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NMR AND MOLECULAR RECOGNITION. PROTEIN-CARBOHYDRATE INTERACTIONS 
JESUS JIMENEZ-BARBERO 
Chemical and Physical Biology 
jjbarbero@cib.csic.es 
jjbarbero@cicbiogune.es 
MADRID 
LILLY SYMPOSIUM 
October 8, 2014
The sugar code: the recognition of carbohydrates by specific 
proteins translates sugar-encoded information into cellular 
responses 
Gabius HJ, André S, Jiménez-Barbero J, Romero A, Solís D. Trends Biochem Sci. 2011, 36:298- 
313 
Solís D, Bovin NV, Davis AP, Jiménez-Barbero J, Romero A, Roy R, Smetana K Jr, Gabius HJ. 
Biochim Biophys Acta. 2014, pii: S0304-4165(14)00120-2. doi: 10.1016/j.bbagen.2014.03.016
From NRDD (2004) 
1 LIGAND STRUCTURE? 
2 RECEPTOR STRUCTURE? 
Complexity and 
Flexibility 
Soluble with 
MW<X0.000
FROM THE PERSPECTIVE OF THE RECEPTOR: 
1 LIGAND STRUCTURE? 
2 RECEPTOR STRUCTURE? 
Complexity and 
Flexibility 
Soluble with 
MW<X0.000 
HSQC and CHEMICAL SHIFT PERTURBATIONS
K16 
M17 
K19 
N28 
1H (ppm) 
15N (ppm) 
E15 
K19 
K16 M17 
E18 
N28 
D2 FGFR 
Control 
Prot 1:0.25 lig 
Prot 1:0.5 lig 
Prot 1:1 lig 
Prot 1:1.5 lig 
Prot 1:2 lig 
N28 
L71 
S70 
E18 
K16 
N13 
E15 
M17 
K19 
FIBROBLAST GROWTH FACTORS 
Fast dissociation: FGFR/HEPARIN 
A. Canales, L. Nieto 
2nd Partner 
JACS 2006, J Biomol NMR 2006, Febs J 2006, 
JACS 2008, Chem Eur J 2011 & ChemBioChem 2013
The ligand’s perspective: 
Saturation Transfer Difference. STD (Meyer and Mayer, Peters, 1999, 2000) 
IS THERE ANY BINDING FOR ANY GIVEN COMPOUND? 
WHICH IS THE BINDING EPITOPE? 
IRRADIATION 
at the aromatic 
or aliphatic 
NMR regions 
At long irradiation times, the saturation is transferred to the bound ligand, first 
to the protons belonging to the ligand epitope, then to the rest of the ligand 
Single Compound or 
Library
170x scale 
The ligand’s perspective: 
Forsmann Disaccharide/h-gal9 
GalNAca1-3GalNAcbOR 
i) 
ii) 
H1’ 
H2’ 
H4β 
H4’ 
linker 
H5 
Me 
Me’ 
linker linker 
Joao Ribeiro 
A.Romero, MJ Maté, HJ Gabius, D. Solís 
Int J Biochem Cell Biol, 2010
Ligand NMR 
based 
methods 
STD 
tr-NOESY 
Computational 
methods 
Docking 
MD 
CORCEMA-ST 
+ 
tr-N STD (epitope) OESY (bound conformer) 
3D structure 
docking 
MD 
Nat Prod Rep 2011, 28, 1118-1125 , Med Chem Commun, 2014, 5, 1280-1289
Tubulin as chemotherapeutic target (with JF Díaz & JM Andreu) 
a-tubulin 
b-tubulin 
α,β-tubulin/taxol 
(EC, PDB code 1JFF), 2001 
Docetaxel 
Taxol 
Epothilone A Epothilone B 
Dictyostatin Discodermolide 
taxol 
Taxol 
Epothilone A Epothilone B 
Docetaxel 
Microtubule stabilizing agents (MSAs) 
J Am Chem Soc. 2006 
ACS Chem Biol. 2013 
& Bacterial Tubulin (FtsZ) 
J Am Chem Soc. 2013 
Paclitaxel (Taxol ®) 
Biophys J. 2011 
Docetaxel (Taxotere ®) 
ACS Chem Biol. 2011 
Epothilone A 
ACS Chem Biol, 2014 Epothilone B 
Dictyostatin, Chem. Eur. J., 2008 Discodermolide, Chem Biol, 2012
HNK 1 epitope – mAntibody (Guillem-Barré Syndrome) 
With N. Nifantev (Moscow), M. Schachner (Hamburg) 
STD spectrum 
reference 
TTOOCCSSYY SSTTDD--TTOOCCSSYY 
J Am Chem Soc., 2012 ;134:426- 
35
Protein 1H 
Ligand 19F 
Ligands: 
Simple fluorinated carbohydrates: Man, Glc, 2FDG, 3FDG 
Receptors: ConA, LCA and PSA 
Methodology: Proof-of-principle 
Chem Eur J 2009 & Eur. J. Org. Chem. 2012 & Submitted 
J. P. Ribeiro, T. Diercks (CIC Biogune) 
K. El Biari 
Perturb Protons at 
the protein 
Observe Fluorine at 
the ligand 
With H.J.Gabius 
D. Solís 
The ligand’s perspective:
conA + 2FDG HF STD 
32x 
scale 
The ligand’s perspective: 
Off resonance (phase mod 180º) 
STD
100 
80 
60 
40 
20 
0 
fractional STDreF [%] 
Following interactions by 19F NMR. 
0 5 10 15 20 
inhibitor concentration [mM] 
Competition experiments 
19 F NMR fluorinated ligand (spy) 
Addition of other possible ligands 
+ ligands 
H.-J. Gabius 
R. Roy 
T. Diercks 
Chem Eur J 2009 
& Eur J Org Chem 2012 & submitted 
The ligand’s perspective:
The interactions 
• Model systems: Small ligands, small proteins
The receptor’s perspective: 
NMR Solution Structure of Hevein and their molecular complexes with chitin oligomers 
The first solution state lectin-oligosaccharide complex by NMR…… (1995-2014….) 
