Microfluidic Approaches for the Characterization of Therapeutic Proteins

Antibodies, repertoires and microdevices in antibody discovery and characterization

Therapeutic antibodies are paramount in treating a wide range of diseases, particularly in auto-immunity, inflammation and cancer, and novel antibody candidates recognizing a vast array of novel antigens are needed to expand the usefulness and applications of these powerful molecules. Microdevices play an essential role in this challenging endeavor at various stages since many general requirements of the overall process overlap nicely with the general advantages of microfluidics. Therefore, microfluidic devices are rapidly taking over various steps in the process of new candidate isolation, such as antibody characterization and discovery workflows. Such technologies can allow for vast improvements in time-lines and incorporate conservative antibody stability and characterization assays, but most prominently screenings and functional characterization within integrated workflows due to high throughput and standardized workflows. First, we aim to provide an overview of the challenges of developing new therapeutic candidates, their repertoires and requirements. Afterward, this review focuses on the discovery of antibodies using microfluidic systems, technological aspects of micro devices and small-scale antibody protein characterization and selection, as well as their integration and implementation into antibody discovery workflows. We close with future developments in microfluidic detection and antibody isolation principles and the field in general.

Trends and challenges in microfluidic methods for protein manipulation-A review

Proteins are important molecules involved in an immensely large number of biological processes. Being capable of manipulating proteins is critical for developing reliable and affordable techniques to analyze and/or detect them. Such techniques would enable the production of therapeutic agents for the treatment of diseases or other biotechnological applications (e.g., bioreactors or biocatalysis). Microfluidic technology represents a potential solution to protein manipulation challenges because of the diverse phenomena that can be exploited to achieve micro- and nanoparticle manipulation. In this review, we discuss recent contributions made in the field of protein manipulation in microfluidic systems using different physicochemical principles and techniques, some of which are miniaturized versions of already established macro-scale techniques.

Variable domain mutational analysis to probe the molecular mechanisms of high viscosity of an IgG1 antibody

Subcutaneous injection is the preferred route of administration for many antibody therapeutics for reasons that include its speed and convenience. However, the small volume limit (typically ≤ 2 mL) for subcutaneous delivery often necessitates antibody formulations at high concentrations (commonly ≥100 mg/mL), which may lead to physicochemical problems. For example, antibodies with large hydrophobic or charged patches can be prone to self-interaction giving rise to high viscosity. Here, we combined X-ray crystallography with computational modeling to predict regions of an anti-glucagon receptor (GCGR) IgG1 antibody prone to self-interaction. An extensive mutational analysis was undertaken of the complementarity-determining region residues residing in hydrophobic surface patches predicted by spatial aggregation propensity, in conjunction with residue-level solvent accessibility, averaged over conformational ensembles from molecular dynamics simulations. Dynamic light scattering (DLS) was used as a medium throughput screen for self-interaction of ~ 200 anti-GCGR IgG1 variants. A negative correlation was found between the viscosity determined at high concentration (180 mg/mL) and the DLS interaction parameter measured at low concentration (2-10 mg/mL). Additionally, anti-GCGR variants were readily identified with reduced viscosity and antigen-binding affinity within a few fold of the parent antibody, with no identified impact on overall developability. The methods described here may be useful in the optimization of other antibodies to facilitate their therapeutic administration at high concentration.

Surface-Induced Protein Aggregation and Particle Formation in Biologics: Current Understanding of Mechanisms, Detection and Mitigation Strategies

Protein stability against aggregation is a major quality concern for the production of safe and effective biopharmaceuticals. Amongst the different drivers of protein aggregation, increasing evidence indicates that interactions between proteins and interfaces represent a major risk factor for the formation of protein aggregates in aqueous solutions. Potentially harmful surfaces relevant to biologics manufacturing and storage include air-water and silicone oil-water interfaces as well as materials from different processing units, storage containers, and delivery devices. The impact of some of these surfaces, for instance originating from impurities, can be difficult to predict and control. Moreover, aggregate formation may additionally be complicated by the simultaneous presence of interfacial, hydrodynamic and mechanical stresses, whose contributions may be difficult to deconvolute. As a consequence, it remains difficult to identify the key chemical and physical determinants and define appropriate analytical methods to monitor and predict protein instability at these interfaces. In this review, we first discuss the main mechanisms of surface-induced protein aggregation. We then review the types of contact materials identified as potentially harmful or detected as potential triggers of proteinaceous particle formation in formulations and discuss proposed mitigation strategies. Finally, we present current methods to probe surface-induced instabilities, which represent a starting point towards assays that can be implemented in early-stage screening and formulation development of biologics.

