Detection of kinase activity using versatile fluorescence quencher probes

Article abstract of DOI:10.1002/anie.201000879

(Figure Presented) Turn off the light! A kinase assay system employs fluorescent peptides and a phosphate-selective fluorescence quencher probe, and can be placed on a microfluidic chip (see picture). The system can be used for real-time kinase monitoring, kinase inhibitor screening, and cancer diagnosis based on abnormal kinase activity observed in patients' samples.

Full text of DOI:10.1002/anie.201000879

Angewandte
Chemie
DOI: 10.1002/anie.201000879
Kinase Assay
Detection of Kinase Activity Using Versatile Fluorescence Quencher
Probes**
Hyun-Woo Rhee, Seung Hwan Lee, Ik-Soo Shin, So Jung Choi, Hun Hee Park, Kyungja Han,
Tai Hyun Park,* and Jong-In Hong*
Protein phosphorylation is the most universal form of
posttranslational modification of cell-signal transduction in
living organisms. The human kinome[1a] comprises 518 protein
kinases that control protein phosphorylation; irregular con-
trol of protein phosphorylation is a major cause of diseases
such as cancer.[1b] Therefore, accurate probing of the kinase
activity of a target protein is crucial for cancer diagnosis and
high-throughput screening of anticancer drugs.[2,3]
For the high-throughput analysis of kinase activity, several
research groups have developed various types of protein or
peptide chips using radioactive labeling[2a] with [33Pg]-adeno-
sine 5’-triphosphate (ATP) or using antibody hybridization.[2b]
However, a crucial problem involved in the use of these on-
chip detection methods[2] is that some kinases show decreased
activities on the surfaces of chips because of reduced enzyme
accessibility to the substrate.[2d]
In recent years, several pharmaceutical and biotechnology
companies have developed homogeneous kinase assay sys-
tems based on fluorescence polarization (FP) for developing
anticancer drugs.[3] These platforms (kinase assay systems)
utilize peptide substrates with an N-terminal fluorophore and
phospho-specific antibodies[3b] or phosphopeptide (or phos-
phoprotein)-binding nanoparticles (IMAP).[3c] However, FP-
based detection has been reported to be very sensitive to
fluorescence interference, and it is liable to produce false
positives when used to screen a large number of com-
pounds.[3d] Furthermore, there are no reports on the real-time
monitoring of kinase activity in cell lysates through FP-based
kinase detection; this is because many cellular components
can bind to the fluorescent peptides and produce false
positives for FP.
Recently, peptide- or protein-linked synthetic fluorescent
probes that are sensitive to certain protein kinases have been
reported by the research groups of Lawrence, Imperiali,
Sames, and Hamachi.[4–7] Ting, Tsien, and co-workers used
fluorescent proteins to develop an in vivo probe system to
detect kinase.[8] These synthetic probes enabled real-time
fluorescence monitoring of the specific activity of kinases in
cellular lysates, and exhibited immense potential for use in the
development of kinase activity inhibitors for certain kinases.
However, it is still difficult to predict and determine the
optimal sites for attaching fluorophores near the phosphory-
lated sites on the substrate peptides or proteins; the attach-
ment of these fluorophores is necessary to induce significant
changes in the fluorescence signal after phosphorylation of
the substrate peptides or proteins by a specific kinase.
Therefore, a general strategy for developing a synthetic
fluorescent kinase probe is desired.
We designed chemosensors Dab-DPA and PTZ-DPA
(Scheme 1) to develop a simple but powerful kinase assay tool
based on fluorescence intensity changes (ON/OFF). Using
these chemosensors, we show for the first time the diagnosis
of chronic myelogenous leukemia (CML) through real-time
fluorescence monitoring of Abelson (Abl) tyrosine kinase
activity and the development of a fluorescence-based homo-
geneous kinase assay system on a microfluidic chip.
As shown in Scheme 1, Dab-DPA consists of a bis(Zn2+-
dipicolylamine) complex and a dabcyl (Dab) fluorescence
quencher, and PTZ-DPA consists of the dipicolylamine
complex and a phenothiazine (PTZ) fluorescence quencher.
Dab and PTZ quench fluorescence by Fꢀrster resonance
energy transfer (FRET)[9] and photoinduced electron transfer
(PET),[10,11g] respectively. The bis(Zn2+-dipicolylamine) com-
plex is a well-known synthetic receptor that strongly and
selectively binds to phosphate in aqueous solution.[11] Dab-
DPA and PTZ-DPA are synthesized in a few steps (see the
Supporting Information).
