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Letter
A Pair of Stereodynamic Chiral Benzylicaldehyde Probes
for Determination of Absolute Configuration of Amino
Acid Residues in Peptides by Mass Spectrometry
Lin Wang, Zhe Jin, Xiayan Wang, Su Zeng, cuirong sun, and Yuanjiang Pan
Anal. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.analchem.7b03804 • Publication Date (Web): 24 Oct 2017
Downloaded from http://pubs.acs.org on October 25, 2017
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Analytical Chemistry
A Pair of Stereodynamic Chiral Benzylicaldehyde Probes for Determination of Absolute
Configuration of Amino Acid Residues in Peptides by Mass Spectrometry
Lin Wang,†,‡,§ Zhe Jin,§ Xiayan Wang,‡ Su Zeng,† Cuirong Sun,†,* Yuanjiang Pan§,*
†
College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
Department of Chemistry and Chemical Engineering, Beijing University of Technology, 100124, Beijing, China
§
Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang China
‡
ABSTRACT: This paper describes a simple method to determine the absolute configuration of amino acids residues in peptides by
mass spectrometry using a newly developed pair of mass-tagged chiral probes without the requirement of reference standards. A
pair of benzylicaldehyde probes, 1-(S)-1H in S configuration and 2-(R)-2D in deuterium-labeled R configuration with the ratio of
1:1, were synthesized for in-situ condensation with amino acid residues and transformed into a pair of stereodynamic imine
products. The characteristic intensity difference observed in mass spectrometry can be used to determine the absolute configuration
and to quantify the enantiomeric composition of chiral amino acid residues. Significant chiral recognition ability was achieved for
eighteen natural chiral amino acids and for one β-amino acid by comparing the ion intensity ratio of imine products I[1-(S)-1H -AA]- to
I[2-(R)-2D-AA]-. For 16 kinds of amino acids, the L form of the amino acids was more reactive with 1-(S)-1H, while D configuration
amino acids preferred to react with 2-(R)-2D. However, for three kinds of amino acid, the opposite result was obtained. The
configurations of the residues in the peptides, Phe-Tyr-Ala, D-Phe-Tyr-Ala, Val-Pro-Phe-D-Leu-Met, Val-Pro-Phe-Leu-D-Met, as
well as in a natural peptide with unknown chirality were determined by acid hydrolysis followed by the present method. In addition,
molecular modeling results illustrate that the recognition process is mainly controlled by kinetic factors. Using the new probes
coupled with a mass spectrometry approach avoids time-consuming workup and separation steps. We expect that the probes could
be applied as tools to determine the absolute configuration of amino acid residues in proteins in future research.
Chiral molecules have attracted considerable attention from
organic and pharmaceutical chemists. Peptides and their basic
amino acid units (AA) are especially interesting because they
are important for the biological functions and activities. Damino acid-containing peptides share the same sequences with
their all-L isomers. But in many cases, the conversion of the
amino acid from the L to D form within peptides and proteins
induces peculiar folding of the peptides, increases their
structural diversity and generally results in modified biological
activity. One of the most elegant examples of protein chirality
and its relation to functionality was provided by Kent et al.1
They demonstrated that D-HIV protease retained activity, but
the enzyme specificity was limited to the substrates and
inhibitors of a chirality opposite to the natural L-form. Besides,
D-amino acids have been identified in bacterial cell wall,2
cone snails,3- 4 and some mammals.5-6 Isomerized aspartyl
residues in β-amyloid peptide Aβ (1-42) at positions 7 and 23
are demonstrated to have relevance in Alzheimer.7 Opioid
peptides, such as natural dermorphin containing a D-Ala
residue, shows better antimicrobial and analgesic activities
than its all L-analog.8 As increasing number of peptides
containing D-amino acids are found exhibiting different
activities compared to peptides containing L-amino acids,
reliable methods that can be used to determine the absolute
configuration of amino acid residues in peptides are highly
desirable.
