) Most importantly, because
the A?42-GFP screen was designed to identify compounds that
inhibit aggregation, it would miss potential therapeutics that
remove toxic oligomers by enhancing their aggregation into
These considerations motivated us to develop a novel method
to screen compounds based solely on their ability to bind to
monomeric A?. Ultimately, whether a small molecule reduces
the toxicity of A? by inhibiting aggregation, accelerating it past
the toxic species, or redirecting it to an alternate pathway, the
compound must first bind the A? peptide.
High-throughput identification of compounds that bind to
specific proteins has been accomplished previously through the
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Chen et al.
reactions. For the current study, SMMs were prepared by
installing an isocyanate on the surface of the slides and then
attaching the small molecules to this group.35-37Because
isocyanate reacts with amines (primary and secondary), thiols,
alcohols (primary and secondary), and several other groups, a
compound possessing several different functional groups can
attach to the surface in a range of orientations with various
functional groups available to interact with the probe. To ensure
that the small molecules are presented at a distance from the
surface sufficient to enable interactions with a soluble probe
(A? peptide in the current study), the isocyanate is separated
from the surface by a polyethylene glycol spacer.
A single SMM slide typically displays 10800 compounds,
allowing for rapid and efficient screening of diverse libraries
of small molecules. SMM slides are probed with a fluorophore-
or epitope-tagged protein (in this case, fluorescently labeled A?
peptide), and compounds that bind the protein are detected by
automated fluorescence read-out (a schematic is shown in Figure
2a).35-37SMMs have been used successfully to identify a wide
range of protein-ligand interactions, including calmodulin and
human immunoglobin G ligands,38,39transcriptional regulators,40,41
and inhibitors of histone deacetylases.42
The SMM technology has several features that make it ideal
as a high-throughput screen for compounds that bind A?. First,
it does not require knowledge of the protein structure or binding
pocket. This unbiased approach is crucial since the structure of
the toxic A? aggregate is not known, and a traditional active
site pocket is not likely to exist. Second, the high sensitivity of
the SMM assay allows the A? peptide to be used at very low
concentrations. This is important because A? aggregation occurs
via a nucleation-dependent mechanism,43and keeping the
peptide below the critical concentration favors the monomeric
form, thereby facilitating the identification of compounds that
interact with A? at or before the earliest steps of aggregation.
An added benefit is that low concentrations of peptide make
the assay relatively inexpensive.
Here we describe the development of SMM technology to
screen libraries of small molecules for compounds that bind
the Alzheimer’s A? peptide. As an initial step toward SMM
assay development, we identified conditions that favor the
monomeric state of A?. Next, two SMM slide sets, one with
natural products and synthetic commercial compounds (NPC)
and the other with diversity-oriented synthesis compounds
(DIV), were screened with fluorescently labeled A?40. Com-
pounds in printed features that bound the peptide were identified
as hits, as described previously.37,44These compounds were
subsequently assayed for their ability to rescue PC12 cells from
A?42-induced toxicity. Further examination of a commercially
available compound revealed dose-dependent rescue of PC12
cells. Finally, we demonstrated that this compound actually
promotes, rather than inhibits, fibrillogenesis. These results
validate the ability of the SMM screen to reveal compounds
that interact with the A? peptide, and may provide leads for
therapeutics that prevent or cure Alzheimer’s disease.
Results and Discussion
Development of an SMM Assay for Binding to A?. Identifying
compounds that interact with A? at or before the earliest stages
of aggregation required that we develop conditions for the SMM
assay wherein the peptide would occur predominantly in its
monomeric form. A?, particularly A?42, is known to aggregate
quickly, and aggregation is considerably faster when the sample
is agitated,45-47as required for the SMM assays. We assessed
the aggregation of A?40 and A?42 with N-terminal fluorescent
tags under conditions typically used for SMM screening, which
include 30 min of gentle agitation (by orbital mixing) at room
temperature. Monomeric and oligomeric states were estimated
using Tris-Tricine SDS-PAGE. Such gels are used routinely
to assess the oligomeric state of A?,48,49and previous reports
indicate that both cell-derived oligomers and those formed in
Vitro resist denaturation by SDS, particularly when gel analysis
is performed at room temperature.50-52Nonetheless, the pos-
sibility that SDS alters the distribution of oligomeric states
cannot be ruled out. With this caveat in mind, we probed the
oligomeric states of our samples using the standard Tris-Tricine
As shown in Figure 1a, fluorescently labeled A?42 formed
more oligomers and larger oligomers than A?40. Distinct
monomer (4 kDa), dimer (8 kDa), trimer (12 kDa), and tetramer
(16 kDa) bands are apparent for A?42 at 9.35 µM, with the
trimer being the most intense oligomeric band, consistent with
previous reports.48Trimer and tetramer bands were also very
faintly apparent for A?42 at 935 nM. In contrast to A?42, A?40
produced only monomer and dimer bands at 9.35 µM, and at
concentrations below 1 µM, A?40 yielded only monomers.
