N, N'-carbonyldiimidazole-mediated DBU-catalyzed one-pot synthesis of urea-tethered glycosyl amino acids and glycoconjugates

Article abstract of DOI:10.1055/s-0030-1259958

An efficient, mild, simple, and alternative one-pot protocol for the synthesis of urea-tethered glycosyl amino acids mediated by N,N'- carbonyldiimidazole employing DBU as a catalyst is described. This protocol is also extended for the synthesis of urea-tethered disaccharides and oligosaccharides. Georg Thieme Verlag Stuttgart - New York.

Full text of DOI:10.1055/s-0030-1259958

1160
LETTER
N,N¢-Carbonyldiimidazole-Mediated DBU-Catalyzed One-Pot Synthesis of
Urea-Tethered Glycosyl Amino Acids and Glycoconjugates
Synthesis of
U
rea-
.
T
ethered Gly
V
cosyl
A
mino
A
cid
.
s
and
Glyco
S
conjugates ureshbabu,* Basavaprabhu
Peptide Research Laboratory, Department of Studies in Chemistry, Central College Campus, Dr. B. R. Ambedkar Veedhi, Bangalore Uni-
versity, Bangalore, 560 001, India
E-mail: hariccb@hotmail.com; E-mail: sureshbabuvommina@rediffmail.com; E-mail: hariccb@gmail.com
Received 8 November 2010
ates, and to avoid the use of carbamoyl chlorides, our
Abstract: An efficient, mild, simple, and alternative one-pot proto-
group recently demonstrated the synthesis of urea-teth-
col for the synthesis of urea-tethered glycosyl amino acids mediated
by N,N¢-carbonyldiimidazole employing DBU as a catalyst is de-
scribed. This protocol is also extended for the synthesis of urea-teth-
ered glycopeptides employing Deoxofluor/TMSN315a and
thioureido-glycopeptides using Bt-CS-Bt.15b In a continu-
ered disaccharides and oligosaccharides.
ation of our interest in the area of glycopeptidomimetics,
we have sought an alternative protocol for the synthesis of
urea-tethered neoglycoconjugates employing N,N¢-carbo-
nyldiimidazole (CDI).
Key words: urea-tethered glycoconjugates, N,N¢-carbonyldiimida-
zole, DBU, base catalysis
CDI16 was introduced as a coupling agent in peptide syn-
thesis and is widely used for amide bond formation. It is
also used in the synthesis of glycosides and their deriva-
tives on solid phase and in reactions involving transfer of
a carbonyl group, imidazole group, and coupling between
different functional groups under various conditions.
Protein glycosylation1 is a ubiquitous process and is the
most complex protein modification.2 Generally, glycosy-
lation involves either the w-hydroxy group of serine3 or
carboxamide functionality of asparagine.4 Glycopeptide
mimetics involving O- and N-glycosyl linkages have been
replaced by a variety of C–C, C–S, and other heteroatom
bonds as well as heterocycles.5 The urea functionality is
one of the most important surrogates for the natural N-gly-
cosyl moiety. This group is of paramount importance in
the synthesis of a library of neoglycoconjugates which are
of biological and pharmaceutical significance.6 Ap-
proaches for the construction of urea-tethered neoglyco-
conjugates are relatively rare. The known strategies
involve either the reaction of a glycosyl amine or amino
sugar with isocyanates7 or their synthetic equivalents such
as carbamates8 and trichloroacetimidates.9 Other methods
include addition of H2O to the glycosyl carbodiimides10 or
by the reaction of sugar isocyanates with amines.11,12 One-
pot protocols have also been reported wherein the in situ
generated sugar isocyanate will react with an appropriate
amine.13 The use of protected glycosyl isocyanates is
widespread. Glycosyl isocyanates have been prepared
through various protocols employing a plethora of re-
agents and conditions which inherently suffer from cer-
tain limitations.12 A method involving the oxidation of
glycosyl isocyanide is a multistep protocol. Acylation of
amines with acid chlorides14 is one of the most important
classes of functionalization reaction used in the prepara-
tion of ureas but the carbamoyl chlorides require phos-
gene for their synthesis, and their relative instability does
not render them suitable for long-term storage.
In an initial study, 2,3,4,6-tetra-O-acetyl-b-D-glu-
cosamine, prepared according to the literature, was treated
with valine methyl ester in anhydrous CH2Cl2, in the pres-
ence of CDI and N-methylmorpholine (NMM) at 0 °C.
The reaction was found to be sluggish and yielded only
20% of the desired product after 24 hours. This is possibly
due to the fact that the intermediate carbamoyl imidazole
is much less reactive towards nucleophilic attack and re-
quires activation as the carbamoylimidazolium salt17 to
effect nucleophilic substitution.
In order to improve the protocol, various bases compatible
with CDI such as triethylamine (Et3N), diisopropylethyl-
amine (DIPEA), 4,4-dimethylaminopyridine (DMAP),
1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) were used
(Table 1). Among them, DBU18 afforded appreciable rate
enhancement with good yields of the desired product
within three hours under mild reaction conditions.
Table 1 Screening of Various Bases for the Synthesis of Urea-Teth-
ered Glycoconjugates
Base
Time (h)
Temp
Yield (%)
18
Et3N
12
12
6
0 °C to r.t.
NMM
DIPEA
DMAP
DBU
0 °C to 50 °C 20
0 °C to r.t.
0 °C to r.t.
0 °C
45
40
88
In order to circumvent the inconvenience associated with
the preparation and handling of reactive glycosyl isocyan-
4
3
SYNLETT 2011, No. 8, pp 1160–1164
x
x.
x
x.
2
0
1
1
Advanced online publication: 18.04.2011
DOI: 10.1055/s-0030-1259958; Art ID: D29910ST
© Georg Thieme Verlag Stuttgart · New York
We presume that, in the first step of the reaction, DBU
acts as a non-nucleophilic base, thereby assisting an

