Chemical Structure and Composition of Major Glycans Covalently Linked to Therapeutic Monoclonal Antibodies by Middle-Down Nuclear Magnetic Resonance

NMR investigations of glycan conformation, dynamics, and interactions

Glycans are ubiquitous in nature, decorating our cells and serving as the initial points of contact with any visiting entities. These glycan interactions are fundamental to host-pathogen recognition and are related to various diseases, including inflammation and cancer. Therefore, understanding the conformations and dynamics of glycans, as well as the key features that regulate their interactions with proteins, is crucial for designing new therapeutics. Due to the intrinsic flexibility of glycans, NMR is an essential tool for unravelling these properties. In this review, we describe the key NMR parameters that can be extracted from the different experiments, and which allow us to deduce the necessary geometry and molecular motion information, with a special emphasis on assessing the internal motions of the glycosidic linkages. We specifically address the NMR peculiarities of various natural glycans, from histo-blood group antigens to glycosaminoglycans, and also consider the special characteristics of their synthetic analogues (glycomimetics). Finally, we discuss the application of NMR protocols to study glycan-related molecular recognition events, both from the carbohydrate and receptor perspectives, including the use of stable isotopes and paramagnetic NMR methods to overcome the inherent degeneracy of glycan chemical shifts.

Assessment of monoclonal antibody glycosylation: a comparative study using HRMS, NMR, and HILIC-FLD

Monoclonal antibodies (mAbs) represent the largest class of therapeutic protein drug products. mAb glycosylation produces a heterogeneous, analytically challenging distribution of glycoforms that typically should be adequately characterized because glycosylation-based product quality attributes (PQAs) can impact product quality, immunogenicity, and efficacy. In this study, two products were compared using a panel of analytical methods. Two high-resolution mass spectrometry (HRMS) workflows were used to analyze N-glycans, while nuclear magnetic resonance (NMR) was used to generate monosaccharide fingerprints. These state-of-the-art techniques were compared to conventional analysis using hydrophilic interaction chromatography (HILIC) coupled with fluorescence detection (FLD). The advantages and disadvantages of each method are discussed along with a comparison of the identified glycan distributions. The results demonstrated agreement across all methods for major glycoforms, demonstrating how confidence in glycan characterization is increased by combining orthogonal analytical methodologies. The full panel of methods used represents a diverse toolbox that can be selected from based on the needs for a specific product or analysis.

The impact of glycosylation on the structure, function, and interactions of CD14

CD14 is an innate immune receptor that senses pathogen-associated molecular patterns, such as lipopolysaccharide, to activate the innate immune response. Although CD14 is known to be glycosylated, detailed understanding about the structural and functional significance of this modification is still missing. Herein, an NMR and MS-based study, assisted by MD simulations, has provided a 3D-structural model of glycosylated CD14. Our results reveal the existence of a key N-glycosylation site at Asn282 that exclusively contains unprocessed oligomannnose N-glycans that perfectly fit the concave cavity of the bent-solenoid shaped protein. This site is not accessible to glycosidases and is fundamental for protein folding and secretion. A second N-site at Asn151 displays mostly complex N-glycans, with the typical terminal epitopes of the host cell-line expression system (i.e. βGal, α2,3 and α2,6 sialylated βGal, here), but also particularities, such as the lack of core fucosylation. The glycan at this site points outside the protein surface, resulting in N-glycoforms fully exposed and available for interactions with lectins. In fact, NMR experiments show that galectin-4, proposed as a binder of CD14 on monocytes to induce their differentiation into macrophages-like cells, interacts in vitro with CD14 through the recognition of the terminal glycoepitopes on Asn151. This work provides key information about CD14 glycosylation, which helps to better understand its functional roles and significance. Although protein glycosylation is known to be dynamic and influenced by many factors, some of the features found herein (presence of unprocessed N-glycans and lack of core Fuc) are likely to be protein specific.