Because of its reduced propensity to aggregate, we opted to
use A?40 for our SMM screens. Because A?40 lacks only two
residues at its C-terminus and has the same core residues as
A?42, we assumed that most compounds capable of binding
A?40 would also bind A?42. To assess whether fluorescently
labeled A?40 would remain monomeric under the conditions
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SMMs for the Discovery of Compounds That Bind AD A? Peptide
of the SMM assay, we incubated the peptide with gentle
agitation for 60 minstwice as long as required for typical SMM
binding experimentssand probed its oligomeric state by
SDS-PAGE. As shown in Figure 1b, at micromolar concentra-
tions, A?40 forms monomers and dimers, but at concentrations
1.17 µM or lower, only monomeric bands are seen. This is
consistent with previous reports that the critical concentration
of amyloid aggregation occurs in the micromolar or high
These results suggest that fluorescently tagged A?40 is largely
monomeric in solution at the concentration (185 nM) and
incubation conditions used for SMM screening. Therefore, initial
encounters between the immobilized small molecule and the
peptide are likely to occur with the latter in its monomeric form.
After the first peptide binds an immobilized small molecule and
becomes attached to the surface, further copies may be recruited
to aggregate onto this immobilized complex.
The SMM Screen Identifies Compounds That Bind A?. The
SMM assay was used to screen two collections of compounds.
The first collection contained natural product and commercial
synthetic compounds (NPC), while the second contained a
library of compounds from a diversity-oriented synthesis (DIV).
A total of 17905 compounds were screened, and all assays were
performed in triplicate. Compounds that bound fluorescently
Figure 2. (a) The SMM binding screen. Compounds are covalently attached in an array of spots on the surface of a slide, and probed with fluorescently
tagged A? peptide. Those compounds that bind A? and withstand several washes are revealed as fluorescent spots. (b) Fluorescent read-out of the NPC-
SMM slide following incubation with fluorescent A?40. Enlargement of a grid section shows compound 2002-H20 binding the peptide (false-colored red)
as well as fluorescent dyes used in grid alignment (false-colored green and red) and nonfluorescing DMSO control spots. The structure of 2002-H20 is
shown with isocyanate-reactive functional groups colored red to indicate the positions available for attachment to the slide. Because two functional groups
(an amine and a phenol) are available for cross-linking, the population displayed on the surface is assumed to include molecules displayed in more than one
orientation, with some exposing the amine and others exposing the phenol for interaction with A?. (c) Three replicate SMM screens of the NPC compound
set show that compound 2002-H20 binds fluorescently labeled A?40 reproducibly and consistently. (d) Histogram of the composite Z-scores of SMM
fluorescence results from 3 replicates of the DIV and NPC slides. Results are divided into 254 bins with compounds shown in blue and DMSO controls in
red. The green box surrounds bins for 79 assay positive compounds with composite Z-scores g 3.4.
oligomeric state of fluorescently labeled A? under SMM agitation condi-
tions. (a) HiLyte Fluor 488-labeled A?42 (lanes 2-5) and HiLyte Fluor
647-labeled A?40 (lanes 6-9) after agitation for 30 min. (b) Fluorescently
labeled A?40 after 60 min agitation. Monomeric A? appears at ∼4 kDa.
Gels were visualized by silver staining.
