Angewandte
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Interestingly, background labeling in HeLa cells was more
most of these proteins were not identified by gel-based off-
evenly distributed with 46, 78, and 85 hits for AA-1, BP-1, and
DA-1, highlighting the importance of cell-line-specific off-
target analysis (Figure S2). A list of all identified proteins is
provided in the Supporting Information.
target profiling,[7] and furthermore, hits of gel studies are
underrepresented here, confirming the relevance of the
proteomic preparation technique for the results of AfBPP
studies.
Considering the increasing application of DA photo-
probes in chemical biology, we synthesized three additional
minimal probes for in-depth analysis (Figure 1A and
Scheme S3). Here, the DA moiety was embedded in different
aliphatic or aromatic scaffolds with the aim of dissecting off-
target binding and connecting protein hits to structural motifs.
All four DAs (DA-1–DA-4), including a close mimic of
a previously reported control compound,[4b] were applied in
gel-based cellular protein profiling. All probes labeled intra-
cellular targets, suggesting sufficient cell permeability (Fig-
ure S3).
Subsequent gel-free, quantitative proteomics studies
revealed a significant influence of the scaffold on protein
binding (Figure S4). Probe DA-2, which contains an aryl
piperazine, exhibited the highest labeling in A549 cells
followed by the aromatic probe DA-1 (Figure 2A). In HeLa
cells, DA-1 and aliphatic DA-4 contributed to the majority of
hits (Figure 2B). Interestingly, DA-3, with an amide bond and
a short aliphatic chain, was most selective in both cell lines,
suggesting that affinity probe design could benefit from such
short alkyl linkers.
To gather comprehensive information on the most prom-
inent DA-specific background targets, we overlaid the
volcano plots for all probes in A549 and HeLa cells. DA-
specific protein targets should thus be extensively enriched
whereas scaffold-specific hits relocate around zero (Fig-
ure 2C; for a detailed explanation, see the Supporting
Information). This mathematical operation revealed a set of
eight and seven significant proteins for A549 and HeLa cells,
respectively, after Benjamini–Hochberg correction (Fig-
ure 2D,E). Satisfyingly, 291 out of 1655 protein groups in
the A549 proteome were annotated as membrane-bound.
Identified hits that are predominantly localized in the
lysosome and mitochondrion can be grouped into three
superfamilies: 1) channels or channel-associated proteins
(e.g., VDAC1 and VDAC2), 2) catabolic enzymes (e.g.,
CTSD), and 3) small-molecule binders (e.g., ALDH1B1).
For example, VDAC1 and VDAC2 are highly abundant
channels with permeability for small molecules. Similarly,
ECH1 and ALDH1B1 are catabolic enzymes known to bind
small molecules. A summary of all non-specific photoprobe
targets is provided in Figure 2F and Table S1. To account for
label-free MS quantification, a rising proteomic technique
independent of SILAC, we applied all DA probes together in
the labeling of intact A549 cells to obtain a comparable
photome list (Figure S5 and Supporting Information). Again,
a good distribution of cytosolic and membrane proteins was
obtained while re-extraction of the insoluble fraction did not
significantly enhance the overall coverage of membrane-
bound proteins (Figure S6).
With a comprehensive photome background list in hand,
we next analyzed the irradiation and concentration depend-
ence of DA photocrosslinking reactions. For this study, we
used the kinase inhibitor SP600125 equipped with a minimal
DA linker, similar as previously reported (Scheme S4).[4b]
Interestingly, while short irradiation times of 5 min and high
probe concentrations of 3 mm enhanced photome labeling,
longer irradiation times (20–30 min) as well as lower concen-
trations (125 nm) minimized background enrichment in this
setting (Figures S7 and S8). Although JNK, a known target of
SP600125, was not among the hits, concentration-dependent
competition with the unmodified drug revealed several
carboxylases that also exhibit ATP binding sites as putative
targets (Figure S9).
For an initial evaluation of the photome list, we re-
analyzed previous results obtained from A549 profiling with
a falcarinol diazirine probe.[8a] A comparison of the proteins
identified with the probe and those found in the photome
classified four out of seven falcarinol hits, including HMOX2
and CTSD, as photome targets (Figure S10). Importantly,
ALDH2, a biochemically confirmed target of falcarinol, stood
out from the photome proteins, which confirms the general
utility of this approach for unbiased target identification.
Finally, we sought to illustrate the applicability of the
photome inventory list in a target identification study with
isoquinoline sulfonamide H8 (Figure 3A), a widely applied
inhibitor of the cAMP-dependent protein kinase (PKA).[12]
H8 and its structurally related analogue H89 are gold
standards in PKA research,[12b] and AfBPP with this molecule
should reveal PKA as a validated positive control.
Based on the lessons learned from the photocrosslinker
comparisons described above, we equipped H8 with a short
aliphatic diazirine alkyne linker (Figure 3B), found to exhibit
minimal background labeling, at the terminal amine. Crys-
tallography data of PKA in complex with H-inhibitors further
indicate that chain extension at this position is tolerated.[13]
However, H8p might alternatively directly bind to the cAMP-
binding pocket of the regulatory subunit. The synthesis of this
probe was conducted through the coupling of the alkyl
diazirine carboxylic acid L4 (for the structure, see Scheme S1)
and N-(2-aminoethyl)isoquinoline-5-sulfonamide (2), which
was prepared according to published procedures,[14] in the
final step (Figure 3B).
A549 SILAC cells were treated with H8p and DMSO
according to established procedures. Proteomics workflow
and analysis revealed the enrichment of 30 proteins matching
our cut-off criteria (Figure 3C). These hits were classified into
three categories according to their enrichment in the photome
overlay (Figure 2D): 1) low confidence (five hits depicted in
red: log2(enrichment) in the photome > 1 and p < 0.05),
2) medium confidence (six hits depicted in orange: 0 <
log2(enrichment) ꢀ 1 and p < 0.05), 3) high confidence (19
remaining hits depicted in gray, which are not significantly
enriched in the photome). Interestingly, medium-and high-
Interestingly, reported abundances (Table S1) revealed
that proteins solely identified in one cell line, such as ECE1 in
HeLa cells, are less expressed in the other cell line, likely
explaining their cell-line-specific DA labeling. Importantly,
Angew. Chem. Int. Ed. 2016, 55, 1 – 7
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