Boronic acids facilitate rapid oxime condensations at neutral pH

Article abstract of DOI:10.1039/c5sc00921a

We report here the discovery and development of boron-assisted oxime formation as a powerful connective reaction for chemical biology. Oximes proximal to boronic acids form in neutral aqueous buffer with rate constants of more than 10⁴ M^-1

Full text of DOI:10.1039/c5sc00921a

Chemical
Science
View Article Online
View Journal | View Issue
EDGE ARTICLE
Boronic acids facilitate rapid oxime condensations
at neutral pH†‡
Cite this: Chem. Sci., 2015, 6, 3329
*
Pascal Schmidt, Cedric Stress and Dennis Gillingham
We report here the discovery and development of boron-assisted oxime formation as a powerful
connective reaction for chemical biology. Oximes proximal to boronic acids form in neutral aqueous
buffer with rate constants of more than 104 Mꢀ1 ꢀ1, the largest to date for any oxime condensation.
s
Received 13th March 2015
Accepted 7th April 2015
Boron's dynamic coordination chemistry confers an adaptability that seems to aid a number of
elementary steps in the oxime condensation. In addition to applications in bioconjugation, the emerging
importance of boronic acids in chemical biology as carbohydrate receptors or peroxide probes, and the
growing list of drugs and drug candidates containing boronic acids suggest many potential applications.
DOI: 10.1039/c5sc00921a
www.rsc.org/chemicalscience
many of its applications. For example the N / B dative inter-
action has been proposed to stabilize otherwise labile Schiff
Introduction
bases, and these iminoboronates have been used in supramo-
lecular chemistry,24,25 enantiomer analysis by NMR,26,27 and
protein labelling.28,29
We selected the 2-formylphenylboronic acid (2-FPBA, 1)
scaffold as a model system to explore boron's inuence on
Bioconjugation reactions create multifunctional molecules
from monofunctional components, a molecular plug-and-play
that is invaluable in modern biological research.1 Still under-
developed, however, are biocompatible (neutral pH, tolerant to
biothiols) coupling reactions that proceed fast enough to allow
substrate ratios near unity at low concentrations (i.e. nM to mM
regime).2 Certainly the fastest biocompatible reaction is the
tetrazine inverse electron demand Diels–Alder with strained
olens,3,4 a recent example of which has achieved an astonish-
ingly high rate constant.5 Despite the availability of faster
reactions the oxime condensation remains a workhorse in
chemical biology due to its simplicity and robustness;6,7 but the
need for added catalysts or low pH to achieve acceptable rates is
a distinct disadvantage.
Recent works by us8 and others9,10 have shown that proximal
functional groups can play a decisive role in oxime condensa-
tions and related reactions.11 Based on these insights, we
hypothesized that the Lewis acidity of boron12 coupled with its
ability to modulate alcohol pKas through coordination
(panel a, Fig. 1),13,14 might facilitate rapid oxime formation
(panel b, Fig. 1). Moreover, boron is a chemically versatile
element and its presence in oxime products would open the
door to many applications in chemical biology. For example
boron compounds have found uses in medicinal chemistry,15,16
cross-coupling reactions17,18 carbohydrate detection,19,20
promoting endocytosis,21 and reactivity-based peroxide
sensing.22,23 Boron's rich coordination chemistry is pivotal for
Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel,
Switzerland. E-mail: dennis.gillingham@unibas.ch
Fig. 1 (A) The unique abilities of boron led to the hypothesis that
proximal boron substituents would have an impact on oxime
condensations; (B) preliminary observations confirming the potential
of boron to accelerate oxime formation.
† Dedicated to Andreas Pfaltz on the occasion of his retirement.
‡ Electronic supplementary information (ESI) available: Detailed kinetic data,
HPLC assays, and characterization data for all new compounds are provided.
