Chemical biology of the sugar code

Differential cellular localization of lectins in the testes of dromedary camel (Camelus dromedarius) during active and inactive breeding seasons

The reproductive activity of the male dromedary camel (Camelus dromedarius) as a seasonal breeder is affected by various seasonal changes that reflect on the reproductive performance. In the current study, we explored a differential cellular localization of lectins in eight dromedary camel testes utilizing lectin histochemistry (LHC). The glycoconjugates' localizations were detected within the testicular tissue utilizing 13 biotin-labeled lectins (PNA, ConA, LCA, RCA120, GS IB4, WGA, BPL, DBA, ECA, PHA-E4, UEA-1, PTL-II, and SBA) distributed into six sets. The cellular structures revealed diverse lectins distribution that may reflect various glycoproteins' structures and their compositional modifications during spermatogenesis. Some of the investigated lectins were restricted to acrosomes of spermatids that will help study different stages during the spermatogenic cycle of dromedary camel, particularly PNA, and ECA. The statistical analysis showed a marked positive correlation between the response intensity of various lectins and the breeding season (P < 0.05). We can conclude that lectins have a fundamental role during camel spermatogenesis and are associated with the reproductive activity of dromedary camel.

Term alpaca placenta glycosylation profile and its correlation with pregnancy maintenance and fetal survival

Alpaca is a South American camelid, particularly present in Peruvian highlands, where oxygen concentration and atmospheric pressure are very low. Due to this fact, gestational physiology has adapted to preserve the conceptus' and mother's health. In this context, several cellular and molecular features play an essential role during and at the end of gestation. Structural carbohydrates act on maternal-fetal communication, recognize exogenous molecules, and contribute to placental barrier selectivity. Therefore, this study aimed to characterize the structural carbohydrate profiles that are present in the term alpaca placenta, kept in their natural habitat of around 4,000 m height. For this propose, 12 term alpaca placentas were collected, and the material was obtained at the time of birth from camelids raised naturally in the Peruvian highlands, in the Cusco region. All placenta samples were processed for histological analysis. A lectin histochemical investigation was performed using 13 biotinylated lectins, allowing us to determine the location of carbohydrates and their intensity on a semi-quantitative scale. Our results demonstrated that during term gestation, the epitheliochorial alpaca placenta shows a high presence of carbohydrates, particularly glucose, α-linked mannose, N-acetylglucosamine β (GlcNAc), galactose (αGal), and N-acetylgalactosamine α (GalNAc), present in the trophoblast, amnion epithelium, and mesenchyme, as well as the presence of sialic acid residues and low affinity for fucose. In fetal blood capillaries, the presence of bi- and tri-antennary complex structures and α-linked mannose was predominated. In conclusion, we characterized the glycosylation profile in the term alpaca placenta. Based on our data, compared to those reported in the bibliography, we suggest that these carbohydrates could participate in the labor of these animals that survive in Peruvian extreme environments.

Regioselective One-Pot Synthesis, Biological Activity and Molecular Docking Studies of Novel Conjugates N-(p-Aryltriazolyl)-1,5-benzodiazepin-2-ones as Potent Antibacterial and Antifungal Agents

Novel 1,2,3-triazolo-linked-1,5-benzodiazepinones were designed and synthesized via a Cu(I)-catalyzed 1,3-dipolar alkyne-azide coupling reaction (CuAAC). The chemical structures of these compounds were confirmed by 1H NMR, 13C NMR, HMBC, HRMS, and elemental analysis. The compounds were screened for their in vitro antibacterial and antifungal activities. Several compounds exhibited good to moderate activities compared to those of established standard drugs. Furthermore, the binding interactions of these active analogs were confirmed through molecular docking.

Current Synthetic Approaches to the Synthesis of Carbasugars from Non-Carbohydrate Sources

Carbasugars are a group of carbohydrate derivatives in which the ring oxygen is replaced by a methylene group, producing a molecule with a nearly identical structure but highly different behavior. Over time, this definition has been extended to include other unsaturated cyclohexenols and carba-, di-, and polysaccharides. Such molecules can be found in bacterial strains and the human body, acting as neurotransmitters (e.g., inositol trisphosphate). In science, there are a wide range of research areas that are affected by, and involve, carbasugars, such as studies on enzyme inhibition, lectin-binding, and even HIV and cancer treatment. In this review article, different methods for synthesizing carbasugars, their derivatives, and similar cyclohexanes presenting comparable characteristics are summarized and evaluated, utilizing diverse starting materials and synthetic procedures.

UniLectin, A One-Stop-Shop to Explore and Study Carbohydrate-Binding Proteins

All eukaryotic cells are covered with a dense layer of glycoconjugates, and the cell walls of bacteria are made of various polysaccharides, putting glycans in key locations for mediating protein-protein interactions at cell interfaces. Glycan function is therefore mainly defined as binding to other molecules, and lectins are proteins that specifically recognize and interact non-covalently with glycans. UniLectin was designed based on insight into the knowledge of lectins, their classification, and their biological role. This modular platform provides a curated and periodically updated classification of lectins along with a set of comparative and visualization tools, as well as structured results of screening comprehensive sequence datasets. UniLectin can be used to explore lectins, find precise information on glycan-protein interactions, and mine the results of predictive tools based on HMM profiles. This usage is illustrated here with two protocols. The first one highlights the fine-tuned role of the O blood group antigen in distinctive pathogen recognition, while the second compares the various bacterial lectin arsenals that clearly depend on living conditions of species even in the same genus. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Searching for the structural details of lectins binding the O blood group antigen Basic Protocol 2: Comparing the lectomes of related organisms in different environments.

