1H and 15N NMR Characterization of the Amine Groups of Heparan Sulfate Related Glucosamine Monosaccharides in Aqueous Solution

Molecular architecture of chitin and chitosan-dominated cell walls in zygomycetous fungal pathogens by solid-state NMR

Zygomycetous fungal infections pose an emerging medical threat among individuals with compromised immunity and metabolic abnormalities. Our pathophysiological understanding of these infections, particularly the role of fungal cell walls in growth and immune response, remains limited. Here we conducted multidimensional solid-state NMR analysis to examine cell walls in five Mucorales species, including key mucormycosis causative agents like Rhizopus and Mucor species. We show that the rigid core of the cell wall primarily comprises highly polymorphic chitin and chitosan, with minimal quantities of β-glucans linked to a specific chitin subtype. Chitosan emerges as a pivotal molecule preserving hydration and dynamics. Some proteins are entrapped within this semi-crystalline chitin/chitosan layer, stabilized by the sidechains of hydrophobic amino acid residues, and situated distantly from β-glucans. The mobile domain contains galactan- and mannan-based polysaccharides, along with polymeric α-fucoses. Treatment with the chitin synthase inhibitor nikkomycin removes the β-glucan-chitin/chitosan complex, leaving the other chitin and chitosan allomorphs untouched while simultaneously thickening and rigidifying the cell wall. These findings shed light on the organization of Mucorales cell walls and emphasize the necessity for a deeper understanding of the diverse families of chitin synthases and deacetylases as potential targets for novel antifungal therapies.

Quality control, safety assessment and preparation approaches of low molecular weight heparin

Low Molecular Weight Heparins (LMWHs) are well-established for use in the prevention and treatment of thrombotic diseases, and as a substitute for unfractionated heparin (UFH) due to their predictable pharmacokinetics and subcutaneous bioavailability. LMWHs are produced by various depolymerization methods from UFH, resulting in heterogeneous compounds with similar biochemical and pharmacological properties. However, the delicate supply chain of UFH and potential contamination from animal sources require new manufacturing approaches for LMWHs. Various LMWH preparation methods are emerging, such as chemical synthesis, enzymatic or chemical depolymerization and chemoenzymatic synthesis. To establish the sameness of active ingredients in both innovator and generic LMWH products, the Food and Drug Administration has implemented a stringent scientific method of equivalence based on physicochemical properties, heparin source material and depolymerization techniques, disaccharide composition and oligosaccharide mapping, biological and biochemical properties, and in vivo pharmacodynamic profiles. In this review, we discuss currently available LMWHs, potential manufacturing methods, and recent progress for manufacturing quality control of these LMWHs.

Solvent-Free Nuclear Magnetic Resonance Spectroscopy of Charged Molecules

Nuclear magnetic resonance (NMR) spectroscopy of small molecules protonated in a solvent-free environment was successfully demonstrated. The method is referred to as solvent-free protonation NMR (SoF-NMR). Leveraging matrix-assisted ionization (MAI), we generated protonated species of aniline, 4-chloroaniline, 4-aminobiphenyl, and benzocaine for NMR analysis under mild pressure and temperature conditions. The SoF-NMR spectra were compared to traditional solution NMR spectra, and the shift changes in nuclear spin resonance frequencies verify that these small molecules are protonated by 3-nitrobenzonitrile (3-NBN). As the sample pressure decreased, new spectral features appeared, indicating the presence of differently charged species. Several advantages of SoF-NMR are highlighted, such as the elimination of H/D exchange in labile protons, resulting in the precise observation of protons that are otherwise transient in solution. Notably, the data on benzocaine show evidence of neutral, N-protonated, and O-protonated species all in the same spectrum. SoF-NMR eliminates the solvent effects and interactions that can hinder important spectral features. Optimizing SoF-NMR will result in more cost-effective and efficient NMR experimentation to monitor high-temperature, solvent-free reactions. SoF-NMR has a viable future application for studying exchangeable protons, intermediates, and products in gas-phase chemistry.

