Small-angle neutron scattering characterization of monoclonal antibody conformations and interactions at high concentrations

Predicting Protein-Protein Interactions of Concentrated Antibody Solutions Using Dilute Solution Data and Coarse-Grained Molecular Models

Protein-protein interactions for solutions of an IgG1 molecule were quantified using static light scattering (SLS) measurements from low to high protein concentrations (c₂). SLS was used to determine second osmotic virial coefficients (B₂₂) at low c₂, and excess Rayleigh profiles (R^ex/K vs. c₂) and zero-q structure factors (S_q=0) as a function of c₂ at higher c₂ for a series of conditions (pH, sucrose concentration, and total ionic strength [TIS]). Repulsive (attractive) interactions were observed at low TIS (high TIS) for pH 5 and 6.5, with increasing repulsions when 5% w/w sucrose was also present. Previously developed and refined coarse-grained antibody models were used to fit model parameters from B₂₂ versus TIS data. The resulting parameters from low-c₂ conditions were used as the sole input to multiprotein Monte Carlo simulations to predict high-c₂R^ex/K and S_q=0 behavior up to 150 g/L. Experimental results at high-c₂ conditions were quantitatively predicted by the simulations for the coarse-grained models that treated antibody molecules as either 6 or 12 (sub) domains, which preserved the basic shape of a monoclonal antibody. Finally, preferential accumulation of sucrose around the protein surface was identified via high-precision density measurements, which self-consistently explained the simulation and experimental SLS results.

Characterization of Monoclonal Antibody-Protein Antigen Complexes Using Small-Angle Scattering and Molecular Modeling

The determination of monoclonal antibody interactions with protein antigens in solution can lead to important insights guiding physical characterization and molecular engineering of therapeutic targets. We used small-angle scattering (SAS) combined with size-exclusion multi-angle light scattering high-performance liquid chromatography to obtain monodisperse samples with defined stoichiometry to study an anti-streptavidin monoclonal antibody interacting with tetrameric streptavidin. Ensembles of structures with both monodentate and bidentate antibody-antigen complexes were generated using molecular docking protocols and molecular simulations. By comparing theoretical SAS profiles to the experimental data it was determined that the primary component(s) were compact monodentate and/or bidentate complexes. SAS profiles of extended monodentate complexes were not consistent with the experimental data. These results highlight the capability for determining the shape of monoclonal antibody-antigen complexes in solution using SAS data and physics-based molecular modeling.

Design and Properties of Genetically Encoded Probes for Sensing Macromolecular Crowding

Cells are highly crowded with proteins and polynucleotides. Any reaction that depends on the available volume can be affected by macromolecular crowding, but the effects of crowding in cells are complex and difficult to track. Here, we present a set of Förster resonance energy transfer (FRET)-based crowding-sensitive probes and investigate the role of the linker design. We investigate the sensors in vitro and in vivo and by molecular dynamics simulations. We find that in vitro all the probes can be compressed by crowding, with a magnitude that increases with the probe size, the crowder concentration, and the crowder size. We capture the role of the linker in a heuristic scaling model, and we find that compression is a function of size of the probe and volume fraction of the crowder. The FRET changes observed in Escherichia coli are more complicated, where FRET-increases and scaling behavior are observed solely with probes that contain the helices in the linker. The probe with the highest sensitivity to crowding in vivo yields the same macromolecular volume fractions as previously obtained from cell dry weight. The collection of new probes provides more detailed readouts on the macromolecular crowding than a single sensor.

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

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

Intermediate scattering function for macromolecules in solutions probed by neutron spin echo

The neutron-spin-echo method (NSE) is a powerful technique for studying internal dynamics of macromolecules in solutions because it can simultaneously probe length and time scales comparable to intramolecular density fluctuations of macromolecules. Recently, there has been increased, strong interest in studying protein internal motions using NSE. The coherent intermediate scattering function (ISF) measured by NSE depends on internal, rotational, and translational motions of macromolecules in solutions. It is thus critical, but highly nontrivial, to separate the internal motion from other motions in order to properly understand protein internal dynamics. Even though many experiments are performed at relatively high concentrations, current theories of calculating the ISF of concentrated protein solutions are either inaccurate or flawed by incorrect assumptions for realistic protein systems with anisotropic shapes. Here, a theoretical framework is developed to establish the quantitative relationship of different motions included in the ISF. This theory based on the dynamic decoupling approximation is applicable to a wide range of protein concentrations, including dilute cases. It is also, in general, useful for studying many other types of macromolecule systems studied by NSE.

Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars

DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed of 196 nucleotides) and to explore the structural signatures of their aggregation process. We report small-angle neutron scattering experiments focused on the evaluation of both the form factor and the temperature evolution of the scattered intensity at a nanostar concentration where the system forms a tetravalent equilibrium gel. We also perform molecular dynamics simulations of one isolated tetramer to evaluate the form factor numerically, without resorting to any approximate shape. The numerical form factor is found to be in very good agreement with the experimental one. Simulations predict an essentially temperature-independent form factor, offering the possibility to extract the effective structure factor and its evolution during the equilibrium gelation.

Structure of colloidal gels at intermediate concentrations: the role of competing interactions

Colloidal gels formed by colloid-polymer mixtures with an intermediate volume fraction (ϕ_c ≈ 0.4) are investigated by confocal microscopy. In addition, we have performed Monte Carlo simulations based on a simple effective pair potential that includes a short-range attractive contribution representing depletion interactions, and a longer-range repulsive contribution describing the electrostatic interactions due to the presence of residual charges. Despite neglecting non-equilibrium effects, experiments and simulations yield similar gel structures, characterised by, e.g., the pair, angular and bond distribution functions. We find that the structure hardly depends on the strength of the attraction if the electrostatic contribution is fixed, but changes significantly if the electrostatic screening is changed. This delicate balance between attractions and repulsions, which we quantify by the second virial coefficient, also determines the location of the gelation boundary.

A critical examination of the decoupling approximation for small-angle scattering from hard ellipsoids of revolution

The decoupling approximation, proposed by Kotlarchyk & Chen [J. Chem. Phys. (1983), 79, 2461–2469], is a first-order correction to the experimentally determined apparent structure factor that is necessary because of concentration effects in polydisperse and/or nonspherical systems. While the approximation is considered accurate for spheres with low polydispersity (<10%), the corresponding limitations for nonspherical particles are unknown. The validity of this approximation is studied for monodisperse dispersions of hard ellipsoids of revolution with aspect ratios ranging from 0.333 to 3 and a guide for its accuracy is provided.

Rheology of clustering protein solutions

High viscosity is a major challenge with protein therapeutics at extremely high concentrations. To overcome this obstacle, it is essential to understand the relationship between the concentration of a protein solution and its viscosity as a function of shear rate and temperature. Here, lysozyme is a model charged globular protein having both short-ranged attraction (SA) and long-ranged repulsion (LR) that promote the formation of dynamic clusters at high concentrations. We report viscosity measurements from a micro-capillary rheometer (using only several microliters of solution) over a wide range of lysozyme solution concentrations, shear rates, and temperatures. Solution structural relaxation dynamics are also probed by dynamic light scattering (DLS). As a result of lysozyme's SALR interactions, the viscosity increased dramatically across all shear rates with increasing concentration and decreasing temperature. While most of the solutions exhibited Newtonian behavior, shear thinning was exhibited at the highest concentration (480 g/l) and lowest temperatures at shear rates above approximately 10(4 )s(-1). The onset shear rate for thinning and a structural relaxation rate estimated from a slow-mode measured by DLS are compared. These measurements provide insights into the properties of protein solutions and their microscopic structural origins.

Aggregation of Antibody Drug Conjugates at Room Temperature: SAXS and Light Scattering Evidence for Colloidal Instability of a Specific Subpopulation