The Development of Vaccines from Synthetic Tumor-Associated Mucin Glycopeptides and their Glycosylation-Dependent Immune Response

Tumor-associated carbohydrate antigens are overexpressed as altered-self in most common epithelial cancers. Their glycosylation patterns differ from those of healthy cells, functioning as an ID for cancer cells. Scientists have been developing anti-cancer vaccines based on mucin glycopeptides, yet the interplay of delivery system, adjuvant and tumor associated MUC epitopes in the induced immune response is not well understood. The current state of the art suggests that the identity, abundancy and location of the glycans on the MUC backbone are all key parameters in the cellular and humoral response. This review shares lessons learned by us in over two decades of research in glycopeptide vaccines. By bridging synthetic chemistry and immunology, we discuss efforts in designing synthetic MUC1/4/16 vaccines and focus on the role of glycosylation patterns. We provide a brief introduction into the mechanisms of the immune system and aim to promote the development of cancer subunit vaccines.

Protein Assembly by Design

Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.

Evidence for Quantum Chemical Effects in Receptor-Ligand Binding Between Integrin and Collagen Fragments - A Computational Investigation With an Impact on Tissue Repair, Neurooncolgy and Glycobiology

The collagen-integrin interactions are mediated by the doubly charged Mg2+ cation. In nature this cation seems to have the optimal binding strength to stabilize this complex. It is essential that the binding is not too weak so that the complex becomes unstable, however, it is also of importance that the ligand-receptor binding is still labile enough so that the ligand can separate from the receptor in a suited environment. In the case of crystal growing for experimentally useful integrin-collagen fragment complexes it turned out that Co2+ cations are ideal mediators to form stable complexes for such experiments. Although, one can argue that Co2+ is in this context an artificial cation, however, it is now of special interest to test the impact of this cation in cell-culture experiments focusing on integrin-ligand interactions. In order to examine, in particular, the role cobalt ions we have studied a Co2+ based model system using quantum chemical calculations. Thereby, we have shown that hybrid and long-range corrected functional, which are approximations provide already a sufficient level of accuracy. It is of interest to study a potential impact of cations on the binding of collagen-fragments including collagens from various species because different integrins have numerous biological functions (e.g. Integrin - NCAM (Neural cell adhesion molecule) interactions) and are triggered by intact and degraded collagen fragments. Since integrin-carbohydrate interactions play a key role when bio-medical problems such as tumor cell adhesion and virus-host cell infections have to be addressed on a sub-molecular level it is essential to understand the interactions with heavy-metal ions also at the sub-atomic level. Our findings open new routes, especially, in the fields of tissue repair and neuro-oncology for example for cell-culture experiments with different ions. Since Co2+ ions seem to bind stronger to integrin than Mg2+ ions it should be feasible to exchange these cations in suited tumor tissues although different cations are present in other metalloproteins which are active in such tissues. Various staining methods can be applied to document the interactions of integrins with carbohydrate chains and other target structures. Thereby, it is possible to study a potential impact of these interactions on biological functions. It was therefore necessary to figure out first which histological-glycobiological experimental settings of tumor cells are suited for our purpose. Since the interactions of several metalloproteins (integrin, ADAM12) with polysialic acid and the HNK-1 epitope play a crucial role in tumor tissues selected staining methods are proper tools to obtain essential information about the impact of the metal ions under study.

Comparative Cellular Localization of Sugar Residues in Bull (Bos taurus) and Donkey (Equus asinus) Testes Using Lectin Histochemistry

Lectins are glycoproteins of a non-immune origin often used as histochemical reagents to study the distribution of glycoconjugates in different types of tissues. In this study, we performed a comparative cellular localization of sugar residues in bull and donkey testes using immunofluorescent lectin histochemistry. We inspected the cellular localization of the glycoconjugates within the testes using 11 biotin-labeled lectins (LCA, ConA, PNA, WGA, DBA, SBA, ECA, BPL, PTL-II, UEA-1, and PHA-E4) classified under six groups. Although the basic testicular structure in both species was similar, the cellular components showed different lectin localization patterns. The statistical analysis revealed no significant association between the intensity of labeling and different variables, including group and type of lectin and type of cell examined, at p < 0.05. However, a stronger response tended to occur in the donkey than in the bull testes (odds ratio: 1.3). These findings may be associated with the different cellular compositions of the glycoproteins and modification changes during spermatogenesis. Moreover, glycoconjugate profiling through lectin histochemistry can characterize some cell-type selective markers that will be helpful in studying bull and donkey spermatogenesis.

Continuous synthesis of bromoalkyl glycosides by Fischer glycosylation in a microreactor

In this study, bromoalkyl glycosides were successfully synthesized in microreactor scale by Fischer glycosylation. Yields between 24 and 40% after purification were achieved using various acidic catalysts and conditions. In some experiments, yields 180% higher than with previously known methods could be achieved. This study showed also that reversed-phase flash chromatography is more successful than normal-phase flash chromatography for the purification of bromoalkyl glycosides. Furthermore, longer bromoalcohols were shown to be more compatible than shorter bromoalcohols under these reaction conditions.

What is the Sugar Code?

A code is defined by the nature of the symbols, which are used to generate information‐storing combinations (e. g. oligo‐ and polymers). Like nucleic acids and proteins, oligo‐ and polysaccharides are ubiquitous, and they are a biochemical platform for establishing molecular messages. Of note, the letters of the sugar code system (third alphabet of life) excel in coding capacity by making an unsurpassed versatility for isomer (code word) formation possible by variability in anomery and linkage position of the glycosidic bond, ring size and branching. The enzymatic machinery for glycan biosynthesis (writers) realizes this enormous potential for building a large vocabulary. It includes possibilities for dynamic editing/erasing as known from nucleic acids and proteins. Matching the glycome diversity, a large panel of sugar receptors (lectins) has developed based on more than a dozen folds. Lectins ‘read’ the glycan‐encoded information. Hydrogen/coordination bonding and ionic pairing together with stacking and C−H/π‐interactions as well as modes of spatial glycan presentation underlie the selectivity and specificity of glycan‐lectin recognition. Modular design of lectins together with glycan display and the nature of the cognate glycoconjugate account for the large number of post‐binding events. They give an entry to the glycan vocabulary its functional, often context‐dependent meaning(s), hereby building the dictionary of the sugar code.

