Glycosaminoglycans: What Remains To Be Deciphered?

Glycosaminoglycans (GAGs) are complex polysaccharides exhibiting a vast structural diversity and fulfilling various functions mediated by thousands of interactions in the extracellular matrix, at the cell surface, and within the cells where they have been detected in the nucleus. It is known that the chemical groups attached to GAGs and GAG conformations comprise “glycocodes” that are not yet fully deciphered. The molecular context also matters for GAG structures and functions, and the influence of the structure and functions of the proteoglycan core proteins on sulfated GAGs and vice versa warrants further investigation. The lack of dedicated bioinformatic tools for mining GAG data sets contributes to a partial characterization of the structural and functional landscape and interactions of GAGs. These pending issues will benefit from the development of new approaches reviewed here, namely (i) the synthesis of GAG oligosaccharides to build large and diverse GAG libraries, (ii) GAG analysis and sequencing by mass spectrometry (e.g., ion mobility-mass spectrometry), gas-phase infrared spectroscopy, recognition tunnelling nanopores, and molecular modeling to identify bioactive GAG sequences, biophysical methods to investigate binding interfaces, and to expand our knowledge and understanding of glycocodes governing GAG molecular recognition, and (iii) artificial intelligence for in-depth investigation of GAGomic data sets and their integration with proteomics

Synthesis and characterization of glucose- and galactose- derived poly-amido-saccharides (PAS)

Polysaccharides are widely diverse in structure and can vary in molecular weight, sugar composition, monomeric sequence, stereochemistry, glycosidic linkage, branching, and functionalization. Due to these attributes, polysaccharides are highly abundant in nature and are found in a variety of applications across biology, chemistry, medicine, and commercial products. As the structural diversity within carbohydrate polymers is challenging to replicate under synthetic means, these materials are commonly isolated from natural resources, which introduces unwanted variation between batch samples and requires extensive purification to isolate final products. Although enzymatic approaches to obtain polysaccharides have been explored, these routes typically require expensive starting materials and cannot introduce non-natural functional groups. While chemical synthetic routes of polysaccharide structures and polymer-mimics have been reported, it is challenging to have synthetic control over molecular weight, stereochemistry, and linkages while maintaining the high density of similar functional groups and rigid pyranose backbone. Poly-amido-saccharides (PASs) are enantiopure carbohydrate polymers in which sugar units are joined by 1,2-amide linkages. By using an anionic ring-opening polymerization of β-lactam monomers, PAS structures are synthesized with control over molecular weight, functional groups, batch-to-batch consistency, and at low polydispersity. Importantly, PAS samples are water-soluble and contain the rigid pyranose backbone as found in natural polysaccharides. As PAS structures are not found in nature, the unnatural peptide linkage between monosaccharide units contributes to their unique structural features and chemical properties. The Grinstaff group has reported PASs to have a robust helical secondary structure; minimal cytotoxicity in different mammalian cell lines; ability to be functionalized on the monomer and polymer level; varying water-solubility depending on its sugar composition; and, potential to be recognized as natural carbohydrates (glucose-derived PAS are recognized by lectin concanavalin A similarly to glucose). Experimental and computational techniques, including circular dichroism, 2D-NMR spectroscopy, and molecular dynamics simulations, were used to explore structure-function relationships between glucose- (glc-) and galactose- (gal-) PAS structures. Cytotoxicity and cellular uptake studies were conducted to investigate their biocompatibility properties. Finally, sulfated glc-PASs structures were explored to possess anticoagulation activity and binding interactions with antithrombin III to serve as heparin-mimics to address current clinical challenges associated with heparin usage.2019-03-17T00:00:00

