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Inert co-solutes, or excipients, are often included in protein biologic formulations to adjust the tonicity of liquid dosage forms intended for subcutaneous delivery. Despite the low concentration of their use, many of these excipients alter protein-protein interactions such as dimerization and aggregation rates of high concentration monoclonal antibody (mAb) therapeutics to varying extents during long-term refrigerated clinical storage, challenging the formulation scientist to make informed excipient selections at the earliest stages of development when protein supply and time are often limited. The objectives of this study were to better understand how isotonic concentrations of excipients influence the dimerization rates of a model mAb stored at refrigerated and room temperatures and explore protein sparing biophysical methods capable of predicting this dependence. Despite their prevalence of use in the biopharmaceutical industry, methods for assessing conformational stability such differential scanning calorimetry and isothermal equilibrium unfolding showed little predictive power and we highlight some of the assumptions and technical challenges of their use with mAbs. Conversely, measures of colloidal stability of the native-state such as preferential interaction coefficients measured by vapor pressure osmometry and solubility assessed by polyethylene-glycol induced precipitation correlated reasonably well with the mAb dimerization data and are most consistent with the excipients tested minimizing dimerization by interacting favorably with the residues comprising the protein-protein association interface.

Isotonic concentrations of inert cosolutes or excipients are routinely used in protein therapeutic formulations to minimize physical instabilities including aggregation, particulation, and precipitation that are often manifested during drug substance/product manufacture and long-term storage. Despite their prevalent use within the biopharmaceutical industry, a more detailed understanding for how excipients modulate the specific protein-protein interactions responsible for these instabilities is still needed so that informed formulation decisions can be made at the earliest stages of development when protein supply and time are limited. In the present report, subisotonic concentrations of the five common formulation excipients, sucrose, proline, sorbitol, glycerol, arginine hydrochloride, and the denaturant urea, were studied for their effect on the room temperature liquid-liquid phase separation of a model monoclonal antibody (mAb-B). Although each excipient lowered the onset temperatures of mAb-B liquid-liquid phase separation to different extents, all six were found to be preferentially excluded from the native state monomer by vapor pressure osmometry, and no apparent correlations to the excipient dependence of mAb-B melting temperatures were observed. These results and those of the effects of solution pH, addition of salt, and impact of a small number of charge mutations were most consistent with a mechanism of local excipient accumulation, to an extent dependent on their type, with the specific residues that mediate mAb-B electrostatic protein-protein interactions. These findings suggest that selection of excipients on the basis of their interaction with the solvent exposed residues of the native state may at times be a more effective strategy for limiting protein-protein interactions at pharmaceutically relevant storage conditions than choosing those that are excluded from the residues of the native state interior.

Inert co‐solutes, or excipients, are often included in protein biologic formulations to adjust the tonicity of liquid dosage forms intended for subcutaneous delivery. Despite the low concentration of their use, many of these excipients alter protein–protein interactions such as dimerization and aggregation rates of high concentration monoclonal antibody (mAb) therapeutics to varying extents during long‐term refrigerated clinical storage, challenging the formulation scientist to make informed excipient selections at the earliest stages of development when protein supply and time are often limited. The objectives of this study were to better understand how isotonic concentrations of excipients influence the dimerization rates of a model mAb stored at refrigerated and room temperatures and explore protein sparing biophysical methods capable of predicting this dependence. Despite their prevalence of use in the biopharmaceutical industry, methods for assessing conformational stability such differential scanning calorimetry and isothermal equilibrium unfolding showed little predictive power and we highlight some of the assumptions and technical challenges of their use with mAbs. Conversely, measures of colloidal stability of the native‐state such as preferential interaction coefficients measured by vapor pressure osmometry and solubility assessed by polyethylene–glycol induced precipitation correlated reasonably well with the mAb dimerization data and are most consistent with the excipients tested minimizing dimerization by interacting favorably with the residues comprising the protein–protein association interface.