Sensitive determination of the configurations of amino acid
residues in peptides or proteins remains a challenge, as this
post-translational modification does not induce any change in
molecular mass. A common approach is to hydrolyze the
chiral peptides using acid or enzyme followed by liquid
chromatography (LC) 9 or capillary electrophoresis (CE)10- 11
by comparing the migration time to the standard. Marfey’s
reagent coupled with LC-MS is one of the most extensively
used method for the determination of the enantiomeric purity
of amino acids, short peptides and drug compounds containing
amine groups.12 This method has enough reproducibility and
accuracy for quantitative analysis. The reaction often takes
one to two hours under mild alkaline conditions and needs to
be protected from light. Meanwhile, the choice of the
stationary phase, internal standard and data interpretation
method can cause a lot of variability. Tandem mass
spectrometry (MS/MS) can also be used to characterize
peptides containing D-amino acids, as peptides with D-amino
acid substitutions often display different collision active
dissociation behaviors13-16 or electron capture dissociation
patterns.17-18 Most MS/MS-based approaches introduce a
functional group for the peptide epimers to better discriminate
between them. A kinetic method described by Cooks et al,
which is based on the dissociation of metal-bound trimeric
complex ions of peptide epimers, allows for good
discrimination.19-21 Sachon et al. demonstrated that acetylation
is an easy protocol for the differentiation of peptide containing
a D-residue close to the N-terminus by matrix-assisted laser
desorption ionization time-of-flight (MALDI-TOF-TOF) mass
spectrometry.22 With this method, Sweedler et al successfully
distinguished
endogenous
D-amino
acid-containing
neuropeptides from individual neurons.23 An alternative
strategy is to label the peptides with a chromophore, and then
to use radical-directed dissociation (RDD) to produce different
backbone dissociation product ions. This method achieves
high chiral recognition values and has the advantage of the
greatest flexibility in terms of charge state selection.24-26 In
addition, the combination of hydrogen/deuterium exchange
and tandem MS was also reported to identify the racemization
sites in immunoglobulin protein.27 Such MS-based approaches
exhibit high sensitivity and good reproducibility. However,
they are not suitable for the analysis of compounds with
unknown chirality, since standards are required to validate the
observed fragmentation pattern. Therefore, it is essential to
develop a fast and sensitive MS-based strategy to characterize
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the absolute configuration of individual amino acid residues in
unknown peptides without using standards.
Figure 1. Structures of the probes.
Chemical derivatization, especially using probes with isotope
labeling, has been proven to be an efficient approach for the
identification of small chiral molecules in complicated
matrixes. 28-30 Herein, a pair of mass-tagged chiral
benzylicaldehyde probes, 1-(S)-1H and 2-(R)-2D, was designed
for determining the absolute configuration of amino acid
residues in peptides, with several structural features shown in
Figure 1. The rationale for the design of these two probes is as
follows. First, the salicylaldehyde ring (the presence of an
adjacent phenol moiety) in the stereodynamic probe can
accelerate the condensation reaction between the formyl unit
and amino group, facilitating efficient enantiomer
recognition.31 Second, the proline unit is an effective skeleton
for designing chiral selectors because of its non-rotational
chiral center. Third, the formation of an imine results in new
stereochemical bias. As we demonstrated below, the pair of
1
H/2D mass-tagged probes is beneficial for the direct
determination of the configuration in one mass spectrum when
the S and R probes are presented in a 1:1 ratio.
For the reaction, a total volume of 500 µL of anhydrous
acetonitrile containing 10 µmol of the probes mixture [1-(S)1
H and 2-(R)-2D, 1:1] and 1 µmol of phenylalanine (Phe) was
stirred at room temperature. The derivatization process is
simple with mild reaction conditions and does not require any
special equipment. A typical full scan mass spectrum for the
analysis of Phe is depicted in Figure 2. A condensation
reaction occurred between Phe and the probes resulting in the
loss of one H2O and the appearance of two product ions at m/z
469 and 474, corresponding to the pair of imines. Interestingly,
the intensity of the ion at m/z 469 (S, S) was higher than that
of the ion at m/z 474 (S, R) for L-Phe (Figure 2B). In contrast,
for D-Phe (Figure 2C), the result was the opposite, with a
higher intensity observed for m/z 474 (R, R). This finding
suggests that the intensity of product ion is related to the
absolute configuration of the amino acid and the reaction is
controlled by the isomeric differences. It should be noted that
the L-Phe tends to produce the light form of the imine(S, S),
while D-Phe tends to produce the heavy isotope-labeled form
of the imine (R, R).
To understand the underlying interactions that cause large
differences in chiral selectivity, reaction rate measurements
were conducted. For kinetic measurements, 1-(S)-1H and 2(R)-2D probes were allowed to react with either L or D Phe for
different time points. Flow injection mass spectra were
recorded to obtain the conversion rate by integrating the imine
peak areas. The changes in the relative amounts of imine
products reflect the different rate constants, which are used to
define the configuration of the starting material according to
the rate difference. It was found that L-Phe reacts faster with
1-(S)-1H than with 2-(R)-2D by a ratio of 6.5, while D-Phe
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prefers to react with 2-(R)-2D by a ratio of 5.9 compared to 1(S)-1H (Figure S26 in the Supporting Information). The results
demonstrated that the pair of probes has stereodynamic
selectivity when reacting with chiral amino acids.
