The role of electrostatics in protein-protein interactions of a monoclonal antibody

The molecular basis for hydrodynamic properties of PEGylated human serum albumin

Polyethylene glycol (PEG) conjugation provides a protective modification that enhances the pharmacokinetics and solubility of proteins for therapeutic use. A knowledge of the structural ensemble of these PEGylated proteins is necessary to understand the molecular details that contribute to their hydrodynamic and colligative properties. Because of the large size and dynamic flexibility of pharmaceutically important PEGylated proteins, the determination of structure is challenging. In addition, the hydration of these conjugates that contain large polymers is difficult to determine with traditional methods that identify only first shell hydration water, which does not account for the complete hydrodynamic volume of a macromolecule. Here, we demonstrate that structural ensembles, generated by coarse-grained simulations, can be analyzed with HullRad and used to predict sedimentation coefficients and concentration-dependent hydrodynamic and diffusion nonideality coefficients of PEGylated proteins. A knowledge of these concentration-dependent properties enhances the ability to design and analyze new modified protein therapeutics. HullRad accomplishes this analysis by effectively accounting for the complete hydration of a macromolecule, including that of flexible polymers.

Combining Scattering Experiments and Colloid Theory to Characterize Charge Effects in Concentrated Antibody Solutions

Charges and their contribution to protein-protein interactions are essential for the key structural and dynamic properties of monoclonal antibody (mAb) solutions. In fact, they influence the apparent molecular weight, the static structure factor, the collective diffusion coefficient, or the relative viscosity, and their concentration dependence. Further, charges play an important role in the colloidal stability of mAbs. There exist standard experimental tools to characterize mAb net charges, such as the measurement of the electrophoretic mobility, the second virial coefficient, or the diffusion interaction parameter. However, the resulting values are difficult to directly relate to the actual overall net charge of the antibody and to theoretical predictions based on its known molecular structure. Here, we report the results of a systematic investigation of the solution properties of a charged IgG1 mAb as a function of concentration and ionic strength using a combination of electrophoretic measurements, static and dynamic light scattering, small-angle X-ray scattering, and tracer particle-based microrheology. We analyze and interpret the experimental results using established colloid theory and coarse-grained computer simulations. We discuss the potential and limits of colloidal models for the description of the interaction effects of charged mAbs, in particular pointing out the importance of incorporating shape and charge anisotropy when attempting to predict structural and dynamic solution properties at high concentrations.

Teaching biologics design using molecular modeling and simulations

Teaching chemistry and biology students about biologics design remains challenging despite its increasing importance in pharmaceutical development. Monoclonal antibodies, commonly called mAbs, are the most popular biologics. They have been developed into drugs to treat various diseases in the past decades. Multiple challenges exist for designing proper formulations to stabilize mAbs, such as preventing aggregation and mitigating viscosity. Molecular modeling and simulations can improve pharmaceutical products by examining the interactions between mAbs and other compounds, such as excipients. To introduce students to biopharmaceuticals, eight students at the Stevens Institute of Technology participated in a semester-long course to learn the challenges of pharmaceutical development and different computational skills to study biologics design. The students started with a limited background in this field. Throughout one semester, they were introduced to various literature and software tools for modeling antibodies and studying their interactions with excipients. This paper aims to develop a course structure to be replicated at other universities and institutions to teach biopharmaceutical development to students.

Sandwich Immuno-RCA Assay with Single Molecule Counting Readout: The Importance of Biointerface Design

The analysis of low-abundance protein molecules in human serum is reported based on counting of the individual affinity-captured analyte on a solid sensor surface, yielding a readout format similar to digital assays. In this approach, a sandwich immunoassay with rolling circle amplification (RCA) is used for single molecule detection (SMD) through associating the target analyte with spatially distinct bright spots observed by fluorescence microscopy. The unspecific interaction of the target analyte and other immunoassay constituents with the sensor surface is of particular interest in this work, as it ultimately limits the performance of this assay. It is minimized by the design of the respective biointerface and thiol self-assembled monolayer with oligoethylene (OEG) head groups, and a poly[oligo(ethylene glycol) methacrylate] (pHOEGMA) antifouling polymer brush was used for the immobilization of the capture antibody (cAb) on the sensor surface. The assay relying on fluorescent postlabeling of long single-stranded DNA that are grafted from the detection antibody (dAb) by RCA was established with the help of combined surface plasmon resonance and surface plasmon-enhanced fluorescence monitoring of reaction kinetics. These techniques were employed for in situ measurements of conjugating of cAb to the sensor surface, tagging of short single-stranded DNA to dAb, affinity capture of the target analyte from the analyzed liquid sample, and the fluorescence readout of the RCA product. Through mitigation of adsorption of nontarget molecules on the sensor surface by tailoring of the antifouling biointerface, optimizing conjugation chemistry, and by implementing weak Coulombic repelling between dAb and the sensor surface, the limit of detection (LOD) of the assay was substantially improved. For the chosen interleukin-6 biomarker, SMD assay with LOD at a concentration of 4.3 fM was achieved for model (spiked) samples, and validation of the ability of detection of standard human serum samples is demonstrated.

Exploring the Combined Action of Adding Pertuzumab to Branded Trastuzumab versus Trastuzumab Biosimilars for Treating HER2+ Breast Cancer

The binding activity of various trastuzumab biosimilars versus the branded trastuzumab towards the glycosylated extracellular domain of the human epidermal growth factor receptor 2 (HER2) target in the presence of pertuzumab was investigated. We employed size exclusion chromatography with tetra-detection methodology to simultaneously determine absolute molecular weight, concentration, molecular size, and intrinsic viscosity. All trastuzumab molecules in solution exhibit analogous behavior in their binary action towards HER2 regardless of the order of addition of trastuzumab/pertuzumab. This analogous behavior of all trastuzumab molecules, including biosimilars, highlights the robustness and consistency of their binding activity towards HER2. Furthermore, the addition of HER2 to a mixture of trastuzumab and pertuzumab leads to increased formation of high-order HER2 complexes, up to concentrations of one order of magnitude higher than in the case of sequential addition. The observed increase suggests a potential synergistic effect between these antibodies, which could enhance their therapeutic efficacy in HER2-positive cancers. These findings underscore the importance of understanding the complex interplay between therapeutic antibodies and their target antigens, providing valuable insights for the development of more effective treatment strategies.

