SUPRAMOLECULAR CHEMISTRY
Group Leader: Ignacio Alfonso
Supramolecular chemistry is the “chemistry beyond the molecule” and deals with the interactions between chemical species in an ordered and hierarchical way, leading to the formation of well-defined supramolecules. We mainly work in the fields of molecular recognition, programmed folding and self-assembling processes, using a large variety of experimental and theoretical approaches. Our scientific activity is inspired by the structural and interactional complexity of living organisms. Trying to understand and apply both forms of complexity in chemical systems, our research encompasses the molecular recognition of biologically relevant molecules, the self-assembly of organic compounds, and the study of dynamic combinatorial chemistry.
Thus, we focus in the discovery, preparation and study of new synthetic receptors for biologically interesting small-molecules and ions (amino acids, anions) and sequences or domains in macrobiomolecules. Typically, we make use of pseudopeptidic molecular cages for the recognition, binding or transport of small molecules. We also employ dynamic combinatorial chemistry for the development of receptors and sensors (including more complex targets, i. e. peptide or DNA sequences) as well as for understanding the behaviour of complex chemical systems. It must be highlighted that aqueous media are used throughout our research to ensure the compatibility of our sensors with biological media
Moreover, we use supramolecular approaches to synthetic procedures, such as templated synthesis or catalysis. Based on our understanding of molecular recognition events and self-assembly, we develop highly efficient asymmetric organocatalysts for organic synthesis. We intend to make water compatible catalysts operational under sustainable conditions
Additionally, we collaborate with several groups (both at IQAC and outside) to study biomolecular and biomimetic systems from a supramolecular point of view.
-
Molecular recognition of species with biological interest
In this project, we propose the synthesis and supramolecular study of abiotic receptors for chemical species with biological interest. We are mainly focused on anionic entities because about 75% of cofactors and enzyme substrates are anionic at physiological pH. Moreover, since many biomolecules are chiral and they are present in nature in enantiopure form, the enantioselective recognition of chiral anions is also a hot topic within our research fields. The corresponding molecular recognition processes are studied using a large variety of experimental (potentiometric, spectroscopic, etc…) and theoretical tools. Besides, we also carry out a deep structural characterization of the supramolecular complexes thus formed. We have studied the molecular recognition of carboxylates, amino acids, short peptides and oligonucleotides with open-chain and macrocyclic synthetic receptors. Lately we have become interested in more complex structures such as biomacromolecules (DNA, peptides, polyamines) that are related to important diseases such as Alzheimer’s or cancer processes.
Staff: Ignacio Alfonso.
-
Constitutional Dynamic Chemistry (CDC)
This project deals with the preparation of dynamic mixtures of interconverting species operating under thermodynamic control. To do that, we use a Dynamic Covalent Chemistry approach, based on the implementation of reversible bonds (such as imine or disulfide bonds). The formation of the different species within these dynamic mixtures depends on the chemical information stored in the corresponding building blocks. Eventually, the chemical system could respond to an external stimulus and adapt its constitution accordingly, after a molecular evolution process. If this stimulus is a target substrate, this methodology allows the identification and isolation of improved synthetic receptors for that target. We are interested in the study of these processes from the conceptual perspective, as well as for synthetic applications in template-assisted processes. The study of the molecular networks that form the different species involved in the library is important from a structural point of view and has implications in the understanding of biological processes and even in the events that conducted to the emergence of life. Using the lessons learned in these Dynamic Covalent Libraries we can access to new receptors and even sensors that give a readable signal in the presence of a relevant analyte.
Staff: Ignacio Alfonso, Jordi Solà.
-
Study of self-assembling properties
Some synthetic molecules are able to hierarchically organize in supramolecular species through non-covalent interactions. These new self-assembled species are usually in the nano-micrometer scales, which give them emerging properties for structural, functional or delivering applications. We are especially interested in understanding the self-assembling process at the molecular level, using a combination of many different experimental techniques. This approach represents the bottom-up approximation to nanotechnology, which is the natural perspective from a chemist’s point of view.
Staff: Ignacio Alfonso
-
Asymmetric Supramolecular Catalysis
Based on our understanding of molecular recognition events and self-assembly, we also develop highly efficient asymmetric organocatalysts for organic synthesis. To this aim, we have developed a methodology based in dynamic chemistry that allows the preparation of multifunctional catalysts by self-assembly of their constituent parts. This strategy permits to generate and investigate multiple catalysts with a limited synthetic effort. We are particularly interested to make water compatible catalysts operational under sustainable conditions.
Staff: Ciril Jimeno, Jordi Solà.