Subsequently, 1-(S)-1H probe was allowed to react with D-Phe
for 120 min to confirm that the imine product (S, R) was
formed. Then probe 2-(R)-2D was added and the imine
products were detected at different time points including 0, 10,
20, 30, 40, 50 and 60 min. Chiral recognition ability (CR) was
defined as the ratio of ion intensity of two imine products I[11
2
(S)- H -AA] to I[2-(R)- D-AA] . The results showed that the amount of
the newly generated (R, R) imine increase quickly and
exceeded the (S, R) imine, until the CR remained stable at
approximately 0.45. The complimentary reaction was started
with probe 2-(R)-2D and 1-(S)-1H was added second. Only a
small amount of newly generated (S, R) imine was detected
(Figure S27 in the Supporting Information). All the results
suggest that the reaction is controlled by kinetic selectivity and
that the intensity of the product ion is related to the absolute
configuration of the amino acid.
Figure 2. (A) The enantioselective condensation reaction
between probes and L-Phe, (B) mass spectra of imines
produced from L-Phe with probes, (C) mass spectra of imines
produced from D-Phe with probes.
Molecular modeling served as a supplementary tool to
understand the stoichiometry of the imines and predict the
chiral stereodynamic behavior. L-Phe was chosen as the
sample to test the chiral selectivity of the pair of probes. The
lowest docking energies represent the most favorable
conformation. Figure 3 depicts representative conformers of
the imine products of L-Phe with 1-(S)-1H and 2-(R)-2D.
Although calculation at the B3LYP/6-31 level cannot give
accurate binding energy information, it is still possible to
obtain the conformations with the lowest energies which are
consistent with experimental results. The result shows that
both the transition state energy and the product energy for the
reaction of 1-(S)-1H and L-Phe are lower than that of the
reaction of 2-(R)-2D and L-Phe, which demonstrates a kinetic
reaction mechanism. Meanwhile, there is an intramolecular
hydrogen bond between the carboxylic acid of Phe and the
carbonyl unit of probe in 1-(S)-1H-L-Phe product. This
effectively shortens the distance between the carboxylic acid
proton Ha and the chiral proton Hb in the probe to 3.86 Å. In
the case of imine resulting from the reaction of L-Phe with 2(R)-2D, no intramolecular hydrogen bond was observed, and
the distance between proton Ha and Hb was 7.67 Å. Taken
together, a kinetically controlled process with a lower-energy
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Analytical Chemistry
transition state and stable product was responsible for the
stereodynamic chiral recognition.
Next, CR for all chiral amino acids were determined except
proline (Pro), which is a secondary amine and cannot react
with the probes. The CR values are shown in Table 1. The L
and D forms of all the 18 chiral amino acids and a β-amino
acid (pregabalin, Pre) could be distinguished based on
different CR values. High chiral selectivity was achieved for
Valine (Val), Isoleucine (Ile), Leucine (Leu), and Methionine
(Met) with 11.1, 10.09, 10.0 and 8.33 for the L configurations
and 0.09, 0.1, 0.1, 0.15 for the D forms, respectively. It
appears that the CR value increases for amino acids with
nonpolar side chains compared to those with polar side chain.
This method presented relatively low chiral selectivity for Asp
and pregabalin with CR values of 1.35 and 1.28, respectively.
Meanwhile, for amino acids in entries 1 to 16, the CR values
reflected the preferred formation of homochiral product. This
means that when CR > 1, the analyte tended to react towards
1-(S)-1H and it would be in the L configuration, while in the
case of CR﹤1, it would be in the D configuration. In contrast,
amino acids in entries 17 to 19 tended to form heterochiral
products, and their configurations could also be identified by
comparing the light and heavy imine intensity peaks in the
spectra. In addition to the high selectivity, the probes are also
sensitive as the limit detection for analysis of Leu is
approximately 10 pg mL-1 using the homemade chip-MS
device shown in Figure S31-32 in the Supporting Information.
