Jesús Jiménez-Barbero

Center for Cooperative Research in Biosciences | CIC bioGUNE · Structural Biology Unit

A set of bicyclic iminosugar C-glycosides, based on an octahydrofuro[3,2-b]pyridine motif, has been synthesized from a C-allyl iminosugar exploiting a debenzylative iodocycloetherification and an iodine nucleophilic displacement as the key steps. The halogen allowed the introduction of a range of aglycon moieties of different sizes bearing several...

Transthyretin (TTR) has a well-established role in neuroprotection in Alzheimer's Disease (AD). We have setup a drug discovery program of small-molecule compounds that act as chaperones enhancing TTR/Amyloid-beta peptide (Aβ) interactions. A combination of computational drug repurposing approaches and in vitro biological assays have resulted in a s...

Acyl group migration is a fundamental phenomenon in carbohydrate chemistry, recently shown to take place also between two non‐adjacent hydroxyl groups, across the glycosidic bond, in a β‐(1→4)‐linked mannan trisaccharide model compound. With the central mannoside unit containing acetyl groups at the O2 and O3 positions, the O2‐acetyl was in the ear...

Glycerol phosphate (GroP)-based teichoic acids (TAs) are antigenic cell-wall components found in both enterococcus and staphylococcus species. Their immunogenicity has been explored using both native and synthetic structures, but no details have yet been reported on the structural basis of their interaction with antibodies. This work represents the...

Repeating carbohydrate patterns are commonly found in Nature in extended oligosaccharides and polysaccharides. When recognized by protein receptors, dissecting the contribution of each repeating unit to the binding event is not easy. Here, the introduction of ¹³C-labels at specific positions of a tri-LacNAc repeating hexasaccharide has been used in...

In glycoproteins, carbohydrates are responsible for the selective interaction and tight regulation of cellular processes, constituting the main information transducer interface in protein–glycoprotein interactions. Increasing experimental and computational evidence suggest that such interactions often induce allosteric changes in the host protein,...

The interaction of multi-LacNAc (Galβ1-4GlcNAc)-containing N-(2-hydroxypropyl) methacrylamide (HPMA) copolymers with human galectin-1 (Gal-1) and the carbohydrate recognition domain (CRD) of human galectin-3 (Gal-3) was analyzed using NMR methods in addition to cryo-electron-microscopy and dynamic light scattering (DLS) experiments. The interaction...

Mucopolysaccharidosis type IIIB is a devastating neurological disease caused by a lack of the lysosomal enzyme, α ‐N‐acetylglucosaminidase (NAGLU), leading to a toxic accumulation of heparan sulfate. Herein we explored a pharmacological chaperone approach to enhance the residual activity of NAGLU in patient fibroblasts. Capitalizing on the three‐di...

A combined chemo‐enzymatic synthesis/NMR‐based methodology is presented to identify, in unambiguous manner, the distinctive binding epitope within repeating sugar oligomers when binding to protein receptors. The concept is based on the incorporation of 13 C‐labels at specific monosaccharide units, selected within a repeating glycan oligomeric struc...

A main clinical parameter of COVID-19 pathophysiology is hypoxia. Here we show that hypoxia decreases the attachment of the receptor binding domain (RBD) and the S1 subunit (S1) of the spike protein of SARS-CoV-2 to epithelial cells. In Vero E6 cells, hypoxia reduces the protein levels of ACE2 and neuropilin-1 (NRP1), which might in part explain th...

Trimethylamine N -oxide (TMAO) is a well-known naturally occurring osmolyte in animals that counteracts the effect of different denaturants related to environmental stress and has recently been associated with severe human chronic diseases. In plants, however, the presence of TMAO has not yet been reported. In this study, we demonstrate that plants...

Carbohydrates (glycans, saccharides, and sugars) are essential molecules in all domains of life. Research on glycoscience spans from chemistry to biomedicine, including material science and biotechnology. Access to pure and well-defined complex glycans using synthetic methods depends on the success of the employed glycosylation reaction. In most ca...