Protein stability, one of the major concerns for therapeutic protein development, can be optimized during process development by evaluating multiple formulation conditions. This can be a costly and lengthy procedure where different excipients and storage conditions are tested for their impact on protein stability. A better understanding of the effects of different formulation conditions at the molecular level will provide information on the local interactions within the protein leading to a more rational design of stable and efficacious formulations. In this study, we examined the roles of the excipients, sucrose and benzyl alcohol, on the conformational dynamics of recombinant human granulocyte colony stimulating factor using hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS). Under physiological pH and temperature, sucrose globally protects the whole molecule from deuterium uptake, whereas benzyl alcohol induces increased deuterium uptake of the regions within the a-helical bundle, with even larger extent. The HDX experiments described were incorporated a set of internal peptides (Zhang et al., 2012. Anal Chem 84:4942–4949) to monitor the differences in intrinsic exchange rates in different formulations. In addition, we discussed the feasibility of implementing HDX-MS with these peptide probes in protein formulation development.

Previous equilibrium and kinetic folding studies of the glycoprotein erythropoietin indicate that sodium chloride increases the conformational stability of this therapeutically important cytokine, ostensibly by stabilizing the native-state [Banks DD, (2011) The Effect of Glycosylation on the Folding Kinetics of Erythropoietin. J Mol Biol 412:536–550]. The focus of the current report is to determine the underlying cause of the salt dependent increase in erythropoietin conformational stability and to understand if it has any impact on aggregation, an instability that remains a challenge to the biotech industry in maintaining the efficacy and shelf-life of protein therapeutics. Isothermal urea denaturation experiments conducted at numerous temperatures in the absence and presence of sodium chloride indicated that salt stabilizes erythropoietin primarily by increasing the difference in enthalpy between the native and unfolded sates. This result, and the finding that the salt induced increases in erythropoietin melting temperatures were independent of the identity of the salt cation and anion, indicates that salt likely increases the conformational stability of erythropoietin at neutral pH by nonspecific shielding of unfavorable electrostatic interaction(s) in the native-state. The addition of salt (even low concentrations of the strong chaotrope salt guanidinium hydrochloride) also exponentially decreased the initial rate of soluble erythropoietin non-native aggregation at 37 °C storage.

In the present report, two formulation strategies, based on different aggregation models, were compared for their ability to quickly predict which excipients (cosolutes) would minimize the aggregation rate of an immunoglobulin G1 monoclonal antibody (mAb-1) stored for long term at refrigerated and room temperatures. The first formulation strategy assumed that a conformational change to an aggregation-prone intermediate state was necessary to initiate the association process and the second formulation strategy assumed that protein self-association was instead controlled by the solubility of the native state. The results of these studies indicate that the stabilizing effect of excipients formulated at isotonic concentrations is derived from their ability to solubilize the native state, not by the increase of protein conformational stability induced by their presence. The degree the excipients solvate the native state was determined from the apparent transfer free energy of the native state from water into each of the excipients. These values for mAb-1 and two additional therapeutic antibodies correlated well to their long-term 4°C and room temperature aggregation data and were calculated using only the literature values for the apparent transfer free energies of the amino acids into the various excipients and the three-dimensional models of the antibodies.

The antibody MAB007 was recently shown to be cysteinylated on an unpaired cysteine residue in the CDR3 variable region. Cysteinylation at this position was not complete and resulted in heterogeneous lots of MAB007 with respect to this posttranslational modification. In this report, a mild redox step was used that effectively removed cysteinylation while keeping native inter and intra-molecular disulfide bonds intact. Biophysical methods were employed to determine what consequences cysteinylation of the variable region had by directly comparing cysteinylated and de-cysteinylated MAB007 antibodies. No differences were detected in secondary structure; however, several pieces of evidence indicated that cysteinylation may result in tertiary or quaternary structural perturbations. These included differences in the cation-exchange chromatography and fluorescence-emission spectra of the cysteinylated and de-cysteinylated antibodies as well as differences in the solvent accessibility of the unpaired cysteine residue determined by labeling experiments. Such structural changes induced by cysteinylation were shown to increase the rate of MAB007 aggregation and to decrease the melting temperature of the Fab region by as much as 6 degrees C. The bioactivity of MAB007 was also shown to be adversely affected by cysteinylation and a direct correlation was made between the percent cysteinylation and biological activity.

