Binding of excipients is a poor predictor for aggregation kinetics of biopharmaceutical proteins

Removal of Excipients from Drug Product may Impact Antibody Characterization of Monoclonal Antibodies

Extensive analytical and functional characterization of a biotherapeutic product is a regulatory requirement, more so for biosimilar products where approval is contingent on the manufacturer's ability to demonstrate comparability of their product to the corresponding reference product. Typical biotherapeutic formulations contain multiple excipients that are meant to stabilize the product and these can impact certain analytical and functional techniques that are typically used in the above-mentioned characterization and comparability exercises. In this study, we elucidate this interference using Trastuzumab (Tmab) reference product, Herclon, and its commercially available biosimilars, Herzuma and Vivitra, as an example. Excipients were removed one at a time from the drug product and impact of this removal on a spectrum of analytical and functional tools was examined. Removal of certain excipients (Trehalose, L-histidine HCl and Polysorbate 20) was found to impact the results of charge variant analysis (cation exchange HPLC), secondary structure analysis (FTIR and far-UV CD spectroscopy), and tertiary structure analysis (near-UV CD and intrinsic FLR spectroscopy) For charge variants, differences up to 3.62% in basic species were observed, while FTIR spectra in the amide I region were significantly impacted. The intrinsic fluorescence spectra displayed major wavelength maxima shifts of up to 6 nm. In view of these results, it is recommended that biosimilar manufacturers consider the impact of differences in formulation in the samples that are being compared as well as the impact of excipient removal, if they are extracting the therapeutic moiety from the drug product for comparability analysis (routinely done by biosimilar manufacturers).

Investigating the Interaction between Excipients and Monoclonal Antibodies PGT121 and N49P9.6-FR-LS: A Comprehensive Analysis

N49P9.6-FR-LS and PGT121 are promising antibodies with significant therapeutic potential against HIV infection, but they are prone to precipitation at concentrations greater than 12 to 13 mg/mL. This study evaluates the influence of six excipients─arginine, alanine, sucrose, trehalose, methionine, and glutamate─on the biophysical stability of antibodies. We employed a comprehensive approach, combining computational mAb-excipient interaction analysis via the site-identification by ligand competitive saturation (SILCS) method with extensive experimental characterization. Our experimental matrix included viscosity measurements across temperature gradients, particle size distribution, zeta potential, pH value, and solution appearance, alongside a short-term stability product study at 30 °C and 65% relative humidity, with assessments at t0 (initial), t1 (14 days), and t2 (28 days). Results indicated that sucrose, arginine, alanine, and trehalose provided varying degrees of stabilization for both antibodies. Conversely, glutamate destabilized PGT121 but stabilized N49P9.6-FR-LS, while methionine had a negative effect on N49P9.6-FR-LS but a positive one on PGT121. SILCS-Biologics analysis suggested that stabilization by these excipients is linked to their ability to occupy regions involved in self-protein interactions. Debye-Hückel-Henry charge calculations further indicated that neutral excipients like sucrose and trehalose could alter mAb charges by affecting buffer binding, influencing aggregation propensity. These findings offer valuable insights for optimizing antibody formulations, ensuring enhanced product stability and therapeutic efficacy for HIV treatment.

Intrinsic Differential Scanning Fluorimetry for Protein Stability Assessment in Microwell Plates

Intrinsic differential scanning fluorimetry (DSF) is essential for analyzing protein thermal stability. Until now, intrinsic DSF was characterized by medium throughput and high consumable costs. Here, we present a microplate-based intrinsic DSF approach that enables the measurement of up to 384 samples in parallel by consuming only 10 μL per sample. We systematically test and benchmark the new intrinsic DSF against gold-standard methods such as differential scanning microcalorimetry and circular dichroism. Using a range of model proteins and sample conditions, we demonstrate the robustness and versatility of the intrinsic DSF method for characterizing protein stability and ranking protein drug candidates. In addition, we demonstrate modulated scanning fluorimetry (MSF) capabilities on the intrinsic DSF hardware that enable simultaneous MSF measurements in 384-microwell plates. Overall, the presented technology is a powerful tool for the early stability analysis of various protein samples and drug candidates.