The NMR signature of maltose-based glycation in full-length proteins

Reducing sugars can spontaneously react with free amines in protein side chains leading to posttranslational modifications (PTMs) called glycation. In contrast to glycosylation, glycation is a non-enzymatic modification with consequences on the overall charge, solubility, aggregation susceptibility and functionality of a protein. Glycation is a critical quality attribute of therapeutic monoclonal antibodies. In addition to glucose, also disaccharides like maltose can form glycation products. We present here a detailed NMR analysis of the Amadori product formed between proteins and maltose. For better comparison, data collection was done under denaturing conditions using 7 M urea-d4 in D2O. The here presented correlation patterns serve as a signature and can be used to identify maltose-based glycation in any protein that can be denatured. In addition to the model protein BSA, which can be readily glycated, we present data of the biotherapeutic abatacept containing maltose in its formulation buffer. With this contribution, we demonstrate that NMR spectroscopy is an independent method for detecting maltose-based glycation, that is suited for cross-validation with other methods.

Unambiguous Identification of Glucose-Induced Glycation in mAbs and other Proteins by NMR Spectroscopy

OBJECTIVE

Glycation is a non-enzymatic and spontaneous post-translational modification (PTM) generated by the reaction between reducing sugars and primary amine groups within proteins. Because glycation can alter the properties of proteins, it is a critical quality attribute of therapeutic monoclonal antibodies (mAbs) and should therefore be carefully monitored. The most abundant product of glycation is formed by glucose and lysine side chains resulting in fructoselysine after Amadori rearrangement. In proteomics, which routinely uses a combination of chromatography and mass spectrometry to analyze PTMs, there is no straight-forward way to distinguish between glycation products of a reducing monosaccharide and an additional hexose within a glycan, since both lead to a mass difference of 162 Da.

METHODS

To verify that the observed mass change is indeed a glycation product, we developed an approach based on 2D NMR spectroscopy spectroscopy and full-length protein samples denatured using high concentrations of deuterated urea.

RESULTS

The dominating β-pyranose form of the Amadori product shows a characteristic chemical shift correlation pattern in 1H-13C HSQC spectra suited to identify glucose-induced glycation. The same pattern was observed in spectra of a variety of artificially glycated proteins, including two mAbs, as well as natural proteins.

CONCLUSION

Based on this unique correlation pattern, 2D NMR spectroscopy can be used to unambiguously identify glucose-induced glycation in any protein of interest. We provide a robust method that is orthogonal to MS-based methods and can also be used for cross-validation.

A Precise qNMR Method for the Rapid Quantification of Lot-to-Lot Variations in Multiple Quality Attributes of Pentosan Polysulfate Sodium

Pentosan polysulfate sodium (PPS) is an orphan drug with anticoagulant activity. PPS is prepared from the chemical processing of xylan extracted from beechwood tree to yield a mixture of 4-6 kDa polysaccharides. The chain is mainly composed of sulfated xylose (Xyl) with branched 4-O-methyl-glucuronate (MGA). During generic drug development, the quality attributes (QAs) including monosaccharide composition, modification, and length need to be comparable to those found in the reference list drug (RLD). However, the range of QA variation of the RLD PPS has not been well characterized. Here, multiple PPS RLD lots were studied using quantitative NMR (qNMR) and diffusion ordered spectroscopy (DOSY) to quantitate the components in the mixture and to probe both inter- and intra-lot precision variability. The DOSY precision assessed using coefficient of variation (CV) was 6%, comparable to PPS inter-lot CV of 5%. The QAs obtained from 1D qNMR were highly precise with a precision CV < 1%. The inter-lot MGA content was 4.8 ± 0.1%, indicating a very consistent botanical raw material source. Other process-related chemical modification including aldehyde at 0.51 ± 0.04%, acetylation at 3.3 ± 0.2% and pyridine at 2.08 ± 0.06%, varied more than MGA content. The study demonstrated that 1D qNMR is a quick and precise method to reveal ranges of variation in multiple attributes of RLD PPS which can be used to assess equivalency with generic formulations. Interestingly, the synthetic process appeared to introduce more variations to the PPS product than the botanical source of the material.

