Top-down approach for the direct characterization of low molecular weight heparins using LC-FT-MS

State-of-the-art chromatographic and mass spectrometric techniques in heparin structural analysis

Heparin is the most extensively used anticoagulant in clinical practice. It is a highly sulfated, linear polysaccharide composed of repeating disaccharide units. As a member of the glycosaminoglycan (GAG) family, heparin's complex structure features significant molecular weight variability, diverse sugar residues, and variable sulfation patterns. Low molecular weight heparins (LMWHs), produced through chemical or enzymatic depolymerization, are distinguished by their reduced molecular weight and offer therapeutic advantages, including lower bleeding risks, reduced immunogenicity, and higher bioavailability following subcutaneous administration. The structural intricacy of heparin-based drugs presents major challenges for quality control, clinical safety, process optimization, and therapeutic expansion. Advanced analytical methods, particularly LC and MS, remain at the forefront of efforts to elucidate the detailed structures of these drugs. This review highlights recent progress in chromatographic and MS-based analysis techniques for heparin and its derivatives, including the application of computational algorithms for structural elucidation. The focus is on the analytical methodologies, their innovations, and limitations, while also exploring how machine learning and bioinformatics tools are shaping the future of heparin quality control and therapeutic application. This comprehensive review provides a reference point for researchers engaged in the structural analysis of heparin-based drugs and offers insights into the future development of novel analytical strategies for improving the safety and efficacy of these critical anticoagulants.

Structural analysis of sulfated fucan from the sea cucumber Holothuria mexicana with the assistance of endo-1,3-fucanase

Sulfated fucan from sea cucumber has received growing interest in recent decades. Insight into the primary structure of sulfated fucan is fundamental to elucidate their bioactivity. The sea cucumber Holothuria mexicana possesses a high market demand, while the structure of its sulfated fucan (Hm-FUC) remains unclear. This study investigates the structural characteristics of Hm-FUC, especially using a tool enzyme of heterologously expressed endo-1,3-fucanase (Fun168D). Hm-FUC demonstrated a 6.12 ± 0.45 % yield from the body wall of dried sea cucumber and a molecular weight of 475.2 ± 0.5 kDa. A set of procedures including enzymatic degradation, glycomics, and NMR analyses were introduced into the structural identification of Hm-FUC. The structure of Hm-FUC was determined to comprise a tetrafucose repeating unit [→3-α-l-Fucp2,4S-1 → 3-α-l-Fucp-1 → 3-α-l-Fucp2S-1 → 3-α-l-Fucp2S-1→]. The well-defined primary structure is beneficial for its application as nutritional component in foods and therapeutic agent in drugs.

Rapid characterization of polysaccharides from marine animals using chemical degradation combined with liquid chromatography mass spectrometry

Glycosaminoglycans of marine origin have exceptional biological activities, but rapid elucidation strategies for precise structures are still lacking. In this study, the optimal conditions for deacetylation of glycosaminoglycans were optimized first. The hydrazinolysis time of 24 h was determined as the final condition, oligosaccharides with a degree of polymerization of 2-14 are mainly produced after hydrazinolysis. Then mixed oligosaccharides generated by deacetylation-deamination cleavage of polysaccharides were detected with hydrophilic interaction chromatography with tandem mass spectrometry (HILIC-MS/MS), and the total ion chromatography showed excellent resolution. The mass spectrometry data were automatically processed by GlycReSoft, and the corresponding matching results were obtained according to the set parameters. A small amount of keratan sulfate exists in oligosaccharides of Teuthida and Salmo salar, and ion peaks corresponding to IdoA-GalNAc4S exist in oligosaccharides of Scophthalmus maximus and Salmo salar. The results of the manual analysis of the mass spectrometry data verified that the HILIC-MS/MS combined with automatic analysis by software adopted in this study could achieve accurate matching and matching of mixed oligosaccharide components. The establishment of a rapid and accurate analysis strategy for the structure of glycosaminoglycans in this study will help the development of its application and standardized industrial production.

Fingerprinting analyses of low molecular weight heparin with an orthogonal MHC 2D LC-MS system

In this work, a synthetical glycan fingerprinting strategy using a multiple heart-cut two-dimensional liquid chromatography system linked to mass spectrometry (MHC 2D LC-MS) was developed to analyze enoxaparin, a widely used low molecular weight heparin (LMWH). Glycans from an enoxaparin standard were prepared offline based on size, and the derived tetra-, hexa-, octa- and decasaccharides were profiled using a qualitative analytical platform. Strong anion exchange chromatography (SAX) was employed as the first-dimensional chromatography (1D) to separate glycans of the same size but with different charges or sequences, while size exclusion chromatography (SEC) was used in the second dimension (2D) for desalting before MS analysis. The retention times (RTs), accurate masses and structural compositions of the glycans were fully characterized. Real samples were analyzed using the same platform but with 1D and 2D exchanged: SEC was used to separate enoxaparin glycans by size, followed by SAX using the same parameters as in the qualitative platform to separate glycans by charge or sequence. Glycans in real samples were identified by matching their RTs to those assigned in the qualitative analysis and semi-quantitated after normalization of peaks in each SAX chromatogram of glycans of different sizes. The analyses were performed automatically and robustly using this synthetical platform, enabling the fingerprinting and differentiation of enoxaparins from various sources. This platform could serve as a powerful tool for structural analysis, quality control, and heparin-related drug development.

Eco-friendly ozonation of alginate: Physicochemical characterization and degradation mechanism exploration through mass spectrometry

The ozone degradation has been proven to be an effective degradation method for alginate, while the degradation mechanism remained to be unconfirmed. In this study, two high-molecular-weight alginates with different mannuronic/guluronic (G/M) ratios, HM and HG (G/M 0.49 vs 1.40), were depolymerized using established ozonation technology platform. Notably, HM can be degraded faster than HG especially within initial 30 min, indicating that the β-1, 4-mannuronic bonds are more susceptible to be ozonated than α-1, 4-guluronic bonds. However, HM/HG degraded to LMWA in 2 h and reached a plateau. Therefore, we employed mass spectrometry (MS) to profile the degraded products of LMWA polymannuronate (PM) and polyguluronate (PG) in more intense conditions. The results indicated that the oxidation process continued until all reducing ends were converted to carboxyl groups. The o-diol could directly oxidize to o-dialdehyde. This study provides a MS based elucidation of the mechanism by which alginate cleaves to oligosaccharides through ozonation.

