Design of a mechanism-based probe for neuraminidase to capture influenza viruses

Article abstract of DOI:10.1002/anie.200501738

(Chemical Equation Presented) Getting a grip on the flu: A mechanism-based probe, 1, for neuraminidase was developed. It is capable of forming a biotinylated adduct with neuraminidase (NA) from Arthrobacter ureafaciens. It also displays an inhibitory effe

Full text of DOI:10.1002/anie.200501738

Communications
Activity Probes
DOI: 10.1002/anie.200501738
Design of a Mechanism-Based Probe for
Neuraminidase To Capture Influenza Viruses**
Chun-Ping Lu, Chien-Tai Ren, Yi-Ning Lai,
Shih-Hsiung Wu,* Wei-Man Wang, Jean-Yin Chen,
and Lee-Chiang Lo*
Influenza viruses, which cause upper respiratory tract prob-
lems in humans, have long been a major threat to public
health.[1] It is estimated that 10–20% of the general popula-
[+] [++]
[*] C.-P. Lu,[+] $ Dr. C.-T. Ren,$ Y.-N. Lai, Prof. S.-H. Wu
Institute of Biological Chemistry, Academia Sinica
Taipei 115 (Taiwan)
Fax: (+886)2-2653-9142
E-mail: shwu@gate.sinica.edu.tw
W.-M. Wang, J.-Y. Chen, Prof. L.-C. Lo
Department of Chemistry, National Taiwan University
Taipei 106 (Taiwan)
Fax: (+886)2-2362-1979
E-mail: lclo@ntu.edu.tw
[+] Institute of Biochemical Sciences, National Taiwan University
Taipei 106, (Taiwan)
[
++] Genomics Research Center, Academia Sinica
Taipei 115 (Taiwan)
[$] These authors contributed equally to this work.
[**] Influenza A virus (A/WSN/33) was a gift from Dr. Shin-Ru Shih,
Chang Gung University, Taiwan) and polyclonal anti-FluA antibody
was a gift from Dr. Hour-Young Chen (Center for Disease Control
Taiwan). Japanese encephalitis virus (JEV, Taiwanese strain, RP-9)
and the mouse monoclonal antibody specific for this virus were
kindly provided by Dr. Yi-Ling Lin (IBMS Academia Sinica).
Zanamivir was a gift from GlaxoWellcome Research and Develop-
ment Ltd. (Stevenage, UK) and from Prof. Ching-Shih Chen (The
Ohio State University, OH). We thank Prof. Yulin Lam for proof-
reading the manuscript. This work was supported by the National
Science Council (Grant nos. NSC92-2113M-001-023 to S.-H.W. and
NSC93-3112-B-002-001 to L.-C.L.).
Supporting information for this article is available on the WWW
under http://www.angewandte.org or from the author.
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tion are affected in seasonal epidemics. Some devastating
outbreaks recorded in history even claimed millions of lives
worldwide.[2] Influenza viruses are typically spherical with a
diameter of about 100 nm.[3] The pathogenic properties of the
viruses have been extensively investigated.[4] Significant
advances in therapeutic treatments and in the detection of
the viruses have been made in recent years as a result of this
information. Among the limited number of proteins that are
encoded by the viral RNA segments, two surface glycopro-
teins, namely, hemagglutinin (HA) and neuraminidase (NA),
have often been the focus of research. These two surface
glycoproteins play important roles in the infection process;
HA is responsible for the binding of viruses to the host cells,
whereas NA is involved in the budding process.[5] Although
the surface antigens of the viruses mutate frequently to avert
attacks from the immune system of the hosts, the critical
catalytic activity of NA has to be maintained for successful
infection and propagation. This special feature makes it an
excellent candidate for research.[6]
NA (sialidase, N-acylneuraminosyl glycohydrolase,
EC 3.2.1.18) is an exo-glycosidase that hydrolyzes the linkage
of sialic acid residues, which are mostly found as terminal
constituents of glycoconjugates. X-ray crystallographic infor-
mation about the active site of NA has revealed important
residues involved in the recognition and binding of sialic
acid.[7] This has assisted in the development of several
reversible inhibitors of NA, such as zanamivir and oseltami-
vir, which have been approved for the treatment of influ-
enza.[8] Recently, McKimm-Breschkin et al. have demon-
strated that ligands derived from biotin-conjugated zanamivir
were able to bind influenza virion on microtiter plates; this
could in turn serve as a basis for a diagnostic method.[9]
Besides influenza viruses, many NA-containing microorgan-
isms are pathogenic and it has been proposed that this enzyme
plays an important role in the pathogenicity of these
infections.[10] We therefore envision that the development of
activity probes that selectively form a covalent linkage with
NA would be of great value, as demonstrated by the
application for capturing the virus particles in this report.