Analytical Techniques for the Characterization and Quantification of Monoclonal Antibodies

Monoclonal antibodies (mAbs) are a fast-growing class of biopharmaceuticals. They are widely used in the identification and detection of cell makers, serum analytes, and pathogenic agents, and are remarkably used for the cure of autoimmune diseases, infectious diseases, or malignancies. The successful application of therapeutic mAbs is based on their ability to precisely interact with their appropriate target sites. The precision of mAbs rely on the isolation techniques delivering pure, consistent, stable, and safe lots that can be used for analytical, diagnostic, or therapeutic applications. During the creation of a biologic, the key quality features of a particular mAb, such as structure, post-translational modifications, and activities at the biomolecular and cellular levels, must be characterized and profiled in great detail. This implies the requirement of powerful state of the art analytical techniques for quality control and characterization of mAbs. Until now, various analytical techniques have been developed to characterize and quantify the mAbs according to the regulatory guidelines. The present review summarizes the major techniques used for the analyses of mAbs which include chromatographic, electrophoretic, spectroscopic, and electrochemical methods in addition to the modifications in these methods for improving the quality of mAbs. This compilation of major analytical techniques will help students and researchers to have an overview of the methodologies employed by the biopharmaceutical industry for structural characterization of mAbs for eventual release of therapeutics in the drug market.

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.

Analytical Similarity Assessment of Biosimilars: Global Regulatory Landscape, Recent Studies and Major Advancements in Orthogonal Platforms

Biopharmaceuticals are one of the fastest-growing sectors in the biotechnology industry. Within the umbrella of biopharmaceuticals, the biosimilar segment is expanding with currently over 200 approved biosimilars, globally. The key step towards achieving a successful biosimilar approval is to establish analytical and clinical biosimilarity with the innovator. The objective of an analytical biosimilarity study is to demonstrate a highly similar profile with respect to variations in critical quality attributes (CQAs) of the biosimilar product, and these variations must lie within the range set by the innovator. This comprises a detailed comparative structural and functional characterization using appropriate, validated analytical methods to fingerprint the molecule and helps reduce the economic burden towards regulatory requirement of extensive preclinical/clinical similarity data, thus making biotechnological drugs more affordable. In the last decade, biosimilar manufacturing and associated regulations have become more established, leading to numerous approvals. Biosimilarity assessment exercises conducted towards approval are also published more frequently in the public domain. Consequently, some technical advancements in analytical sciences have also percolated to applications in analytical biosimilarity assessment. Keeping this in mind, this review aims at providing a holistic view of progresses in biosimilar analysis and approval. In this review, we have summarized the major developments in the global regulatory landscape with respect to biosimilar approvals and also catalogued biosimilarity assessment studies for recombinant DNA products available in the public domain. We have also covered recent advancements in analytical methods, orthogonal techniques, and platforms for biosimilar characterization, since 2015. The review specifically aims to serve as a comprehensive catalog for published biosimilarity assessment studies with details on analytical platform used and critical quality attributes (CQAs) covered for multiple biotherapeutic products. Through this compilation, the emergent evolution of techniques with respect to each CQA has also been charted and discussed. Lastly, the information resource of published biosimilarity assessment studies, created during literature search is anticipated to serve as a helpful reference for biopharmaceutical scientists and biosimilar developers.

2D NMR peak profiling to compare chemical differences between batches of pentosan polysulfate sodium

Pentosan Polysulfate Sodium (PPS) is a semi-synthetic polysulfated xylan sourced from beechwood tree barks. PPS, which is mainly composed of a xylose chain with branched O-methyl-glucuronate (MGA), can have heterogeneity in monosaccharide species, sequence and chemical modifications including sulfation and acetylation. The monosaccharide composition in polysaccharide therapeutics is a frequently quoted quality attribute (QA), which has been assessed using two-dimensional (2D) ¹H-¹³C HSQC NMR. However, the sensitivity of 2D NMR for the assessment of PPS inter-lot variability from the same manufacturer was unclear and questions remained whether 2D NMR had sufficient sensitivity to distinguish normal batch to batch variations in this QA. Here, a 2D peak profile method was applied to compare high-resolution semi-quantitative (semi-q) HSQC spectra with the inclusion of intermediate precision spectra collected on two PPS drug lots released 29 months apart (where one of the lots was expired). The semi-q HSQC NMR confirmed the mass equivalence of total polysaccharides, O-Methyl and acetyl groups between the two lots. The 2D spectral peak profile results readily identified significant lot-to-lot differences (p < 0.05) in relative distribution among most monosaccharide species, in addition to heterogeneity in MGA distribution and acetyl transfer from PPS to free acetate in the expired lot. Precisely measured chemical QAs are prerequisites to establish normal batch variation in the innovator product, providing important reference ranges for complex generic drug developers. Overall, high-resolution semi-q HSQC NMR may provide a sensitive tool to measure fine chemical differences in polysaccharide therapeutics needed to establish chemical QAs and compare batches without concerns of intrinsic NMR method variation.