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.

Application of chromatography in purification and structural analysis of natural polysaccharides: A review

Polysaccharides are widely distributed in natural sources from monocytic microorganisms to higher animals, and are found in a variety of biological activities in recent decades. Natural polysaccharides have the characteristics of large molecular weight, diverse composition, and complex structure, so their purification and structural analysis are difficult issues in research. Chromatography as a powerful separation technique, plays an irreplaceable role in the separation and structural analysis of natural polysaccharides, especially in the purification of polysaccharides, the separation of hydrolysates, and the analysis of monosaccharide composition. The separation mechanisms and application of different chromatographic methods in the studies of polysaccharides were summarized in this review. Moreover, the advantages and drawbacks of various chromatography methods were discussed as well.

MsPHep: An online application for low molecular weight heparin rapid characterization based on liquid chromatography-tandem mass spectrometry

Low-molecular-weight heparins (LMWHs) are important anticoagulants widely used in clinic. Since they are comprised of complex and heterogenous glycan chains, liquid chromatography-tandem mass spectrometry (LC-MS) is commonly used for structural analysis and quality control of LMWHs to ensure their safety and efficacy. Yet, the structural complexity arising from the parent heparin macromolecules, as well as the different depolymerization methods used for preparing LMWHs, makes processing and assigning the LC-MS data of LWMHs very tedious and challenging. We therefore developed, and here report, an open-source and easy-to-use web application, MsPHep, to facilitate the LMWH analysis based on LC-MS data. MsPHep is compatible with various LMWHs and chromatographic separation methods. With the HepQual function, MsPHep is capable of annotating both the LMWH compound and its isotopic distribution from mass spectra. Moreover, the HepQuant function enables automatic quantification of LMWH compositions without prior knowledge or any database generation. To demonstrate the reliability and system stability of MsPHep, we tested various types of LMWHs that were analyzed with different chromatographic methods coupled to MS. The results show that MsPHep has its own advantages compared to another public tool GlycReSoft for LMWH analysis, and it is available online under an open-source license at https://ngrc-glycan.shinyapps.io/MsPHep.

Spectroscopic Characterization, Cyclic Voltammetry, Biological Investigations, MOE, and Gaussian Calculations of VO(II), Cu(II), and Cd(II) Heteroleptic Complexes

A novel hydrazone ligand (o-H₂BMP) N-(benzo[d]thiazol-2-yl)-3-oxo-3-(2-(1-(pyridin-2-yl)ethylidene)hydrazinyl)propanamide alongside its Cu(II), Cd(II), and VO(II) complexes were prepared and structurally characterized via various spectroscopic analyses (Fourier transform infrared spectroscopy, UV-visible spectroscopy, ¹H/¹³C NMR spectroscopy, liquid chromatography coupled to mass spectrometry, and electron paramagnetic resonance spectroscopy) as well as by elemental analysis, thermal gravimetry analysis/differential thermal analysis, and magnetic moment measurements. Powder X-ray diffraction analysis was also performed for the free ligand and its metal complexes to determine the crystallographic structures and atomic spacing. It also provided information on unit cell dimensions and the average crystallite size. Furthermore, geometric optimization and computational studies were carried out by applying Gaussian (09) software based on density-functional theory coupled with the B3LYP functional and LANL2DZ/6-31+G(d,p) mixed basis set to evaluate some distinct features such as molecular electrostatic potential, E _HOMO, and E _LUMO. Moreover, electrochemical measurements were performed for Cu(II) in the absence/presence of the chelating agent to predict the effect of complexation interaction in the solution state study. As part of the biological examination, antioxidant and antimicrobial assays were conducted for each compound individually, in addition to cytotoxicity evaluations via MTT assays for all isolated complexes compared to the corresponding metal salts. The MOE (molecular operating environment) approach was also applied to model the interface between the isolated compounds and proteins that were expressed in breast cancer at the atomic level.

[Advances in heparin structural analysis by chromatography technologies]

Heparin （Hp） is the most widely used anticoagulant drug in the clinics， with an annual global output of over 10 billion dollars. Hp， a member of the glycosaminoglycans （GAGs）， is prepared from porcine intestinal mucosa via extraction， separation， and purification. Hp is a linear polysaccharide with repeating disaccharide units. Low-molecular-weight heparins （LMWHs） are depolymerized from Hp via chemical or enzymatic degradation. Compared with Hp， LMWHs exhibit less bleeding side effect， milder immunogenicity， and higher bioavailability when injected subcutaneously. In general， Hps， including LMWHs， are high complex drugs with large molecular weights （MWs）， inhomogeneous MW distributions， and structural heterogeneity， including different degrees and locations of sulfonation， and unique residues generated from different production processes. Thus， developing efficient analytical methods to elucidate the structures of Hps and characterize or quantitate their properties is extremely challenging. Unfortunately， this problem limits their quality control， production optimization， clinical safety monitoring， and new applications. Research has constantly sought to elucidate the complicated structures of Hp drugs. Among the structural analysis and quality control methods of Hp currently available， chromatographic methods are the most widely studied and used. However， no literature thoroughly summarizes the specific applications of chromatographic methods in the structural analysis， manufacturing process， and quality control of Hp drugs. This paper systematically organizes and describes recent research progresses of the chromatographic methods used to analyze Hp drugs， including the identification and composition of monosaccharides， disaccharides， oligosaccharides， and polysaccharides. The applications， innovations， and limitations of these chromatographic methods are also summarized in this review. The insights obtained in this study will help production and quality control personnel， as well as drug researchers， obtain a deeper understanding of the complex structures of Hp drugs. This paper also provides a comprehensive reference for the structural analysis and quality control of Hps， proposes ideas for the development of new quality control methods， and lays a strong foundation for the in-depth structural elucidation of Hp drugs.