Figure 3. The stable structure of transition state and the
products from L-Phe with 1-(S)-1H and 2-(R)-2D. Calculations
were performed at B3LYP/6-31 level.32
Quantitative analysis, especially when one enantiomer
comprises only a few percent of a mixture, remains a
challenge. The capability of this method for quantitative
analysis was investigated for Phe. L/D ratio were chosen at
100:0, 95:5, 90:10, 75:25, 65:35, 50:50, 35:65, 25:75, 10:90,
5:95 and 0:100,. Analysis of each sample required only one
measurement of a single MS spectrum. A linear relationship
between ee and ln(I[1-(S)-1H-Phe]-/I[2-(R)-2D-Phe]-.) was obtained with
a correlation coefficient (r2) of 0.9916. Similar results were
obtained for Leu and Val with correlation coefficients of
0.9912 and 0.9874, respectively, indicating that the method
has the potential to quantify the relative percentage of the L
and D forms in a mixture (Figure S28 in the Supporting
Information).
D-Amino acids are promising candidates as biomarkers for
several diseases including chronic kidney disease and
Alzheimer disease.33- 34 A sensitive and feasible analysis
method for determining trace D amino acids from a mixture is
essential. In the following step, the probes were employed to
determine the absolute configuration of individual amino acids
from an amino acid mixture. A mixture containing Ala, Val,
Leu, Met, Phe and Trp of “unknown” configuration was
analyzed using the above-described method. Each chiral
amino acid formed a pair of imine products that could be
detected by mass spectrometry. The high abundance ions at
m/z 393, 421, 435, 453, 469 and 508, were observed as shown
in Figure 4 (A). The CR values suggested that all the six
amino acids components were in the L configuration. Mixtures
containing 5% D-Val were allowed to react with the probes,
and the D-configuration could be clearly identified (Figure
S29 in the Supporting Information).
Table 1. Chiral selectivity of amino acids with probes.
Entry
Amino acid
CR[a]
Amino acid
CR
1
L-Val
11.1
D-Val
0.09
2
L-Ile
10.09
D-Ile
0.10
0.10
3
L-Leu
10.0
D-Leu
4
L-Met
8.33
D-Met
0.15
0.29
5
L-Gln
4.76
D-Gln
6
L-Ala
3.03
D-Ala
0.35
7
L-Lys
3.03
D-Lys
0.31
8
L-Phe
2.86
D-Phe
0.40
9
L-Tyr
2.38
D-Tyr
10
L-Asn
2.22
D-Asn
0.42
0.45
11
L-Glu
2.08
D-Glu
0.55
12
L-Cys
1.85
D-Cys
0.54
13
L-Trp
1.56
D-Trp
0.60
0.65
14
L-Arg
1.53
D-Arg
15
L-Asp
1.35
D-Asp
0.75
0.86
16
L-Pregabalin
1.28
D-Pregabalin
17
L-His
0.31
D-His
3.58
18
L-Ser
0.64
D-Ser
1.70
19
L-Thr
0.71
D-Thr
1.34
[a] CR= I[1-(S)-1H-AA]-/I[2-(R)-2D-AA]-.I represents relative abundance %.
The experiments were carried out in triplicate. Each reaction used a 10fold excess of the pair of reagents and the standard deviations for the
multiple runs are all less than 8 %.
Next, amino acid residues in peptides were analyzed
using this method. As MS has established itself as an
indispensable tool for peptide and protein sequence
analysis using electron-transfer dissociation and
collisional induced dissociation approaches,35-36 we only
focused on determining the configuration of the residues
in this work. A pair of peptides with the same amino acid
sequences but different configurations was analyzed. To
determine the configuration of each amino acid residue,
the peptide samples were first hydrolyzed with hot 6 M
HCl37 and then neutralized with Na2CO3. Hydrolysis
products were allowed to react with 10-fold excess of the
probes followed by MS analysis. The results for the
tripeptides pairs are shown in Figure 4 (B) and (C).
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Figure 4. The full scan mass spectrum analysis of (A) amino acid mixtures, (B) Phe-Tyr-Ala, (C) D-Phe-Tyr-Ala, (D) Val-Pro-PheD-Leu-Met, (E) Val-Pro-Phe-Leu-D-Met, and (F) Tyr-D-Ala-Phe-Gly-Tyr-Pro-Ser-NH2. The higher abundant imine products are
marked with star style.