See DOI: 10.1039/c5sc00921a
This journal is © The Royal Society of Chemistry 2015
Chem. Sci., 2015, 6, 3329–3333 | 3329

View Article Online
Chemical Science
Edge Article
Table 1 Probing the importance of boron positioning and substitution
on oxime condensations
oxime condensations (Fig. 1). 2-FPBA has previously been
shown to modify lysine residues or N-termini in proteins in a
process controlled by rapid equilibria.29 Little is known,
however, about the analogous condensation with a-effect
nucleophiles. We have found two cases of alkoxy-
iminoboronates (AIBs),27,30 two cases of O-alkylAIBs31,32 and two
cases of the related hydrazinoiminoboronates;30,33 but in each of
those studies the coupling itself was not of central importance
and therefore not examined in detail. Herein we describe that
O-alkylAIBs form with remarkable speed and selectivity in
neutral aqueous buffer. The reaction is unaffected by proteins,
carbohydrates, biothiols, and human serum, and has an equi-
Entry Ar
X
Product
Conc (mM) Convb (%)
1c
Ph
H
100
100
<5
librium constant of >108 Mꢀ1
.
2
H
H
>98
Results and discussion
3
4
10
>98
>98
As shown in panel b of Fig. 1, when 2-FPBA was reacted with
O-benzylhydroxylamine in a 1 : 1 ratio at neutral pH at 10 mM
the reaction was nearly complete aer the rst proton NMR
measurement (>90% conversion at ꢁ3.5 minutes), or HPLC
injection (ꢁ1 minute, see entry 3, Table 1). These observations
imply a rate upwards of 103 Mꢀ1 sꢀ1 – several orders of
magnitude faster than normal oxime condensations at neutral
pH,34 prompting us to explore the importance of boronic acid
positioning on reaction efficacy. Comparing entries 1–6 in Table
1 makes it clear that the 2-FPBA motif is crucial for an efficient
reaction: the corresponding meta- and para-substituted FPBAs
behaved similar to benzaldehyde, delivering nearly undetect-
able levels of oxime aer 90 minutes (cf. entry 1 with 5 and 6).
More complex hydroxylamines, such as the pentapeptide shown
in entry 4, were also excellent substrates, delivering complete
conversion aer the rst injection. Condensations with ketones
were slower than with 2-FPBA (entry 7), but still faster than
normal ketoxime condensations. Pinacol boronate esters also
gave complete conversion aer one minute (compares entries
2 & 8) but the hydrolysed boronic acid 2a was the main product
with only 10% of pinacol ester oxime 2f observed; aer ninety
minutes only 2a was present. The ketoximine pinacol product
(entry 9), on the other hand, was more stable and comprised
97% of the product aer the rst injection (the remainder being
2e); aer thirty minutes 2g had also completely hydrolysed to
2e. The ability to use pinacol esters is valuable since these are
readily obtained from Pd-catalysed routes to boronic esters, and
their deprotections in organic solvents are oen tricky.
H
H
100
5c
100
<5
6c
7
H
100
100
<5
94
Me
8
H
100
100
>98d
>98
9
Me
a
Time is approximate since samples are injected directly aer mixing.
b
c
Determined by reverse phase HPLC analysis under neutral conditions.
d
Injections at 90 minutes still show <5% conversion. At the rst
injection approximately 10% of the pinacol ester oxime is observed,
but only the hydrolysed product is detected at 90 minutes. KPi
potassium phosphate buffer.
¼
The reaction is fast and displays second order kinetics. We
established the rate in three independent ways: HPLC, NMR,
and uorescence quenching. While the time resolution and showed excellent linearity in inverse concentration plots
sensitivity of HPLC and NMR could provide only a lower bound (see Fig. 2) and gave a rate constant of z11 000 Mꢀ1 sꢀ1
–
for the rate constant, uorescence quenching gave a more several orders of magnitude faster than the fastest neutral pH
quantitative assessment. A hydroxylamine bearing a lissamine oxime condensations.34 Although uorescence quenching is an
uorophore and a 2-FPBA connected to a quencher were indirect measurement technique, HPLC injections of aliquots
prepared (see Fig. 2 for the structures and the ESI pages S10–11‡ from the assay mixture showed only product and starting
for synthetic details). Scouting experiments suggested that materials (indicating a clean reaction) and gave conversions
monitoring at 100 nM would be required to obtain sufficient qualitatively in agreement with the uorescence measurements.