W23 W23 
W21 
S19 Y30 
Y30 N 
C 
Exposed site 
Preorganized 
Enthalpy driven 
Hydrogen bonds 
Van der Waals 
CH-p (Acc Chem Res, 2013)
The receptor’s perspective: 
Binding Properties of hevein-like aromatic mutants with Chitotriose 
Similar Binding Mode 
Phe18 
Enthalpy driven 
Ka298K [M-1] DH [KJ/mol]DS[J/molK] 
[KJ/molK] 
Ac-AMP2 Nal18 3500 -63.9 -146.6 
Ac-AMP2 W18 1700 -54.1 -119.0 
Ac-AMP2 F18 1200 -50.1 -109.0 
Y27 
Y20 
Trp18 
Nal18 
Dr. Muraki, Tsukuba, Ac-AMP2 
enthalpy-entropy compensation
CH-p sugar/aromatic interactions take place in water even for 
simple monosaccharide/aromatic systems 
M C Fernández-Alonso, G Cuevas 
Dispersion, electrostatic, hydrophobic 
J. Am. Chem. Soc. 2005, 7379 
Critical points Accounts Chem Res 2013 
(AIM)
D.Díaz, K. Ramírez, C. Fernández-Alonso, G. Cuevas 
Dispersion, electrostatic, hydrophobic 
J. Am. Chem. Soc. 2005 
Pure Appl Chem, 2008, 
Aromatic aminoacids, Chem Eur J 2008 
Protected sugars, J. Am. Chem. Soc, 2009 
Reactivity (Dynamic Combinatorial Chemistry), J. Am. Chem. Soc, 2013 
OVERVIEW: Acc. Chem. Res, 2013,
The ligand’s perspective: 
19F NMR: WGA/chitin interactions (with N. Reichardt, CIC biomaGUNE) 
19 F NMR, FREE AND BOUND 
2 1 
1H NMR, FREE AND BOUND 
1H spectrum of ligand 2 
19F NMR STD (submitted)
The interactions 
• Increasing complexity. Larger systems
FIBROBLAST GROWTH FACTORS AND THEIR INTERACTIONS: 
HEPARIN, HEPARAN SULFATE, AND FGFR 
-Cell proliferation 
-Differentiation 
-Angiogenesis 
-Wound healing 
ANGIOGENESIS 
FGFR 
cis 
membrane 
FGFR 
Signalling 
autophosphorylation 
Extracellular 
matrix 
citoplasm 
heparin 
FGF1 
HS 
trans 
FIBROBLAST GROWTH FACTORS 
It is known that in FGF activation: 
• heparin 
• specific trasmembrane receptors (FGFRs) 
A. Canales, L. Nieto 
M. Martin-Lomas, P. Nieto, J. Angulo (Seville) 
G. Gimenez-Gallego, I. Fernández (Madrid) 
Both the ligand’s and receptor’s perspective:
asymmetric structure symmetric structure 
FGF1 
FGF1-FGFR2-heparin 
2:2:1 
Pellegrini et al. 
Nature 2000, 407, 1029-1034 
TRANS: ASYMMETRIC 
heparin 
FGF2-FGFR1-heparin 
2:2:2 
Schlessinger et al. 
Mol.Cell 2000, 6, 743-750 
CIS: SYMMETRIC 
FGFR2 
FGFR2 
heparin 
X-RAY STRUCTURES 
Ig2 
Ig3 Ig3 
Ig2 
FGF2 
FGFR1 
FIBROBLAST GROWTH FACTORS
L145 
FGF1 residues 
affected by the 
addition of FGFR-Ig2 
that are not involved 
in protein-protein 
interactions in this 
structure 
1st Partner 2nd Partner 
Protein-protein 
interaction 
surfaces 
asymmetric 
model 
Y108 
D102 
FGF1/ FGFR-Ig2 secondary binding site 
+ + 
15N FGF1 unlabelled 
FGFR Ig2 
pentasaccharide 
15N FGF1 + pentasaccharide (1:2) 
15N FGF1+ pentasaccharide + FGFR Ig2 (1:2:0.25) 
G140 
E104 
L145 
E56 
F53 
V104 
L147 
M149 
L21 
E105 
Y139E104 G140 
Protein-protein 
interaction 
surfaces 
symmetric 
model 
15N-1H HSQC 
L28 
L147 
E104 
G140 
Y108 
F36 
TERNARY COMPLEX INTERACTIONS: from the FGF1 viewpoint 
TERNARY COMPLEX INTERACTIONS: 
Only the symmetryc complex explains all the NMR experimental observations 
FIBROBLAST GROWTH FACTORS 
JACS 2006, J Biomol NMR 2006, Febs J 2006, JACS 2008, Chem Eur J 2011 & ChemBioChem 
2013
The Sugar: The bound 
conformation 
13C-double filtered-NOESY 
CHAIR-BOAT EQUILIBRIUM 
IN THE BOUND STATE! 
Conformational dynamics (ligand 
plasticity) is essential for 
bioactivity 
FGF, JACS, 2005; 
5.05.105.205.305.405.05.105.205.305.403.03.504.04.50 
OH 
H1I5 
H5 
H5 
H2 
NH 
H2 
H1I1 
H3,4 
H3 
H4 
H1G6 
¯ 
H1G2 
¯ 
H1G4 
H1I3 
H2 
H4 
H3 
H5 
H2 
H4 
H2,3 
H3,4 
H2,5 
H4 
H3 
OH 
OH 
HG6 
1HG2 
¯ 1¯ 
HI3 
1H1I5 
H1G4 
HO 
O 
O 
NH 
HO 
O 
-O3SO 
O 
-OOC 
O 
O 
HO 
OH 
OSO3 
- 
H H 
H 
H 
H H 
H 
H 
H 
O 
OH 
HO 
O 
H 
-OOC 
O 
O 
NH 
HO 
H 
H 
H H 
H 
H 
H H 
O 
-O3SO 
O 
-OOC 
H 
H 
H 
H 
H 
iPr 
SO3 
- 
Ac 
SO3 
- 
GlcN-6 IdoA-5 GlcN-4 IdoA-3 GlcN-2 IdoA-1 
H1I5-H6G4 
A B 
10 .0 7.5 5.0 2.5 0.0 
0.0 
2.5 
5.0 
7.5 
10.0 
0 
FGFR, Chem Eur J, 2011 & ChemBioChem, 2013 
A. Canales, L. Nieto 
First Partner
Mimicking conformational plasticity: The use of fluorine-containing glycans 
With M. Sollogoub (UPMC, Paris) 
19F-NMR spectra, RT 
Idose-like (1, 3, 5, 6) & Glc-like (2, 4, 7) 
________________________________________________________________ 
19F-NMR spectra, VT 
INCREASING TEMP, DECREASING TEMP
Mimicking conformational plasticity: The use of fluorine-containing glycans 
With M. Sollogoub (UPMC, Paris) 
The Ido-like fluoro-saccharides also mimic the dynamic behavior of natural sugars! 
Regular carbasugars display one unique (4C1 chair) conformation (Widmalm, 2010)! 