Studies of the folding mechanisms of monomeric proteins have been a major focus in efforts to describe the protein folding code: how a protein’s primary structure encodes its unique, three-dimensional structure as well as the pathway to this native state from an unfolded, random coil ensemble of states. The folding kinetics of small, single-domain model systems can often be described by a rapid, two-state mechanism (for reviews, see Jackson 1998; Plaxco et al. 2000; Daggett and Fersht 2003). In contrast, the folding kinetics of larger, multidomain monomeric proteins are often more complex, requiring the coordination of long-range interdomain and short-range intradomain interactions (for reviews, see Kim and Baldwin 1990; Matthews 1993; Wallace and Matthews 2002). Significant insights have been gained from monomeric folding systems regarding the intramolecular forces responsible for the productive formation and stabilization of secondary and tertiary structures as the folding energy landscape is successfully and efficiently traversed. However, it is not yet clear how these insights apply to the intermolecular association reactions that stabilize the quaternary structure of oligomeric proteins. Oligomeric proteins are prevalent in biology and offer evolutionary advantages such as the potential of increased thermostability relative to mono mers and sensitive regulation through allostery and cooper ativity in ligand binding. The folding of oligomeric proteins requires that the protein folding code direct the formation of intramolecular secondary and tertiary structure as well as the productive quaternary interactions necessary for biologi cal function. Folding experiments on large, oligomeric en zymes demonstrated the complexity of this coordination of multiple levels of structure formation (for reviews, see Jaenicke 1987; Jaenicke and Lilie 2000). A lack of reversibil ity, often resulting from aggregation, is a complication in the folding of many proteins, and particularly oligomeric systems. Protein concentration-dependent, nonproductive aggregation reactions often kinetically compete with on pathway, partially folded, kinetic intermediates in large oligomeric proteins (Seckler 2000). In vivo, this competition between productive folding and aggregation is often offset by the assistance of chaperones. Given these complexities, recent efforts have focused on smaller oligomeric folding model systems. Small (less than 60 residues per monomer), dimeric, two-state folding sys tems have been identified, for example the P22 Arc repres sor (Milla and Sauer 1994; Srivastava and Sauer 2000) and the GCN-4-derived leucine zipper peptides (Zitzewitz et al 1995, 2000). However, just as with monomeric systems, larger dimers, containing subdomains, tend to traverse more complicated folding landscapes, with transient kinetic inter mediates and sometimes parallel pathways. Examples in clude ketosteroid isomerases (Kim et al. 2001a,b), Esche richia coli Trp repressor (Gittelman and Matthews 1990; Mann et al. 1995; Gloss et al. 2001), glutathione transfer ases (Wallace et al. 1998; Wallace and Dirr 1999), and bacterial luciferase (Clark et al. 1997; Noland et al. 1999; Inlow and Baldwin 2002). Both monomeric and dimeric kinetic intermediates have been observed, but as yet, no clear rules are discernable for the prediction of the features of the folding landscape of dimeric proteins. This article investigates the folding reactions of the his tone fold motif, using the (H3–H4)2 tetramer (Fig. 1 ▶) as model system. The histone fold is a dimerization motif found in several important protein–DNA complexes. The fold was first structurally characterized in the eukaryotic heterodimers of the core nucleosome—the (H3–H4)2 tetramer and the H2A–H2B heterodimer (Arents et al. 1991; Luger et al. 1997a). The motif is also seen in the struc tures of homodimeric archael histones (Starich et al. 1996; Zhu et al. 1998; Decanniere et al. 2000) and some of the TATA-binding protein Associated Factors (TAFs) of the TFIID complex (Xie et al. 1996; Birck et al. 1998). Sequence alignments have suggested that many other DNA binding proteins may also contain the histone fold dimerization motif (Arents and Moudrianakis 1995; Baxevanis et al. 1995). Figure 1. Ribbon structure of the histone fold and the dimer–dimer interface of the H3–H4 tetramer. The H3 monomers, from residues 38–135 of 135, are shown in a lighter gray; the darker-colored H4 monomers encompass residues 20–102 ... The histone fold contains a long central α-helix that is flanked on both the N and C termini by short β-loops and shorter α-helices (Arents et al. 1991; Luger et al. 1997a). The histone monomers associate to form dimers in a head-to-tail fashion called the “handshake motif” (Arents and Moudrianakis 1995). Two H3–H4 dimers then dimerize with one another through a four-helix bundle of their H3 C-terminal helical regions. Thus, the folding of the (H3–H4)2 tetramer requires the coordinated folding of four polypeptide chains and the assembly of two dimerization interfaces. To date, biophysical characterization of the eukaryotic histones has focused on the equilibrium stabilities of the oligomers (Baxevanis et al. 1991; Karantza et al. 1995, 1996 Karantza et al. 2001; Gloss and Placek 2002; Placek and Gloss 2002; Banks and Gloss 2003). The equilibrium stability of recombinant (H3–H4)2 tetramer was determined by GdnHCl-induced denaturation, using fluorescence and circular dichroism spectroscopies (Banks and Gloss 2003). At moderate ionic strength (μ ~ 0.2 M), H3–H4 is unstable, with little native baseline in the unfolding transition. Therefore, tri-methylamine-N-oxide (TMAO) was used to stabilize the tetramer to obtain accurate thermodynamic parameters. The equilibrium unfolding of the (H3–H4)2 tetramer was best described by a three-state mechanism, with well-folded H3–H4 dimers as a populated intermediate. When compared to the structurally similar H2A–H2B dimer, the H3–H3′ tetramer interface and the H3–H4 histone fold are strikingly less stable (Banks and Gloss 2003). This article provides the first report of kinetic folding studies and a proposed folding mechanism for an oligomer containing the histone fold.

