Biosensor binding data and its applicability to the determination of active concentration

Multi-temperature experiments to ease analysis of heterogeneous binder solutions by surface plasmon resonance biosensing

Surface Plasmon Resonance (SPR) biosensing is a well-established tool for the investigation of binding kinetics between a soluble species and an immobilized (bio)molecule. While robust and accurate data analysis techniques are readily available for single species, methods to exploit data collected with a solution containing multiple interactants are scarce. In a previous study, our group proposed two data analysis algorithms for (1) the precise and reliable identification of the kinetic parameters of N interactants present at different ratios in N mixtures and (2) the estimation of the composition of a given mixture, assuming that the kinetic parameters and the total concentration of all interactants are known. Here, we extend the first algorithm by reducing the number of necessary mixtures. This is achieved by conducting experiments at different temperatures. Through the Van't Hoff and Eyring equations, identifying the kinetic and thermodynamic parameters of N binders becomes possible with M mixtures with M comprised between 2 and N and at least N/M temperatures. The second algorithm is improved by adding the total analyte concentration as a supplementary variable to be identified in an optimization routine. We validated our analysis framework experimentally with a system consisting of mixtures of low molecular weight drugs, each competing to bind to an immobilized protein. We believe that the analysis of mixtures and composition estimation could pave the way for SPR biosensing to become a bioprocess monitoring tool, on top of expanding its already substantial role in drug discovery and development.

Multiplexed, High-Sensitivity Measurements of Antibody Affinity Using Interferometric Reflectance Imaging Sensor

Anthrax lethal factor (LF) is one of the enzymatic components of the anthrax toxin responsible for the pathogenic responses of the anthrax disease. The ability to screen multiplexed ligands against LF and subsequently estimate the effective kinetic rates (kon and koff) and complementary binding behavior provides critical information useful in diagnostic and therapeutic development for anthrax. Tools such as biolayer interferometry (BLI) and surface plasmon resonance imaging (SPRi) have been developed for this purpose; however, these tools suffer from limitations such as signal jumps when the solution in the chamber is switched or low sensitivity. Here, we present multiplexed antibody affinity measurements obtained by the interferometric reflectance imaging sensor (IRIS), a highly sensitive, label-free optical biosensor, whose stability, simplicity, and imaging modality overcomes many of the limitations of other multiplexed methods. We compare the multiplexed binding results obtained with the IRIS system using two ligands targeting the anthrax lethal factor (LF) against previously published results obtained with more traditional surface plasmon resonance (SPR), which showed consistent results, as well as kinetic information previously unattainable with SPR. Additional exemplary data demonstrating multiplexed binding and the corresponding complementary binding to sequentially injected ligands provides an additional layer of information immediately useful to the researcher.

On the Use of Surface Plasmon Resonance-Based Biosensors for Advanced Bioprocess Monitoring

Biomanufacturers are being incited by regulatory agencies to transition from a quality by testing framework, where they extensively test their product after their production, to more of a quality by design or even quality by control framework. This requires powerful analytical tools and sensors enabling measurements of key process variables and/or product quality attributes during production, preferably in an online manner. As such, the demand for monitoring technologies is rapidly growing. In this context, we believe surface plasmon resonance (SPR)-based biosensors can play a role in enabling the development of improved bioprocess monitoring and control strategies. The SPR technique has been profusely used to probe the binding behavior of a solution species with a sensor surface-immobilized partner in an investigative context, but its ability to detect binding in real-time and without a label has been exploited for monitoring purposes and is promising for the near future. In this review, we examine applications of SPR that are or could be related to bioprocess monitoring in three spheres: biotherapeutics production monitoring, vaccine monitoring, and bacteria and contaminant detection. These applications mainly exploit SPR’s ability to measure solution species concentrations, but performing kinetic analyses is also possible and could prove useful for product quality assessments. We follow with a discussion on the limitations of SPR in a monitoring role and how recent advances in hardware and SPR response modeling could counter them. Mainly, throughput limitations can be addressed by multi-detection spot instruments, and nonspecific binding effects can be alleviated by new antifouling materials. A plethora of methods are available for cell growth and metabolism monitoring, but product monitoring is performed mainly a posteriori. SPR-based biosensors exhibit potential as product monitoring tools from early production to the end of downstream processing, paving the way for more efficient production control. However, more work needs to be done to facilitate or eliminate the need for sample preprocessing and to optimize the experimental protocols.