Paucimannosidic glycans are restricted to the core structure [Man1-3GlcNAc2Fuc0-1] of N-glycans and are rarely found in mammalian tissues. Yet, especially [Man2-3GlcNAc2Fuc1] have been found significantly upregulated in tumors, including in colorectal and liver cancer. Mannitou IgM is a murine monoclonal antibody that was previously shown to recogn...

The tandem-repeat Galectin-4 (Gal-4) contains two different domains covalently linked through a short flexible peptide. Both domains have been shown to bind preferentially to A and B histo blood group antigens with different affinities, although the binding details are not yet available. The biological relevance of these associations is unknown, al...

Galectins bind various pathogens through recognition of distinct carbohydrate structures. In this work, we examined the binding of four human galectins to the Gram-negative bacteria Klebsiella pneumoniae (Kpn) and non-typeable Haemophilus influenzae (NTHi), which display different surface glycans. In particular, Kpn cells are covered by a polysacch...

Interactions of glycan‐specific epitopes to human lectin receptors represent novel immune checkpoints for investigating cancer and infection diseases. By employing a multidisciplinary approach that combines isothermal titration calorimetry, NMR spectroscopy, molecular dynamics simulations, and X‐ray crystallography, we disclosed the molecular deter...

Glycosylation of polyphenols may increase their aqueous solubility, stability, bioavailability and pharmacological activity. Herein, we used a mutant of sucrose phosphorylase from Thermoanaerobacterium thermosaccharolyticum engineered to accept large polyphenols (variant TtSPP_R134A) to produce phloretin glucosides. The reaction was performed using...

Capitalizing on a recently reported iminosugar-based aza-crown (ISAC) accessed by a double Staudinger azaWittig coupling reaction, we have expanded the structural diversity of this new family of sweet cyclam analogs. Replacement of the two secondary amines linking the iminosugar units by two amide bonds obtained a cyclodimerization with BOP and DIP...

Nuclear magnetic resonance spectroscopy is powerful technique for the study of the conformation, dynamics and interactions of glycans and provides extremely valuable information to disentangle the mechanism of biological processes in which carbohydrates are involved. Recent developments in NMR hardware and novel methodological developments in the f...

The sialic acid-binding immunoglobulin-type of lectins (Siglecs) are receptors that recognize sialic acid-containing glycans. In the majority of the cases, Siglecs are expressed on immune cells and play a critical role in regulating immune cell signaling. Over the years, it has been shown that the sialic acid-Siglec axis participates in immunologic...

Molecular recognition of carbohydrates is a key step in essential biological processes. Carbohydrate receptors can distinguish monosaccharides even if they only differ in a single aspect of the orientation of the hydroxyl groups or harbor subtle chemical modifications. Hydroxyl-by-fluorine substitution has proven its merits for chemically mapping t...

Calix[4]arene PTX008 is an angiostatic agent that inhibits tumor growth in mice by binding to galectin-1, a β-galactoside-binding lectin. To assess the affinity profile of PTX008 for galectins, we used 15 N,1 H HSQC NMR spectroscopy to show that PTX008 also binds to galectin-3 (Gal-3), albeit more weakly. We identified the contact site for PTX008 o...

The mechanistic study of one‐step sulfoxide glycosylations enabled by the employment of 13C‐labelled glycosyl‐donors and low‐temperature NMR revealed the internal dynamics between all reaction intermediates involved in this process, which are represented in the accompanying image as a molecular rollercoaster. The formation and stability of donor/ac...

Significance The elucidation of structural epitopes is key to understanding the mechanisms of action of vaccines. Here a multidisciplinary approach was used to map the glycan epitope of Neisseria meningitidis serogroup A capsular polysaccharide, a component of marketed vaccines, with a monoclonal antibody capable of triggering human complement-medi...