The 10-20% Tris-Tricine SDS-PAGE gels showing the
17018 J. AM. CHEM. SOC. 9 VOL. 132, NO. 47, 2010
Chen et al.
labeled A?40 yielded spots exhibiting fluorescence at 632 nm
(false-colored red). Rhodamine features exhibiting fluorescence
at 532 nm (false-colored green) were used for grid alignment.
Fluorescence read-out results for the NPC slide screened with
the A?40 probe are shown in Figure 2b. Zooming in on a section
of the slide shows the rhodamine grid alignment spots, non-
fluorescing DMSO control spots, and the distinct, uniform red
fluorescence of a representative compound that bound A?.
Figure 2c shows that this compound, hereafter referred to as
2002-H20, bound A?40 in all three replicates.
Primary SMM assay positives were annotated using fluores-
cence signal as described previously by Seiler et al.44The
fluorescence intensity values from each replica slide were
background subtracted and converted to a Z-score, or standard
score representing the number of standard deviations that an
observationshere, the fluorescence of a grid spotsis above or
below the mean value.36,37,44Z-scores from the three replicas
performed for each slide set were combined to produce a
composite Z-score for each compound. These values, and the
composite Z-scores for DMSO control spots, were plotted in a
histogram (Figure 2d) with the results divided into 254 bins.
The resulting shape of the compound histogram, shown in blue,
is normal with a center around zero and a small shoulder on
the right side. The DMSO control histogram (red) also exhibits
a normal distribution centered on zero. Compounds binding A?
with a composite Z-score of 3.4 or greater were identified as
“hits” and selected for follow-up testing. From the 17905
compounds assayed from the DIV and NPC libraries, 79
compounds with a composite Z-score above the threshold value
were chosen for additional studies.
Inhibition of A?42-Induced Cytotoxicity. The 79 hits identi-
fied in the SMM screens were assayed for their ability to inhibit
A?42-induced killing of PC12 cells. We chose inhibition of
cytotoxicitysrather than biophysical studies of A? aggregationsas
our initial follow-up assay because it makes no assumptions
about the precise mechanism of A? toxicity, and thus allows a
less biased search for compounds that may ultimately lead to
therapeutics. Because A?42 is known to be a more important
contributor to AD-associated neurotoxicity than A?40, we used
the longer peptide to assay for inhibition of A?-induced cell
death. These assays were performed using pure peptide, not
linked to the fluorescent probe used in the SMM screen.
Therefore, any compounds that were isolated in the SMM screen
because of binding to the fluorophore tag would be weeded out
at this stage.
PC12 cells were incubated with A?42 and the SMM assay
positive compounds, and cell viability was assessed using the
MTT assay, which is based on the reduction of the yellow
tetrazolium salt MTT (3-(4,5-dimethylthiazol-2yl)-2,5-diphe-
nyltetrazolium bromide) to purple formazan crystals in meta-
bolically active cells. Briefly, PC12 cells were grown to
confluence and incubated for 24 h in the presence of 20 µM
A?42 and 100 µM of the hit compounds solubilized in DMSO.
MTT was added, and after incubation and solubilization, the
difference between absorbance at the formazan wavelength (570
nm) and the MTT absorbance (670 nm) was taken as a measure
of relative cell viability. At concentrations of 100 µM, 44 of
the 79 SMM hit compounds were found to reduce the toxicity
of A?42 in PC12 cells, with 15 of these compounds increasing
cell viability by >30%. These results for the top 15 rescuers
are shown in Figure 3 (toxicity rescue data for all 79 hit
compounds can be found in Supporting Information, Table S1).
As shown, one compound, 1462-B09, rescued cell viability to
nearly 100%, almost eliminating A?-induced toxicity entirely.
Another compound, 2002-H20, increases cell survival by 41%.
Compound 2002-H20 was chosen for further study as it
reproducibly binds A?40 in the SMM assays (Figure 2c), is
readily soluble in DMSO, and is commercially available.
Structural Features of Compound 2002-H20. The structure
of compound 2002-H20 is shown in Figure 4. With multiple
aromatic groups and several sites for hydrogen bonding, it shares
features with compounds identified previously as amyloid
aggregation inhibitors.55-57Its structure also bears some
resemblance to thioflavin-T (ThT), a fluorescent dye used to
bind and detect amyloid fibrils,58and Pittsburgh Compound-B,
which is used to image amyloid in the brains of AD patients.59
These compounds all contain a central phenyl ring and an
attached benzoxazole or benzothiazole. These similarities to
compounds previously known to bind A? support the efficacy
(53) Harper, J. D.; Lansbury, P. T. Annu. ReV. Biochem. 1997, 66, 385–
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2005, 44, 12709–12718.
