Artículos (Instituto de Investigaciones Químicas (IIQ) – CIC Cartuja)

URI permanente para esta colecciónhttps://hdl.handle.net/11441/10959

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Protocols for Monitoring Condensate Formation and Dynamics between the Phase-separating Proteins SET/TAF-Iβ and Cytochrome c
(Elsevier, 2025) Casado Combreras, Miguel Ángel; Rosa Acosta, Miguel Ángel de la; Díaz Moreno, Irene; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Ministerio de Ciencia, Innovación y Universidades (MICIU). España; Junta de Andalucía; Ministerio de Educación. España
The targeting of several nuclear stress-response factors by translocated cytochrome c upon genotoxic stress has been demonstrated in recent years to involve liquid-liquid phase separation. This protocol addresses the need to investigate the mechanisms and features of phase separation of the histone chaperone SET/TAF-Iβ induced by cytochrome c. We provide steps for protein purification and fluorescent labeling, condensate formation, imaging, quantification, and evaluation of their dynamics by fluorescence recovery after photobleaching (FRAP). This protocol can be broadly applied to other protein complexes.
Effect of Electrostatic Immobilization on the Electrochemistry of Human and Horse Cytochrome c
(Elsevier, 2025) Olloqui Sariego, José Luis; Márquez Escudero, Inmaculada; Guerra Castellano, Alejandra; Molero Casado, Miguel; Rosa Acosta, Miguel Ángel de la; Calvente Pacheco, Juan José; Díaz Moreno, Irene; Andreu Fondacabe, Rafael Jesús; Universidad de Sevilla. Departamento de Química Física; Ministerio de Ciencia, Innovación y Universidades (MICIU). España
Protein film voltammetry is a sensitive tool to characterize the electron transfer properties of redox proteins in a variety of environments and conformational states. Here, a detailed voltammetric study aimed to explore the effect of electrostatic immobilization on the electron transfer thermodynamics and kinetics of adsorbed human- and horse- cytochrome c was carried out. For this purpose, the two cytochromes were adsorbed on thiol monolayers (SAM) with different immobilization strengths and donor–acceptor distances. While thermodynamic redox parameters do not seem to be affected by the monolayer thickness and charge density, electron transfer kinetics are significantly modulated by the protein immobilization strength. Stronger protein–SAM electrostatic interactions result in lower electron transfer rates in both non-adiabatic and friction kinetic regimes. This behavior is further characterized by smaller pre-exponential factors and activation enthalpies in Arrhenius type plots. These kinetic results in the physiologically relevant non-adiabatic electron transfer regime are shown to be consistent with the recently developed Matyushov's theoretical formulation of protein electron transfer. Moreover, a comparison between the kinetic parameters of the two cytochrome variants supports the hypothesis that differences between their electron transfer rates originate in their structural flexibility to accommodate the conformational changes required to form the precursor complex between cytochrome and a negatively charged redox partner.
Light-responsive glycosidase inhibitors: Tuning enzyme selectivity and switching factors through integrated chemical and optoglycomic strategies
(Elsevier, 2025-07-15) Rivero Barbarroja, Gonzalo; Maisonneuve, Stéphane; Xie, Juan; García Fernández, José Manuel; Ortiz Mellet, Carmen; Universidad de Sevilla. Departamento de Química Orgánica; Ministerio de Ciencia, Innovación y Universidades (MICIU). España
Photopharmacology leverages light-responsive drugs to achieve spatiotemporal control over their activation and interactions with biological targets. This high level of precision is particularly crucial for therapeutic strategies that require sequential drug-target binding and dissociation, such as pharmacological chaperones (PCs) for lysosomal storage disorders (LSDs). PCs must tightly bind misfolded glycosidases in the endoplasmic reticulum (ER) to promote proper folding, yet efficiently dissociate in the lysosome to restore enzymatic function. Here, we demonstrate that azobenzene-equipped, photoswitchable sp2-iminosugars can fulfill these criteria by exploiting differential E-/Z-isomer interactions with aglycone-accommodating regions of target glycosidases. A diversity-oriented strategy was implemented, incorporating variations in glycomimetic portions, linkers, azobenzene substitution patterns, distal substituents, and valency to fine-tune light and temperature responsiveness. This approach yielded derivatives capable of selectively switching between α- and β-glucosidase inhibition, as well as conjugates exhibiting reversible nanomolar inhibition of human glucocerebrosidase, the dysfunctional enzyme in Gaucher disease, with remarkable switching factors under conditions that mirror the scenario at the ER and the lysosome. The results expand the scope of optoglycomics by providing a framework for designing photocommutators that enable reversible glycosidase modulation and laying the foundation for next-generation photoresponsive glycosidase inhibitors with therapeutic potential in LSDs and broader biomedical applications.
