Effects of Salts from the Hofmeister Series on the Conformational Stability, Aggregation Propensity, and Local Flexibility of an IgG1 Monoclonal Antibody

Low-field NMR Works as a Rapid, Automatic, Non-Invasive and Wide-Scale Coverage Technique for Aggregates Indication in Biomacromolecule Development

Protein aggregation is challenging for biopharmaceutical drug, because it affects the stability of protein formulations in real-time. However, current techniques for protein aggregate indication meet a number of limitations including limited aggregate size range, complex pre-treatments and lack of chromatographic approaches. Herein, a rapid, automatic, non-invasive and wide-scale coverage technique for aggregates indication is developed to overcome these challenges. Firstly, the response of low-field nuclear magnetic resonance (LF-NMR) to the aggregates is explored by making a comparison with certain established techniques. LF-NMR achieves a high sensitivity of water proton transverse relaxation rate (R2 of H2O, hereinafter referred as R2(H2O)) to protein aggregates from nanometer to micrometer. Then, the quantitative relationship between R2(H2O) and aggregates is investigated furtherly. R2(H2O) could serve as an all-size coverage protein aggregates indicator during development. As a non-invasive method, LF-NMR does not need any sample handling. It takes only 44 s for one test, and saves a lot of manpower, materials and costs. Compared with other established analytical techniques, the technique developed here could be a powerful tool for a rapid, automatic, non-invasive and wide-scale coverage technique for aggregates indication in biomacromolecule development.

Interpretation of Hydrogen/Deuterium Exchange Mass Spectrometry

This paper sheds light on the meaning of hydrogen/deuterium exchange-mass spectrometry (HDX-MS) data. HDX-MS data provide not structural information but dynamic information on an analyte protein. First, the reaction mechanism of backbone amide HDX reaction is considered and the correlation between the parameters from an X-ray crystal structure and the protection factors of HDX reactions of cytochrome c is evaluated. The presence of H-bonds in a protein structure has a strong influence on HDX rates which represent protein dynamics, while the solvent accessibility only weakly affects the HDX rates. Second, the energy diagrams of the HDX reaction at each residue in the presence and absence of perturbation are described. Whereas the free energy change upon mutation can be directly measured by the HDX rates, the free energy change upon ligand binding may be complicated due to the presence of unbound analyte protein in the protein-ligand mixture. Third, the meanings of HDX and other biophysical techniques are explained using a hypothetical protein folding well. The shape of the protein folding well describes the protein dynamics and provides Boltzmann distribution of open and closed states which yield HDX protection factors, while a protein's crystal structure represents a snapshot near the bottom of the well. All biophysical data should be consistent yet provide different information because they monitor different parts of the same protein folding well.

Modeling the behavior of monoclonal antibodies on hydrophobic interaction chromatography resins

Monoclonal antibodies (mAbs) require a high level of purity for regulatory approval and safe administration. High-molecular weight (HMW) species are a common impurity associated with mAb therapies. Hydrophobic interaction chromatography (HIC) resins are often used to remove these HMW impurities. Determination of a suitable HIC resin can be a time and resource-intensive process. In this study, we modeled the chromatographic behavior of seven mAbs across 13 HIC resins using measurements of surface hydrophobicity, surface charge, and thermal stability for mAbs, and hydrophobicity and zeta-potential for HIC resins with high fit quality (adjusted R2 > 0.80). We identified zeta-potential as a novel key modeling parameter. When using these models to select a HIC resin for HMW clearance of a test mAb, we were able to achieve 60% HMW clearance and 89% recovery. These models can be used to expedite the downstream process development for mAbs in an industry setting.

Interaction between preservatives and a monoclonal antibody in support of multidose formulation development

Multidose formulations have patient-centric advantages over single-dose formats. A major challenge in developing multidose formulations is the prevention of microbial growth that can potentially be introduced during multiple drawings. The incorporation of antimicrobial preservatives (APs) is a common approach to inhibit this microbial growth. Selection of the right preservative while maintaining drug product stability is often challenging. We explored the effects of three APs, 1.1 % (w/v) benzyl alcohol, 0.62 % (w/v) phenol, and 0.42 % (w/v) m-cresol, on a model immunoglobulin G1 monoclonal antibody, termed the "NIST mAb." As measured by hydrogen exchange-mass spectrometry (HX-MS) and differential scanning calorimetry, conformational stability was decreased in the presence of APs. Specifically, flexibility (faster HX) was significantly increased in the CH2 domain (HC 238-255) across all APs. The addition of phenol caused the greatest conformational destabilization, followed by m-cresol and benzyl alcohol. Storage stability studies conducted by subvisible particle (SVP) analysis at 40 °C over 4 weeks further revealed an increase in SVPs in the presence of phenol and m-cresol but not in the presence of benzyl alcohol. However, as monitored by size exclusion chromatography, there was neither a significant change in the monomeric content nor an accumulation of soluble aggregate in the presence of APs.

Hydrogen-Deuterium Exchange Dynamics of NISTmAb Measured by Small Angle Neutron Scattering

Understanding protein dynamics and conformational stability holds great significance in biopharmaceutical research. Hydrogen-deuterium exchange (HDX) is a quantitative methodology used to examine these fundamental properties of proteins. HDX involves measuring the exchange of solvent-accessible hydrogens with deuterium, which yields valuable insights into conformational fluctuations and conformational stability. While mass spectrometry is commonly used to measure HDX on the peptide level, we explore a different approach using small-angle neutron scattering (SANS). In this work, SANS is demonstrated as a complementary and noninvasive HDX method (HDX-SANS). By assessing subtle changes in the tertiary and quaternary structure during the exchange process in deuterated buffer, along with the influence of added electrolytes on protein stability, SANS is validated as a complementary HDX technique. The HDX of a model therapeutic antibody, NISTmAb, an IgG1κ, is monitored by HDX-SANS over many hours using several different formulations, including salts from the Hofmeister series of anions, such as sodium perchlorate, sodium thiocyanate, and sodium sulfate. The impact of these formulation conditions on the thermal stability of NISTmAb is probed by differential scanning calorimetry. The more destabilizing salts led to heightened conformational dynamics in mAb solutions even at temperatures significantly below the denaturation point. HDX-SANS is demonstrated as a sensitive and noninvasive technique for quantifying HDX kinetics directly in mAb solution, providing novel information about mAb conformational fluctuations. Therefore, HDX-SANS holds promise as a potential tool for assessing protein stability in formulation.

