Assessing the Utility of Circular Dichroism and FTIR Spectroscopy in Monoclonal-Antibody Comparability Studies

Impact of imperfect data on protein secondary structure estimates from Far-UV circular dichroism spectra

Circular dichroism [CD] is widely used to rapidly assess protein structure. Deconvolution of the far-UV CD spectrum is widely used to quantify the secondary structural elements [SSEs]. Multiple algorithms are available for this. Imperfections in the experimental CD spectra arising from spectral noise, instrument miscalibration, spectral offsets and non-linearity will impact on the accuracy and precision of derived secondary structure estimates. Analytical validation for use in regulated environments, such as biopharmaceuticals, requires that the impact of imperfect data on these estimates be understood. Limited information on the impact of poor data were available. A series of noise-free simulated spectral datasets with modified intensity, wavelength, noise and intensity linearity and offsets were created from entries in the Protein Circular Dichroism Data Bank. These datasets were analysed using the BeStSel, on-line resource to estimate secondary structure. Data imperfections caused significant change in SSEs, but the spectral range is also important. This study emphasises the importance of analytical method validation and justifiable estimates of uncertainty when reporting results. The datasets created are made available as a resource to validate other secondary structure estimation programs.

Comprehensive characterization of higher order structure changes in methionine oxidized monoclonal antibodies via NMR chemometric analysis and biophysical approaches

The higher order structure (HOS) of monoclonal antibodies (mAbs) is an important quality attribute with strong contribution to clinically relevant biological functions and drug safety. Due to the multi-faceted nature of HOS, the synergy of multiple complementary analytical approaches can substantially improve the understanding, accuracy, and resolution of HOS characterization. In this study, we applied one- and two-dimensional (1D and 2D) nuclear magnetic resonance (NMR) spectroscopy coupled with chemometric analysis, as well as circular dichroism (CD), differential scanning calorimetry (DSC), and fluorescence spectroscopy as orthogonal methods, to characterize the impact of methionine (Met) oxidation on the HOS of an IgG1 mAb. We used a forced degradation method involving concentration-dependent oxidation by peracetic acid, in which Met oxidation is site-specifically quantified by liquid chromatography-mass spectrometry. Conventional biophysical techniques report nuanced results, in which CD detects no change to the secondary structure and little change in the tertiary structure. Yet, DSC measurements show the destabilization of Fab and Fc domains due to Met oxidation. More importantly, our study demonstrates that 1D and 2D NMR and chemometric analysis can provide semi-quantitative analysis of chemical modifications and resolve localized conformational changes with high sensitivity. Furthermore, we leveraged a novel 15N-Met labeling technique of the antibody to directly observe structural perturbations at the oxidation sites. The NMR methods described here to probe HOS changes are highly reliable and practical in biopharmaceutical characterization.

Preparation and in vitro investigation of prostate-specific membrane antigen targeted Lycopene loaded niosomes on prostate cancer cells

In this study, it's aimed to develop prostate-specific membrane antigen (PSMA) targeted niosomes with a multifunctional theranostic approach. With this aim, PSMA-targeted niosomes were synthesized by a thin-film hydration method followed by bath sonication. Drug-loaded niosomes (Lyc-ICG-Nio) were coated with DSPE-PEG-COOH (Lyc-ICG-Nio-PEG) and subsequently anti-PSMA antibody conjugated to niosomes (Lyc-ICG-Nio-PSMA) with amide bond formation. Dynamic light scattering (DLS) analysis showed that the hydrodynamic diameter of Lyc-ICG-Nio-PSMA was approximately 285 nm and it was found with transmission electron microscopy (TEM) that the niosome formulation was spherical. Encapsulation efficiency was 45% and %65 upon dual encapsulation of ICG and lycopene. The results of fourier-transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) demonstrated that PEG coating and antibody coupling were successfully done. In vitro studies showed that cell viability decreased when lycopene was entrapped into niosomes applied while the total apoptotic cell population rose slightly. When Lyc-ICG-Nio-PSMA was applied to cells, decreased cell viability and enhanced apoptotic effect were seen compared to those for Lyc-ICG-Nio. In conclusion, it was demonstrated that targeted niosomes displayed improved cellular association and decreased cell viability on PSMA+ cells.