Unambiguous identification of α-Gal epitopes in intact monoclonal antibodies by NMR spectroscopy

The α-Gal epitope consisting of the terminal trisaccharide Galα1,3Galβ1,4GlcNAc exposed on cell or protein surfaces can cause severe immune reactions, such as hypersensitivity reactions, in humans. This epitope is also called the xenotransplantation epitope because it is one of the main reasons for the rejection of non-human organ transplants by the human innate immune response. Recombinant therapeutic proteins expressed in murine cell lines may contain α-Gal epitopes, and therefore their absence or presence needs to be tightly monitored to minimize any undesired adverse effects. The analytical identification of α-Gal epitopes in glycoproteins using the common standard techniques based on liquid chromatography and mass spectrometry is challenging, mainly due to the isobaricity of hexose stereoisomers. Here, we present a straightforward NMR approach to detect the presence of α-Gal in biotherapeutics based on a quick screen with sensitive ¹H-¹H TOCSY spectra followed by a confirmation using ¹H-¹³C HSQC spectra.Abbreviations: α-Gal: α1,3-linked galactose; AGC: automatic gain control; CHO: Chinese hamster ovary; CE: capillary electrophoreses coupled to mass spectrometry; COSY: correlation spectroscopy; DSS: 2,2-dimethyl-2-silapentane-5-sulfonate; DTT: dithiothreitol; GlcNAc: N-acetyl glusomamine; HCD: higher-energy collisional dissociation; HMBC: heteronuclear multiple-bond correlation; HPLC: high-performance liquid chromatography; HSQC: heteronuclear single-quantum corre; LacNAc: N-acetyl lactosamine; mAb: monoclonal antibody; MS: mass spectrometry; NMR: nuclear magnetic resonance; NOESY: 2D) nuclear Overhauser spectroscopy; PEG: polyethylenglycol; pH*: observed pH meter reading without correction for isotope effects; PTM: post-translational modification; TCEP: tris(2-carboxyethyl) phosphine hydrochloride; TOCSY: total correlation spectroscopy; xCGE-LIF: multiplex capillary gel electrophoresis with laser-induced fluorescence detection.

Hydrazide-assisted directional antibody conjugation of gold nanoparticles to enhance immunochromatographic assay

The analytical performance of immunochromatographic assay (ICA) is usually determined by the biological activity of antibody and gold nanoparticle conjugates (AuNP probes). However, conventional probes are constructed using the nondirectional coupling method that can cause the improper orientation of antibodies with the poor accessibility of antigen-binding sites. To address these issues, we report a site-specific directional coupling strategy to enhance the bioactivity of AuNP probes through the specific covalent binding of the aldehyde group in the Fc domain of antibodies with the hydrazide group modified on the surface of AuNPs. Through this design, the antibodies can be erected on the AuNP surface to fully expose the Fab domain and achieve the maximized functional availability. Leveraging these AuNP probes as ICA labels, we demonstrate an improved detection of the hepatitis B surface antigen with less used amount of labeled antibody (0.2 mg/pmol AuNPs), shorter reaction time (10 min), better antibody bioactivity, and higher detection sensitivity (2 ng/mL) compared with the carbodiimide method. Overall, this work provides great promise for the design and the construction of high-performance probes to enhance the detection performance of ICA sensors.