Exploring a Novel Anti-Inflammatory Therapy for Diabetic Retinopathy Based on Glyco-Zeolitic-Imidazolate Frameworks
(Multidisciplinary Digital Publishing Institute (MDPI), 2025-06-17) Díaz Paredes, Elena; Martín Loro, Francisco; Rodríguez Marín, Rocío; Gómez Jaramillo, Laura; Sánchez Fernández, Elena Matilde; Carrillo Carrión, Carolina; Arroba, Ana I.; Universidad de Sevilla. Departamento de Química Orgánica; Ministerio de Ciencia, Innovación y Universidades (MICIU). España; Instituto de Salud Carlos III
Diabetic retinopathy is an ocular disease caused by changes in the expression of inflammatory mediators and increased oxidative stress in the retina and is the leading cause of vision loss in diabetic patients. Currently, there is no treatment capable of reversing retinal damage, which represents a significant burden on the quality of life of patients. (1R)-1-Dodecylsulfonyl-5N,6O-oxomethylidenenojirimycin stands outs as a prototype of the sp2-iminoglycolipids family for its beneficial neuroprotective effect against this chronic eye disease. Critical issues related to the low solubility and bioavailability of this glycolipid in biological settings are overcome by its encapsulation in a Zeolitic-Imidazolate Framework (ZIF) structure, resulting in homogeneous and biocompatible GlycoZIF nanoparticles. Cell studies show an enhanced cellular uptake compared with the free glycolipid, and importantly, its bioactivity is preserved once released inside cells. Methods: Extensive in vitro and ex vivo assays with diabetic retinopathy models unveil the mechanistic pathways of the designed GlycoZIF. Results: A reduction in proinflammatory mediators, increased heme oxygenase-1 level, inhibition of NLRP3 inflammasome, and reduced reactive gliosis is shown. Conclusions: These findings demonstrate for the first time the potential of Glyco-modified ZIFs for the treatment of diabetes-related ocular problems by controlling the immune-mediated inflammatory response.
Selective H/D Exchange in E–H (E = Si, Ge, Sn) Bonds Catalyzed by 1,2,3-Triazolylidene-Stabilized Nickel Nanoparticles
(American Chemical Society, 2025) Molinillo, Pablo; Gálvez Del Postigo, Ana; Puyo, Maxime; Vattier Lagarrigue, María Florencia; Beltrán, Ana M.; Rendón Márquez, Nuria; Lara Muñoz, Patricia; Suárez, Andrés; Universidad de Sevilla. Departamento de Química Inorgánica; Universidad de Sevilla. Departamento de Ingeniería y Ciencia de los Materiales y del Transporte; Ministerio de Ciencia e Innovación (MICIN). España; European Union (UE)
Nickel nanoparticles (Ni·MIC) stabilized with mesoionic 1,2,3-triazolylidene (MIC) ligands were prepared via decomposition of the [Ni(COD)2] (COD = 1,5-cyclooctadiene) complex with H2 (3 bar) in the presence of 0.2 or 0.5 equiv of ligand. The obtained monodisperse and small-sized (3.2–3.8 nm) nanoparticles were characterized by high-resolution transmission electron microscopy (TEM, HRTEM) and inductively coupled plasma (ICP) analysis. Further analysis of the nickel nanoparticles by X-ray photoelectron spectroscopy (XPS) demonstrated the coordination of the MIC ligands to the metal surface. Finally, the Ni·MIC nanoparticles were applied in the isotopic H/D exchange in hydrides of group 14 elements (Si, Ge, Sn) using D2 gas under relatively mild conditions (1.0–1.8 mol % Ni, 1 bar D2, 55 °C). High and chemoselective deuterium incorporation at the E–H (E = Si, Ge, Sn) bond in these derivatives was observed.