Scientific staff
Ignacio Alfonso
Scientific Researcher
ignacio.alfonso@iqac.csic.es
Ciril Jimeno
Tenured Scientist
ciril.jimeno@iqac.csic.es
Jordi Solà
Tenured Scientist
jordi.sola@iqac.csic.es
Lab people
Daniel Carbajo
Postdoctoral Researcher
daniel.carbajo@iqac.csic.es
Silvia Pujals
Ramon & Cajal Researcher
silvia.pujals@iqac.csic.es
Mónica Martínez
Postdoctoral Researcher
monica.martinez@iqac.csic.es
- A super-resolution and transmission electron microscopy correlative approach to study intracellular trafficking of nanoparticles
Andrian, T., Muela, Y., Delgado, L., Albertazzi, L., Pujals, S.
Nanoscale, 15 (35), pp. 14615-14627
- Super-resolution imaging of antibody-conjugated biodegradable periodic mesoporous organosilica nanoparticles for targeted chemotherapy of prostate cancer
Das, P., Pujals, S., Ali, L.M.A., Gary-Bobo, M., Albertazzi, L., Durand, J.-O.
Nanoscale, 15 (28), pp. 12008-12024. 2023
- Synaptic oligomeric tau in Alzheimer’s disease — A potential culprit in the spread of tau pathology through the brain
Martí Colom-Cadena,Caitlin Davies,Sònia Sirisi, Ji-Eun Lee, Elizabeth M. Simzer, Makis Tzioras, Marta Querol-Vilaseca, Érika Sánchez-Aced, Ya Yin Chang, Kristjan Holt, Robert I. McGeachan, Jamie Rose, Jane Tulloch, Lewis Wilkins, Colin Smith, Teodora Andrian, Olivia Belbin, Sílvia Pujals, Mathew H. Horrocks, Alberto Lleó and Tara L. Spires-Jones
Neuron 111, 1–14, 2023 - An introduction to one- and two-dimensional lineshape analysis of chemically exchanging systems
Christopher A. Waudby, Ignacio Alfonso
Journal of Magnetic Resonance Open 16–17 (2023) 100102
- An introduction to one- and two-dimensional lineshape analysis of chemically exchanging systems
Waudby, C.A., Alfonso, I.
Journal of Magnetic Resonance Open, 16-17, art. no. 100102, 2023.
- Multivalent effect of peptide functionalized polymeric nanoparticles towards selective prostate cancer targeting
Murar, M., Pujals, S., Albertazzi, L.
Nanoscale Advances, 5 (5), pp. 1378-1385. 2023
- Pseudopeptidic host adaptation in peptide recognition unveiled by ion mobility mass spectrometry
Lucia Tapia, Yolanda Pérez, Jordi Solà, Santiago V. Luis, Ignacio Alfonso and Cristian Vicent
Analyst, 2022,147, 5546-5556
- A Degenerate Metal-Templated Catalytic System with Redundant Functional Groups for the Asymmetric Aldol Reaction
Alba Sors-Vendrell, Albert Ortiz, Diego Meneses, Ignacio Alfonso, Jordi Solà and Ciril Jimeno
J. Org. Chem. 2022, 87, 7509−7513
- Dynamic Combinatorial Optimization of In Vitro and In Vivo Heparin Antidotes
Daniel Carbajo, Yolanda Pérez, Marta Guerra-Rebollo, Eva Prats, Jordi Bujons, and Ignacio Alfonso
J. Med. Chem. 2022, 65, 4865−4877
- Structure-Activity Studies of Novel Di-substituted [1,2,5]oxadiazolo [3,4-b]pyrazine Analogs Targeting the A-loop Regulatory Site of p38 MAP Kinase
Carrasco, E., Gomez-Gutierrez, P., Campos, P.M., Vega, M., Messeguer, A., Perez, J.J.
Current Medicinal Chemistry, 29 (9), pp. 1640-1653. 2022
- Inhibition of Sema-3A Promotes Cell Migration, Axonal Growth, and Retinal Ganglion Cell Survival
Anat Nitzan; Miriam Corredor-Sanchez; Ronit Galron; Limor Nahary, Mary Safrin; Marina Bruzel; Alejandra Moure; Roman Bonet; Yolanda Pérez; Jordi Bujons; Enriqueta Vallejo-Yague; Hagit Sacks; Michael Burnet; Ignacio Alfonso; Angel Messeguer; Itai Benhar; Ari Barzilai; Arieh S. Solomon
Translational Vision Science & Technology November 2021, Vol.10, 16
- Molecular cages for biological applications
Lucía Tapia, Ignacio Alfonso and Jordi Solà
Org. Biomol. Chem., 2021,19, 9527-9540
- Semaphorin 3A—Glycosaminoglycans Interaction as Therapeutic Target for Axonal Regeneration
Pérez, Y.; Bonet, R.; Corredor, M.; Domingo, C.; Moure, A.; Messeguer, À.; Bujons, J.; Alfonso, I.