Constant domain polymorphisms influence monoclonal antibody stability and dynamics

The constant regions of clinical monoclonal antibodies are derived from a select number of allotypes found in IgG subclasses. Despite a long-term acknowledgment that this diversity may impact both antibody function and developability, there is a lack of data on the stability of variants carrying these mutations. Here, we generated a panel of IgG1, IgG2, and IgG3 antibodies with 32 unique constant region alleles and performed a systematic comparison of stability using red edge excitation shift (REES). This technique exploits the fluorescent properties of tryptophan residues to measure antibody structural dynamics which predict flexibility and the propensity to unfold. Our REES measurements revealed broad stability differences between subclasses with IgG3 possessing the poorest overall stability. Further interrogation of differences between variants within each subclass enabled the high-resolution profiling of individual allotype stabilities. Crucially, these observed differences were not found to be linked to N297-linked glycan heterogeneity. Our work demonstrates diverse stabilities (and dynamics) for a range of naturally occurring constant domain alleles and the utility of REES as a method for rapid and sensitive antibody stability profiling, requiring only laboratory spectrophotometry equipment.

Analytical Techniques for the Characterization and Quantification of Monoclonal Antibodies

Monoclonal antibodies (mAbs) are a fast-growing class of biopharmaceuticals. They are widely used in the identification and detection of cell makers, serum analytes, and pathogenic agents, and are remarkably used for the cure of autoimmune diseases, infectious diseases, or malignancies. The successful application of therapeutic mAbs is based on their ability to precisely interact with their appropriate target sites. The precision of mAbs rely on the isolation techniques delivering pure, consistent, stable, and safe lots that can be used for analytical, diagnostic, or therapeutic applications. During the creation of a biologic, the key quality features of a particular mAb, such as structure, post-translational modifications, and activities at the biomolecular and cellular levels, must be characterized and profiled in great detail. This implies the requirement of powerful state of the art analytical techniques for quality control and characterization of mAbs. Until now, various analytical techniques have been developed to characterize and quantify the mAbs according to the regulatory guidelines. The present review summarizes the major techniques used for the analyses of mAbs which include chromatographic, electrophoretic, spectroscopic, and electrochemical methods in addition to the modifications in these methods for improving the quality of mAbs. This compilation of major analytical techniques will help students and researchers to have an overview of the methodologies employed by the biopharmaceutical industry for structural characterization of mAbs for eventual release of therapeutics in the drug market.

Challenges and Strategies for a Thorough Characterization of Antibody Acidic Charge Variants

Heterogeneity of therapeutic Monoclonal antibody (mAb) drugs are due to protein variants generated during the manufacturing process. These protein variants can be critical quality attributes (CQAs) depending on their potential impact on drug safety and/or efficacy. To identify CQAs and ensure the drug product qualities, a thorough characterization is required but challenging due to the complex structure of biotherapeutics. Past characterization studies for basic and acidic variants revealed that full characterizations were limited to the basic charge variants, while the quantitative measurements of acidic variants left gaps. Consequently, the characterization and quantitation of acidic variants are more challenging. A case study of a therapeutic mAb1 accounted for two-thirds of the enriched acidic variants in the initial characterization study. This led to additional investigations, closing the quantification gaps of mAb1 acidic variants. This work demonstrates that a well-designed study with the right choices of analytical methods can play a key role in characterization studies. Thus, the updated strategies for more complete antibody charge variant characterization are recommended.