Separations of Carbohydrates with Noncovalent Shift Reagents by Frequency-Modulated Ion Mobility-Orbitrap Mass Spectrometry

An increased focus on characterizing the structural heterogeneity of carbohydrates has been driven by their many significant roles in extant life and potential roles in chemical evolution and the origin of life. In this work, multiplexed drift tube ion mobility-Orbitrap mass spectrometry methods were developed to analyze mixtures of disaccharides modified with noncovalent shift reagents. Since traditional coupling of atmospheric pressure drift tube ion mobility cells with Orbitrap mass analyzers suffers from low duty cycles (<0.1%), a frequency modulation scheme was applied to improve the signal-to-noise ratios (SNR). Several parameters such as the resolution setting and maximum injection time of the Orbitrap analyzer and the magnitude and duration of the frequency sweep were investigated for their impact on the sensitivity gains and resolution of disaccharide-shift reagent adducts. The sweep time and disaccharide concentration had a positive correlation with SNR. The magnitude of the frequency sweep had a negative correlation with SNR. However, increasing the frequency sweep improved the resolution of mixtures of disaccharide analytes. Application of frequency-modulated ion mobility-Orbitrap mass spectrometry to four noncovalently modified glucose dimers allowed for the differentiation of three out of these four analytes.

Nanoparticles for Directed Immunomodulation: Mannose-Functionalized Glycodendrimers Induce Interleukin-8 in Myeloid Cell Lines

New therapeutic strategies for personalized medicine need to involve innovative pharmaceutical tools, for example, modular nanoparticles designed for direct immunomodulatory properties. We synthesized mannose-functionalized poly(propyleneimine) glycodendrimers with a novel architecture, where freely accessible mannose moieties are presented on poly(ethylene glycol)-based linkers embedded within an open-shell maltose coating. This design enhanced glycodendrimer bioactivity and led to complex functional effects in myeloid cells, with specific induction of interleukin-8 expression by mannose glycodendrimers detected in HL-60 and THP-1 cells. We concentrated on explaining the molecular mechanism of this phenomenon, which turned out to be different in both investigated cell lines: in HL-60 cells, transcriptional activation via AP-1 binding to the promoter predominated, while in THP-1 cells (which initially expressed less IL-8), induction was mediated mainly by mRNA stabilization. The success of directed immunomodulation, with synthetic design guided by assumptions about mannose-modified dendrimers as exogenous regulators of pro-inflammatory chemokine levels, opens new possibilities for designing bioactive nanoparticles.

Structural Diversities of Lectins Binding to the Glycosphingolipid Gb3

Glycolipids are present on the surfaces of all living cells and thereby represent targets for many protein receptors, such as lectins. Understanding the interactions between lectins and glycolipids is essential for investigating the functions of lectins and the dynamics of glycolipids in living membranes. This review focuses on lectins binding to the glycosphingolipid globotriaosylceramide (Gb3), an attractive host cell receptor, particularly for pathogens and pathogenic products. Shiga toxin (Stx), from Shigella dysenteriae or Escherichia coli, which is one of the most virulent bacterial toxins, binds and clusters Gb3, leading to local negative membrane curvature and the formation of tubular plasma membrane invaginations as the initial step for clathrin-independent endocytosis. After internalization, it is embracing the retrograde transport pathway. In comparison, the homotetrameric lectin LecA from Pseudomonas aeruginosa can also bind to Gb3, triggering the so-called lipid zipper mechanism, which results in membrane engulfment of the bacterium as an important step for its cellular uptake. Notably, both lectins bind to Gb3 but induce distinct plasma membrane domains and exploit mainly different transport pathways. Not only, several other Gb3-binding lectins have been described from bacterial origins, such as the adhesins SadP (from Streptococcus suis) and PapG (from E. coli), but also from animal, fungal, or plant origins. The variety of amino acid sequences and folds demonstrates the structural versatilities of Gb3-binding lectins and asks the question of the evolution of specificity and carbohydrate recognition in different kingdoms of life.

An Octa-Urea [Pd2 L4 ]4+ Cage that Selectively Binds to n-octyl-α-D-Mannoside

Designing compounds for the selective molecular recognition of carbohydrates is a challenging task for supramolecular chemists. Macrocyclic compounds that incorporate isophtalamide or bisurea spacers linking two aromatic moieties have proven effective for the selective recognition of all-equatorial carbohydrates. Here, we explore the molecular recognition properties of an octa-urea [Pd2 L4 ]4+ cage complex (4). It was found that small anions like NO3- and BF4- bind inside 4 and inhibit binding of n-octyl glycosides. When the large non-coordinating anion 'BArF ' was used, 4 showed excellent selectivity towards n-octyl-α-D-Mannoside with binding in the order of Ka ≈16 M-1 versus non-measurable affinities for other glycosides including n-octyl-β-D-Glucoside (in CH3 CN/H2 O 91 : 9).

Non-carbohydrate strategies to inhibit lectin proteins with special emphasis on galectins

Lectins are a family of glycan-binding proteins, many of which have been established as key targets for therapeutic intervention. They play a central role in many physiological and cellular processes. With the advances in protein crystallography, NMR spectroscopy and computational power over the past couple of decades, the carbohydrate-receptor interactions are now well understood and characterized. Nevertheless, designing efficient carbohydrate inhibitors is a laborious endeavour. They are known to have weak affinities, unsuitable pharmacokinetic properties and highly cumbersome/complex synthetic routes. To circumvent these issues many non-carbohydrate strategies have been reported. Galectins are a sub-family of lectin proteins which have been recognized as crucial targets for a wide variety of diseases. Many candidates targeting galectins are currently in advanced stages of clinical trials. There have been a few reports of non-carbohydrate inhibitors targeting galectins which comprise of peptide-based inhibitors and a recent flourish of heterocyclic inhibitors. In this review, we have briefly highlighted the strategies like fragment-based drug-design and high-throughput screens utilized to identify non-carbohydrate based antagonists for proteins wherein the presence of a sugar was believed to be essential. Additionally, we have described the literature pertaining to non-carbohydrate inhibitors of galectins and how previous reports on rational substitution of a sugar motif could aid in design of heterocyclics that inhibit lectins/galectins. We have concluded with remarks on challenges, gap in our understanding and future perspectives concerned with rational design of non-carbohydrate molecules targeting lectins/galectins.