Data evaluation for surface-sensitive label-free methods to obtain real-time kinetic and structural information of thin films: A practical review with related software packages

Interfacial layers are important in a wide range of applications in biomedicine, biosensing, analytical chemistry and the maritime industries. Given the growing number of applications, analysis of such layers and understanding their behavior is becoming crucial. Label-free surface sensitive methods are excellent for monitoring the formation kinetics, structure and its evolution of thin layers, even at the nanoscale. In this paper, we review existing and commercially available label-free techniques and demonstrate how the experimentally obtained data can be utilized to extract kinetic and structural information during and after formation, and any subsequent adsorption/desorption processes. We outline techniques, some traditional and some novel, based on the principles of optical and mechanical transduction. Our special focus is the current possibilities of combining label-free methods, which is a powerful approach to extend the range of detected and deduced parameters. We summarize the most important theoretical considerations for obtaining reliable information from measurements taking place in liquid environments and, hence, with layers in a hydrated state. A thorough treamtmaent of the various kinetic and structural quantities obtained from evaluation of the raw label-free data are provided. Such quantities include layer thickness, refractive index, optical anisotropy (and molecular orientation derived therefrom), degree of hydration, viscoelasticity, as well as association and dissociation rate constants and occupied area of subsequently adsorbed species. To demonstrate the effect of variations in model conditions on the observed data, simulations of kinetic curves at various model settings are also included. Based on our own extensive experience with optical waveguide lightmode spectroscopy (OWLS) and the quartz crystal microbalance (QCM), we have developed dedicated software packages for data analysis, which are made available to the scientific community alongside this paper.

Bulk-Effect-Free Method for Binding Kinetic Measurements Enabling Small-Molecule Affinity Characterization

Optical technologies for label-free detection are an attractive solution for monitoring molecular binding kinetics; however, these techniques measure the changes in the refractive index, making it difficult to distinguish surface binding from a change in the refractive index of the analyte solution in the proximity of the sensor surface. The solution refractive index changes, due to solvents, temperature changes, or pH variations, can create an unwanted background signal known as the bulk effect. Technologies such as biolayer interferometry and surface plasmon resonance offer no bulk-effect compensation, or they alternatively offer a reference channel to correct in postprocessing. Here, we present a virtually bulk-effect-free method, without a reference channel or any computational correction, for measuring kinetic binding using the interferometric reflectance imaging sensor (IRIS), an optical label-free biomolecular interaction analysis tool. Dynamic spectral illumination engineering, through tailored LED contributions, is combined with the IRIS technology to minimize the bulk effect, with the potential to enable kinetic measurements of a broader range of analytes. We demonstrate that the deviation in the reflectivity signal is reduced to ∼8 × 10^-6 for a solution change from phosphate-buffered saline (PBS) (n = 1.335) to 1% dimethyl sulfoxide (DMSO) in PBS (n = 1.336). As a proof of concept, we applied the method to a biotin-streptavidin interaction, where biotin (MW = 244.3 Da) was dissolved at a final concentration of 1 μM in a 1% solution of DMSO in PBS and flowed over immobilized streptavidin. Clear binding results were obtained without a reference channel or any computational correction.

Calibration-free concentration analysis for quantification of anti-drug specific antibodies in polyclonal positive control antibodies and in clinical samples

Highly sensitive assays for anti-drug antibodies (ADAs) are both a regulatory requirement and requisite for proper evaluation of the effects of immunogenicity on clinical efficacy and safety. Determination of ADA assay sensitivity depends on positive control antibodies to represent naturally occurring or treatment-induced ADA responses. An accurate determination of the proportion of drug-specific antibodies in these polyclonal positive control batches is critical for correct evaluation of assay sensitivity. Target purification of positive control antibodies is commonly applied but infers the risk to lose a proportion of the antibodies. This may lead to an incorrect estimate of the ADA assay sensitivity, especially if high-affinity antibodies are lost that may be representative of natural ADAs with clinical implication. The Surface Plasmon Resonance platform on the Biacore™ systems offers methods for real-time analysis of biomolecular interactions without introducing any modifications to the analysed material. Calibration-free concentration analysis (CFCA) is such an application for determination of the proportion of drug-specific antibodies, which allows direct determination of active antibody concentrations, as defined by the ligand, in a flow-based system. Here, we present a novel CFCA method for ADA quantification developed and validated using polyclonal positive control antibodies against endogenous human insulin, insulin degludec (Tresiba®) and turoctocog alfa (NovoEight®). We find that CFCA precisely and accurately measures concentrations of drug-specific IgG antibodies with a precision of ±10% and 90%-112% recovery of expected values of monoclonal positive control antibodies. Additionally, we have achieved a more accurate measure of the sensitivity of a cell-based bioassay for in vitro neutralising ADAs using the specific concentration determined with CFCA. Moreover, we effectively quantified serum anti-insulin antibodies in high-titre clinical samples from individuals with diabetes mellitus. This application extends the relevance of the CFCA technology to analysis of immunogenicity for accurate quantification of ADAs in both the polyclonal positive control and in clinical samples.