Beyond Rule-of-five: Permeability Assessment of Semipeptidic Macrocycles

Compounds beyond the rule-of-five are generating interest as they expand the molecular toolbox for modulating targets previously considered "undruggable". Macrocyclic peptides are an efficient class of molecules for modulating protein-protein interactions. However, predicting their permeability is difficult as they differ from small molecules. Although constrained by macrocyclization, they generally retain some conformational flexibility associated with an enhanced ability to cross biological membranes. In this study, we investigated the relationship between the structure of semi-peptidic macrocycles and their membrane permeability through structural modifications. Based on a scaffold of four amino acids and a linker, we synthesized 56 macrocycles incorporating modifications in either stereochemistry, N-methylation, or lipophilicity and assessed their passive permeability using the parallel artificial membrane permeability assay (PAMPA). Our results show that some semi-peptidic macrocycles have adequate passive permeability even with properties outside the Lipinski rule of five. We found that N-methylation in position 2 and the addition of lipophilic groups to the side chain of tyrosine led to an improvement in permeability with a decrease in tPSA and 3D-PSA. This enhancement could be attributed to the shielding effect of the lipophilic group on some regions of the macrocycle, which in turn, facilitates a favorable macrocycle conformation for permeability, suggesting some degree of chameleonic behavior.

Synthesis and Characterization of Multi-Reducing-End Polysaccharides

Site-specific modification is a great challenge for polysaccharide scientists. Chemo- and regioselective modification of polysaccharide chains can provide many useful natural-based materials and help us illuminate fundamental structure-property relationships of polysaccharide derivatives. The hemiacetal reducing end of a polysaccharide is in equilibrium with its ring-opened aldehyde form, making it the most uniquely reactive site on the polysaccharide molecule, ideal for regioselective decoration such as imine formation. However, all natural polysaccharides, whether they are branched or not, have only one reducing end per chain, which means that only one aldehyde-reactive substituent can be added. We introduce a new approach to selective functionalization of polysaccharides as an entrée to useful materials, appending multiple reducing ends to each polysaccharide molecule. Herein, we reduce the approach to practice using amide formation. Amine groups on monosaccharides such as glucosamine or galactosamine can react with carboxyl groups of polysaccharides, whether natural uronic acids like alginates, or derivatives with carboxyl-containing substituents such as carboxymethyl cellulose (CMC) or carboxymethyl dextran (CMD). Amide formation is assisted using the coupling agent 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMTMM). By linking the C2 amines of monosaccharides to polysaccharides in this way, a new class of polysaccharide derivatives possessing many reducing ends can be obtained. We refer to this class of derivatives as multi-reducing-end polysaccharides (MREPs). This new family of derivatives creates the potential for designing polysaccharide-based materials with many potential applications, including in hydrogels, block copolymers, prodrugs, and as reactive intermediates for other derivatives.

Primary Structure of Glycans by NMR Spectroscopy

Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a 1H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.

PplD is a de-N-acetylase of the cell wall linkage unit of streptococcal rhamnopolysaccharides

The cell wall of the human bacterial pathogen Group A Streptococcus (GAS) consists of peptidoglycan decorated with the Lancefield group A carbohydrate (GAC). GAC is a promising target for the development of GAS vaccines. In this study, employing chemical, compositional, and NMR methods, we show that GAC is attached to peptidoglycan via glucosamine 1-phosphate. This structural feature makes the GAC-peptidoglycan linkage highly sensitive to cleavage by nitrous acid and resistant to mild acid conditions. Using this characteristic of the GAS cell wall, we identify PplD as a protein required for deacetylation of linkage N-acetylglucosamine (GlcNAc). X-ray structural analysis indicates that PplD performs catalysis via a modified acid/base mechanism. Genetic surveys in silico together with functional analysis indicate that PplD homologs deacetylate the polysaccharide linkage in many streptococcal species. We further demonstrate that introduction of positive charges to the cell wall by GlcNAc deacetylation protects GAS against host cationic antimicrobial proteins.