Experimentally Observed Conformational Changes in Antibodies Due to Binding and Paratope-epitope Asymmetries

Understanding binding related changes in antibody conformations is important for epitope prediction and antibody refinement. The increase of available data in the PDB allowed a more detailed investigation of the conformational landscape for free and bound antibodies. A dataset containing a total of 835 unique PDB entries of antibodies that were crystallized in complex with their antigen and in a free state was constructed. It was examined for binding related conformation changes. We present further evidence supporting the theory of a pre-existing-equilibrium in experimental data. Multiple sequence alignments did not show binding induced tendencies in the solvent accessibility of residues in any specific position. Evaluating the changes in solvent accessibility per residue revealed a certain binding induced increase for several amino acids. Antibody-antigen interaction statistics were established and quantify a significant directional asymmetry between many interacting antibody and antigen residue pairs, especially a richness in tyrosine in the antibody epitope compared to its paratope. This asymmetry could potentially facilitate an increase in the success rate of computationally guided antibody refinement.

Influence of cadmium ion on denaturation kinetics of hen egg white-lysozyme under thermal and acidic conditions

To study the influence of Cd(II) ions on denaturation kinetics of hen egg white lysozyme (HEWL) under thermal and acidic conditions, spontaneous Raman spectroscopy in conjunction with Thioflavin-T fluorescence, AFM imaging, far-UV circular dichroism spectroscopy, and transmittance assays was conducted. Four distinctive Raman spectral markers for protein tertiary and secondary structures were recorded to follow the kinetics of conformational transformation. Through comparing variations of these markers in the presence or absence of Cd(II) ions, Cd(II) ions show an ability to efficiently accelerate the disruption of tertiary structure, and meanwhile, to promote the direct formation of organized β-sheets from the uncoiling of α-helices by skipping intermediate random coils. More significantly, with the action of Cd(II) ions, the initially resulting oligomers with disordered structures tend to assemble into aggregates with random structures like gels more than amyloid fibrils, along with a so-called "off-pathway" denaturation pathway. Our results advance the in-depth understanding of corresponding ion-specific effects.

Effects of Salts and Surface Charge on the Biophysical Stability of a Low pI Monoclonal Antibody

The impact of five representative Hofmeister salts (NaCl, KCl, MgCl₂, Na₂SO₄, and NaSCN) on the thermal stability and aggregation kinetics of a slightly acidic monoclonal antibody (mAb) were investigated under different pH conditions. The thermal stability of the mAb was assessed by measuring the lowest unfolding transition temperature, T_m, with differential scanning fluorimetry. MgCl₂ and NaSCN significantly decreased T_m at all three charged states of the mAb, but to the greatest extent when the mAb surface charge was net positive. Non-native aggregation kinetics was monitored by measuring Rayleigh light scattering. When the mAb surface charge was net positive or net neutral, the nucleation rate increased non-monotonically with MgCl₂ and NaSCN but decreased monotonically with NaCl, KCl, and Na₂SO₄. By contrast, when the mAb surface was negatively charged, there were only minor changes in the nucleation rate with all salts tested. Furthermore, there was less structural perturbation and slower aggregation rates when the mAb was net negatively charged than when it was net neutrally or positively charged. The observed salt effects on thermal unfolding are consistent with ion-specific mechanisms dominated by short-range amide backbone binding. On the other hand, the salt effects on nucleation rates appear to be influenced by both amide backbone binding and long-range electrostatic binding of ions to charged amino acid side chains.

Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section

The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field of structural biology over the past two decades. An IM-MS workflow applied to a given target analyte provides mass, charge, and conformation, and all three of these can be used to discern structural information. While mass and charge are determined in mass spectrometry (MS), it is the addition of ion mobility that enables the separation of isomeric and isobaric ions and the direct elucidation of conformation, which has reaped huge benefits for structural biology. In this review, where we focus on the analysis of proteins and their complexes, we outline the typical features of an IM-MS experiment from the preparation of samples, the creation of ions, and their separation in different mobility and mass spectrometers. We describe the interpretation of ion mobility data in terms of protein conformation and how the data can be compared with data from other sources with the use of computational tools. The benefit of coupling mobility analysis to activation via collisions with gas or surfaces or photons photoactivation is detailed with reference to recent examples. And finally, we focus on insights afforded by IM-MS experiments when applied to the study of conformationally dynamic and intrinsically disordered proteins.

Probing Antibody Structures by Hydrogen/Deuterium Exchange Mass Spectrometry

Hydrogen/deuterium exchange (HDX) followed by mass spectrometry detection (MS) provides a fast, reliable, and detailed solution for the assessment of a protein structure. It has been widely recognized as an indispensable tool and already approved by several regulatory agencies as a structural technique for the validation of protein biopharmaceuticals, including antibody-based drugs. Antibodies are of a key importance in life and medical sciences but considered to be challenging analytical targets because of their compact structure stabilized by disulfide bonds and due to the presence of glycosylation. Despite these difficulties, there are already numerous excellent studies describing MS-based antibody structure characterization. In this chapter, we describe a universal HDX-MS workflow. Deeper attention is paid to sample handling, optimization procedures, and feasibility stages, as these elements of the HDX experiment are crucial for obtaining reliable detailed and spatially well-resolved information.