Quantifying Protein Shape to Elucidate Its Influence on Solution Viscosity in High-Concentration Electrolyte Solutions

Therapeutic proteins with a high concentration and low viscosity are highly desirable for subcutaneous and certain local injections. The shape of a protein is known to influence solution viscosity; however, the precise quantification of protein shape and its relative impact compared to other factors like charge-charge interactions remains unclear. In this study, we utilized seven model proteins of varying shapes and experimentally determined their shape factors (v) based on Einstein's viscosity theory, which correlate strongly with the ratios of the proteins' surface area to the 2/3 power of their respective volumes, based on protein crystal structures resolved experimentally or predicted by AlphaFold. This finding confirms the feasibility of computationally estimating protein shape factors from amino acid sequences alone. Furthermore, our results demonstrated that, in high-concentration electrolyte solutions, a more spherical protein shape increases the protein's critical concentration (C*), the transition concentration beyond which protein viscosity increases exponentially relative to concentration increases. In summary, our work elucidates protein shape as a key determinant of solution viscosity through quantitative analysis and comparison with other contributing factors. This provides insights into molecular engineering strategies to optimize the molecular design of therapeutic proteins, thus optimizing their viscosity.

Impact of Glycosylation on Protein-Protein Self-Interactions of Monoclonal Antibodies

Protein self-interactions measured via second osmotic virial coefficients (B22) and dynamic light scattering interaction parameter values (kD) are often used as metrics for assessing the favorability of protein candidates and different formulations during monoclonal antibody (MAb) product development. Model predictions of B22 or kD typically do not account for glycans, though glycosylation can potentially impact experimental MAb self-interactions. To the best of our knowledge, the impact of MAb glycosylation on the experimentally measured B22 and kD values has not yet been reported. B22 and kD values of two fully deglycosylated MAbs and their native (i.e., fully glycosylated) counterparts were measured by light scattering over a range of pH and ionic strength conditions. Significant differences between B22 and kD of the native and deglycosylated forms were observed at a range of low to high ionic strengths used to modulate the effect of electrostatic contributions. Differences were most pronounced at low ionic strength, indicating that electrostatic interactions are a contributing factor. Though B22 and kD values were statistically equivalent at high ionic strengths where electrostatics were fully screened, we observed protein-dependent qualitative differences, which indicate that steric interactions may also play a role in the observed B22 and kD differences. A domain-level coarse-grained molecular model accounting for charge differences was considered to potentially provide additional insight but was not fully predictive of the behavior across all of the solution conditions investigated. This highlights that both the level of modeling and lack of inclusion of glycans may limit existing models in making quantitatively accurate predictions of self-interactions.

Electrostatically Mediated Attractive Self-Interactions and Reversible Self-Association of Fc-Fusion Proteins

Attractive self-interactions and reversible self-association are implicated in many problematic solution behaviors for therapeutic proteins, such as irreversible aggregation, elevated viscosity, phase separation, and opalescence. Protein self-interactions and reversible oligomerization of two Fc-fusion proteins (monovalent and bivalent) and the corresponding fusion partner protein were characterized experimentally with static and dynamic light scattering as a function of pH (5 and 6.5) and ionic strength (10 mM to at least 300 mM). The fusion partner protein and monovalent Fc-fusion each displayed net attractive electrostatic self-interactions at pH 6.5 and net repulsive electrostatic self-interactions at pH 5. Solutions of the bivalent Fc-fusion contained higher molecular weight species that prevented quantification of typical interaction parameters (B22 and kD). All three of the proteins displayed reversible self-association at pH 6.5, where oligomers dissociated with increased ionic strength. Coarse-grained molecular simulations were used to model the self-interactions measured experimentally, assess net self-interactions for the bivalent Fc-fusion, and probe the specific electrostatic interactions between charged amino acids that were involved in attractive electrostatic self-interactions. Mayer-weighted pairwise electrostatic energies from the simulations suggested that attractive electrostatic self-interactions at pH 6.5 for the two Fc-fusion proteins were due to cross-domain interactions between the fusion partner domain(s) and the Fc domain.

Ions Adsorbed at Amorphous Solid/Solution Interfaces Form Wigner Crystal-like Structures

When a surface is immersed in a solution, it usually acquires a charge, which attracts counterions and repels co-ions to form an electrical double layer. The ions directly adsorbed to the surface are referred to as the Stern layer. The structure of the Stern layer normal to the interface was described decades ago, but the lateral organization within the Stern layer has received scant attention. This is because instrumental limitations have prevented visualization of the ion arrangements except for atypical, model, crystalline surfaces. Here, we use high-resolution amplitude modulated atomic force microscopy (AFM) to visualize in situ the lateral structure of Stern layer ions adsorbed to polycrystalline gold, and amorphous silica and gallium nitride (GaN). For all three substrates, when the density of ions in the layer exceeds a system-dependent threshold, correlation effects induce the formation of close packed structures akin to Wigner crystals. Depending on the surface and the ions, the Wigner crystal-like structure can be hexagonally close packed, cubic, or worm-like. The influence of the electrolyte concentration, species, and valence, as well as the surface type and charge, on the Stern layer structures is described. When the system parameters are changed to reduce the Stern layer ion surface excess below the threshold value, Wigner crystal-like structures do not form and the Stern layer is unstructured. For gold surfaces, molecular dynamics (MD) simulations reveal that when sufficient potential is applied to the surface, ion clusters form with dimensions similar to the Wigner crystal-like structures in the AFM images. The lateral Stern layer structures presented, and in particular the Wigner crystal-like structures, will influence diverse applications in chemistry, energy storage, environmental science, nanotechnology, biology, and medicine.