Synthetic heparan sulfate ligands for vascular endothelial growth factor to modulate angiogenesis

We report the discovery of a potential heparan sulfate (HS) ligand to target several growth factors using 13 unique HS tetrasaccharide ligands. By employing an HS microarray and SPR, we deciphered the crucial structure-binding relationship of these glycans with the growth factors BMP2, VEGF₁₆₅, HB-EGF, and FGF2. Notably, GlcNHAc(6-O-SO₃^-)-IdoA(2-O-SO₃^-) (HT-2,6S-NAc) tetrasaccharide showed strong binding with the VEGF₁₆₅ growth factor. In vitro vascular endothelial cell proliferation, migration and angiogenesis was inhibited in the presence of VEGF₁₆₅ and HT-2,6S-NAc or HT-6S-NAc, revealing the potential therapeutic role of these synthetic HS ligands.

Molecular imaging of cancer by glucosamine chemical exchange saturation transfer MRI: A preclinical study

Glucosamine (GlcN) was recently proposed as an agent with an excellent safety profile to detect cancer with the chemical exchange saturation transfer (CEST) MRI technique. Translation of the GlcN CEST method to the clinical application requires evaluation of its sensitivity to the different frequency regions of irradiation. Hence, imaging of the GlcN signal was established for the full Z spectra recorded following GlcN administration to mice bearing implanted 4T1 breast tumors. Significant CEST effects were observed at around 1.5, 3.6 and -3.4 ppm, corresponding to the hydroxyl, amine/amide exchangeable protons and for the Nuclear Overhauser Enhancement (NOE), respectively. The sources of the observed CEST effects were investigated by identifying the GlcN metabolic products as observed by ¹³ C NMR spectroscopy studies of extracts from the same tumor model following treatment with [UL-¹³ C] -GlcN·HCl. The CEST contribution can be attributed to several phosphorylated products of GlcN, including uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc), which is a substrate for the O-linked and N-linked glycosylated proteins that may be associated with the increase of the NOE signal. The observation of a significant amount of lactate among the metabolic products hints at acidification as one of the sources of the enhanced CEST effect of GlcN. The proposed method may offer a new approach for clinical molecular imaging that enables the detection of metabolically active tumors and may play a role in other diseases.

Structural and spectral characterisation of 2-amino-2H-[1,2,3]triazolo[4,5-g]quinoline-4,9-dione polymorphs. Cytotoxic activity and molecular docking study with NQO1 enzyme

Depending on temperature, the 2-amino-2H-[1,2,3]triazolo[4,5-g]quinoline-4,9-dione forms two polymorphic structures, which differ in the spatial arrangement of the amine group. Both polymorphs were investigated using different experimental methods as well as various quantum chemical calculations in order to characterise their molecular structures. We used X-ray diffraction, FT-IR and NMR (solid-state and liquid) methods supplemented by the density functional theory (DFT) calculations, molecular electrostatic potential (MEP) and molecular orbital (HOMO, LUMO) analyses. It was found that the arrangement of the amine group affected the crystal structure, formation of H-bonds, the amine and carbonyl vibration bands in the FT-IR spectra, chemical shift of amine group in ¹⁵N CP/MAS NMR and chemical shift of amine protons in ¹H NMR spectra. Both polymorphs were tested on anticancer activity against a panel of human cancer cell lines. Comparing the activity of both compounds showed that activity against MCF-7, MDA-MB-231 and Caco-2 lines depend on the arrangement of the amine group. Moreover, both polymorphs exhibited the highest activity against cell line with high NQO1 protein level, such as: A549, MCF-7 and Caco-2. The molecular docking was used to examine the probable interaction between the ligand of the tested polymorphs and the NQO1 enzyme. The analysis showed that ligands formed a hydrophobic interaction with tryptophan (Trp105), phenylalanine (Phe126 and Phe178) and tyrosine (Tyr 126).