High-Pressure, Low-Temperature Induced Unfolding and Aggregation of Monoclonal Antibodies: Role of the Fc and Fab Fragments

The effects of high pressure and low temperature on the stability of two different monoclonal antibodies (MAbs) were examined in this work. Fluorescence and small-angle neutron scattering were used to monitor the in situ effects of pressure to infer shifts in tertiary structure and characterize aggregation prone intermediates. Partial unfolding was observed for both MAbs, to different extents, under a range of pressure/temperature conditions. Fourier transform infrared spectroscopy was also used to monitor ex situ changes in secondary structure. Preservation of native secondary structure after incubation at elevated pressures and subzero ° C temperatures was independent of the extent of tertiary unfolding and reversibility. Several combinations of pressure and temperature were also used to discern the respective contributions of the isolated Ab fragments (Fab and Fc) to unfolding and aggregation. The fragments for each antibody showed significantly different partial unfolding profiles and reversibility. There was not a simple correlation between stability of the full MAb and either the Fc or Fab fragment stabilities across all cases, demonstrating a complex relationship to full MAb unfolding and aggregation behavior. That notwithstanding, the combined use of spectroscopic and scattering techniques provides insights into MAb conformational stability and hysteresis in high-pressure, low-temperature environments.

Quantitative Hydrogen/Deuterium Exchange Mass Spectrometry

This Account describes considerations for the data generation, data analysis, and data interpretation of a hydrogen/deuterium exchange-mass spectrometry (HDX-MS) experiment to have a quantitative argument. Although HDX-MS has gained its popularity as a biophysical tool, the argument from its data often remains qualitative. To generate HDX-MS data that are more suitable for a quantitative argument, the sequence coverage and sequence resolution should be optimized during the feasibility stage, and the time window coverage and time window resolution should be improved during the HDX stage. To extract biophysically meaningful values for a certain perturbation from medium-resolution HDX-MS data, there are two major ways: (i) estimating the area between the two deuterium buildup curves using centroid values with and without the perturbation when plotted against log time scale and (ii) dissecting into multiple single-exponential curves using the isotope envelopes. To have more accurate arguments for an HDX-MS perturbation study, (i) false negatives due to sequence coverage, (ii) false negatives due to time window coverage, (iii) false positives due to sequence resolution, and (iv) false positives due to allosteric effects should be carefully examined.

Interaction of Aluminum-adjuvanted Recombinant P[4] Protein Antigen With Preservatives: Storage Stability and Backbone Flexibility Studies

Eight antimicrobial preservatives used in parenteral multidose formulations (thimerosal, 2-phenoxy ethanol, phenol, benzyl alcohol, m-cresol, chlorobutanol, methyl paraben, propyl paraben) were examined for their effects on the storage stability (4 °C, 25 °C) of an Alhydrogel® (AH) adjuvanted formulation of the non-replicating rotavirus vaccine (NRRV) recombinant P[4] protein antigen. The stability of AH-adsorbed P[4] was monitored for antigen-antibody binding, conformational stability, and antigen-adjuvant interaction via competitive ELISA, DSC, and SDS-PAGE, respectively. There was an unexpected correlation between increasing storage stability of the AH-adsorbed P[4] and preservative hydrophobicity (log P) (e.g., the parabens and chlorobutanol were least destabilizing). We used hydrogen exchange-mass spectrometry (HX-MS) to better understand the destabilizing effects of temperature and preservative on backbone flexibility of AH-adsorbed P[4]. Thimerosal addition immediately increased the backbone flexibility across much of the AH-adsorbed P[4] protein backbone (except the N-terminal P2 region and residues G¹⁷-Y³⁸), and further increase in P[4] backbone flexibility was observed after storage (4 °C, 4 weeks). HX-MS analysis of AH-adsorbed P[4] stored for 4 weeks at 25 °C revealed structural alterations in some regions of the epitope involved in P[4] specific mAb binding. These combined results are discussed in terms of a generalized workflow for multi-dose vaccine formulation development for recombinant protein antigens.

Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems

Solution-phase hydrogen/deuterium exchange (HDX) coupled to mass spectrometry (MS) is a widespread tool for structural analysis across academia and the biopharmaceutical industry. By monitoring the exchangeability of backbone amide protons, HDX-MS can reveal information about higher-order structure and dynamics throughout a protein, can track protein folding pathways, map interaction sites, and assess conformational states of protein samples. The combination of the versatility of the hydrogen/deuterium exchange reaction with the sensitivity of mass spectrometry has enabled the study of extremely challenging protein systems, some of which cannot be suitably studied using other techniques. Improvements over the past three decades have continually increased throughput, robustness, and expanded the limits of what is feasible for HDX-MS investigations. To provide an overview for researchers seeking to utilize and derive the most from HDX-MS for protein structural analysis, we summarize the fundamental principles, basic methodology, strengths and weaknesses, and the established applications of HDX-MS while highlighting new developments and applications.