_______________________________________________________________ 
________________________________________________________________ 
4 2S C1 5a 
Luca Unione, with S. Martín-Santamaría (computations), submitted
Mimicking conformational behaviour: The use of fluorine-containing glycans 
With M. Sollogoub (UPMC, Paris) 
Gem-difluoro-sugars also mimic the dynamic behavior of disaccharides around the glycosidic linkage 
________________________________________________________________ 
s*C1-C5a 
s*C1-C2 s*C1-C2 
s*C1-C2 
s*C1-O1 
F 
F 
O O O 
s*C1-CF2 
R 
O 
O R 
O R 
O R 
O 
R 
R 
F 
F 
Glycoside Carbasugar gem-diF-carbasugar 
Exo 
Non Exo 
HO 
HOH 
O 
OH 
HOO O 
HO 
HO OMe 
HO F 
F 
The exo-anomeric effect governs 
the conformational behavior of 
glycans around the glycosidic linkage 
C-glycosyl 
Asensio et al. JACS 1999, Chem Eur J 2000 
________________________________________________________________ 
________________________________________________________________ 
Luca Unione, with S. Martín-Santamaría (computations), Angew Chem Int Ed Engl. 2014 ;53:9597
Mimicking conformational behaviour: The use of fluorine-containing glycans 
With M. Sollogoub (UPMC, Paris) 
Gem-difluoro-sugars also mimic the dynamic behavior of disaccharides around the glycosidic linkage 
________________________________________________________________ 
The Gem-difluoro-maltose analogue displays the natural exo-anomeric conformation 
The carbasugar analogue shows a major equilibrium around the glycosidic torsions 
________________________________________________________________ 
Luca Unione, with S. Martín-Santamaría (computations), Angew Chem Int Ed Engl. 2014; 53:9597
GGllyyccaannss iinn NNaattuurree 
Asn 
n 
N-glycans - lectins 
Lys-Val-Ala-Asn-Lys- 
Thr 
Neu5Ac 
Gal 
Man 
GlcNAc 
Ana Ardá & Pilar Blasco 
From simple molecules with single epitopes to complex molecules 
with multiple epitopes 
The importance of lectin architecture 
The importance of single or multi domain protein domains
Glycopeptide binding: beyond binary complexes 
A. Ardá, J. J. Hernández-Gay 
Chem Eur J (2010), 16, 10715 
with C. Unverzagt & HJ Gabius
BIANTENNARY N-GLYCANS: MULTIPLE EPITOPES! 
NATURAL BIANTENNARY 
OLIGOSACCHARIDES: NO 
HEVEIN BINDING BY 
with C. Unverzagt (Bayreuth) & HJ Gabius (München) STD!!!!
BIANTENNARY N-GLYCANS AND MULTIDOMAIN LECTINS: WGA, a dimer of 4 HEVEINS 
THERE IS BINDING! 
But… 
The sialyl residues do not 
contribute 
to the binding event….. 
Although WGA has been considered 
a 
Sialic acid binding protein! 
MACROSCOPIC STUDIES ONLY PROVIDE PARTIAL ANSWERS!
NATURAL BIANTENNARY OLIGOSACCHARIDES AND LARGE LECTINS: WGA (8 HEVEINS) 
With C. Unverzagt, H.-J. Gabius 
A. Ardá, P. Blasco 
MACROSCOPIC STUDIES ONLY PROVIDE PARTIAL ANSWERS! 
J. Am. Chem. Soc . (2013)
To finish: 
Conformation and Recognition. N-Glycans 
Few key NOEs and long range Js, not easy to get. 
Why not trying additional tools?
from G. Otting, Annu. Rev. Biophys . 2010, 39, 387–405 
O 
HO O 
HO 
OH 
HN 
HN 
O 
HO 
OH 
HN 
CO2H 
N 
N 
CO2H 
CO2H 
CO2H 
O 
HN 
O O 
O 
Paramagnetic probes: Lanthanides
Using other NMR parameters. THE USE OF LANTHANIDES: PCS and PRE 
Carbohydrate probe design 
O 
6´ 
4´ 5´ 
HO O 
4 5 
HO 
OH 
HN 
HN 
O 
HO 
OH 
HN 
CO2H 
N 
N 
CO2H 
CO2H 
CO2H 
O 
HN 
O O 
O 
2 1 
3 
6 
1´ 
3´ 2´ 
A. Canales, A. Mallagaray, J. Pérez-Castells 
O 
6´ 
4´ 5´ 
HO O 
6 
4 5 
HO 
OH 
HN 
HN 
O 
HO 
OH 
HN 
CO2H 
N 
N 
CO2H 
CO2H 
CO2H 
O O 
O 
1´ 1 
3´ 2´ 
3 2 
b- aminochitobiose derivatives 
A. Canales, A. Mallagaray, Chem. Commun, 2011, 47(25), 7179-81 
Lactose derivative 
JACS (2014)
THE USE OF LANTHANIDES: DISACCHARIDE CONFORMATION 
H1 
Lactose derivative 
La+3 complex 
Dy+3 complex 
2 
1,8 
1,6 
1,4 
1,2 
1 
0,8 
0,6 
0,4 
0,2 
0 
0 0,2 0,4 0,6 0,8 1 1,2 1,4 1,6 1,8 2 
1,0 
0,5 
Dd = +1.78 
Mspin calculation 
1H PCS exp 
1H PCS calc 
Qfactor= 0.006 
1H-13C HSQC 
Dy+3 
1,0 
0,5 
A. Canales, A. Berbís, SYNTHESIS: A. Mallagaray, J. Pérez-Castells 
0,0 
0,0 
H5' H4' H3' H2' H1' H5 H4 H3 H2 H1 
1H PCS 
ppm 
PCS H4´ 
0.27 ppm 
d (H4´-Dy3+) = 20.1 Å 
J.Am.Chem.Soc. 2014, 136, 8011-7
h-Galectin 3 binding studies (HJ Gabius, München) 
Orange residues disappear due to PRE 
Green residues shift d(Dy-HN S237) 31 Å 
VII GERMN Biennial meeting 
G235 
E165 
W181 
S237 
D178 
1H-15N HSQC 
Gal-3 + lactose derivative + La3+ 
Gal-3 + lactose derivative + Dy3+ 
G235 
E165 
W181 
S237 
D178 
Dy3+ 
0.05 ppm 
J.Am.A. Canales, A. Berbís, SYNTHESIS: A. Mallagaray, J. Pérez-Castells Chem.Soc. 2014, 136(22), 8011-7
Complex type N-glycans 
-Folding control. 
-Cell adhesion. 
-Inmune response. 