Conformation And Binding Aspects Of Sulfated Carbohydrates By Liquid-State Nmr

Liquid-state NMR has long been an important tool for understanding the conformations and interactions of biomacromolecules. To date these conclusions have primarily been focused upon nucleotides and peptides with little information regarding the conformational structures of carbohydrates. Through the methods described in this manuscript the accurate conformational analysis of a sulfated fucan from Lytechinus variegatus has been assessed. This was achieved through a combination of NOESY spectroscopy and assessment of chemical exchange in hydroxyl protons undergoing fast chemical exchange with excess solvent. This is accomplished through usage of super- cooled H2O: acetone solvent and T1 inversion recovery. This methodology was optimized in L-fucose and applied to the sulfated fucan for normalization of NOE information for derivatization of distance restraints. Molecular dynamics modeling further confirmed these structures as supported. Furthermore, the structure-activity relationships between glycosaminoglycan oligosaccharides and their binding partners have been heavily studied. Usage of saturation transfer difference NMR has allowed robust conclusions towards understanding the impact of chain length, position of sulfates, and carbohydrate composition on the complex formation between the sulfated polysaccharides and their binding partners

Synthetic glycans for structural studies: the importance of the modification pattern

Carbohydrates are the most abundant organic compounds in nature. They serve as energy sources, regulate a plethora of biological processes, and are essential structural components in animals, plants and microorganisms. The structural diversity of carbohydrates results in materials with extremely different properties. Still, structure-property correlations are hardly established for carbohydrates due to the difficulty in obtaining pure, well-defined molecules and the lack of suitable analytical methods. A comprehensive understanding of carbohydrate function requires a detailed understanding and thorough elucidation of the carbohydrate's structure. The ultimate goal of this thesis is to establish correlations between the structure and the properties of carbohydrates and shine light on how small modifications affect the shape of carbohydrates. To achieve this goal, automated glycan assembly (AGA) is used as a platform to produce well-defined oligosaccharide probes. Molecular dynamic (MD) simulations are performed to address conformational aspects of oligosaccharides at the atomic level and to support the structural analysis

Exploring the Multifaceted Roles of Glycosaminoglycans (GAGs) - New Advances and Further Challenges

Glycosaminoglycans are linear, anionic polysaccharides (GAGs) consisting of repeating disaccharides. GAGs are ubiquitously localized throughout the extracellular matrix (ECM) and to the cell membranes of cells in all tissues. They are either conjugated to protein cores in the form of proteoglycans, e.g., chondroitin/dermatan sulfate (CS/DS), heparin/heparan sulfate (Hep/HS) and keratan sulfate (KS), as well as non-sulfated hyaluronan (HA). By modulating biological signaling GAGs participate in the regulation of homeostasis and also participate in disease progression. The book, entitled “Exploring the multifaceted roles of glycosaminoglycans (GAGs)—new advances and further challenges”, features original research and review articles. These articles cover several GAG-related timely topics in structural biology and imaging; morphogenesis, cancer, and other disease therapy and drug developments; tissue engineering; and metabolic engineering. This book also includes an article illustrating how metabolic engineering can be used to create the novel chondroitin-like polysaccharide.A prerequisite for communicating in any discipline and across disciplines is familiarity with the appropriate terminology. Several nomenclature rules exist in the field of biochemistry. The historical description of GAGs follows IUPAC and IUB nomenclature. New structural depictions such as the structural nomenclature for glycan and their translation into machine-readable formats have opened the route for cross-references with popular bioinformatics resources and further connections with other exciting “omics” fields

Toward Improving Understanding of the Structure and Biophysics of Glycosaminoglycans

Glycosaminoglycans (GAGs) are the linear carbohydrate components of proteoglycans (PGs) that mediate PG bioactivities, including signal transduction, tissue morphogenesis, and matrix assembly. To understand GAG function, it is important to understand GAG structure and biophysics at atomic resolution. This is a challenge for existing experimental and computational methods because GAGs are heterogeneous, conformationally complex, and polydisperse, containing up to 200 monosaccharides. Molecular dynamics (MD) simulations come close to overcoming this challenge but are only feasible for short GAG polymers. To address this problem, we developed an algorithm that applies conformations from unbiased all-atom explicit-solvent MD simulations of short GAG polymers to rapidly construct 3-D atomic-resolution models of GAGs of arbitrary length. MD simulations of GAG 10-mers (i.e., polymers containing 10 monosaccharides) and 20-mers were run and conformations of all monosaccharide rings and glycosidic linkages were analyzed and compared to existing experimental data. These analyses demonstrated that (1) MD-generated GAG conformations are in agreement with existing experimental data; (2) MD-generated GAG 10-mer ring and linkage conformations match those in corresponding GAG 20-mers, suggesting that these conformations are representative of those in longer GAG biopolymers; and (3) rings and linkages in GAG 10- and 20-mers behave randomly and independently in MD simulation. Together, these findings indicate that MD-generated GAG 20-mer ring and linkage conformations can be used to construct thermodynamically-correct models of GAG polymers. Indeed, our findings demonstrate that our algorithm constructs GAG 10- and 20-mer conformational ensembles that accurately represent the backbone flexibility seen in MD simulations. Furthermore, within a day, our algorithm constructs conformational ensembles of GAG 200-mers that we would reasonably expect from MD simulation, demonstrating the efficiency of the algorithm and reduction in its time and computational cost compared to simulation. While there are other programs that can quickly construct atomic-resolution models of GAGs, those programs use conformations from short GAG subunits in solid state. Our findings suggest that GAG 20-mers are more flexible than short GAG subunits, meaning our program constructs ensembles that more accurately represent GAG polymer backbone flexibility and provide valuable insights toward improving the understanding of the structure and biophysics of GAGs