Comparative study on quantitation of human myoglobin by both isotope dilution mass spectrometry and surface plasmon resonance based on calibration-free analysis

The activity of proteins rather than the concentration of proteins in biopharmaceutical and in vitro diagnostics are often the primary focus. Nonetheless, development of a calibration-free concentration analysis (CFCA) approach that accurately quantifies the concentration of proteins based on molecular interactions with specific monoclonal antibodies and without the requirement of external calibrators would be beneficial to diagnostics. Generally, only analytes that interact with the antibody (Ab) are quantified by CFCA. Moreover, protein concentrations measured by CFCA usually vary when different Abs are used, and are lower than those obtained by amino acid analysis because any non-native state population of the target protein is not captured by the Ab. To achieve comparable results between CFCA and traditional amino acid analysis (AAA), an Ab that recognizes the target protein irrespective of its conformation should be used. In this report, three different monoclonal antibodies were used to quantify purified human myoglobin in solution by CFCA. The concentrations obtain by the Abs (i.e., 2.985, 2.912, 3.032 mg mL^-1) were comparable with that obtained by AAA. Moreover, isotope dilution mass spectrometry (IDMS) gave a human myoglobin concentration of 2.851 mg mL^-1, which is also in agreement with the results from CFCA. The performance of CFCA was evaluated by measuring various parameters, including within-day and between-day precision. The results demonstrated that the active concentration measured by CFCA is comparable with that of IDMS when the appropriate Ab is used. Recommended procedures for performing the new CFCA approach are provided. This study shows that CFCA represents a primary method for accurate protein concentration determination, which should aid the development of certified reference materials. Graphical abstract.

Surface Plasmon Resonance for Investigating Molecular Interactions with RNA

Surface plasmon resonance (SPR)-based instruments have become gold-standard tools for investigating molecular interactions involving macromolecules. The major advantage is that the measured signal is sensitive to changes in mass. Therefore, all kinds of complexes can be analyzed including those with compounds as small as cations. SPR is mainly used to determine the dissociation equilibrium constant and the binding rates of a reaction if slow enough. SPR is well suited for analysis molecular interactions with nucleic acids because these negatively charged macromolecules do not have a tendency to stick to the sensor chip surface as some proteins can do. To illustrate the use of SPR with RNA molecules, we describe methods that we used for monitoring the interaction between the protein Rop from E. coli and two RNA-RNA loop-loop complexes. One is derived from the natural target of Rop, RNAI-RNAII. The other one is an RNA-RNA complex formed between a shortened version of the TAR element of HIV-1 and a structured RNA, TAR^* rationally designed to interact with TAR through loop-loop interactions. These methods can be easily adapted to other complexes involving RNA molecules and to other SPR instruments.

VHH characterization. Comparison of recombinant with chemically synthesized anti-HER2 VHH

In the continuous exploration of the VHH chemistry, biochemistry and therapeutic future use, we investigated two different production strategies of this small antibody-like protein, using an anti-HER2 VHH as a model. The total chemical synthesis of the 125 amino-acid peptide was performed with reasonable yield, even if optimization will be necessary to upgrade this kind of production. In parallel, we expressed the same sequence in two different hosts: Escherichia coli and Pichia pastoris. Both productions were successful and led to a fair amount of VHHs. The integrity and conformation of the VHH were characterized by complementary mass spectrometry approaches, while surface plasmon resonance experiments were used to assess the VHH recognition capacity and affinity toward its "antigen." Using this combination of orthogonal techniques, it was possible to show that the three VHHs-whether synthetic or recombinant ones-were properly and similarly folded and recognized the "antigen" HER2 with similar affinities, in the nanomolar range. This opens a route toward further exploration of modified VHH with unnatural amino acids and subsequently, VHH-drug conjugates.