β-Cyclodextrin-based geometrically frustrated amphiphiles as one-component, cell-specific and organ-specific nucleic acid delivery systems
(Elsevier, 2025-01-01) Rivero Barbarroja, Gonzalo; López Fernández, José; Juárez Gonzálvez, Inmaculada; Fernández Clavero, C.; Di Giorgio, Christophe; Vélaz, Itziar; Ortiz Mellet, Carmen; García Fernández, José M.; Universidad de Sevilla. Departamento de Química Orgánica; Ministerio de Ciencia, Innovación y Universidades (MICIU). España; Agencia Estatal de Investigación. España; European Union (UE)
We introduce an innovative β-cyclodextrin (βCD)-prototype for delivering nucleic acids: “geometrically frustrated amphiphiles (GFAs).” GFAs are designed with cationic centers evenly distributed across the primary O6 and secondary O2 positions of the βCD scaffold, while hydrophobic tails are anchored at the seven O3 positions. Such distribution of functional elements differs from Janus-type architectures and enlarges the capacity for accessing strictly monodisperse variants. Changes at the molecular level can then be correlated with preferred self-assembly and plasmid DNA (pDNA) co-assembly behaviors. Specifically, GFAs undergo pH-dependent transition between bilayered to monolayered vesicles or individual molecules. GFA-pDNA nanocomplexes exhibit topological and internal order characteristics that are also a function of the GFA molecular architecture. Notably, adjusting the pKa of the cationic heads and the hydrophilic-hydrophobic balance, pupa-like arrangements implying axial alignments of GFA units flanked by quasi-parallel pDNA segments are preferred. In vitro cell transfection studies revealed remarkable differences in relative performances, which corresponded to distinct organ targeting outcomes in vivo. This allowed for preferential delivery to the liver and lung, kidney or spleen. The results collectively highlight cyclodextrin-based GFAs as a promising class of molecular vectors capable of finely tuning cell and organ transfection selectivity
STD NMR Epitope Perturbation by Mutation Unveils the Mechanismof YM155 as an Arginine-Glycosyltransferases Inhibitor Effective inTreating Enteropathogenic Diseases
(American Chemical Society, 2025-03) Ramírez Cárdenas, Jonathan; Taleb, Víctor; Calvaresi, Valeria; Struwe, WB; El Qaidi, Samir; Zhu, Congrui; Muñoz García, Juan Carlos; Angulo Álvarez, Jesús; Universidad de Sevilla. Departamento de Química Orgánica; Ministerio de Ciencia, Innovación y Universidades (MICIU). España; Agencia Estatal de Investigación. España; European Union (UE); Gobierno de Aragón
Enteropathogenic arginine-glycosyltransferases(Arg-GTs) alter higher eukaryotic proteins by attaching a GlcNAcresidue to arginine acceptor sites, disrupting essential pathwayssuch as NF-κB signaling, which promotes bacterial survival. Theseenzymes are potential drug targets for treating related diseases. Inthis study, we present a novel STD NMR Epitope Perturbation byMutation spectroscopic approach that, in combination withhydrogen−deuterium exchange mass spectrometry (HDX-MS),and molecular dynamics simulations, shows that the highly potentbroad-spectrum anticancer drug YM155 serves as a potentialnoncompetitive inhibitor of these enzymes. It induces aconformation of the arginine acceptor site unfavorable for GlcNActransfer, which underlies the molecular mechanism by which thiscompound exerts its inhibitory function. Finally, we also demonstrate that YM155 effectively treats enteropathogenic diseases in amouse model, highlighting its therapeutic potential. Overall, our data suggest that this compound can be repurposed to not only treatcancer but also infectious diseases.