Coupling a hydrophobic drug onto monoclonal antibodies via lysine residues is a common route to prepare antibody-drug conjugates (ADC), a promising class of biotherapeutics. But a few chemical modifications on protein surface often increase aggregation propensity, without a clear understanding of the aggregation mechanisms at stake (loss of colloidal stability, self-assemblies, denaturation, etc.), and the statistical nature of conjugation introduces polydispersity in the ADC population, which raises questions on whether the whole ADC population becomes unstable. To characterize the average interactions between ADC, we monitored small-angle X-ray scattering in solutions of monoclonal IgG1 human antibody drug conjugate, with average degree of conjugation of 0, 2, or 3 drug molecules per protein. To characterize stability, we studied the kinetics of aggregation at room temperature. The intrinsic Fuchs stability ratio of the ADC was estimated from the variation over time of scattered light intensity and hydrodynamic radius, in buffers of varying pH, and at diverse sucrose (0% or 10%) and NaCl (0 or 100 mM) concentrations. We show that stable ADC stock solutions became unstable upon pH shift, well below the pH of maximum average attraction between IgGs. Data indicate that aggregation can be ascribed to a fraction of ADC population usually representing less than 30 mol % of the sample. In contrast to the case of (monodisperse) monoclonal antibodies, our results suggest that a poor correlation between stability and average interaction parameters should be expected as a corollary of dispersity of ADC conjugation. In practice, the most unstable fraction of the ADC population can be removed by filtration, which affects remarkably the apparent stability of the samples. Finally, the lack of correlation between the kinetic stability and variations of the average inter-ADC interactions is tentatively attributed to the uneven nature of charge distributions and the presence of patches on the drug-modified antibodies.

Coacervation and precipitation in polysaccharide-protein systems

Precipitation poses a consistent problem for the growing applications of biopolymer coacervation, but the relationship between the two types of phase separation is not well understood. To clarify this relationship, we studied phase separation as a function of pH and ionic strength, in three systems of proteins with anionic polysaccharides: β-lactoglobulin (BLG)/hyaluronic acid (HA); BLG/tragacanthin (TG); and monoclonal antibody (mAb)/HA. We found that coacervation and precipitation are intrinsically different phenomena, responsive to different factors, but their simultaneity (for example with changing pH) may be confused with transitions from one state to another. We propose that coacervate does not literally turn into precipitate, but rather that both coacervate and precipitate are in equilibrium with free protein and polyanion, so that dissolution of one and formation of the other can overlap in time. While protein-polyanion complexes must achieve neutrality for coacervation, precipitation only requires tight binding which leads to the expulsion of counterions and water molecules. The pH-dependence of phase separation, considered in terms of protein and polyion charge, revealed that the electrostatic magnitude of the protein's polymer-binding site ("charge patch") plays a key role in the strength of interaction. These findings were supported by the inhibition of precipitation, seen when the bulky side chains of TG impede close protein-polymer interactions.

Effect of Hierarchical Cluster Formation on the Viscosity of Concentrated Monoclonal Antibody Formulations Studied by Neutron Scattering

Recently, reversible cluster formation was identified as an underlying cause of anomalously large solution viscosities observed in some concentrated monoclonal antibody (mAb) formulations, which poses a major challenge to the use of subcutaneous injection for some mAbs. A fundamental understanding of the structural and dynamic origins of high viscosities in concentrated mAb solutions is thus of significant relevance to mAb applications in human health care, as well as being of scientific interest. Herein, we present a detailed investigation of an IgG1-based mAb to relate the short-time dynamics and microstructure to significant viscosity changes over a range of pharmaceutically relevant physiochemical conditions. The combination of light scattering, small-angle neutron scattering, and neutron spin echo measurement techniques conclusively demonstrates that, upon addition of Na2SO4, these antibodies form strongly bound reversible dimers at dilute concentrations that interact with each other to form large, loosely bound, transient clusters when concentrated. This hierarchical structure formation in solution causes a significant increase in the solution viscosity.

Structural Changes and Aggregation Mechanisms for Anti-Streptavidin IgG1 at Elevated Concentration

Non-native protein aggregation may occur during manufacturing and storage of protein therapeutics, and this may decrease drug efficacy or jeopardize patient safety. From a regulatory perspective, changes in higher order structure due to aggregation are of particular interest but can be difficult to monitor directly at elevated protein concentrations. The present report focuses on non-native aggregation of antistreptavidin (AS) IgG1 at 30 mg/mL under solution conditions that prior work at dilute concentrations (e.g., 1 mg/mL) indicated would result in different aggregation mechanisms. Time-dependent aggregation and structural changes were monitored in situ with dynamic light scattering, small-angle neutron scattering, and Raman scattering and ex situ with far-UV circular dichroism and second-derivative UV spectroscopy. The effects of adding 0.15 M (∼5 w/w %) sucrose were also assessed. The addition of sucrose decreased monomer loss rates but did not change protein-protein interactions, aggregation mechanism(s), or aggregate structure and morphology. Consistent with prior results, altering the pD or salt concentration had the primary effect of changing the aggregation mechanism. Overall, the results provide a comparison of aggregate structure and morphology created via different growth mechanisms using orthogonal techniques and show that the techniques agree at least qualitatively. Interestingly, AS-IgG1 aggregates created at pD 5.3 with no added salt formed the smallest aggregates but had the largest structural changes compared to other solution conditions. The observation that the larger aggregates were also those with less structural perturbation compared to folded AS-IgG1 might be expected to extend to other proteins if the same strong electrostatic repulsions that mediate aggregate growth also mediate structural changes of the constituent proteins within aggregates.