Altered glycosylation in cancer: A promising target for biomarkers and therapeutics

Glycosylation is a well-regulated cell and microenvironment specific post-translational modification. Several glycosyltransferases and glycosidases orchestrate the addition of defined glycan structures on the proteins and lipids. Recent advances and systemic approaches in glycomics have significantly contributed to a better understanding of instrumental roles of glycans in health and diseases. Emerging research evidence recognized aberrantly glycosylated proteins as the modulators of the malignant phenotype of cancer cells. The Cancer Genome Atlas has identified alterations in the expressions of glycosylation-specific genes that are correlated with cancer progression. However, the mechanistic basis remains poorly explored. Recent researches have shown that specific changes in the glycan structures are associated with 'stemness' and epithelial-to-mesenchymal transition of cancer cells. Moreover, epigenetic changes in the glycosylation pattern make the tumor cells capable of escaping immunosurveillance mechanisms. The deciphering roles of glycans in cancer emphasize that glycans can serve as a source for the development of novel clinical biomarkers. The ability of glycans in intervening various stages of tumor progression and the biosynthetic pathways involved in glycan structures constitute a promising target for cancer therapy. Advances in the knowledge of innovative strategies for identifying the mechanisms of glycan-binding proteins are hoped to hold great potential in cancer therapy. This review discusses the fundamental role of glycans in regulating tumorigenesis and tumor progression and provides insights into the influence of glycans in the current tactics of targeted therapies in the clinical setting.

Effects of Stereochemistry and Hydrogen Bonding on Glycopolymer-Amyloid-β Interactions

Saccharide stereochemistry plays an important role in carbohydrate functions such as biological recognition processes and protein binding. Synthetic glycopolymers with pendant saccharides of controlled stereochemistry provide an attractive approach for the design of polysaccharide-inspired biomaterials. Acrylamide-based polymers containing either β,d-glucose or β,d-galactose pendant groups, designed to mimic GM1 ganglioside saccharides, and their small-molecule analogues were used to evaluate the effect of stereochemistry on glycopolymer solution aggregation processes alone and in the presence of Aβ42 peptide using dynamic light scattering, gel permeation chromatography-multiangle laser light scattering, and fluorescence assays. Fourier transform infrared and nuclear magnetic resonance (NMR) were employed to determine hydrogen bonding patterns of the systems. The galactose-containing polymer displayed significant intramolecular hydrogen bonding and self-aggregation and minimal association with Aβ42, while the glucose-containing glycopolymers showed intermolecular interactions with the surrounding environment and association with Aβ42. Saturation transfer difference NMR spectroscopy demonstrated different binding affinities for the two glycopolymers to Aβ42 peptide.

Galectins and their involvement in ocular disease and development

Galectins are carbohydrate binding proteins with high affinity to ß-galactoside containing glycoconjugates. Understanding of the functions of galectins has grown steadily over the past decade, as a result of substantial advancements in the field of glycobiology. Galectins have been shown to be versatile molecules that participate in a range of important biological systems, including inflammation, neovascularisation and fibrosis. These processes are of particular importance in ocular tissues, where a major theme of recent research has been to divert diseases away from pathways which result in loss of function into pathways of repair and regeneration. This review summarises our current understanding of galectins in the context important ocular diseases, followed by an update on current clinical studies and future directions.

UniLectin3D, a database of carbohydrate binding proteins with curated information on 3D structures and interacting ligands

Lectins, and related receptors such as adhesins and toxins, are glycan-binding proteins from all origins that decipher the glycocode, i.e. the structural information encoded in the conformation of complex carbohydrates present on the surface of all cells. Lectins are still poorly classified and annotated, but since their functions are based on ligand recognition, their 3D-structures provide a solid foundation for characterization. UniLectin3D is a curated database that classifies lectins on origin and fold, with cross-links to literature, other databases in glycosciences and functional data such as known specificity. The database provides detailed information on lectins, their bound glycan ligands, and features their interactions using the Protein–Ligand Interaction Profiler (PLIP) server. Special care was devoted to the description of the bound glycan ligands with the use of simple graphical representation and numerical format for cross-linking to other databases in glycoscience. We conceived the design of the database architecture and the navigation tools to account for all organisms, as well as to search for oligosaccharide epitopes complexed within specified binding sites. UniLectin3D is accessible at https://www.unilectin.eu/unilectin3D.

Principles of Information Storage in Small-Molecule Mixtures

Molecular data systems have the potential to store information at dramatically higher density than existing electronic media. Some of the first experimental demonstrations of this idea have used DNA, but nature also uses a wide diversity of smaller non-polymeric molecules to preserve, process, and transmit information. In this paper, we present a general framework for quantifying chemical memory, which is not limited to polymers and extends to mixtures of molecules of all types. We show that the theoretical limit for molecular information is two orders of magnitude denser by mass than DNA, although this comes with different practical constraints on total capacity. We experimentally demonstrate kilobyte-scale information storage in mixtures of small synthetic molecules, and we consider some of the new perspectives that will be necessary to harness the information capacity available from the vast non-genomic chemical space.

Revisiting the Language of Glycoscience: Readers, Writers and Erasers in Carbohydrate Biochemistry

The roles of carbohydrates in nature are many and varied. However, the lack of template encoding in glycoscience distances carbohydrate structure, and hence function, from gene sequence. This challenging situation is compounded by descriptors of carbohydrate structure and function that have tended to emphasise their complexity. Herein, we suggest that revising the language of glycoscience could make interdisciplinary discourse more accessible to all interested parties.