Figure 3. Relative rescue scores for the top 15 compounds, which (at 100
µM) reduced the toxicity of A?42 to PC12 cells. Viability of cells in the
absence of A? or exogenous compounds was scaled (A570-670) 0.716) to
100% and viability of cells exposed to A?42 alone (A570-670) 0.496) was
scaled as 0%. As shown in gray, compound 2002-H20 increased viability
by 41%. Cell viability was assayed using the MTT assay. Compound
identities and toxicity data for all 79 compounds provided in Supporting
Figure 4. The benzoxazole motif in compound 2002-H20 is similar to the
benzothiazole motif in Pittsburgh Compound-B and thioflavin-T, two
compounds that bind A? and are used routinely to detect amyloid. Another
SMM hit compound, 2002-G12, contains similar benzimidozole motifs and
reduced A?42 toxicity by 76% (Figure 3).
J. AM. CHEM. SOC. 9 VOL. 132, NO. 47, 2010
SMMs for the Discovery of Compounds That Bind AD A? Peptide
of the SMM method for isolating A? binders. Similar structural
features also occur in another SMM hit, compound 2002-G12,
which contains a central phenyl ring with two benzimidizole
substituents and reduced A?-induced toxicity by 76% (Figure
3). Though this compound was no longer available for purchase
from the original commercial supplier, analogues with benzi-
midizole groups were tested and found to produce statistically
significant improvements in the viability of PC12 cells exposed
to A?42 (data not shown).
Compound 2002-H20 Exhibits Dose Dependent Inhibition
of A?42-Induced Cytotoxicity. The MTT assay was used to
assess the dose dependence of 2002-H20-mediated rescue of
PC12 cells from A?42-induced toxicity. As shown in Figure 5,
concentrations e3.13 µM were ineffective. However, beginning
at 6.25 µM, a dose-dependent increase in cell viability was
observed with concentrations g12.5 µM producing statistically
significant rescue of PC12 cells exposed to A?42. The greatest
improvement was at the high dose of 100 µM 2002-H20, with
cell viability increased to 65% of the level of cells that were
not incubated with A?42.
Compound 2002-H20 Does Not Affect Cell Viability. To
assess the effect of compound 2002-H20 on cell viability, it
was added to PC12 cells in the absence of A?42. As shown in
Figure 6, the compound does not appear to affect viability and
there are no concentration-dependent trends. Variations in
viability above and below 100% are likely due to the inherent
noise of the MTT assay.
Analogues of Compound 2002-H20. To assess whether
analogues of compound 2002-H20 inhibit A?42-induced cyto-
toxicity, we evaluated 21 related molecules. Compounds were
tested at a concentration of 50 µM for their ability to reduce
the toxicity of 20 µM A?42 in PC12 cells. Thirteen of these
compounds showed statistically significant rescue, but no
significant trends in functional groups were revealed. Only one
analogue was more effective than compound 2002-H20 itself
(Supporting Information, Table S2 and Figure S1).
Mode of Action for 2002-H20-Mediated Rescue of A?42-
Induced Cytotoxicity. Compound 2002-H20 was identified by
the SMM assay for its ability to bind A?42. Further character-
ization showed that it enhances the viability of PC12 cells
exposed to A?42. To explore the mechanism by which 2002-
H20 binding reduces A?42 toxicity, we investigated its impact
on peptide aggregation in Vitro. Compound 2002-H20 was
incubated at concentrations of either 50 or 100 µM with
synthetic A?42 at 20 µM. Amyloid formation was monitored
by the Congo red (CR) spectral shift assay, and by transmission
electron microscopy (TEM). When CR binds amyloid fibrils, it
produces a characteristic spectral shift that enables quantization
of amyloid.60As shown in Figure 7a, compound 2002-H20
produces a dose-dependent increase in the CR signal. TEM
images (Figure 7b) confirm that fibril formation is enhanced
by compound 2002-H20. In the absence of 2002-H20, the
predominant aggregates are short fibrils, protofibrils, and
oligomeric aggregates. However, in the presence of 50 µM 2002-
H20, A?42 forms long fibrils. Increasing the 2002-H20 con-
centration to 100 µM leads to dense fibrillar networks.