Critical examination of the colloidal particle model of globular proteins

Recent studies of globular protein solutions have uniformly adopted a colloidal view of proteins as particles, a perspective that neglects the polymeric primary structure of these biological macromolecules, their intrinsic flexibility, and their ability to sample a large configurational space. While the colloidal perspective often serves as a useful idealization in many cases, the macromolecular identity of proteins must reveal itself under thermodynamic conditions in which the native state is no longer stable, such as denaturing solvents and high protein concentrations where macromolecules tend to have screened excluded volume, charge, and hydrodynamic interactions. Under extreme pH conditions, charge repulsion interactions within the protein chain can overcome the attractive hydrogen-bonding interactions, holding it in its native globular state. Conformational changes can therefore be expected to have great significance on the shear viscosity and other rheological properties of protein solutions. These changes are not envisioned in conventional colloidal protein models and we have initiated an investigation of the scattering and rheological properties of model proteins. We initiate this effort by considering bovine serum albumin because it is a globular protein whose solution properties have also been extensively investigated as a function of pH, temperature, ionic strength, and concentration. As we anticipated, near-ultraviolet circular dichroism measurements and intrinsic viscosity measurements clearly indicate that the bovine serum albumin tertiary structure changes as protein concentration and pH are varied. Our findings point to limited validity of the colloidal protein model and to the need for further consideration and quantification of the effects of conformational changes on protein solution viscosity, protein association, and the phase behavior. Small-angle Neutron Scattering measurements have allowed us to assess how these conformational changes influence protein size, shape, and interprotein interaction strength.

Pattern formation in binary fluid mixtures induced by short-range competing interactions

Molecular dynamics simulations and integral equation calculations of a simple equimolar mixture of diatomic molecules and monomers interacting via attractive and repulsive short-range potentials show the existence of pattern formation (microheterogeneity), mostly due to depletion forces away from the demixing region. Effective site-site potentials extracted from the pair correlation functions using an inverse Monte Carlo approach and an integral equation inversion procedure exhibit the features characteristic of a short-range attractive and a long-range repulsive potential. When charges are incorporated into the model, this becomes a coarse grained representation of a room temperature ionic liquid, and as expected, intermediate range order becomes more pronounced and stable.

Explaining the non-newtonian character of aggregating monoclonal antibody solutions using small-angle neutron scattering

A monoclonal antibody solution displays an increase in low shear rate viscosity upon aggregation after prolonged incubation at 40°C. The morphology and interactions leading to the formation of the aggregates responsible for this non-Newtonian character are resolved using small-angle neutron scattering. Our data show a weak repulsive barrier before proteins aggregate reversibly, unless a favorable contact with high binding energy occurs. Two types of aggregates were identified after incubation at 40°C: oligomers with radius of gyration ∼10 nm and fractal submicrometer particles formed by a slow reaction-limited aggregation process, consistent with monomers colliding many times before finding a favorable strong interaction site. Before incubation, these antibody solutions are Newtonian liquids with no increase in low shear rate viscosity and no upturn in scattering at low wavevector, whereas aggregated solutions under the same conditions have both of these features. These results demonstrate that fractal submicrometer particles are responsible for the increase in low shear rate viscosity and low wavevector upturn in scattered intensity of aggregated antibody solutions; both are removed from aggregated samples by filtering.

