ABSTRACT
Biopharmaceutical molecules such as monoclonal antibodies (mAbs) undergo a series of complex processing steps to obtain the nal product. Specically, proteinbased biotherapeutics can undergo steps such as production, harvest, purication, refolding, freeze-thaw, drying, formulation, lling, nebulization, and shipping to obtain the nal product. These processing steps and factors such as high concentrations, variable temperatures, pH extremes, varying ionic strength, agitation, light, shear stresses, air-liquid interface, and a variety of solid-liquid interfaces subject the drug molecules to many stresses and cause them to degrade.1 Advances in analytical chemistry have identied many degradation pathways that occur in protein therapeutics over time. These pathways, which depend not only on the above-mentioned factors, but also on the protein sequence-structure, generate either physical instability or chemical instability, or both. The physical degradation pathway includes unfolding, dissociation, denaturation, precipitation, and aggregation, while the chemical degradation pathway includes oxidation, deamidation, aspartate isomerization, and peptide bond hydrolysis. Quite often, protein degradation pathways are synergistic; that is, a chemical degradation event triggers a physical degradation event, such as when oxidation of a labile residue in the protein is followed by protein aggregation. These degradations not only lead to protein drug product heterogeneity, but also might lead to immunogenicity when administered to patients, reduced target binding, altered pharmacokinetics, and so forth.2,3
In this chapter, the current understanding and computational tools for prediction of degradation, such as aggregation-, oxidation-, and deamidation-prone sites, are discussed. Since, among these pathways, protein aggregation is one of the most common pathways of degradation, a large section of this chapter is devoted to computational tools for addressing protein aggregation.