isochronous NMR shifts 
N-glycans pseudosymmetry 
Complex type 
Gal GlcNAc aMan 
H2 GlcNAc 
(A+B) 
H4 Gal 
(A+B) 
H4 aMan 
(A+B) 
H4 GlcNAc 
(A+B) 
H2 Gal 
(A+B) 
H5 GlcNAc 
(A+B) 
d (13C) ppm 
d (1H) ppm 
Ln3+ = La3+ 
1H-13C HSQC
Breaking pseudosymmetry in complex N-glycans with paramagnetic lanthanides and PCS 
PCS 0.10 ppm 
B 
H2 GlcNAc 
(A+B) 
B 
0,5 
0,5 
Gal GlcNAc aMan 
A B 
GlcNAc 
aMan 
bMan 
Gal GlcNAc aMan 
H2 bMan 
H4 Gal A 
(A+B) 
H4 GlcNAc 
(A+B) 
A 
0,5 
B 
H4 aMan 
(A+B) 
A B 
B 
H3 bMan 
Gal 
H2 aMan B PCS 0.41 ppm 
PCS 0.29 ppm 
H2 Gal 
(A+B) 
0,5 
0,5 
A B 
H5 GlcNAc 
(A+B) 
A B 
A 
d  (1H) ppm  d  (13C) ppm  
A 
1H PCS 
ppm 
0,0 
H5 H4 H3 H2 H1 
0,0 
H5 H4 H3 H2 H1 
0,0 
H5 H4 H3 H2 H1 
1H PCS 
ppm 
0,5 
0,0 
H5 H4 H3 H2 H1 
0,0 
H5 H4 H3 H2 H1 
0,0 
H5 H4 H3 H2 H1 
1H-13C HSQC 
N-glycan derivative + Dy3+ 
N-glycan derivative + La3+ 
A. Canales, with C. Unverzagt and I. Boos Angew Chem. Int. Ed. 2013, 52, 13789
1,2 
1 
0,8 
0,6 
0,4 
0,2 
0 
0 0,1 0,2 0,3 0,4 0,5 0,6 0,7 0,8 0,9 1 
Green gg 180 
Red gt 180 
1-3 branch 
1H PCSs exp 
1H PCSs calc 
A. Canales, with C. Unverzagt & I Boos Angew Chem Int Ed, 2013
Gal GlcNAc B 
h-Galectin 3 binding studies. Impossible in the diamagnetic sample 
1H-13C HSQC nonasaccharide + 1H-13C HSQC nonasaccharide + + hGal3 
H1GalA H1GalB H1GalA H1GalB 
H1GlcNAcA H1GlcNAcB H1GlcNAcA H1GlcNAcB 
HSQC rows GalB 
H4GalA H4GalB 
4 H3GlcNAcA H3GlcNAcB 
H1GalA H1GalB 
H3bMan3 
GlcNAcB 
GalAGlcNAcA 
Angew Chem. Int. Ed. 2013, 52, 13789-93 
A 
B 
A 
CR_D_ _h_G_a_l_e_c_ti_n_-3________________________________________________________
Further challenge: Tetraantennary N-glycan 
1H-13C HSQC La3+ 
1H-13C HSQC Dy3+ 
H1 aManC H1 GlcNAc 
H1 Gal 
A-D 
H1 aManA 
A+C 
H1 GlcNAc 
B+D 
A C 
D B 
A D B C 
H1 bMan 
H1 GlcNAc2 
D 
C 
B 
A 3 2 1 
The chemical shifts of the four Galactose moieties are isochronous 
The chemical shifts of the four GlcNAc units are isochronous in pairs (A, C & B, D)
Overall fitting A, B, C and D arms 
gg_gt/gg_gg 60/40 Qf 0.16 single tensor 
R2 = 0,9459 
1,400 
1,200 
1,000 
0,800 
0,600 
0,400 
0,200 
gg_gt PCS (Exp, calc) 
H1 GlcNAc C (0.4, 0.46) 
H2 GlcNAc C (0.38, 0.31) 
H3 GlcNAc C (0.42, 0.42) 
H5 GlcNAc C (0.44,0.45) 
H1 Mana 1-6 (0.43, 0.43) 
H1 GlcNAc A 
(0.18, 0.12) 
H1 GlcNAc B 
(0.29, 0.22) 
H1 Gal C (0.28, 0.27) 
C 
D 
A 
B What about the interaction with a 
receptor? 
A. Canales, with C. Unverzagt & I. Boos 
submitted 
0,000 
0,000 0,200 0,400 0,600 0,800 1,000 1,200 1,400
Line broadening upon addition of h-galectin3 HSQC rows 
H4 GalA H4 GalD H4 GalB H4 GalC 
% intensity 
respect to the 
sample without 
protein 
89% 56% 33% 34% 
HSQC 1H-13C tetraantennary N-glycan +Dy3+ HSQC 1H-13C tetraantennary N-glycan +Dy3+ +gal3, Molar ratio 12:1 
H2 GalA H2 GalD H2 GalB 
76% 
55% 44% 
H2 GalC 
46% 
B 
A 
C 
D 
B and C arms are more affected, followed by arm D 
Branch A is basically non-accesible to hGal3 
A. Canales, with C. Unverzagt & I. Boos 
submitted
B 
A 
C 
D 
A and D arms are less 
accessible to potential 
binders than C and B 
Paramagnetic lanthanides: 
Breaking pseudosymmetry and unraveling “hidden” molecular recognition features 
19F-containing glycomimetics: 
Mimicking conformational behavior and plasticity 
Unraveling the key role of carbohydrate-aromatic interactions for sugar recognition 
Applications of NMR techniques for addressing molecular recognition events, 
from the ligand (1H and 19F) and receptor’s perspective
J. Jiménez-Barbero, F. J. Cañada 
CIB-CSIC, Madrid, SPAIN 
FORMER MEMBERS 
J. L. Asensio (IQOG) 
J. F. Espinosa, A Rivera 
P Vidal, L Calle (Lilly) 
A. Poveda (UAM) 
M. Martín-Pastor (USC) 
J. I. Santos (UPV-SS) 
F. Corzana (La Rioja) 
J. Pérez-Castells, CEU 
N. Aboitiz (Army) 
E. Montero (UK) 
P. Groves, F. Marcelo (Lisbon) 
S. Mari (Milano) 
M. Fontanella (Padova) 
C. Venturi (Florence) 
V. Gargiulo, C de Castro 
R Marchetti (Napoli) 
M. Politi (Genoa) 
G. Cuevas, M. I. Chavez, M Morando 
B. Domínguez, K. Ramírez (UNAM) 
V. García-Aparicio, J. J. Hdez-Gay 
A. García-Herrero (Canada) 
K. Martínez-Mayorga, JL Medina (Florida) 
J. Ribeiro (Grenoble) 
L. Nieto (Eindhoven) 
V. Roldós (Montevideo) 
A. Mallagaray (Luebeck) 
LANTHANIDES 
C. Unverzagt (Bayreuth) 
J. Pérez-Castells (USP-CEU) 
HML, Galectins 
H.-J. Gabius (München) 
S-I. Nishimura (Sapporo) 
Heparin/FGF/FGFR 
M. Martín-Lomas (BMG) 
G. Giménez-Gallego (CIB) 
P.M. Nieto (IIQ) 
R. J. Linhardt (NY) 
Hevein, Chitin 
A. Rdgez-Romero (UNAM) 
G. Asensio (Valencia) 
D. Andreu (Barcelona) 
M. Vila (Barcelona) 
M. Muraki (Tsukuba) 
€ 
•MINECO (Spain) 
•CAM (Madrid) 
•FP6, FP7, H2020 (EU): 
•GlycoHit 
•Dynano 
•Glycopharm 
•TOLLerant 
•COST BM1003, CM1102 
•Mizutani 
•Cariplo 
•Pharmamar, Rovi, Vertex, 
ImmunoTek, Syngenta 
•Marató TV3 
•CSIC (PIF) 
CIB-CSIC (2014) 
Ana Ardá 
Angeles Canales 
Ana Manzano 
Carmen Fernández-Alonso 
Alberto Fernández-Tejada 
Dolores Díaz 
Pilar Blasco 
Khouzaima El Biari 
Alvaro Berbís 
Luca Unione 
Javier Sastre 
Silvia Galante 
Beatriz Fernández de Toro 
Modeling 
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Dr. Jesús Jiménez Barbero - Simposio Internacional 'Química: respuestas para un mundo mejor'