The effects of intramolecular and intermolecular electrostatic repulsions on the stability and aggregation of NISTmAb revealed by HDX-MS, DSC, and nanoDSF

The stability and aggregation of NIST monoclonal antibody (NISTmAb) were investigated by hydrogen/deuterium exchange mass spectrometry (HDX-MS), differential scanning calorimetry (DSC), and nano-differential scanning fluorimetry (nanoDSF). NISTmAb was prepared in eight formulations at four different pHs (pH 5, 6, 7, and 8) in the presence and absence of 150 mM NaCl and analyzed by the three methods. The HDX-MS results showed that NISTmAb is more conformationally stable at a pH near its isoelectric point (pI) in the presence of NaCl than a pH far from its pI in the absence of NaCl. The stabilization effects were global and not localized. The midpoint temperature of protein thermal unfolding transition results also showed the C_H 2 domain of the protein is more conformationally stable at a pH near its pI. On the other hand, the onset of aggregation temperature results showed that NISTmAb is less prone to aggregate at a pH far from its pI, particularly in the absence of NaCl. These seemingly contradicting results, higher conformational stability yet higher aggregation propensity near the pI than far away from the pI, can be explained by intramolecular and intermolecular electrostatic repulsion using Lumry-Eyring model, which separates folding/unfolding equilibrium and aggregation event. The further a pH from the pI, the higher the net charge of the protein. The higher net charge leads to greater intramolecular and intermolecular electrostatic repulsions. The greater intramolecular electrostatic repulsion destabilizes the protein and the greater intermolecular electrostatic repulsion prevents aggregation of the protein molecules at pH far from the pI.

Protein-protein interactions and reduced excluded volume increase dynamic binding capacity of dual salt systems in hydrophobic interaction chromatography

Deploying two salts in hydrophobic interaction chromatography can significantly increase dynamic binding capacities. Nevertheless, the mechanistic understanding of this phenomenon is lacking. Here, we investigate whether surface tension or ionic strength govern dynamic binding capacities of the chromatographic resin Toyopearl Butyl-650 M in dual salt systems. Small-angle X-ray scattering was employed to analyze the model proteins and the protein-resin adduct in the respective dual salt systems. The dual salt systems incorporate sodium citrate and a secondary sodium salt (acetate, sulfate, or phosphate). As model proteins, we used lysozyme, GFP, and a monoclonal antibody (adalimumab). Moreover, for the protein-resin adduct, we determined the model parameters of a self-avoiding random walk model fitted into the pair density distribution function of the SAXS data. Ionic strength is more predictive for dynamic binding capacities in HIC dual salt systems than surface tension. However, dynamic binding capacities still differ by up to 30 % between the investigated dual salt systems. The proteins exhibit extensive protein-protein interactions in the studied dual salt HIC buffers. We found a correlation of protein-protein interactions with the well-known Hofmeister series. For systems with elevated protein-protein interactions, adsorption isotherms deviate from Langmuirian behavior. This highlights the importance of lateral protein-protein interactions in protein adsorption, where monomolecular protein layers are usually assumed. SAXS analysis of the protein-resin adduct indicates an inverse correlation of the binding capacity and the excluded volume parameter. This is indicative of the deposition of proteins in the cavities of the stationary phase. We hypothesize that increasing protein-protein interactions allow the formation of attractive clusters and multilayers in the cavities, respectively.

Protein A does not induce allosteric structural changes in an IgG1 antibody during binding

Affinity chromatography is widely used for antibody purification in biopharmaceutical production. Although there is evidence suggesting that affinity chromatography might induce structural changes in antibodies, allosteric changes in structure have not been well-explored. Here, we used hydrogen exchange-mass spectrometry (HX-MS) to reveal conformational changes in the NIST mAb upon binding with a protein A (ProA) matrix. HX-MS measurements of NIST mAb bound to in-solution and resin forms of ProA revealed regions of the C_H2 and C_H3 domains with increased protection from HX upon ProA binding, consistent with the known ProA binding region. In-solution ProA experiments revealed regions in the F_ab with increased HX uptake when the ProA:mAb molar ratio was increased to 2:1, suggesting an allosterically induced increase in backbone flexibility. Such effects were not observed with lower ProA concentration (1:1 molar ratio) or when ProA resin was used, suggesting some kind of change in binding mode. Since all pharmaceutical processes use ProA bound to resin, our results rule out reversible allosteric effects on the NIST mAb during interaction with resin ProA. However, irreversible effects cannot be ruled out since the NIST mAb was previously exposed to ProA during its original purification.

Comparison of Huggins Coefficients and Osmotic Second Virial Coefficients of Buffered Solutions of Monoclonal Antibodies

The Huggins coefficient kH is a well-known metric for quantifying the increase in solution viscosity arising from intermolecular interactions in relatively dilute macromolecular solutions, and there has been much interest in this solution property in connection with developing improved antibody therapeutics. While numerous kH measurements have been reported for select monoclonal antibodies (mAbs) solutions, there has been limited study of kH in terms of the fundamental molecular interactions that determine this property. In this paper, we compare measurements of the osmotic second virial coefficient B22, a common metric of intermolecular and interparticle interaction strength, to measurements of kH for model antibody solutions. This comparison is motivated by the seminal work of Russel for hard sphere particles having a short-range "sticky" interparticle interaction, and we also compare our data with known results for uncharged flexible polymers having variable excluded volume interactions because proteins are polypeptide chains. Our observations indicate that neither the adhesive hard sphere model, a common colloidal model of globular proteins, nor the familiar uncharged flexible polymer model, an excellent model of intrinsically disordered proteins, describes the dependence of kH of these antibodies on B22. Clearly, an improved understanding of protein and ion solvation by water as well as dipole-dipole and charge-dipole effects is required to understand the significance of kH from the standpoint of fundamental protein-protein interactions. Despite shortcomings in our theoretical understanding of kH for antibody solutions, this quantity provides a useful practical measure of the strength of interprotein interactions at elevated protein concentrations that is of direct significance for the development of antibody formulations that minimize the solution viscosity.