Light-controlled assembly and disassembly of cyclodextrin-bisazobenzene supramolecular complexes
(Elsevier, 2025-04-16) Fernández Clavero, Carlos; Rivero Barbarroja, Gonzalo; Carmona, Thais; García Iriepa, C.; Marcelo, Gema; Tros de Ilarduya, Conchita; Ortiz Mellet, Carmen; García Fernández, José M.; Benito, Juan M.; Mendicuti, Francisco; Universidad de Sevilla. Departamento de Química Orgánica; Ministerio de Ciencia, Innovación y Universidades (MICINN). España; Agencia Estatal de Investigación. España; European Union (UE); Universidad de Alcalá
The inclusion complexation of a water soluble bis-azobenzene derivative (bis-Azo) and its monotopic analog (mono-Azo) with α-, β-, and γ-cyclodextrins (CyDs) was investigated as a prototype for light-responsive selfassembling systems. Using spectroscopic techniques (UV–vis, induced circular dichroism, 1 H NMR), computational methods (molecular mechanics and dynamics), and thermodynamic analyses, we examined the photoswitching properties, stability, and structural dynamics of these systems. The azobenzene moieties in the Eisomer of mono-Azo and bis-Azo consistently showed strong affinity for the αCyD cavity, characterized by high association constants. In contrast, no complex formation was observed upon photoinduced E-to-Z isomerization. For bis-Azo, this implies the formation of supramolecular αCyD dimers, with the spatial separation between the oppositely oriented host components determined by the connector linking the two azobenzene moieties in the Econfigured ditopic guest. This complex disassembles upon photoswitching, driven by the structural disruption associated with the Z-form. Both the E-and Z-isomers fitted in the cavity of βCyD, with moderate selectivity towards the E-form. A similar scenario was found for complexes with γCyD when using low concentrations of the host. Interestingly, at high concentrations γCyD formed low-solubility pseudopolyrotaxane-type supramolecular architectures with bis-Azo, which were disrupted upon Z-isomer photoisomerization. All the complexes demonstrated high fatigue resistance, maintaining structural integrity after multiple isomerization cycles. This work advances the design of stimuli-responsive preorganized supramolecular systems, with potential applications in nucleic acid delivery through dual pH/light-sensitive mechanisms.
The two yeast cytochrome c isoforms differentially regulate supercomplex assembly and mitochondrial electron flow
(Elsevier, 2025-06) Guerra Castellano, Alejandra; Aneas, Manuel; Tamargo Azpilicueta, Joaquín; Márquez Escudero, Inmaculada; Olloqui Sariego, José Luis; Calvente Pacheco, Juan José; Rosa Acosta, Miguel Ángel de la; Díaz Moreno, Irene; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Universidad de Sevilla. Departamento de Química Física; Ministerio de Ciencia, Innovación y Universidades (MICIU). España; Junta de Andalucía
Mitochondria play a crucial role in cellular energy production, signaling and homeostasis. Respiratory supercomplexes represent evolutionary well-conserved, stable associations between membrane complexes and molecules, including proteins and lipids, within the inner mitochondrial membrane. They dynamically respond to metabolic demands and enhance the electron transfer rate, thereby reducing the production of ROS. Recent research has unveiled cytochrome c, a mobile electron carrier between complexes III and IV, as a potential key player in orchestrating the formation of these supra-associations. This study centers on elucidating the role of cytochrome c in modulating the assembly of supercomplexes, using the Saccharomyces cerevisiae yeast as a model system for mitochondrial metabolism. BN-PAGE and mass spectrometry-based proteomic analysis were employed to examine supercomplex organization in yeast strains expressing different cytochrome c isoforms, grown under fermentative and respiratory conditions. Our results demonstrate that both isoforms of cytochrome c contribute to supercomplex assembly, with isoform-2 significantly improving electron transfer and lowering ROS levels. We propose a model in which cytochrome c acts as a scaffold for the recruitment of assembly factors, facilitating the formation of higher order supercomplexes such as III2IV2. This model highlights cytochrome c's role beyond electron transfer, as it regulates supercomplex assembly and mitochondrial homeostasis.