Approaches to expand the conventional toolbox for discovery and selection of antibodies with drug-like physicochemical properties

Antibody drugs should exhibit not only high-binding affinity for their target antigens but also favorable physicochemical drug-like properties. Such drug-like biophysical properties are essential for the successful development of antibody drug products. The traditional approaches used in antibody drug development require significant experimentation to produce, optimize, and characterize many candidates. Therefore, it is attractive to integrate new methods that can optimize the process of selecting antibodies with both desired target-binding and drug-like biophysical properties. Here, we summarize a selection of techniques that can complement the conventional toolbox used to de-risk antibody drug development. These techniques can be integrated at different stages of the antibody development process to reduce the frequency of physicochemical liabilities in antibody libraries during initial discovery and to co-optimize multiple antibody features during early-stage antibody engineering and affinity maturation. Moreover, we highlight biophysical and computational approaches that can be used to predict physical degradation pathways relevant for long-term storage and in-use stability to reduce the need for extensive experimentation.

Mathematical modeling and process analytical technology for continuous chromatography of biopharmaceutical products

Chromatography is a widely used separation method that is inherently a batch operation. However, the demand for higher productivity and lower cost and labor has prompted industries such as the petrochemical and food industries to transition from batch to continuous chromatography. Growing market competition in the biopharmaceutical industry and the rise of novel biotherapeutics modalities have brought about promising continuous chromatography methods as well as next-generation tools to enable continuous operation in bioprocessing. While these continuous chromatography methods outperform their batch counterpart, their implementation presents challenges due to their greater complexity. This review discusses two key technologies that are essential for the implementation of continuous chromatography: mathematical modeling and novel process analytical technologies. Mechanistic-based models not only aid in process development and optimization but also allow for greater process control and automation.

Non-specificity as the sticky problem in therapeutic antibody development

Antibodies are highly potent therapeutic scaffolds with more than a hundred different products approved on the market. Successful development of antibody-based drugs requires a trade-off between high target specificity and target binding affinity. In order to better understand this problem, we here review non-specific interactions and explore their fundamental physicochemical origins. We discuss the role of surface patches - clusters of surface-exposed amino acid residues with similar physicochemical properties - as inducers of non-specific interactions. These patches collectively drive interactions including dipole-dipole, π-stacking and hydrophobic interactions to complementary moieties. We elucidate links between these supramolecular assembly processes and macroscopic development issues, such as decreased physical stability and poor in vivo half-life. Finally, we highlight challenges and opportunities for optimizing protein binding specificity and minimizing non-specificity for future generations of therapeutics.

Microscale Diffusiophoresis of Proteins

Living systems are characterized by their spatially highly inhomogeneous nature which is susceptible to modify fundamentally the behavior of biomolecular species, including the proteins that underpin biological functionality in cells. Spatial gradients in chemical potential are known to lead to strong transport effects for colloidal particles, but their effect on molecular scale species such as proteins has remained largely unexplored. Here, we improve on existing diffusiophoresis microfluidic technique to measure protein diffusiophoresis in real space. The measurement of proteins is made possible by two ameliorations. First, a label-free microscope is used to suppress label interference. Second, improvements in numerical methods are developed to meet the particular challenges posed by small molecules. We demonstrate that individual proteins can undergo strong diffusiophoretic motion in salt gradients in a manner which is sufficient to overcome diffusion and which leads to dramatic changes in their spatial organization on the scale of a cell. Moreover, we demonstrate that this phenomenon can be used to control the motion of proteins in microfluidic devices. These results open up a path towards a physical understanding of the role of gradients in living systems in the spatial organization of macromolecules and highlight novel routes towards protein sorting applications on device.

