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. 2024 Nov 4;21(11):5497-5509.
doi: 10.1021/acs.molpharmaceut.4c00332. Epub 2024 Oct 21.

Molecular Dynamics Simulations Reveal How Competing Protein-Surface Interactions for Glycine, Citrate, and Water Modulate Stability in Antibody Fragment Formulations

Affiliations

Molecular Dynamics Simulations Reveal How Competing Protein-Surface Interactions for Glycine, Citrate, and Water Modulate Stability in Antibody Fragment Formulations

Akash Pandya et al. Mol Pharm. .

Abstract

The design of stable formulations remains a major challenge for protein therapeutics, particularly the need to minimize aggregation. Experimental formulation screens are typically based on thermal transition midpoints (Tm), and forced degradation studies at elevated temperatures. Both approaches give limited predictions of long-term storage stability, particularly at low temperatures. Better understanding of the mechanisms of action for formulation of excipients and buffers could lead to improved strategies for formulation design. Here, we identified a complex impact of glycine concentration on the experimentally determined stability of an antibody Fab fragment and then used molecular dynamics simulations to reveal mechanisms that underpin these complex behaviors. Tm values increased monotonically with glycine concentration, but associated ΔSvh measurements revealed more complex changes in the native ensemble dynamics, which reached a maximum at 30 mg/mL. The aggregation kinetics at 65 °C were similar at 0 and 20 mg/mL glycine, but then significantly slower at 50 mg/mL. These complex behaviors indicated changes in the dominant stabilizing mechanisms as the glycine concentration was increased. MD revealed a complex balance of glycine self-interaction, and differentially preferred interactions of glycine with the Fab as it displaced hydration-shell water, and surface-bound water and citrate buffer molecules. As a result, glycine binding to the Fab surface had different effects at different concentrations, and led from preferential interactions at low concentrations to preferential exclusion at higher concentrations. During preferential interaction, glycine displaced water from the Fab hydration shell, and a small number of water and citrate molecules from the Fab surface, which reduced the protein dynamics as measured by root-mean-square fluctuation (RMSF) on the short time scales of MD. By contrast, the native ensemble dynamics increased according to ΔSvh, suggesting increased conformational changes on longer time scales. The aggregation kinetics did not change at low glycine concentrations, and so the opposing dynamics effects either canceled out or were not directly relevant to aggregation. During preferential exclusion at higher glycine concentrations, glycine could only bind to the Fab surface through the displacement of citrate buffer molecules already favorably bound on the Fab surface. Displacement of citrate increased the flexibility (RMSF) of the Fab, as glycine formed fewer bridging hydrogen bonds to the Fab surface. Overall, the slowing of aggregation kinetics coincided with reduced flexibility in the Fab ensemble at the very highest glycine concentrations, as determined by both RMSF and ΔSvh, and occurred at a point where glycine binding displaced neither water nor citrate. These final interactions with the Fab surface were driven by mass action and were the least favorable, leading to a macromolecular crowding effect under the regime of preferential exclusion that stabilized the dynamics of Fab.

Keywords: Fab; aggregation; enthalpy change; formulation; melting temperature; preferential interaction; stability.

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Conflict of interest statement

The authors declare no competing financial interest.

Figures

Figure 1
Figure 1
Effect of glycine concentration on the conformational stability of A33 Fab. The change in van’t Hoff entropies (ΔSvh) and the thermal transition midpoint temperatures (Tm) for 3 mg/mL A33 Fab as a function of glycine concentration in 20 mM sodium citrate, pH 4.5, were determined from thermal unfolding profiles.
Figure 2
Figure 2
Concentration-dependent self-association of glycine, and interactions with citrate in MD simulations. (A) Monomeric fraction of glycine decreases, while dimer & Nmer populations increase with increasing bulk glycine concentration. (B) Number of hydrogen bonds formed between citrate and glycine as a function of the bulk glycine concentration.
Figure 3
Figure 3
Quantifying the interactions of glycine and citrate with Fab during MD simulations. (A) Preferential Interaction Coefficient (Γ23) as a function of glycine bulk concentration. (B) Number of hydrogen bonds formed between excipients (citrate and glycine) and A33 Fab as a function of the bulk glycine concentration.
Figure 4
Figure 4
Surface mapping of Fab-Gly and Fab-citrate interactions, and the residue-level ΔRMSF. (A) Glycine contact frequencies mapped onto the Fab surface. (B) Citrate contact frequencies were mapped onto the Fab surface. (C) Residue level ΔRMSF (%) relative to 0 mg/mL Gly.
Figure 5
Figure 5
Global average ΔRMSF (%) as a function of glycine concentration for the whole protein, backbone, or side chain atoms. RMSF at each condition is the global average RMSF for all residues of Fab.
Figure 6
Figure 6
Global average ΔRMSF (%) as a function of glycine concentration by location within the protein. (A) Exposed and Buried A33 Fab residues. (B–E) Overall, backbone, and side chain for VH (B), VL (C), CH1 (D), CL (E) domain residues.
Figure 7
Figure 7
Snapshots of citrate and glycine interacting with the K39, K42, and K45 hotspot. (A) 0 mg/mL glycine. (B) 20 mg/mL glycine. At 20 mg/mL, interactions with both citrate and glycine are observed simultaneously.

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