Pathways to Metal-Ligand Cooperation in Quinoline-Based Titanium(IV) Pincers: Nonelectrophilic N-methylation, Deprotonation, and Dihydropyridine Formation
(American Chemical Society, 2021-06-07) Fandos, Rosa; Rodríguez Delgado, Antonio; Rodríguez, Ana; Romero, Iván; Organero, Juan Ángel; Álvarez González, Eleuterio; Universidad de Sevilla. Departamento de Química Inorgánica; Junta de Castilla-La Mancha; Ministerio de Economía y Competitividad (MINECO). España
A series of titanium(IV) complexes stabilized by quinoline-based pincer ligands have been synthesized and characterized. The reaction of [TiCp*Me3] with 8-hydroxy-2-quinolinecarboxaldehyde results in [TiCp*Me{κ3-N,O,O-(OCH)(8-O-N-Me-quin)}] (1), which shows an uncommon N-methylation/dearomatization of the pyridinic ring; in contrast, when 8-hydroxy-2-quinolinemethanol reacts with the same Ti(IV) trimethyl derivative, the expected monoalkyl complex [TiCp*Me{κ3-N,O,O-(OCH2)(8-O-quin)}] (2) is formed. The pincer ligand in 2 can be dearomatized by deprotonation of the methylene fragment, yielding [TiCp*Me{κ3-N,O,O-(OCH)(8-O-quin)}][Li(Et2O)] (3·Et2O) and [TiCp*Me{k3-N,O,O-(OCH)(8-O-quin)}][Li(Py)2] (3·2Py), or by incorporation of a hydride group into the para position of the pyridinic ring, giving [TiCp*Me{κ3-N,O,O-(OCH2)(4-H-8-O-quin)}][Li·THF] (5). Compounds 1, [TiCp*{κ3-N,O,O-(OCH2)(4-H-8-O-quin)}]2 (6), and [TiCp*{κ3-N,O,O-(OCH2)(4-H-8-O-quin)}]2[Li·THF]2(μ-O)] (7) have been studied by X-ray diffraction. Additionally, DFT quantum mechanical calculations were performed on complexes 1 and 2.
Sweet MOFs: exploring the potential and restraints of integrating carbohydrates with metal-organic frameworks for biomedical applications
(Royal Soc Chemistry, 2025-03-04) Zuliani, A; Ramos, V.; Escudero Belmonte, Alberto; Khiar, Noureddine; Universidad de Sevilla. Departamento de Química Inorgánica; Junta de Andalucía; Ministerio de Ciencia e Innovación (MICIN). España; European Union (UE)
The unique features of metal–organic frameworks (MOFs) such as biodegradability, reduced toxicity and high surface area offer the possibility of developing smart nanosystems for biomedical applications through the simultaneous functionalization of their structure with biologically relevant ligands and the loading of biologically active cargos, ranging from small drugs to large biomacromolecules, into their pores. Aiming to develop efficient, naturally inspired biocompatible systems, recent research has combined organic and materials chemistry to design innovative composites that exploit carbohydrate chemistry for the functionalization and structural modification of MOFs. Scientific investigation in the field has seen a significant rise in the past five years, and it is becoming crucial to acknowledge both the limits and benefits of this approach for future investigation. In this review, the latest research results merging carbohydrates and MOFs are discussed, with a particular emphasis on the advances in the field and the remaining challenges, including addressing sustainability and real-case applicability.
Fluorinated Man9 as a High Mannose Mimetic to Unravel Its Recognition by DC-SIGN Using NMR
(American Chemical Society, 2023-11-08) Silva Díaz, Adrián; Ramírez Cárdenas, Jonathan; Muñoz García, Juan Carlos; de la Fuente, M. Carmen; Thépaut, Michel; Fieschi, Franck; Ramos Soriano, Javier; Angulo Álvarez, Jesús; Rojo, Javier; Universidad de Sevilla. Departamento de Química Orgánica; Ministerio de Ciencia e Innovación (MICIN). España; Agencia Estatal de Investigación. España; European Union (UE)
Lectins are capable of reading out the structural information contained in carbohydrates through specific recognition processes. Determining the binding epitope of the sugar is fundamental to understanding this recognition event. Nuclear magnetic resonance (NMR) is a powerful tool to obtain this structural information in solution; however, when the sugar involved is a complex oligosaccharide, such as high mannose, the signal overlap found in the NMR spectra precludes an accurate analysis of the interaction. The introduction of tags into these complex oligosaccharides could overcome these problems and facilitate NMR studies. Here, we show the preparation of the Man9 of high mannose with some fluorine tags and the study of the interaction with its receptor, dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN). This fluorinated ligand has allowed us to apply heteronuclear two-dimensional (2D) 1H,19F STD-TOCSYreF NMR experiments, using the initial slope approach, which has facilitated the analysis of the Man9/DC-SIGN interaction, unequivocally providing the binding epitope.