  • 1. NMR AND MOLECULAR RECOGNITION. PROTEIN-CARBOHYDRATE INTERACTIONS JESUS JIMENEZ-BARBERO Chemical and Physical Biology jjbarbero@cib.csic.es jjbarbero@cicbiogune.es MADRID LILLY SYMPOSIUM October 8, 2014
  • 2. The sugar code: the recognition of carbohydrates by specific proteins translates sugar-encoded information into cellular responses Gabius HJ, André S, Jiménez-Barbero J, Romero A, Solís D. Trends Biochem Sci. 2011, 36:298- 313 Solís D, Bovin NV, Davis AP, Jiménez-Barbero J, Romero A, Roy R, Smetana K Jr, Gabius HJ. Biochim Biophys Acta. 2014, pii: S0304-4165(14)00120-2. doi: 10.1016/j.bbagen.2014.03.016
  • 3. From NRDD (2004) 1 LIGAND STRUCTURE? 2 RECEPTOR STRUCTURE? Complexity and Flexibility Soluble with MW<X0.000
  • 4. FROM THE PERSPECTIVE OF THE RECEPTOR: 1 LIGAND STRUCTURE? 2 RECEPTOR STRUCTURE? Complexity and Flexibility Soluble with MW<X0.000 HSQC and CHEMICAL SHIFT PERTURBATIONS
  • 5. K16 M17 K19 N28 1H (ppm) 15N (ppm) E15 K19 K16 M17 E18 N28 D2 FGFR Control Prot 1:0.25 lig Prot 1:0.5 lig Prot 1:1 lig Prot 1:1.5 lig Prot 1:2 lig N28 L71 S70 E18 K16 N13 E15 M17 K19 FIBROBLAST GROWTH FACTORS Fast dissociation: FGFR/HEPARIN A. Canales, L. Nieto 2nd Partner JACS 2006, J Biomol NMR 2006, Febs J 2006, JACS 2008, Chem Eur J 2011 & ChemBioChem 2013
  • 6. The ligand’s perspective: Saturation Transfer Difference. STD (Meyer and Mayer, Peters, 1999, 2000) IS THERE ANY BINDING FOR ANY GIVEN COMPOUND? WHICH IS THE BINDING EPITOPE? IRRADIATION at the aromatic or aliphatic NMR regions At long irradiation times, the saturation is transferred to the bound ligand, first to the protons belonging to the ligand epitope, then to the rest of the ligand Single Compound or Library
  • 7. 170x scale The ligand’s perspective: Forsmann Disaccharide/h-gal9 GalNAca1-3GalNAcbOR i) ii) H1’ H2’ H4β H4’ linker H5 Me Me’ linker linker Joao Ribeiro A.Romero, MJ Maté, HJ Gabius, D. Solís Int J Biochem Cell Biol, 2010
  • 8. Ligand NMR based methods STD tr-NOESY Computational methods Docking MD CORCEMA-ST + tr-N STD (epitope) OESY (bound conformer) 3D structure docking MD Nat Prod Rep 2011, 28, 1118-1125 , Med Chem Commun, 2014, 5, 1280-1289
  • 9. Tubulin as chemotherapeutic target (with JF Díaz & JM Andreu) a-tubulin b-tubulin α,β-tubulin/taxol (EC, PDB code 1JFF), 2001 Docetaxel Taxol Epothilone A Epothilone B Dictyostatin Discodermolide taxol Taxol Epothilone A Epothilone B Docetaxel Microtubule stabilizing agents (MSAs) J Am Chem Soc. 2006 ACS Chem Biol. 2013 & Bacterial Tubulin (FtsZ) J Am Chem Soc. 2013 Paclitaxel (Taxol ®) Biophys J. 2011 Docetaxel (Taxotere ®) ACS Chem Biol. 2011 Epothilone A ACS Chem Biol, 2014 Epothilone B Dictyostatin, Chem. Eur. J., 2008 Discodermolide, Chem Biol, 2012
  • 10. HNK 1 epitope – mAntibody (Guillem-Barré Syndrome) With N. Nifantev (Moscow), M. Schachner (Hamburg) STD spectrum reference TTOOCCSSYY SSTTDD--TTOOCCSSYY J Am Chem Soc., 2012 ;134:426- 35
  • 11. Protein 1H Ligand 19F Ligands: Simple fluorinated carbohydrates: Man, Glc, 2FDG, 3FDG Receptors: ConA, LCA and PSA Methodology: Proof-of-principle Chem Eur J 2009 & Eur. J. Org. Chem. 2012 & Submitted J. P. Ribeiro, T. Diercks (CIC Biogune) K. El Biari Perturb Protons at the protein Observe Fluorine at the ligand With H.J.Gabius D. Solís The ligand’s perspective:
  • 12. conA + 2FDG HF STD 32x scale The ligand’s perspective: Off resonance (phase mod 180º) STD
  • 13. 100 80 60 40 20 0 fractional STDreF [%] Following interactions by 19F NMR. 0 5 10 15 20 inhibitor concentration [mM] Competition experiments 19 F NMR fluorinated ligand (spy) Addition of other possible ligands + ligands H.-J. Gabius R. Roy T. Diercks Chem Eur J 2009 & Eur J Org Chem 2012 & submitted The ligand’s perspective:
  • 14. The interactions • Model systems: Small ligands, small proteins
  • 15. The receptor’s perspective: NMR Solution Structure of Hevein and their molecular complexes with chitin oligomers The first solution state lectin-oligosaccharide complex by NMR…… (1995-2014….) W23 W23 W21 S19 Y30 Y30 N C Exposed site Preorganized Enthalpy driven Hydrogen bonds Van der Waals CH-p (Acc Chem Res, 2013)
  • 16. The receptor’s perspective: Binding Properties of hevein-like aromatic mutants with Chitotriose Similar Binding Mode Phe18 Enthalpy driven Ka298K [M-1] DH [KJ/mol]DS[J/molK] [KJ/molK] Ac-AMP2 Nal18 3500 -63.9 -146.6 Ac-AMP2 W18 1700 -54.1 -119.0 Ac-AMP2 F18 1200 -50.1 -109.0 Y27 Y20 Trp18 Nal18 Dr. Muraki, Tsukuba, Ac-AMP2 enthalpy-entropy compensation
  • 17. CH-p sugar/aromatic interactions take place in water even for simple monosaccharide/aromatic systems M C Fernández-Alonso, G Cuevas Dispersion, electrostatic, hydrophobic J. Am. Chem. Soc. 2005, 7379 Critical points Accounts Chem Res 2013 (AIM)
  • 18. D.Díaz, K. Ramírez, C. Fernández-Alonso, G. Cuevas Dispersion, electrostatic, hydrophobic J. Am. Chem. Soc. 2005 Pure Appl Chem, 2008, Aromatic aminoacids, Chem Eur J 2008 Protected sugars, J. Am. Chem. Soc, 2009 Reactivity (Dynamic Combinatorial Chemistry), J. Am. Chem. Soc, 2013 OVERVIEW: Acc. Chem. Res, 2013,
  • 19. The ligand’s perspective: 19F NMR: WGA/chitin interactions (with N. Reichardt, CIC biomaGUNE) 19 F NMR, FREE AND BOUND 2 1 1H NMR, FREE AND BOUND 1H spectrum of ligand 2 19F NMR STD (submitted)
  • 20. The interactions • Increasing complexity. Larger systems