NMR-based metabolite studies with 15N amino acids

¹⁵N labeled amino acids are routinely used to label proteins or nucleic acids for study by NMR. However, NMR studies of ¹⁵N labeled amino acids in metabolite studies have not been pursued extensively, presumably due to line broadening present under standard experimental conditions. In this work, we show that lowering the temperature to −5 °C allows facile characterization of ¹⁵N-labeled amino acids. Further, we show that this technique can be exploited to measure ¹⁵NH₃ produced in an enzyme catalyzed reaction and the transport and metabolism of individual amino acids in mammalian cell culture. With respect to ¹³C-labeled amino acids, ¹⁵N-labeled amino acids are less costly and enable direct characterization of nitrogen metabolism in complex biological systems by NMR. In summary, the present work significantly expands the metabolite pools and their reactions for study by NMR.

Multivariate analysis applied to complex biological medicines

A biological medicine (or biologicals) is a term for a medicinal compound that is derived from a living organism. By their very nature, they are complex and often heterogeneous in structure, composition and biological activity. Some of the oldest pharmaceutical products are biologicals, for example insulin and heparin. The former is now produced recombinantly, with technology being at a point where this can be considered a defined chemical entity. This is not the case for the latter, however. Heparin is a heterogeneous polysaccharide that is extracted from the intestinal mucosa of animals, primarily porcine, although there is also a significant market for non-porcine heparin due to social and economical reasons. In 2008 heparin was adulterated with another sulfated polysaccharide. Unfortunately this event was disastrous and resulted in a global public health emergency. This was the impetuous to apply modern analytical techniques, principally NMR spectroscopy, and multivariate analyses to monitor heparin. Initially, traditional unsupervised multivariate analysis (principal component analysis (PCA)) was applied to the problem. This was able to distinguish animal heparins from each other, and could also separate adulterated heparin from what was considered bona fide heparin. Taught multivariate analysis functions by training the analysis to look for specific patterns within the dataset of interest. If this approach was to be applied to heparin, or any other biological medicine, it would have to be taught to find every possible alien signal. The opposite approach would be more efficient; defining the complex heterogeneous material by a library of bona fide spectra and then filtering test samples with these spectra to reveal alien features that are not consistent with the reference library. This is the basis of an approach termed spectral filtering, which has been applied to 1D and 2D-NMR spectra, and has been very successful in extracting the spectral features of adulterants in heparin, as well as being able to differentiate supposedly biosimilar products. In essence, the filtered spectrum is determined by subtracting the covariance matrix of the library spectra from the covariance matrix of the library spectra plus the test spectrum. These approaches are universal and could be applied to biological medicines such as vaccine polysaccharides and monoclonal antibodies.

Investigation of the Amide Proton Solvent Exchange Properties of Glycosaminoglycan Oligosaccharides

One-dimensional ¹H NMR experiments were conducted for aqueous solutions of glycosaminoglycan oligosaccharides to measure the amide proton temperature coefficients and activation energy barriers for solvent exchange and evaluate the effect of pH on the solvent exchange properties. A library of mono- and oligosaccharides was prepared by enzymatic depolymerization of amide-containing polysaccharides and by chemical modification of heparin and heparan sulfate saccharides including members that contain a 3- O-sulfated glucosamine residue. The systematic evaluation of this saccharide library facilitated assessment of the effects of structural characteristics, such as size, sulfation number and site, and glycosidic linkage, on amide proton solvent exchange rates. Charge repulsion by neighboring negatively charged sulfate and carboxylate groups was found to have a significant impact on the catalysis of amide proton solvent exchange by hydroxide. This observation leads to the conclusion that solvent exchange rates must be interpreted within the context of a given chemical environment. On their own, slow exchange rates do not conclusively establish the involvement of a labile proton in a hydrogen bond, and additional supporting experimental evidence such as reduced temperature coefficients is required.