Conformational and Structural characterization of carbohydrates and their interactions studied by NMR

Carbohydrates, either free or as glycans conjugated with other biomolecules, participate in many essential biological processes. Their apparent simplicity in terms of chemical functionality hides an extraordinary diversity and structural complexity. Deeply deciphering at the atomic level their structures is essential to understand their biological function and activities, but it is still a challenging task in need of complementary approaches and no generalized procedures are available to address the study of such complex, natural glycans. The versatility of Nuclear Magnetic Resonance spectroscopy (NMR) often makes it the preferred choice to study glycans and carbohydrates in solution media. The most basic NMR parameters, namely chemical shifts, coupling constants and nuclear Overhauser effects, allow defining short or repetitive chain sequences and characterize their structures and local geometries either in the free state or when interacting with other biomolecules, rendering additional information on the molecular recognition processes. The increased accessibility to carbohydrate molecules extensively or selectively labeled with 13C boosts the resolution and detail that analyzed glycan structures can reach. In turn, structural information derived from NMR, complemented with molecular modeling and theoretical calculations can also provide dynamic information on the conformational flexibility of carbohydrate structures. Furthermore, using partially oriented media or paramagnetic perturbations, it has been possible to introduce additional long-range observables rendering structural information on longer and branched glycan chains. In this review, we provide examples of these studies and an overview of the recent and most relevant NMR applications in the glycobiology field.

LC-MS/MS-based non-isotopically paired labeling (NIPL) strategy for the qualification and quantification of monosaccharides

Investigation into monosaccharides is critical for studies of oligosaccharides structure and function in biological processes. However, monosaccharides quantification is still challenge due to their isomeric structure and high hydrophilic properties. Besides, it was difficult to obtain isotopic internal standards (IS) of each monosaccharide in complex matrixes. Herein, we developed a novel strategy for the qualification and quantification of monosaccharides in urine using two structure analogs 1-(4-methylphenyl)-3-methyl-5-pyrazolone (MPMP) and1-phenyl-3-methyl-5-pyrazolone (PMP) as non-isotopically paired labeling (NIPL) reagents by liquid chromatograph-tandem mass spectrometry (LC-MS/MS). The derivatized monosaccharides by NIPL method not only had sufficient retention time differences on reversed-phase column, but also exhibited predominant product ion pairs (m/z 189 & m/z 175) in the multiple reaction monitoring (MRM) mode. In this method, PMP labeled standards were adopted as one-to-one internal standards (ISs). 12 urinary monosaccharides were successfully determined and the linear ranges expanded five orders of magnitude with limit of quantification (LOQ) varied from 0.09 ng mL^-1 to 0.36 ng mL^-1 as well as the accuracy higher than 98.15% and the relative standard derivation (RSD) lower than 7.92%. With assistance of multivariate analysis, the targeted monosaccharide biomarkers were firstly obtained for the diagnosis of bladder cancer. By the inexpensive NIPL reagents-MPMP/PMP, the developed strategy possessed the specific advantages of low cost, simple operation, high sensitivity and high accuracy for the qualification and quantitation of monosaccharides. As expected, this method will provide an alternative application potential for targeted metabolomics analysis.

Comprehensive Assessment of Protein and Excipient Stability in Biopharmaceutical Formulations Using 1H NMR Spectroscopy

Biopharmaceutical proteins are important drug therapies in the treatment of a range of diseases. Proteins, such as antibodies (Abs) and peptides, are prone to chemical and physical degradation, particularly at the high concentrations currently sought for subcutaneous injections, and so formulation conditions, including buffers and excipients, must be optimized to minimize such instabilities. Therefore, both the protein and small molecule content of biopharmaceutical formulations and their stability are critical to a treatment's success. However, assessing all aspects of protein and small molecule stability currently requires a large number of analytical techniques, most of which involve sample dilution or other manipulations which may themselves distort sample behavior. Here, we demonstrate the application of 1H nuclear magnetic resonance (NMR) spectroscopy to study both protein and small molecule content and stability in situ in high-concentration (100 mg/mL) Ab formulations. We show that protein degradation (aggregation or fragmentation) can be detected as changes in 1D 1H NMR signal intensity, while apparent relaxation rates are specifically sensitive to Ab fragmentation. Simultaneously, relaxation-filtered spectra reveal the presence and degradation of small molecule components such as excipients, as well as changes in general solution properties, such as pH. 1H NMR spectroscopy can thus provide a holistic overview of biopharmaceutical formulation content and stability, providing a preliminary characterization of degradation and acting as a triaging step to guide further analytical techniques.