LETTER
Synthesis of Urea-Tethered Glycosyl Amino Acids and Glycoconjugates
1161
amine to form the carbamoyl imidazole. In the subsequent
step, DBU behaves as nucleophilic catalyst where it adds
to the carbamoyl imidazole intermediate with the release
of imidazole byproduct.18 The carbamoyl–DBU-linked
intermediate then generates an isocyanate that subse-
quently reacts with the incoming sugar amine resulting in
the formation of the urea (Scheme 1).
O
N
N
N
N
O
CDI
R1
NH2
R1
N
N
N
H
DBU
OR
O
During the course of reaction, an aliquot of reaction mix-
ture was taken and analyzed by IR spectroscopy and was
found to exhibit an absorption peak at nmax = 1670–1685
cm–1 which corresponds to the carbamoyl imidazole. Dur-
ing the second addition of DBU prior treatment with sugar
amine, as monitored through IR, indicated the disappear-
ance of the peak at nmax = 1670 cm–1 with the appearance
of another strong absorption peak at nmax = 2246 cm–1,
confirming the intermediacy of the isocyanate.
N
O
HN
R''O
RO
N
N
H
N
R1
N
H
OR
DBU
OR
O
O
RO
RO
NH2
R1
N
N
OR
H
R1
N
C
O
N+
Finally, IR analysis of the product showed two absorption
peaks at nmax = 1650 cm–1 and 1560 cm–1, which are char-
acteristic of the urea functionality. The structure of the fi-
N
N
1
nal product was confirmed through H NMR and 13C
Scheme 1 Possible mechanism proposed for the synthesis of urea-
tethered glycoconjugates mediated by CDI under DBU base catalysis
NMR analyses. The same protocol was extended to urea-
tethered pseudo-disaccharides and oligosaccharides
which possess diverse biological as well as pharmaceuti-
cal applications.19 The mild reaction conditions employed
in the above-mentioned protocol (Scheme 2) were found
The protocol worked well with the secondary amine of
proline methyl ester (1c), the w-amine of lysine (1f), 2,3-
Dap ester (1d), 2,4-Dab ester (1e), and amines of mono-
and disaccharides 1g–j to yield the corresponding urea-
tethered glycoconjugates in excellent yields (Table 2).
1
to be epimerization-free as evidenced by H NMR and
HPLC analyses.20
OR2
O
O
N
N
R3O
NH2
N
N
OR2
N
N
R2O
O
O
OR2
O
DBU
CDI
DBU
anhyd CH2Cl2
0 °C, 3 h
O
R3O
R2O
R1 NH2
R1
N
N
R1
N
R1
N
N
N
N
H
H
H
H
OR2
N
3a,b,d,g–i R2 = R3 = Ac
3c,e,f R2 = R3 = Bn
OAc
O
AcO
O
3j R2 = Ac, R3
=
AcO
OAc
Scheme 2 Synthesis of urea-tethered glycoconjugates
Table 2 List of Urea-Tethered Glycoconjugates21
Entry
Amine
Urea-tethered glycoconjugate
Yield (%)
OAc
H
H
AcO
AcO
O
N
N
COOMe
1
OAc
92
O
H2N
COOMe
COOMe
1a
3a
OAc
H
H
AcO
O
N
N
COOMe
2
88
AcO
H2N
OAc
O
1b
3b
Synlett 2011, No. 8, 1160–1164 © Thieme Stuttgart · New York