A multifaceted approach to understanding protein-buffer interactions in biopharmaceuticals

The excipient selection process plays a crucial role in biopharmaceutical formulation development to ensure the long-term stability of the drug product. Though there are numerous options approved by regulatory authorities, only a subset is commonly utilized. Previous research has proposed various stabilization mechanisms, including protein-excipient interactions. However, identifying these interactions remains challenging due to their weak and transient nature. In this study, we present a comprehensive approach to identify such interactions. Using the 1HT2 CPMG (Carr-Purcel-Meiboom-Gill) filter experiment we identified interactions of rituximab with certain buffers and amino acids, shedding light on its Fc fragment instability that manifested during the enzymatic cleavage of the antibody. Moreover, chemometric analyses of 2D NMR fingerprints revealed interactions of selected excipients with antibody fragments. Furthermore, molecular dynamics simulations revealed potential interacting hotspots without NMR spectra assignment. Our results highlight the importance of an orthogonal methods approach to uncovering these critical interactions, advancing our understanding of excipient stabilization mechanisms and rational formulation design in biopharmaceutics.

Characterizing Interactions Between Small Peptides and Dimethyl Sulfoxide Using Infrared Spectroscopy and Computational Methods

This study provides a comprehensive analysis of the interactions between dimethyl sulfoxide (DMSO) and two small peptides, diglycine and N-acetyl-glycine-methylamide (NAGMA), in aqueous solutions using FTIR spectroscopy and density functional theory (DFT) calculations. ATR-FTIR spectroscopy and DFT results revealed that DMSO does not form direct bonds with the peptides, suggesting that DMSO indirectly influences both peptides by modifying the surrounding water molecules. The analysis of HDO spectra allowed for the isolation of the contribution of water molecules that were simultaneously altered by the peptide and DMSO, and it also explained the changes in the hydration shells of the peptides in the presence of DMSO. In the DMSO-diglycine system, DMSO contributes to the additional strengthening of water hydrogen bonds in the reinforced hydration sphere of diglycine. In contrast, DMSO has a more moderate effect on the water molecules surrounding NAGMA due to the similarity of their hydration shells, leading to a slight weakening of the hydrogen bonds in the NAGMA hydration sphere. DFT/ONIOM calculations confirmed these observations. These findings demonstrated that DMSO influences peptide stability differentially based on their structural characteristics.

Effect of surfactants on lactate dehydrogenase aqueous solutions: A comparative study of poloxamer 188, polysorbate 20 and 80

The effect of three commonly used surfactants, poloxamer 188 (P188), polysorbate 20 and 80 (PS20 and PS80), on the stability of a model protein, lactate dehydrogenase (LDH), was compared in aqueous solutions. In the absence of a surfactant, protein solution revealed a gradual decrease in surface tension as a function of time. The addition of surfactant resulted in a rapid decrease in the surface tension. This suggested that the surface behavior was dictated by the surfactant. PS20 and PS80 were more effective than P188 in preventing LDH adsorption on the solution surface. The advantage of polysorbates over P188 was also evident from the higher LDH tetramer recovery after shaking (room temperature, 30 h), especially when the surfactants were used at concentrations ≤ 0.01% w/v. However, PS20 and PS80 accelerated protein unfolding during quiescent storage at 40 °C. Based on circular dichroism results, polysorbates perturbed the tertiary structure of LDH but not the secondary structure, while P188 did not impact the protein structure and stability. Polysorbates were more effective in stabilizing LDH against mechanical stress (shaking), but their adverse effects on protein conformational stability need to be carefully evaluated.

Interactions between the protein barnase and co-solutes studied by NMR

Protein solubility and stability depend on the co-solutes present. There is little theoretical basis for selection of suitable co-solutes. Some guidance is provided by the Hofmeister series, an empirical ordering of anions according to their effect on solubility and stability; and by osmolytes, which are small organic molecules produced by cells to allow them to function in stressful environments. Here, NMR titrations of the protein barnase with Hofmeister anions and osmolytes are used to measure and locate binding, and thus to separate binding and bulk solvent effects. We describe a rationalisation of Hofmeister (and inverse Hofmeister) effects, which is similar to the traditional chaotrope/kosmotrope idea but based on solvent fluctuation rather than water withdrawal, and characterise how co-solutes affect protein stability and solubility, based on solvent fluctuations. This provides a coherent explanation for solute effects, and points towards a more rational basis for choice of excipients.

