Synthesis and X-ray single crystal structure of a bivalent glycocluster

Article abstract of DOI:10.1039/b313934d

The crystal structure of a bivalent glycocluster containing aromatic amides reveals that alkylation of secondary amides alters amide configuration and thus carbohydrate presentation. This also facilitates non covalent interactions (azide-azide, carbonyl-p

Full text of DOI:10.1039/b313934d

Synthesis and X-ray single crystal structure of a bivalent glycocluster
Manuela Tosin, Helge Müller-Bunz and Paul V. Murphy*
Centre for Synthesis and Chemical Biology, Department of Chemistry, Conway Institute of Biomolecular and
Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland. E-mail: paul.v.murphy@ucd.ie;
Fax: +353-1-7162105; Tel: +353-1-7162504
Received (in Cambridge, UK) 3rd November 2003, Accepted 7th January 2004
First published as an Advance Article on the web 28th January 2004
The crystal structure of a bivalent glycocluster containing
aromatic amides reveals that alkylation of secondary amides
alters amide configuration and thus carbohydrate presentation.
This also facilitates non covalent interactions (azide–azide,
carbonyl–pyranose and aromatic–pyranose) and thus carbohy-
drate–carbohydrate stacking.
The carbohydrates stacked and adopted a cis‡ or U-shaped
conformation. Carbohydrate stacking was mediated by non-
covalent interactions (Table 1 and Fig. 3). Selected interatomic
distances that provide evidence for intramolecular van der Waals
interactions and other close contacts are given in Table 1: there
were clear interactions between (i) the oxygen atom of both
pyranoses with aromatic carbon and hydrogen atoms; (ii) the E-syn
2-acetate carbonyl oxygen atom with E-anti pyranose ring protons
and (iii) the two azide groups.
Qualitative NOE data obtained for 6 in D2O or for 9 in CDCl3 do
not provide evidence that the amides are E-anti or E-syn; i.e. there
are no NOEs observed between H-5 and aromatic protons or
between H-4 and aromatic protons as would be expected (the H-5
of the E-anti pyranose was 3.16 Å and the H-4 of the E-syn
pyranose was 2.51 Å from the nearest aromatic protons in the
crystal structure of 7). The observation of both E-syn and E-anti
conformations in the solid state structure of 7 would indicate that
two signal sets of equal intensity should be observed if the structure
was the same in solution. However this is not the case for 7 or 8,
where there is only one major set of signals in the NMR spectra of
each compound. This could be due to both amides preferring to
adopt E-anti conformers in solution (supported by NOE) or that the
rate of E-anti/E-syn interconversion is too rapid to be detected by
NMR. Qualitative NOE data obtained for 7 (CDCl3) and 8 (D2O)
indicate that the E-anti amide is preferred in solution as an NOE
There is little published work concerning the 3D structures of
bivalent or higher order multivalent carbohydrate ligands. Such
ligands1,2 are relevant for the development of inhibitors or
promoters of carbohydrate mediated biological processes.3–11
Interest is not confined to the glycobiology area as applications for
bivalent ligands include modulation of signal transduction12 and as
leads for development of new antibiotics.13 There are recent
indications that multivalent ligands with increased rigidity can have
enhanced affinity and selectivities,14 suggesting that 3D structure–
activity relationships will be interesting. Earlier work15 has led us
to investigate the synthesis of bivalent carbohydrates such as 5–8
whose structure would depend on the conformational and config-
urational preferences displayed by their amides. It was expected
that secondary amides (e.g. 1 where R1 = H) (Fig. 1) would adopt
the Z-configuration whereas it was unclear whether a steric
interaction between the pyranose and the alkyl group would lead to
tertiary amides (R1 = alkyl) preferring to adopt the E-configura-
tion.16 If so then alkylation of the amide would alter the structural
space occupied by the carbohydrates. We are interested in such
bivalent compounds as scaffolding onto which ligands can be
grafted for presentation to receptors. Alterations in the scaffold
structure would also alter presentation of the grafted ligands. The
concept of using carbohydrates as biologically relevant scaffolds
has been introduced and validated previously.17 The synthesis of
bivalent compounds 5–8 is described herein and the structure of
tertiary amide 7 has been determined in the solid state.
The acid 2, prepared from
-glucuronic acid,18 was the starting
D
point for the synthetic work (Scheme 1, 2). This was first converted
to the b-azide 3 in three steps: preparation of the acid chloride was
followed by synthesis of the allyl ester and subsequent introduction
of the azide. The protection of the carboxylic acid as an ester was
necessary to preclude formation of the a-azide for reasons that we
have previously reported.18 Removal of the allyl ester protecting
group from 3,19 followed by preparation of the acid chloride 4 and
its reaction with phenylene-1,4-diamine gave 5. Deacetylation of 5
gave 6 whereas alkylation of 5 and deprotection gave the bivalent
tertiary amide 8.
Scheme 1 Reagents and conditions: (i) oxalyl chloride, DMF, CH2Cl2; (ii)
allyl alcohol, C5H5N; (iii) TMSN3, SnCl4, CH2Cl2; (iv) Pd(PPh3)4,
pyrrolidine, MeCN; (v) 1,4-phenylenediamine, C5H5N, CH2Cl2; (vi)
NaOMe, MeOH; (vii) NaH, MeI, DMF.
Crystals suitable for X-ray diffraction were obtained for 7 and
the solid state structure was determined.† One of the amides of 7
was found to be E-anti whereas the other amide was E-syn (Fig. 2).
Fig. 1 Amide structure and nomenclature.
Fig. 2 X-ray single crystal structure of 7.
494
C h e m . C o m m u n . , 2 0 0 4 , 4 9 4 – 4 9 5
T h i s j o u r n a l i s © T h e R o y a l S o c i e t y o f C h e m i s t r y 2 0 0 4