The origins of nonideality exhibited by monoclonal antibodies and Fab fragments in human serum

The development of therapeutic antibodies remains challenging, time-consuming, and expensive. A key contributing factor is a lack of understanding of how proteins are affected by complex biological environments such as serum and plasma. Nonideality due to attractive or repulsive interactions with cosolutes can alter the stability, aggregation propensity, and binding interactions of proteins in solution. Fluorescence correlation spectroscopy (FCS) can be used to measure apparent second virial coefficient (B2,app ) values for therapeutic and model monoclonal antibodies (mAbs) that capture the nature and strength of interactions with cosolutes directly in undiluted serum and similar complex biological media. Here, we use FCS-derived B2,app measurements to identify the components of human serum responsible for nonideal interactions with mAbs and Fab fragments. Most mAbs exhibit neutral or slightly attractive interactions with intact serum. Generally, mAbs display repulsive interactions with albumin and mildly attractive interactions with IgGs in the context of whole serum. Crucially, however, these attractive interactions are much stronger with pooled IgGs isolated from other serum components, indicating that the effects of serum nonideality can only be understood by studying the intact medium (rather than isolated components). Moreover, Fab fragments universally exhibited more attractive interactions than their parental mAbs, potentially rendering them more susceptible to nonideality-driven perturbations. FCS-based B2,app measurements have the potential to advance our understanding of how physiological environments impact protein-based therapeutics in general. Furthermore, incorporating such assays into preclinical biologics development may help de-risk molecules and make for a faster and more efficient development process.

Retrospective rationalization of disparities between the concentration dependence of diffusion coefficients obtained by boundary spreading and dynamic light scattering

This study establishes the existence of substantial agreement between published results from traditional boundary spreading measurements (including synthetic boundary measurements in the analytical ultracenrifuge) on two globular proteins (bovine serum albumin, ovalbumin) and the concentration dependence of diffusion coefficient predicted for experiments conducted under the operative thermodynamic constraints of constant temperature and solvent chemical potential. Although slight negative concentration dependence of the translational diffusion coefficient is the experimentally observed as well as theoretically predicted, the extent of the concentration dependence is within the limits of experimental uncertainty inherent in diffusion coefficient measurement. Attention is then directed toward the ionic strength dependence of the concentration dependence coefficient ([Formula: see text]) describing diffusion coefficients obtained by dynamic light scattering, where, in principle, the operative thermodynamic constraints of constant temperature and pressure preclude consideration of results in terms of single-solute theory. Nevertheless, good agreement between predicted and published experimental ionic strength dependencies of [Formula: see text] for lysozyme and an immunoglobulin is observed by a minor adaptation of the theoretical treatment to accommodate the fact that thermodynamic activity is monitored on the molal concentration scale because of the constraint of constant pressure that pertains in dynamic light scattering experiments.

Experimental support for reclassification of the light scattering second virial coefficient from macromolecular solutions as a hydrodynamic parameter

This investigation examines the source of the disparity between experimental values of the light scattering second virial coefficient [Formula: see text] (mL.mol/g2) for proteins and those predicted on the statistical mechanical basis of excluded volume. A much better theoretical description of published results for lysozyme is obtained by considering the experimental parameters to monitor the difference between the thermodynamic excluded volume term and its hydrodynamic counterpart. This involves a combination of parameters quantifying concentration dependence of the translational diffusion coefficient obtained from dynamic light scattering measurements. That finding is shown to account for observations of a strong correlation between [Formula: see text] (mL/g), where M2 is the molar mass (molecular weight) of the macromolecule and the diffusion concentration parameter [Formula: see text] (mL/g). On the grounds that [Formula: see text] is regarded as a hydrodynamic parameter, the same status should be accorded the light scattering second virial coefficient rather than its current incorrect thermodynamic designation as [Formula: see text] (mL.mol/g2), or just B, the osmotic second virial coefficient for protein self-interaction.

Chemometrics in Protein Formulation: Stability Governed by Repulsion and Protein Unfolding

Therapeutic proteins can be challenging to develop due to their complexity and the requirement of an acceptable formulation to ensure patient safety and efficacy. To date, there is no universal formulation development strategy that can identify optimal formulation conditions for all types of proteins in a fast and reliable manner. In this work, high-throughput characterization, employing a toolbox of five techniques, was performed on 14 structurally different proteins formulated in 6 different buffer conditions and in the presence of 4 different excipients. Multivariate data analysis and chemometrics were used to analyze the data in an unbiased way. First, observed changes in stability were primarily determined by the individual protein. Second, pH and ionic strength are the two most important factors determining the physical stability of proteins, where there exists a significant statistical interaction between protein and pH/ionic strength. Additionally, we developed prediction methods by partial least-squares regression. Colloidal stability indicators are important for prediction of real-time stability, while conformational stability indicators are important for prediction of stability under accelerated stress conditions at 40 °C. In order to predict real-time storage stability, protein-protein repulsion and the initial monomer fraction are the most important properties to monitor.