Triggering of the immune response to MCF7 cell line using conjugated antibody with bacterial antigens: In-vitro and in-vivo study

The current study intended to trigger the immune response to cancer cells by using antibodies conjugated with bacterial antigens. The protein membrane of the MCF7 cell line was extracted and specific antibodies against cell membrane antigens was produced in rabbits. The specific antibodies were purified using chromatography methods and linked to E. coli antigens or doxorubicin using Diethylenetriamine pentaacetate (DTPA) linker. After confirmation of the conjugation process using SDS-PAGE and ATR-FTIR methods, the MCF7 and HUVEC cells were treated with various concentrations of the prepared conjugated antibodies along with human serum. The toxicity of each treatment against MCF7 and HUVEC cells was evaluated using the MTT assay. Also, polylactic acid scaffolds that contain 10×10⁴ MCF7 cells were surgically placed in the peritoneal cavity of the rats. After treatment of each group, induction of the inflammatory responses was evaluated on stained histological sections of the scaffolds. The lowest cytotoxic doses of the antigen conjugated-antibody, doxorubicin-conjugated-antibody was 4 and 1 μg/mL, respectively. Doxorubicin conjugated antibodies displayed greater toxicity on both MCF7 and HUVEC cells. The in vivo finding revealed that the inflammatory cells were significantly higher in treating animals with antigen conjugated-antibody. The current synthetic agent stimulated the serum toxicity and induced an inflammatory response to MCF7 cell lines. Targeting of the bacterial antigens on tumor sites by immune system elements, could limit the growth of the tumor cells.

Magnetic resonance imaging of tumor-infiltrating lymphocytes by anti-CD3-conjugated iron oxide nanoparticles

Immune checkpoint blockade, considered a revolutionary approach in cancer treatment, is only effective in patients with high tumor-infiltrating lymphocytes (TILs). This work aimed to investigate the feasibility of targeted contrast agent (CA) based on dextran-coated superparamagnetic iron oxide nanoparticles (SPIONs-DEX) for TILs detection by magnetic resonance imaging (MRI) studies. To do so, we synthesized an MRI CA by conjugating SPIONs-DEX to an anti-CD3 monoclonal antibody via cyanogen bromide as a cross-linker. In vitro assessments demonstrated the higher labeling efficiency of the developed CA to CD3+ lymphocytes compared to SPIONs-DEX. In vivo MRI of a xenograft model of CD3+ lymphocytes revealed the significant signal loss after the intravenous injection of the bioconjugate by ~ 34% and 21% in T 2 * -weighted and T 2 -weighted images, respectively. The histopathological evaluation of xenograft tumors confirmed the labeling of lymphocytes by the targeted CA. This approach could open up a new horizon in the non-invasive assessment of TILs to identify patients eligible for immunotherapy.

Rapid antibody conformational screening by matrix assisted laser desorption ionization hydrogen-deuterium exchange mass spectrometry

Recent advances in the field of cancer biology have accelerated the discovery and development of novel biopharmaceuticals. At the forefront of these drug development efforts are high-throughput screening, compressed timelines and limited sample quantities, all characteristic of the discovery space. To meet program targets, large numbers of protein variants must be produced, screened, and characterized, presenting a daunting analytical challenge. Additionally, higher-order structure is paramount for protein function and must be monitored as a critical quality attribute. Matrix Assisted Laser Desorption Ionization MS has been utilized as an ultra-fast, automatable, sample-sparing analytical tool for biomolecules. Our group has published applications integrating Hydrogen-Deuterium Exchange MS with Matrix Assisted Laser Desorption Ionization MS for the rapid conformational characterization of small proteins, the current work expands this application to monoclonal and bi-specific antibodies. This study demonstrates the ability of the methodology Matrix Assisted Laser Desorption Ionization Hydrogen-Deuterium Exchange MS to detect conformational differences between bi-specific antibodies from different expression host. These conformational differences were validated by orthogonal techniques including Circular Dichroism, Nuclear Magnetic Resonance and Size-Exclusion Chromatography Hydrogen-Deuterium Exchange MS. This work demonstrates the utility of applying the developed methodology as a rapid conformational screening tool to triage samples for further analytical characterization. This article is protected by copyright. All rights reserved.

