Redox-based probes for protein tyrosine phosphatases

Article abstract of DOI:10.1002/anie.201007871

Three in one: The design strategy for redox-based probes (RBPs) that detect the reversible oxidation of protein tyrosine phosphatases (PTPs) includes a "warhead" that forms a covalent adduct with the oxidized active site cysteine of PTPs, a synthetic module that directs binding to the PTP active site, and a chemical reporter tag used for the identification, purification, or direct visualization of the probe-labeled proteins (see picture). Copyright

Full text of DOI:10.1002/anie.201007871

DOI: 10.1002/anie.201007871
Chemoselective Redox Probes
Redox-Based Probes for Protein Tyrosine Phosphatases**
Stephen E. Leonard, Francisco J. Garcia, David S. Goodsell, and Kate S. Carroll*
Over the past two decades, it has been established that growth
factors, cytokines, and a host of other ligands trigger the
production of hydrogen peroxide (H2O2) in nonphagocytic
cells through their corresponding membrane receptors.[1]
Such H2O2 generation has been demonstrated to regulate
many basic cellular processes including growth, differentia-
tion, adhesion, migration, senescence, and autophagy.[2] Once
formed, H2O2 promotes autophosphorylation of the mem-
brane receptor and induction of the signaling cascade.
Landmark publications from the Finkel and Rhee labo-
ratories were the first to demonstrate an essential role for
reactive oxygen species (ROS) growth factor receptor-medi-
ated signal transduction.[3] As illustrated in Figure 1, ligand
stimulation leads to a transient burst of H2O2 and a net
increase in tyrosine phosphorylation of numerous proteins,
including the growth factor receptor itself.[4] Likewise,
application of peroxide scavengers such as N-acetyl cysteine
Figure 1. Proposed model for redox-dependent signal transduction.
After ligand stimulation the H2O2 level increases through cytosolic
proteins and subsequent activation of membrane-bound NADPH
oxidase (Nox). Increased H2O2 production can lead to oxidation of
specific reactive Cys residues within proteins, with concomitant
modulation of the protein function. In PTPs, oxidation results in
inactivation (and unopposed kinase action) until the H2O2 level
declines and phosphatase activity is restored by reduction of the Cys
residue. Trx=thioredoxin, TR=thioredoxin reductase, Grx=glutare-
doxin, GR=glutaredoxin reductase.
or catalase inhibits ligand-induced tyrosine phosphorylation.
In large part, these effects are believed to arise from oxidative
inhibition of protein tyrosine phosphatases (PTPs), which
function as antagonists of protein tyrosine kinases and return
membrane receptors to their resting state.[5]
There are about 80 members of the PTP superfamily,
including the tyrosine (Tyr)-specific enzymes and dual-
specificity phosphatases (DSPs), which also recognize serine
(Ser) and threonine (Thr).[6] The catalytic activity of PTPs
depends upon an invariant active site cysteine (Cys) within
the conserved signature motif [His-Cys-(X)5-Arg-(Ser/Thr)]
(His = histidine, Arg = arginine; X = any residue) located at
the bottom of the active site pocket.[7] Owing to the environ-
ment of the active site, the catalytic Cys residue exhibits a
remarkably low pKa (4.5 to 5.5) and is present as the thiolate
anion at physiological pH. The low pKa serves to enhance the
nucleophilicity of this residue, but also renders it susceptible
to oxidation and enzymatic inactivation.[8] Consequently,
oxidative inhibition of PTPs promotes phosphorylation-
dependent signaling cascades.
[*] F. J. Garcia, Dr. K. S. Carroll
Biochemical evidence indicates that upon exposure to
H2O2, the catalytic Cys residue is converted into the sulfenic
acid form and results in PTP inactivation (Figure 1).[9] This
oxo form can react with a backbone amide to form a cyclic
sulfenyl amide for classical PTPs or an adjacent thiol in DSPs
to form an intramolecular disulfide.[10] The activity of PTPs
can be restored through the action of cellular antioxidants,
such as the thioredoxin and glutaredoxin reducing sys-
tems.[5,11] Thus, oxidation of the catalytic Cys is reversible
and represents a dynamic mechanism of PTP regulation.