Polymorphic protein phase transitions driven by surface anisotropy

Phase transitions of proteins are strongly influenced by surface chemical modifications or mutations. Human γD-crystallin (HGD) single-mutants have been extensively studied because they are associated with the onset of juvenile cataract. However, they have also provided a rich library of molecules to examine how specific inter-protein interactions direct protein assembly, providing new insights and valuable experimental data for coarse-grained patchy-particle models. Here, we demonstrate that the addition of new inter-protein interactions by mutagenesis is additive and increases the number and variety of condensed phases formed by proteins. When double mutations incorporating two specific single point mutations are made, the properties of both single mutations are retained in addition to the formation of a new condensed phase. We find that the HGD double-mutant P23VC110M self-assembles into spherical particles with retrograde solubility, orthorhombic crystals, and needle/plate shape crystals, while retaining the ability to undergo liquid-liquid phase separation. This rich polymorphism is only partially predicted by the experimental data on the constituent single mutants. We also report a previously un-characterized amorphous protein particle, with unique properties that differ from those of protein spherulites, protein particulates previously described. The particles we observe are amorphous, reversible with temperature, tens of microns in size, and perfectly spherical. When they are grown on pristine surfaces, they appear to form by homogeneous nucleation, making them unique, and we believe a new form of protein condensate. This work highlights the challenges in predicting protein behavior, which has frustrated rational assembly and crystallization but also provides rich data to develop new coarse-grained models to explain the observed polymorphism.

Events at the Interface: How Do Interfaces Modulate the Dynamics and Functionalities of Guest Molecules?

Chemical and biological interfaces are of various types, which could be between two materials of the same and/or different states, two phases of the same material, biological substrates and the outer environment, surfactant or polymeric membranes and the bulk, and so forth. Small-molecule guests frequently interact with such interfaces that decide their functionalities. The structural and behavioral properties undergo considerable characteristic changes, which control their final course of action in the targeted application. This Perspective will discuss mainly the chemical interfaces constituted by the surfactants, polymers, lipids, and nucleic acids and their impacts on the dynamics of small-molecule guests. Some specific and interesting phenomena and future prospects will be elucidated in this Perspective.

Predicting Experimental B22 Values and the Effects of Histidine Charge States for Monoclonal Antibodies Using Coarse-Grained Molecular Simulations

Static light scattering (SLS) was used to characterize five monoclonal antibodies (MAbs) as a function of total ionic strength (TIS) at pH values between 5.5 and 7.0. Second osmotic virial coefficient (B₂₂) values were determined experimentally for each MAb as a function of TIS using low protein concentration SLS data. Coarse-grained molecular simulations were performed to predict the B₂₂ values for each MAb at a given pH and TIS. To include the effect of charge fluctuations of titratable residues in the B₂₂ calculations, a statistical approach was introduced in the Monte Carlo algorithm based on the protonation probability based on a given pH value and the Henderson-Hasselbalch equation. The charged residues were allowed to fluctuate individually, based on the sampled microstates and the influence of electrostatic interactions on net protein-protein interactions during the simulations. Compared to static charge simulations, the new approach provided improved results compared to experimental B₂₂ values at pH conditions near the pK_a of titratable residues.

Oligomeric interactions maintain active-site structure in a noncooperative enzyme family

The evolutionary benefit accounting for widespread conservation of oligomeric structures in proteins lacking evidence of intersubunit cooperativity remains unclear. Here, crystal and cryo-EM structures, and enzymological data, demonstrate that a conserved tetramer interface maintains the active-site structure in one such class of proteins, the short-chain dehydrogenase/reductase (SDR) superfamily. Phylogenetic comparisons support a significantly longer polypeptide being required to maintain an equivalent active-site structure in the context of a single subunit. Oligomerization therefore enhances evolutionary fitness by reducing the metabolic cost of enzyme biosynthesis. The large surface area of the structure-stabilizing oligomeric interface yields a synergistic gain in fitness by increasing tolerance to activity-enhancing yet destabilizing mutations. We demonstrate that two paralogous SDR superfamily enzymes with different specificities can form mixed heterotetramers that combine their individual enzymological properties. This suggests that oligomerization can also diversify the functions generated by a given metabolic investment, enhancing the fitness advantage provided by this architectural strategy.

NMR and dynamic light scattering give different diffusion information for short-living protein oligomers. Human serum albumin in water solutions of metal ions

Diffusive behavior of human serum albumin (HSA) in the presence of Mg²⁺ and Cu²⁺ ions was studied by pulsed field gradient nuclear magnetic resonance (PFG NMR) and dynamic light scattering (DLS). According to NMR data yielding measurements of HSA self-diffusion coefficient, a weighted average of the protein monomers and oligomers diffusion mobility in the presence of metal ions was observed. While the short-time collective diffusion measured by DLS showed one type of diffusing species in ion-free HSA solution and two molecular forms of HSA in the presence of metal ions. The light intensity correlation function analysis showed that HSA oligomers have a limited lifetime (lower limit is about 0.4 ms) intermediate between characteristic time scales of PFG NMR and DLS experiments. For a theoretical description of concentration dependence of HSA self- and collective diffusion coefficients, the phenomenological approach based on the frictional formalism of non-equilibrium thermodynamics was used (Vink theory), allowing analysis of the solvent-solute and solute-solute interactions in protein solutions. In the presence of metal ions, a significant increase of HSA protein-protein friction coefficient was shown. Based on theoretical analysis of collective diffusion data, the positive values of second virial coefficients A₂ for HSA monomers were obtained. The A₂ values were found to be higher for the HSA with metal ions compared with the ion-free HSA solution. This is due to the more pronounced contribution of repulsion in protein-protein interactions of HSA monomers in the presence of Mg²⁺ and Cu²⁺ ions.

