Quadrupole Dalton-Based Controlled Proteolysis Method for Characterization of Higher Order Protein Structure

Limited Proteolysis Coupled with Mass Spectrometry for Simultaneous Evaluation of a Large Number of Protein Variants for Their Impact on Conformational Stability

A stable molecular structure is important in the development of a protein candidate into a therapeutic product. A therapeutic protein often contains many different variants; some of them may have an impact on the conformational stability of the protein. Conventionally, to evaluate the impact of a variant on stability, the variant must be enriched to a reasonable purity, and then its stability characterized by chromatographic or biophysical techniques. However, it is often impractical to purify and characterize each variant in a therapeutic protein. A workflow, based on limited proteolysis followed by MS detection, was established to simultaneously assess the impact of a large number of variants on conformational stability without enrichment. Because a less stable domain is more susceptible to proteolytic degradation, conformational stability of the domain can be reported from the release rate of a proteolytic peptide. A kinetic model is established to quantitatively determine the extent of domain stabilization/destabilization of different variants. The methodology is demonstrated by examining variants known to affect the stability of immunoglobulin domains, such as different N-glycoforms, methionine oxidations, and sequence variants. With this methodology, near 100 variants may be evaluated within 2 days in a single experiment. Insights into the sequence-stability relationship will be obtained by monitoring the large number of low-level sequence variants, facilitating engineering of more stable molecules.

A multi-angular view on the impact of protein unfolding on biophysical structural data

The performance of biophysical methods used for the characterization of protein higher order structure (HOS) is key to ensure reliable structural data for drug applications, as these methods are not routinely validated. To assess the analytical performance characteristics, the impact of increasing amounts of heat-denatured material (HDM) on HOS data obtained for a monoclonal antibody (mAb) and its cysteine-conjugated antibody-drug conjugate (ADC) by a set of biophysical methods routinely used in the pharmaceutical industry was evaluated. Relationships between structural data generated by these methods were established using statistical correlation analysis. Most individual methods revealed a linear correlation with increasing amounts of HDM, in the presence of intact mAb or ADC. Overall, Pearson correlation analysis showed strong correlations between the biophysical data obtained. Moreover, biophysical methods that are generally claimed to be orthogonal, were confirmed to provide similar structural insights based on the data obtained. Some methods were capable of differentiating the impact of structural change and/or onset of protein aggregation between the mAb and the ADC. Our results underline the capabilities and performance of the biophysical characterization methods investigated, thereby substantiating these are 'scientifically sound' and 'fit for purpose': the interrogation of protein HOS as part of pharmaceutical development.

Native peptide mapping - A simple method to routinely monitor higher order structure changes and relation to functional activity

In the biopharmaceutical environment, controlling the Critical Quality Attributes (CQA) of a product is essential to prevent changes that affect its safety or efficacy. Physico-chemical techniques and bioassays are used to screen and monitor these CQAs. The higher order structure (HOS) is a CQA that is typically studied using techniques that are not commonly considered amenable to quality control laboratories. Here, we propose a peptide mapping-based method, named native peptide mapping, which could be considered as straightforward for HOS analysis and applicable for IgG4 and IgG1 antibodies. The method was demonstrated to be fit-for-purpose as a stability-indicating assay by showing differences at the peptide level between stressed and unstressed material. The unfolding pathway induced by a heat stress was also studied via native peptide mapping assay. Furthermore, we demonstrated the structure–activity relationship between HOS and biological activity by analyzing different types of stressed samples with a cell-based assay and the native peptide mapping. The correlation between both sets of results was highlighted by monitoring peptides located in the complementary-determining regions and the relative potency of the biotherapeutic product. This relationship represents a useful approach to interrogate the criticality of HOS as a CQA of a drug.