State-of-the-art glycosaminoglycan characterization

Glycosaminoglycans (GAGs) are heterogeneous acidic polysaccharides involved in a range of biological functions. They have a significant influence on the regulation of cellular processes and the development of various diseases and infections. To fully understand the functional roles that GAGs play in mammalian systems, including disease processes, it is essential to understand their structural features. Despite having a linear structure and a repetitive disaccharide backbone, their structural analysis is challenging and requires elaborate preparative and analytical techniques. In particular, the extent to which GAGs are sulfated, as well as variation in sulfate position across the entire oligosaccharide or on individual monosaccharides, represents a major obstacle. Here, we summarize the current state-of-the-art methodologies used for GAG sample preparation and analysis, discussing in detail liquid chromatograpy and mass spectrometry-based approaches, including advanced ion activation methods, ion mobility separations and infrared action spectroscopy of mass-selected species.

A Cluster Sequencing Strategy To Determine the Consensus Affinity Domains in Heparin for Its Binding to Specific Proteins

Glycosaminoglycans (GAGs) have high negative charge and are biologically and pharmaceutically important because their high charge promotes a strong interaction with many proteins. Due to the inherent heterogeneity of GAGs, multiple oligosaccharides, containing certain common domains, often can interact with clusters of basic amino acid residues on a target protein. The specificity of many GAG-protein interactions remains undiscovered since there is insufficient structural information on the interacting GAGs. Herein, we establish a cluster sequencing strategy to simultaneously deduce all major sequences of the affinity GAG oligosaccharides, leading to a definition of the consensus sequence they share that corresponds to the specific binding domain for the target protein. As a proof of concept, antithrombin III-binding oligosaccharides were examined, resulting in a heptasaccharide domain containing the well-established anticoagulant pentasaccharide sequence. Repeating this approach, a new pentasaccharide domain was discovered corresponding to the heparin motif responsible for binding interferon-γ (IFNγ). Our strategy is fundamentally important for the discovery of saccharide sequences needed in the development of novel GAG-based therapeutics.

Commercial Low Molecular Weight Heparins - Patent Ecosystem and Technology Paradigm for Quality Characterization

Heparin is a subject of ever-growing interest for laboratory researchers and pharmaceutical industry. One of the driving factors is its critical life-saving drug status, which during the COVID-19 pandemic has assumed a central role in disease treatment and/or prevention. Apart, heparin is one amongst few drugs enjoying a "demand constant" status. In 2020, heparin market size was valued to US$6.5 bn., and given the ongoing stability in the COVID-19 health crisis, it is expected to reach US$11.43 bn. by 2027 with yearly growth rate momentum (CAGR) of 3.9% during the forecast period (Pepi et al., Mol Cell Proteomics 20:100,025, 2021). As patent is a limited monopoly, every year, many patents on low molecular weight heparin (LMWH; a chemically or enzymatically degraded product of unfractionated heparin) are losing market exclusivity worldwide, inviting the generic/biosimilar drug manufacturers to capture market share with cheaper drug products. By tracking patent expiration, drugs in patent litigation, regulatory setbacks for innovator companies (such as those seeking data exclusivity or patent term extension), or other unexpected events affecting market demand and competition, generics can make investment decisions in manufacturing off-patent LMWH drug products of commercial significance. However, given the US Food and Drug Administration (FDA), European Medicine Agency (EMA), Drug Regulatory Authority of Pakistan (DRAP), and other regulatory authorities scientifically rigorous standards for generic/biosimilar LMWH drug products marketing approval, the market is secured and momentous for drug makers that could demonstrate through scientific and clinical dataset that the generic/biosimilar LMWH drug product is of the same quality and purity as the innovator drug product. This study presents an overview of the patent landscape of commercially available LMWHs and advanced analytical techniques for their structural and biochemical characterization for quality control and quality assurance during manufacturing and post-marketing. The study also covers FDA, EMA, Health Canada, and DRAP's current approaches to evaluating the generic/biosimilar LMWH drug products for quality, safety including immunogenicity, and efficacy.

Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties

Sulfation pattern and molecular weight (MW) play a key role in the biological actions of sulfated glycans. Besides anticoagulant effects, certain sulfated glycans can also exhibit anti-SARS-CoV-2 properties. To develop a more selective antiviral carbohydrate, an efficient strategy to separate these two actions is required. In this work, low MW fractions derived from the red alga Botryocladia occidentalis sulfated galactan (BoSG) were generated, structurally characterized, and tested for activity against SARS-CoV-2 and blood coagulation. The lowest MW fraction was found to be primarily composed of octasaccharides of monosulfated monosaccharides. Unlike heparin or native BoSG, we found that hydrolyzed BoSG products had weak anticoagulant activities as seen by aPTT and inhibitory assays using purified cofactors. In contrast, lower MW BoSG-derivatives retained anti-SARS-CoV-2 activity using SARS-CoV-2 spike (S)-protein pseudotyped lentivirus vector in HEK-293T-hACE2 cells monitored by GFP. Surface plasmon resonance confirmed that longer chains are necessary for BoSG to interact with coagulation cofactors but is not required for interactions with certain S-protein variants. We observed distinct affinities of BoSG derivatives for the S-proteins of different SARS-CoV-2 strains, including WT, N501Y (Alpha), K417T/E484K/N501Y (Gamma), and L542R (Delta) mutants, and stronger affinity for the N501Y-containing variants. Docking of the four possible monosulfated BoSG disaccharides in interactions with the N501Y mutant S-protein predicted potential binding poses of the BoSG constructs and favorable binding in close proximity to the 501Y residue. Our results demonstrate that depolymerization and fractionation of BoSG are an effective strategy to segregate its anticoagulant property from its anti-SARS-CoV-2 action.

Informatics Ecosystems to Advance the Biology of Glycans

Glycomics researchers have identified the need for integrated database systems for collecting glycomics information in a consistent format. The goal is to create a resource for knowledge discovery and dissemination to wider research communities. This has the potential and has exhibited initial success, to extend the research community to include biologists, clinicians, chemists, and computer scientists. This chapter discusses the technology and approach needed to create integrated data resources and informatics ecosystems to empower the broader community to leverage extant glycomics data. The focus is on glycosaminoglycan (GAGs) and proteoglycan research, but the approach can be generalized. The methods described span the development of glycomics standards from CarbBank to Glyco Connection Tables. Integrated data sets provide a foundation for novel methods of analysis such as machine learning and deep learning for knowledge discovery. The implications of predictive analysis are examined in relation to disease biomarker to expand the target audience of GAG and proteoglycan research.