Structural Insights into the Molecular Evolution of the Archaeal Exo-β-d-Glucosaminidase

The archaeal exo-β-d-glucosaminidase (GlmA), a thermostable enzyme belonging to the glycosidase hydrolase (GH) 35 family, hydrolyzes chitosan oligosaccharides into monomer glucosamines. GlmA is a novel enzyme in terms of its primary structure, as it is homologous to both GH35 and GH42 β-galactosidases. The catalytic mechanism of GlmA is not known. Here, we summarize the recent reports on the crystallographic analysis of GlmA. GlmA is a homodimer, with each subunit comprising three distinct domains: a catalytic TIM-barrel domain, an α/β domain, and a β1 domain. Surprisingly, the structure of GlmA presents features common to GH35 and GH42 β-galactosidases, with the domain organization resembling that of GH42 β-galactosidases and the active-site architecture resembling that of GH35 β-galactosidases. Additionally, the GlmA structure also provides critical information about its catalytic mechanism, in particular, on how the enzyme can recognize glucosamine. Finally, we postulate an evolutionary pathway based on the structure of an ancestor GlmA to extant GH35 and GH42 β-galactosidases.

1H NMR characterization of chitin tetrasaccharide in binary H2O:DMSO solution: Evidence for anomeric end-effect propagation

Chitin oligosaccharides, composed of homogeneous β(1 → 4)-linked N-acetyl-D-glucosamine (GlcNAc) sequences, is a well-known elicitor of plant immune defense, and also occur as structural elements of chitosan and nodulation (Nod) factor. Detailed microstructure characterization is required for understanding the function mode of these bioactive molecules. Herein, experimental conditions for detection and elucidation of the ¹H NMR resonances of amide groups in chitin oligosaccharides are presented. The binary mixture of 70% H₂O: 30% DMSO‑d₆ was found to be the optimal solvent for amide proton measurements in homogeneous GlcNAc sequences, facilitating differentiation of the local chemical microenvironments of all four amide groups of the chitin tetrasaccharide. Experimental evidence that anomeric end-effect triggers amide proton resonance differentiation at the adjacent residue has potential to provide important insights into the solution structure of chitin and other amino sugars containing GlcNAc sequences.

Design, synthesis, and biomedical applications of synthetic sulphated polysaccharides

This review summarizes the synthetic methods to sulphated polysaccharides, describes their compositional and structural diversity in regards to activity, and showcases their biomedical applications.

Recent innovations in the structural analysis of heparin

Heparin, the widely used anticoagulant drug, is unusual among major pharmaceutical agents being neither single chemical entity nor a defined mixture of compounds. Its composition, while conforming to approximate average disaccharide composition or sulfation levels, exhibits heterogeneity and variability depending on the source, as well as its geographical origin. Furthermore, individual polysaccharide chains, whose physico-chemical properties are extremely similar, cannot be separated with current state-of-the-art techniques, presenting a challenge to those interested in the quality control of heparin, in ensuring its provenance and safety, and those with an interest in investigating the relationships between its structure and biological activity. The review consists of two main sections: The first is the Introduction, comprising (i) The History, Occurrence and Use of Heparin and (ii) Approaches to Structure-Activity Relationships. The second section is Improved Techniques for Structural Analysis, comprising; (i) Separation and Identification, (ii) Spectroscopic Methods, (iii) Enzymatic Approaches and (iv) Other Physico-Chemical Approaches. The ~60 references cover recent technological advances in the study of heparin structural analysis, largely since 2010.

