Coarse-Grained Modeling of Antibodies from Small-Angle Scattering Profiles

Abstract

Predicting the concentrated solution behavior for monoclonal antibodies requires developing and using minimal models to describe their shape and interaction potential. Toward this end, the small-angle X-ray scattering (SAXS) profiles for a monoclonal antibody (COE-03) have been measured under solution conditions chosen to produce weak self-association. The experiments are complemented with molecular simulations of a three-bead antibody model with and without interbead attraction. The scattering profile is extracted directly from the molecular simulation to avoid using the decoupling approximation. We examine the ability of the three-bead model to capture features of the scattering profile and the dependence of compressibilty on protein concentration. The three-bead model is able to reproduce generic features of the experimental structure factor as a function of wave vector S(k) including a well-defined shoulder, which is a consequence of the planar structure of the antibody, and a well-defined minimum in S(k) at k ∼ 0.025 Å. We also show the decoupling approximation is incapable of accounting for highly anisotropic shapes. The best-fit parameters obtained from matching spherical models to simulated scattering profiles are protein concentration dependent, which limits their applicability for predicting thermodynamic properties. Nevertheless, the experimental compressibility curves can be accurately reproduced by an appropriate parametrization of the Baxter adhesive model, indicating the model provides a semiempirical equation of state for the antibody. The results provide insights into how equations of state can be improved for antibodies by accounting for their anisotropic shapes.

Self-Interaction of Human Serum Albumin: A Formulation Perspective

“…The spherical assumption was examined in a computational study for a monoclonal antibody by comparing the structure factor profiles and osmotic compressibility of a three-bead model for the protein to that of an equivalent hard sphere with the same osmotic second virial coefficient. 65 For excluded volume systems, the osmotic compressibility is proportional to the fraction of overlapping particle configurations. Because the three-bead model and the sphere have the same osmotic second virial coefficient, the osmotic compressibility is similar at low protein concentrations, where only two-body interactions are significant.…”

Engineering Stability, Viscosity, and Immunogenicity of Antibodies by Computational Design

“…180,181,185 SAXS has been used to study self-association of antibody molecules in solution, and the resulting scattering profiles have been interpreted based on simple spherical models interacting through potentials comprised of long-rage repulsion and short-range attraction. [185][186][187] Corbett et al 188 have gone one step further by using CGMD simulations with a 3-bead model, which was able to reproduce features of SAXS profiles that were not captured by spherical models.…”

Potential and limits of a colloid approach to protein solutions

“…45,[126][127][128][129][130] A number of studies have made attempts to characterize cluster formation in mAb solutions, and to interpret antibody solution properties through analogies with colloids. [129][130][131][132][133][134][135][136][137] This is by no means straightforward due to the nonspherical shape and internal flexibility of mAbs, since interactions between proteins are frequently treated based on spherical approximations, and in particular the enormous effect that specific, directional interactions can have are often not considered.…”