Disease-specific glycosaminoglycan patterns in the extracellular matrix of human lung and brain

A wide variety of diseases throughout the mammalian organism is characterized by abnormal deposition of various components of the extracellular matrix (ECM), including the heterogeneous family of glycosaminoglycans (GAGs), which contribute considerably to the ECM architecture as part of the so-called proteoglycans. The GAG's unique sulfation pattern, derived from highly dynamic and specific modification processes, has a massive impact on critical mediators such as cytokines and growth factors. Due to the strong connection between the specific sulfation pattern and GAG function, slight alterations of this pattern are often associated with enormous changes at the cell as well as at the organ level. This review aims to investigate the connection between modifications of GAG sulfation patterns and the wide range of pathological conditions, mainly focusing on a range of chronic diseases of the central nervous system (CNS) as well as the respiratory tract.

HepParser: An Intelligent Software Program for Deciphering Low-Molecular-Weight Heparin Based on Mass Spectrometry

Low-molecular-weight heparins (LMWHs) are considered to be the most successful carbohydrate-based drugs because of their wide use as anticoagulants in clinics. The efficacy of anticoagulants made by LMWHs mainly depends on the components and structures of LMWHs. Therefore, deciphering the components and identifying the structures of LMWHs are critical to developing high-efficiency anticoagulants. However, most LMWHs are mixtures of linear polysaccharides which are comprised of several disaccharide repeating units with high similarity, making it extremely challenging to separate and decipher each component in LMWHs. Here, we present a new algorithm named hepParser to decipher the main components of LMWHs automatically and precisely based on the liquid chromatography/mass spectrometry (LC/MS) data. When tested on the general LMWH using hepParser, profiling of the oligosaccharides with different degrees of polymerization (dp’s) was completed with high accuracy within 1 minute. When compared with the results of GlycReSoft on heparan sulfate samples, hepParser achieved more comprehensive and reasonable results automatically.

High sensitivity analysis of nanogram quantities of glycosaminoglycans using ToF-SIMS

Glycosaminoglycans (GAGs) are important biopolymers that differ in the sequence of saccharide units and in post polymerisation alterations at various positions, making these complex molecules challenging to analyse. Here we describe an approach that enables small quantities (<200 ng) of over 400 different GAGs to be analysed within a short time frame (3-4 h). Time of flight secondary ion mass spectrometry (ToF-SIMS) together with multivariate analysis is used to analyse the entire set of GAG samples. Resultant spectra are derived from the whole molecules and do not require pre-digestion. All 6 possible GAG types are successfully discriminated, both alone and in the presence of fibronectin. We also distinguish between pharmaceutical grade heparin, derived from different animal species and from different suppliers, to a sensitivity as low as 0.001 wt%. This approach is likely to be highly beneficial in the quality control of GAGs produced for therapeutic applications and for characterising GAGs within biomaterials or from in vitro cell culture.

Discovery of exolytic heparinases and their catalytic mechanism and potential application

Heparinases (Hepases) are critical tools for the studies of highly heterogeneous heparin (HP)/heparan sulfate (HS). However, exolytic heparinases urgently needed for the sequencing of HP/HS chains remain undiscovered. Herein, a type of exolytic heparinases (exoHepases) is identified from the genomes of different bacteria. These exoHepases share almost no homology with known Hepases and prefer to digest HP rather than HS chains by sequentially releasing unsaturated disaccharides from their reducing ends. The structural study of an exoHepase (BIexoHep) shows that an N-terminal conserved DUF4962 superfamily domain is essential to the enzyme activities of these exoHepases, which is involved in the formation of a unique L-shaped catalytic cavity controlling the sequential digestion of substrates through electrostatic interactions. Further, several HP octasaccharides have been preliminarily sequenced by using BIexoHep. Overall, this study fills the research gap of exoHepases and provides urgently needed tools for the structural and functional studies of HP/HS chains.

Analysis of the Glycosaminoglycan Chains of Proteoglycans

Glycosaminoglycans (GAGs) are heterogeneous, negatively charged, macromolecules that are found in animal tissues. Based on the form of component sugar, GAGs have been categorized into four different families: heparin/heparan sulfate, chondroitin/dermatan sulfate, keratan sulfate, and hyaluronan. GAGs engage in biological pathway regulation through their interaction with protein ligands. Detailed structural information on GAG chains is required to further understanding of GAG-ligand interactions. However, polysaccharide sequencing has lagged behind protein and DNA sequencing due to the non-template-driven biosynthesis of glycans. In this review, we summarize recent progress in the analysis of GAG chains, specifically focusing on techniques related to mass spectroscopy (MS), including separation techniques coupled to MS, tandem MS, and bioinformatics software for MS spectrum interpretation. Progress in the use of other structural analysis tools, such as nuclear magnetic resonance (NMR) and hyphenated techniques, is included to provide a comprehensive perspective.

Coupling Liquid Chromatography and Tandem Mass Spectrometry to Electrophoresis for In-Depth Analysis of Glycosaminoglycan Drugs: Heparin and the Multicomponent Sulodexide

Glycosaminoglycans (GAGs) contribute to the treatment of many human diseases, especially in the field of thrombosis, because of their anticoagulant activity. GAGs interrupt the coagulation process by interacting with multiple coagulation factors through defined sequences within their linear and negatively charged chains, which are not fully elucidated. Numerous methods have been developed to characterize the structure of pharmaceutical GAGs, including intravenously or subcutaneously administered heparin and orally administered sulodexide. However, most currently available methods only focus on the oligosaccharide portion or analyze the whole mixture because longer-chain polysaccharides are extremely difficult to resolve by chromatographic separation. We have established two novel electrophoresis-mass spectrometry methods to provide a panoramic view of the structures of pharmaceutical GAGs. In the first method, an in-gel digestion procedure was developed to recover GAGs from the polyacrylamide gels, while in the second method, a strong anion exchange ultrafiltration procedure was developed to extract multiple GAG species from the agarose gels. Both procedures are compatible with liquid chromatography-tandem mass spectrometry, and structural information, such as disaccharide composition and chain length, can be revealed for each GAG fraction. The applications of these two methods on analysis of two different GAG drugs, heparin and sulodexide, were demonstrated. The current study offers the first robust tool to directly elucidate the structure of larger GAG chains with more biological importance rather than obtaining a vague picture of all chains as a mixture, which is fundamental for better understanding the structure-activity relationship and quality control of the GAG drugs.