An Efficient Conjugation Approach for Coupling Drugs to Native Antibodies via the PtII Linker Lx for Improved Manufacturability of Antibody-Drug Conjugates

The PtII linker [ethylenediamineplatinum(II)]2+ , coined Lx, has emerged as a novel non-conventional approach to antibody-drug conjugates (ADCs) and has shown its potential in preclinical in vitro and in vivo benchmark studies. A crucial improvement of the Lx conjugation reaction from initially <15 % to ca. 75-90 % conjugation efficiency is described, resulting from a systematic screening of all relevant reaction parameters. NaI, a strikingly simple inorganic salt additive, greatly improves the conjugation efficiency as well as the conjugation selectivity simply by exchanging the leaving chloride ligand on Cl-Lx-drug complexes (which are direct precursors for Lx-ADCs) for iodide, thus generating I-Lx-drug complexes as more reactive species. Using this iodide effect, we developed a general and highly practical conjugation procedure that is scalable: our lead Lx-ADC was produced on a 5 g scale with an outstanding conjugation efficiency of 89 %.

Tutorial: Chemistry of Hydrogen/Deuterium Exchange Mass Spectrometry

Chemistry related to hydrogen/deuterium exchange-mass spectrometry (HDX-MS) for the analysis of proteins is described. First, the HDX rates of various functional groups in proteins are explained by reviewing the observed rates described in the literature, followed by estimating rates of all types of heteroatom hydrogens in proteins using proton transfer theory and the pK_a values. The estimated HDX rates match well with the respective observed rates for most functional groups, with the exception of indole and amide groups. The discrepancies between the observed and estimated HDX rates for these groups are explained by the reaction mechanisms. Second, the factors that affect the HDX rates of backbone amide hydrogen, including side chain, N- and C-terminals, pH, temperature, organic solvent, and isotopes, are discussed. These factors are important for the proper design of exchange reactions and downstream process as well as the analysis and interpretation of HDX-MS data.

In-Use Interfacial Stability of Monoclonal Antibody Formulations Diluted in Saline i.v. Bags

The use of monoclonal antibodies (mAbs) for the treatment of a variety of diseases is rapidly growing each year. Many mAbs are administered intravenously using i.v. bags containing 0.9% NaCl (normal saline). We studied the aggregation propensity of these antibody solutions in saline and compared it with a low ionic strength formulation buffer. The mAb studied in this work is prone to aggregate, and is known to form a viscoelastic network at the air-solution interface. We observed that this interfacial elasticity increased when formulated in saline. In the bulk, the mAbs exhibited a tendency to self-associate that was higher in saline. We also studied the aggregation of the mAbs in the presence of polysorbate-20, typically added to formulations to mitigate interfacial aggregation. We observed that with surfactants, the presence of salt in the buffer led to a greater mAb adsorption at the interface and resulted in the formation of more particulate aggregates. Our results show that the addition of salt to the buffer led to differences in the interfacial aggregation in mAb formulations, showing that stress studies used to screen for mAb aggregation intended for i.v. administration should be performed in conditions representative of their intended route of administration.

Cation Specific Effects on the Domain-Domain Interaction of Heterogeneous Dimeric Protein Revealed by FRET Analysis

Specific monovalent cation effects on the domain-domain interaction of heterogeneous dimeric protein were investigated using green fluorescent protein (GFP)-glutathione-s-transferase (GST) fusion protein as a model protein. Conjugating N-terminal of GST domain with a fluorescence probe Cyanine3, complementary increase and decrease of fluorescence intensities of Cyanine3 and GFP were recognized on the exclusive excitation of GFP and further the fluorescence decay of GFP was remarkably accelerated to show that an excellent Förster type of resonance excitation energy transfer (FRET) pair was constructed between GFP- and GST-domain. The spectral overlap integral and critical distance of the FRET pair were estimated to be 5.96×10¹³ M^-1cm³ and 62.5 Å, respectively. The FRET rate and efficiency evaluated by fluorescence lifetime of the energy donor, GFP, were influenced by the monovalent cations included in the buffer solution to suggest that the domain-domain interactions of GFP-GST fusion protein would be susceptible to cation species and their concentrations. The order affecting the domain-domain interaction was estimated to be Li⁺>NH₄⁺ >Na⁺>K⁺>Cs⁺, almost corresponding to the reverse Hofmeister series.

FTIR Spectroscopy Study of the Secondary Structure Changes in Human Serum Albumin and Trypsin under Neutral Salts

The effect of neutral salts on protein conformation was first analyzed by Hofmeister in 1888, however, even today this phenomenon is not completely understood. To clarify this effect, we studied changes in the secondary structure of two proteins: human serum albumin with predominantly α-helical structure and porcine pancreas β-trypsin with the typical β-structural arrangement in aqueous solutions of neutral salts (KSCN, KCl, (NH₄)₂SO₄). The changes in the secondary structure were studied at 23 °C and 80 °C by using the second derivative deconvolution method of the IR spectra. Our results demonstrated that the ability of the salts to stabilize/destabilize these two proteins correlates with the Hofmeister series of ions. At the same time, some exceptions were also observed. The destabilization of the native structures of both α-helical albumin and β-structural trypsin upon interaction with neutral salts leads to the formation of intermolecular β-sheets typical for amyloid fibrils or amorphous aggregates. Thus, our quantitative FTIR-spectroscopy analysis allowed us to further clarify the mechanisms and complexity of the neutral salt actions on protein structures which may lead to strategies preventing unwelcome misfolding of proteins.