Plasmonic biosensors fabricated by galvanic displacement reactions for monitoring biomolecular interactions in real time

Optical sensors are prepared by reduction of gold ions using freshly etched hydride-terminated porous silicon, and their ability to specifically detect binding between protein A/rabbit IgG and asialofetuin/Erythrina cristagalli lectin is studied. The fabrication process is simple, fast, and reproducible, and does not require complicated lab equipment. The resulting nanostructured gold layer on silicon shows an optical response in the visible range based on the excitation of localized surface plasmon resonance. Variations in the refractive index of the surrounding medium result in a color change of the sensor which can be observed by the naked eye. By monitoring the spectral position of the localized surface plasmon resonance using reflectance spectroscopy, a bulk sensitivity of 296 nm ± 3 nm/RIU is determined. Furthermore, selectivity to target analytes is conferred to the sensor through functionalization of its surface with appropriate capture probes. For this purpose, biomolecules are deposited either by physical adsorption or by covalent coupling. Both strategies are successfully tested, i.e., the optical response of the sensor is dependent on the concentration of respective target analyte in the solution facilitating the determination of equilibrium dissociation constants for protein A/rabbit IgG as well as asialofetuin/Erythrina cristagalli lectin which are in accordance with reported values in literature. These results demonstrate the potential of the developed optical sensor for cost-efficient biosensor applications. Graphical abstract.

Organic acid shift reagents for the discrimination of carbohydrate isobars by ion mobility-mass spectrometry

Traveling wave and drift tube ion mobility were utilized to separate isomeric disaccharides. Organic acid shift reagents were necessary to increase the resolution of these separations for mixture analysis.

The Sialic Acid-Dependent Nematocyst Discharge Process in Relation to Its Physical-Chemical Properties Is A Role Model for Nanomedical Diagnostic and Therapeutic Tools

Formulas derived from theoretical physics provide important insights about the nematocyst discharge process of Cnidaria (Hydra, jellyfishes, box-jellyfishes and sea-anemones). Our model description of the fastest process in living nature raises and answers questions related to the material properties of the cell- and tubule-walls of nematocysts including their polysialic acid (polySia) dependent target function. Since a number of tumor-cells, especially brain-tumor cells such as neuroblastoma tissues carry the polysaccharide chain polySia in similar concentration as fish eggs or fish skin, it makes sense to use these findings for new diagnostic and therapeutic approaches in the field of nanomedicine. Therefore, the nematocyst discharge process can be considered as a bionic blue-print for future nanomedical devices in cancer diagnostics and therapies. This approach is promising because the physical background of this process can be described in a sufficient way with formulas presented here. Additionally, we discuss biophysical and biochemical experiments which will allow us to define proper boundary conditions in order to support our theoretical model approach. PolySia glycans occur in a similar density on malignant tumor cells than on the cell surfaces of Cnidarian predators and preys. The knowledge of the polySia-dependent initiation of the nematocyst discharge process in an intact nematocyte is an essential prerequisite regarding the further development of target-directed nanomedical devices for diagnostic and therapeutic purposes. The theoretical description as well as the computationally and experimentally derived results about the biophysical and biochemical parameters can contribute to a proper design of anti-tumor drug ejecting vessels which use a stylet-tubule system. Especially, the role of nematogalectins is of interest because these bridging proteins contribute as well as special collagen fibers to the elastic band properties. The basic concepts of the nematocyst discharge process inside the tubule cell walls of nematocysts were studied in jellyfishes and in Hydra which are ideal model organisms. Hydra has already been chosen by Alan Turing in order to figure out how the chemical basis of morphogenesis can be described in a fundamental way. This encouraged us to discuss the action of nematocysts in relation to morphological aspects and material requirements. Using these insights, it is now possible to discuss natural and artificial nematocyst-like vessels with optimized properties for a diagnostic and therapeutic use, e.g., in neurooncology. We show here that crucial physical parameters such as pressure thresholds and elasticity properties during the nematocyst discharge process can be described in a consistent and satisfactory way with an impact on the construction of new nanomedical devices.

Translation of genome to glycome: role of the Golgi apparatus

Glycans are one of the four biopolymers of the cell and they play important roles in cellular and organismal physiology. They consist of both linear and branched structures and are synthesized in a nontemplated manner in the secretory pathway of mammalian cells with the Golgi apparatus playing a key role in the process. In spite of the absence of a template, the glycans synthesized by a cell are not a random collection of possible glycan structures but a distribution of specific glycans in defined quantities that is unique to each cell type (Cell type here refers to distinct cell forms present in an organism that can be distinguished based on morphological, phenotypic and/or molecular criteria.) While information to produce cell type-specific glycans is encoded in the genome, how this information is translated into cell type-specific glycome (Glycome refers to the quantitative distribution of all glycan structures present in a given cell type.) is not completely understood. We summarize here the factors that are known to influence the fidelity of glycan biosynthesis and integrate them into known glycosylation pathways so as to rationalize the translation of genetic information to cell type-specific glycome.

Selenoglycosides as Lectin Ligands: 77 Se-Edited CPMG-HSQMBC NMR Spectroscopy To Monitor Biomedically Relevant Interactions

The fundamental importance of protein-glycan recognition calls for specific and sensitive high-resolution techniques for their detailed analysis. After the introduction of 19 F NMR spectroscopy to study the recognition of fluorinated glycans, a new 77 Se NMR spectroscopy method is presented for complementary studies of selenoglycans with optimised resolution and sensitivity, in which direct NMR spectroscopy detection on 77 Se is replaced by its indirect observation in a 2D 1 H,77 Se HSQMBC spectrum. In contrast to OH/F substitution, O/Se exchange allows the glycosidic bond to be targeted. As an example, selenodigalactoside recognition by three human galectins and a plant toxin is readily indicated by signal attenuation and line broadening in the 2D 1 H,77 Se HSQMBC spectrum, in which CPMG-INEPT long-range transfer ensures maximal detection sensitivity, clean signal phases, and reliable ligand ranking. By monitoring competitive displacement of a selenated spy ligand, the selective 77 Se NMR spectroscopy approach may also be used to screen non-selenated compounds. Finally, 1 H,77 Se CPMG-INEPT transfer allows further NMR sensors of molecular interaction to be combined with the specificity and resolution of 77 Se NMR spectroscopy.