An inexpensive and quick deoxygenation system for measuring protein phosphorescence is described. Oxygen was first reduced to less than 1 ppb from nitrogen or other inert gas by passing through an oxygen trap. The oxygen-free gas was routed through stainless steel tubing directly into the sample compartment of the phosphorimeter. Flexible tubing, coupled to the stainless steel tubing, was run through the septum of a cuvette sealed with a gray butyl rubber lyophilization stopper. The flexible tubing allowed for manipulation of the cuvette during alternate cycles of vacuuming and nitrogen equilibration. Utility of the system was demonstrated by measuring the phosphorescence lifetimes of N-acetyl-L-tryptophanamide, alkaline phosphatase, human serum albumin, and recombinant human serum albumin. Phosphorescence lifetimes of 2 ms for N-acetyl-L-tryptophanamide, almost double that previously reported, were routinely achieved while a lifetime of 1.84 s was obtained for alkaline phosphatase, well within the reported range of 1.5-2s. Human serum albumin, which contains a single tryptophan, showed a biexponential decay with lifetimes of 4.33 and 17 ms, in contrast to previous reports of a biexponential decay with rates of 0.2 and 0.9 ms. Recombinant human serum albumin was even more striking with lifetimes of 4.60 and 68.2 ms. The data are explained based on the recently published X-ray crystallographic structure of human serum albumin. The simplicity and reproducibility of the system should make this technique practical for most biochemical labs.

To compare the stability of structurally related dimers and to aid in understanding the thermodynamics of nucleosome assembly, the equilibrium stabilities of the recombinant wild-type H3-H4 tetramer and H2A-H2B dimer have been determined by guanidinium-induced denaturation, using fluorescence and circular dichroism spectroscopies. The unfolding of the tetramer and dimer are highly reversible. The unfolding of the H2A-H2B dimer is a two-state process, with no detected equilibrium intermediates. The H3-H4 tetramer is unstable at moderate ionic strengths (mu approximately 0.2 M). TMAO (trimethylamine-N-oxide) was used to stabilize the tetramer; the stability of the H2A-H2B dimer was determined under the same solvent conditions. The equilibrium unfolding of H3-H4 was best described by a three-state mechanism, with well-folded H3-H4 dimers as a populated intermediate. When compared to H2A-H2B, the H3-H3 tetramer interface and the H3-H4 histone fold are strikingly less stable. The free energy of unfolding, in the absence of denaturant, for the H3-H4 and H2A-H2B dimers are 12.4 and 21.0 kcal mol(-)(1), respectively, in 1 M TMAO. It is postulated that the difference in stability between the histone dimers, which contain the same fold, is the result of unfavorable tertiary interactions, most likely the partial to complete burial of three salt bridges and burial of a charged hydrogen bond. Given the conservation of these buried interactions in histones from yeast to mammals, it is speculated that the H3-H4 tetramer has evolved to be unstable, and this instability may relate to its role in nucleosome dynamics.