PTZ is a good fluorescence quencher but there are very
few reports on its use as such, except for the isoalloxazine ring
of flavins.[10,11g] To prove that PTZ can be used as a general
fluorescence quencher for other fluorophores, such as car-
boxyfluorescein (FAM) or tetramethyrhodamine (TMR), we
performed electrochemical analyses of PTZ, FAM, and TMR.
Figure 1a shows the cyclic voltammograms of 1 mm PTZ,
TMR, and FAM; the Pt-disk working electrode is immersed
in acetonitrile with 0.1m tetrabutylammonium hexafluoro-
phosphate (TBAPF6) as supporting electrolyte. The observed
waves are assigned to the oxidation of PTZ and the
fluorophores (TMR and FAM). PTZ undergoes nearly
Nernstian oxidation at E1/2,ox = 0.63 V with a peak separation
[*] Dr. H.-W. Rhee, S. H. Lee, Dr. I.-S. Shin, S. J. Choi, Prof. Dr. T. H. Park,
Prof. Dr. J.-I. Hong
Department of Chemistry
School of Chemical & Biological Engineering
Seoul National University, Seoul 151-747 (Korea)
Fax: (+82)2-889-1568
E-mail: thpark@snu.ac.kr
jihong@snu.ac.kr
Dr. H. H. Park, Prof. Dr. K. Han
Department of Clinical Pathology
Catholic University Medical College, Seoul (Korea)
[**] This study was supported by a National Research Foundation (NRF)
grant funded by the MEST (Grant Nos. 2009-0080734, 2009-
0081997, 2010-0000825, WCU project R32-2009-000-10213-0).
H.-W.R. is the recipient of POSCO T.J. Park postdoctoral fellowship.
Gleevec was provided by Novartis.
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.201000879.
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Figure 1. a) Cyclic voltammograms of 1) PTZ, 2) TMR, and 3) FAM, all
1 mm in acetonitrile (supporting electrolyte: 0.1m TBAPF6), at a scan
rate of 200 mVsÀ1. b) Energy diagram of the quencher (PTZ) and
fluorophores (TMR and FAM). The HOMO value corresponds to the
oxidation potential. The LUMO values that correspond to the reduc-
tion potentials were estimated from the calculated emission energies
of fluorophores (Es =1239.81/lmax eV). c) UV/Vis absorption spectra of
Dab-DPA (10 mm), Dab (10 mm), PTZ (10 mm), and PTZ-DPA (10 mm)
in acetonitrile. Inset: PTZ-DPA (100 mm, left) and Dab-DPA (100 mm,
right) in buffer solution. SCE=saturated calomel electrode.
efficient only at very short distances.[12] Furthermore, in the
visible-light range, PTZ has a negligible molar extinction
coefficient (e = 5740 cmÀ1mÀ1, lmax = 316 nm), whereas Dab
Scheme 1. Top: Chemical structures of Dab-DPA and PTZ-DPA.
Bottom: Detection of protein kinase activity based on fluorescence
intensity (ON/OFF) using PTZ-DPA. Dab=dabcyl, DPA=bis(Zn2+
dipicolylamine) complex, PTZ=phenothiazine.
-
has a high molar extinction coefficient (e = 44000 cmÀ1mÀ1
,
lmax = 436 nm); because of this high coefficient, inner filter
effects[9a,b] become significant at high concentrations. In our
experiment, Dab-DPA shows a far-red-shifted absorption
of 71 mV. The peak current ratio is approximately unity
(ipc/ipa=0.97) at a scan rate of 200 mVsÀ1; this suggests that the
oxidation results in a stable radical cation. However, the
cyclic voltammograms recorded during the oxidation of TMR
show successive irreversible oxidation waves in the range of
0.87–1.96 V under the same conditions as for the oxidation of
PTZ. Therefore, the half-wave potential of the first oxidation
wave was estimated to be 0.93 V by means of differential
pulse voltammetry. FAM undergoes reversible oxidation at
band (e = 80600 cmÀ1mÀ1
, lmax = 512 nm), but PTZ-DPA
shows almost no absorption in the visible range. Therefore,
PTZ is expected to be a more suitable fluorescence quencher
for a selective quenching system.