Although the model presented in Figure 1 is supported by
a number of elegant studies, it is also well-known that the rate
of reaction of a PTP with H2O2 is about 105 times slower than
the equivalent reaction with peroxiredoxin, an antioxidant
enzyme.[9,10] This raises the question of whether a nonenzy-
matic reaction can account for the formation of the sulfenic
acid in PTPs.[12] This apparent discrepancy may reflect the
possibility that enzymatic H2O2 generation needs to occur in
close proximity to PTPs so that the concentration of the
Department of Chemistry, The Scripps Research Institute
130 Scripps Way, Jupiter, FL 33458 (USA)
Fax: (+1)561-228-2919
E-mail: kcarroll@scripps.edu
Dr. D. S. Goodsell
Department of Molecular Biology
The Scripps Research Institute, La Jolla, CA 92037 (USA)
S. E. Leonard
Chemical Biology Graduate Program, University of Michigan
Ann Arbor, MI 49109 (USA)
[**] We acknowledge funding from the Camille and Henry Dreyfus
Teacher–Scholar Awards Program (to K.S.C.) and the American
Heart Association Scientist Development Award (award number
0835419N to K.S.C.). We thank Prof. M. Saper for providing the
YopH expression plasmid and for helpful discussion, Jesse Song for
providing technical assistance, and Prof. A. Barrios for helpful
discussion.
Supporting information for this article (including all experimental
procedures) is available on the WWW under http://dx.doi.org/10.
1002/anie.201007871.
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Communications
oxidant is high enough to make the rate of the uncatalyzed
reaction physiologically relevant, or oxidation of the Cys
residue may be catalyzed by another enzyme. Evidence to
support or revise these proposals will require a better
understanding of the mechanisms that underlie cellular
compartmentalization, information about the extent of
in situ oxidation of PTPs, and/or the discovery of a specific
Cys oxidase.
These outstanding questions, coupled with the physiolog-
ical importance of PTPs, and their therapeutic relevance to
diseases such as cancer and diabetes have motivated the
development of methods for monitoring reversible PTP
oxidation.[13] The majority of these approaches rely on the
loss of reactivity with thiol-modifying reagents or the
restoration of labeling by reducing agents. These techniques
require that free thiols are completely blocked by alkylating
agents prior to the reduction step and are thus limited to
enrichment from protein extracts. Methods to decrease
oxidation artifacts after cell lysis have been reported;[13b]
however, they require specialized reagents or equipment,
and other issues such as loss of labile modifications and
temporal resolution are not addressed.
Figure 2. Redox-based probes (RBPs) for detecting reversible PTP
oxidation. a) The design strategy for RBP includes the cyclic 1,3-
diketone warhead, a synthetic module that directs binding to the PTP
active site, and an azide reporter tag for downstream analysis.
b) Structures of the parent compound DAz-1 2 and the focused RBP
library (3–8) synthesized and evaluated in this study.
Direct labeling methods that exploit the selective reaction
of sulfenic acid and 5,5-dimethyl-1,3-cyclohexanedione
(dimedone, 1) and related analogues have also been used to
monitor PTP oxidation (Scheme 1).[14] Recently, we have
reported the development of azide- and alkyne-based ana-
approach to detect PTP oxidation is inspired by the extensive
use of activity-based probes to monitor phosphatase and
protease activity.[18] We anticipated that integrating a binding
module into the dimedone scaffold would provide a redox-
based probe, termed RBP, designed to react only with the
oxidized form of PTPs. Modification of PTP targets by such
probes would provide a direct measure of oxidation and
enable their purification and identification, thereby aiding in
the elucidation of the biological roles of PTP oxidation in
physiological and pathophysiological redox-mediated signal
transduction pathways. Along these lines, we selected a series
of synthetic binding modules known to target the active site of
a broad range of enzymes from the PTP superfamily (Fig-
ure 2b). The phenyl 3 and benzyl 4 derivatives are modeled
after the phosphotyrosine ring present in the native substrate.
