1. GMR Literature Highlights 03-10-2013
Samuele Staderini

2. Molecular recognition of
carbohydrates
• Key role in biological processes
• Dedicated classes of biomolecules (lectins, antibodies…) govern
interaction between living cells and other cells or pathogens
• Specific recognition of epitopes of saccharidic chains (usually
terminal mono- or oligosaccharides)
Development of articial biomimetic
receptors to:
1. Mimic the natural ones
2. Understand recognition mechanism
3. Develop new therapeutic and
diagnostic tools
The sugar code: fundamentals of glycosciences (Ed.: H.-J.Gabius), Wiley.VCH, Weinheim, 2009
Carbohydrates in chemistry and biology, Part I, Vol.2 (Eds.: B.Ernst, G.W. Hart, P. Sinaÿ), Wiley-VCH,
Weinheim, 2000

3. Mannosides are recognized by several lectins and are involved in
infections caused by high-risk pathogenes like:
• Yeasts (Candida)
• Bacteria (Tubercolosis)
• Viruses (HIV and Hepatitis HCV)
Recognition of terminal oligomannosides on pathogen surface
enhance potent antiviral activity to:
• Lectins (cyanovirin-N, microvirin, actinovirin)
• Andibodies (2G12, PGT128)
• Natural non-peptidic molecules (benanomicin A, pradimicin A)
Mono-mannosides and
Di-mannosides
Carbohydrates in chemistry and biology, Part II, Vol.4 (Eds.: B.Ernst, G.W. Hart, P. Sinaÿ), Wiley-VCH,
Weinheim, 2000, pp. 533-609

4. Di-mannosides: a relevant
example (HIV infection)
Oligomannose
glycan
Other sugars
Terminal α-
dimannoside motif:
the smaller
fragment required
for lectin
recognition
The binding of the DC-SIGN lectin of immune system dendritic cells
to the viral glycoprotein gp120 on the HIV envelope triggers the
infection of human cells by the virus
R.A.Dwek, Nature, 2007, 446, 1038-1045

5. Mannosides synthetic
receptors
C.Nativi, O.Francesconi, G.Gabrielli, A.Vacca, S.Roelens, Chem. Eur. J., 2011, 17, 4814-4820
Aminopyrrolic tripodal structures
High affinity and
selectivity for
• Polar solvent, but not water
• Octyl chain ensure solubility in polar organic solvents
• Different recognition properties by two enantiomers
Mono-mannosides
Dimannosides: Ditopic structure bridging two units by an
appropriate linker

6. Oct(αMan)αMan
Dimannosides synthesis
C.Nativi, O.Francesconi, G.Gabrielli, A.Vacca, S.Roelens, Chem. Eur. J., 2011, 17, 4814-4820
a) n-octanol,TMSOTf, DCM,
0 C, 15 min, 61%
b) MeONa 1M sol. In MeOH,
RT, 45 min, 95%
c) Compound 2,TMSOTf,
DCM, 0 C, 50 min, 60%
d) MeONa 1M sol. In MeOH,
RT, 1.5h, then H2,
[Pd(OH)2]/C, DCM/MeOH
1:1, RT, 16h, 84%

7. Dimannosides synthesis
Y.Ito,T.Ogawa, Angew. Chem. Int. Ed. Engl., 1994, 33, 1765
IAD: Intramolecular aglycone
delivery
a) n-octanol, DDQ, DCM, RT,
1h
b) DTBMP, AgOTf, SnCl2,
DCM, RT, 3,5h, 72%
c) Compound 2,TMSOTf,
DCM, 0 C, 1h, 63%
d) K2CO3, MeOH, RT, 3h, then
H2, [Pd(OH)2]/C,
DCM/MeOH 1:1, RT, 16h,
71%
Oct(αMan)βMan