Examining polymer-protein biophysical interactions with small-angle x-ray scattering and quartz crystal microbalance with dissipation

Polymer-protein hybrids can be deployed to improve protein solubility and stability in denaturing environments. While previous work used robotics and active machine learning to inform new designs, further biophysical information is required to ascertain structure-function behavior. Here, we show the value of tandem small-angle x-ray scattering (SAXS) and quartz crystal microbalance with dissipation (QCMD) experiments to reveal detailed polymer-protein interactions with horseradish peroxidase (HRP) as a test case. Of particular interest was the process of polymer-protein complex formation under thermal stress whereby SAXS monitors formation in solution while QCMD follows these dynamics at an interface. The radius of gyration (Rg ) of the protein as measured by SAXS does not change significantly in the presence of polymer under denaturing conditions, but thickness and dissipation changes were observed in QCMD data. SAXS data with and without thermal stress were utilized to create bead models of the potential complexes and denatured enzyme, and each model fit provided insight into the degree of interactions. Additionally, QCMD data demonstrated that HRP deforms by spreading upon surface adsorption at low concentration as shown by longer adsorption times and smaller frequency shifts. In contrast, thermally stressed and highly inactive HRP had faster adsorption kinetics. The combination of SAXS and QCMD serves as a framework for biophysical characterization of interactions between proteins and polymers which could be useful in designing polymer-protein hybrids.

Insights into the Stabilization of Interferon Alpha by Two Surfactants Revealed by STD-NMR Spectroscopy

Surfactants are commonly used in biopharmaceutical formulations to stabilize proteins against aggregation. However, the choice of a suitable surfactant for a particular protein is decided mostly empirically, and their mechanism of action on molecular level is largely unknown. Here we show that a straightforward label-free method, saturation transfer difference (STD) nuclear magnetic resonance (NMR) spectroscopy, can be used to detect protein-surfactant interactions in formulations of a model protein, interferon alpha. We find that polysorbate 20 binds with its fatty acid to interferon, and that the binding is stronger at pH closer to the isoelectric point of the protein. In contrast, we did not detect interactions between poloxamer 407 and interferon alpha. Neither of the two surfactants affected the tertiary structure and the thermal stability of the protein as evident from circular dichroism and nanoDSF measurements. Interestingly, both surfactants inhibited the formation of subvisible particles during long-term storage, but only polysorbate 20 reduced the amount of small soluble aggregates detected by size-exclusion chromatography. This proof-of-principle study demonstrates how STD-NMR can be employed to quickly assess surfactant-protein interactions and support the choice of surfactant in protein formulation.

Investigation of the pH-dependent aggregation mechanisms of GCSF using low resolution protein characterization techniques and advanced molecular dynamics simulations

Granulocyte-colony stimulating factor (GCSF) is a widely used therapeutic protein to treat neutropenia. GCSF has an increased propensity to aggregate if the pH is increased above 5.0. Although GCSF is very well experimentally characterized, the exact pH-dependent aggregation mechanism of GCSF is still under debate. This study aimed to model the complex pH-dependent aggregation behavior of GCSF using state-of-the-art simulation techniques. The conformational stability of GCSF was investigated by performing metadynamics simulations, while the protein-protein interactions were investigated using coarse-grained (CG) simulations of multiple GCSF monomers. The CG simulations were directly compared with small-angle X-ray (SAXS) data. The metadynamics simulations demonstrated that the orientations of Trp residues in GCSF are dependent on pH. The conformational change of Trp residues is due to the loss of Trp-His interactions at the physiological pH, which in turn may increase protein flexibility. The helical structure of GCSF was not affected by the pH conditions of the simulations. Our CG simulations indicate that at pH 4.0, the colloidal stability may be more important than the conformational stability of GCSF. The electrostatic potential surface and CG simulations suggested that the basic residues are mainly responsible for colloidal stability as deprotonation of these residues causes a reduction of the highly positively charged electrostatic barrier close to the aggregation-prone long loop regions.