The CR data and TEM images shown in Figure 7 confirm
that compound 2002-H20 affects the aggregation pathway of
A?42. However, rather than inhibiting aggregation, 2002-H20
seems to accelerate fibril formation. These results suggest that
2002-H20 inhibits cytotoxicity by driving A?42 aggregation
toward fibrils, thereby reducing the presence of toxic oligomers.
A number of previous studies described compounds that
increase A? aggregation. For example, Williams et al. screened
a collection of 640 small molecules and isolated a compound
that stabilizes protofibrils.61Necula et al. examined compounds
previously identified as aggregation inhibitors and found that
several of these compounds reduced oligomer formation, but
promoted fibrillization.62In a related study of the phenothiazine
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Figure 5. Dose-dependence of compound 2002-H20’s ability to rescue
PC12 cells from A?42-induced toxicity. A 100% rescue scaled as the
absorbance difference of cells incubated in buffer without peptide (A570-670
) 0.976) and 0% as absorbance difference of cells with 20 µM A?42 and
no 2002-H20 (A570-670 ) 0.389). An asterisk (*) indicates statistical
significance as determined by the two-tailed Student’s t test (p < 0.05) and
error bars reflect standard error from the average of three measurements.
Figure 6. Viability of PC12 cells exposed to compound 2002-H20 at
varying concentrations. One-hundred percent is scaled as the measured
viability of cells not exposed to exogenous compound or peptide, but
incubated in buffer with 1% (v/v) DMSO (A570-670) 0.976). Average of
three measurements with standard error reported.
17020J. AM. CHEM. SOC. 9 VOL. 132, NO. 47, 2010
Chen et al.
compound, methylene blue, they proposed a causative link
between the promotion of fibril formation and reduced oligo-
merization.30The potential for the enhancement of fibril
formation as a novel therapeutic strategy was suggested by
Cheng et al., who found that accelerating fibril formation in
transgenic AD mice led to reduced oligomerization and im-
proved behavioral outcomes.29Our finding that a compound
isolated for its ability to bind A?42 can both increase fibril
formation and decrease A?42-induced toxicity supports the
potential efficacy of this strategy.
Compound 2002-H20 Might Have Been Missed by Other
High-Throughput Screens. The advantages of the SMM screen
are highlighted by the realization that compound 2002-H20
would not have been found by previously reported high-
throughput screens for inhibitors of A? aggregation.
We found that the most commonly used assay for A?
aggregationsThT fluorescenceswas ineffective in the presence
of 2002-H20 because the compound and ThT fluoresce at similar
wavelengths (data not shown). Indeed, recent studies suggest
that ThT assays are often prone to errors in the presence of
compounds that absorb or fluoresce in the same region of the
spectrum.63However, even if the fluorescence of 2002-H20 and
ThT did not overlap and the compound did not affect ThT
fluorescence, a ThT-based assay that screens for inhibition of
fibrillization would have missed 2002-H20, which actually
promotes fibril formation.
Most of the screens described in the literature aim to isolate
compounds that alter the aggregation of A?.31,32,64Screens that
isolate inhibitors of aggregation would miss compounds like
2002-H20, which favor fibrils. Conversely, screens for enhancers
of aggregation would miss compounds that stabilize monomeric
A?. In both cases, novel molecules that may ultimately provide
leads for Alzheimer’s therapeutics would have been missed by
screens biased to favor either inhibitors or enhancers of
aggregation. In contrast, the SMM screen described here makes
no assumptions about whether aggregation to a particular state
is advantageous or detrimental and isolates compounds based
solely on their ability to interact with A?.
Our primary aim in this study was to develop the SMM assay
as a screen for compounds that may ultimately lead to
therapeutics for Alzheimer’s disease, and as described above,
the assay effectively identified molecules that reduce the
cytotoxicity of A?42. Further examination of one of those
compounds revealed dose-dependent rescue of A?-challenged
PC12 cells, with a concomitant increase in fibril formation.