Impact of Imperfect Data on the Performance of Algorithms to Compare Near-Ultraviolet Circular Dichroism Spectra

There is growing interest in the use of algorithms to objectively compare near-UV spectra of protein biopharmaceuticals in a regulated environment. Such use will require that the methods be validated, with International Conference on the Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH) Q2(R1) currently being the key document. A key aspect of such validation is to understand how robust the method is to experimental variation. Noise-free simulated spectra, obtained by fitting multiple Gaussian peaks to experimental data obtained from a pharmaceutical protein, were used to assess the robustness of several algorithms in response to spectral data "imperfections". Sources and magnitudes of these imperfections were derived from published inter-laboratory studies. Spectral noise, wavelength calibration errors, intensity variation, and spectral offset errors were "titrated" into the noise-free simulated spectrum and imperfect data sets were compared with the simulated data using a variety of published algorithms, including Pearson, Prestrelski, and derivative correlation algorithms, and spectral overlap, spectral difference and weighted spectral difference methods, to understand how robust outputs are to imperfect data. Algorithm was assessed by comparing their sensitivity to imperfect data against the pairwise statistical variation between 20 replicate spectra.

Assessment of the Higher-Order Structure of Formulated Monoclonal Antibody Therapeutics by 2D Methyl Correlated NMR and Principal Component Analysis

Characterization of the higher-order structure (HOS) of protein therapeutics, and in particular of monoclonal antibodies, by 2D ¹ H-¹³ C methyl correlated NMR has been demonstrated as precise and robust. Such characterization can be greatly enhanced when collections of spectra are analyzed using multivariate approaches such as principal component analysis (PCA), allowing for the detection and identification of small structural differences in drug substance that may otherwise fall below the limit of detection of conventional spectral analysis. A major limitation to this approach is the presence of aliphatic signals from formulation or excipient components, which result in spectral interference with the protein signal of interest; however, the recently described Selective Excipient Reduction and Removal (SIERRA) filter greatly reduces this issue. Here we will outline how basic 2D ¹ H-¹³ C methyl-correlated NMR may be combined with the SIERRA approach to collect 'clean' NMR spectra of formulated monoclonal antibody therapeutics (i.e., drug substance spectra free of interfering component signals), and how series of such spectra may be used for HOS characterization by direct PCA of the series spectral matrix. © 2020 U.S. Government. Basic Protocol 1: NMR data acquisition Basic Protocol 2: Full spectral matrix data processing and analysis Support Protocol: Data visualization and cluster analysis.

Glycoconjugate vaccine batch consistency assessed by objective comparison of circular dichroism spectra

Circular dichroism (CD) spectra of biopharmaceutical protein, or protein conjugate, products contain information about their secondary and tertiary structures, which can answer to increasing regulatory interest in demonstrating consistent higher order structures of production batches. Widespread routine use of CD in a regulatory environment requires objective, statistically based, and validated methods to analyse and compare spectra against product specifications. Correlation approaches to compare spectra, developed and tested on monoclonal antibodies, are here used to assess the consistency of Hib PRP-CRM197 glycoconjugate immunogen batches, by analysis of historical data sets. Deconvolution of spectra into Gaussian peaks was used to model the spectrum and allow a more detailed description of spectral differences. Two groups of spectra [and hence samples] were distinguished. The analyses are discussed in the context of spectral comparison approaches, inter-laboratory studies, potential regulatory use and sources of uncertainty between spectra. Data analysis methods implemented here can also support stability and formulation studies.