Strategies for the Development of Glycomimetic Drug Candidates

Carbohydrates are a structurally-diverse group of natural products which play an important role in numerous biological processes, including immune regulation, infection, and cancer metastasis. Many diseases have been correlated with changes in the composition of cell-surface glycans, highlighting their potential as a therapeutic target. Unfortunately, native carbohydrates suffer from inherently weak binding affinities and poor pharmacokinetic properties. To enhance their usefulness as drug candidates, 'glycomimetics' have been developed: more drug-like compounds which mimic the structure and function of native carbohydrates. Approaches to improve binding affinities (e.g., deoxygenation, pre-organization) and pharmacokinetic properties (e.g., limiting metabolic degradation, improving permeability) have been highlighted in this review, accompanied by relevant examples. By utilizing these strategies, high-affinity ligands with optimized properties can be rationally designed and used to address therapies for novel carbohydrate-binding targets.

Anti-adhesive effects of human soluble thrombomodulin and its domains

We reported previously that leukocyte β2 integrins (LFA-1 and Mac-1) bind to the serine/threonine-rich domain of thrombomodulin (TM) expressed on vascular endothelial cells (VECs). Recombinant human soluble TM (rhsTM, TMD123) has been approved as a therapeutic drug for septic disseminated intravascular coagulation. However, the roles of TMD123 on the adhesion of leukocyte integrins to VECs remain unclear. In the current study, we have revealed that an integrin-dependent binding between human peripheral blood mononuclear cells (PBMCs) and VECs was inhibited by TMD123. Next, using mutant proteins composed of isolated TM extracellular domains, we examined the structural characteristics responsible for the anti-adhesion properties of TMD123. Namely, we investigated whether the effects of the binding of TM and leukocytes was inhibited by the administration of TMD123. In fact, we confirmed that TMD123, TMD1, and TMD3 inhibited the binding of PBMCs to the immobilized recombinant proteins TMD123 and TMD3. These results indicate that TMD123 inhibited the adhesion of leukocytes to endothelial cells via β2 integrins and endothelial TM. Moreover, since TMD1 might bind to leukocytes via other adhesion receptors than integrins, TMD1 and TMD3 appear to inhibit leukocyte binding to TM on VECs via different mechanisms. In summary, TMD123 (rhsTM), TMD1 or TMD3 is a promising treatment option for sepsis that attenuates integrin-dependent binding of leukocytes to VECs, and may inhibit the undesirable adhesion and migration of leukocytes to VECs in sepsis.

Sialylated Oligosaccharides and Glycoconjugates of Human Milk. The Impact on Infant and Newborn Protection, Development and Well-Being

Human milk not only has nutritional value, but also provides a wide range of biologically active molecules, which are adapted to meet the needs of newborns and infants. Mother’s milk is a source of sialylated oligosaccharides and glycans that are attached to proteins and lipids, whose concentrations and composition are unique. Sialylated human milk glycoconjugates and oligosaccharides enrich the newborn immature immune system and are crucial for their proper development and well-being. Some of the milk sialylated oligosaccharide structures can locally exert biologically active effects in the newborn’s and infant’s gut. Sialylated molecules of human milk can be recognized and bound by sialic acid-dependent pathogens and inhibit their adhesion to the epithelial cells of newborns and infants. A small amount of intact sialylated oligosaccharides can be absorbed from the intestine and remain in the newborn’s circulation in concentrations high enough to modulate the immunological system at the cellular level and facilitate proper brain development during infancy. Conclusion: The review summarizes the current state of knowledge on sialylated human milk oligosaccharides and glycoconjugates, discusses the significance of sialylated structures of human milk in newborn protection and development, and presents the advantages of human milk over infant formula.

A Descriptive Study of Lectin Histochemistry of the Placenta in Cattle following Inoculation of Neospora caninum

The aim of this study was to describe the lectin-binding pattern in the placentas of cows infected experimentally with Neospora caninum. Four cows were inoculated intravenously with 1 × 10⁸ tachyzoites of the NC-1 strain of N. caninum at 150 ± 7 days of pregnancy. Two control cows were administered a placebo. An indirect fluorescence antibody test (IFAT) was performed on serum samples obtained before and after the inoculation. The cows were killed at 30 and 37 days post inoculation. Samples of placenta were taken for histopathology and lectin histochemistry. Fetal tissues and fluids were collected for histopathology and IFAT, respectively. All infected cows had high antibody titres. All fetuses had characteristic histopathological lesions, including non-suppurative meningoencephalitis, myocarditis, hepatitis and myositis, suggesting N. caninum infection. Only two infected fetuses developed specific antibodies. Mild non-suppurative inflammatory infiltrates were recorded in the placentae. Differences in the lectin-binding pattern were observed between infected animals and controls in the glycocalyx (CON-A and WGA) and apical cytoplasm (RCA-I and CON-A) of the trophoblastic cells; giant trophoblastic cells (CON-A and DBA); glycocalyx (PNA, WGA) and apical cytoplasm (CON-A, WGA, PNA, DBA and RCA-I) of endometrial cells; trophoblast of the interplacentomal region (WGA); endothelium (CON-A, SBA, RCA-1 and WGA); and finally, mesenchyme (CON-A, RCA-1, SBA, PNA and DBA). These findings indicate that there is a distinctive pattern of lectin binding in the placenta of cattle infected with N. caninum. The direct effect of the presence of the protozoa as well as the altered expression of cytokines could explain these changes in the maternofetal interface.