Glycosaminoglycans: What Remains To Be Deciphered?

Glycosaminoglycans (GAGs) are complex polysaccharides exhibiting a vast structural diversity and fulfilling various functions mediated by thousands of interactions in the extracellular matrix, at the cell surface, and within the cells where they have been detected in the nucleus. It is known that the chemical groups attached to GAGs and GAG conformations comprise “glycocodes” that are not yet fully deciphered. The molecular context also matters for GAG structures and functions, and the influence of the structure and functions of the proteoglycan core proteins on sulfated GAGs and vice versa warrants further investigation. The lack of dedicated bioinformatic tools for mining GAG data sets contributes to a partial characterization of the structural and functional landscape and interactions of GAGs. These pending issues will benefit from the development of new approaches reviewed here, namely (i) the synthesis of GAG oligosaccharides to build large and diverse GAG libraries, (ii) GAG analysis and sequencing by mass spectrometry (e.g., ion mobility-mass spectrometry), gas-phase infrared spectroscopy, recognition tunnelling nanopores, and molecular modeling to identify bioactive GAG sequences, biophysical methods to investigate binding interfaces, and to expand our knowledge and understanding of glycocodes governing GAG molecular recognition, and (iii) artificial intelligence for in-depth investigation of GAGomic data sets and their integration with proteomics

Marine Polysaccharides Volume 1

The field of marine polysaccharides is constantly evolving, due to progress in the discovery and production of new marine polysaccharides. Seaweed remains the most abundant source of polysaccharides, but recent advances in biotechnology have allowed the production of large quantities of polysaccharides from a variety of micro-algae, by controlling growth conditions and tailoring the production of bioactive compounds in a bioreactor. Of particular interest are polysaccharides produced by micro-organisms from extreme marine environments, due to their recognized different biochemistry. Extracellular polysaccharides (EPSs) with unique properties produced by a number of micro-algae are known. The first volume is a collection of papers concerning the identification and characterization of novel marine polysaccharides. It is divided into three chapters; the first two are dedicated to polysaccharides from different marine sources (algae, micro-algae, animals), while the third one gathers information on the isolation, characterization and bioactivity of new EPSs

Sulfated seaweed polysaccharides as multifunctional materials in drug delivery applications

In the last decades, the discovery of metabolites from marine resources showing biological activity has increased significantly. Among marine resources, seaweed is a valuable source of structurally diverse bioactive compounds. The cell walls of marine algae are rich in sulfated polysaccharides, including carrageenan in red algae, ulvan in green algae and fucoidan in brown algae. Sulfated polysaccharides have been increasingly studied over the years in the pharmaceutical field, given their potential usefulness in applications such as the design of drug delivery systems. The purpose of this review is to discuss potential applications of these polymers in drug delivery systems, with a focus on carrageenan, ulvan and fucoidan. General information regarding structure, extraction process and physicochemical properties is presented, along with a brief reference to reported biological activities. For each material, specific applications under the scope of drug delivery are described, addressing in privileged manner particulate carriers, as well as hydrogels and beads. A final section approaches the application of sulfated polysaccharides in targeted drug delivery, focusing with particular interest the capacity for macrophage targeting