Model for Counterion Binding and Charge Reversal on Protein Surfaces

The structural stability and solubility of proteins in liquid therapeutic formulations is important, especially since new generations of therapeutics are designed for efficacy before consideration of stability. We introduce an electrostatic binding model to measure the net charge of proteins with bound ions in solution. The electrostatic potential on a protein surface is used to separately group together acidic and basic amino acids into patches, which are then iteratively bound with oppositely charged counterions. This model is aimed toward formulation chemists for initial screening of a range of conditions prior to lab-work. Computed results compare well with experimental zeta potential measurements from the literature covering a range of solution conditions. Importantly, the binding model reproduces the charge reversal phenomenon that is observed with polyvalent ion binding to proteins and its dependence on ion charge and concentration. Intriguingly, protein sequence can be used to give similarly good agreement with experiment as protein structure, interpreted as resulting from the close proximity of charged side chains on a protein surface. Further, application of the model to human proteins suggests that polyanion binding and overcharging, including charge reversal for cationic proteins, is a general feature. These results add to evidence that addition of polyanions to protein formulations could be a general mechanism for modulating solution stability.

Double-edged effects of aluminium ions on amyloid fibrillation of hen egg-white lysozyme

Elucidating the effects of Al(III) ions on amyloid fibrillation is important to understand the association between metal ions and Alzheimer's disease. Here, Raman spectroscopy was applied to investigate amyloid fibrillation of hen egg-white lysozymes during thermal incubation with Al(III) ions or acids, combined with atomic force microscopy and thioflavin T fluorescence assays. Kinetics of conformational changes in lysozymes were assessed by monitoring six characteristic Raman spectral markers. The peak of Phe residues at 1003 cm^-1 and two bands of Trp residues at 759 cm^-1 and 1340-1360 cm^-1 corresponded to the lysozyme tertiary structure, whereas two NC_αC stretching vibrations at 899 cm^-1 and 935 cm^-1 and an amide I band were associated with the lysozyme skeleton. There may be a four-stage transformation mechanism underlying the kinetics of amyloid fibrillation of lysozymes with the thermal/Al(III) treatment. Comparison of kinetics under thermal/Al(III) and thermal/acid conditions revealed double-edged roles of Al(III) ions in amyloid fibrillation of lysozymes. Specifically, in addition to postponing α-helix degradation, Al(III) ions accelerated conformational transformations from α-helices to organized β-sheets. The present investigation sheds light on the controversial effects of Al(III) ions on amyloid fibrillation of lysozymes.

Current Trends in Biotherapeutic Higher Order Structure Characterization by Irreversible Covalent Footprinting Mass Spectrometry

BACKGROUND

Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing class of drugs capable of treating a wide range of diseases. Therapeutic function and solutionstability are linked to the proper three-dimensional organization of the primary sequence into Higher Order Structure (HOS) as well as the timescales of protein motions (dynamics). Methods that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant protein-protein interactions and assessing properly folded structures. Irreversible covalent protein footprinting Mass Spectrometry (MS) tools, such as site-specific amino acid labeling and hydroxyl radical footprinting are analytical techniques capable of monitoring the side chain solvent accessibility influenced by tertiary and quaternary structure. Here we discuss the methodology, examples of biotherapeutic applications, and the future directions of irreversible covalent protein footprinting MS in biotherapeutic research and development.

CONCLUSION

Bottom-up mass spectrometry using irreversible labeling techniques provide valuable information for characterizing solution-phase protein structure. Examples range from epitope mapping and protein-ligand interactions, to probing challenging structures of membrane proteins. By paring these techniques with hydrogen-deuterium exchange, spectroscopic analysis, or static-phase structural data such as crystallography or electron microscopy, a comprehensive understanding of protein structure can be obtained.

Do soft anions promote protein denaturation through binding interactions? A case study using ribonuclease A

It has long been known that large soft anions like bromide, iodide and thiocyanate are protein denaturing agents, but their mechanism of action is still unclear. In this work we have investigated the protein denaturing properties of these anions using Ribonuclease A (RNase A) as a model protein system. Salt-induced perturbations to the protein folding free energy were determined using differential scanning calorimetry and the results demonstrate that the addition of sodium iodide and sodium thiocyanate significantly decreases the melting temperature of the protein. In order to account for this reduction in protein stability, we show that the introduction of salts that contain soft anions to the aqueous solvent perturbs the protein unfolding free energy through three mechanisms: (a) screening Coulomb interactions that exist between charged protein residues, (b) Hofmeister effects, and (c) specific anion binding to CH and CH2 moieties in the protein polypeptide backbone. Using the micellization of 1,2-hexanediol as a ruler for hydrophobicity, we have devised a practical methodology that separates the Coulomb and Hofmeister contributions of salts to the protein unfolding free energy. This allowing us to isolate the contribution of soft anion binding interactions to the unfolding process. The analysis shows that binding contributions have the largest magnitude, confirming that it is the binding of soft anions to the polypeptide backbone that is the main promoter of protein unfolding.

Probing Conformational Diversity of Fc Domains in Aggregation-Prone Monoclonal Antibodies

PURPOSE

Fc domains are an integral component of monoclonal antibodies (mAbs) and Fc-based fusion proteins. Engineering mutations in the Fc domain is a common approach to achieve desired effector function and clinical efficacy of therapeutic mAbs. It remains debatable, however, whether molecular engineering either by changing glycosylation patterns or by amino acid mutation in Fc domain could impact the higher order structure of Fc domain potentially leading to increased aggregation propensities in mAbs.

METHODS

Here, we use NMR fingerprinting analysis of Fc domains, generated from selected Pfizer mAbs with similar glycosylation patterns, to address this question. Specifically, we use high resolution 2D [¹³C-¹H] NMR spectra of Fc fragments, which fingerprints methyl sidechain bearing residues, to probe the correlation of higher order structure with the storage stability of mAbs. Thermal calorimetric studies were also performed to assess the stability of mAb fragments.

RESULTS

Unlike NMR fingerprinting, thermal melting temperature as obtained from calorimetric studies for the intact mAbs and fragments (Fc and Fab), did not reveal any correlation with the aggregation propensities of mAbs. Despite >97% sequence homology, NMR data suggests that higher order structure of Fc domains could be dynamic and may result in unique conformation(s) in solution.