Effects of amino acid additives on protein solubility - insights from desorption and direct electrospray ionization mass spectrometry

Naturally occurring amino acids have been broadly used as additives to improve protein solubility and inhibit aggregation. In this study, improvements in protein signal intensity obtained with the addition of L-serine, and structural analogs, to the desorption electrospray ionization mass spectrometry (DESI-MS) spray solvent were measured. The results were interpreted at the hand of proposed mechanisms of solution additive effects on protein solubility and dissolution. DESI-MS allows for these processes to be studied efficiently using dilute concentrations of additives and small amounts of proteins, advantages that represent real benefits compared to classical methods of studying protein stability and aggregation. We show that serine significantly increases the protein signal in DESI-MS when native proteins are undergoing unfolding during the dissolution process with an acidic solvent system (p-value = 0.0001), or with ammonium bicarbonate under denaturing conditions for proteins with high isoelectric points (p-value = 0.001). We establish that a similar increase in the protein signal cannot be observed with direct ESI-MS, and the observed increase is therefore not related to ionization processes or changes in the physical properties of the bulk solution. The importance of the presence of serine during protein conformational changes while undergoing dissolution is demonstrated through comparisons between the analyses of proteins deposited in native or unfolded states and by using native state-preserving and denaturing desorption solvents. We hypothesize that direct, non-covalent interactions involving all three functional groups of serine are involved in the beneficial effect on protein solubility and dissolution. Supporting evidence for a direct interaction include a reduction in efficacy with D-serine or the racemic mixture, indicating a non-bulk-solution physical property effect; insensitivity to the sample surface type or relative placement of serine addition; and a reduction in efficacy with any modifications to the serine structure, most notably the carboxyl functional group. An alternative hypothesis, also supported by some of our observations, could involve the role of serine clusters in the mechanism of solubility enhancement. Our study demonstrates the capability of DESI-MS together with complementary ESI-MS experiments as a novel tool for understanding protein solubility and dissolution and investigating the mechanism of action for solubility-enhancing additives.

Towards an improved prediction of concentrated antibody solution viscosity using the Huggins coefficient

The viscosity of a monoclonal antibody solution must be monitored and controlled as it can adversely affect product processing, packaging and administration. Engineering low viscosity mAb formulations is challenging as prohibitive amounts of material are required for concentrated solution analysis, and it is difficult to predict viscosity from parameters obtained through low-volume, high-throughput measurements such as the interaction parameter, k_D, and the second osmotic virial coefficient, B₂₂. As a measure encompassing the effect of intermolecular interactions on dilute solution viscosity, the Huggins coefficient, k_h, is a promising candidate as a parameter measureable at low concentrations, but indicative of concentrated solution viscosity. In this study, a differential viscometry technique is developed to measure the intrinsic viscosity, [η], and the Huggins coefficient, k_h, of protein solutions. To understand the effect of colloidal protein-protein interactions on the viscosity of concentrated protein formulations, the viscometric parameters are compared to k_D and B₂₂ of two mAbs, tuning the contributions of repulsive and attractive forces to the net protein-protein interaction by adjusting solution pH and ionic strength. We find a strong correlation between the concentrated protein solution viscosity and the k_h but this was not observed for the k_D or the b₂₂, which have been previously used as indicators of high concentration viscosity. Trends observed in [η] and k_h values as a function of pH and ionic strength are rationalised in terms of protein-protein interactions.

Thermodynamic Origin of Differential Excipient-Lysozyme Interactions

Understanding the intricate interplay of interactions between proteins, excipients, ions and water is important to achieve the effective purification and stable formulation of protein therapeutics. The free energy of lysozyme interacting with two kinds of polyanionic excipients, citrate and tripolyphosphate, together with sodium chloride and TRIS-buffer, are analysed in multiple-walker metadynamics simulations to understand why tripolyphosphate causes lysozyme to precipitate but citrate does not. The resulting multiscale decomposition of energy and entropy components for water, sodium chloride, excipients and lysozyme reveals that lysozyme is more stabilised by the interaction of tripolyphosphate with basic residues. This is accompanied by more sodium ions being released into solution from tripolyphosphate than for citrate, whilst the latter instead has more water molecules released into solution. Even though lysozyme aggregation is not directly probed in this study, these different mechanisms are suspected to drive the cross-linking between lysozyme molecules with vacant basic residues, ultimately leading to precipitation.

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.