Chemical probes that are able to form covalent linkages
with hydrolase subfamilies have proven to be a powerful tool
in modern proteomics studies.[11] We have previously devel-
oped activity probes for hydrolases such as phosphatases and
b-glucosidase.[12] The concept for the design of these activity
probes originated from suicide substrates, or mechanism-
based inhibitors, of enzymes.[13] This approach is unique as the
probes themselves are also the substrates of the correspond-
ing hydrolases. The probes can be selectively activated once
the recognition head is cleaved by the targeting hydrolase,
thereby leading to covalent modifications of the hydrolase.[14]
More importantly and closely related to this report, the
mechanism-based approach has been successfully applied in
the screening and selection of biocatalysts from phage-
displayed libraries, such as in the selection of mutant b-
lactamases and in the search for catalytic antibodies with b-
galactosidase activity.[15] Earlier studies have shown that
compound 1 was a mechanism-based inhibitor of Clostridium
perfringens NA.[16] We thus developed probe 2 as a mecha-
nism-based probe for NA. Probe 2 carries four structural units
in its design; a sialic acid recognition head, which is connected
to an ortho-difluoromethylphenyl latent trapping device, a
linker, and a biotin reporter group. The biotin reporter group
serves two functions. On one hand, it is used to visualize the
labeled NA after Western blotting with streptavidin-conju-
gated peroxidase chemiluminescence. On the other hand, it
could be used to attach the probe to the microtiter plates
through avidin–biotin interactions during the virus-capturing
study. When the designated glycosidic bond is cleaved by NA,
the released intermediate 3 would undergo 1,4-elimination
with removal of a fluoride ion to generate a reactive quinone
methide, 4. The highly reactive quinone methide intermediate
4 would alkylate nearby nucleophiles of the enzyme, thereby
resulting in biotinylated adduct 5 (Scheme 1). Since the viral
surface is spiked with NA, covalent attachment through NA
would then lead to the capture of virus particles.
Scheme 1. Mechanism for selective activation and alkylation of neura-
minidase with probe 2.
The synthesis of probe 2 begins with a commercially
available N-acetylneuraminic acid 6 (Scheme 2). All the
synthetic procedures were combinations of efforts from
previous publications.[17] In brief, fully protected glycosyl
chloride 8 was prepared and used directly for coupling with 2-
hydroxy-5-nitrobenzaldahyde in
a CHCl3/H2O biphasic
system by using tetrabutylammonium bromide as the phase-
transfer catalyst to give compound 9. The formyl group of
compound 9 could be converted into the difluoromethyl
moiety of the trapping device by the DAST reagent. The
structure of the difluoromethylphenyl group in compound 10
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shown by the lack of labeled bands
(Lane 2). In the absence of the probe,
neither NA nor BSA was biotinylated
(Lanes 3 and 4). This result firmly
supports the alkylation process de-
scribed in Scheme 1. The actual label-
ing site was not further determined in
this study, because a number of bio-
logical applications utilizing the same
latent trapping device have already
established the covalent-bond-form-
ing feature.[15,19] Moreover, Lee and
co-workers recently used this activity-
probe approach to characterize the
catalytic domain of b-galactosidases
from Xanthomonas manihotis, Escher-
ichia coli, and Bacillus circulans, with
the identification of mainly single
modifications on Arg, Glu, and Glu
residues, respectively.[20]
Scheme 2. Synthesis of probe 2 for neuraminidase. Conditions: a) MeOH, IR-120 (H+) resin, 92%; b) AcCl,
AcOH; c) 2-hydroxy-5-nitrobenzaldehyde, Cs2CO3, Bu4NBr, H2O/CHCl3, 67% for two steps; d) DAST,
CH2Cl2, 47%; e) H2, 5% Pd/C, MeOH, 95%; f) succinic anhydride, TEA, CH2Cl2, 94%; g) EDCI, HOBt, 13,
DIEA, DMF, 75%; h) Na2CO3, MeOH; aqueous Na2CO3, 52%. TFA=trifluoroacetic acid; TEA=triethyl-
amine; EDCI=3-(3-dimethylaminopropyl)-1-ethylcarbodiimide; HOBt=1-hydroxy-1H-benzotriazole;
DIEA=N,N-diisopropylethylamine; DMF=N,N-dimethylformamide; DAST=(diethylamino)sulfur trifluor-
ide.