ATR-FTIR spectroscopy and spectroscopic imaging for the analysis of biopharmaceuticals

Attenuated Total Reflection Fourier Transform Infrared (ATR-FTIR) spectroscopy is a label-free, non-destructive technique that can be applied to a vast range of biological applications, from imaging cancer tissues and live cells, to determining protein content and protein secondary structure composition. This review summarises the recent advances in applications of ATR-FTIR spectroscopy to biopharmaceuticals, the application of this technique to biosimilars, and the current uses of FTIR spectroscopy in biopharmaceutical production. We discuss the use of ATR-FTIR spectroscopic imaging to investigate biopharmaceuticals, and finally, give an outlook on the possible future developments and applications of ATR-FTIR spectroscopy and spectroscopic imaging to this field. Throughout the review comparisons will be made between FTIR spectroscopy and alternative analytical techniques, and areas will be identified where FTIR spectroscopy could perhaps offer a better alternative in future studies. This review focuses on the most recent advances in the field of using ATR-FTIR spectroscopy and spectroscopic imaging to characterise and evaluate biopharmaceuticals, both in industrial and academic research based environments.

Formulation of nanoliposome-encapsulated bevacizumab (Avastin): Statistical optimization for enhanced drug encapsulation and properties evaluation

Bevacizumab (Avastin®), an anti-vascular endothelial growth factor, is one of the most effective drugs widely used to inhibit ocular angiogenesis. Nanoliposomes were recruited to improve the accessibility of bevacizumab (BVZ) during treatment. To optimize drug entrapment efficiency (DEE %), the effect of some independent variables was evaluated utilizing response surface methodology. The optimized formulation containing BVZ (NLP-BVZ) was characterized, and its safety was assessed. Employingarising retinalpigment epithelial (ARPE) cells, the permeability of the nanoliposome was analyzed. Structural stability and integrity of NLP-BVZ were also estimated with different methods. Optimal condition for the maximum DEE (39.9%) was obtained with cholesterol/DPPC (1,2-Dipalimitoyl-Sn-glycero-3-phosphocholine) (%w/w) 13.64, BVZ/DPPC (%w/w) 83.78 and 9 freeze-thaw cycles. Neutral fabricated NLP-BVZ with an average size of 141.5 ± 45.8 nm showed a smooth spherical structure and released the drug in a slow and sustained fashion. The formulation exhibited no obvious effect against human umbilical vein endothelial cells (HUVECs) and ARPEs. Additionally, the pattern of the circular dichroism (CD) and intrinsic fluorescence spectra confirmed the structural integrity of protein remained conserved after encapsulation. Taken together, the analysis indicated that the process of entrapment into nanoliposome meaningfully made the drug safer, more stable, and, therefore, appropriate for treating ocular disorders.

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.

Temperature-dependent irreversible conformational change of recombinant ADAMTS13 upon metal ion chelation

BACKGROUND

The catalytic domain of ADAMTS13 possesses one Zn2+ and up to three putative Ca2+ binding sites and can be inactivated by chelating agents. Although replenishment with an appropriate metallic cation is thought to restore the enzyme's proteolytic activity fully, ADAMTS13 stability in a metal ion-depleting environment has not been explored.

OBJECTIVES

To address the stability of ADAMTS13 in citrated human plasma.

METHODS

ADAMTS13 activity was measured using the FRETS-VWF73 fluorogenic assay. The molar ratio of metals bound to ADAMTS13 was determined by size exclusion chromatography inductively coupled plasma mass spectrometry (SEC-ICP-MS). Higher-order structural changes were analyzed using Fourier-transformed infrared spectroscopy and dynamic light scattering.

RESULTS

ADAMTS13 was stable at room temperature for up to 24 hours irrespective of the presence of citrate (0.38%). However, at 37°C, citrate caused a time-dependent activity decrease. No ADAMTS13 activity decrease was seen in heparinized plasma, but the addition of citrate again caused ADAMTS13 instability at 37°C. Scavenging of citrate by the addition of Ca2+ or Zn2+ prior to but not postincubation prevented the activity decrease of the enzyme. The SEC-ICP-MS analyses showed that ADAMTS13 only bound Zn2+ and that its reduced activity correlated with a gradual loss of bound Zn2+ . Concomitant higher-order structural analyses demonstrated structural changes in ADAMTS13 that are typical of less-ordered protein structures.