Additional scaffolds that are common to many known PTP
inhibitors include naphthalene (in 5), biphenyl (in 6),
diphenyl ether (in 7), and benzy phenyl ether (in 8).[19]
Accordingly, we prepared compounds 3–8 (see the Support-
ing Information) and evaluated their target-binding affinity
and ability to monitor PTP oxidation.
To test our compounds of interest, we used recombinant
Yersinia phosphatase (YopH). The enzyme is a representative
member of the classical PTP superfamily and has been
extensively characterized in vitro.[20] Like other PTPs, YopH
harbors a catalytic Cys residue in its active site, Cys403 that is
characterized by a low pKa (ca. 5). Since sulfenic acid
modification of YopH had not been previously documented,
initial experiments were directed toward determining
whether Cys403 was susceptible to oxidation by H2O2.
Analogous to other redox-sensitive PTPs, we expected that
Scheme 1. Selective reaction between a protein sulfenic acid and
dimedone (1).
logues of dimedone, such as DAz-1 (2, Scheme 1) that enable
trapping and tagging of sulfenic acid modified proteins
directly in cells.[14b,15] The azide or alkyne chemical reporter
group can be used for bioorthogonal Staudinger and Huisgen
[3+2] cycloaddition coupling reactions for downstream anal-
ysis of labeled proteins. These reagents have been successfully
deployed for global profiling of protein sulfenic acid modi-
fications.[15,16] Although dimedone-based probes have shown
wide utility for investigating Cys oxidation, the modest
reaction rate and the low cellular abundance of signaling
proteins have hampered the detection of oxidized PTPs.[16,17]
Herein, we present a solution to this issue and report on the
design of new redox-based probes (RBPs) for direct detection
of PTP oxidation with significantly increased sensitivity and
selectivity.
Our overall strategy for targeting reversible PTP oxida-
tion is to create a trifunctional probe that consists of: 1) a
“warhead” bearing a cyclic 1,3-diketone group that forms a
covalent adduct with the active-site cysteine of PTPs, 2) a
module that directs binding to the PTP target, and 3) a
reporter tag used for the identification, purification, or direct
visualization of the probe-labeled proteins (Figure 2a). This
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Table 1: Inhibition constants for DAz-1 2 and compounds 3–8 with
oxidation of Cys403 would manifest itself as a loss of catalytic
activity. We evaluated this proposal in steady-state assays
using the fluorogenic substrate, 4-methylumbelliferyl phos-
phate (4-MUP). As shown in Figure 3a, the YopH activity
was detected as fluorescence signal owing to dephosphoryla-
YopH.[a]
Entry
Ki [mm]
DAz-1 2
>12000
162.1
2710
3
4
5
6
7
8
47.1
2.9
21.4[b]
113.3[b]
[a] Ki values represent the average of at least three independent
experiments and the standard deviation was ꢀ25%. [b] Compounds
exhibited aggregation-based inhibition.
biphenyl derivative 6 conferred a 4135-fold increase in the
binding affinity and was the most potent inhibitor of the series
(Ki = 2.9 mm). Finally, the diphenyl ether in 7 and the benzyl
phenyl ether in 8 showed Ki values in the mid-micromolar
range.
In many cases, protein aggregation is a common mecha-
nism of promiscuous chemical inhibitors.[23] The kinetic assays
were therefore repeated with 0.02% Triton-X 100 detergent.
Inhibition by 2–6 was found to be independent of the enzyme
and detergent concentration. By contrast, compounds 7 and 8
both demonstrated a > 15-fold decrease in potency when
detergent was present in the assay buffer. These data are
consistent with aggregation-based inhibition of YopH by 7
and 8. Promiscuous inhibition has been observed previously
in scaffolds that contain the diphenyl ether or benzyl phenyl
ether functional groups.[23,24]
Compounds 3–8 were then tested for detecting sulfenic
acid modification of YopH, and compared against DAz-1. For
these experiments, the PTP was oxidized and then incubated
for 15 min with each probe. The bioorthogonally labeled
protein was detected through reaction of the azido group with
phosphine-biotin (p-biotin) through the Staudinger liga-
tion.[25] The products of these reactions were resolved by
SDS-PAGE and analyzed by streptavidin-HRP western blot.