CONCLUSION

The overall glycosylation pattern of these mAbs being similar, these conformation(s) could be linked to the inherent plasticity of the Fc domain, and may act as early transients to the overall aggregation of mAbs.

Interrogating the Osmotic Pressure of Self-Crowded Bovine Serum Albumin Solutions: Implications of Specific Monovalent Anion Effects Relative to the Hofmeister Series

The free-solvent-based (FSB) model and osmotic pressure were used to probe the ion binding and protein hydration for self-crowded bovine serum albumin in 0.15 M NaF, NaCl, NaI, and NaSCN solutions. All experiments were conducted with solutions at pH 7.4. The regressed results of the FSB model behavior to the measured osmotic pressure were excellent, albeit, the osmotic pressure data for NaSCN were noisy. The resulting ion binding and hydration were realistic values and the covariance of the two parameters was exceptionally low, providing substantial credibility to the FSB model. The results showed that the kosmotropic F^- and neutral Cl^- solutions generated significantly higher ion binding and protein hydration than the chaotropic solutions of I^- and SCN^-. Further, the ionic strength ratio and resulting hydration implied that the chaotropic solutions had substantially higher aggregation than the other salts investigated. Overall, the FSB model provides an additional, complementary tool to contribute to the analysis of crowded protein solutions relative to anions in the Hofmeister series as it can interrogate crowded solutions directly; something that is not possible with many measurement techniques.

Conformational Assessment of Adnectin and Adnectin-Drug Conjugate by Hydrogen/Deuterium Exchange Mass Spectrometry

Higher-order structure (HOS) characterization of therapeutic protein-drug conjugates for comprehensive assessment of conjugation-induced protein conformational changes is an important consideration in the biopharmaceutical industry to ensure proper behavior of protein therapeutics. In this study, conformational dynamics of a small therapeutic protein, adnectin 1, together with its drug conjugate were characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS) with different spatial resolutions. Top-down HDX allows detailed assessment of the residue-level deuterium content in the payload conjugation region. HDX-MS dataset revealed the ability of peptide-based payload/linker to retain deuterium in HDX experiments. Combined results from intact, top-down, and bottom-up HDX indicated no significant conformational changes of adnectin 1 upon payload conjugation. Graphical Abstract ᅟ.

Impact of Glycosylation on the Local Backbone Flexibility of Well-Defined IgG1-Fc Glycoforms Using Hydrogen Exchange-Mass Spectrometry

We have used hydrogen exchange-mass spectrometry to characterize local backbone flexibility of 4 well-defined IgG1-Fc glycoforms expressed and purified from Pichia pastoris, 2 of which were prepared using subsequent in vitro enzymatic treatments. Progressively decreasing the size of the N-linked N297 oligosaccharide from high mannose (Man8-Man12), to Man5, to GlcNAc, to nonglycosylated N297Q resulted in progressive increases in backbone flexibility. Comparison of these results with recently published physicochemical stability and Fcγ receptor binding data with the same set of glycoproteins provide improved insights into correlations between glycan structure and these pharmaceutical properties. Flexibility significantly increased upon glycan truncation in 2 potential aggregation-prone regions. In addition, a correlation was established between increased local backbone flexibility and increased deamidation at asparagine 315. Interestingly, the opposite trend was observed for oxidation of tryptophan 277 where faster oxidation correlated with decreased local backbone flexibility. Finally, a trend of increasing C'E glycopeptide loop flexibility with decreasing glycan size was observed that correlates with their FcγRIIIa receptor binding properties. These well-defined IgG1-Fc glycoforms serve as a useful model system to identify physicochemical stability and local backbone flexibility data sets potentially discriminating between various IgG glycoforms for potential applicability to future comparability or biosimilarity assessments.

Modification of the kinetic stability of immunoglobulin G by solvent additives

Biophysical properties of antibody-based biopharmaceuticals are a critical part of their release criteria. In this context, finding the appropriate formulation is equally important as optimizing their intrinsic biophysical properties through protein engineering, and both are mutually dependent. Most previous studies have empirically tested the impact of additives on measures of colloidal stability, while mechanistic aspects have usually been limited to only the thermodynamic stability of the protein. Here we emphasize the kinetic impact of additives on the irreversible denaturation steps of immunoglobulins G (IgG) and their antigen-binding fragments (Fabs), as these are the key committed steps preceding aggregation, and thus especially informative in elucidating the molecular parameters of activity loss. We examined the effects of ten additives on the conformational kinetic stability by differential scanning calorimetry (DSC), using a recently developed three-step model containing both reversible and irreversible steps. The data highlight and help to rationalize different effects of the additives on the properties of full-length IgG, analyzed by onset and aggregation temperatures as well as by kinetic parameters derived from our model. Our results further help to explain the observation that stabilizing mutations in the antigen-binding fragment (Fab) significantly affect the kinetic parameters of its thermal denaturation, but not the aggregation properties of the full-length IgGs. We show that the proper analysis of DSC scans for full-length IgGs and their corresponding Fabs not only helps in ranking their stability in different formats and formulations, but provides important mechanistic insights for improving the conformational kinetic stability of IgGs.

MS-based conformation analysis of recombinant proteins in design, optimization and development of biopharmaceuticals

Mass spectrometry (MS)-based methods for analyzing protein higher order structures have gained increasing application in the field of biopharmaceutical development. The predominant methods used in this area include native MS, hydrogen deuterium exchange-MS, covalent labeling, cross-linking and limited proteolysis. These MS-based methods will be briefly described in this article, followed by a discussion on how these methods contribute at different stages of discovery and development of protein therapeutics.