Pharmaceuticals 2021, 14, 906.
- Modulation of Src Kinase Activity by Selective Substrate Recognition with Pseudopeptidic Cages
Tapia, L., Solozabal, N., Solà, J., Pérez, Y., Miller, W.T., Alfonso, I.
Chemistry - A European Journal, 27 (37), pp. 9542-9549, 2021
- Discovery of novel 2,3,5-trisubstituted pyridine analogs as potent inhibitors of IL-1β via modulation of the p38 MAPK signaling pathway
Carrasco, E., Gomez-Gutierrez, P., Campos, P.M., Vega, M., Messeguer, A., Perez, J.J.
European Journal of Medicinal Chemistry, 223, art. no. 113620, 2021
- Amino Acylguanidines as Bioinspired Catalysts for the Asymmetric Aldol Reaction
Ciril Jimeno
Molecules 2021, 26(4), 826
- Dynamic Stereoselection of Peptide Helicates and Their Selective Labeling of DNA Replication Foci in Cells
Dr, Jacobo Gómez‐González, Dr. Yolanda Pérez, Dr. Giuseppe Sciortino, Lorena Roldan‐Martín, Prof. José Martínez‐Costas, Prof. Jean‐Didier Maréchal, Dr. Ignacio Alfonso, Prof. Miguel Vázquez López, Prof. M. Eugenio Vázquez
Angew. Chem. Int. Ed. 2021, 60,2–10
- Spontaneous macrocyclization through multiple dynamic cyclic aminal formation
Carbajo, D., Ruiz-Sánchez, A.J., Nájera, F., Pérez-Inestrosa, E., Alfonso, I.
Chemical Communications, 57 (10), pp. 1190-1193. 2021
- Spontaneous macrocyclization through multiple dynamic cyclic aminal formation
Daniel Carbajo, Antonio Jesús Ruiz-Sánchez, Francisco Nájera, Ezequiel Pérez-Inestrosa and Ignacio Alfonso
Chem. Commun., 2021,57, 1190-1193
- Centrally Active Multitarget Anti-Alzheimer Agents Derived from the Antioxidant Lead CR-6
Pérez-Areales, F.J., Garrido, M., Aso, E., Bartolini, M., De Simone, A., Espargaró, A., Ginex, T., Sabate, R., Pérez, B., Andrisano, V., Puigoriol-Illamola, D., Pallàs, M., Luque, F.J., Loza, M.I., Brea, J., Ferrer, I., Ciruela, F., Messeguer, A., Muñoz-Torrero, D.
Journal of medicinal chemistry, 63 (17), pp. 9360-9390. 2020
- Desulfitative Thioalkylation of Alkenes
Cao, L., Jimeno, C., Renaud, P.
Advanced Synthesis and Catalysis, 2020
- MCR-ALS analysis of 1H NMR spectra by segments to study the zebrafish exposure to acrylamide
Pérez, Y., Casado, M., Raldúa, D., Prats, E., Piña, B., Tauler, R., Alfonso, I., Puig-Castellví, F.
Analytical and Bioanalytical Chemistry, 2020
- Live-Cell-Templated Dynamic Combinatorial Chemistry
Carbajo, D., Pérez, Y., Bujons, J., Alfonso, I.
Angewandte Chemie - International Edition, 2020.
- Live‐Cell‐Templated Dynamic Combinatorial Chemistry
Daniel Carbajo, Yolanda Pérez, Jordi Bujons, Ignacio Alfonso
Angew. Chem. Int. Ed.. doi:10.1002/anie.202004745
- Molecular Recognition of Zwitterions with Artificial Receptors
Alfonso, I., Solà, J.
Chemistry - An Asian Journal, 2020
- Synthesis of second-generation self-assembling Gemini Amphiphilic Pseudopeptides
Lotfallah, A.H., Isabel Burguete, M., Alfonso, I., Luis, S.V.
Journal of Colloid and Interface Science, 564, pp. 52-64. 2020
- Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain
Raldúa, D., Casado, M., Prats, E., Faria, M., Puig-Castellví, F., Pérez, Y., Alfonso, I., Hsu, C.-Y., Arick II, M.A., Garcia-Reyero, N., Ziv, T., Ben-Lulu, S., Admon, A., Piña, B.