Developments in Mass Spectrometry for Glycosaminoglycan Analysis: A Review

This review covers recent developments in glycosaminoglycan (GAG) analysis via mass spectrometry (MS). GAGs participate in a variety of biological functions, including cellular communication, wound healing, and anticoagulation, and are important targets for structural characterization. GAGs exhibit a diverse range of structural features due to the variety of O- and N-sulfation modifications and uronic acid C-5 epimerization that can occur, making their analysis a challenging target. Mass spectrometry approaches to the structure assignment of GAGs have been widely investigated, and new methodologies remain the subject of development. Advances in sample preparation, tandem MS techniques (MS/MS), online separations, and automated analysis software have advanced the field of GAG analysis. These recent developments have led to remarkable improvements in the precision and time efficiency for the structural characterization of GAGs.

Recent advances in biotechnology for heparin and heparan sulfate analysis

Heparan sulfate (HS) is a class of linear, sulfated, anionic polysaccharides, called glycosaminoglycans (GAGs), which present on the mammalian cell surfaces and extracellular matrix. HS GAGs display a wide range of critical biological functions, particularly in cell signaling. HS is composed of repeating units of 1 → 4 glucosidically linked uronic acid and glucosamine residues. Heparin, a pharmacologically important version of HS, having higher sulfation and a higher content of iduronic acid than HS, is a widely used clinical anticoagulant. However, due to their heterogeneity and complex structure, HS and heparin are very challenging to analyze, limiting biological studies and even resulting in safety concerns in their therapeutic application. Therefore, reliable methods of structural analysis of HS and heparin are critically needed. In addition to the structural analysis of heparin, its concentration in blood needs to be closely monitored to avoid complications such as thrombocytopenia or hemorrhage caused by heparin overdose. This review summarizes the progress in biotechnological approaches in the structural characterization of HS and heparin over the past decade and includes the development of the ultrasensitive approaches for detection and measurement in biological samples.

In vitro fermentation and isolation of heparin-degrading bacteria from human gut microbiota

Heparin and its derivative are commonly used as injectable anticoagulants in clinical procedures, but possess poor oral bioavailability. To explore the role of gut microbiota in the poor oral effect of heparin, the degradation profiles of heparin on six human gut microbiota were investigated. The heparin-degradation ability varied significantly among individuals. Furthermore, two strains of heparin-degrading bacteria, Bacteroides ovatus A2 and Bacteroides cellulosilyticus B19, were isolated from the gut microbiota of different individuals and the degradation products of the isolates were profiled. The ΔUA2S-GlcNS6S was the major end product with almost no desulfation. 3-O-sulfo group-containing tetrasaccharides were detected, which indicated that the antithrombin binding site was broken and this explained the lost anticoagulant activity of heparin. Collectively, the present study assessed the degradation profiles of heparin by human gut microbiota and provided references for the development of oral administration of heparin from a gut microbiota perspective.

A heparin derivatives library constructed by chemical modification and enzymatic depolymerization for exploitation of non-anticoagulant functions

Non-anticoagulant biological functions of heparin-based drugs have drawn increasing attention. However, the exploration into the non-anticoagulant activities of various low molecular weight heparins was associated with bleeding risks in clinical practice and often led to controversial conclusions due to the structural differences. In this study, we aimed to establish a process to produce a library of heparin derivatives with structural diversity and reduced/abolished anticoagulant activity through the combination of chemical modifications and enzymatic cleavage of heparins. The depolymerization characteristics of various selectively modified heparin derivatives by three heparinases were comprehensively analyzed. The order of periodate treatment and heparinase-I depolymerization was proved to significantly change the structural characteristics of the oligosaccharide products. Finally, among several heparin derivatives that screened in the bleomycin-induced cell apoptosis model, the low molecular weight partially 6-O-/N-desulfated heparins showed the strongest anti-apoptotic activities. This study provided a useful approach for future development of novel heparin-derivative medications.

Enzymatic depolymerization of streptococcus pneumoniae type 8 polysaccharide

Although there have been decades of research on streptococcus pneumoniae, it is still among the leading cause of infectious disease in the world. As a type of capsular polysaccharide (CPS) of streptococcus pneumoniae, pneumococcal polysaccharides are essential components for colonization and virulence in mammalian hosts. This study aimed to characterize the CPS structure of type 8 streptococcus pneumoniae, which is one of the most fatal serotypes. In this work, heparinase I&III was used to successfully digest pneumococcal type 8 polysaccharide (Pn8P). We characterized the oligosaccharide generated from the enzymatic depolymerization of Pn8P by size exclusion chromatography, mass spectrometry and nuclear magnetic resonance. This is the first study to enzymatically depolymerize and characterize Pn8P.

Living with Breakthrough: Two-Dimensional Liquid-Chromatography Separations of a Water-Soluble Synthetically Grafted Bio-Polymer

In this study, we evaluate the use of various two-dimensional liquid chromatographic methods to characterize water-soluble, synthetically grafted bio-polymers, consisting of long poly(acrylic acid) chains and short maltodextrin grafts. The confirmation of the presence of grafting and the estimation of its extent is challenging. It is complicated by the limited solubility of polymers, their structural dispersity and chemical heterogeneity. Moreover, the starting materials (and other reagents, reaction products and additives) may be present in the product. Reversed-phase liquid chromatography (RPLC), hydrophilic-interaction liquid chromatography (HILIC) and size-exclusion chromatography (SEC) were used to characterize the product, as well as the starting materials. Additionally, fractions were collected for off-line characterization by infrared spectroscopy and mass spectrometry. The one-dimensional separation methods were found to be inconclusive regarding the grafting question. Breakthrough (the early elution of polymer fractions due to strong injection solvents) is shown to be a perpetual problem. This issue is not solved by comprehensive two-dimensional liquid chromatography (LC × LC), but information demonstrating the success of the grafting reaction could be obtained. SEC × RPLC and HILIC × RPLC separations are presented and discussed.