1162
V. V. Sureshbabu, Basavaprabhu
LETTER
Table 2 List of Urea-Tethered Glycoconjugates21 (continued)
Entry
3
Amine
Urea-tethered glycoconjugate
Yield (%)
OBn
H
N
BnO
BnO
O
COOMe
N
COOMe
NHCbz
75
N
H
OBn
O
O
O
1c
3c
OAc
NH2
H
N
H
N
AcO
O
4
82
AcO
COOMe
CbzHN
COOMe
OAc
1d
3d
OBn
NH2
H
N
H
N
BnO
O
COOMe
NHCbz
5
6
7
73
75
86
BnO
CbzHN
COOMe
OBn
1e
3e
OBn
NH2
H
H
BnO
BnO
O
N
N
COOMe
NHBoc
BocHN
COOMe
OBn
O
1f
3f
OAc
OAc
OAc
O
H
N
H
N
AcO
AcO
O
O
AcO
AcO
OAc
OAc
NH2
OAc
OAc
OAc
O
O
1g
3g
OAc
NH2
H
N
H
N
AcO
AcO
O
AcO
O
OMe
OAc
8
77
OAc
O
O
O
O
MeO
O
1h
3h
OAc
OAc
O
OAc
OAc
OAc
O
O
OAc
OAc
AcO
H
H
N
9
70
66
AcO
AcO
O
O
AcO
N
O
OAc
OAc
O
AcO
NH2
OAc
OAc
OAc
OAc
O
1i
3i
OAc
OBn
O
OBn
OBn
OAc
O
OBn
O
O
O
AcO
OBn
OBn
BnO
BnO
H
H
AcO
O
10
O
AcO
O
N
N
O
BnO
NH2
OAc
OBn
OBn
OBn
OAc
OBn
OBn
O
1j
3j
In conclusion, we have developed an efficient, mild, and Acknowledgment
alternative one-pot protocol for the synthesis of urea-teth-
We thank the Department of Science and Technology (DST) (Grant
No. SR/S1/OC-26/2008) New Delhi, India for financial support.
ered glycoconjugates mediated by CDI in the presence of
DBU as catalyst. This circumvents the isolation of reac-
tive glycosyl isocyanates and affords high purity products
in excellent yields under mild conditions.
Synlett 2011, No. 8, 1160–1164 © Thieme Stuttgart · New York

LETTER
Synthesis of Urea-Tethered Glycosyl Amino Acids and Glycoconjugates
1163
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(20) The epimerization study was carried out by 1H NMR and
HPLC analyses of the glycosyl ureas 3k and 3l synthesized
by the protocol described below.
Glucosamine (2a),was converted into two epimeric glycosyl
ureas 3k and 3l as outlined in Scheme 3 by coupling
separately with L-Ala-OMe (1k) and D-Ala-OMe (1l),
respectively. An equimolar mixture of these two epimers
was obtained by coupling with the racemic mixture of L- and
D-Ala-OMe. The 1H NMR spectrum of 3k and 3l contained
distinct methyl group doublets at d = 1.52, 1.54 ppm and d =
1.55, 1.58 ppm, respectively; whereas the epimeric mixture
showed CH3 group signals at d = 1.51, 1.54 ppm and d =
1.56, 1.59 ppm corresponding to two doublets. Additionally,
HPLC analysis of the pure L- and D-Ala-OMe-derived
glycosyl ureas 3k and 3l showed single peaks at different
tR values i.e., tR = 9.23 and tR = 9.61 (method: gradient 0.1%
TFA H2O–MeCN; MeCN 30–100% in 30 min),
respectively.
L-isomer
OAc
O
H2N
COOMe
1k
H
N
H
N
AcO
AcO
COOMe
COOMe
OAc
O
OAc
O
O
CDI, DBU
3k
AcO
AcO
NH2
anhyd CH2Cl2
0 °C
OAc
O
OAc
H
N
H
N
2a
AcO
AcO
D-isomer
OAc
3l
H2N
COOMe
1l
Scheme 3
Synlett 2011, No. 8, 1160–1164 © Thieme Stuttgart · New York