Recent Developments in Solid-Phase Strategies towards Synthetic, Sequence-Defined Macromolecules

Sequence-control in synthetic polymers is an important contemporary research area because it provides the opportunity to create completely novel materials for structure-function studies. This is especially relevant for biomimetic polymers, bioactive and information security materials. The level of control is strongly dependent and inherent upon the polymerization technique utilized. Today, the most established method yielding monodispersity and monomer sequence-definition is solid-phase synthesis. This Focus Review highlights recent advances in solid-phase strategies to access synthetic, sequence-defined macromolecules. Alternatives strategies towards sequence-defined macromolecules are also briefly summarized.

Glycans and glycosaminoglycans in neurobiology: key regulators of neuronal cell function and fate

The aim of the present study was to examine the roles of l-fucose and the glycosaminoglycans (GAGs) keratan sulfate (KS) and chondroitin sulfate/dermatan sulfate (CS/DS) with selected functional molecules in neural tissues. Cell surface glycans and GAGs have evolved over millions of years to become cellular mediators which regulate fundamental aspects of cellular survival. The glycocalyx, which surrounds all cells, actuates responses to growth factors, cytokines and morphogens at the cellular boundary, silencing or activating downstream signaling pathways and gene expression. In this review, we have focused on interactions mediated by l-fucose, KS and CS/DS in the central and peripheral nervous systems. Fucose makes critical contributions in the area of molecular recognition and information transfer in the blood group substances, cytotoxic immunoglobulins, cell fate-mediated Notch-1 interactions, regulation of selectin-mediated neutrophil extravasation in innate immunity and CD-34-mediated new blood vessel development, and the targeting of neuroprogenitor cells to damaged neural tissue. Fucosylated glycoproteins regulate delivery of synaptic neurotransmitters and neural function. Neural KS proteoglycans (PGs) were examined in terms of cellular regulation and their interactive properties with neuroregulatory molecules. The paradoxical properties of CS/DS isomers decorating matrix and transmembrane PGs and the positive and negative regulatory cues they provide to neurons are also discussed.

"One-Pot" Protection, Glycosylation, and Protection-Glycosylation Strategies of Carbohydrates

Carbohydrates, which are ubiquitously distributed throughout the three domains of life, play significant roles in a variety of vital biological processes. Access to unique and homogeneous carbohydrate materials is important to understand their physical properties, biological functions, and disease-related features. It is difficult to isolate carbohydrates in acceptable purity and amounts from natural sources. Therefore, complex saccharides with well-defined structures are often most conviently accessed through chemical syntheses. Two major hurdles, regioselective protection and stereoselective glycosylation, are faced by carbohydrate chemists in synthesizing these highly complicated molecules. Over the past few years, there has been a radical change in tackling these problems and speeding up the synthesis of oligosaccharides. This is largely due to the development of one-pot protection, one-pot glycosylation, and one-pot protection-glycosylation protocols and streamlined approaches to orthogonally protected building blocks, including those from rare sugars, that can be used in glycan coupling. In addition, new automated strategies for oligosaccharide syntheses have been reported not only for program-controlled assembly on solid support but also by the stepwise glycosylation in solution phase. As a result, various sugar molecules with highly complex, large structures could be successfully synthesized. To summarize these recent advances, this review describes the methodologies for one-pot protection and their one-pot glycosylation into the complex glycans and the chronological developments associated with automated syntheses of oligosaccharides.

Overview of Piezoelectric Biosensors, Immunosensors and DNA Sensors and Their Applications

Piezoelectric biosensors are a group of analytical devices working on a principle of affinity interaction recording. A piezoelectric platform or piezoelectric crystal is a sensor part working on the principle of oscillations change due to a mass bound on the piezoelectric crystal surface. In this review, biosensors having their surface modified with an antibody or antigen, with a molecularly imprinted polymer, with genetic information like single stranded DNA, and biosensors with bound receptors of organic of biochemical origin, are presented and discussed. The mentioned recognition parts are frequently combined with use of nanoparticles and applications in this way are also introduced. An overview of the current literature is given and the methods presented are commented upon.

Designing the new generation of intelligent biocompatible carriers for protein and peptide delivery

Therapeutic proteins and peptides have revolutionized treatment for a number of diseases, and the expected increase in macromolecule-based therapies brings a new set of challenges for the pharmaceutics field. Due to their poor stability, large molecular weight, and poor transport properties, therapeutic proteins and peptides are predominantly limited to parenteral administration. The short serum half-lives typically require frequent injections to maintain an effective dose, and patient compliance is a growing issue as therapeutic protein treatments become more widely available. A number of studies have underscored the relationship of subcutaneous injections with patient non-adherence, estimating that over half of insulin-dependent adults intentionally skip injections. The development of oral formulations has the potential to address some issues associated with non-adherence including the interference with daily activities, embarrassment, and injection pain. Oral delivery can also help to eliminate the adverse effects and scar tissue buildup associated with repeated injections. However, there are several major challenges associated with oral delivery of proteins and peptides, such as the instability in the gastrointestinal (GI) tract, low permeability, and a narrow absorption window in the intestine. This review provides a detailed overview of the oral delivery route and associated challenges. Recent advances in formulation and drug delivery technologies to enhance bioavailability are discussed, including the co-administration of compounds to alter conditions in the GI tract, the modification of the macromolecule physicochemical properties, and the use of improved targeted and controlled release carriers.

Covalent Strategies for Targeting Messenger and Non-Coding RNAs: An Updated Review on siRNA, miRNA and antimiR Conjugates

Oligonucleotide-based therapy has become an alternative to classical approaches in the search of novel therapeutics involving gene-related diseases. Several mechanisms have been described in which demonstrate the pivotal role of oligonucleotide for modulating gene expression. Antisense oligonucleotides (ASOs) and more recently siRNAs and miRNAs have made important contributions either in reducing aberrant protein levels by sequence-specific targeting messenger RNAs (mRNAs) or restoring the anomalous levels of non-coding RNAs (ncRNAs) that are involved in a good number of diseases including cancer. In addition to formulation approaches which have contributed to accelerate the presence of ASOs, siRNAs and miRNAs in clinical trials; the covalent linkage between non-viral vectors and nucleic acids has also added value and opened new perspectives to the development of promising nucleic acid-based therapeutics. This review article is mainly focused on the strategies carried out for covalently modifying siRNA and miRNA molecules. Examples involving cell-penetrating peptides (CPPs), carbohydrates, polymers, lipids and aptamers are discussed for the synthesis of siRNA conjugates whereas in the case of miRNA-based drugs, this review article makes special emphasis in using antagomiRs, locked nucleic acids (LNAs), peptide nucleic acids (PNAs) as well as nanoparticles. The biomedical applications of siRNA and miRNA conjugates are also discussed.