Figure 4a shows that the majority of compounds exhibited an
increase in labeling relative to DAz-1.[26] The most significant
increase in YopH sulfenic acid detection was observed for 3,
5, and 6. Notably, probe 6 exhibited the most potent Ki value
and also showed the most robust detection of oxidized YopH.
Naphthalene derivative 5, which displayed the second highest
binding activity, also demonstrated enhanced sulfenic acid
detection. By contrast, compounds 4, 7, and 8 showed
moderate to no reaction with the oxidized protein. The
apparent lack of reactivity for compounds 7 and 8 is most
likely due to the formation of promiscuous aggregates.
Additional control experiments also verified that chemical
reduction of YopH or pretreatment of the oxidized protein
with dimedone inhibited incorporation of the azido probe, as
expected (see Figure S4 in the Supporting Information).
Our next goal was to assess the selectivity of probes 5 and
6, relative to DAz-1, for detecting sulfenic acid modifications
in non-PTP proteins. For this purpose, we used the metabolic
Figure 3. Analysis of YopH PTP oxidation by H2O2. a) YopH was
inactivated by the addition of H2O2 in the absence of a reducing agent.
H2O2-inactivated YopH could be reactivated through DTT treatment.
Dimedone (1) forms a covalent adduct with the sulfenic acid form of
YopH, which prevents reactivation of YopH by DTT. b) The observed
rate of YopH inactivation plotted as a function of the H2O2 concen-
tration. The second-order rate constant for oxidation of Cys403 by
H2O2 was about 10mÀ1 sÀ1
.
tion of 4-MUP. Exposure to 100 equivalents of H2O2 for 1 h
abolished the phosphatase activity and subsequent addition of
dithiothreitol (DTT) resulted in substantial restoration of the
PTP function. These results are indicative of reversible
modification of Cys403 with sulfenic acid. To verify the
identity of the modification at the active-site Cys, oxidized
YopH was incubated with dimedone, which reacts with
sulfenic acids to form a covalent adduct that is nonreducible
by thiols. As expected, dimedone treatment inhibited the PTP
activity, which could not be restored by incubation with DTT.
Mass spectrometry analysis also confirmed formation of the
adduct in a stoichiometry of 1:1 (see Figure S1 in the
Supporting Information). Having established that YopH is
susceptible to oxidation, we determined the second-order rate
constant for the reaction of Cys403 with H2O2 to be about
10mÀ1 sÀ1, consistent with values obtained for other PTPs
(Figure 3b).[9]
Next, we examined the ability of compounds 3–8, and the
parent compound DAz-1, to reversibly inhibit activity of
YopH. To this end, the dissociation constants (Ki) for
inhibition were determined by conducting the assays under
reducing conditions, in the absence of H2O2. The resulting
data fit well to a simple model of competitive inhibition[21] and
the Ki values are summarized in Table 1. No significant
inhibition by DAz-1 was observed at concentrations up to
12 mm,[22] consistent with the absence of an active-site-
targeted binding module. The phenyl compound 3 was
moderately active, with a 130-fold increase in the binding
affinity relative to DAz-1. By contrast, the benzyl analogue 4
exhibited weak binding. The naphthalene analogue 5 showed
a 255-fold increase in the affinity relative to DAz-1. The
enzyme
glyceraldehyde
3-phosphate
dehydrogenase
(GAPDH). This protein forms a sulfenic acid modification
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Communications
Figure 5. The binding conformation of RBP 6 with YopH predicted by
AutoDock. a) Molecular surface representation of YopH (PDB code:
3BLT) colored by the polarity of the atoms. RBP 6 is given in a ball-
and-stick representation. b) Detailed view of hypothetical interactions
between YopH and RBP 6. The cyclic diketone is shown with carbon in
yellow and oxygen in green. Hydrogen bonds are shown as thin blue
lines. Images were created with the Python Molecular Viewer.[30]
Figure 4. Analysis of RBP selectivity for oxidized YopH. a) RBPs detect
sulfenic acid in oxidized YopH with increased sensitivity over the
parent compound DAz-1 2. YopH was oxidized with H2O2 and
incubated with compounds 2–8 or DMSO alone (–). Top: Following p-
biotin conjugation, reactions were analyzed by streptavidin-HRP west-
ern blot. Bottom: Equal loading was verified by Ponceau S staining.