Direct and simultaneous recognition of the positional isomers of aminobenzenesulfonic acid by TIMS-TOF-MS

Positional isomer recognition is a challenging scientific issue. Fast and accurate detection of isomers is required for understanding their chemical properties. Here, we describe a method for simultaneous recognition of three positional isomers of 2-aminobenzenesulfonic acid (2-ABSA), 3-ABSA, and 4-ABSA using trapped ion mobility spectroscopy-time-of-flight mass spectrometry (TIMS-TOF-MS). The three ABSA positional isomers were recognized by measuring the different ion mobility of the ternary complexes of [β-cyclodextrin (CD)+ABSA + Li]⁺ or [λ-CD + ABSA + Na]⁺, because their different collision cross-sections or different spatial conformations. The collision-induced dissociation mechanism of the different complexes of [β-CD + ABSA + Li]⁺ and [λ-CD + ABSA + Na]⁺ using tandem mass spectrometry exhibited the same dissociation process with slightly different dissociation energies, which the smaller cross-section requires higher collision energy that means the smaller complex with tighter and more stable conformation than a larger complex for the ABSA complexes. In addition, relative quantification of the ABSA isomers was studied by measuring any two of the three ABSA isomer complexes at different molar ratio of 10:1 to 1:10 in the μM range, good linearity (R² > 0.99) with precision between 2.14% and 2.58%, and accuracy ≥ 97.1% were obtained. The method for fast determination and recognition of ABSA positional isomers by combination with CD and alkali metal ions possesses the advantages of being simple, direct, rapid, sensitive, cost-effective, and needs no chemical derivatives or chromatographic separation before analysis. Therefore, the proposed method would be a powerful tool for the analysis of ABSA isomers or even other positional isomers.

Minor N-Glycan Mapping of Monoclonal Antibody Therapeutics Using Middle-Down NMR Spectroscopy

The N-glycosylation pattern of Asn-297 may have impacts on monoclonal antibody (mAb) drug plasma clearance, antibody-dependent cell mediated cytotoxicity (ADCC), and complement-dependent cytotoxicity (CDC). Notably, the changes in the relative abundance of certain minor glycans, like the afucosylation, high-mannose, or galactosylation are known to change mAb properties and functions. Here, a middle-down NMR spectroscopy based analytical procedure was applied to assess the composition and structure of glycans on adalimumab and trastuzumab without glycan cleavage from the mAbs. The anomeric 2D ¹H-¹³C spectra showed distinct patterns that could be used to profile and differentiate mAb glycan compositions. Specifically, the anomeric C1/H1 resonances from N-acetylglucosamine (GlcNAc2 and -5) and mannose (Man4) were identified as characteristic peaks for key glycan anomeric linkages and branching states. They were also utilized for measuring the relative abundance of minor glycans of total afucosylation (aFuc%), high mannose (HM%), and branch specific galactosylation (Gal_1-3% and Gal_1-6%). The obtained total aFuc% value of 11-12% was similar between the two mAbs; however, trastuzumab had significantly lower level of high mannose and a higher level of galactosylation than adalimumab. Overall, the 2D-NMR measurements provided functionally relevant mAb glycan composition and structure information. The method was deemed fit-for-purpose for assessment of these mAb quality attributes and involved fewer chemical preparation steps than the classical approaches that cleave glycans prior to making measurements.

NMR of glycoproteins: profiling, structure, conformation and interactions

In glycoproteins, carbohydrates are responsible for the selective interaction and tight regulation of cellular processes, constituting the main information transducer interface in protein-glycoprotein interactions. Increasing experimental and computational evidence suggest that such interactions often induce allosteric changes in the host protein, underlining the importance of studying intact glycoproteins. Technical issues have precluded such studies for years but, nowadays, a promising era is emerging where NMR spectroscopy, among other techniques, allows the characterization of the composition, structure and segmental dynamics of glycoproteins. In this review, we discuss such advances and highlight some selected examples. This novel technology unravels multiple new functional mechanisms, subtly hidden within the sugar code.