The extremely halophilic Archae require near-saturating concentrations of salt in the external environment and in their cytoplasm, potassium being the predominant intracellular cation. The proteins of these organisms have evolved to function in concentrations of salt that inactivate or precipitate homologous proteins from non-halophilic species. It has been proposed that haloadaptation is primarily due to clustering of acidic residues on the surface of the protein, and that these clusters bind networks of hydrated ions. The dihydrofolate reductases from Escherichia coli (ecDHFR) and two DHFR isozymes from Haloferax volcanii (hvDHFR1 and hvDHFR2) have been used as a model system to compare the effect of salts on a mesophilic and halophilic enzyme. The KCl-dependence of the activity and substrate affinity was investigated. ecDHFR is largely inactivated above 1M KCl, with no major effect on substrate affinity. hvDHFR1 and hvDHFR2 unfold at KCl concentrations below approximately 0.5M. Above approximately 1M, the KCl dependence of the hvDHFR activities can be attributed to the effect of salt on substrate affinity. The abilities of NaCl, KCl, and CsCl to enhance the stability to urea denaturation were determined, and similar efficacies of stabilization were observed for all three DHFR variants. The DeltaG degrees (H(2)O) values increased linearly with increasing KCl and CsCl concentrations. The increase of DeltaG degrees (H(2)O) as a function of the smallest cation, NaCl, is slightly curved, suggesting a minor stabilization from cation binding or screening of electrostatic repulsion. At their respective physiological ionic strengths, the DHFR variants exhibit similar stabilities. Salts stabilize ecDHFR and the hvDHFRs by a common mechanism, not a halophile-specific mechanism, such as the binding of hydrated salt networks. The primary mode of salt stabilization of the mesophilic and halophilic DHFRs appears to be through preferential hydration and the Hofmeister effect of salt on the activity and entropy of the aqueous solvent. In support of this conclusion, all three DHFRs are similarly stabilized by the non-ionic cosolute, sucrose.

Prescreening methods are needed in the biotechnology industry for rapid selection of protein therapeutic candidates and formulations of low aggregation propensity. In recent reports solubility measurements have shown promise as one such method, although the connection between protein solubility and non-native aggregation is not well understood. In the present investigation, recombinant human granulocyte colony stimulating factor (rhGCSF) was used to explore this relationship since it was previously shown to rapidly undergo non-native aggregation/precipitation under physiological conditions in a reaction attenuated by the addition of sucrose [Krishnan, S.; et al. Biochemistry 2002, 41, 6422-6431]. Strong correlations were found between rhGCSF non-native aggregation and both solubility and thermal stability as a function of sucrose concentration. We believe these results make sense in the context of an rhGCSF aggregation mechanism where loss of monomer to insoluble aggregate is limited by association to an observable dimer from a less soluble (and aggregation competent) intermediate species that exists in a temperature sensitive pre-equilibrium with the native monomer. Both solubility and measures of conformational stability report on the position of this equilibrium and therefore the concentration of reactive intermediate. Interestingly, aggregation also correlated with rhGCSF solubility as a function of salting-in concentrations of phosphate since both are dependent on the colloidal stability of the reactive intermediate but not with conformational stability. In lieu of a complete understanding of the aggregation processes that limit protein therapeutic shelf life, these results highlight the potential of using simple solubility measurements as an additional tool in the biotechnology prescreening repertoire.