Rational Design of Dual-Domain Binding Inhibitors for N-Acetylgalactosamine Transferase 2 with Improved Selectivity over the T1 and T3 Isoforms
(American Chemical Society, 2024-09-11) Compañón, Ismael; Ballard, Collin J.; Lira Navarrete, Enardi; Santos, Tanausú; Monaco, Serena; Muñoz García, Juan Carlos; Angulo Álvarez, Jesús; Ghirardello, Mattía; Universidad de Sevilla. Departamento de Química Orgánica; Agencia Estatal de Investigación. España; Universidad de La Rioja; Gobierno de Aragón; European Union (UE)
The GalNAc-transferase (GalNAc-T) family, consisting of 20 isoenzymes, regulates the O-glycosylation process of mucin glycopeptides by transferring GalNAc units to serine/threonine residues. Dysregulation of specific GalNAc-Ts is associated with various diseases, making these enzymes attractive targets for drug development. The development of inhibitors is key to understanding the implications of GalNAc-Ts in human diseases. However, developing selective inhibitors for individual GalNAc-Ts represents a major challenge due to shared structural similarities among the isoenzymes and some degree of redundancy among the natural substrates. Herein, we report the development of a GalNAc-T2 inhibitor with higher potency compared to those of the T1 and T3 isoforms. The most promising candidate features bivalent GalNAc and thiophene moieties on a peptide chain, enabling binding to both the lectin and catalytic domains of the enzyme. The binding mode was confirmed by competitive saturation transfer difference NMR experiments and validated through molecular dynamics simulations. The inhibitor demonstrated an IC50 of 21.4 μM for GalNAc-T2, with 8- and 32-fold higher selectivity over the T3 and T1 isoforms, respectively, representing a significant step forward in the synthesis of specific GalNAc-T inhibitors tailored to the unique structural features of the targeted isoform.
Fluorinated trehalose analogues for cell surface engineering and imaging of Mycobacterium tuberculosis
(2024-08-12) Guy, Collette S.; Gott, James A.; Ramírez Cárdenas, Jonathan; de Wolf, Cristopher; Furze, Christopher M.; West, Geoff; Muñoz García, Juan Carlos; Angulo Álvarez, Jesús; Fullam, Elizabeth; Universidad de Sevilla. Departamento de Química Orgánica; Ministerio de Ciencia e Innovación (MICIN). España; Agencia Estatal de Investigación. España; European Union (UE)
The sensitive, rapid and accurate diagnosis of Mycobacterium tuberculosis (Mtb) infection is a central challenge in controlling the global tuberculosis (TB) pandemic. Yet the detection of mycobacteria is often made difficult by the low sensitivity of current diagnostic tools, with over 3.6 million TB cases missed each year. To overcome these limitations there is an urgent need for next-generation TB diagnostic technologies. Here we report the use of a discrete panel of native 19F-trehalose (F-Tre) analogues to label and directly visualise Mtb by exploiting the uptake of fluorine-modified trehalose analogues via the mycobacterial trehalose LpqY-SugABC ATP-binding cassette (ABC) importer. We discovered the extent of modified F-Tre uptake correlates with LpqY substrate recognition and characterisation of the interacting sites by saturation transfer difference NMR coupled with molecular dynamics provides a unique glimpse into the molecular basis of fluorine-modified trehalose import in Mtb. Lipid profiling demonstrated that F-Tre analogues modified at positions 2, 3 and 6 are incorporated into mycobacterial cell-surface trehalose-containing glycolipids. This rapid one-step labelling approach facilitates the direct visualisation of F-Tre-labelled Mtb by Focused Ion Beam (FIB) Secondary Ion Mass Spectrometry (SIMS), enabling detection of the Mtb pathogen. Collectively, our findings highlight that F-Tre analogues have potential as tools to probe and unravel Mtb biology and can be exploited to detect and image TB.
Fast Quantitative Validation of 3D Models of Low-Affinity Protein-Ligand Complexes by STD NMR Spectroscopy
(American Chemical Society, 2024-06-07) Nepravishta, Ridvan; Ramírez Cárdenas, Jonathan; Rocha, Gabriel; Walpole, Samuel; Hicks, Thomas; Monaco, Serena; Muñoz García, Juan Carlos; Angulo Álvarez, Jesús; Universidad de Sevilla. Departamento de Química Orgánica; Biotechnology and Biological Sciences Research Council (BBSRC). U. K.; Agencia Estatal de Investigación. España; Ministerio de Ciencia e Innovación (MICIN). España; European Union (UE)
Low-affinity protein–ligand interactions are important for many biological processes, including cell communication, signal transduction, and immune responses. Structural characterization of these complexes is also critical for the development of new drugs through fragment-based drug discovery (FBDD), but it is challenging due to the low affinity of fragments for the binding site. Saturation transfer difference (STD) NMR spectroscopy has revolutionized the study of low-affinity receptor–ligand interactions enabling binding detection and structural characterization. Comparison of relaxation and exchange matrix calculations with 1H STD NMR experimental data is essential for the validation of 3D structures of protein–ligand complexes. In this work, we present a new approach based on the calculation of a reduced relaxation matrix, in combination with funnel metadynamics MD simulations, that allows a very fast generation of experimentally STD-NMR-validated 3D structures of low-affinity protein–ligand complexes.