Identification and Quantification of Oxidation Products in Full-Length Biotherapeutic Antibodies by NMR Spectroscopy

Therapeutic proteins are an indispensable class of drugs and often therapeutics of last resort. They are sensitive to oxidation, which is of critical concern, because it can affect drug safety and efficacy. Protein oxidation, with methionine and tryptophan as the most susceptible moieties, is mainly monitored by HPLC–MS techniques. However, since several oxidation products display the same mass difference, their identification by MS is often ambiguous. Therefore, an alternative analytical method able to unambiguously identify and, ideally, also quantify oxidation species in proteins is highly desired. Here, we present an NMR-based approach to monitor oxidation in full-length proteins under denaturing conditions, as demonstrated on two biotherapeutic monoclonal antibodies (mAbs). We show that methionine sulfoxide, methionine sulfone, N-formylkynurenine, kynurenine, oxindolylalanine, hydroxypyrroloindole, and 5-hydroxytryptophan result in characteristic chemical shift correlations suited for their identification and quantification. We identified the five most abundant oxidation products in forced degradation studies of two full-length therapeutic mAbs and can also unambiguously distinguish oxindolylalanine from 5-hydroxytryptophan, which are undistinguishable by MS due to the same mass shift. Quantification of the abundant methionine sulfoxide by NMR and MS gave highly comparable values. These results underline the suitability of NMR spectroscopy for the identification and quantification of critical quality attributes of biotherapeutics.

Regional Metabolic Patterns of Abnormal Postoperative Behavioral Performance in Aged Mice Assessed by 1H-NMR Dynamic Mapping Method

Abnormal postoperative neurobehavioral performance (APNP) is a common phenomenon in the early postoperative period. The disturbed homeostatic status of metabolites in the brain after anesthesia and surgery might make a significant contribution to APNP. The dynamic changes of metabolites in different brain regions after anesthesia and surgery, as well as their potential association with APNP are still not well understood. Here, we used a battery of behavioral tests to assess the effects of laparotomy under isoflurane anesthesia in aged mice, and investigated the metabolites in 12 different sub-regions of the brain at different time points using proton nuclear magnetic resonance (1H-NMR) spectroscopy. The abnormal neurobehavioral performance occurred at 6 h and/or 9 h, and recovered at 24 h after anesthesia/surgery. Compared with the control group, the altered metabolite of the model group at 6 h was aspartate (Asp), and the difference was mainly displayed in the cortex; while significant changes at 9 h occurred predominantly in the cortex and hippocampus, and the corresponding metabolites were Asp and glutamate (Glu). All changes returned to baseline at 24 h. The altered metabolic changes could have occurred as a result of the acute APNP, and the metabolites Asp and Glu in the cortex and hippocampus could provide preliminary evidence for understanding the APNP process.

Glycan structures and their interactions with proteins. A NMR view

Carbohydrate molecules are essential actors in key biological events, being involved as recognition points for cell-cell and cell-matrix interactions related to health and disease. Despite outstanding advances in cryoEM, X-ray crystallography and NMR still remain the most employed techniques to unravel their conformational features and to describe the structural details of their interactions with biomolecular receptors. Given the intrinsic flexibility of saccharides, NMR methods are of paramount importance to deduce the extent of motion around their glycosidic linkages and to explore their receptor-bound conformations. We herein present our particular view on the latest advances in NMR methodologies that are permitting to magnify their applications for deducing glycan conformation and dynamics and understanding the recognition events in which there are involved.

Unambiguous Identification of Pyroglutamate in Full-Length Biopharmaceutical Monoclonal Antibodies by NMR Spectroscopy