Polysaccharide Sequence Influences the Specificity and Catalytic Activity of Glucuronyl C5-Epimerase

Heparin is a widely used biotherapeutic produced from animal tissues. However, it might be possible to produce a bioengineered version using a multienzyme process, relying on the isolation of the E. coli K5 capsule heparosan and its chemical conversion to N-sulfoheparosan, NSH. Glucuronyl C5-epimerase, the first enzyme that acts on NSH, catalyzes the reversible conversion of glucuronic acid (GlcA) to iduronic acid (IdoA). Using full-length NSH, containing different amounts of N-acetylglucosamine (GlcNAc) residues, we demonstrate that C5-epimerase specificity relates to polysaccharide sequence, particularly the location of GlcNAc residues within the chain. We leveraged the deuterium exchange and the novel β-glucuronidase heparanase BP, which cleaves at the GlcA residue. Liquid chromatography-mass spectrometry and gel permeation chromatography of partial/complete heparanase BP digestion products from various NSH substrates treated with C5-epimerase provide information on C5-epimerase activity and action pattern. This study provides insight into optimizing the large-scale production of bioengineered heparin.

Characterization of a Novel Porphyranase Accommodating Methyl-galactoses at Its Subsites

Porphyran is the major polysaccharide of laver and mainly composed of 3-linked β-d-galactopyranose (G) and 4-linked α-l-galactopyranose-6-sulfate (L6S) units. Structural heterogeneity of porphyran highly originates from the natural methylation on the O-6 position of G units (GMe). Here, a GH16 porphyranase Por16C_Wf was cloned from a porphyran-related polysaccharide utilization locus of Wenyingzhuangia fucanilytica and expressed in Escherichia coli. It hydrolyzed porphyran in a random endo-acting manner. Using a glycomics strategy combining liquid chromatography-mass spectrometry and glycoinformatics, the subsite specificity was clarified. Por16C_Wf accommodated both G and GMe at subsites -1 and +2. This is the first report on the sequence of porphyranases hydrolyzing consecutive methyl-porphyranobiose moieties, which shed light on the diversity in subsite specificity of porphyranases. Por16C_Wf was the first characterized enzyme in subfamily 14 of the GH16 family. The defined and novel activity of Por16C_Wf implied that it could serve as a favorable tool in the full degradation and structural investigation of porphyran.

Filter-entrapment enrichment pull-down assay for glycosaminoglycan structural characterization and protein interaction

Heparins are the most pharmaceutically important polysaccharides. These heparin-based anticoagulant/antithrombotic agents include unfractionated heparins, low molecular weight heparins (LMWHs) and ultralow molecular weight heparins (ULMWHs). Heparins exhibit their pharmacological and biological activities through interaction with heparin-binding proteins. The prototypical heparin-binding protein is antithrombin III (AT), responsible for heparin's anticoagulant/antithrombotic activity. This study describes a filter-trapping method to isolate the chains in enoxaparin, a LMWH, which bind to AT. We demonstrate this method using the ULMWH, fondaparinux, which consists of a single well defined AT binding site. The interacting chains of enoxaparin are then characterized by activity assays, top-down liquid chromatography-mass spectrometry, and capillary zone electrophoresis mass spectrometry. This filter-trapping assay is an improvement over affinity chromatography for isolating heparin chains interacting with heparin binding proteins.

Non-anticoagulant Heparin as a Pre-exposure Prophylaxis Prevents Lyme Disease Infection

Lyme disease (LD) is caused by the spirochete Borrelia burgdorferi sensu lato (Bbsl). After transmission to humans by ticks, Bbsl spreads to multiple organs, leading to arthritis, carditis, and neuroborreliosis. No effective prophylaxis against human LD prior to tick exposure is currently available. Thus, a pre-exposure prophylaxis (PrEP) against LD is needed. The establishment of LD bacteria at diverse sites is dictated partly by the binding of Bbsl to proteoglycans (PGs) and glycosaminoglycans (GAGs) in tissues. The drug heparin is structurally similar to these GAGs and inhibits Bbsl attachment to PGs, GAGs, cells, and tissues, suggesting its potential to prevent LD. However, the anticoagulant activity of heparin often results in hemorrhage, hampering the development of this compound as LD PrEP. We have previously synthesized a non-anticoagulant version of heparin (NACH), which was verified for safety in mice and humans. Here, we showed that NACH blocks Bbsl attachment to PGs, GAGs, and mammalian cells. We also found that treating mice with NACH prior to the exposure of ticks carrying Bbsl followed by continuous administration of this compound prevents tissue colonization by Bbsl. Furthermore, NACH-treated mice develop greater levels of IgG and IgM against Bbsl at early stages of infection, suggesting that the upregulation of antibody immune responses may be one of the mechanisms for NACH-mediated LD prevention. This is one of the first studies examining the ability of a heparin-based compound to prevent LD prior to tick exposure. The information presented might also be extended to prevent other infectious diseases agents.

Mass spectrometric evidence for the mechanism of free-radical depolymerization of various types of glycosaminoglycans

Glycosaminoglycans (GAGs) are large, complex carbohydrate molecules that interact with a wide range of proteins involved in physiological and pathological processes. Several naturally derived GAGs have emerged as potentially useful therapeutics in clinical applications. Natural polysaccharides, however, generally have high molecular weights with a degree of polydispersity, making it difficult to investigate their structural properties. In this study, we establish a free-radical-mediated micro-reaction system and use hydrophilic interaction chromatography (HILIC)-Fourier transform mass spectrometry (FTMS) to profile the degraded products of various types of GAGs, heparin, chondroitin sulfate A, NS-heparosan, and oversulfated chondroitin sulfate (OSCS), to reveal the free-radical degradation mechanism of GAGs. The results show that the bulk fragments of GAGs generated by free-radical degradation can maintain their basic structural units and sulfate substituents. In addition, an abundance of oligomers modified with oxidation at their reducing ends or by dehydration also appeared. We discovered that these modifications were related in terms of the degree of sulfation and the α- or β-linkage of HexNY (Y = SO₃^- or Ac), and especially that the different linkage of the disaccharide unit is the main factor in modification. In addition, the method based on micro-free-radical reaction and HILIC-FTMS is both effective and sensitive, thus suggesting its broad practical value for the structural characterization and in the biological structure-function studies of GAGs.