The transformation of glycals into 2,3-unsaturated glycosyl derivatives, reported by Ferrier in 1962, is supposed to involve an α,β unsaturated glycosyl cation, an elusive ionic species that has still to be observed experimentally. Herein, while combination of TfOH and flow conditions failed to observe this ionic species, its extended lifetime in s...

Unprecedent structural details of the glycans of the RBD of SARS‐CoV‐2 spike glycoprotein have been revealed by NMR spectroscopy. Unexpected and non‐previously reported glycoepitopes have been detected. The interaction of the RBD glycoprotein with diverse human lectins has been scrutinized by exploiting the NMR signature of the ¹³C‐glycans. Our ana...

The cyclic allyloxycarbenium ion, the key intermediate in the Ferrier rearrangement, has been generated and accumulated under TfOH flow conditions. It is stable in superacid HF/SbF5 solutions. Its long‐lived character in these non‐nucleophilic conditions allowed its full characterization by low‐temperature NMR supported by DFT calculations. This io...

Bacterial infections are the cause of different severe health conditions and new therapies to combat these pathogens have been widely investigated. Carbohydrates, being complex structures covering the surface of bacteria, are considered relevant targets for antibody and vaccine development. The biological activities in pathogenesis of bacterial cap...

Glycosyl sulfoxides have gained recognition in the total synthesis of complex oligosaccharides and as model substrates for dissecting the mechanisms involved. While these donors are usually reacted under pre-activation conditions, an experimentally more convenient single-step protocol has also been reported, whereby the activation is performed in t...

This chapter is dedicated to the presentation of different examples of the application of solution NMR to the study of conformation, dynamics of sugar molecules (oligo and polysaccharides, glycopeptides and glycomimetics) including the investigation of glycan-related molecular recognition events. It is not our intention to be exhaustive, rather to...

The glycan structures of the receptor binding domain of the SARS-CoV2 spike glycoprotein expressed in human HEK293F cells have been studied by using NMR. The different possible interacting epitopes have been deeply analysed and characterized, providing evidence of the presence of glycan structures not found in previous MS-based analyses. The intera...

The dynamic adaptability of tetragonal prismatic nanocapsule 1 8+ in the selective separation of fullerenes and endohedral metallofullerenes (EMFs) remains unexplored. Therefore, the essential molecular details of the fullerene recognition and binding process into the coordination capsule and the origins of fullerene selectivity remain elusive. In...

Background: Transthyretin (TTR) is a tetrameric, amyloid-β (Aβ)-binding protein which reduces Aβ toxicity. The TTR/Aβ interaction can be enhanced by a series of small molecules that stabilize its tetrameric form. Hence, TTR stabilizers might act as disease-modifying drugs in Alzheimer's disease. Objective: We monitored the therapeutic efficacy o...

Among glycan-binding proteins, galectins, β-galactoside-binding lectins, exhibit relevant biological roles and are implicated in many diseases, such as cancer and inflammation. Their involvement in crucial pathologies makes them interesting targets for drug discovery. In this review, we gather the last approaches toward the specific design of glyco...

Fluorinated glycomimetics are frequently employed to study and eventually modulate protein–glycan interactions. However, complex glycans and their glycomimetics may display multiple binding epitopes that enormously complicate the access to a complete picture of the protein–ligand complexes. We herein present a new methodology based on the synergic...

The protein transthyretin (TTR) modulates Abeta (Aβ) peptides deposition and processing and this physiological effect is further enhanced by treatment with iododiflunisal (IDIF), a small‐molecule compound (SMC) with TTR tetramer stabilization properties that behaves as chaperone of the complex. This knowledge has prompted us to design and optimize...

The aggregation kinetics of Aβ1–40 peptide was characterized using a synergistic approach by a combination of nuclear magnetic resonance, thioflavin-T fluorescence, transmission electron microscopy and dynamic light scattering. A major finding is the experimental detection of high molecular weight oligomers (HMWO) that converts into fibrils nuclei....