CONCLUSIONS

Zn2+ is required to stabilize ADAMTS13 structure at physiologic temperature, thereby preventing irreversible loss of enzyme activity. This finding is particularly important to consider when using citrated human plasma as a source of ADAMTS13 in clinical settings.

Current Trends in Biotherapeutic Higher Order Structure Characterization by Irreversible Covalent Footprinting Mass Spectrometry

BACKGROUND

Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing class of drugs capable of treating a wide range of diseases. Therapeutic function and solutionstability are linked to the proper three-dimensional organization of the primary sequence into Higher Order Structure (HOS) as well as the timescales of protein motions (dynamics). Methods that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant protein-protein interactions and assessing properly folded structures. Irreversible covalent protein footprinting Mass Spectrometry (MS) tools, such as site-specific amino acid labeling and hydroxyl radical footprinting are analytical techniques capable of monitoring the side chain solvent accessibility influenced by tertiary and quaternary structure. Here we discuss the methodology, examples of biotherapeutic applications, and the future directions of irreversible covalent protein footprinting MS in biotherapeutic research and development.

CONCLUSION

Bottom-up mass spectrometry using irreversible labeling techniques provide valuable information for characterizing solution-phase protein structure. Examples range from epitope mapping and protein-ligand interactions, to probing challenging structures of membrane proteins. By paring these techniques with hydrogen-deuterium exchange, spectroscopic analysis, or static-phase structural data such as crystallography or electron microscopy, a comprehensive understanding of protein structure can be obtained.

Enhanced Precision of Circular Dichroism Spectral Measurements Permits Detection of Subtle Higher Order Structural Changes in Therapeutic Proteins

Protein higher order structure (HOS) is an essential quality attribute to ensure protein stability and proper biological function. Protein HOS characterization is performed during comparability assessments for product consistency as well as during forced degradation studies for structural alteration upon stress. Circular dichroism (CD) spectroscopy is a widely used technique for measuring protein HOS, but it remains difficult to assess HOS with a high degree of accuracy and precision. Moreover, once spectral changes are detected, interpreting the differences in terms of specific structural attributes is challenging. Spectral normalization by the protein concentration remains one of the largest sources of error and reduces the ability to confidently detect differences in CD spectra. This work develops a simple method to enhance the precision of the CD spectral measurements through normalization of the CD spectra by the protein concentration determined directly from the CD measurement. This method is implemented to successfully detect small CD spectral changes in multiple forced degradation studies as well as comparability assessments during biologics drug development. Furthermore, the interpretation of CD spectral changes in terms of HOS differences are provided based on orthogonal data in conjunction with structural insights gained through in silico homology modeling of the protein structure.

A comparison of biophysical characterization techniques in predicting monoclonal antibody stability

With the rapid growth of biopharmaceutical product development, knowledge of therapeutic protein stability has become increasingly important. We evaluated assays that measure solution-mediated interactions and key molecular characteristics of 9 formulated monoclonal antibody (mAb) therapeutics, to predict their stability behavior. Colloidal interactions, self-association propensity and conformational stability were measured using effective surface charge via zeta potential, diffusion interaction parameter (kD) and differential scanning calorimetry (DSC), respectively. The molecular features of all 9 mAbs were compared to their stability at accelerated (25°C and 40°C) and long-term storage conditions (2-8°C) as measured by size exclusion chromatography. At accelerated storage conditions, the majority of the mAbs in this study degraded via fragmentation rather than aggregation. Our results show that colloidal stability, self-association propensity and conformational characteristics (exposed tryptophan) provide reasonable prediction of accelerated stability, with limited predictive value at 2-8°C stability. While no correlations to stability behavior were observed with onset-of-melting temperatures or domain unfolding temperatures, by DSC, melting of the Fab domain with the CH2 domain suggests lower stability at stressed conditions. The relevance of identifying appropriate biophysical assays based on the primary degradation pathways is discussed.