Investigating the dynamics and polyanion binding sites of fibroblast growth factor-1 using hydrogen-deuterium exchange mass spectrometry

In this study, we examined the local dynamics of acidic fibroblast growth factor (FGF-1) as well as the binding sites of various polyanions including poly-sulfates (heparin and low MW heparin) and poly-phosphates (phytic acid and ATP) using hydrogen-deuterium exchange mass spectrometry (HX-MS). For local dynamics, results are analyzed at the peptide level as well as in terms of buried amides employing crystallographic B-factors and compared with a residue level heat map generated from HX-MS results. Results show that strand 4 and 5 and the turn between them to be the most flexible regions as was previously seen by NMR. On the other hand, the C-terminal strands 8, 9, and 10 appear to be more rigid which is also consistent with crystallographic B-factors as well as local dynamics studies conducted by NMR. Crystal structures of FGF-1 in complex with heparin have shown that heparin binds to N-terminal Asn18 and to C-terminal Lys105, Tryp107, Lys112, Lys113, Arg119, Pro121, Arg122, Gln127, and Lys128 indicating electrostatic forces as dominant interactions. Heparin binding as determined by HX-MS is consistent with crystallography data. Previous studies have also shown that other polyanions including low MW heparin, phytic acid and ATP dramatically increase the thermal stability of FGF-1. Using HX-MS, we find other poly anions tested bind in a similar manner to heparin, primarily targeting the turns in the lysine rich C-terminal region of FGF-1 along with two distinct N-terminal regions that contains lysines and arginines/histidines. This confirms the interactions between FGF-1 and polyanions are primary directed by electrostatics.

Understanding the Increased Aggregation Propensity of a Light-Exposed IgG1 Monoclonal Antibody Using Hydrogen Exchange Mass Spectrometry, Biophysical Characterization, and Structural Analysis

This work compares the conformational stability, backbone flexibility, and aggregation propensity of monomer and dimer fractions of an IgG1 monoclonal antibody (mAb) generated on UVA light exposure for up to 72 h collected by preparative size-exclusion chromatography, compared with unstressed control. UVA light exposure induced covalent aggregation, and fragmentation as measured by size-exclusion chromatography, sodium dodecyl sulfate polyacrylamide gel electrophoresis, and extensive oxidation of specific methionine residues (Met 257, Met 433, and Met 109) in both size fractions identified by reverse phase chromatography coupled to mass spectrometry. Compared with unstressed mAb, both the monomer and dimer fractionated from 72 h UVA light-exposed mAb had decreased thermal melting temperatures (T_m1) by 1.4°C as measured by differential scanning calorimetry, minor changes in tertiary structure as measured by near-UV CD, increased monomer loss, and aggregation on accelerated storage at 35°C. Hydrogen/deuterium exchange mass spectrometry identified local segments with increased flexibility in C_H2 and C_H3 domains of both size fractions, and decreased flexibility in few segments of F_ab and C_H1 domains in the dimer fraction. Segment 247-256 in heavy chain, an established aggregation hotspot in IgG1 mAbs had large increase in flexibility in both size fractions compared with unstressed mAb.

Analysis of IgG kinetic stability by differential scanning calorimetry, probe fluorescence and light scattering

Monoclonal antibodies of the immunoglobulin G (IgG) type have become mainstream therapeutics for the treatment of many life-threatening diseases. For their successful application in the clinic and a favorable cost-benefit ratio, the design and formulation of these therapeutic molecules must guarantee long-term stability for an extended period of time. Accelerated stability studies, e.g., by employing thermal denaturation, have the great potential for enabling high-throughput screening campaigns to find optimal molecular variants and formulations in a short time. Surprisingly, no validated quantitative analysis of these accelerated studies has been performed yet, which clearly limits their application for predicting IgG stability. Therefore, we have established a quantitative approach for the assessment of the kinetic stability over a broad range of temperatures. To this end, differential scanning calorimetry (DSC) experiments were performed with a model IgG, testing chaotropic formulations and an extended temperature range, and they were subsequently analyzed by our recently developed three-step sequential model of IgG denaturation, consisting of one reversible and two irreversible steps. A critical comparison of the predictions from this model with data obtained by an orthogonal fluorescence probe method, based on 8-anilinonaphthalene-1-sulfonate binding to partially unfolded states, resulted in very good agreement. In summary, our study highlights the validity of this easy-to-perform analysis for reliably assessing the kinetic stability of IgGs, which can support accelerated formulation development of monoclonal antibodies by ranking different formulations as well as by improving colloidal stability models.

Protein Partial Molar Volumes in Multicomponent Solutions from the Perspective of Inverse Kirkwood-Buff Theory

Inverse Kirkwood-Buff (KB) solution theory can be used to relate macroscopic quantities with molecular scale interactions and correlation functions, in the form of KB integrals. Protein partial specific volumes ([Formula: see text]) from high-precision density measurements can be used to quantify solvent-solute and solute-solute KB integrals. Currently, general expressions for [Formula: see text] as a function of cosolute concentration (c₃) have been provided for only binary and ternary solutions. We derive a general multicomponent expression for [Formula: see text] in terms of the relevant KB integrals for the case of low (infinite dilution) protein concentration but arbitrary cosolute concentrations. To test the utility of treating a quaternary system with a pseudoternary approximation, α-Chymotrypsinogen (aCgn) solutions with a series of solutes (NaCl, sucrose, and trehalose) were compared as a function of solute concentration with and without buffer present. Comparison between those ternary and quaternary solutions shows equivalent results within experimental uncertainty and suggests the pseudoternary approximation may be reasonable. In the case of aCgn, doing so also revealed that the preferential interactions can depend on pH. Analysis of steric contributions also provides an example that illustrates how KB integrals allow one to interpret [Formula: see text] in terms of contributions from molecular volume, excluded volume, and hydration/solvation effects.