The interaction of human galectin‐1 with a variety of oligosaccharides, from di‐ (N‐acetyllactosamine) to tetra‐saccharides (blood B type‐II antigen) has been scrutinized by using a combined approach of different NMR experiments, molecular dynamics (MD) simulations, and isothermal titration calorimetry. Ligand‐ and receptor‐based NMR experiments as...

Noscapine is a natural alkaloid that is used as an antitussive medicine. However, it also acts as a weak anticancer agent in certain in vivo models through a mechanism that is largely unknown. Here, we performed structural studies and show that the cytotoxic agent 7A-O-demethoxy-amino-noscapine (7A-aminonoscapine) binds to the colchicine site of tu...

The parasitic worm, Schistosoma mansoni, expresses unusual fucosylated glycans in a stage‐dependent manner that can be recognized by the human innate immune receptor DC‐SIGN, thereby shaping host immune responses . We have developed a synthetic approach for mono‐ and bis‐ fucosylated Lac diNA c (LDN‐F and LDN‐DF, respectively), which are epitopes e...

The exopolymer (EPSp) produced by the strain B. licheniformis IDN-EC was isolated and characterized using different techniques (MALDI-TOF, NMR, ATR-FTIR, TGA, DSC, SEM). The results showed that the low molecular weight EPSp contained a long polyglutamic acid and an extracellular teichoic acid polysaccharide. The latter was composed of poly(glycerol...

Glycosylations promoted by triflate-generating reagents are widespread synthetic methods for the construction of glycosidic scaffolds and glycoconjugates of biological and chemical interest. These processes are thought to proceed with the participation of a plethora of activated high energy intermediates such as the α- and β-glycosyl triflates, or...

Fluorinated carbohydrates have become indispensable in glycosciences. This contribution provides an overview of how fluorine introduction modifies physical and chemical properties of carbohydrates along with selected examples of its applications.

Invited for the cover of this issue is the group of Roberto Adamo at GlaxoSmithKline Research Center, Siena, and colleagues at The University of the Basque Country and Basque Research Technology Alliance. The image depicts a tactical plan with the different elements of the research as part of the team. Read the full text of the article at 10.1002/c...

Group B Streptococcus III has been considered a model of highly complex glycan epitope. Based on the X‐ray crystallographic structure of a polysaccharide fragment‐mAb complex, a hexasaccharide was synthesized comprising the positions involved in binding. After conjugation to a carrier protein and in vivo testing, the oligosaccharide was as efficaci...

Carbohydrates play a pivotal role in intercellular communication processes. In particular, glycan antigens are key for sustaining homeostasis, helping leukocytes to distinguish damaged tissues and invading pathogens from healthy tissues. From a structural perspective, this cross‐talk is fairly complex, and multiple membrane proteins guide these rec...

Long-chain alkyl glucosides, such as octyl and decyl β-D-glucopyranosides (OG and DG, respectively), are regarded as a new generation of biodegradable, non-ionic surfactants. Previously, the mutants of Dalbergia cochinchinensis Pierre dalcochinase showed potential in the synthesis of oligosaccharides and alkyl glucosides. In this study, the N189 F...

The first synthesis of 3-deoxy-3-fluoro-l-fucose is presented, which employs a d- to l-sugar translation strategy, and involves an enzymatic oxidation of 3-deoxy-3-fluoro-l-fucitol. Enzymatic activation (FKP) and glycosylation using an -1,2...

Galactosaminogalactan (GAG) is a prominent cell wall component of the opportunistic fungal pathogen Aspergillus fumigatus . GAG is a heteropolysaccharide composed of a ‐1,4‐linked galactose, galactosamine and N ‐acetylgalactosamine residues. To enable biochemical studies, a library of GAG‐fragments was constructed featuring specimens containing a ‐...

Retaining glycoside hydrolases cleave their substrates through stereochemical retention at the anomeric position. Typically, this involves two-step mechanisms using either an enzymatic nucleophile via a covalent glycosyl enzyme intermediate or neighboring-group participation by a substrate-borne 2-acetamido neighboring group via an oxazoline interm...