We also compared the inhibitory
effect of probe 2 and zanamivir on the
activity of NA from influenza A virus
(A/WSN/33, H1N1), as well as from
Arthrobacter ureafaciens (AU), Clos-
was supported by its 1H NMR spectroscopic data which
showed a triplet at d = 6.86 ppm with a coupling constant of
2JH,F = 54.9 Hz, a typical value for H–F coupling. A triplet at
d = 109.9 ppm (1JC,F = 237.2 Hz) in the 13C NMR spectrum of
10 further confirmed the presence of the CHF2 moiety. The
nitro group of compound 10 was then reduced by catalytic
hydrogenation to give amine 11. Attachment of the linker and
biotin reporter group yielded the fully protected probe 14.
Final deprotection under alkaline conditions offered the
desired probe 2 after LH-20 purification.
tridium perfringens (CP), and Vibro cholerae (VC; Figure 2).
Both compounds were tested at 3.3 mm in the NA inhibi-
tion assays with 2’-(4-methylumbelliferyl)-a-d-N-acetyl-
Probe 2 was first tested for its ability to biotinylate NA
obtained from Arthrobacter ureafaciens. Arthrobacter ureafa-
ciens neuraminidase (0.8 U, Sigma) was incubated in the
presence or absence of probe 2 (200 mm) at 48C in 100 mm
ammonium acetate buffer (10 mL). Bovine serum albumin
(BSA) was used as a negative control. Labeled samples were
applied to a 10% polyacrylamide gel, which was then
subjected to sodium dodecylsulfate (SDS) PAGE. After
electrophoresis, the proteins were
Figure 2. Inhibition study of NA activities from A. ureafaciens (AU),
C. perfringens (CP), V. cholerae (VC), and influenza A virus (Inf A) with
probe 2 (gray), zanamivir (white), and the control (black). Virus,
suspended in 32.5 mm b-morpholinoethanesulfonic acid buffer
(pH 6.5) was incubated with either probe 2 or zanamivir (3.3 mm) at
room temperature for 45 min and then incubated with MUNANA at
378C for 30 min. The residual NA activity is expressed as the
percentage of activity relative to that obtained in the absence of
reagent. Assays for AU, CP, and VC were similarly carried out, except
in 80 mm acetate buffer (pH 5.0).
transferred from the gel onto a poly-
vinylidene fluoride (PVDF) mem-
brane. The PVDF membrane was
blocked, washed, and developed by
using the enhanced chemilumines-
cence (ECL). Western blotting pro-
tocols as recommended by the sup-
plier (Amersham Biosciences). The
result of the Western blot analysis
only shows biotinylated proteins
(Figure 1). In this experiment, three
biotinylated bands corresponding to
neuraminic acid (MUNANA, Sigma) as the substrate.[21] All
samples were measured in duplicate and fluorometric deter-
minations were performed with a fluorometer (ThermoLab
systems, Sweden). The excitation wavelength was 355 nm and
the emission wavelength was 460 nm. Probe 2 inhibited all
four NA activities (H1N1, AU, CP, VC) with IC50 values of
1.7, 0.68, 0.08, and 0.53 mm, respectively. These results
indicate that probe 2 interferes with the activity of NA
isolated from various sources at the active site, regardless of
the variations the enzymes might have. On the other hand,
Figure 1. Western blot
analysis of probe 2
labeling the Arthro-
bacter ureafaciens neu-
isoenzymes at 88, 66, and 52 KDa
were observed for NA (Lane 1).[18]
raminidase.