data at early reaction conversion (runs at 500 nM show second In addition, the fact that 10 and 1 mM reactions monitored by 1H
order behavior only in the rst 100 seconds, see page S26 in the NMR showed >90% conversion at the earliest possible
ESI‡ for details). Triplicate rate measurements at 100 nM measurements (see Fig. 1, and the ESI Scheme S1‡ for 1 mM
3330 | Chem. Sci., 2015, 6, 3329–3333
This journal is © The Royal Society of Chemistry 2015

View Article Online
Edge Article
Chemical Science
case) provides independent verication of a rate constant
>104 Mꢀ1 sꢀ1 since the rst half-life would have to be less than
90 seconds. The general pH dependence, with a maximum in
the range of 4.5–5, is consistent with normal oxime formation35
except there is a distortion in the sigmoidal shape at higher pH
(i.e. 7.2 & 8). The asymmetry in the pH dependence curve is
inverted in comparison to a typical oxime condensation
(acetone with hydroxylamine),35 which shows
a
more
pronounced drop-off in rate at higher pH than at lower pH.
Based on the build-up of a tetrahedral intermediate at higher
pH, Jencks attributed this pH dependence to the need for a
proton in the dehydration step.35 Although we have thus far not
been able to detect intermediates, we speculate that the near-
neutral pKa of amine-substituted aqueous boronates14,36
provides the ideal environment for acceleration of the normally
rate-limiting dehydration.
The products are stable and undergo slow equilibration at
neutral pH. Proton NMR analysis of compound 2a (from entry 2
in Table 1) in pH 7.2 phosphate buffer led to little change in
concentration (<5%) over the course of three days (see panel a in
Fig. 3). We also tested whether 2a was in equilibrium with the
starting materials by adding to the NMR sample a ve-fold
excess of O-methylhydroxylamine. As shown in panel b of Fig. 3,
O-methylhydroxylamine leads to a new oxime product, with
equilibrium being established aer 10–15 hours at 100 mM in
pH 7.2 phosphate buffer. Although the equilibrium constant is
too large to allow a static equilibrium measurement, kꢀ1 can be
calculated directly from the exchange rate between oximes
(4.2 ꢂ 0.4 ꢃ 10ꢀ5 sꢀ1). From this value and the k1 value obtained
from uorescence quenching (Fig. 2) an equilibrium constant
of 2.6 ꢂ 0.3 ꢃ 108 Mꢀ1 can be estimated. The reversibility assay
shown in Fig. 3 would not be able to distinguish between
hydrolysis and direct O-methylhydroxylamine attack; therefore
Fig. 3 (A) Product 2a shows no detectable decomposition after three
days in 10 mM phosphate buffer at pH 7.2. (B) Product 2a exchanges
with O-methylhydroxylamine, reaching equilibrium over several hours
in 10 mM phosphate buffer at pH 7.2.
we also ran the experiment by adding a different boronic acid to
2a instead of O-methylhydroxylamine: the exchange kinetics are
the same within experimental error, corroborating the hydro-
lysis-based mechanism (see the ESI pages S36 and S37‡ for
details).
For practical applications it is important for
a bio-
conjugation to proceed in complex environments. We therefore
explored the efficacy of the boron-assisted oxime ligation in the
presence of common interfering additives (sugars, biothiols,
proteins, human serum). The additives led to no detectable
reduction in reaction efficiency (see Table 2) with the exception
of human serum. Interestingly in human serum the boronic
acid in 2a partially oxidized to a phenol, leading to an apparent
loss of material: aer the rst injection 80% of 2a was present
while aer 18 h only 20% remained (see the ESI Fig. S13‡ for
details). Even in the oxidized product, however, the oxime was
still intact and if both components are added together the mass
balance is nearly complete. Furthermore, lysozyme, which has
previously been shown to react with 2-FPBA,29 showed no
modication according to LC-MS, indicating that the hydroxyl-
amine entirely outcompetes nucleophilic amino acid function-
alities for 2-FPBA (see Fig. S12 in the ESI‡).
Fig. 2 Fluorescence quenching assay to determine rate constants and
pH dependence. All measurements were done in triplicate and are
corrected by subtracting a control measurement where everything
was identical except that the dabcyl moiety lacked a 2-FPBA function.
