Characterization of free thiol variants of an IgG1 by reversed phase ultra high pressure liquid chromatography coupled with mass spectrometry

Development of a Novel Label-Free Subunit HILIC-MS Method for Domain-Specific Free Thiol Identification and Quantitation in Therapeutic Monoclonal Antibodies

Cysteine residues are crucial for the formation of conserved disulfide bonds in therapeutic monoclonal antibodies (mAbs), which are essential for their folding and structural stability. The presence of free thiols in mAbs can indicate incomplete disulfide bond formation, potentially impacting the molecule's conformational stability. Free thiol quantitation has been achieved using labeling-based strategies such as maleimide and haloalkyl derivatives at both intact and peptide levels. However, intact-level measurement only provides total free thiol levels, while peptide-level measurement is time-consuming and more prone to assay-induced artifacts. In this study, we present a novel label-free HILIC-MS method that separates free thiol species at the subunit level, followed by free thiol localization by the MS2 fragmentation pattern. This allows for facile identification and quantitation of intrachain free thiols at domain-specific resolution. Compared to bottom-up approaches, this subunit HILIC-MS method excels in simpler sample preparation and higher throughput and enables chain-specific free thiol analysis for bispecific mAbs. This method can be readily applied for screening mAb candidates with elevated levels of free thiols in early-stage developability assessment and facilitating an effective comparability evaluation of mAb samples during process development.

A new metric for relating macroscopic chromatograms to microscopic surface dynamics: the distribution function ratio (DFR)

Heterogeneous stationary phase chemistry causes chromatographic tailing that lowers separation efficiency and complicates optimizing mobile phase conditions. Model-free metrics are attractive for assessing optimal separation conditions due to the low quantity of information required, but often do not reveal underlying mechanisms that cause tailing, for example, heterogeneous retention modes. We report a new metric, which we call the Distribution Function Ratio (DFR), based on a graphical comparison between the chromatogram and Gaussian cumulative distribution functions, achieving correspondence to ground truth surface dynamics with a single chromatogram. Using a Monte Carlo framework, we show that the DFR can predict the prevalence of heterogeneous retention modes with high precision when the relative desorption rate between modes is known, as in during surface dynamics experiments. Ground truth comparisons reveal that the DFR outperforms both the asymmetry factor and skewness by yielding a one-to-one correspondence with heterogeneous retention mode prevalence over a broad range of experimentally realistic values. Perhaps of more value, we illustrate that the DFR, when combined with the asymmetry factor and skewness, can estimate microscopic surface dynamics, providing valuable insights into surface chemistry using existing chromatographic instrumentation. Connecting ensemble results to microscopic quantities through the lens of simulation establishes a new chemistry-driven route to measuring and advancing separations.

Extended characterization of unpaired cysteines in an IgG1 monoclonal antibody by LC-MS analysis

The development of comprehensive methods to characterize unpaired cysteines in monoclonal antibodies (mAbs) is very important for understanding structural heterogeneity, impurity, and stability. In this paper, unpaired cysteines observed in a therapeutic antibody (mAb1) were thoroughly studied by Liquid Chromatography-Mass Spectrometry (LC-MS) methods at the intact mAb, domain, and peptide levels. Three cysteine variants were observed at the intact mAb level with each variant containing two unpaired cysteines. Variants containing four or six unpaired cysteines were not observed. Domain analysis indicated that two Fab variants, each containing two unpaired cysteines, were present while the third variant contained two unpaired cysteines on the Fc region. Peptide mapping analysis localized the six unpaired cysteines to Cys22/Cys96, Cys146/Cys202, and Cys369/Cys427 in the heavy chain. No significant changes were observed for these unpaired cysteines in mAb1 under high pH and heat-stressed conditions. Structural analysis and molecular modeling revealed that these unpaired cysteines were buried inside the three-dimensional structure. The integrated LC-MS methods together with stress studies and structural analysis may potentially be applied to the analysis of unpaired cysteines in other mAbs.

In Vivo Reoxidation Kinetics of Free Thiols in Multiple Domains of IgG1 Antibodies in Rats

While free thiols in monoclonal antibodies (mAbs) have been extensively characterized by in vitro studies to probe its effect on antibody function and stability, their in vivo biotransformation has not been comprehensively studied. In this study, a panel of five recombinant IgG1 mAbs with elevated free thiols in the VH, VL, and CH2 domains were intravenously administered into Wistar rats. In vivo biotransformation of thirty-five free thiol sites in total (7 disulfide pairs in VL, CL, VH, CH1, HH, CH2, CH3 domains across the 5 mAbs) were monitored using a denaturing differential isotopic tagging procedure on immunopurified timepoints followed by LC-MS of tryptic digests. The free thiol levels in two VH domain and one CH2 domain disulfide sites decreased in vivo following first order kinetics. Free thiol levels of the remaining 32 sites were remarkably stable in vivo. Further analytical characterization highlighted a positive association between a free thiol's solvent accessibility and a free thiol's reoxidation propensity. The data and discussion presented here shed valuable insights into the in vivo fate of free thiols in several recombinant IgG1s and its implications for free thiols as a product quality attribute in therapeutic mAb products.

Making Sharper Peaks for Reverse-Phase Liquid Chromatography of Proteins

Protein separations have gained increasing interest over the past two decades owing to the dramatic growth of proteins as therapeutics and the completion of the Human Genome Project. About every decade, the field of protein high-performance liquid chromatography (HPLC) seems to mature, having reached what appears to be a theoretical limit. But then scientists well versed in the basic principles of HPLC invented a way around the limit, generating another decade of exciting progress. There is still the need for higher resolution and better compatibility with mass spectrometry because it is an essential tool for identification of proteins and their modifications. To make advances, the fundamental principles need to be understood. This review covers recent advances and current needs in the context of the principles that underlie the many contributions to peak broadening.

Qualitative and quantitative characterization of protein biotherapeutics with liquid chromatography mass spectrometry

In the last decade, the advancement of liquid chromatography mass spectrometry (LC/MS) techniques has enabled their broad application in protein characterization, both quantitatively and qualitatively. Owing to certain important merits of LC/MS techniques (e.g., high selectivity, flexibility, and rapid method development), LC/MS assays are often deemed as preferable alternatives to conventional methods (e.g., ligand-binding assays) for the analysis of protein biotherapeutics. At the discovery and development stages, LC/MS is generally employed for two purposes absolute quantification of protein biotherapeutics in biological samples and qualitative characterization of proteins. For absolute quantification of a target protein in bio-matrices, recent work has led to improvements in the efficiency of LC/MS method development, sample treatment, enrichment and digestion, and high-performance low-flow-LC separation. These advances have enhanced analytical sensitivity, specificity, and robustness. As to qualitative analysis, a range of techniques have been developed to characterize intramolecular disulfide bonds, glycosylation, charge variants, primary sequence heterogeneity, and the drug-to-antibody ratio of antibody drug conjugate (ADC), which has enabled a refined ability to assess product quality. In this review, we will focus on the discussion of technical challenges and strategies of LC/MS-based quantification and characterization of biotherapeutics, with the emphasis on the analysis of antibody-based biotherapeutics such as monoclonal antibodies (mAbs) and ADCs. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:734-754, 2017.