b) RBPs do not increase the general sulfenic acid reactivity. Top:
GAPDH was incubated with 2, 5, 6, or DMSO alone (–) followed by
conjugation to p-biotin and analyzed by streptavidin-HRP western blot.
Bottom: Equal loading was verified by reprobing the blot with an
antibody against GAPDH. The bar graphs summarize the relative
signal intensities from replicate experiments quantified by densitome-
try, normalized to 6, and analyzed by Student’s t-test. Error bars
represent standard errors of the mean: ***) indicates that P<0.001
and *) indicates that P<0.05 when compared against detection with
the parent compound, DAz-1 2.
group present in RBP 6 has been identified as a core structure
in many bioactive compounds and is considered a privileged
scaffold.[29] Along these lines, an opportunity for future design
will be to evaluate the potency of substituted biphenyls and
create molecules that interact more closely with the PTP
surface.
In summary, we have developed a suite of redox-based
probes that target the active site of YopH and PTP1B, which
are both members of the classical PTP superfamily. Although
indirect and direct methods to detect protein sulfenic acids
have previously been reported,[15,27a,31] our study provides the
first example of a cyclic 1,3-diketone, dimedone-like warhead
to develop probes with enhanced targeting specificity. In
terms of reversible inhibition, the potency of RBPs 5 and 6 are
comparable or exceed that of other known YopH and PTP1B
inhibitors.[19] Future studies will focus on the application of
RBPs to investigate PTP regulation and redox signaling in
living systems. Finally, we note that the strategy employed to
identify RBPs in this study may also represent an attractive
starting point into the inhibitor- or tool-development cycle for
other classes of proteins with redox-sensitive Cys residues.
at Cys149, which has been detected in previous studies by
dimedone and related azido analogues.[16,27] Oxidized
GAPDH was incubated with DAz-1, 5, or 6 followed by p-
biotin conjugation and western blot analysis. Figure 4b shows
that sulfenic acid modification of GAPDH is detected with
equal efficiency by the azido probe. Similar results were
obtained with the thiol peroxidase, Gpx3 (data not shown).
Finally, we examined the ability of compounds 5 and 6 to
inhibit and detect reversible oxidation of PTP1B, another
redox-sensitive tyrosine phosphatase.[8] Compounds 5 and 6
inhibited PTP1B with Ki values of (0.67 Æ 0.19) mm and
(61.5 Æ 7.0) mm, respectively. By contrast, PTP1B activity
was not affected by DAz-1. Importantly, 5 and 6 showed
enhanced detection of oxidized PTP1B, relative to DAz-1 (see
Figure S5 in the Supporting Information). Taken together,
these data establish that 5 and 6 are RBPs against YopH and
PTP1B, thereby validating our general approach.
To gain molecular insight into interactions between YopH
and RBP 6, we performed docking simulations using Auto-
Dock.[28] As shown in Figure 5, the two oxygen atoms of the
cyclic diketone are predicted to form hydrogen bonds with
several active-site residues. In addition, the docking analysis
suggests that aromatic stacking interactions can occur
between the phenyl rings of RBP 6 and the side chain of
Phe229. The remaining portion of the compound (i.e., the
chemical reporter group) appears largely exposed to the
solvent. Future structural studies of YopH in complex with
RBP 6 should provide further insights into interactions that
can facilitate active-site targeting. Interestingly, the biphenyl
Received: December 14, 2010
Published online: April 18, 2011
Keywords: chemoselectivity · cysteine oxidation ·
.
protein modifications · redox chemistry · tyrosine phosphatase
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