Assessment of Therapeutic Antibody Developability by Combinations of In Vitro and In Silico Methods

Although antibodies have become the fastest-growing class of therapeutics on the market, it is still challenging to develop them for therapeutic applications, which often require these molecules to withstand stresses that are not present in vivo. We define developability as the likelihood of an antibody candidate with suitable functionality to be developed into a manufacturable, stable, safe, and effective drug that can be formulated to high concentrations while retaining a long shelf life. The implementation of reliable developability assessments from the early stages of antibody discovery enables flagging and deselection of potentially problematic candidates, while focussing available resources on the development of the most promising ones. Currently, however, thorough developability assessment requires multiple in vitro assays, which makes it labor intensive and time consuming to implement at early stages. Furthermore, accurate in vitro analysis at the early stage is compromised by the high number of potential candidates that are often prepared at low quantities and purity. Recent improvements in the performance of computational predictors of developability potential are beginning to change this scenario. Many computational methods only require the knowledge of the amino acid sequences and can be used to identify possible developability issues or to rank available candidates according to a range of biophysical properties. Here, we describe how the implementation of in silico tools into antibody discovery pipelines is increasingly offering time- and cost-effective alternatives to in vitro experimental screening, thus streamlining the drug development process. We discuss in particular the biophysical and biochemical properties that underpin developability potential and their trade-offs, review various in vitro assays to measure such properties or parameters that are predictive of developability, and give an overview of the growing number of in silico tools available to predict properties important for antibody development, including the CamSol method developed in our laboratory.

Measuring Self-Association of Antibody Lead Candidates with Dynamic Light Scattering

In this method chapter, we provide a brief overview of the key methods available to measure self-association of monoclonal antibodies (mAbs) and explain for which experimental throughputs they are usually applied. We then focus on dynamic light scattering (DLS) and describe experimental details on how to measure the diffusion interaction parameter (k_D) which is occasionally referred to as the gold standard for measuring self-association of proteins. The k_D is a well-established parameter to predict solution viscosity, which is one of the most critical developability parameters of mAbs. Finally, we present a pH and excipient screen that is designed to measure self-association with DLS under conditions that are relevant for bioprocessing and formulation of mAbs. The presented light scattering methods are well suited for lead candidate selections where it is essential to select mAbs with high developability potential for progression toward first human dose.

Design of millidevices to expedite apparent solubility measurements

A fast, automated and accurate millidevice for determination of the apparent solubility of proteins and impurities and different industrially relevant precipitating agents.

A small-volume microcapillary rheometer

We demonstrate a capillary device used to measure the shear rate-dependent viscosity of microliter scale volumes. Liquid samples are driven pneumatically through a microcapillary and partially fill a larger glass capillary. The glass capillary is mounted on an optical linear sensor to track the air-liquid meniscus in real time and trigger the reversal of flow direction by switching a pneumatic valve. Each transit provides a volumetric flow rate measurement, which is used with the pressure drop to determine viscosity as a function of shear rate. A given sample of at least 50 μL can be measured over at least 2 to 3 decades in shear rate, in the range of 10 to 10⁵ s^-1, and be essentially fully recovered. Validation by comparison to reference measurements is performed using samples of Newtonian and non-Newtonian fluid, with viscosity ranging from 1 to 100 mPa s. The range of operation and uncertainty arising from instrumentation, meniscus effects, and inertial effects are discussed. The performance of this rheometer is advantageous, especially for use and reuse of small volumes.

Design of Biopharmaceutical Formulations Accelerated by Machine Learning

In addition to activity, successful biological drugs must exhibit a series of suitable developability properties, which depend on both protein sequence and buffer composition. In the context of this high-dimensional optimization problem, advanced algorithms from the domain of machine learning are highly beneficial in complementing analytical screening and rational design. Here, we propose a Bayesian optimization algorithm to accelerate the design of biopharmaceutical formulations. We demonstrate the power of this approach by identifying the formulation that optimizes the thermal stability of three tandem single-chain Fv variants within 25 experiments, a number which is less than one-third of the experiments that would be required by a classical DoE method and several orders of magnitude smaller compared to detailed experimental analysis of full combinatorial space. We further show the advantage of this method over conventional approaches to efficiently transfer historical information as prior knowledge for the development of new biologics or when new buffer agents are available. Moreover, we highlight the benefit of our technique in engineering multiple biophysical properties by simultaneously optimizing both thermal and interface stabilities. This optimization minimizes the amount of surfactant in the formulation, which is important to decrease the risks associated with corresponding degradation processes. Overall, this method can provide high speed of converging to optimal conditions, the ability to transfer prior knowledge, and the identification of new nonlinear combinations of excipients. We envision that these features can lead to a considerable acceleration in formulation design and to parallelization of operations during drug development.