Hierarchical Exploration of Drying Patterns Formed in Drops Containing Lysozyme, PBS, and Liquid Crystals

Biological systems, by nature, are highly complex. These systems exhibit diverse hierarchical spatial and temporal features when driven far from equilibrium. The generated features are susceptible to the initial conditions that largely depend on vast parameter space. Extracting information on their properties and behavior thus becomes far too complex. This work seeks to examine the drying kinetics of the drops containing a globular protein (xlysozyme (Lys)), phosphate buffer saline (PBS), and thermotropic liquid crystal (LCs). The drying evolution and the morphological crack patterns of these drops are examined using high-resolution microscopy, textural image analysis, and statistical methods. This study observes that the textural parameters can identify the (i) phase separation of the salts present in the PBS and (ii) the LCs’ birefringence during the drying evolution. This birefringence activities of the LCs slow down when the initial PBS concentration is increased from 0.25 to 1× despite using a fixed volume of LCs. To comprehend such a surprising effect, the combinations of (i) Lys+PBS and (ii) PBS+LCs are thoroughly examined. A phase diagram is established as a function of initial concentrations of Lys and PBS. The scanning electron microscopic images of Lys+PBS reveal that the tuning between lysozyme and salt concentrations in PBS plays a significant role in determining the morphological patterns. The Lys drops with and without LCs exhibit two distinct regions: the peripheral ring (“coffee-ring”) and the central ones. This phase-separated ring formation indicates that the film containing Lys and salts might have formed on top of these LCs in the central region, which reduces the optical response (birefringence) of LCs. A physical mechanism is proposed in this paper to anticipate the redistributions of LCs in a multi-component system such as Lys+PBS+LCs.

Exploring Nucleation Pathways in Distinct Physicochemical Environments Unveiling Novel Options to Modulate and Optimize Protein Crystallization

The scientific discussion about classical and nonclassical nucleation theories has lasted for two decades so far. Recently, multiple nucleation pathways and the occurrence and role of metastable intermediates in crystallization processes have attracted increasing attention, following the discovery of functional phase separation, which is now under investigation in different fields of cellular life sciences, providing interesting and novel aspects for conventional crystallization experiments. In this context, more systematic investigations need to be carried out to extend the current knowledge about nucleation processes. In terms of the data we present, a well-studied model protein, glucose isomerase (GI), was employed first to investigate systematically the early stages of the crystallization process, covering condensing and prenucleation ordering of protein molecules in diverse scenarios, including varying ionic and crowding agent conditions, as well as the application of a pulsed electric field (pEF). The main method used to characterize the early events of nucleation was synchronized polarized and depolarized dynamic light scattering (DLS/DDLS), which is capable of collecting the polarized and depolarized component of scattered light from a sample suspension in parallel, thus monitoring the time-resolved evolution of the condensation and geometrical ordering of proteins at the early stages of nucleation. A diffusion interaction parameter, KD, of GI under varying salt conditions was evaluated to discuss how the proportion of specific and non-specific protein–protein interactions affects the nucleation process. The effect of mesoscopic ordered clusters (MOCs) on protein crystallization was explored further by adding different ratios of MOCs induced by a pEF to fresh GI droplets in solution with different PEG concentrations. To emphasize and complement the data and results obtained with GI, a recombinant pyridoxal 5-phosphate (vitamin B6) synthase (Pdx) complex of Staphylococcus aureus assembled from twelve monomers of Pdx1 and twelve monomers of Pdx2 was employed to validate the ability of the pEF influencing the nucleation of complex macromolecules and the effect of MOCs on adjusting the crystallization pathway. In summary, our data revealed multiple nucleation pathways by tuning the proportion of specific and non-specific protein interactions, or by utilizing a pEF which turned out to be efficient to accelerate the nucleation process. Finally, a novel and reproducible experimental strategy, which can adjust and facilitate a crystallization process by pEF-induced MOCs, was summarized and reported for the first time.

Phase stability of aqueous mixtures of bovine serum albumin with low molecular mass salts in presence of polyethylene glycol

The stability of bovine serum albumin (BSA) solutions against phase separation caused by cooling the system is studied under the combined influence of added poly(ethylene glycol) (PEG) and alkali halide salts in water as solvent. The phase stability of the system depends on the concentration of the added PEG and its molecular mass, the concentration of the low molecular mass electrolyte and its nature, as also on the pH of the solution. More specifically, the addition of NaCl to the BSA-PEG mixture promotes phase separation at pH = 4.0, where BSA carries the net positive charge in aqueous solution, and it increases the stability of the solution at pH=4.6, i.e., near the isoionic point of the protein. Moreover, at pH = 4.6, the cloud-point temperature decreases in the order from NaF to NaI and from LiCl to CsCl. The order of the salts at pH = 4.0 is exactly reversed: LiCl and NaF show the weakest effect on the cloud-point temperature and the strongest decrease in stability is caused by RbCl and NaNO3. An attempt is made to correlate these observations with the free energies of hydration of the added salt ions and with the effect of adsorption of salt ions on the protein surface on the protein-protein interactions. Kosmotropic salt ions decrease the phase stability of BSA-PEG-salt solutions at pH < pI, while exactly the opposite is true at pH = pI.

Measuring Self-Association of Antibody Lead Candidates with Dynamic Light Scattering

In this method chapter, we provide a brief overview of the key methods available to measure self-association of monoclonal antibodies (mAbs) and explain for which experimental throughputs they are usually applied. We then focus on dynamic light scattering (DLS) and describe experimental details on how to measure the diffusion interaction parameter (k_D) which is occasionally referred to as the gold standard for measuring self-association of proteins. The k_D is a well-established parameter to predict solution viscosity, which is one of the most critical developability parameters of mAbs. Finally, we present a pH and excipient screen that is designed to measure self-association with DLS under conditions that are relevant for bioprocessing and formulation of mAbs. The presented light scattering methods are well suited for lead candidate selections where it is essential to select mAbs with high developability potential for progression toward first human dose.