Observation of small cluster formation in concentrated monoclonal antibody solutions and its implications to solution viscosity

Monoclonal antibodies (mAbs) are a major class of biopharmaceuticals. It is hypothesized that some concentrated mAb solutions exhibit formation of a solution phase consisting of reversibly self-associated aggregates (or reversible clusters), which is speculated to be responsible for their distinct solution properties. Here, we report direct observation of reversible clusters in concentrated solutions of mAbs using neutron spin echo. Specifically, a stable mAb solution is studied across a transition from dispersed monomers in dilute solution to clustered states at more concentrated conditions, where clusters of a preferred size are observed. Once mAb clusters have formed, their size, in contrast to that observed in typical globular protein solutions, is observed to remain nearly constant over a wide range of concentrations. Our results not only conclusively establish a clear relationship between the undesirable high viscosity of some mAb solutions and the formation of reversible clusters with extended open structures, but also directly observe self-assembled mAb protein clusters of preferred small finite size similar to that in micelle formation that dominate the properties of concentrated mAb solutions.

Role of anisotropic interactions for proteins and patchy nanoparticles

Protein–protein interactions are inherently anisotropic to some degree, with orientation-dependent interactions between repulsive and attractive or complementary regions or “patches” on adjacent proteins. In some cases it has been suggested that such patch–patch interactions dominate the thermodynamics of dilute protein solutions, as captured by the osmotic second virial coefficient (B₂₂), but delineating when this will or will not be the case remains an open question. A series of simplified but exactly solvable models are first used to illustrate that a delicate balance exists between the strength of attractive patch–patch interactions and the patch size, and that repulsive patch–patch interactions contribute significantly to B₂₂ for only those conditions where the repulsions are long-ranged. Finally, B₂₂ is reformulated, without approximations, in terms of the density of states for a given interaction energy and particle–particle distance. Doing so illustrates the inherent balance of entropic and energetic contributions to B₂₂. It highlights that simply having strong patch–patch interactions will only cause anisotropic interactions to dominate B₂₂ solution properties if the unavoidable entropic penalties are overcome, which cannot occur if patches are too small. The results also indicate that the temperature dependence of B₂₂ may be a simple experimental means to assess whether a small number of strongly attractive configurations dominate the dilute solution behavior.

Improving monoclonal antibody selection and engineering using measurements of colloidal protein interactions

A limitation of using mAbs as therapeutic molecules is their propensity to associate with themselves and/or with other molecules via nonaffinity (colloidal) interactions. This can lead to a variety of problems ranging from low solubility and high viscosity to off-target binding and fast antibody clearance. Measuring such colloidal interactions is challenging given that they are weak and potentially involve diverse target molecules. Nevertheless, assessing these weak interactions-especially during early antibody discovery and lead candidate optimization-is critical to preventing problems that can arise later in the development process. Here we review advances in developing and implementing sensitive methods for measuring antibody colloidal interactions as well as using these measurements for guiding antibody selection and engineering. These systematic efforts to minimize nonaffinity interactions are expected to yield more effective and stable mAbs for diverse therapeutic applications. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 103:3356-3363, 2014.

Protein aggregation and its impact on product quality

Protein pharmaceutical products are typically active as folded monomers that are composed of one or more protein chains, such as the heavy and light chains in monoclonal antibodies that are a mainstay of current drug pipelines. There are numerous possible aggregated states for a given protein, some of which are potentially useful, while most of which are considered deleterious from the perspective of pharmaceutical product quality and performance. This review provides an overview of how and why different aggregated states of proteins occur, how this potentially impacts product quality and performance, fundamental approaches to control aggregate formation, and the practical approaches that are currently used in the pharmaceutical industry.

Generalized phase behavior of cluster formation in colloidal dispersions with competing interactions

Colloidal liquids interacting with short range attraction and long range repulsion, such as proposed for some protein solutions, have been found to exhibit novel states consisting of equilibrium particle clusters. Monte Carlo simulations are performed for two physically meaningful inter-particle potentials across a broad range of interaction parameters, temperatures and volume fractions to locate the conditions where clustered states are found. A corresponding states phase behavior is identified when normalized by the critical point of an appropriately selected reference attractive fluid. Clustered fluid states and cluster percolated states are found exclusively within the two phase region of the state diagram for a reference attractive fluid, confirming the underlying intrinsic relation between clustered states and bulk phase separation. Clustered and cluster percolated states consistently exhibit an intermediate range order peak in their structure factors with a magnitude above 2.7, leading to a semi-empirical rule for identifying clustered fluids in scattering experiments.