Differential Solvent DEEP-STD NMR and MD Simulations Enable the Determinants of the Molecular Recognition of Heparin Oligosaccharides by Antithrombin to Be Disentangled
(MDPI, 2024-04-26) Parafioriti, Michela; Elli, Stefano; Muñoz García, Juan Carlos; Ramírez Cárdenas, Jonathan; Yates, Edwin A.; Angulo Álvarez, Jesús; Guerrini, Marco; Universidad de Sevilla. Departamento de Química Orgánica; Fundación G. Ronzoni. Italia; Ministerio de Ciencia e Innovación (MICIN). España; Agencia Estatal de Investigación. España; European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER)
The interaction of heparin with antithrombin (AT) involves a specific sequence corresponding to the pentasaccharide GlcNAc/NS6S-GlcA-GlcNS3S6S-IdoA2S-GlcNS6S (AGA*IA). Recent studies have revealed that two AGA*IA-containing hexasaccharides, which differ in the sulfation degree of the iduronic acid unit, exhibit similar binding to AT, albeit with different affinities. However, the lack of experimental data concerning the molecular contacts between these ligands and the amino acids within the protein-binding site prevents a detailed description of the complexes. Differential epitope mapping (DEEP)-STD NMR, in combination with MD simulations, enables the experimental observation and comparison of two heparin pentasaccharides interacting with AT, revealing slightly different bound orientations and distinct affinities of both glycans for AT. We demonstrate the effectiveness of the differential solvent DEEP-STD NMR approach in determining the presence of polar residues in the recognition sites of glycosaminoglycan-binding proteins.
Organocatalytic Applications of Sulfonyl Squaramides in Anion-Recognition Strategies
(Willey, 2024-10-16) Benítez Narváez, Manuel; Matador Martínez, Esteban; Velázquez Muñoz, Marta; Lassaletta, José M.; Fernández Fernández, Rosario Fátima; Monge Fernández, David; Universidad de Sevilla. Departamento de Química Orgánica; Ministerio de Ciencia e Innovación (MICIN). España; European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER); Junta de Andalucía
A modular, 3-steps protocol for the synthesis of N-sulfonyl squaramides has been developed. The strategic installation of a tetrahedral, electron-withdrawing sulfonyl group into the squaramido core allowed the prevention of undesired self-aggregations, therefore upgrading the solubility in common organic solvents, and moreover, enhancing their H-bond donor abilities for molecular recognition. These unique features have been efficiently exploited in two different ion-pairing reactions: (i) the challenging C4-selective dearomatization of 2-picoline with silyl ketene acetals and (ii) the tritylation of N-methylindole. Furthermore, their catalytic activities have been directly compared with other common and well-established (thio)urea analogues and related H-bond donors, revealing that highly acidic designs are essential to reach optimal catalytic performances.
Ni‐Catalyzed (2+2+2) Cycloaddition of Alkynes to Form Arenes and Pyridines at Low Catalyst Loadings
(Willey, 2024-10-09) Martín García, María Trinidad; Maya Díaz, Celia María; Galindo del Pozo, Agustín; Nicasio Jaramillo, María del Carmen; Universidad de Sevilla. Departamento de Química Inorgánica; Ministerio de Ciencia e Innovación (MICIN). España; Agencia Estatal de Investigación. España
We report the Ni-catalyzed cyclotrimerization of terminal alkynes at very low loadings of catalysts (0.05 mol% for all substrates). The nickel catalyst containing a terphenyl phosphine ligand allows carrying out the reactions at room temperature in only 30 min, providing the arene products as a single regioisomer in most cases. The Ni complex is also competent for the synthesis of polysubstituted pyridines through the cycloadditions of diynes and nitriles at mild temperatures (25 ° or 50 °C) and low Ni loadings (1 mol%). Experimental data and computational studies support the involvement of monoligated PNi species in all fundamental steps of the catalytic cycle.