An accelerated surface-mediated stress assay of antibody instability for developability studies

High physical stability is required for the development of monoclonal antibodies (mAbs) into successful therapeutic products. Developability assays are used to predict physical stability issues such as high viscosity and poor conformational stability, but protein aggregation remains a challenging property to predict. Among different types of stresses, air–water and solid–liquid interfaces are well known to potentially trigger protein instability and induce aggregation. Yet, in contrast to the increasing number of developability assays to evaluate bulk properties, there is still a lack of experimental methods to evaluate antibody stability against interfaces. Here, we investigate the potential of a hydrophobic nanoparticle surface-mediated stress assay to assess the stability of mAbs during the early stages of development. We evaluate this surface-mediated accelerated stability assay on a rationally designed library of 14 variants of a humanized IgG4, featuring a broad span of solubility values and other developability properties. The assay could identify variants characterized by high instability against agitation in the presence of air–water interfaces. Remarkably, for the set of investigated molecules, we observe strong correlations between the extent of aggregation induced by the surface-mediated stress assay and other developability properties of the molecules, such as aggregation upon storage at 45°C, self-association (evaluated by affinity-capture self-interaction nanoparticle spectroscopy) and nonspecific interactions (estimated by cross-interaction chromatography, stand-up monolayer chromatography (SMAC), SMAC*). This highly controlled surface-mediated stress assay has the potential to complement and increase the ability of the current set of screening techniques to assess protein aggregation and developability potential of mAbs during the early stages of drug development.

Abbreviations:AC-SINS: Affinity-Capture Self-Interaction Nanoparticle Spectroscopy; AMS: Ammonium sulfate precipitation; ANS: 1-anilinonaphtalene-8-sulfonate; CIC: Cross-interaction chromatography; DLS: Dynamic light scattering; HIC: Hydrophobic interaction chromatography; HNSSA: Hydrophobic nanoparticles surface-stress assay; mAb: Monoclonal antibody; NP: Nanoparticle; SEC: Size exclusion chromatography; SMAC: Stand-up monolayer chromatography; WT: Wild type

Label-free methods for optical in vitro characterization of protein-protein interactions

Protein-protein interactions are involved in the regulation and function of the majority of cellular processes. As a result, much effort has been aimed at the development of methodologies capable of quantifying protein-protein interactions, with label-free methods being of particular interest due to the associated simplified workflows and minimisation of label-induced perturbations. Here, we review recent advances in optical technologies providing label-free in vitro measurements of affinities and kinetics. We provide an overview and comparison of existing techniques and their principles, discussing advantages, limitations, and recent applications.

Applications of Microfluidic Devices in the Diagnosis and Treatment of Cancer: A Review Study

Many cancer-related deaths are reported annually due to a lack of appropriate diagnosis and treatment strategies. Microfluidic technology, as new creativity has a great impact on automation and miniaturization via handling a small volume of materials and samples (in microliter to femtoliter range) to set up the system. Microfluidic devices not only detect various cancer-diagnostic factors from biological fluids but also can produce proper nanoparticles for drug delivery. With the contribution of microfluidics; multiple treatments for cancer such as chemotherapy, radiation therapy, and gene delivery can be implemented and studied. Hence, Microfluidics can be worth for the cancer field because of its high Throughput, high sensitivity, less material use, and low expense. In this review study, we intend to look at positive microfluidics prospects, features, benefits, and clinical applications.

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.

Analysis of biomolecular condensates and protein phase separation with microfluidic technology

An increasing body of evidence shows that membraneless organelles are key components in cellular organization. These observations open a variety of outstanding questions about the physico-chemical rules underlying their assembly, disassembly and functions. Some molecular determinants of biomolecular condensates are challenging to probe and understand in complex in vivo systems. Minimalistic in vitro reconstitution approaches can fill this gap, mimicking key biological features, while maintaining sufficient simplicity to enable the analysis of fundamental aspects of biomolecular condensates. In this context, microfluidic technologies are highly attractive tools for the analysis of biomolecular phase transitions. In addition to enabling high-throughput measurements on small sample volumes, microfluidic tools provide for exquisite control of self-assembly in both time and space, leading to accurate quantitative analysis of biomolecular phase transitions. Here, with a specific focus on droplet-based microfluidics, we describe the advantages of microfluidic technology for the analysis of several aspects of phase separation. These include phase diagrams, dynamics of assembly and disassembly, rheological and surface properties, exchange of materials with the surrounding environment and the coupling between compartmentalization and biochemical reactions. We illustrate these concepts with selected examples, ranging from simple solutions of individual proteins to more complex mixtures of proteins and RNA, which represent synthetic models of biological membraneless organelles. Finally, we discuss how this technology may impact the bottom-up fabrication of synthetic artificial cells and for the development of synthetic protein materials in biotechnology.