These findings highlight the benefits of a screen optimized to
reveal binding to A? without bias toward a specific type of
interaction, and further suggest the potential for the SMM
method as a tool for exploring the A? aggregation pathway.
For example, future examination of small molecules that bind
A? in the SMM assay, but fail to rescue cells from A?-induced
toxicity may reveal compounds that stabilize toxic aggregates.
With further development, such compounds may prove useful
as probes for the intermediates that cause Alzheimer’s disease.
Additional applications can be envisioned with the SMM assay
having potential as an efficient and versatile screen for isolating
compounds that interact with intermediates at various stages of
the A? aggregation pathway.
Materials and Methods
Materials. Fluorescently tagged amyloid-? peptide was pur-
chased from Anaspec (San Jose, CA), diluted to a stock concentra-
tion of 9.35 µM in 8 mM NaOH, and used without additional
purification. A?40 labeled at the N-terminus with HiLyte-Fluor 647
was reported by Anaspec to have a purity of greater than 90%,
and A?42 labeled at the N-terminus with HiLyte-Fluor 488 had a
reported purity of greater than 95%. Nonfluorescently labeled crude
amyloid-? peptides, synthesized via FMOC synthesis, were pur-
chased from the Keck Institute at Yale University (New Haven,
(63) Hudson, S. A.; Ecroyd, H.; Kee, T. W.; Carver, J. A. FEBS J. 2009,
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Figure 7. Compound 2002-H20 increases amyloid fibril formation of synthetic A?42. (a) Congo red spectral shift. (b) Transmission electron microscopy.
For both experiments, 20 µM of synthetic A?42 was incubated with the indicated concentration of compound 2002-H20. Incubations were at 37 °C with
gentle agitation for 24 h.
J. AM. CHEM. SOC. 9 VOL. 132, NO. 47, 2010
SMMs for the Discovery of Compounds That Bind AD A? Peptide
CT) and purified as described below. SMM slides were prepared Download full-text
Peptide Purification. Purification of crude peptides was ac-
complished via reverse phase-HPLC with a C4 column (Grace
Vydac 214TP152022; Deerfield, IL). A two-solvent system was
run at 60 °C. Solvent A was 95% ultrapure H2O, 5% acetonitrile,
and 0.1% trifluoroacetic acid (TFA); and solvent B was 50%
ultrapure H2O, 50% acetonitrile, and 0.1% TFA. Purified peptides
were disaggregated with TFA and 1,1,1,3,3,3-hexafluoro-2-isopro-
panol, which were applied successively and removed under a gentle
argon stream.66Disaggregated peptides were stored as a lyophilized
film at -20 °C.
SDS-PAGE Electrophoresis. The 9.35 µM stocks of fluores-
cently labeled peptides from Anaspec were diluted in 1× PBS to
the indicated concentrations, and the pH of all dilutions was checked
with pH paper and adjusted to 7-8 with 20% formic acid. The
peptides were incubated for 30 or 60 min with gentle orbital
shaking, combined with sample buffer, and loaded without boiling
onto 10-20% Tris-Tricine gels (precast Ready Gels, Biorad;
Hercules, CA). Electrophoresis was performed at 100 V and gels
were developed with silver staining.