was of L configuration and another was D, the ratio would be
Both spectra displayed similar peaks at m/z 393, 398, 469, 474,
approximately 1. The high abundance ion at m/z 469 resulting
485, and 490, and the only difference was the ratio of the peak
from Phe and 1-(S)-1H, indicated that Phe is of the L
configuration. Another mass-tagged ion pair at m/z 409 and
abundances for m/z 469 to 474. When compared with the CRs
414 was the imine products from the reaction of Ser with the
of the free amino acids in Table 1, the configurations of Tyr
and Ala residues in the two peptides were determined to be Lprobes, with CR ﹤ 1 indicating that the Ser residue is also of
configuration. Phe was in the L configuration in Figure 4 (B)
the L configuration. In the peptide, Pro is a secondary amine,
and the D configuration in Figure 4 (C).
which could not be identified with the probes. There is also no
To further verify the feasibility of the method, two “unknown”
need to identify the chirality of Gly because it is an achiral
peptides without L control peptides were tested. For the Valamino acid. Thus, we were able to distinguish the
Pro-Phe-D-Leu-Met peptide, the results clearly showed five
configuration of each amino acid residue within the peptide on
strong peaks at m/z 421, 440, 453 and 469 (Figure 4D). The
the basis of the CR value, without comparing to other peptides
ratio of ion intensity of 435 to 440 is ﹤1, indicating that the
or standards.
Leu residue in the peptide is of the D configuration, and the
In summary, we have developed a pair of stereodynamic
other amino acid residues were all of the L configuration. In
benzylicaldehyde probes that exhibit capability not only for
the case of Val-Pro-Phe-Leu-D-Met, the ion at m/z 458 was
the analysis of chiral amino acid mixtures, but also for the
much higher than the ion at m/z 453, indicating that the Met
determination of the configurations of amino acid residue in
residue is of the D configuration, and the other amino acids
chiral peptides based on the ion abundance ratios of imine
such as Val, Phe and Leu were all of the L configuration
products
in a single mass spectrum. The probes produce a pair
(Figure 4E). It should be mentioned that Pro does not react
of
distinct
mass spectrometry signals upon condensation with
with the pair of probes. Racemization of amino acids must be
amino
acid
residues in peptides which can be correlated to the
considered in the process of acid hydrolysis. Acid hydrolysis
substrate
chirality
and quantification of enantiomer. They were
of Val-Pro-Phe-D-Leu-Met with 6M HCl of in H2O and 6M of
found
to
work
well
with both α-amino acids and β-amino acids.
DCl in D2O were investigated. If isomerization occurred, a
deuterium-labeled amino acid would be produced in 6M of
Most importantly, this straightforward strategy is capable of
DCl with a molecular mass 1 Da more than that produced in 6
determining the absolute configurations of amino acid residues
M of HCl. The results demonstrated that isomerization under
in peptides without using standards. In comparison with
acidic conditions did not occur and had no influence on the
Marfey’s reagent, analysis of residue configurations using the
chiral determination (Figure S30 in the Supporting
new probes is accurate with minimal sample handlings, and
Information). Therefore, each of the configurations of the
without time-consuming workup and separation steps. The
constituent amino acids can be determined by this practical
probes
still need to be improved as they may lose some
strategy without using standard.
racemic
site information when used to analyze large proteins
Furthermore, a nature peptide dermorphin (Try-D-Ala-Phein
complex
biological samples. The development of other new
Gly-Tyr-Pro-Ser-NH2) containing a D-Ala residue was
and
versatile
probes for detecting the configurations of
analyzed using this strategy. Ala is the smallest chiral amino
acid, and its chirality is difficult to determine. As described
residues in proteins remains an active area of research in our
above, D-Ala prefers to react with probe 2-(R)-2D to produce
laboratory.
the labeled imine, which is 5 mass units larger than the
unlabeled imine. As shown in Figure 4 (F), the expected peaks
of the derivative from the Ala residue can be clearly detected
ASSOCIATED CONTENT
at m/z 393 (S, R) and 398 (R, R), and the intensity of the ion at
Supporting Information
m/z 398 was higher than that of m/z 393, confirming the D
The Supporting Information is available free of charge on the
configuration. In the meantime, for the Tyr analysis, the peak
ACS Publications website.
at m/z 485 was higher than the peak at m/z 490, which means
that both Tyr residues had L configurations, because if one
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Synthesis and derivative procedure and other supporting figures
and tables (PDF).
AUTHOR INFORMATION
Corresponding Author
* Cuirong Sun; Telephone (86) 571-88208868; Fax (86) 57188208868; E-mail: suncuirong@zju.edu.cn
* Yuanjiang Pan; Telephone (86) 571-87951285; Fax (86) 57187951285; E-mail: panyuanjiang@zju.edu.cn
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENT
This work was supported by the National Natural Science
Foundation of China (81230080, 21472171, 21605002).
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