Bisecting GlcNAc restricts conformations of branches in model N-glycans with GlcNAc termini

Bisected N-glycans play significant roles in tumor migration and Alzheimer's disease through modulating the action and localization of their carrier proteins. Such biological functions are often discussed in terms of the conformation of the attached N-glycans with or without bisecting GlcNAc. To obtain insights into the effects of bisecting GlcNAc on glycan conformation, a systematic NMR structural analysis was performed on two pairs of synthetic N-glycans, with and without bisecting GlcNAc. The analysis reveals that terminal GlcNAcs and bisecting GlcNAc cooperate to restrict the conformations of both the α1-3 and α1-6 branches of N-glycans. ¹H and ¹³C chemical shift comparisons suggest that bisecting GlcNAc directly modulates local conformation. Unique NOE correlations between core-mannose and the α1-3 branch mannose as well as the ³J_C-H constant of the glycoside linkage indicate that bisecting GlcNAc restricts the conformation of the 1-3 branch. The angles of the glycosidic bonds between core-mannose and α1-6 branch mannose derived from ³J_C-H and ³J_H-H coupling constants show that terminal GlcNAcs restrict the distribution of the ψ angle to 180° and the bisecting GlcNAc increases the distribution of the ω angle +60° in the presence of terminal GlcNAcs. It is feasible that restriction of branch conformations by bisecting GlcNAc has important consequences for protein-glycan interplay and following biological events.

Exploring the Role of Solvent on Carbohydrate-Aryl Interactions by Diffusion NMR-Based Studies

Carbohydrate-protein interactions play an important role in many molecular recognition processes. An exquisite combination of multiple factors favors the interaction of the receptor with one specific type of sugar, whereas others are excluded. Stacking CH-aromatic interactions within the binding site provide a relevant contribution to the stabilization of the resulting sugar-protein complex. Being experimentally difficult to detect and analyze, the key CH-π interaction features have been very often dissected using a variety of techniques and simple model systems. In the present work, diffusion NMR spectroscopy has been employed to separate the components of sugar mixtures in different solvents on the basis of their differential ability to interact through CH-π interactions with one particular aromatic cosolute in solution. The experimental data show that the properties of the solvent did also influence the diffusion behavior of the sugars present in the mixture, inhibiting or improving their separation. Overall, the results showed that, for the considered monosaccharide derivatives, their diffusion coefficient values and, consequently, their apparent molecular sizes and/or shapes depend on the balance between solute/cosolute as well as solute/solvent interactions. Thus, in certain media and in the presence of the aromatic cosolute, the studied saccharides that are more suited to display CH-π interactions exhibited a lower diffusion coefficient than the noncomplexing sugars in the mixture. However, when dissolved in another medium, the interaction with the solvent strongly competes with that of the aromatic cosolute.

Harnessing chondroitin sulphate in composite scaffolds to direct progenitor and stem cell function for tissue repair

This review details the inclusion of chondroitin sulphate in bioscaffolds for superior functional properties in tissue regenerative applications.

Computational Chemistry Tools in Glycobiology: Modelling of Carbohydrate–Protein Interactions

Molecular modelling provides a major impact in the field of glycosciences, helping in the characterisation of the molecular basis of the recognition between lectins from pathogens and human glycoconjugates, and in the design of glycocompounds with anti-infectious properties. The conformational properties of oligosaccharides are complex, and therefore, the simulation of these properties is a challenging task. Indeed, the development of suitable force fields is required for the proper simulation of important problems in glycobiology, such as the interatomic interactions responsible for oligosaccharide and glycoprotein dynamics, including O-linkages in oligo- and polysaccharides, and N- and O-linkages in glycoproteins. The computational description of representative examples is discussed, herein, related to biologically active oligosaccharides and their interaction with lectins and other proteins, and the new routes open for the design of glycocompounds with promising biological activities.

Enzymatic Synthesis of N-Acetyllactosamine (LacNAc) Type 1 Oligomers and Characterization as Multivalent Galectin Ligands

Repeats of the disaccharide unit N-acetyllactosamine (LacNAc) occur as type 1 (Galβ1, 3GlcNAc) and type 2 (Galβ1, 4GlcNAc) glycosylation motifs on glycoproteins and glycolipids. The LacNAc motif acts as binding ligand for lectins and is involved in many biological recognition events. To the best of our knowledge, we present, for the first time, the synthesis of LacNAc type 1 oligomers using recombinant β1,3-galactosyltransferase from Escherichia coli and β1,3-N-acetylglucosaminyltranferase from Helicobacter pylori. Tetrasaccharide glycans presenting LacNAc type 1 repeats or LacNAc type 1 at the reducing or non-reducing end, respectively, were conjugated to bovine serum albumin as a protein scaffold by squarate linker chemistry. The resulting multivalent LacNAc type 1 presenting neo-glycoproteins were further studied for specific binding of the tumor-associated human galectin 3 (Gal-3) and its truncated counterpart Gal-3∆ in an enzyme-linked lectin assay (ELLA). We observed a significantly increased affinity of Gal-3∆ towards the multivalent neo-glycoprotein presenting LacNAc type 1 repeating units. This is the first evidence for differences in glycan selectivity of Gal-3∆ and Gal-3 and may be further utilized for tracing Gal-3∆ during tumor progression and therapy.