  • 21. FIBROBLAST GROWTH FACTORS AND THEIR INTERACTIONS: HEPARIN, HEPARAN SULFATE, AND FGFR -Cell proliferation -Differentiation -Angiogenesis -Wound healing ANGIOGENESIS FGFR cis membrane FGFR Signalling autophosphorylation Extracellular matrix citoplasm heparin FGF1 HS trans FIBROBLAST GROWTH FACTORS It is known that in FGF activation: • heparin • specific trasmembrane receptors (FGFRs) A. Canales, L. Nieto M. Martin-Lomas, P. Nieto, J. Angulo (Seville) G. Gimenez-Gallego, I. Fernández (Madrid) Both the ligand’s and receptor’s perspective:
  • 22. asymmetric structure symmetric structure FGF1 FGF1-FGFR2-heparin 2:2:1 Pellegrini et al. Nature 2000, 407, 1029-1034 TRANS: ASYMMETRIC heparin FGF2-FGFR1-heparin 2:2:2 Schlessinger et al. Mol.Cell 2000, 6, 743-750 CIS: SYMMETRIC FGFR2 FGFR2 heparin X-RAY STRUCTURES Ig2 Ig3 Ig3 Ig2 FGF2 FGFR1 FIBROBLAST GROWTH FACTORS
  • 23. L145 FGF1 residues affected by the addition of FGFR-Ig2 that are not involved in protein-protein interactions in this structure 1st Partner 2nd Partner Protein-protein interaction surfaces asymmetric model Y108 D102 FGF1/ FGFR-Ig2 secondary binding site + + 15N FGF1 unlabelled FGFR Ig2 pentasaccharide 15N FGF1 + pentasaccharide (1:2) 15N FGF1+ pentasaccharide + FGFR Ig2 (1:2:0.25) G140 E104 L145 E56 F53 V104 L147 M149 L21 E105 Y139E104 G140 Protein-protein interaction surfaces symmetric model 15N-1H HSQC L28 L147 E104 G140 Y108 F36 TERNARY COMPLEX INTERACTIONS: from the FGF1 viewpoint TERNARY COMPLEX INTERACTIONS: Only the symmetryc complex explains all the NMR experimental observations FIBROBLAST GROWTH FACTORS JACS 2006, J Biomol NMR 2006, Febs J 2006, JACS 2008, Chem Eur J 2011 & ChemBioChem 2013
  • 24. The Sugar: The bound conformation 13C-double filtered-NOESY CHAIR-BOAT EQUILIBRIUM IN THE BOUND STATE! Conformational dynamics (ligand plasticity) is essential for bioactivity FGF, JACS, 2005; 5.05.105.205.305.405.05.105.205.305.403.03.504.04.50 OH H1I5 H5 H5 H2 NH H2 H1I1 H3,4 H3 H4 H1G6 ¯ H1G2 ¯ H1G4 H1I3 H2 H4 H3 H5 H2 H4 H2,3 H3,4 H2,5 H4 H3 OH OH HG6 1HG2 ¯ 1¯ HI3 1H1I5 H1G4 HO O O NH HO O -O3SO O -OOC O O HO OH OSO3 - H H H H H H H H H O OH HO O H -OOC O O NH HO H H H H H H H H O -O3SO O -OOC H H H H H iPr SO3 - Ac SO3 - GlcN-6 IdoA-5 GlcN-4 IdoA-3 GlcN-2 IdoA-1 H1I5-H6G4 A B 10 .0 7.5 5.0 2.5 0.0 0.0 2.5 5.0 7.5 10.0 0 FGFR, Chem Eur J, 2011 & ChemBioChem, 2013 A. Canales, L. Nieto First Partner
  • 25. Mimicking conformational plasticity: The use of fluorine-containing glycans With M. Sollogoub (UPMC, Paris) 19F-NMR spectra, RT Idose-like (1, 3, 5, 6) & Glc-like (2, 4, 7) ________________________________________________________________ 19F-NMR spectra, VT INCREASING TEMP, DECREASING TEMP
  • 26. Mimicking conformational plasticity: The use of fluorine-containing glycans With M. Sollogoub (UPMC, Paris) The Ido-like fluoro-saccharides also mimic the dynamic behavior of natural sugars! Regular carbasugars display one unique (4C1 chair) conformation (Widmalm, 2010)! _______________________________________________________________ ________________________________________________________________ 4 2S C1 5a Luca Unione, with S. Martín-Santamaría (computations), submitted
  • 27. Mimicking conformational behaviour: The use of fluorine-containing glycans With M. Sollogoub (UPMC, Paris) Gem-difluoro-sugars also mimic the dynamic behavior of disaccharides around the glycosidic linkage ________________________________________________________________ s*C1-C5a s*C1-C2 s*C1-C2 s*C1-C2 s*C1-O1 F F O O O s*C1-CF2 R O O R O R O R O R R F F Glycoside Carbasugar gem-diF-carbasugar Exo Non Exo HO HOH O OH HOO O HO HO OMe HO F F The exo-anomeric effect governs the conformational behavior of glycans around the glycosidic linkage C-glycosyl Asensio et al. JACS 1999, Chem Eur J 2000 ________________________________________________________________ ________________________________________________________________ Luca Unione, with S. Martín-Santamaría (computations), Angew Chem Int Ed Engl. 2014 ;53:9597
  • 28. Mimicking conformational behaviour: The use of fluorine-containing glycans With M. Sollogoub (UPMC, Paris) Gem-difluoro-sugars also mimic the dynamic behavior of disaccharides around the glycosidic linkage ________________________________________________________________ The Gem-difluoro-maltose analogue displays the natural exo-anomeric conformation The carbasugar analogue shows a major equilibrium around the glycosidic torsions ________________________________________________________________ Luca Unione, with S. Martín-Santamaría (computations), Angew Chem Int Ed Engl. 2014; 53:9597
  • 29. GGllyyccaannss iinn NNaattuurree Asn n N-glycans - lectins Lys-Val-Ala-Asn-Lys- Thr Neu5Ac Gal Man GlcNAc Ana Ardá & Pilar Blasco From simple molecules with single epitopes to complex molecules with multiple epitopes The importance of lectin architecture The importance of single or multi domain protein domains
  • 30. Glycopeptide binding: beyond binary complexes A. Ardá, J. J. Hernández-Gay Chem Eur J (2010), 16, 10715 with C. Unverzagt & HJ Gabius
  • 31. BIANTENNARY N-GLYCANS: MULTIPLE EPITOPES! NATURAL BIANTENNARY OLIGOSACCHARIDES: NO HEVEIN BINDING BY with C. Unverzagt (Bayreuth) & HJ Gabius (München) STD!!!!