The Structure of an Archaeal β-Glucosaminidase Provides Insight into Glycoside Hydrolase Evolution

The archaeal exo-β-d-glucosaminidase (GlmA) is a dimeric enzyme that hydrolyzes chitosan oligosaccharides into monomer glucosamines. GlmA is a member of the glycosidase hydrolase (GH)-A superfamily-subfamily 35 and is a novel enzyme in terms of its primary structure. Here, we present the crystal structure of GlmA in complex with glucosamine at 1.27 Å resolution. The structure reveals that a monomeric form of GlmA shares structural homology with GH42 β-galactosidases, whereas most of the spatial positions of the active site residues are identical to those of GH35 β-galactosidases. We found that upon dimerization, the active site of GlmA changes shape, enhancing its ability to hydrolyze the smaller substrate in a manner similar to that of homotrimeric GH42 β-galactosidase. However, GlmA can differentiate glucosamine from galactose based on one charged residue while using the "evolutionary heritage residue" it shares with GH35 β-galactosidase. Our study suggests that GH35 and GH42 β-galactosidases evolved by exploiting the structural features of GlmA.

Investigating the relationship between temperature, conformation and calcium binding in heparin model oligosaccharides

Glycosaminoglycans such as heparan sulfate (HS) are major components of the cell surface and extracellular matrix (ECM) of all multicellular animals, connecting cells to each other as well as to their environment. The ECM must, therefore, both sense and accommodate changes to external conditions. Heparin, a model compound for HS, responds to increased temperatures, involving changes in the populations of conformational states with implications for the binding of HS to proteins, cations and, potentially, for its activity. A fully ¹³C and ¹⁵N labelled model octasasccharide; D-GlcNS6S α(1-4) L-IdoA2S [α(1-4) D-GlcNS6S α(1-4) L-IdoA2S]₂ α(1-4) D-GlcNS6S α(1-4) L-IdoA1,6an, was studied by ¹H, ¹³C and ¹⁵N NMR, revealing complex changes in chemical shifts and conformation, over temperatures (280-305 K), comfortably within the range relevant to terrestrial biology. These complex conformational changes indicated an interaction between the carboxylate group of L-iduronate and D-glucosamine residues that was susceptible to temperature changes in this range, while the well-documented hydrogen bond between the N-sulfamido group of glucosamine and the hydroxyl group at position-3 of iduronate remained intact. Unexpectedly, despite the presence of similar thermally-induced conformational changes in a heparin octasaccharide fraction in the sodium ion form, its subsequent binding to calcium ions and their resulting conformation was stringently maintained, as judged by comparisons of ¹H NMR chemical shifts.

¹H and (15)N NMR Analyses on Heparin, Heparan Sulfates and Related Monosaccharides Concerning the Chemical Exchange Regime of the N-Sulfo-Glucosamine Sulfamate Proton

Heparin and heparan sulfate are structurally related glycosaminoglycans (GAGs). Both GAGs present, although in different concentrations, N-sulfo-glucosamine (GlcNS) as one of their various composing units. The conditional fast exchange property of the GlcNS sulfamate proton in these GAGs has been pointed as the main barrier to its signal detection via NMR experiments, especially ¹H-¹⁵N HSQC. Here, a series of NMR spectra is collected on heparin, heparan sulfate and related monosaccharides. The N-acetyl glucosamine-linked uronic acid types of these GAGs were properly assigned in the ¹H-¹⁵N HSQC spectra. Dynamic nuclear polarization (DNP) was employed in order to facilitate 1D spectral acquisition of the sulfamate ¹⁵N signal of free GlcNS. Analyses on the multiplet pattern of scalar couplings of GlcNS ¹⁵N has helped to understand the chemical properties of the sulfamate proton in solution. The singlet peak observed for GlcNS happens due to fast chemical exchange of the GlcNS sulfamate proton in solution. Analyses on kinetics of alpha-beta anomeric mutarotation via ¹H NMR spectra have been performed in GlcNS as well as other glucose-based monosaccharides. 1D ¹H and 2D ¹H-¹⁵N HSQC spectra recorded at low temperature for free GlcNS dissolved in a proton-rich solution showed signals from all exchangeable protons, including those belonging to the sulfamate group. This work suits well to the current grand celebration of one-century-anniversary of the discovery of heparin.