Self-Interactions of Two Monoclonal Antibodies: Small-Angle X-ray Scattering, Light Scattering, and Coarse-Grained Modeling

Using light scattering (LS), small-angle X-ray scattering (SAXS), and coarse-grained Monte Carlo (MC) simulations, we studied the self-interactions of two monoclonal antibodies (mAbs), PPI03 and PPI13. With LS measurements, we obtained the osmotic second virial coefficient, B₂₂, and the molecular weight, M_w, of the two mAbs, while with SAXS measurements, we studied the mAbs' self-interaction behavior in the high protein concentration regime up to 125 g/L. Through SAXS-derived coarse-grained representations of the mAbs, we performed MC simulations with either a one-protein or a two-protein model to predict B₂₂. By comparing simulation and experimental results, we validated our models and obtained insights into the mAbs' self-interaction properties, highlighting the role of both ion binding and charged patches on the mAb surfaces. Our models provide useful information about mAbs' self-interaction properties and can assist the screening of conditions driving to colloidal stability.

ATP and Tri-Polyphosphate (TPP) Suppress Protein Aggregate Growth by a Supercharging Mechanism

A common strategy to increase aggregation resistance is through rational mutagenesis to supercharge proteins, which leads to high colloidal stability, but often has the undesirable effect of lowering conformational stability. We show this trade-off can be overcome by using small multivalent polyphosphate ions, adenosine triphosphate (ATP) and tripolyphosphate (TPP) as excipients. These ions are equally effective at suppressing aggregation of ovalbumin and bovine serum albumin (BSA) upon thermal stress as monitored by dynamic and static light scattering. Monomer loss kinetic studies, combined with measurements of native state protein–protein interactions and ζ-potentials, indicate the ions reduce aggregate growth by increasing the protein colloidal stability through binding and overcharging the protein. Out of three additional proteins studied, ribonuclease A (RNaseA), α-chymotrypsinogen (α-Cgn), and lysozyme, we only observed a reduction in aggregate growth for RNaseA, although overcharging by the poly-phosphate ions still occurs for lysozyme and α-Cgn. Because the salts do not alter protein conformational stability, using them as excipients could be a promising strategy for stabilizing biopharmaceuticals once the protein structural factors that determine whether multivalent ion binding will increase colloidal stability are better elucidated. Our findings also have biological implications. Recently, it has been proposed that ATP also plays an important role in maintaining intracellular biological condensates and preventing protein aggregation in densely packed cellular environments. We expect electrostatic interactions are a significant factor in determining the stabilizing ability of ATP towards maintaining proteins in non-dispersed states in vivo.

Surface Exposed Free Cysteine Suppresses Crystallization of Human γD-Crystallin

Human γD-crystallin (HGD) has remarkable stability against condensation in the human lens, sometimes over a whole lifetime. The native protein has a surface exposed free cysteine that forms dimers (Benedek, 1997; Ramkumar et al., 1864)^1,2 without specific biological function and leads to further protein association and/or aggregation, which creates a paradox for understanding its stability. Previous work has demonstrated that chemical modification of the protein at the free cysteine (C110), increases the temperature at which liquid-liquid phase separation occurs (LLPS), lowers protein solubility and suggests an important role for this amino acid in maintaining its long-term resistance to condensation. Here we demonstrate that mutation of the cysteine does not alter the structure or solubility (liquidus) line for the protein, but dramatically increases the protein crystal nucleation rate following LLPS, suggesting that the free cysteine has a vital role in suppressing crystallization in the human lens.

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.

Cluster Percolation Causes Shear Thinning Behavior in Concentrated Solutions of Monoclonal Antibodies

High-concentration (>100 g/L) solutions of monoclonal antibodies (mAbs) are typically characterized by anomalously large solution viscosity and shear thinning behavior for strain rates ≥10³ s^-1. Here, the link between protein-protein interactions (PPIs) and the rheology of concentrated solutions of COE-03 and COE-19 mAbs is studied by means of static and dynamic light scattering and microfluidic rheometry. By comparing the experimental data with predictions based on the Baxter sticky hard-sphere model, we surprisingly find a connection between the observed shear thinning and the predicted percolation threshold. The longest shear relaxation time of mAbs was much larger than that of model sticky hard spheres within the same region of the phase diagram, which is attributed to the anisotropy of the mAb PPIs. Our results suggest that not only the strength but also the patchiness of short-range attractive PPIs should be explicitly accounted for by theoretical approaches aimed at predicting the shear rate-dependent viscosity of dense mAb solutions.

A coarse-grained xDLVO model for colloidal protein-protein interactions

Colloidal protein-protein interactions (PPIs) of attractive and repulsive nature modulate the solubility of proteins, their aggregation, precipitation and crystallization. Such interactions are very important for many biotechnological processes, but are complex and hard to control, therefore, difficult to be understood in terms of measurements alone. In diluted protein solutions, PPIs can be estimated from the osmotic second virial coefficient, B22, which has been calculated using different methods and levels of theory. The most popular approach is based on the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory and its extended versions, i.e. xDLVO. Despite much efforts, these models are not fully quantitative and must be fitted to experiments, which limits their predictive value. Here, we report an extended xDLVO-CG model, which extends existing models by a coarse-grained representation of proteins and the inclusion of an additional ion-protein dispersion interaction term. We demonstrate for four proteins, i.e. lysozyme (LYZ), subtilisin (Subs), bovine serum albumin (BSA) and immunoglobulin (IgG1), that semi-quantitative agreement with experimental values without the need to fit to experimental B22 values. While most likely not the final step in the nearly hundred years of research in PPIs, xDLVO-CG is a step towards predictive PPIs calculations that are transferable to different proteins.