1164
V. V. Sureshbabu, Basavaprabhu
LETTER
(21) General Procedure for the Preparation of 3a–f
To a suspension of N,N¢-carbonyldiimidazole (1.2 mmol) in
anhydrous CH2Cl2 (10 mL) was added amino acid ester (1.0
mmol) and DBU (0.2 mmol), and the reaction mixture was
stirred at ambient temperature for 6–7 min. The glycosyl
amine (1.0 mmol) and DBU (0.3 mmol) was then added at
0 °C, and the resulting mixture was stirred for about 3 h at
0 °C. After completion of the reaction, the resulting solution
was diluted with CH2Cl2 (10 mL) and washed with citric acid
(2 × 10 mL), H2O (2 × 10 mL), and brine (10 mL). The
organic layer was dried over anhyd Na2SO4, filtered, and
evaporated to obtain the crude product. Pure urea-tethered
glycoconjugate was obtained as a solid on column
chromatography eluting with EtOAc–hexane (4:6).
The procedure followed for the synthesis of 3g–j is similar
to that described above with the only difference being the
use of 0.6 mmol DBU during the addition of the second
amine component.
Hz, 6.0 Hz, 1 H), 4.88 (t, J = 9.6 Hz, 1 H), 5.10 (t, J = 9.4 Hz,
1 H), 5.15 (t, J = 9.3 Hz, 1 H), 5.12–5.22 (br, 1 H), 5.33 (d,
J = 9.6 Hz, 1 H), 5.40–5.53 (br, 1 H), 7.04–7.16 (m, 2 H),
7.22– 7.35 (m, 3 H) ppm. 13C NMR (75 MHz, CDCl3): d =
21.0, 21.2, 38.0, 53.1, 54.5, 62.6, 69.5, 70.2, 73.2, 74.3, 81.6,
128.4, 129.1, 130.3, 136.8, 156.5, 169.8, 170.1, 171.0,
171.6, 173.8 ppm.
Spectroscopic Data for Compound 3h
White solid. IR (KBr): nmax = 1669, 1558, 1229 cm–1. 1H
NMR (400 MHz, CDCl3): d = 1.31 (s, 3 H), 1.49 (s, 3 H),
2.00 (s, 3 H), 2.02 (s, 3 H), 2.06 (s, 3 H), 2.09 (s, 3 H), 2.14
(s, 3 H), 3.32 (dd, J = 14.6, 5.8 Hz, 1 H), 3.41 (s, 3 H), 3.52
(ddd, J = 15.0, 5.8, 2.6 Hz, 1 H), 3.78 (ddd, J = 10.8, 5.6, 2.4
Hz, 1 H), 3.86 (ddd, J = 10.0, 4.2, 2.2 Hz, 1 H), 4.18 (dd,
J = 12.6, 2.0 Hz, 1 H), 4.20 (d, J = 5.8 Hz, 1 H), 4.24 (dd,
J = 7.6, 5.5 Hz, 1 H), 4.35 (dd, J = 12.6, 4.0 Hz, 1 H), 4.90
(dd, J = 10.5, 7.5 Hz, 1 H), 4.93 (t, J = 9.5 Hz, 1 H), 4.97 (s,
1 H), 5.12 (t, J = 6.0 Hz, 1 H), 5.15 (t, J = 9.7 Hz, 1 H), 5.19
(t, J = 9.4 Hz, 1 H), 5.36 (t, J = 9.4 Hz, 1 H), 5.47 (br d,
J = 9.5 Hz, 1 H) ppm. 13C NMR (100 MHz, CDCl3): d =
20.9, 21.5, 21.9, 26.8, 27.9, 42.4, 57.3, 63.9, 68.6, 70.5, 72.1,
73.3, 75.8, 76.7, 77.9, 82.1, 99.6, 110.8, 158.2, 170.4, 170.9,
172.0, 173.9, 174.5 ppm.
Spectroscopic Data for Compound 3a
White solid. IR (KBr): nmax = 3385, 1748, 1655, 1560, 1231
cm–1. 1H NMR (300 MHz, CDCl3): d = 2.00 (s, 3 H), 2.03 (s,
3 H), 2.05 (s, 3 H), 2.07 (s, 3 H), 3.06 (d, 2 H), 3.69 (s, 3 H),
3.77 (ddd, J = 10.0, 4.3, 2.1 Hz, 1 H), 4.10 (dd, J = 12.3, 1.8
Hz, 1 H), 4.29 (dd, J = 12.3, 4.6 Hz, 1 H), 4.71 (q, J = 7.0
Synlett 2011, No. 8, 1160–1164 © Thieme Stuttgart · New York

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