Scientific Reports, 10 (1), art. no. 312, 2020
- pH‐dependent chloride transport by pseudopeptidic cages for the selective killing of cancer cells in acidic microenvironments
Ignacio Alfonso, Lucía Tapia, Yolanda Pérez, Michael Bolte, Josefina Casas, Jordi Solà, Roberto Quesada
Angew. Chem. Int. Ed. 10.1002/anie.201905965
- pH‐Dependent Chloride Transport by Pseudopeptidic Cages for the Selective Killing of Cancer Cells in Acidic Microenvironments
Tapia, L., Pérez, Y., Bolte, M., Casas, J., Solà, J., Quesada, R., Alfonso, I.
Angewandte Chemie - International Edition, 58 (36), pp. 12465-12468. 2019
- Structurally Selective Assembly of a Specific Macrobicycle from a Dynamic Library of Pseudopeptidic Disulfides
Dr. María Lafuente, Dr. Ignacio Alfonso, Dr. Jordi Solà
ChemSystemsChem, 2019,6,e1900002
- Carboxylate-functionalized foldamer inhibitors of HIV-1 integrase and Topoisomerase 1: artificial analogues of DNA mimic proteins
Corvaglia, V., Carbajo, D., Prabhakaran, P., Ziach, K., Mandal, P.K., Santos, V.D., Legeay, C., Vogel, R., Parissi, V., Pourquier, P., Huc, I.
Nucleic Acids Research, 47 (11), pp. 5511-5521. 2019
- An efficient dynamic asymmetric catalytic system within a zinc-templated network
Anna Serra-Pont, Ignacio Alfonso, Jordi Solà and Ciril Jimeno
Chem. Commun., 2019,55, 7970-7973
- Axonal and Myelin Neuroprotection by the Peptoid BN201 in Brain Inflammation
Villoslada, P., Vila, G., Colafrancesco, V., Moreno, B., Fernandez-Diez, B., Vazquez, R., Pertsovskaya, I., Zubizarreta, I., Pulido-Valdeolivas, I., Messeguer, J., Vendrell-Navarro, G., Frade, J.M., López-Sánchez, N., Teixido, M., Giralt, E., Masso, M., Dugas, J.C., Leonoudakis, D.,Lariosa-Willingham, K.D., Steinman, L., Messeguer, A.
Neurotherapeutics, . 2019
- Comparative analysis of 1H NMR and 1H–13C HSQC NMR metabolomics to understand the effects of medium composition in yeast growth
Puig-Castellví, F., Pérez, Y., Piña, B., Tauler, R., Alfonso, I.
Anal. Chem., 2018, 90 (21), pp 12422–12430
- Dynamic Covalent Identification of an Efficient Heparin Ligand
Corredor M, Carbajo D, Domingo C, Pérez Y, Bujons J, Messeguer A, Alfonso I.
Angew Chem Int Ed 2018, 57, 11973-11977.
- A dynamic chemical network for cystinuria diagnosis
M. Lafuente, M.J. Solà, I. Alfonso.
Angew. Chem. Int. Ed. 57, 1-5, 2018 - Deciphering the Underlying Metabolomic and Lipidomic Patterns Linked to Thermal Acclimation in Saccharomyces cerevisiae
Puig-Castellví, F., Bedia, C., Alfonso, I., Piña, B., Tauler, R.
J Prot Research 2018, 17 (6), 2034-2044.
- Unraveling the multistimuli responses of a complex dynamic system of pseudopeptidic macrocycles.
Valdivielso, A. M.; Puig-Castellví, F.; Atcher, J.; Solà, J.; Tauler, R.; Alfonso, I.
Chem. Eur. J., 23, 10789-10799, 2017 HOT PAPER & FRONT COVER
- Concentration Effect in the Asymmetric Michael Addition of Acetone to Nitrostyrenes Catalyzed by Primary Amine Thioureas
Günler, Z. I.; Alfonso, I.; Jimeno, C.; Pericàs, M. A.
Synthesis, 49, 319-325, 2017
- Pseudopeptidic Compounds for the Generation of Dynamic Combinatorial Libraries of Chemically Diverse Macrocycles in Aqueous Media
Atcher, J.; Solà, J.; Alfonso, I.
Org. Biomol. Chem., 15, 213-219, 2017.
- Untargeted Assignment and Automatic Integration of 1H NMR Metabolomic Dataset Using a Multivariate Curve Resolution Approach
Puig-Castellví, F; Alfonso, I.; Tauler, R.