Toward a Suite of Coarse-Grained Models for Molecular Simulation of Monoclonal Antibodies and Therapeutic Proteins

A series of coarse-grained models for molecular simulation of proteins are considered, with emphasis on the application of predicting protein-protein self-interactions for monoclonal antibodies (MAbs). As an illustrative example and for quantitative comparison, the models are used to predict osmotic virial coefficients over a broad range of attractive and repulsive self-interactions and solution conditions for a series of MAbs where the second osmotic virial coefficient has been experimentally determined in prior work. The models are compared based on how well they can predict experimental behavior, their computational burdens, and scalability. An intermediate-resolution model is also introduced that can capture specific electrostatic interactions with improved efficiency and similar or improved accuracy when compared to the previously published models. Guidance is included for the selection of coarse-grained models more generally for capturing a balance of electrostatic, steric, and short-ranged nonelectrostatic interactions for proteins from low to high concentrations.

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.

Microwell Plate-Based Dynamic Light Scattering as a High-Throughput Characterization Tool in Biopharmaceutical Development

High-throughput light scattering instruments are widely used in screening of biopharmaceutical formulations and can be easily incorporated into processes by utilizing multi-well plate formats. High-throughput plate readers are helpful tools to assess the aggregation tendency and colloidal stability of biological drug candidates based on the diffusion self-interaction parameter (k_D). However, plate readers evoke issues about the precision and variability of determined data. In this article, we report about the statistical evaluation of intra- and inter-plate variability (384-well plates) for the k_D analysis of protein and peptide solutions. ANOVA revealed no significant differences between the runs. In conclusion, the reliability and precision of k_D was dependent on the plate position of the sample replicates and k_D value. Positive k_D values (57.0 mL/g, coefficients of variation (CV) 8.9%) showed a lower variability compared to negative k_D values (−14.8 mL/g, CV 13.4%). The variability of k_D was not reduced using more data points (120 vs. 30). A k_D analysis exclusively based on center wells showed a lower CV (<2%) compared to edge wells (5–12%) or a combination of edge and center wells (2–5%). We present plate designs for k_D analysis within the early formulation development, screening up to 20 formulations consuming less than 50 mg of active pharmaceutical ingredient (API).

Temperature Dependence of Protein Solution Viscosity and Protein-Protein Interactions: Insights into the Origins of High-Viscosity Protein Solutions

Protein solution viscosity (η) as a function of temperature was measured at a series of protein concentrations under a range of formulation conditions for two monoclonal antibodies (MAbs) and a globular protein (aCgn). Based on theoretical arguments, a strong temperature dependence for protein-protein interactions (PPI) indicates highly anisotropic, short-ranged attractions that could lead to higher solution viscosities. The semi-empirical Ross-Minton model was used to determine the apparent intrinsic viscosity, shape, and "crowding" factors for each protein as a function of temperature and formulation conditions. The apparent intrinsic viscosity was independent of temperature for aCgn, while a slight decrease with increasing temperature was observed for the MAbs. The temperature dependence of solution viscosity was analyzed using the Andrade-Eyring equation to determine the effective activation energy of viscous flow (E_a,η). While E_a,η values were different for each protein, they were independent of formulation conditions for a given protein. PPI were quantified via the osmotic second virial coefficient (B₂₂) and the protein diffusion interaction parameter (k_D) as a function of temperature under the same formulation conditions as the viscosity measurements. Net interactions ranged from strongly attractive to repulsive by changing formulation pH and ionic strength for each protein. Overall, larger activation energies for PPI corresponded to larger activation energies for η, and those were predictive of the highest η values at higher protein concentrations.

Analysis of antibody self-interaction by bio-layer interferometry as tool to support lead candidate selection during preformulation and developability assessments

Developability assessment of therapeutic mAb candidates before entering CMC development mitigates the risk of later failure because of manufacturing and stability issues. For mAbs derived from library based screenings, such evaluation starts with the first panning and ends with the selection of a lead candidate. This candidate should show, amongst others, high affine target binding and beneficial conformational as well as chemical stability. In addition, colloidal stability, reflected by the self-interaction propensity, should be superior in order to reduce aggregate formation and unacceptably high viscosity at elevated protein concentrations. Here, we present a study demonstrating the application of self-interaction bio-layer interferometry (SI-BLI) in a developability assessment, including the evaluation of preformulations. We reveal that the formulation rankings based on SI-BLI, DLS and viscosity measurements correlate. SI-BLI provides a deeper understanding of influencing factors on mAb self-interaction such as ionic strength or cation species. The attractive mAb self-interaction propensity was significantly more suppressed by Mg²⁺ compared to Na⁺. SI-BLI can be performed in high throughput with minimal material and sample preparation needs. Therefore, it can be applied in early stages of developability assessment going beyond the use of a platform formulation and a small number of analysis, to screen more parameters before proceeding with candidate selection and further extensive development.

Anomalous Salt Dependence Reveals an Interplay of Attractive and Repulsive Electrostatic Interactions in α-synuclein Fibril Formation

α-Synuclein (α-syn) is an intrinsically disordered protein with a highly asymmetric charge distribution, whose aggregation is linked to Parkinson’s disease. The effect of ionic strength was investigated at mildly acidic pH (5.5) in the presence of catalytic surfaces in the form of α-syn seeds or anionic lipid vesicles using thioflavin T fluorescence measurements. Similar trends were observed with both surfaces: increasing ionic strength reduced the rate of α-syn aggregation although the surfaces as well as α-syn have a net negative charge at pH 5.5. This anomalous salt dependence implies that short-range attractive electrostatic interactions are critical for secondary nucleation as well as heterogeneous primary nucleation. Such interactions were confirmed in Monte Carlo simulations of α-syn monomers interacting with surface-grafted C-terminal tails, and found to be weakened in the presence of salt. Thus, nucleation of α-syn aggregation depends critically on an attractive electrostatic component that is screened by salt to the extent that it outweighs the screening of the long-range repulsion between negatively charged monomers and negative surfaces. Interactions between the positively charged N-termini of α-syn monomers on the one hand, and the negatively C-termini of α-syn on fibrils or vesicles surfaces on the other hand, are thus critical for nucleation.