We performed fluorescence titration experiments on Dab-
DPA and PTZ-DPA by using ten fluorescent peptides
(Table 1). FAM-abl showed nonspecific fluorescence quench-
ing with both Dab-DPA and PTZ-DPA because the anionic
fluorescein could bind to the bis(Zn2+-dipicolylamine) com-
plex in Dab-DPA and PTZ-DPA, regardless of the peptide
phosphorylation (see the Supporting Information). However,
PTZ-DPA showed a higher fluorescence quenching ratio
(0.72) than Dab-DPA (0.59) for nonphosphorylated and
phosphorylated TMR–peptides (Figure 2a; see the Support-
ing Information). TMR-cas, which has a À7 net charge, is
expected to bind to PTZ-DPA more strongly than other
nonphosphorylated peptides; however, TMR-p-cas showed a
more distinct fluorescence quenching with PTZ-DPA than
did TMR-cas, because PTZ-DPA bound strongly to TMR-
p-cas rather than to TMR-cas (Figure 2b). Other nonphos-
phorylated and phosphorylated TMR–peptides were also
clearly distinguished by PTZ-DPA (Figure 2b).
E
1/2,ox = 1.01 V.
Compared to TMR and FAM, PTZ has a less-positive
oxidation potential that can be correlated to the higher value
of the highest occupied molecular orbital (HOMO) of the
PTZ molecule compared to those of TMR and FAM.
Therefore, when TMR or FAM is photochemically excited,
an electron of PTZ can be easily transferred to the ground
state of the excited TMR* or FAM*, thereby quenching its
fluorescence emission (Figure 1b). This observation provides
an explanation to understand why PTZ can be used as a
versatile quencher by the mechanism of PET for fluorophores
including TMR and FAM. PTZ, which is a PET quencher, can
be used to develop a more selective detection system than
that developed by using Dab, which is a FRET quencher,
because fluorescence quenching by electron transfer is
These results encouraged us to attempt real-time fluores-
cence monitoring of the activities of several kinases (PKA,
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the Supporting Information).[13] As expected, the peptide
Table 1: Fluorescent peptides in kinase assay with PTZ-DPA.
phosphorylation rate increased with the amount of kinase
added to the reaction solutions. Furthermore, the calmodulin-
dependent kinase II showed almost no activity when cal-
modulin was not added to the reaction solution (Figure 3b).
We also performed control experiments in which fluores-
cent peptides (TMR-pka, TMR-cam) were incubated with
Abl kinase. As expected, the fluorescence of TMR-pka and
TMR-cam did not decrease upon the addition of PTZ-DPA
(Figure S11A, Supporting Information); this was because
these peptides could not be phosphorylated by Abl kinase.
Furthermore, the fluorescence of TMR-abl incubated with
PKA did not decrease but rather increased[14] upon the
addition of PTZ-DPA, which might be caused by nonspecific
interaction between fluorescent peptides and unsuitable
kinases (see Figure S13 in the Supporting Information).
Therefore, we concluded that the fluorescence of fluorescent
peptides decreases upon treatment with PTZ-DPA only when
they are phosphorylated by suitable kinases. This orthogon-
ality between peptide substrates and kinases can be very
useful for an in vitro assay of target kinases in cellular lysates.
Note that both Dab-DPA and PTZ-DPA also bind to ATP
and adenosine 5’-diphosphate (ADP), which are the substrate
and by-product, respectively, of the protein kinase reaction.
This can interfere with monitoring of peptide phosphorylation
by Dab-DPA and PTZ-DPA. Nevertheless, the problem can
be solved if a higher concentration of the quencher probe
(100 mm) than those of ATP (2 mm) and the fluorescent
peptides (1 mm) is used for the estimation of peptide
phosphorylation.
We also carried out fluorescent screening of kinase
inhibitors such as Gleevec (imatinib mesylate, Abl kinase
inhibitor)[15a] and A3-hydrochloride (PKA inhibitor).[15b] As
shown in Figure S11B in the Supporting Information, we
found that the reaction rate decreased upon the addition of
each inhibitor to the corresponding enzymatic reaction
mixture. As shown in our experimental data, we obtained
the IC50 value (820 nm; Figure S12, Supporting Information)
of Gleevec, which is comparable to that obtained in other
studies.[16] These results show the potential for the utilization
of quencher probes in high-throughput screening for drug
development.
