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peted after treatment with 200 nm AA-CW236. Finally, probe
20 also proved useful for measuring the activity of AA-
CW236 directly in living MCF7 cells (Figure S7). The gel-
based profile indicates that MGMT was completely inhibited
after treatment of cells with 100 nm of AA-CW236 for ten
hours.
MS-based profiling methods offer a clear advantage over
gel-based techniques, because a much higher number of
proteins can be detected and quantified in one single experi-
ment.[17] Therefore, we performed a competitive activity-
based protein profiling experiment in MCF7 proteomes in
combination with quantification by stable isotope labeling of
amino acids in culture (SILAC). We used the MGMT
inhibitor AA-CW236 at two different concentrations,
200 nm (Table S2) and 1 mm (Table S3), and the broad-profile
CMT probe 1 for subsequent proteomic enrichment. Intrigu-
ingly, among the combined 1039 quantified proteins and even
at 1 mm concentration, only MGMT was found to be greater
than 66% competed (SILAC ratio of 0.12 = 88% competi-
tion; Figure 3D). Moreover, we conducted an additional
competitive proteomics experiment based on the catch-and-
release strategy recently reported by us, using iodoacetamide
(IAA) alkyne as a general cysteine-reactive enrichment
probe,[18] but applying dimethyl labeling (DML) as an
alternative method for stable-isotope-based quantification.
This method allows selective enrichment and quantification
of cysteine-containing and IAA-modified peptides rather
than of whole proteins. Again, after treatment with 200 nm
AA-CW236, among all 1245 enriched and quantified pep-
tides, only one peptide, which contained the MGMT active-
site cysteine, was found to be greater than 66% competed
(Figure 3D, Table S4). This is remarkable considering that the
human proteome contains thousands of cysteines that are
capable of reacting with electrophilic probes.[18,19] In fact, even
highly optimized and clinically approved kinase inhibitors
bind to numerous off-target cysteines.[20] For comparison,
when lomeguatrib (200 nm) was used as a competitor, we
observed several other > 66% competed peptides originating
from proteins such as the arginine tRNA ligase RARS,
guanine nucleotide binding protein GNB2, and dynamin-2
(Figure S8, Table S5).
To understand the molecular basis for the observed
potency of AA-CW236 towards hMGMT, we performed
covalent docking using a high-resolution X-ray structure of
hMGMT (PDB: 1EH6) and the protein-ligand docking
program GOLD[21] (Figure 4A). The predicted optimal bind-
ing mode suggests a key interaction between the trifluor-
omethoxy group of AA-CW236 and Tyr114 as well as an
additional potential interaction between the triazole group
and Ser159. Whereas the predicted binding mode for AA-
CW236 yielded a GoldScore of 46.0, significantly lower values
(35–40) were calculated for the less active derivatives 8, 9, and
11, thus supporting the proposed model. Moreover, to further
investigate the role of the CF3 group in hMGMT binding, we
prepared two structurally close derivatives of AA-CW236
that lack this functionality. Subsequent gel-based IC50 meas-
urements confirmed that these compounds are indeed sig-
nificantly less active than AA-CW236 (Figure S9).
Figure 3. Evaluation of the proteome-wide selectivity of AA-CW236.
A) The clickable CMT probe AA-CW159A labels WT GFP-hMGMT, but
not the C145A mutant. B) Chemical structure of the clickable CMT
probe 20 (AA-CW538). C) Gel-based profiling of the MGMT activity
and AA-CW236 selectivity in proteomes of different human cancer cell
lines. Proteomes were treated with DMSO or 200 nm AA-CW236 for
1 h followed by 30 mm AA-CW538. D) Evaluation of the AA-CW236
selectivity by quantitative proteomics. Shown are scatter plots with
SILAC and DML ratios. Left: SILAC ratios from the competitive
experiment with 200 nm (n=3) or 1 mm (n=4) AA-CW236 treatment
followed by 10 mm AA-CW159A. Right: DML ratios from the compet-
itive experiment with 200 nm AA-CW236 (n=6) followed by 10 mm IAA
alkyne. RatiosÆSEM for MGMT are shown.
lysates with overexpressed hMGMT and the CMT probe
1 (Figure S4). We observed complete competition of MGMT
after treatment with 300 nm AA-CW236, whereas no other
targets of probe 1 were visibly affected. Whereas the broad-
profile probe 1 proved useful for experiments with overex-
pressed MGMT, it did not allow gel-based detection of native
MGMTactivity owing to comparably low expression levels of
this protein. Therefore, we prepared the expectedly more
MGMT-directed probe 20 (AA-CW538), a clickable deriva-
tive of the inhibitor AA-CW236 (Scheme S1).
With the new probe in hand, we were finally able to detect
the native MGMT activity in various cancer cell lines
(Figures 3C, S6). Consistent with the literature,[15] high
MGMTactivity levels were observed in breast-cancer-derived
MCF7 cells. Furthermore, we found very high activity in colon
cancer Caco-2 cells and acute lymphoblastic leukemia
RPMI 8402 cells. The gel-based assay for profiling the
MGMT activity with probe AA-CW538 should also be
applicable to clinical samples and represent a significant
improvement in terms of convenience and throughput over
currently existing radioactive and northern blot based
MGMT activity assays.[16] Remarkably, although many other
proteins were also labeled by the probe AA-CW538 at 30 mm
concentration, only the MGMT band was selectively com-
Angew. Chem. Int. Ed. 2016, 55, 2911 –2915
ꢀ 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
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