Anal. Chim. Acta, 964, 55-66, 2017
- Entropy-driven homochiral self-sorting of a dynamic library
Atcher, J.; Bujons, J.; Alfonso, I.
Chem. Commun., 53, 4274-4277, 2017
- A copper-templated, bifunctional organocatalyst: a strongly cooperative dynamic system for the aldol reaction
Serra-Pont, A.; Alfonso, I.; Solà, J.; Jimeno, C.
Org. Biomol. Chem., 15, 6584-6591, 2017
- From Simplicity to Complex Systems with Bioinspired Pseudopeptides
Alfonso, I.
Chem. Commun., 52, 239-250, 2016
- Cationic Peptides and Peptidomimetics Bind Glycosaminoglycans as Potential Sema3A Pathway Inhibitors
Corredor, M.; Bonet, R.; Moure, A.; Domingo, C.; Bujons, J.; Alfonso, I.; Pérez, Y.; Messeguer, A.
Biophys. Journal, 110, 1291-1303, 2016
- Anion Recognition and Induced Self-Assembly of an -Cyclic Peptide To Form Spherical Clusters
Rodríguez-Vázquez, N.; Amorín, M.; Alfonso. I.; Granja, J. R.
Angew. Chem. Int. Ed, 55, 4504-4508, 2016
- Trichloromethanesulfonyl chloride: a convenient chlorinating reagent for aldehydes
Jimeno, L. Cao, P. Renaud.
Org. Chem., 81, 1251-1255, 2016
- Deciphering the Roles of Multiple Additives in Organocatalyzed Michael Additions
Günler, Z. I.; Companyó, X.; Alfonso, I.; Burés, J.; Jimeno, C.; Pericàs, M. A.
Chem. Commun., 52, 6821-6824, 2016
- Water in asymmetric organocatalytic systems: a global perspective
C. Jimeno
Org. Biomol. Chem., 14, 6147-6164, 2016
- Metal driven assembly of peptidic foldamers: formation of molecular tapes
Solà, J.; Bolte, M.; Alfonso, I.
CrystEngComm, 18, 3793- 3798, 2016
- Pseudopeptidic fluorescent on-off pH sensor based on pyrene excimer emission: Imaging of acidic cellular organelles
Faggi, E.; Serra-Vinardell, J.; Pandey, M.D.; Casas, J.; Fabriàs, G.; Luis, S. V.; Alfonso, I.
Sensor Actuat. B-Chem., 234, 633-640, 2016
- A regioselective synthesis of a new family of β-lactams bearing a triazole moiety as potential apoptosis inhibitors
Garrido, M.; Corredor, M.; Orzáez, M.; Alfonso, I.; Messeguer, A.
ChemistryOpen, 5, 485-494, 2016
- Synthesis and in vitro, ex-vivo and in vivo activity of hybrid compounds linking a potent ROS and RNS scavenger activity with diverse substrates addressed to pass across the blood-brain barrier
L. Vázquez-Jiménez, M. Garrido, M. Miceli, E. Prats, A. Ferrer-Montiel, M. Teixidó, C. Jimeno, A. Messeguer
Eur. J. Med. Chem., 123, 788-802, 2016
- 1H NMR metabolomic study of auxotrophic starvation in yeast using Multivariate Curve Resolution-Alternating Least Squares for Pathway Analysis
Puig-Castellví, F.; Alfonso, I.; Piña, B.; Tauler, R.
Sci. Rep.-UK, 6, 30982, 2016
- Supramolecular Protection from the Enzymatic Tyrosine Phosphorylation in a Polypeptide
Faggi, E.; Pérez, Y.; Luis, S. V.; Alfonso, I.
Chem. Commun., 52, 8142-8145, 2016
- AuNP−Polymeric Ionic Liquid Composite Multicatalytic Nanoreactors for One-Pot Cascade Reactions
Montolio, S.; Vicent, C.; Aseyev, V.; Alfonso, I.; Burguete, M. I.; Tenhu, H.; García-Verdugo, E.; Luis, S. V.
ACS Catal., 6, 7230-7237, 2016
- RENOVACIÓN Y MEJORA DEL ESPECTRÓMETRO DE 400MHZ DEL SERVICIO DE RMN DEL IQAC-CSIC
Referencia: EQC2018-004579-P
Entidad Financiadora: Feder / Ministerio de Ciencia, Innovación y Universidades / Agencia Estatal de Investigación
Investigador Principal: Ignacio Alfonso
Concesión: 2018
El proyecto sufragará el coste de la mejora y renovación del Espectrómetro de 400 MHz del Servicio de RMN del IQAC-CSIC