A Sustainable Lecithin-based Ligand for the Bio-functionalization of Iron and Hybrid Metal Organic Frameworks (MOFs) Nanoparticles with the Sugar Mannose
(Royal Society of Chemistry, 2024) Cova, Camilla María; Ramos, V.; Escudero Belmonte, Alberto; Holgado, J. P.; Khiar, N.; Zuliani, A.; Universidad de Sevilla. Departamento de Química Inorgánica; Junta de Andalucía; Ministerio de Ciencia e Innovación (MICIN). España; European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER); European Cooperation in Science and Technology (COST)
The functionalization of nanoparticles with specific ligands, such as antibodies, peptides, and small molecules, plays a critical role in achieving targeted delivery, enhancing biocompatibility, and controlling drug release. However, to date, practically no attention has been paid to the design of green ligands. Herein, an innovative approach to develop a sustainable ligand for nanoparticle functionalization is reported. Its synthesis involved a photochemical thio-ene “click” reaction between the natural compounds phosphatidylcoline, the main component of lecithin, and cysteine, followed by a reductive amination with mannose, a sugar of growing interest for biomedical targeting, in a continuous flow hydrogenation reactor. Comprehensive characterization techniques, including nuclear magnetic resonance (NMR), mass spectrometry (MS), Fourier-transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS) and elemental analysis, confirmed the structure and properties of the novel ligand. The environmental sustainability of the ligand was evaluated determining some green metrics using the EATOS software. The obtained E-factor was compared with a conventional PEG-based ligand. The newly developed lecithin-derived ligand was successfully used to functionalize diverse NP platforms, including the MOFs MIL-101(Fe), PCN-222, UiO-66, and iron nanoparticles (in the form of akaganeite), demonstrating its potential in nanomedicine applications.
Synthesis, Characterization, and Preliminary In Vitro Anticancer Activity of Zinc Complexes Containing Amino Acid-Derived Imidazolium-Based Dicarboxylate Ligands
(Multidisciplinary Digital Publishing Institute (MDPI), 2025-03-30) Carrasco Carrasco, Carlos Jesús; Pastor Navarro, Antonio; Conejo Argandoña, María del Mar; Álvarez González, Eleuterio; Calderón Montaño, José Manuel; López Lázaro, Miguel; Galindo del Pozo, Agustín; Universidad de Sevilla. Departamento de Química Inorgánica; Universidad de Sevilla. Departamento de Farmacología; Ministerio de Ciencia e Innovación (MICIN). España
Coordination polymers containing zinc and imidazolium-based dicarboxylate ligands, [LR]−, were synthesized by reacting zinc acetate with HLR compounds, 1. The resulting complexes were characterized and structurally identified using single-crystal X-ray diffraction, revealing polymeric structures for the complexes [Zn(LR)2]n (R = Gly, 2a; βAla, 2b) and [Zn(LLeu)2(H2O)2]n (2c). In these structures, the [LR]− ligands adopt a bridging monodentate μ-κ1-O1,κ1-O3 coordination mode, resulting in distorted tetrahedral (2a, 2b) or octahedral (2c) geometries around the zinc center. When the synthesis was carried out in the presence of amino acids, mixed ligand complexes [Zn(LR)(aa)(H2O)]n (R = aa = Val, 2d, and R = aa = Ile, 2e) were formed. Complexes 2d–2e were also structurally characterized using single-crystal X-ray crystallography, revealing that the ligand [LR]− maintained the same coordination mode, while the zinc center adopted a five-coordinated geometry. The cytotoxic activity of complexes 2a–2e was evaluated against three cancer cell lines and one non-cancerous cell line. Remarkably, these complexes exhibited higher toxicity against cancer cells than against the non-cancerous cell line, and they showed greater selectivity than carboplatin, a commonly used chemotherapy drug. Although, in general, these complexes did not surpass the selectivity of gemcitabine, complex 2c stood out for exhibiting a selectivity index value similar to that of gemcitabine against melanoma cells. Among the series, compounds 2a–2c demonstrated the highest activity, with 2a being the only complex with some selective activity against lung cancer. Complex 2b was the most active, though with low selectivity, while complex 2c exhibited the highest selectivity for melanoma and bladder cancer (selectivity index of 3.0).

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