This journal is © The Royal Society of Chemistry 2015
Chem. Sci., 2015, 6, 3329–3333 | 3331

View Article Online
Chemical Science
Edge Article
Table 2 Tolerance of the condensation to biological interfering agents
Entry Additive (conc)
Normalized 2a integralb (%) Signicance
1
2
3
4
5
None
100
98
—
Glutathione (5 mM)
Biothiols do not interfere
Boron chelators do not interfere
Amino acid side-chains cannot compete with O-alkylhydroxylamine for 2-FPBA
Sucrose (100 mM & 5 mM) 106/92c
Lysozyme (100 mM)
Human serum (20% v/v)
105
80d
Reaction is compatible with complex media
a
c
b
Time is approximate since samples are injected directly aer mixing. Determined by reverse phase HPLC analysis under neutral conditions.
This reaction was also performed by pre-mixing the boronic acid with the sucrose, with no measurable change in conjugation efficiency.
Human serum leads to oxidation of the boronic acid to a phenol by a Baeyer–Villiger type reaction. The 80% number represents only the
d
measurement of 2a, when the phenol is included nearly complete mass balance is observed. KPi ¼ potassium phosphate buffer.
3 M. Blackman, M. Royzen and J. Fox, J. Am. Chem. Soc., 2008,
130, 13518–13519.
Conclusions
4 N. Devaraj and R. Weissleder, Acc. Chem. Res., 2011, 44, 816–
827.
5 A. Darko, S. Wallace, O. Dmitrenko, M. M. Machovina,
R. A. Mehl, J. W. Chin and J. M. Fox, Chem. Sci., 2014, 5,
3770–3776.
6 K. Lang and J. W. Chin, Chem. Rev., 2014, 114, 4764–4806.
7 D. M. Patterson, L. A. Nazarova and J. A. Prescher, ACS Chem.
Biol., 2014, 9, 592–605.
8 P. Schmidt, L. Zhou, K. Tishinov, K. Zimmermann and
D. Gillingham, Angew. Chem., Int. Ed., 2014, 53, 10928–
10931.
9 P. Crisalli and E. T. Kool, Org. Lett., 2013, 15, 1646–1649.
10 E. T. Kool, D.-H. Park and P. Crisalli, J. Am. Chem. Soc., 2013,
135, 17663–17666.
11 P. I. Kitov, D. F. Vinals, S. Ng, K. F. Tjhung and R. Derda,
J. Am. Chem. Soc., 2014, 136, 8149–8152.
12 B. E. Collins, S. Sorey, A. E. Hargrove, S. H. Shabbir,
V. M. Lynch and E. V. Anslyn, J. Org. Chem., 2009, 74,
4055–4060.
13 W. Ni, G. Kaur, G. Springsteen, B. Wang and S. Franzen,
Bioorg. Chem., 2004, 32, 571–581.
A great advantage of the present method over many coupling
reactions is the simplicity and ready availability of the starting
materials. There are commercial libraries of phenylboronic acid
and boronic ester compounds, many of which contain an
aldehyde or can be trivially elaborated to incorporate one.
Furthermore, the widespread use of oxime conjugations for
connective processes at high concentration means that a variety
of O-alkylhydroxylamines are also available. A shortcoming of
the present method in comparison to the classical oxime
condensation is the size of required 2-FBPA motif. Although for
most applications this should present no difficulties, examples
where the compactness of the oxime is critical (such as, for
example, as a functional isostere of peptide bonds)37 would not
be possible. The ability to run conjugations at 1 : 1 ratios of
partners at biological pH means that either or both components
can be complex, precious materials. Although we have focused
on oxime condensation for proof-of-concept the coordinating
properties of boron in aqueous media could potentially be
exploited to accelerate other important reactions whose rates
are limited by the kinetics of Schiff base formation.11
14 A. Adamczyk-Wo´zniak, K. M. Borys, I. D. Madura,
Acknowledgements
˙
A. Pawełko, E. Tomecka and K. Zukowski, New J. Chem.,
We are grateful to the University of Basel for start-up funds that
support this work.
2013, 37, 188–194.
15 C. T. Liu, J. W. Tomsho and S. J. Benkovic, Bioorg. Med.
Chem., 2014, 22, 4462–4473.