Probe 2 had no effect on BSA, as
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zanamivir effectively inhibited viral NA activity with an IC50
value of 2–3 nm, but it displayed weak inhibitory effects on
the three bacterial NA activities, a result suggesting that the
original strong binding interactions could be greatly compro-
mised by possible variations in the active site. It must be
emphasized that although one of the targets in this study, the
influenza virus, is the same as one in the study of McKimm-
Breschkin et al.,[9] the concept and approach of the current
strategy offers a versatile alternative for future applications.
The labeling event in this study was a result of an activation
step forming the reactive quinone methide and did not rely on
the strong noncovalent binding which is a critical requirement
in the previous approach, a fact which makes the current
approach a more general one in targeting NA activities. It is
especially worth noting that the advantage of the current
approach becomes more prominent with the advent of
zanamivir-resistant viruses.[22]
Having established the efficacy of probe 2 to biotinylate
NA and thus influenza virus A virions, we next studied the
capturing performance by utilizing the covalent-bond-form-
ing feature. The tests were carried out by a modified ELISA
method as described previously.[9] Briefly, a streptavidin-
coated 96-well ELISA plate (NUNC Immobilizer) was
saturated with probe 2. BSA–biotin conjugate provided a
negative control. After 1 hour of incubation, the plate was
blocked with 0.1% BSA/phosphate-buffered saline (PBS) for
1 hour and washed with PBS. Serial twofold dilutions of
influenza A virus (A/WSN/33) were added and incubated for
1 hour at room temperature. After another wash, the
captured viruses were detected by treatment with a polyclonal
anti-FluA antibody, followed by a goat anti-rabbit IgG
horseradish peroxidase (HRP) conjugate and a NeA-Blue
tetramethylbenzidine substrate (TMB, Clinical Science Prod-
ucts, Inc.). The results indicated that probe 2 bound to the
microplate wells could successfully capture influenza virus A
and the intensity of the responding signal was proportional to
the number of virus particles present (Figure 3). The wells
loaded with BSA–biotin conjugate gave a negative response.
The possibility of any noncovalent bindings could be ruled out
by the modest IC50 value (1.7 mm) on the viral NA. More
importantly, when the same procedure was applied to a
mixture of influenza virus and a non-NA-containing Japanese
encephalitis virus, only influenza virus was selectively cap-
tured and detected on the plate, a result strongly supporting
the theory that the capture of virus particles was both probe
and NA dependent. This conclusion was further supported by
the experiment during which probe 2 failed to biotinylate
influenza viruses that were preincubated with zanamivir,
which effectively blocked the active site of NA on the viral
surface. The results represent the first example of the use of a
covalent-bond-forming mechanism for the capture of influ-
enza virus particles. In addition, such covalent interactions
between captured virus particles and the probe are known to
be tolerant to harsh conditions,[15] thus making this method-
ology amenable for further manipulations.
In summary, we have designed and synthesized a mech-
anism-based activity probe 2 for neuraminidase, which uses a
latent quinone methide as the trapping device and forms a
biotinylated adduct with Arthrobacter ureafaciens neuramin-
idase in a model study. By taking advantage of the essential
role played by the NA activity in the life cycle of the influenza
virus, we evaluated the interaction between probe 2 and the
virus. The covalent-labeling event led to diminished NA
activities. Furthermore, it serves as the basis for capturing
influenza virus particles on microplate wells. This novel
approach of capturing the influenza virus, which provides a
stronger interaction between virus and the stationary phase,
will certainly offer opportunities for developing new applica-
tions, such as rapid screening of antibodies against this group
of viruses, and the development of sensitive and rapid
diagnostic methods.
Received: December 15, 2004
Revised: May 20, 2005
Published online: October 7, 2005
Keywords: activity probes · hydrolases · influenza viruses ·
.
mechanism-based labeling · sialic acids
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