  • 32. BIANTENNARY N-GLYCANS AND MULTIDOMAIN LECTINS: WGA, a dimer of 4 HEVEINS THERE IS BINDING! But… The sialyl residues do not contribute to the binding event….. Although WGA has been considered a Sialic acid binding protein! MACROSCOPIC STUDIES ONLY PROVIDE PARTIAL ANSWERS!
  • 33. NATURAL BIANTENNARY OLIGOSACCHARIDES AND LARGE LECTINS: WGA (8 HEVEINS) With C. Unverzagt, H.-J. Gabius A. Ardá, P. Blasco MACROSCOPIC STUDIES ONLY PROVIDE PARTIAL ANSWERS! J. Am. Chem. Soc . (2013)
  • 34. To finish: Conformation and Recognition. N-Glycans Few key NOEs and long range Js, not easy to get. Why not trying additional tools?
  • 35. from G. Otting, Annu. Rev. Biophys . 2010, 39, 387–405 O HO O HO OH HN HN O HO OH HN CO2H N N CO2H CO2H CO2H O HN O O O Paramagnetic probes: Lanthanides
  • 36. Using other NMR parameters. THE USE OF LANTHANIDES: PCS and PRE Carbohydrate probe design O 6´ 4´ 5´ HO O 4 5 HO OH HN HN O HO OH HN CO2H N N CO2H CO2H CO2H O HN O O O 2 1 3 6 1´ 3´ 2´ A. Canales, A. Mallagaray, J. Pérez-Castells O 6´ 4´ 5´ HO O 6 4 5 HO OH HN HN O HO OH HN CO2H N N CO2H CO2H CO2H O O O 1´ 1 3´ 2´ 3 2 b- aminochitobiose derivatives A. Canales, A. Mallagaray, Chem. Commun, 2011, 47(25), 7179-81 Lactose derivative JACS (2014)
  • 37. THE USE OF LANTHANIDES: DISACCHARIDE CONFORMATION H1 Lactose derivative La+3 complex Dy+3 complex 2 1,8 1,6 1,4 1,2 1 0,8 0,6 0,4 0,2 0 0 0,2 0,4 0,6 0,8 1 1,2 1,4 1,6 1,8 2 1,0 0,5 Dd = +1.78 Mspin calculation 1H PCS exp 1H PCS calc Qfactor= 0.006 1H-13C HSQC Dy+3 1,0 0,5 A. Canales, A. Berbís, SYNTHESIS: A. Mallagaray, J. Pérez-Castells 0,0 0,0 H5' H4' H3' H2' H1' H5 H4 H3 H2 H1 1H PCS ppm PCS H4´ 0.27 ppm d (H4´-Dy3+) = 20.1 Å J.Am.Chem.Soc. 2014, 136, 8011-7
  • 38. h-Galectin 3 binding studies (HJ Gabius, München) Orange residues disappear due to PRE Green residues shift d(Dy-HN S237) 31 Å VII GERMN Biennial meeting G235 E165 W181 S237 D178 1H-15N HSQC Gal-3 + lactose derivative + La3+ Gal-3 + lactose derivative + Dy3+ G235 E165 W181 S237 D178 Dy3+ 0.05 ppm J.Am.A. Canales, A. Berbís, SYNTHESIS: A. Mallagaray, J. Pérez-Castells Chem.Soc. 2014, 136(22), 8011-7
  • 39. Complex type N-glycans -Folding control. -Cell adhesion. -Inmune response. isochronous NMR shifts N-glycans pseudosymmetry Complex type Gal GlcNAc aMan H2 GlcNAc (A+B) H4 Gal (A+B) H4 aMan (A+B) H4 GlcNAc (A+B) H2 Gal (A+B) H5 GlcNAc (A+B) d (13C) ppm d (1H) ppm Ln3+ = La3+ 1H-13C HSQC
  • 40. Breaking pseudosymmetry in complex N-glycans with paramagnetic lanthanides and PCS PCS 0.10 ppm B H2 GlcNAc (A+B) B 0,5 0,5 Gal GlcNAc aMan A B GlcNAc aMan bMan Gal GlcNAc aMan H2 bMan H4 Gal A (A+B) H4 GlcNAc (A+B) A 0,5 B H4 aMan (A+B) A B B H3 bMan Gal H2 aMan B PCS 0.41 ppm PCS 0.29 ppm H2 Gal (A+B) 0,5 0,5 A B H5 GlcNAc (A+B) A B A d (1H) ppm d (13C) ppm A 1H PCS ppm 0,0 H5 H4 H3 H2 H1 0,0 H5 H4 H3 H2 H1 0,0 H5 H4 H3 H2 H1 1H PCS ppm 0,5 0,0 H5 H4 H3 H2 H1 0,0 H5 H4 H3 H2 H1 0,0 H5 H4 H3 H2 H1 1H-13C HSQC N-glycan derivative + Dy3+ N-glycan derivative + La3+ A. Canales, with C. Unverzagt and I. Boos Angew Chem. Int. Ed. 2013, 52, 13789
  • 41. 1,2 1 0,8 0,6 0,4 0,2 0 0 0,1 0,2 0,3 0,4 0,5 0,6 0,7 0,8 0,9 1 Green gg 180 Red gt 180 1-3 branch 1H PCSs exp 1H PCSs calc A. Canales, with C. Unverzagt & I Boos Angew Chem Int Ed, 2013
  • 42. Gal GlcNAc B h-Galectin 3 binding studies. Impossible in the diamagnetic sample 1H-13C HSQC nonasaccharide + 1H-13C HSQC nonasaccharide + + hGal3 H1GalA H1GalB H1GalA H1GalB H1GlcNAcA H1GlcNAcB H1GlcNAcA H1GlcNAcB HSQC rows GalB H4GalA H4GalB 4 H3GlcNAcA H3GlcNAcB H1GalA H1GalB H3bMan3 GlcNAcB GalAGlcNAcA Angew Chem. Int. Ed. 2013, 52, 13789-93 A B A CR_D_ _h_G_a_l_e_c_ti_n_-3________________________________________________________
  • 43. Further challenge: Tetraantennary N-glycan 1H-13C HSQC La3+ 1H-13C HSQC Dy3+ H1 aManC H1 GlcNAc H1 Gal A-D H1 aManA A+C H1 GlcNAc B+D A C D B A D B C H1 bMan H1 GlcNAc2 D C B A 3 2 1 The chemical shifts of the four Galactose moieties are isochronous The chemical shifts of the four GlcNAc units are isochronous in pairs (A, C & B, D)
  • 44. Overall fitting A, B, C and D arms gg_gt/gg_gg 60/40 Qf 0.16 single tensor R2 = 0,9459 1,400 1,200 1,000 0,800 0,600 0,400 0,200 gg_gt PCS (Exp, calc) H1 GlcNAc C (0.4, 0.46) H2 GlcNAc C (0.38, 0.31) H3 GlcNAc C (0.42, 0.42) H5 GlcNAc C (0.44,0.45) H1 Mana 1-6 (0.43, 0.43) H1 GlcNAc A (0.18, 0.12) H1 GlcNAc B (0.29, 0.22) H1 Gal C (0.28, 0.27) C D A B What about the interaction with a receptor? A. Canales, with C. Unverzagt & I. Boos submitted 0,000 0,000 0,200 0,400 0,600 0,800 1,000 1,200 1,400
  • 45. Line broadening upon addition of h-galectin3 HSQC rows H4 GalA H4 GalD H4 GalB H4 GalC % intensity respect to the sample without protein 89% 56% 33% 34% HSQC 1H-13C tetraantennary N-glycan +Dy3+ HSQC 1H-13C tetraantennary N-glycan +Dy3+ +gal3, Molar ratio 12:1 H2 GalA H2 GalD H2 GalB 76% 55% 44% H2 GalC 46% B A C D B and C arms are more affected, followed by arm D Branch A is basically non-accesible to hGal3 A. Canales, with C. Unverzagt & I. Boos submitted
  • 46. B A C D A and D arms are less accessible to potential binders than C and B Paramagnetic lanthanides: Breaking pseudosymmetry and unraveling “hidden” molecular recognition features 19F-containing glycomimetics: Mimicking conformational behavior and plasticity Unraveling the key role of carbohydrate-aromatic interactions for sugar recognition Applications of NMR techniques for addressing molecular recognition events, from the ligand (1H and 19F) and receptor’s perspective