Synthesis of 3-O-Sulfated Disaccharide and Tetrasaccharide Standards for Compositional Analysis of Heparan Sulfate

3-O-Sulfation on the glucosamine sugar unit in heparan sulfate (HS) is linked to various biological functions, including the anticoagulant activity to treat thrombotic disorders in hospitals. The 3-O-sulfated glucosamine is biosynthesized by heparan sulfate glucosamine 3-sulfotransferases. Because of its biological significance, there is a need for 3-O-sulfated oligosaccharide standards to facilitate the compositional analysis of HS. These oligosaccharides must contain a Δ^4,5-unsaturated uronic acid (ΔUA) residue at the nonreducing end, which is due to the depolymerization reaction catalyzed by heparin lyases used during the compositional analysis procedure. Here, we describe a protocol for the preparation of one 3-O-sulfated disaccharide (compound 4) and three 3-O-sulfated tetrasaccharides (compound 1-3) in a milligram scale. The synthesis of 3-O-sulfated disaccharide and tetrasaccharide standards was completed by degrading synthetic octasaccharides using heparin lyases. Further analysis revealed that 3-O-sulfated oligosaccharide standards are labile under basic conditions, confirming the findings from a previous study. The unwanted degradation was reduced by decreasing the pH in the presence of phosphate buffer. The 3-O-sulfated oligosaccharide standards are reagents to characterize 3-O-sulfation in HS derived from biological sources.

Bottom-up analysis using liquid chromatography-Fourier transform mass spectrometry to characterize fucosylated chondroitin sulfates from sea cucumbers

Fucosylated chondroitin sulfates (FCSs) from sea cucumbers have repetitive structures that exhibit minor structural differences based on the organism from which they are recovered. A detailed characterization of FCSs and their derivatives is important to establish their structure-activity relationship in the development of new anticoagulant drugs. In the current study, online hydrophilic interaction chromatography-Fourier transform mass spectrometry (FTMS) was applied to analyze the FCS oligosaccharides generated by selective degradation from four species of sea cucumbers, Isostichopus badionotus, Pearsonothuria graeffei, Holothuria mexicana and Acaudina molpadioides. These depolymerized FCS fragments were quantified and compared using the glycomics software package, GlycReSoft. The quantified fragments mainly had trisaccharide-repeating compositions and showed significant differences in fucosylation (including its sulfation) among different species of sea cucumbers. Detailed analysis of FTMS ion peaks and top-down nuclear magnetic resonance spectroscopy of native FCS polysaccharides verified the accuracy of this method. Thus, a new structural model for FCS chains from these different sea cucumbers was defined. This bottom-up approach provides rich detailed structural analysis and provides quantitative information with high accuracy and reproducibility and should be suitable for the quality control in FCSs as well as their oligosaccharides.

High resolution MALDI-TOF-MS and MS/MS: Application for the structural characterization of sulfated oligosaccharides

Sulfated oligosaccharides are involved in important biological events that are often modulated by specific sequences and sulfation patterns, but their structural analysis remains challenging. Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) analysis of three different sulfated oligosaccharides (Fondaparinux, the octasulfated pentasaccharide, a disulfated heparin-derived tetrasaccharide 1, and an octasulfated maltoheptaose) 2 was performed using the 2-(4-hydroxyphenylazo)benzoic acid-tetramethylguanidinium (HABA-TMG₂) matrix. High resolution mass spectrometry of the main ions observed was successful, and this was complemented by tandem mass spectrometry (MS/MS) analysis for structural assessment. Despite sulfate losses, fully sulfated molecular ions were observed and these allowed the determination of oligosaccharide structures: UA-GlcNAc-UA(2S)-AnhMan(6S) for compound 1 and (Glc6S)₆-Glc (1S,6S) for compound 2.

CE-MS for anionic metabolic profiling: An overview of methodological developments

The efficient profiling of highly polar and charged metabolites in biological samples remains a huge analytical challenge in metabolomics. Over the last decade, new analytical techniques have been developed for the selective and sensitive analysis of polar ionogenic compounds in various matrices. Still, the analysis of such compounds, notably for acidic ionogenic metabolites, remains a challenging endeavor, even more when the available sample size becomes an issue for the total analytical workflow. In this paper, we give an overview of the possibilities of capillary electrophoresis-mass spectrometry (CE-MS) for anionic metabolic profiling by focusing on main methodological developments. Attention is paid to the development of improved separation conditions and new interfacing designs in CE-MS for anionic metabolic profiling. A complete overview of all CE-MS-based methods developed for this purpose is provided in table format (Table 1) which includes information on sample type, separation conditions, mass analyzer and limits of detection (LODs). Selected applications are discussed to show the utility of CE-MS for anionic metabolic profiling, especially for small-volume biological samples. On the basis of the examination of the reported literature in this specific field, we conclude that there is still room for the design of a highly sensitive and reliable CE-MS method for anionic metabolic profiling. A rigorous validation and the availability of standard operating procedures would be highly favorable in order to make CE-MS an alternative, viable analytical technique for metabolomics.

Recent Developments in the Separation of Low Molecular Weight Heparin Anticoagulants

The general function of anticoagulants is to prevent blood clotting and growing of the existing clots in blood vessels. In recent years, there has been a significant improvement in developing methods of prevention as well as pharmacologic and surgical treatment of thrombosis. For over the last two decades, low molecular weight heparins (LMWHs) have found their application in the antithrombotic diseases treatment. These types of drugs are widely used in clinical therapy. Despite the biological and medical importance of LMWHs, they have not been completely characterized in terms of their chemical structure. Due to both, the structural complexity of these anticoagulants and the presence of impurities, their structural characterization requires the employment of advanced analytical techniques. Since separation techniques play the key role in these endeavors, this review will focus on the presentation of recent developments in the separation of LMWH anticoagulants.