The transglycosylation activity of a novel commercial β-galactosidase from Bifidobacterium bifidum (Saphera) was evaluated. The optimal conditions of operation of this enzyme, measured with o-nitrophenyl-β-D-galactopyranoside, were 40 °C and pH around 6.0. Although at low lactose concentrations the character of this enzyme was basically hydrolytic,...

The completely stereoselective assembly of fungal Aspergillus fumigatus galactosaminogalactans, incorporating α‐Gal, α‐GalN and α‐GalNac residues up to dodecasaccharides, is reported. Structural studies reveal a non‐canonical C−H⋅⋅⋅O hydrogen bond to stabilize the elongated, linear structure that displays the Gal‐functional groups to the outside of...

A new family of chiral C2 symmetric tetraazamacrocycles, coined ISAC for IminoSugar Aza-Crown, incorporating two iminosugars adopting a 4C1 conformation is disclosed. Multinuclear NMR experiments on the corresponding Cd2+ complex show that the ISAC is a strong chelator in water and its tetramine cavity adopts a conformation similar to that of the p...

The plasma protein transthyretin (TTR) modulates Abeta (Aβ) peptides deposition, processing and toxicity. We have shown that this physiological effect is enhanced in mice by treatment with compounds such as iododiflunisal (IDIF) which is a good TTR ligand and tetrameric stabilizer. Isothermal Titration Calorimetry (ITC) is a powerful technique for...

We report the design, synthesis, immunological evaluation, and conformational analysis of new saponin variants as promising vaccine adjuvants. These studies have provided expedient synthetic access to streamlined adjuvant-active saponins and yielded molecular-level insights into saponin conformation that correlated with their in vivo adjuvant activ...

Designed repeat proteins catalyze the 1,3-dipolar reaction between an imine and a deficient dipolarophile in THF solution to form unnatural nitroproline esters, a reaction that no enzyme can catalyze. NMR studies and mutation experiments show that both acidic and basic residues can catalyze the reaction. The diastereocontrol of the reaction depen...

Carbohydrate molecules are essential actors in key biological events, being involved as recognition points for cell-cell and cell-matrix interactions related to health and disease. Despite outstanding advances in cryoEM, X-ray crystallography and NMR still remain the most employed techniques to unravel their conformational features and to describe...

To investigate the structural features determining the immunospecificity of Group B Streptococcus Ia and Ib polysaccharides, synthetic fragments were obtained by a newly developed regioselective approach. the Ia and Ib polysaccharides differ only in the connection of the Neu5Acα2‐3Gal side chain to the GlcNAc backbone unit. Combining synthesis, com...

Metschnikowia reukaufii is a widespread yeast able to grow in the plants’ floral nectaries, an environment of extreme conditions with sucrose concentrations exceeding 400 g l−1, which led us into the search for enzymatic activities involved in this sugar use/transformation. New oligosaccharides were produced by transglucosylation processes employin...

It is well settled that the amyloidogenic properties of the plasma protein transporter transthyretin (TTR) can be modulated by compounds that stabilize its native tetrameric conformation. TTR is also present in cerebrospinal fluid where it can bind to Aβ-peptides and prevent Aβ aggregation. We have previously shown that treatment of Alzheimer’s Dis...

Group B Streptococcus serotypes Ia and Ib capsular polysaccharides are key targets for vaccine development. In spite of their immunospecifity these polysaccharides share high structural similarity. Both are composed of the same monosaccharide residues and differ only in the connection of the Neu5Acα2‐3Gal side chain to the GlcNAc unit, which is a β...

div>Retaining glycoside hydrolases cleave glycoconjugates into their component sugars through stereochemical retention at the anomeric position. Typically, this involves two-step mechanisms using either an enzymatic nucleophile via a covalent glycosyl enzyme intermediate, or neighboring group participation by a substrate-borne 2-acetamido neighbori...