The Nuclear Magnetic Resonance and Molecular Recognition (NMRMR) group led by Prof. Cañada is interested, from a general point of view, in the study of molecular recognition processes with special emphasis on carbohydrate-receptor interactions applying and developing methodologies based on NMR with the main objective of characterizing the structure and dynamics of carbohydrates, proteins, their complexes and, in general, other biomolecules in solution. The achievement of this objective will allow both understanding at atomic scale the participation and importance of carbohydrates in essential biological processes and facilitating the design of new molecules and/or analogues of carbohydrates in order to modulate those processes.
With the focus on reaching these objectives of characterization of the processes of molecular recognition, the NMRMR group follows a multidisciplinary approach, beyond its specialization in the use and development of methodologies based on NMR, which covers organic synthesis, molecular biology and computational chemistry within a collaborative strategy with other research groups either at CIB or from other national and international research institutions.
The group has been established at CIB since 2002 and has a close collaboration with the group of Prof. Jiménez Barbero, who led the group at CIB until 2014, now based at CICbioGUNE (Bilbao).
From the beginning, the NMRMR group has been conducting studies on the interactions of carbohydrates with different types of receptors: lectins with mammalian (Galectins and C-lectins), viral (adenovirus and influenza virus with sialylated oligosacharides) or plant origins (hevein domains, concanavalin, ricin and others), glycosidases (characterization of substrates, reaction products and inhibitors) and antibodies (against glycogen and tumor antigens). In this context, the group is carrying out a collaborative project with the company Inmunotek with the objective of developing antineoplastic or anti-allergic vaccines that incorporate carbohydrates
Experiments based on chemical shift perturbation (CSP), saturation transfer difference (STD), transferred nuclear Overhausser effect (TR-NOE), diffusion Coefficient-based strategies (DOSY Diffusion Ordered Spectroscopy) and relaxation time perturbation (T2 filters) have been developed and used routinely in those studies. In favorable cases, the characterization by NMR techniques of the three-dimensional solution structures of the receptors and their complexes with carbohydrates has also been carried out.
On the other hand, the group continues to develop new strategies based on the observation by NMR of other nuclei such as fluorine (19F) or in the provocation of perturbations in the usual nuclei (1H, 13C, 15N) by chemical labeling, either of ligands or receptors, with paramagnetic cations (as lanthanides)
These NMR methodologies have been extended to the study of other biological systems not directly related to carbohydrates in collaboration with other groups at CIB (e.g. tubulin, vimentin, FTsZ, oxidases) or external, national and international (chemical models of nucleic acid-carbohydrate recognition, carbohydrate artificial receptors, peptidoglycan and bacterial polysaccharides structures).
Mónico, A. Martínez-Senra, E., Cañada, FJ. Zorrilla, S. Pérez-Sala, D. . Drawbacks of Dialysis Procedures for Removal of EDTA. PLoS One. 18, 12
Ardá, A., Coelho, H., De Toro, B.F., Galante, S., Gimeno, A., Poveda, A., Sastre, J., Unione, L., Valverde, P., Javier Cañada, F., Jiménez-Barbero, J. . Recent advances in the application of NMR methods to uncover the conformation and recognition features of glycans. Carbohydrate Chemistry. 42:47-82.
Gimeno, A., Reichardt, N.-C., Cañada, F.J., Perkams, L., Unverzagt, C., Jiménez-Barbero, J., Ardá, A. . NMR and Molecular Recognition of N-Glycans: Remote Modifications of the Saccharide Chain Modulate Binding Features. ACS Chemical Biology. 12:1104-1112.
Sáez-Calvo, G.; Sharma, A.; Balaguer, F.; Barasoain, I.; Rodríguez-Salarichs, J. Olieric, N.; Muñoz-Hernández, H; Berbís, M.A.; Wendeborn, S.; Peñalva, M.A.; Matesanz, R. Canales, A.; Prota, A.E.; Jímenez-Barbero, J.; Andreu, J.M.; Lamberth, C.; Steinmetz, M.O. and Díaz, J.F. . Triazolopyrimidines Are Microtubule-Stabilizing Agents that Bind the Vinca Inhibitor Site of Tubulin. Cell Chemical Biology, 24 (6), 737-750
Espaillat, A., Forsmo, O., El Biari, K., Björk, R., Lemaitre, B., Trygg, J., Cañada, F.J., De Pedro, M.A., Cava, F. . Chemometric Analysis of Bacterial Peptidoglycan Reveals Atypical Modifications That Empower the Cell Wall against Predatory Enzymes and Fly Innate Immunity. Journal of the American Chemical Society. 138:9193-9204.
Boutet, Julien, Blasco, Pilar, Guerreiro, Catherine, Thouron, Françoise, Dartevelle , Sylvie, Nato , Farida, Cañada, F. Javier, Ardá, Ana, Phalipon, Armelle, Jiménez-Barbero, Jesús, Mulard, Laurence A. . Detailed Investigation of the Immunodominant Role of O-Antigen Stoichiometric O-Acetylation as Revealed by Chemical Synthesis, Immunochemistry, Solution Conformation and STD-NMR Spectroscopy for Shigella flexneri 3a. Chem. Eur. J. 22:10892-10911.