Substrate
Target kinase
Sequence
FAM-abl
FAM-p-abl
TMR-abl
TMR-p-abl
TMR-pka
TMR-p-pka
TMR-cam
TMR-p-cam
TMR-cas
Abl kinase
–
Abl kinase
FAM-KKGEAIYAAPFA-NH2
FAM-KKGEAI-pY-AAPFA-NH2
TMR-KKGEAIYAAPFA-NH2
TMR-KKGEAI-pY-AAPFA-NH2
TMR-LRRASLG-OH
–
PKA[a]
–
TMR-LRRA-pS-LG-OH
CaMKII[b]
TMR-KKALRRQETVDAL-OH
TMR-KKALRRQE-pT-VDAL-OH
TMR-RRADDSDDDDD-OH
TMR-RRADD-pS-DDDDD-OH
–
CKII[c]
–
TMR-p-cas
[a] Protein kinase A catalytic subunit. [b] Ca2+/calmodulin-dependent
kinase II. [c] Casein kinase II. NH2 and OH in the C terminal of peptides
indicate amides and acids, respectively.
Figure 2. a) Fluorescence quenching of TMR-abl or TMR-p-abl upon
the addition of PTZ-DPA or Dab-DPA in aqueous HEPES (10 mm,
pH 7.4) buffer solution. TMR-abl, 1 mm (c); TMR-abl 1 mm+PTZ-
DPA 100 mm (b); TMR-abl 1 mm+DabDPA 100 mm (d); TMR-p-
abl 1 mm+PTZ-DPA 100 mm (b); TMR-p-abl 1 mm+DabDPA
100 mm (d). b) Fluorescence titration curves of peptides (1 mm
each) upon the addition of PTZ-DPA (0.01–100 mm, 10 mm HEPES,
&
pH 7.4). The x axis is a log scale. TMR-pka (&); TMR-p-pka ( ); TMR-
~
~
^
^
abl ( ); TMR—p-abl ( ); TMR-cam ( ); TMR-p-cam ( ); TMR-cas
*
*
( ); TMR-p-cas ( ). HEPES=4-(2-hydroxyethyl)-1-piperazineethanesul-
fonic acid.
Abl kinase, CaMKII, casein kinase II) by using PTZ-DPA.
The fluorescence intensity of TMR–peptides (1 mm) in an
enzymatic reaction mixture decreased rapidly with time upon
the addition of PTZ-DPA (100 mm; Figure 3 and Figure S7 in
The quencher probes PTZ-DPA and TMR-abl were also
used for the diagnosis of CML.[17] It is well known that
aberrant Abl kinase activity (Bcr-Abl)[17a,b] is one of the major
factors that cause myeloid leukemia. At present, most of the
CML diagnosis methods, such as cytogenetic analysis[17c] or
polymerase chain reaction analysis for the Bcr-Abl gene,[17c]
are performed at the genomic level. However, detecting Abl
kinase activity directly from patientsꢁ bone marrow samples is
also crucial. We performed blind tests by using four bone
marrow samples from CML patients and from a healthy
person.[18]
As shown in Figure 4a, we achieved distinctive real-time
fluorescence monitoring of Abl kinase activity in the sample
lysates by using PTZ-DPA. From the obtained data, we could
clearly discriminate the sample of a patient from that of a
healthy subject; the rates of phosphorylation of TMR-abl in
the case of CML patients were higher than those in the case of
Figure 3. Real-time fluorescence monitoring of various kinase activities
with PTZ-DPA using TMR–peptides. a) Abl protein kinase. b) Calm-
odulin-dependent kinase II (CaMKII).
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other fluorescent peptide substrates can be powerful tools for
cancer diagnosis.
Because our kinase activity detection method using PTZ-
DPA is based on fluorescence intensity (ON/OFF), we
believe that a kinase assay system can be built on microfluidic
chips, in which only a few nanoliters of a solution are required
for detection.[19] In these microfluidic chips (Figure 5a and b),
an enzymatic reaction mixture is incubated for 1 h, diluted
(20 mm TMR–peptide, 40 mm ATP, with or without kinase and
kinase reaction buffer), and allowed to flow through the
upper half of the mixing circle; the PTZ-DPA solution
(200 mm, pH 7.4, 10 mm HEPES) flowed through the lower
half. The two parts were mixed sequentially for 1 min with the
help of electronically controlled N2-gas valves for 1 min.