8. Synthesis of receptors - 1
a) N-BOC-trans-1,2-diaminocycloexane, MeOH,DCM 1:1, 70°C,
7,5h, then NaBH4, RT, 1h, 78%
b) TFA, DCM, 1.5h, 91%
c) Pyrrole-2,5-dialdehyde, CHCl3, 70°C, 12h, then NaBH4, MeOH,
RT, 1h, 63%

9. Synthesis of receptors - 2
The gem-dimethyl group induced a convenient twisting
of pyrrolic moieties. On the other hand, the single
carbon hinge may impose conformational restrictions

10. Synthesis of receptors - 3
In addition to providing a more flexible linker, the
hydrogen-bonding ability of the aminic group may result
beneficial to the recognition properties

11. Synthesis of receptors - 4
Rigid and non-hydrogen bonding moiety served as
reference to evaluate the impact of hydrogen-bonding
group and the role of size and rigidity of the linker

12. Synthesis of receptors - 5
Replacing diaminocyclohexane fragment with a simple amine
moiety, the narrowest cleft in the receptor set has been obtained
a) NaOAc, DMF, 100°C, 2h, >99%
b) K2CO3, MeOH, RT, 70h, >99%
c) Pyridinium chlorochromate (PCC), DC, RT, 2h, 95%
d) N-BOC-1,2-diaminocyclohexane, DCM, 80°C, 15h, then
NaBH4, MeOH, RT, 3h, >99%
e) TFA, DCM, RT, 3h, 63%

13. Synthesis of receptors - 6
f) Pyrrole-2,5-dicarboaldehyde, CHCl3, RT, 15h, then NaBH4,MeOH,
RT, 1,5h, 96%
g) PhP3, H2O,THF, RT, 15h, 87%
h) Pyrrole-2,5-dicarboaldehyde, CHCl3, RT, 15h, then NaBH4,MeOH,
RT, 1h, 70%

14. Recognition studies
A.Vacca, O.Francesconi, S.Roelens, Chem. Rec., 2012, 12, 544-566

15. 1H-NMR spectroscopic titration

18. Recognition studies:
conclusions
• Substantial contribution from pyrrolic groups on the linker
• Twisted bridge of receptor 9 is determinant to the matching to
the ligand
• Flexible linker of 12 seems to favor the adaptivity of the receptor
at the expenses of selectivity
• Receptor 16 behaves like 12 but with weaker affinity.
Altogether, bridging monotopic binding units with a linker
of appropriate size and flexibility and endowed with
effective binding groups proved to be a successful
strategy

19. Structural studies and ITC
binding studies
• Receptors showing the best affinity results have been tested in
more competitive solvent (DMF/CDCl3 40/60): affinity decreases,
but follow the same trend.
• Binding affinities were confirmed by isothermal titration
calorimetry (ITC) showing generally good agreements with NMR
data.
• The complex of receptor (S)-9 with Oct(αMan)βMan was selected
as a representative system and its structural features were studied
at 50 C in CDCl3 /[D7]DMF 60:40 by NMR techniques (HSQC, DQ-
COSY andTOCSY 2D spectra)
• Several intermolecular hydrogen bonds between pyrrolic/aminc
NH groups of the receptor and OH groups of the disaccharide
could be found in the structure of the complex.
• Both monosaccharidic units are interacting with monotopic
subunits of the ditopic receptor.

20. Structural studies and ITC
binding studies

21. Recognition studies: Results
• All ditopic receptors consistently bound dimannosides more
effectively than monomannosides, whereas the opposite was
true for the monotopic receptor
• Linker play a crucial role: receptor 15 gave the worst results of
the set. On the other hand receptor 9 gave the best affinity of
the whole set.
• Receptor 9 shows an outstanding enantioselectivity towards β-
dimannoside with the (S) enantiomer more effective than the (R)
one by two orders of magnitude
• The best affinity for α-dimannoside is shown by receptor 12, but
it shows neither good enantioselectivity neither α/β
discrimination

23. IAD: Intramolecular Aglycone
delivery