Comparison of hydrothermal depolymerization and oligosaccharide profile of fucoidan and fucosylated chondroitin sulfate from Holothuria floridana

To minimize undesired pharmacological activities and improve the bioavailability, the fucoidan and fucosylated chondroitin sulfate (FCS) from Holothuria floridana were depolymerized under hydrothermal conditions and the mechanism underlying hydrothermal depolymerization was proposed. Our results demonstrated that fucoidan and FCS from Holothuria floridana were able to be gradually depolymerized without desulfation at 100-121 °C by control of pH at 5-6 to obtain controlled molecular weight. It was the first time to find that pH also plays a key role on the hydrothermal depolymerization of fucoidan and FCS. The monosaccharide composition, FT-IR and NMR analysis showed that the structure of the optimized hydrothermal depolymerized fucoidan and FCS remained almost unchanged. By comparison, FCS was more difficult to be depolymerized than fucoidan under the same hydrothermal condition. The oligosaccharide profile in depolymerized fucoidan and FCS by HILIC-MS analysis further revealed that FCS was depolymerized with preferential cleavage of β-1 → 4 glycosidic linkage and decarboxylation on glucuronic acid during hydrothermal treatment, which was quite different with the random fracture type of fucoidan due to their different structure. These results indicated that hydrothermal depolymerization and action mechanism of fucoidan and FCS from sea cucumber were quite different for their different structure.

Non-Anticoagulant Low Molecular Weight Heparins for Pharmaceutical Applications

Heparin is a polypharmacological agent with anticoagulant activity. Periodate oxidation of the nonsulfated glucuronic acid residue results in non-anticoagulant heparin derivative (NACH) of reduced molecular weight. Similar treatment of a low molecular weight heparin, dalteparin, also removes its anticoagulant activity, affording a second heparin derivative (D-NACH). A full structural characterization of these two derivatives reveals their structural differences. SPR studies display their ability to bind to several important heparin-binding proteins, suggesting potential new therapeutic applications.

Comparison of Low-Molecular-Weight Heparins Prepared From Ovine Heparins With Enoxaparin

Heparin and its low-molecular-weight heparin derivatives are widely used clinical anticoagulants. These drugs are critical for the practice of medicine in applications, including kidney dialysis, cardiopulmonary bypass, and in the management of venous thromboembolism. Currently, these drugs are derived from livestock, primarily porcine intestine and less frequently bovine intestine and bovine lung. The worldwide dependence on the pig as a single dominant animal species has made the supply chain for this critical drug quite fragile, leading to the search for other sources of these drugs, including the expanded use of bovine tissues. A number of laboratories are now also examining the similarities between heparin and low-molecular-weight heparins prepared from porcine and ovine tissues. This study was designed to compare low-molecular-weight heparin prepared from ovine heparin through chemical β-elimination, a process currently used to prepare the low-molecular-weight heparin, enoxaparin. Using top-down, bottom-up, and compositional analyses as well as bioassays, low-molecular-weight heparin derived from ovine intestine was shown to closely resemble enoxaparin. Moreover, the compositions of daughter low-molecular-weight heparins prepared from three unfractionated ovine parent heparins were compared. Ovine enoxaparins had similar molecular weight and in vitro anticoagulant activities as Lovenox. Some disaccharide compositional, oligosaccharide composition at the reducing and nonreducing ends and intact chain compositional differences could be observed between porcine enoxaparin and ovine low-molecular-weight heparin. The similarity of these ovine and porcine heparin products suggests that their preclinical evaluation and ultimately clinical assessment is warranted.

Systematic analysis of enoxaparins from different sources with online one- and two-dimensional chromatography

Enoxaparin, one of the most important low-molecular-weight heparins (LMWHs), is widely used as a clinical anticoagulant.

Heparosan-coated liposomes for drug delivery

Liposomal encapsulation is a useful drug delivery strategy for small molecules, especially chemotherapeutic agents such as doxorubicin. Doxil® is a doxorubicin-containing liposome ("dox-liposome") that passively targets drug to tumors while reducing side effects caused by free drug permeating and poisoning healthy tissues. Polyethylene glycol (PEG) is the hydrophilic coating of Doxil® that protects the formulation from triggering the mononuclear phagocyte system (MPS). Evading the MPS prolongs dox-liposome circulation time thus increasing drug deposition at the tumor site. However, multiple doses of Doxil® sometimes activate an anti-PEG immune response that enhances liposome clearance from circulation and causes hypersensitivity, further limiting its effectiveness against disease. These side effects constrain the utility of PEG-coated liposomes in certain populations, justifying the need for investigation into alternative coatings that could improve drug delivery for better patient quality of life and outcome. We hypothesized that heparosan (HEP; [-4-GlcA-β1-4-GlcNAc-α1-]n) may serve as a PEG alternative for coating liposomes. HEP is a natural precursor to heparin biosynthesis in mammals. Also, bacteria expressing an HEP extracellular capsule during infection escape detection and are recognized as "self," not a foreign threat. By analogy, coating drug-carrying liposomes with HEP should camouflage the delivery vehicle from the MPS, extending circulation time and potentially avoiding immune-mediated clearance. In this study, we characterize the postmodification insertion of HEP-lipids into liposomes by dynamic light scattering and coarse-grain computer modeling, test HEP-lipid immunogenicity in rats, and compare the efficacy of drug delivered by HEP-coated liposomes to PEG-coated liposomes in a human breast cancer xenograft mouse model.

Preparation of low molecular weight heparins from bovine and ovine heparins using nitrous acid degradation

Low molecular weight heparins (LMWHs) are important anticoagulant drugs. Nitrous acid degradation is a major approach to produce LMWHs, such as dalteparin. Due to the foreseeable shortage of porcine intestinal mucosa heparin and other potential risks, expansion of other animal tissues for heparin preparation is necessary. Heparins from different tissues differ in structure and bioactivity potency, and these variations may be carried over to the LMWH products. Sophisticated analytical techniques have been applied to compare various versions of dalteparins produced from porcine intestinal, bovine lung and ovine intestinal heparins to elucidate the effects of different animal tissues starting materials and processing conditions on the properties of final dalteparin products. With adjusted depolymerization conditions, versions of dalteparins that qualify under the European Pharmacopeia (EP) specifications were manufactured using non-porcine heparins. Dissimilarities among the three interspecies animal tissue heparin-derived dalteparins regarding fine structures are also disclosed, and their origins are discussed.