Ippel, H., Miller, M.C., Vértesy, S., Zheng, Y., Cañada, F.J., Suylen, D., Umemoto, K., Romanò, C., Hackeng, T., Tai, G., Leffler, H., Kopitz, J., André, S., Kübler, D., Jiménez-Barbero, J., Oscarson, S., Gabius, H.-J., Mayo, K.H. . Intra- and intermolecular interactions of human galectin-3: Assessment by full-assignment-based NMR. Glycobiology. 26:888-903.
Manzano, A.I., Javier Cañada, F., Cases, B., Sirvent, S., Soria, I., Palomares, O., Fernández-Caldas, E., Casanovas, M., Jiménez-Barbero, J., Subiza, J.L. . Structural studies of novel glycoconjugates from polymerized allergens (allergoids) and mannans as allergy vaccines. Glycoconjugate Journal. 33:93-101.
Jiménez-Moreno, E., Montalvillo-Jiménez, L., Santana, A.G., Gómez, A.M., Jiménez-Osés, G., Corzana, F., Bastida, A., Jiménez-Barbero, J., Canada, F.J., Gómez-Pinto, I., González, C., Asensio, J.L. . Finding the Right Candidate for the Right Position: A Fast NMR-Assisted Combinatorial Method for Optimizing Nucleic Acids Binders. Journal of the American Chemical Society. 138:6463-6474.
Rompiendo las fronteras del reconocimiento molecular de carbohidratos mediante RMN. Proteínas, anticuerpos y acidos nucleicos.MINECO, CTQ2015-64597-C2-2-P 2016-2018
Nueva vacuna antineoplásica basada en el carbohidrato tumoral Ca10
MINECO, RETOS COLABORACIÓN, RTC-2015-3805-1 01/11/2015 Hasta: 31/10/2018
Coordinador: Empresa INMUNOTEK
El proyecto está siendo financiado con fondos FEDER, con el objetivo de promover el desarrollo tecnológico, la innovación y una investigación de calidad
RMN y reconocimiento molecular. Interacciones Proteina-Carbohidrato y ácido nucleico-carbohidrato
MECC CTQ2012-32025 --enero 2013-diciembre 2015
During last years, we have contributed to the study of diverse molecular recognition processes of sugars by lectins, enzymes, antibodies and nucleic acids. These studies have been disseminated to the Society on a number of publications, book chapters and reviews and on many lectures at symposia and institutions. Also, all PhD and Postdoctoral associates have presented several dozens of posters and oral communications at National and International symposia. We have performed rigorous analysis of the interactions which take place at a variety of binding sites on different systems and, in some cases, deduced the thermodynamic parameters of the interactions. Generalization is still difficult and more work seems necessary also to define the importance of motion and dynamics for the interaction to take place and to make use of the knowledge to effectively design better ligands and inhibitors. We have employed till now model lectins and synthetic models (artificial lectins) as well as designed saccharides to interact with nucleic acids. We have pioneered the use of trNOE to deduce the bioactive conformation of saccharides and glycomimetics and the employment of STD experiments to validate the ligand epitope. We have demonstrated that in most cases, by employing flexible ligands, the architecture of the binding site rules the recognition process and that the same analogue might be recognized in three different geometries by three distinct receptors. Also, in the glycosidase context, we have determined for the first time, the bioactive conformation of a competitive inhibitor bound to an enzyme in solution as well as the bound conformation of a natural substrate to a mutated inactive enzyme. Indeed, we demonstrated that the enzyme selects a high energy conformation of the substrate, within the pathway towards the transition state to minimize the energy needs for the hydrolysis to take place. From the viewpoint of the conformational study of sugars, glycomimetics, lectins and their interactions, we have performed key developments and Concepts that have been recognized by invitations in different forums. The first NMR structure in solution of a lectin/sugar complex was published by us, as well as the first experimental characterization of the energy value of the stereoelectronic component of the exo-anomeric effect. Also, we have recently provided definitive proof of the importance of CH-pi interactions for sugar recognition by receptors. From the methodology viewpoint we have been the first group to demonstrate that intact cells may be employed to deduce binding features of the interactions between receptors and ligands, without prior requirement of purification of the protein. New developments are hopefully expected from our group.
Team. At present: 3 PhD students, 1 post-docs, 1 full professors. The group has trained 13 PhD students in the last 10 years. The research group in Madrid has a long-standing experience and international reputation in the application of NMR methods to the study of the three dimensional structure of proteins and their complexes with carbohydrates and glycomimetics. Apart of NMR, the team has also access to other techniques, which may allow deducing other physicochemical parameters relevant to the study of intermolecular interactions.
Prof J. Cañada (PhD in Chemistry) is full Professor from CSIC from 2007. He has published more than 100 publications and has delivered a variety of lectures at national and international meetings and Institutions. He has supervised 5 PhD Thesis. His expertise is in the molecular recognition, NMR, biochemistry and molecular biology fields.