Biophysical Characterization of Binary Therapeutic Monoclonal Antibody Mixtures

Coformulations containing two therapeutic monoclonal antibodies (mAbs) could offer various benefits like enhanced therapeutic efficacy and better patient compliance. However, there are very few published studies on coformulations and binary mixtures of mAbs. It remains unclear to what extent mAbs with different physicochemical properties can be combined in solution without detrimental effects on protein stability. Here, we present a study including six model mAbs of the IgG1 subclass that are commercially available. In silico and biophysical characterization shows that the proteins have different physicochemical properties. Thus, their combinations represent various scenarios for coformulation development. We prepared all possible binary mixtures of the six mAbs and determined several biophysical parameters that are assessed during early-stage protein drug product development. The measured biophysical parameters are indicative of the conformational protein stability (inflection points of the thermal protein unfolding transitions) and the colloidal protein stability (aggregation onset temperatures and interaction parameter k_D from dynamic light scattering). Remarkably, all 15 binary mAb mixtures do not exhibit biophysical parameters that indicate inferior conformational or colloidal stability compared to the least stable mAb in the mixture. Our findings suggest that the coformulation of some therapeutic monoclonal antibodies of the IgG1 subclass could be possible in a straightforward way as severe detrimental effects on the stability of these proteins in binary mixtures were not observed.

Protein aggregation and immunogenicity of biotherapeutics

Recombinant proteins are the mainstay of biopharmaceuticals. A key challenge in the manufacturing and formulation of protein biologic products is the tendency for the active pharmaceutical ingredients to aggregate, resulting in irreversible drug loss, and an increase in immunogenicity risk. While the molecular mechanisms of protein aggregation have been discussed extensively in the literature, knowledge gaps remain in connecting the phenomenon in the context of immunogenicity of biotherapeutics. In this review, we discussed factors that drive aggregation of pharmaceutical recombinant proteins, and highlighted methods of prediction and mitigation that can be deployed through the development stages, from formulation to bioproduction. The purpose is to stimulate new dialogs that would bridge the interface between physical characterizations of protein aggregates in biotherapeutics and the functional attributes of the immune system.

Amplification of Salt-Induced Protein Diffusiophoresis by Varying Salt from Potassium to Sodium to Magnesium Chloride in Water

Salt-induced diffusiophoresis is the migration of a macromolecule or a colloidal particle induced by a concentration gradient of salt in water. Here, the effect of salt type on salt-induced diffusiophoresis of the protein lysozyme at pH 4.5 and 25 °C was examined as a function of salt concentration for three chloride salts: NaCl, KCl, and MgCl₂. Diffusiophoresis coefficients were calculated from experimental ternary diffusion coefficients on lysozyme-salt-water mixtures. In all cases, diffusiophoresis of this positively charged protein occurs from high to low salt concentration. An appropriate mass transfer process was theoretically examined to show that concentration gradients of MgCl₂ produce significant lysozyme diffusiophoresis. This is attributed to the relatively low mobility of Mg²⁺ ions compared to that of Cl^- ions at low salt concentration and a strong thermodynamic nonideality of this salt at high salt concentration. These findings indicate that MgCl₂ concentration gradients could be exploited for protein manipulation in solution (e.g., using microfluidic technologies) with applications to protein adsorption and purification. The dependence of lysozyme diffusiophoresis on salt type was theoretically examined and linked to protein charge. The effect of salts on hydrogen-ion titration curves was experimentally characterized to understand the role of salt type on protein charge. Our results indicate that binding of Mg²⁺ ions to lysozyme further enhances protein diffusiophoresis.

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.

Determination of Protein-Protein Interactions in a Mixture of Two Monoclonal Antibodies

The coformulation of monoclonal antibody (mAb) mixtures provides an attractive route to achieving therapeutic efficacy where the targeting of multiple epitopes is necessary. Controlling and predicting the behavior of such mixtures requires elucidating the molecular basis for the self- and cross-protein-protein interactions and how they depend on solution variables. While self-interactions are now beginning to be well understood, systematic studies of cross-interactions between mAbs in solution do not exist. Here, we have used static light scattering to measure the set of self- and cross-osmotic second virial coefficients in a solution containing a mixture of two mAbs, mAbA and mAbB, as a function of ionic strength and pH. mAbB exhibits strong association at a low ionic strength, which is attributed to an electrostatic attraction that is enhanced by the presence of a strong short-ranged attraction of nonelectrostatic origin. Under all solution conditions, the measured cross-interactions are intermediate self-interactions and follow similar patterns of behavior. There is a strong electrostatic attraction at higher pH values, reflecting the behavior of mAbB. Protein-protein interactions become more attractive with an increasing pH due to reducing the overall protein net charges, an effect that is attenuated with an increasing ionic strength due to the screening of electrostatic interactions. Under moderate ionic strength conditions, the reduced cross-virial coefficient, which reflects only the energetic contribution to protein-protein interactions, is given by a geometric average of the corresponding self-coefficients. We show the relationship can be rationalized using a patchy sphere model, where the interaction energy between sites i and j is given by the arithmetic mean of the i-i and j-j interactions. The geometric mean does not necessarily apply to all mAb mixtures and is expected to break down at a lower ionic strength due to the nonadditivity of electrostatic interactions.

Brownian Dynamics Simulations of Biological Molecules

Brownian dynamics (BD) is a technique for carrying out computer simulations of physical systems that are driven by thermal fluctuations. Biological systems at the macromolecular and cellular level, while falling in the gap between well-established atomic-level models and continuum models, are especially suitable for such simulations. We present a brief history, examples of important biological processes that are driven by thermal motion, and those that have been profitably studied by BD. We also present some of the challenges facing developers of algorithms and software, especially in the attempt to simulate larger systems more accurately and for longer times.