16 R. Smoum, A. Rubinstein, V. M. Dembitsky and M. Srebnik,
Chem. Rev., 2012, 112, 4156–4220.
Notes and references
1 D. M. Patterson, L. A. Nazarova and J. A. Prescher, ACS Chem.
Biol., 2014, 9, 592–605.
17 J. M. Chalker, C. S. C. Wood and B. G. Davis, J. Am. Chem.
Soc., 2009, 131, 16346–16347.
2 F. Saito, H. Noda and J. W. Bode, ACS Chem. Biol., 2015, DOI:
10.1021/cb5006728.
3332 | Chem. Sci., 2015, 6, 3329–3333
This journal is © The Royal Society of Chemistry 2015

View Article Online
Edge Article
Chemical Science
18 R. M. Yusop, A. Unciti-Broceta, E. M. V. Johansson, 28 P. M. S. D. Cal, R. F. M. Frade, V. Chudasama, C. Cordeiro,
´
´
R. M. Sanchez-Martın and M. Bradley, Nat. Chem., 2011, 3,
S. Caddick and P. M. P. Gois, Chem. Commun., 2014, 50,
5261–5263.
239–243.
19 M. Dowlut and D. G. Hall, J. Am. Chem. Soc., 2006, 128, 4226– 29 P. M. S. D. Cal, J. B. Vicente, E. Pires, A. V. Coelho,
4227.
L. S. F. Veiros, C. Cordeiro and P. M. P. Gois, J. Am. Chem.
Soc., 2012, 134, 10299–10305.
´
´
20 A. Pal, M. Berube and D. G. Hall, Angew. Chem., Int. Ed., 2010,
49, 1492–1495.
30 M. J. S. Dewar and R. C. Dougherty, J. Am. Chem. Soc., 1964,
86, 433–436.
31 H. E. Dunn, J. C. Catlin and H. R. Snyder, J. Org. Chem., 1968,
33, 4483–4486.
32 R. J. Mears, H. E. Sailes, J. P. Watts and A. Whiting, J. Chem.
Soc., Perkin Trans. 1, 2000, 3250–3263.
33 M. Li, H. Ge, R. L. Arrowsmith, V. Mirabello, S. W. Botchway,
W. Zhu, S. I. Pascu and T. D. James, Chem. Commun., 2014,
50, 11806–11809.
21 G. A. Ellis, M. J. Palte and R. T. Raines, J. Am. Chem. Soc.,
2012, 134, 3631–3634.
22 M. C. Y. Chang, A. Pralle, E. Y. Isacoff and C. J. Chang, J. Am.
Chem. Soc., 2004, 126, 15392–15393.
23 B. C. Dickinson and C. J. Chang, J. Am. Chem. Soc., 2008, 130,
9638–9639.
24 M. Hutin, G. Bernardinelli and J. R. Nitschke, Chem.–Eur. J.,
2008, 14, 4585–4593.
´
25 C. Arnal-Herault, A. Pasc, M. Michau, D. Cot, E. Petit and 34 A. Dirksen and P. E. Dawson, Bioconjug. Chem., 2008, 19,
M. Barboiu, Angew. Chem., Int. Ed., 2007, 46, 8409–8413. 2543–2548.
26 Y. Perez-Fuertes, A. M. Kelly, A. L. Johnson, S. Arimori, 35 W. P. Jencks, in Progress in Physical Organic Chemistry, John
S. D. Bull and T. D. James, Org. Lett., 2006, 8, 609–612. Wiley & Sons, Inc., 1964, pp. 63–128.
27 D. A. Tickell, M. F. Mahon, S. D. Bull and T. D. James, Org. 36 A. Adamczyk-Wo´zniak, K. M. Borys, K. Czerwinska,
´
´
´
Lett., 2013, 15, 860–863.
B. Gierczyk, M. Jakubczyk, I. D. Madura, A. Sporzynski and
E. Tomecka, Spectrochim. Acta, Part A, 2013, 116, 616–621.
37 K. Rose, J. Am. Chem. Soc., 1994, 116, 30–33.
This journal is © The Royal Society of Chemistry 2015
Chem. Sci., 2015, 6, 3329–3333 | 3333