In biopharmaceutical process development, it is desirable to identify sites of covalent degradations to ensure product consistency. One characterization method used for therapeutic immunoglobulin gamma (IgG) 1 antibodies is limited LysC proteolysis followed by reversed-phase LC/MS. Limited LysC proteolysis leads to high efficiency cleavage at the C-terminal side of the hinge lysine 222 residue, generating Fab and Fc fragments. In this report, we show that IgG 1 samples incubated under mildly acidic conditions at elevated temperatures were partially resistant to LysC cleavage at the hinge and resulted in a species where one of the Fab arms remained connected to the Fc region (Fab-Fc). The growth of the Fab-Fc species was proportional to the duration and storage temperature of the incubation period and correlated with the amount of isomerization of the aspartic acid residue preceding lysine 222, determined by peptide mapping. The isomerization rates of samples stored for up to one year at 4 degrees C, 6 months at 29 or 37 degrees C, or 3 months at 45 degrees C were determined, and the activation energy for this conversion was calculated to be approximately 33 kJ mol(-1). The apparent isomerization rate constant was only 0.02 week(-1) for samples stored at 4 degrees C, which resulted in a modest increase from 5.1 to 6.0% isoD after twenty four weeks of storage and, hence, is not a significant concern under normal storage conditions typically used for monoclonal antibodies. However, when stored at 29 degrees C, the apparent rate constant of this reaction was found to be 0.06 week(-1) and resulted in an increase from 5.1 to 21.1% isoD after twenty four weeks of storage and is a major degradant in stressed IgG 1 antibodies.

Stability studies of protein therapeutics are often accelerated by storing potential formulations at elevated temperatures where the rates of various chemical and physical degradation pathways are increased. An often overlooked caveat of using these studies is the potential degradation of the formulation components themselves. In this report, we show that the monoclonal antibody MAB001 aggregated at a faster rate when formulated with sucrose compared to samples that contained sorbitol or no excipient during accelerated stability studies following an initial lag phase where the rates of aggregate formation were similar in all formulations. The duration of the lag phase was both pH and temperature dependent and a significant increase of protein glycation was noticed during this time. These observations indicate that the enhanced rate of antibody aggregation in sucrose containing formulations is likely due to protein glycation following sucrose hydrolysis under accelerated conditions. This hypothesis was confirmed by demonstrating that antibody directly glycated with glucose aggregated at a faster rate than nonglycated antibody stored in the identical formulation. These findings question the utility of using accelerated stability data for predicting protein stability in sucrose containing formulations stored at 2–8°C, where no glycation or change in aggregation rate was observed. © 2009 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 98:4501–4510, 2009

This report describes what to our knowledge is the first kinetic folding studies of erythropoietin, a glycosylated four-helical bundle cytokine responsible for the regulation of red blood cell production. Kinetic responses for folding and unfolding reactions initiated by manual mixing were monitored by far-ultraviolet circular dichroism and fluorescence spectroscopy, and folding reactions initiated by stopped-flow mixing were monitored by fluorescence. The urea concentration dependence of the observed kinetics were best described by a three-state model with a transiently populated intermediate species that is on-pathway and obligatory. This folding scheme was further supported by the excellent agreement between the free energy of unfolding and m-value calculated from the microscopic rate constants derived from this model and these parameters determined from separate equilibrium unfolding experiments. Compared to the kinetics of other members of the four-helical bundle cytokine family, erythropoietin folding and unfolding reactions were slower and less susceptible to aggregation. We tentatively attribute these slower rates and protection from association events to the large amount of carbohydrate attached to erythropoietin at four sites.

MAB007, an IgG1 monoclonal antibody, is unique because of the presence of a free cysteine residue in the Fab region at position 104 on the heavy chain in the CDR3 region. Mass spectrometric analysis of intact MAB007 showed multiple peaks varying in mass by 120-140 Da that cannot be fully attributed to glycosylation isoforms typically present in IgG molecules. Limited proteolysis of MAB007 with Lys-C led to a single cleavage at the C-terminus of a lysine residue in the hinge region of the heavy chain at position 222, generating free Fab and Fc fragments. Reversed-phase liquid chromatography/mass spectrometry analysis of the Fab and Fc fragments revealed several modifications. The Fab fraction showed cysteinylation of a free cysteine in the CDR3 region resulting in a mass shift of 119 Da. Using limited proteolysis, we also identified modifications resulting in a mass increase of 127 Da in the Fc region, corresponding to C-terminal lysine variants in the heavy chain. Other modifications, such as oxidation (+16 Da) and succinimide formation (-17 Da), were also detected in the Fab fragment. The cysteinylation observed after limited proteolysis was confirmed by peptide mapping coupled with tandem mass spectrometry analysis.