Table 1 Selected interatomic distances in X-ray single crystal structure of
7
Temperature 293(2) K. Wavelength 0.71073 Å. Crystal system, or-
thorhombic. Space group, P212121 (#19). Unit cell dimensions a
11.977(2), b = 15.047(3), c = 21.319(4) Å. Volume 3842.2(12) Å3. Z = 4,
calculated density = 1.367 Mg m23. Absorption coefficient, 0.111 mm21
=
Atom X – Atom Y
Distance/Å
.
F(000), 1656. Crystal size, 0.50 3 0.10 3 0.02 mm. Theta range for data
collection, 1.66 to 19.00 deg. Limiting indices, 210 @ h @ 10, 213 @ k @
13, 213 @ l @ 19. Reflections collected/unique 8199/3077 [R(int) =
0.1058]. Completeness to theta = 19.00, 99.8%. Absorption correction,
numerical max. and min. transmission 0.9978 and 0.9465. Refinement
method, full-matrix least-squares on F2. Data/restraints/parameters
3077/0/225. Goodness-of-fit on F2 0.997. Final R indices [I > 2s(I)] R1 =
0.0947, wR2 = 0.2260. R indices (all data) R1 = 0.1456, wR2 = 0.2455.
Absolute structure parameter fixed at 0.5 to avoid correlation with other
parameters. Largest diff. peak and hole 0.570 and 20.410 e Å23. CCDC
223648. See http://www.rsc.org/suppdata/cc/b3/b313934d/ for crystallo-
graphic data in .cif or other electronic format.
O2A–H1
O2A–H3
O2A–H5
O1A–Hc
O1–Ha
N1–N1A
N1–N2A
O1A–aromatic C2aA
O1A–aromatic C1aA
O1–aromatic C2a
O1–aromatic C1a
2.57 (1)
2.46 (1)
3.01 (1)
2.78 (1)
2.52 (1)
3.22 (2)
3.22 (2)
2.97 (2)
2.85 (2)
3.04 (2)
3.31 (2)
1H-NMR data for 5–8: 5 (300 MHz, CDCl3): d 8.30 (s, 2H, NH), 7.44
(s, 4H, aromatic H), 5.33 (apt t, 2H, J2,3 9.0, J3,4 9.0, H-3), 5.24 (apt t, 2H,
H-4), 4.97 (apt t, 2H, J1,2 8.9, H-2), 4.87 (d, 2H, H-1), 4.15 (d, 2H, J4,5 9.5,
H-5), 2.11, 2.08, 2.03 (each s, each 6H, each COCH3); 6 (300 MHz, D2O):
d 7.55 (s, 4H, Ar H), 4.92 (d, 2H, J1,2 8.8, H-1), 4.16 (d, 2H, J4,5 9.5, H-5),
3.73 (apt t, 2H, J3,4 9.3, H-4), 3.65 (apt t, 2H, J2,3 9.0, H-3), 3.40 (apt t, 2H,
H-2); 7 (300 MHz, CDCl3): d 7.42 (s, 4H, aromatic H), 5.50 (apt t, 2H, J3,4
9.4, H-4), 5.15 (apt t, 2H, J2,3 9.2, H-3), 5.24 (apt t, 2H, H-4), 4.87 (apt t, 2H,
H-2), 4.22 (d, 2H, J1,2 8.3, H-1), 4.11 (d, 2H, J4,5 9.2, H-5), 3.35 (s, 6H,
NCH3), 2.02 (2s, 12H, COCH3), 2.00 (s, 12H, COCH3); 8 (300 MHz, D2O):
d 7.55 (s, 4H, Ar H), 4.53 (d, 2H, J1,2 8.3, H-1), 4.04 (d, 2H, J4,5 9.7, H-5),
3.81 (apt t, 2H, J3,4 9.3, H-4), 3.38 (s, 3H, NCH3), 3.37 (overlapping signals,
8H, H-2 and NCH3), 3.28 (apt t, 2H, J2,3 9.0, H-3).
‡ Cis is defined as the carbohydrate groups being on the same side of the
plane defined by the aromatic ring. One referee referred to it as U-
shaped.
1 Y. V. Lee, R. R. Townsend, M. R. Hardy, J. Lönngren, J. Arnarp, M.
Haraldsson and H. Lönn, J. Biol. Chem., 1983, 258, 199.
2 M. Mammen, S.-K. Choi and G. M. Whitesides, Angew. Chem., Int. Ed.,
1998, 37, 2754.
3 C. H. Wong, Acc. Chem. Res., 1999, 32, 376.
4 H. Kamitakahara, T. Suzuki, N. Nishigori, Y. Suzuki, O. Kanie and C.-
H. Wong, Angew. Chem., Int. Ed., 1998, 37, 1524.
Fig. 3 Van der Waals surfaces were calculated using Macromodel 8.1 for 7.
Shown are the (a) azide–azide and carbonyl–pyranose proton interactions
and (b) pyranose oxygen–aromatic interactions.