Biotherapeutic proteins are an indispensable class of pharmaceuticals that present a high degree of structural complexity and are prone to chemical modifications during production, processing, and storage, which have to be tightly controlled. Pyroglutamate (pGlu), a cyclization product of N-terminal Gln or Glu residues, is a widespread post-translational modification in proteins, including monoclonal antibodies (mAbs). The unambiguous identification and quantification of this modification in proteins is challenging, since the mass difference of -17 Da or -18 Da, when formed from Gln or Glu, respectively, is not unique. Moreover, deamidation and dehydration occur not only during cyclization to pGlu, but also during other reactions leading to different types of modifications, like succinimide or isopeptide bond moieties due to cross-linking between Asn or Gln and Lys side chains. Here we report the unambiguous identification and quantification of pGlu in intact mAbs with natural isotope distribution by NMR spectroscopy. The assignment of all ¹H, ¹³C and ¹⁵N random coil chemical shifts of pGlu in short reference peptides led to the identification of unique chemical shift pairs that are distinct from the random coil chemical shifts of the natural amino-acid residues. These characteristic correlations are suited for the detection of pGlu in denatured proteins. We achieved complete denaturation of mAbs using a straightforward protocol, and could detect and quantify pGlu, in agreement with available mass spectrometric data. The application to the mAbs rituximab and adalimumab illustrates the potential of our approach for the characterization of biotherapeutics containing isotopes at natural abundance.

Characterizing Post-Translational Modifications and Their Effects on Protein Conformation Using NMR Spectroscopy

The diversity of the cellular proteome substantially exceeds the number of genes coded by the DNA of an organism because one or more residues in a majority of eukaryotic proteins are post-translationally modified (PTM) by the covalent conjugation of specific chemical groups. We now know that PTMs alter protein conformation and function in ways that are not entirely understood at the molecular level. NMR spectroscopy has been particularly successful as an analytical tool in elucidating the themes underlying the structural role of PTMs. In this Perspective, we focus on the NMR-based characterization of three abundant PTMs: phosphorylation, acetylation, and glycosylation. We detail NMR methods that have found success in detecting these modifications at a site-specific level. We also highlight NMR studies that have mapped the conformational changes ensuing from these PTMs as well as evaluated their relation to function. The NMR toolbox is expanding rapidly with experiments available to probe not only the average structure of biomolecules but also how this structure changes with time on time scales ranging from picoseconds to seconds. The atomic resolution insights into the biomolecular structure, dynamics, and mechanism accessible from NMR spectroscopy ensure that NMR will continue to be at the forefront of research in the structural biology of PTMs.

Glycoprofile Analysis of an Intact Glycoprotein As Inferred by NMR Spectroscopy

Protein N-glycosylation stands out for its intrinsic and functionally related heterogeneity. Despite its biomedical interest, Glycoprofile analysis still remains a major scientific challenge. Here, we present an NMR-based strategy to delineate the N-glycan composition in intact glycoproteins and under physiological conditions. The employed methodology allowed dissecting the glycan pattern of the IgE high-affinity receptor (FcεRIα) expressed in human HEK 293 cells, identifying the presence and relative abundance of specific glycan epitopes. Chemical shifts and differences in the signal line-broadening between the native and the unfolded states were integrated to build a structural model of FcεRIα that was able to identify intramolecular interactions between high-mannose N-glycans and the protein surface. In turn, complex type N-glycans reflect a large solvent accessibility, suggesting a functional role as interaction sites for receptors. The interaction between intact FcεRIα and the lectin hGal3, also studied here, confirms this hypothesis and opens new avenues for the detection of specific N-glycan epitopes and for the studies of glycoprotein-receptor interactions mediated by N-glycans.

The NMR signature of gluconoylation: a frequent N-terminal modification of isotope-labeled proteins

N-terminal gluconoylation is a moderately widespread modification in recombinant proteins expressed in Escherichia coli, in particular in proteins bearing an N-terminal histidine-tag. This post-translational modification has been investigated mainly by mass spectrometry. Although its NMR signals must have been observed earlier in spectra of ¹³C/¹⁵N labeled proteins, their chemical shifts were not yet reported. Here we present the complete ¹H and ¹³C chemical shift assignment of the N-terminal gluconoyl post-translational modification, based on a selection of His-tagged protein constructs (CCL2, hnRNP A1 and Lin28) starting with Met-Gly-...-(His)₆. In addition, we show that the modification can hydrolyze over time, resulting in a free N-terminus and gluconate. This leads to the disappearance of the gluconoyl signals and the appearance of gluconate signals during the NMR measurements. The chemical shifts presented here can now be used as a reference for the identification of gluconoylation in recombinant proteins, in particular when isotopically labeled.