Sym021, a promising anti-PD1 clinical candidate antibody derived from a new chicken antibody discovery platform

Discovery of therapeutic antibodies is a field of intense development, where immunization of rodents remains a major source of antibody candidates. However, high orthologue protein sequence homology between human and rodent species disfavors generation of antibodies against functionally conserved binding epitopes. Chickens are phylogenetically distant from mammals. Since chickens generate antibodies from a restricted set of germline genes, the possibility of adapting the Symplex antibody discovery platform to chicken immunoglobulin genes and combining it with high-throughput humanization of antibody frameworks by “mass complementarity-determining region grafting” was explored. Hence, wild type chickens were immunized with an immune checkpoint inhibitor programmed cell death 1 (PD1) antigen, and a repertoire of 144 antibodies was generated. The PD1 antibody repertoire was successfully humanized, and we found that most humanized antibodies retained affinity largely similar to that of the parental chicken antibodies. The lead antibody Sym021 blocked PD-L1 and PD-L2 ligand binding, resulting in elevated T-cell cytokine production in vitro. Detailed epitope mapping showed that the epitope recognized by Sym021 was unique compared to the clinically approved PD1 antibodies pembrolizumab and nivolumab. Moreover, Sym021 bound human PD1 with a stronger affinity (30 pM) compared to nivolumab and pembrolizumab, while also cross-reacting with cynomolgus and mouse PD1. This enabled direct testing of Sym021 in the syngeneic mouse in vivo cancer models and evaluation of preclinical toxicology in cynomolgus monkeys. Preclinical in vivo evaluation in various murine and human tumor models demonstrated a pronounced anti-tumor effect of Sym021, supporting its current evaluation in a Phase 1 clinical trial.

Abbreviations: ADCC, antibody-dependent cellular cytotoxicity; CD, cluster of differentiation; CDC, complement-dependent cytotoxicity; CDR, complementarity determining region; DC, dendritic cell; ELISA, enzyme-linked immunosorbent assay; FACS, fluorescence activated cell sorting; FR, framework region; GM-CSF, granulocyte-macrophage colony-stimulating factor; HRP, horseradish peroxidase; IgG, immunoglobulin G; IL, interleukin; IFN, interferon; mAb, monoclonal antibody; MLR, mixed lymphocyte reaction; NK, natural killer; PBMC, peripheral blood mono-nuclear cell; PD1, programmed cell death 1; PDL1, programmed cell death ligand 1; RT-PCR, reverse transcription polymerase chain reaction; SEB, Staphylococcus Enterotoxin B; SPR, surface Plasmon Resonance; VL, variable part of light chain; VH, variable part of heavy chain

Interpretation of results from the competitive Biacore procedure for characterizing immunochemical interactions in solution

Rigorous consideration of the consequences of antibody bivalence in the published competitive kinetic procedure for quantifying the solution characteristics of an antigen-antibody interaction in solution has rendered redundant the practice of substituting the Fab fragment for the antibody to ensure validity of the analysis of results in terms of theory developed for a univalent analyte. Although the quantitative expressions differ for univalent and bivalent analytes, the additional contribution arising from bivalence is likely to be well within the limits of experimental uncertainty in the measured binding constant.

Surrogate potency assays: Comparison of binding profiles complements dose response curves for unambiguous assessment of relative potencies

Surface plasmon resonance (SPR) systems are widely used for detailed characterization of antibody activities including antigen and Fc-receptor binding. During the later stages of development, where the focus is to ensure that established critical quality attributes (CQAs) are maintained during cell culture, purification and formulation processes, analysis is simplified, and relative potencies are often determined. Here, simulation of binding data revealed that relative potency values, determined via parallel line analysis (PLA) and half maximal effective concentration (EC50) analysis accurately reflect changes in active concentration only if binding kinetics remain unchanged. Changes in the association rate constant shifted dose response curves, and therefore relative potencies, in the same way as changes in analyte concentration do. However, for interactions characterized by stable binding, changes in the dissociation rate constant did not result in any shift, suggesting that this type of change may go unnoticed in the dose response curve. Thus, EC50 and PLA analyses of dose response curves obtained with an anti-TNF-α antibody were complemented with the Biacore functionality for sensorgram comparison analysis, whereby changes in antigen and Fc-receptor binding profiles could be detected. Next, analysis of temperature stressed TNF-α antibody revealed that calibration free concentration analysis (CFCA) data correlated perfectly with relative potency values. Together, these results demonstrate that combinations of SPR based dose response curves, sensorgram comparison and CFCA can be used to strengthen the confidence in relative potency assessments, and suggest that SPR can potentially be used as a surrogate potency assay in the quality control of biotherapeutic medicines.

Foreword to 'Quantitative and analytical relations in biochemistry'-a special issue in honour of Donald J. Winzor's 80th birthday

The purpose of this special issue is to honour Professor Donald J. Winzor's long career as a researcher and scientific mentor, and to celebrate the milestone of his 80th birthday. Throughout his career, Don has been renowned for his development of clever approximations to difficult quantitative relations governing a range of biophysical measurements. The theme of this special issue, 'Quantitative and analytical relations in biochemistry', was chosen to reflect this aspect of Don's scientific approach.