Small Molecule Microarray Assay. SMM slides were incubated
with a slow circular orbit for 30 min at room temperature in 5 mL
of 185 nM HiLyte 647-labeled A?40 (diluted from the 9.35 µM
stock in 1× PBS-T, 0.1% Tween-20). Following incubation, slides
were rinsed successively in PBS-T, PBS, and DI H2O for 2 min
each, and then spun dry for 30 s with a slide spinner (Labnet
International; Woodbridge, NJ). A GenePix 4200A microarray
scanner (Molecular Devices; Sunnyvale, CA) was used to scan the
slides with an excitation wavelength of 532 nm (green emission
filter, 557-592 nm) and an excitation wavelength of 635 nm (red
emission filter, 650-690 nm). All SMM experiments were per-
formed in triplicate, and analyzed using a standard pipeline output
for high-throughput screens at the Broad Institute.44
Cell Viability. Rat pheochromocytoma (PC12) cells, purchased
from ATCC (Rockville, MD), were grown on collagen-coated Petri
dishes (Falcon) in complete media (82.5% F12K, 15% horse serum,
2.5% fetal bovine serum; ATCC) in a humidified incubator at 37 °C
and 5% CO2 (HERAcell, Thermo Scientific). Once they reached
confluence, cells were harvested by spraying through an 18.5 gauge
needle, resuspended in fresh complete media and plated onto tissue
24 h to allow cell attachment. One milligram of synthetic A?42,
purified as described above, was dissolved in 100 µL of cell culture
grade DMSO (ATCC), sonicated briefly to ensure complete solubili-
zation, and then diluted to 200 µM with 1.0 mL of sterile 1× PBS
(Invitrogen). Ten microliters of this A?42 stock solution was then
added to each 100 µL well to give a final peptide concentration of 20
µM. In assaying for their ability to reduce A?42-induced toxicity,
compounds solubilized in DMSO were added at 1% (v/v) to the wells
to reach the final concentrations indicated. One percent (v/v) DMSO
without compound was added to wells containing 20 µM A?42 for a
toxicity control and to wells containing only buffer without peptide
for a cell viability control. Plates were then incubated with A?42 and
compounds for an additional 24 h and cell viability was assessed with
the MTT Cell Profileration kit from Roche, as directed.67,68Following
overnight incubation, absorbance was measured at 570 and 670 nm
using a microplate reader (Thermo Varioskan), and A570 nm- A670 nm
was calculated to evaluate relative formazan dye formation, which is
directly correlated to cell viability. The absorbance difference without
A?42 or exogenous compound was scaled as 100% cell viability in
all experiments. In trials assessing the relative rescue ability of
compounds, the absorbance difference calculated with A?42 only and
no compound was scaled as 0% rescue ability. Where indicated,
the potential cytotoxicity of the compounds alone.
Congo Red Spectral Shift Assay. Samples (0.5 mg) of purified
A?42 were solubilized in 300 µL of DMSO with sonication. Five
(final concentration: 50 mM NaH2PO4/100 mM NaCl, pH 7.2-7.4)
bringing the final peptide concentration to 20 µM. To remove
contaminants and pre-existing aggregates, the samples were filtered
with a 0.22 µm low-protein binding syringe filter (Millex-GV;
CA) was solubilized in DMSO to 10 and 5 mM concentrations, and
added to samples to bring the final compound concentration to 100
and 50 µM. Samples were incubated in 15 mL horizontal polypropy-
lene tubes with shaking (∼200 rpm) on a Barnstead/Lab-line titer plate
shaker (Dubuque, IA). Samples containing only 2002-H20 without
peptide were prepared and incubated in the same fashion in order to
evaluate for any effect of the compound alone on the Congo red
spectral shift. After 24 h incubation, 400 µL aliquots were removed
and mixed with 400 µL of a 34 µM Congo red (CR) solution (0.01 M
PBS/10% EtOH, solution syringe filtered and CR concentration
measured as described by Klunk et al.69). Comparable samples with
0.01 M PBS/10% EtOH lacking Congo red were also prepared to
correct for light scattering due to A? and 2002-H20. After 30 min of
room temperature incubation, samples were mixed by pipetting and
absorbance was measured at 403 and 541 nm. The concentration of
CR bound to A? fibrils (in M) was calculated with background
subtraction for light scattering from the absorbance of samples without
Electron Microscopy. The same samples prepared for the Congo
red assay were also used for transmission electron microscopy
(TEM). Formvar carbon-coated Cu grids were floated on a drop of
each sample for 2 min, washed twice for 2 min with DI water, and
stained for 2 min with 1% uranyl acetate. Grids were imaged with
a Zeiss 912ab electron microscope (Thornwood, NY).
the cell viability assay and Margaret Bisher for assistance with electron
microscopy. This research was funded by Grant 5R21AG028462 from
the NIH, Award IIRG-08-89944 from the Alzheimer’s Association
and Contract N01-CO-12400 from the NCI Initiative for Chemical
Supporting Information Available: Complete refs 11 and 59;
table of all 79 SMM hit compounds with composite Z and
toxicity rescue scores; detailed results from study of structural
analogs of compound 2002-H20. This material is available free
of charge via the Internet at http://pubs.acs.org.
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