Insight into Heterogeneous Distribution of Protein Aggregates at the Surface Layer Using Attenuated Total Reflection-Fourier Transform Infrared Spectroscopic Imaging

Monoclonal antibodies (mAbs) have been used as therapeutics for the last few decades. It is necessary to investigate the stability of these mAbs under stress conditions and to elucidate aggregation mechanisms as a means of developing approaches which minimize the problem. Attenuated total reflection (ATR)-FTIR spectroscopic imaging allows probing of a sample at a depth of penetration of around 0.5-5 μm, which makes it suitable for the study of aggregated proteins when accumulated as a layer close to the surface of the ZnSe internal reflection element (IRE). Here, macro ATR-FTIR spectroscopic imaging, along with a variable angle of incidence accessory, have been used to differentiate between the secondary structure of proteins in bulk solution and those that have precipitated onto or near the ZnSe IRE surface. IgG spectra obtained from protein samples in individual wells have been averaged, extracted, and preprocessed, and the Amide I bands of the protein samples were compared and further analyzed to reveal protein distribution at the ZnSe IRE surface. These findings show depth profiling of IgG aggregates at the ZnSe IRE surface (0.5-5 μm) and do not follow a trend of decreasing protein presence with an increasing angle of incidence or increasing depth of penetration, suggesting an irregular distribution of aggregates in the z-direction.

Accelerated Aggregation Studies of Monoclonal Antibodies: Considerations for Storage Stability

Aggregation of mAbs is a crucial concern with respect to their safety and efficacy. Among the various properties of protein aggregates, it is emerging that their size can potentially impact their immunogenicity. Therefore, stability studies of antibody formulations should not only evaluate the rate of monomer loss but also determine the size distribution of the protein aggregates, which in turn depends on the aggregation mechanism. Here, we study the aggregation behavior of different formulations of 2 monoclonal immunoglobulins (IgGs) in the temperature range from 5°C to 50°C over 52 weeks of storage. We show that the aggregation kinetics of both antibodies follow non-Arrhenius behavior and that the aggregation mechanisms change between 40°C and 5°C, leading to different types of aggregates. Specifically, for a given monomer conversion, dimer formation dominates at low temperatures, while larger aggregates are formed at higher temperatures. We further show that the stability ranking of different molecules as well as of different formulations is drastically different at 40°C and 5°C while it correlates better between 30°C and 5°C. Our findings have implications for the level of information provided by accelerated aggregation studies with respect to protein stability under storage conditions.

Scalable Production and Isolation of Extracellular Vesicles: Available Sources and Lessons from Current Industrial Bioprocesses

Potential applications of extracellular vesicles (EVs) are attracting increasing interest in the fields of medicine, cosmetics, and nutrition. However, the manufacturing of EVs is currently characterized by low yields. This limitation severely hampers progress in research at the laboratory and clinical scales, as well as the realization of successful and cost-effective EV-based products. Moreover, the high level of heterogeneity of EVs further complicates reproducible manufacturing on a large scale. In this review, possible directions toward the scalable production of EVs are discussed. In particular, two strategies are considered: i) the optimization of upstream unit operations and ii) the exploitation of well-established and mature technologies already in use in other industrial bioprocesses.

Sensitivity analysis of the variability of amyloid aggregation profiles

The variability of amyloid aggregation profiles is linearly proportional to the duration of the aggregation process, and arises from a perturbation of one or more of the initial conditions.

Third generation antibody discovery methods: in silico rational design

Owing to their outstanding performances in molecular recognition, antibodies are extensively used in research and applications in molecular biology, biotechnology and medicine. Recent advances in experimental and computational methods are making it possible to complement well-established in vivo (first generation) and in vitro (second generation) methods of antibody discovery with novel in silico (third generation) approaches. Here we describe the principles of computational antibody design and review the state of the art in this field. We then present Modular, a method that implements the rational design of antibodies in a modular manner, and describe the opportunities offered by this approach.