  • 47. J. Jiménez-Barbero, F. J. Cañada CIB-CSIC, Madrid, SPAIN FORMER MEMBERS J. L. Asensio (IQOG) J. F. Espinosa, A Rivera P Vidal, L Calle (Lilly) A. Poveda (UAM) M. Martín-Pastor (USC) J. I. Santos (UPV-SS) F. Corzana (La Rioja) J. Pérez-Castells, CEU N. Aboitiz (Army) E. Montero (UK) P. Groves, F. Marcelo (Lisbon) S. Mari (Milano) M. Fontanella (Padova) C. Venturi (Florence) V. Gargiulo, C de Castro R Marchetti (Napoli) M. Politi (Genoa) G. Cuevas, M. I. Chavez, M Morando B. Domínguez, K. Ramírez (UNAM) V. García-Aparicio, J. J. Hdez-Gay A. García-Herrero (Canada) K. Martínez-Mayorga, JL Medina (Florida) J. Ribeiro (Grenoble) L. Nieto (Eindhoven) V. Roldós (Montevideo) A. Mallagaray (Luebeck) LANTHANIDES C. Unverzagt (Bayreuth) J. Pérez-Castells (USP-CEU) HML, Galectins H.-J. Gabius (München) S-I. Nishimura (Sapporo) Heparin/FGF/FGFR M. Martín-Lomas (BMG) G. Giménez-Gallego (CIB) P.M. Nieto (IIQ) R. J. Linhardt (NY) Hevein, Chitin A. Rdgez-Romero (UNAM) G. Asensio (Valencia) D. Andreu (Barcelona) M. Vila (Barcelona) M. Muraki (Tsukuba) € •MINECO (Spain) •CAM (Madrid) •FP6, FP7, H2020 (EU): •GlycoHit •Dynano •Glycopharm •TOLLerant •COST BM1003, CM1102 •Mizutani •Cariplo •Pharmamar, Rovi, Vertex, ImmunoTek, Syngenta •Marató TV3 •CSIC (PIF) CIB-CSIC (2014) Ana Ardá Angeles Canales Ana Manzano Carmen Fernández-Alonso Alberto Fernández-Tejada Dolores Díaz Pilar Blasco Khouzaima El Biari Alvaro Berbís Luca Unione Javier Sastre Silvia Galante Beatriz Fernández de Toro Modeling S. Martín-Santamaría (USP-CEU, Madrid) NMR (800 MHz) M. Bruix (IQFR)

Editor's Notes

  1. Para ello, se llevo a cabo una aproximación combinada de métodos de RMN basados en la observación del ligando, como son el STD y el NOESY transferido. Y de métodos computacionales como Docking, DM, y Corcema-ST. Mapping the binding sites of microtubule-stabilizing agents by using an integrated NMR and computational approach. Docetaxel, a semisynthetic analogue of taxol that present better solubility than taxol, was chosen for this study. Docetaxel differs from Taxol at two positions in its chemical structure. It has a hydroxyl functional group on carbon 10, whereas Taxol has an acetate ester and a tert-butyl substitution exists on the phenylpropionate side chain. The carbon 10 functional group change causes docetaxel to be more lipid soluble than Taxol Docking was used to investigate the possible binding conformations of the ligands within the taxol binding domain of β-tubulin. The tubulin samples were prepared by removing sucrose, Mg2+, and H2O
  2. De estos agentes estabilizantes de MTb Tal vez el mas conocido sea el taxol. Este se pudo cristalizar en presencia de láminas de tubulina permitio identificar el sitio de union del taxol a la subunidad beta aunque al ser una estructura de muy baja resolucion, no se pudo caracterizar bien la conformacion del ligando. Se sabe que estas moleculas tan diversas compiten por el mismo sitio de union a la tubulina, pero no se tiene mucha informacion de como se unen a la proteina, y ni siquiera si son capaces de unirse a la forma no polimerizada de la proteina. Por ello sigue teniendo mucha importancia el estudio estructural de estas moleculas en el estado asociado, para el diseño de farmacos mejores-. Taxol (paclitaxel, Figure 1), a highly functionalized diterpenoid isolated from Taxus brevifolia (Pacific Yew tree), was the first compound recognized to interact specifically and reversibly with the β-subunit of the tubulin heterodimer, promoting microtubule stabilization and consequently, blocking cells in the mitotic phase of the cell cycle. Here are shown other promising anticancer agents that competitively inhibit the binding of paclitaxel to tubulin polymers, indicating an overlapping binding site in the β-tubulin cavity, which can accommodate a variety of structurally diverse MSAAs in unique and independent ways. But no much information is know about how these ligands bind to the protein at the molecular level. In addition, microtubule structure determination both in the presence and in the absence of MSAs remains a challenge for structural biology. The complexity of this system, where different aggregation states of the alpha beta-heterodimer can coexist in solution.Since the size of the protien is too big to be observable by NMR, we have been studied this system from a NMR ligand based approach. Los Taxanos son terpenos complejos producidos porlas plantas del género Taxus (tejos). Originalmente se aislaron de Taxus brevifolia, aunque actualmente son sintetizados de modo artificial. Su mecanismo principal de acción es la alteración de la función de los microtúbulos celulares mediante la estabilización de su formación. Los microtúbulos son esenciales para la reproducción celular por mitosis, de modo que mediante su inactivación se inhibe la división celular. Paclitaxel—utilizado en el tratamiento del cáncer de pulmón, cáncer de ovario, cáncer de mama y formas avanzadas del sarcoma de Kaposi.[6] Docetaxel—Utilizado para tratar cáncer de mama, de ovario y cáncer de pulmón de células no pequeñas.[7] [8]
  3. But not only the chemical nature is important is important. I´m swicth into lectins now, to show other factors that regulate the interactions between sugar and carbohydrates.