5 P. I. Kitov, J. M. Sadowska, G. Mulvey, G. D. Armstrong, H. Ling, N.
S. Pannu, R. J. Read and D. R. Bundle, Nature, 2000, 403, 669.
6 B. Liu and R. Roy, J. Chem. Soc., Perkin Trans. 1, 2001, 773.
7 S. Andre, R. J. Pieters, I. Vrasidas, H. Kaltner, L. Kuwabara, F. T. Liu
and R. M. J. Liskamp, Chem. Bio. Chem., 2001, 2, 822.
8 L. L. Kiessling and N. L. Pohl, Chem. Biol., 1996, 3, 71.
9 G. Kretzschmar, U. Sprengard, H. Kunz, E. Bartnik, W. Schmidt, A.
Toepfer, B. Horsch, M. Krause and D. Seiffge, Tetrahedron, 1995, 51,
13015.
10 J. C. Sacchettini, L. G. Baum and C. F. Brewer, Biochemistry, 2001, 40,
3009.
11 J. B. Corbell, J. L. Lundquist and E. J. Toone, Tetrahedron: Asymmetry,
2000, 11, 95.
12 J. D. Klemm, S. L. Schreiber and G. R. Crabtree, Annu. Rev. Immunol.,
1998, 21, 418–422.
13 J. H. Rao and G. M. Whitesides, J. Am. Chem. Soc., 1997, 119,
10286–10290.
14 I. Vrasidas, S. Andre, P. Valentini, C. Bock, M. Lensch, H. Kaltner, R.
M. J. Liskamp, H. J. Gabius and R. J. Pieters, Org. Biomol. Chem., 2003,
1, 803–810.
crosspeak is observed between H-5 and aromatic protons but not
between the methyl group and H-4 or H-5. An NOE enhancement
between H-4 and aromatic proton would be expected if there was a
significant population of E-syn in solution and it would be expected
to be stronger than that observed between H-5 and the aromatic
protons based on distances observed in the solid state structure
(provided above); this NOE was not observed. The existence of
both E and Z isomers would be expected to be detected by the
1
presence of at least two signal sets in the H-NMR as has been
observed for diastereomeric tertiary amides previously.18 The
major set of signals observed for 7 and 8 is assigned to the EE
isomer. It is not evident from the NMR spectra of 7 or 8 if a cis or
U-shaped conformation where both amides are E-anti is the only
structure that exists in solution. A trans or S-shaped conformation
would be possible and calculations (Macromodel 8.1) indicate it is
a low energy conformation.
15 P. V. Murphy, H. Bradley, M. Tosin, N. Pitt, G. M. Fitzpatrick and W.
K. Glass, J. Org. Chem., 2003, 68, 5693 and cited references.
16 R. Yamasaki, A. Tanatani, I. Azumaya, S. Saito, K. Yamaguchi and H.
Kagechika, Org. Lett., 2003, 5, 1265 and cited references.
17 R. Hirschmann, K. C. Nicolaou, S. Pietranico, J. Salvino, E. Leahy, P.
A. Sprengeler, G. Furst, A. B. Smith, C. D. Strader, M. A. Cascieri, M.
R Candelore, C. Donaldson, W. Vale and L. Maechler, J. Am. Chem.
Soc., 1992, 114, 9217.
In summary, amide modification in these bivalent structures
alters amide configuration and thus carbohydrate presentation. A
consequence is that non-covalent interactions are facilitated and
observed in the solid state.
Notes and references
†
Crystal data and structure refinement for 7. Crystals were obtained
18 M. Tosin and P. V. Murphy, Org. Lett., 2002, 4, 3675.
19 H. Kunz and H. Waldmann, Angew. Chem., Int. Ed., 1984, 23, 71.
from CH2Cl2 and petroleum ether (1 : 3). C32H38N8O16. M = 790.70.
C h e m . C o m m u n . , 2 0 0 4 , 4 9 4 – 4 9 5
495