Mutational probing of protein aggregates to design aggregation-resistant proteins

Characterizing and Minimizing Aggregation and Particle Formation of Three Recombinant Fusion-Protein Bulk Antigens for Use in a Candidate Trivalent Rotavirus Vaccine

In a companion paper, the structural integrity, conformational stability, and degradation mechanisms of 3 recombinant fusion-protein antigens comprising a non-replicating rotavirus (NRRV) vaccine candidate (currently being evaluated in early-stage clinical trials) are described. In this work, we focus on the aggregation propensity of the 3 NRRV antigens coupled to formulation development studies to identify common frozen bulk candidate formulations. The P2-VP8-P[8] antigen was most susceptible to shaking and freeze-thaw-induced aggregation and particle formation. Each NRRV antigen formed aggregates with structurally altered protein (with exposed apolar regions and intermolecular β-sheet) and dimers containing a non-native disulfide bond. From excipient screening studies with P2-VP8-P[8], sugars or polyols (e.g., sucrose, trehalose, mannitol, sorbitol) and various detergents (e.g., Pluronic F-68, polysorbate 20 and 80, PEG-3350) were identified as stabilizers against aggregation. By combining promising additives, candidate bulk formulations were optimized to not only minimize agitation-induced aggregation, but also particle formation due to freeze-thaw stress of P2-VP8-P[8] antigen. Owing to limited material availability, stabilization of the P2-VP8-P[4] and P2-VP8-P[6] was confirmed with the lead candidate P2-VP8-P[8] formulations. The optimization of these bulk NRRV candidate formulations is discussed in the context of subsequent drug product formulations in the presence of aluminum adjuvants.

Ionic liquids and protein folding-old tricks for new solvents

One important aspect of the green chemistry revolution has been the use of ionic liquids as the solvent in liquid-phase enzymatic catalysis. An essential requirement for protein enzyme function is the correct folding of the polypeptide chain into its functional "native" state. Quantitative assessment of protein structure may be carried out either empirically, or by using model-based characterization procedures, in which the parameters are defined in terms of a standard reference state. In this short note, we briefly outline the nature of the parameters associated with different empirical and model-based characterization procedures and point out factors which affect their interpretation when using a base solvent different from water. This review principally describes arguments developed by Wakayama et al., Protein Solubility and Amorphous Aggregation: From Academic Research to Applications in Drug Discovery and Bioindustry, 2019, edited by Y. Kuroda and F. Arisaka; CMC Publishing House. Sections of that work are translated from the original Japanese and republished here with the full permission of CMC Publishing Corporation.

Biophysical studies of protein solubility and amorphous aggregation by systematic mutational analysis and a helical polymerization model

At concentrations above solubility, a protein aggregates, most often into amorphous aggregates, and loses its function. However, unlike amyloidogenic aggregates, which are β-sheeted fibrillar aggregates often related to neurodegenerative diseases, amorphous aggregates, where proteins aggregate/oligomerize without forming specific high-order structures, are rarely the focus of biophysical studies. Hence, protein solubility with respect to amorphous aggregation remains to be fully characterized from a biophysical viewpoint. Here, I briefly describe the structural nature of proteins in amorphous aggregates before discussing systematic mutational analyses that aim to rationalize the contribution of individual amino acids to the solubility of a protein. The discussion is expected to demonstrate that protein solubility, and, accordingly, amorphous aggregation, can be understood using thermodynamic and biophysical rationales similar to those used in the study of protein stability or, more recently, amyloidogenesis. Finally, I will argue that the mathematical formalism of the helical polymerization model (HPM) proposed by Oosawa, Kasai, and Asakura's group can be readily adapted to provide a thermodynamic description of a system containing amorphous aggregates and soluble particles. The HPM and HPM-derived models imply the presence of nuclei or seeds for amorphous aggregates, similar to those hypothesized in crystallogenesis and amyloidogenesis.

Identification of Protein-Excipient Interaction Hotspots Using Computational Approaches

Protein formulation development relies on the selection of excipients that inhibit protein–protein interactions preventing aggregation. Empirical strategies involve screening many excipient and buffer combinations using force degradation studies. Such methods do not readily provide information on intermolecular interactions responsible for the protective effects of excipients. This study describes a molecular docking approach to screen and rank interactions allowing for the identification of protein–excipient hotspots to aid in the selection of excipients to be experimentally screened. Previously published work with Drosophila Su(dx) was used to develop and validate the computational methodology, which was then used to determine the formulation hotspots for Fab A33. Commonly used excipients were examined and compared to the regions in Fab A33 prone to protein–protein interactions that could lead to aggregation. This approach could provide information on a molecular level about the protective interactions of excipients in protein formulations to aid the more rational development of future formulations.