Then, the fluorescence of the mixture was measured under a
fluorescence stereo microscope (see the Supporting Informa-
tion). As expected, the fluorescence of each TMR–peptide
was quenched by PTZ-DPA only when the peptide was
phosphorylated with PKA (Figure 5c and d), Abl kinase
(Figure 5e and f), or CaMKII (Figure 5g and h). We also
monitored the dephosphorylation of TMR-p-pka by alkaline
phosphatase (ALP) in the microfluidic chips (Figure 5i and j).
To the best of our knowledge, this is the first report of a
homogeneous kinase assay involving the use of microfluidic
chips.
In conclusion, we have demonstrated a novel fluorescent
kinase assay based on the use of selective fluorescence
quencher probes (Dab-DPA, PTZ-DPA) for phosphorylated
fluorescent peptides. With this probe, we can perform kinase
inhibitor tests and diagnose CML on the basis of the detection
of Abl kinase activity in the patientsꢁ myelogenous samples.
We also developed the first homogeneous fluorescent kinase
assay system on microfluidic chips. This detection system
involves the use of a quencher probe and has the potential to
be applied to the development of kinase inhibitors by high-
Figure 4. a) Fluorescence detection of phosphorylation of TMR-abl in
^
CML patient samples by using PTZ-DPA. CML, chronic phase ( );
&
control (person; ); CML, chronic phase, resistant to drugs ( ); CML,
*
~
complete hematological response ( ). b) Karyotype of a control
sample (healthy person). c) Karyotype of a CML (chronic phase)
sample.
a healthy person. Furthermore, negligible Abl kinase activity
was observed in the sample of a person with a complete
hematologic response to CML. We also performed a conven-
tional cytogenetic study (Figure 4b and c; see the Supporting
Information) to check for the presence of Philadelphia
chromosomes[18b] in the samples that were determined by
our sensing system to belong to the healthy person (Fig-
ure 4b) or to CML patients (chronic phase, Figure 4c). To the
best of our knowledge, this is the first use of synthetic probes
for cancer diagnosis. Our results show that PTZ-DPA and
Figure 5. Kinase assay on a microfluidic chip: a) microfluidic chip design; b) microfluidic mixing circle: kinase reaction mixture pathway (red,
upper half circle), PTZ-DPA solution pathway (gray, lower half circle), closed valve (black), opened valve (white); c) 10 mm TMR-pka, 20 mm ATP,
no PKA, 100 mm PTZ-DPA; d) 10 mm TMR-pka, 20 mm ATP, 12.0 UmLÀ1 PKA, 100 mm PTZ-DPA, 10 mm MgCl2, reaction buffer of (c,d): 10 mm
MgCl2, pH 7.5, 50 mm Tris–HCl; e) 10 mm TMR-abl, 20 mm ATP, no Abl kinase, 100 mm PTZ-DPA; f) 10 mm TMR-abl, 20 mm ATP, 10 UmLÀ1 Abl
kinase, 100 mm PTZ-DPA, reaction buffer of (e,f): 50 mm Tris–HCl, 10 mm MgCl2, 2 mm DTT, 1 mm EGTA, 0.01% Brij 35; g) 10 mm TMR-cam,
20 mm ATP, no CaMKII, 100 mm PTZ-DPA; h) 10 mm TMR-cam, 20 mm ATP, 5.0 UmLÀ1 CaMKII, 100 mm PTZ-DPA, reaction buffer of (g,h): 50 mm
Tris–HCl, 10 mm MgCl2, 2 mm DTT, 0.1 mm Na2EDTA, 1.2 mm calmodulin, 2 mm CaCl2; i) 10 mm TMR-p-pka, 100 mm PTZ-DPA, no ALP; j) 10 mm
TMR-p-pka, 2.5 mgmLÀ1 ALP, 100 mm PTZ-DPA, reaction buffer of (i,j): 10 mm MgCl2, pH 7.5, 50 mm Tris–HCl. DTT=dithiothreitol, EGTA=
ethylene glycol tetraacetic acid, EDTA=ethylenediamine tetraacetic acid.
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[13] The phosphorylation of TMR-abl by Abl kinase was also
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b) Philadelphia chromosome is an abnormal chromosomal
translocation caused by the juxtapositioning of part of the
BCR gene from chromosome 22 (region q11) to the Abl1 gene
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22. See Ref. [16].
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Received: February 12, 2010
Revised: April 14, 2010
Published online: June 10, 2010
Keywords: cancer · fluorescence · fluorescent probes · kinases ·
.
phosphorylation
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