Elucidating the weak protein-protein interaction mechanisms behind the liquid-liquid phase separation of a mAb solution by different types of additives

A workflow for the development of template-assisted membrane crystallization downstream processing for monoclonal antibody purification

Monoclonal antibodies (mAbs) are commonly used biologic drugs for the treatment of diseases such as rheumatoid arthritis, multiple sclerosis, COVID-19 and various cancers. They are produced in Chinese hamster ovary cell lines and are purified via a number of complex and expensive chromatography-based steps, operated in batch mode, that rely heavily on protein A resin. The major drawback of conventional procedures is the high cost of the adsorption media and the extensive use of chemicals for the regeneration of the chromatographic columns, with an environmental cost. We have shown that conventional protein A chromatography can be replaced with a single crystallization step and gram-scale production can be achieved in continuous flow using the template-assisted membrane crystallization process. The templates are embedded in a membrane (e.g., porous polyvinylidene fluoride with a layer of polymerized polyvinyl alcohol) and serve as nucleants for crystallization. mAbs are flexible proteins that are difficult to crystallize, so it can be challenging to determine the optimal conditions for crystallization. The objective of this protocol is to establish a systematic and flexible approach for the design of a robust, economic and sustainable mAb purification platform to replace at least the protein A affinity stage in traditional chromatography-based purification platforms. The procedure provides details on how to establish the optimal parameters for separation (crystallization conditions, choice of templates, choice of membrane) and advice on analytical and characterization methods.

Conformational Changes and Drivers of Monoclonal Antibody Liquid-Liquid Phase Separation

Liquid-liquid phase separation is a phenomenon within biology whereby proteins can separate into dense and more dilute phases with distinct properties. Three antibodies that undergo liquid-liquid phase separation were characterized in the protein-rich and protein-poor phases. In comparison to the protein-poor phase, the protein-rich phase demonstrates more blue-shift tryptophan emissions and red-shifted amide I absorbances. Large changes involving conformational isomerization around disulfide bonds were observed using Raman spectroscopy. Amide I and protein fluorescence differences between the phases persisted to temperatures above the critical temperature but ceased at the temperature at which aggregation occurred. In addition, large changes occurred in the structural organization of water molecules within the protein-rich phase for all three antibodies. It is hypothesized that as the proteins have the same chemical potential in both phases, the protein viscosity is higher in the protein-rich phase resulting in slowed diffusion dependent protein aggregation in this phase. For all three antibodies we performed accelerated stability studies and found that the protein-rich phase aggregated at the same rate or slower than the protein-poor phase.

Advanced Formulations/Drug Delivery Systems for Subcutaneous Delivery of Protein-Based Biotherapeutics

Multiple advanced formulations and drug delivery systems (DDSs) have been developed to deliver protein-based biotherapeutics via the subcutaneous (SC) route. These formulations/DDSs include high-concentration solution, co-formulation of two or more proteins, large volume injection, protein cluster/complex, suspension, nanoparticle, microparticle, and hydrogel. These advanced systems provide clinical benefits related to efficacy and safety, but meanwhile, have more complicated formulations and manufacturing processes compared to conventional solution formulations. To develop a fit-for-purpose formulation/DDS for SC delivery, scientists need to consider multiple factors, such as the primary indication, targeted site, immunogenicity, compatibility, biopharmaceutics, patient compliance, etc. Next, they need to develop appropriate formulation (s) and manufacturing processes using the QbD principle and have a control strategy. This paper aims to provide a comprehensive review of advanced formulations/DDSs recently developed for SC delivery of proteins, as well as some knowledge gaps and potential strategies to narrow them through future research.

Opalescence Measurements: Improvements in Fundamental Knowledge, Identifying Sources of Analytical Biases, and Advanced Applications for the Development of Therapeutic Proteins

Opalescence of biopharmaceutical solutions can indicate suboptimal colloidal stability and is therefore a generally undesirable attribute that requires investigation and potentially remediation. While there are numerous instrumentation options available for measuring opalescence, cross-instrument comparisons and detailed knowledge of analytical biases have been limited.  Here, we highlight key findings from a multi-instrument investigation where differences in reported opalescence values are explained with particular emphasis on how the optical configuration and detector properties of each instrument affect the response of the sample and the primary formazin standards required for instrument calibration. In doing so, the particle size distribution, angular-dependent light scattering properties and refractive index of the primary formazin standard material are characterized and presented. Finally, the advanced application of a 90° angle light scattering instrument is presented as a suitable approach for making low volume, temperature controlled, nephelometric measurements of opalescence.  Moreover, we demonstrate how this approach enables the simultaneous evaluation of key physical properties, such as hydrodynamic size, that are pertinent to investigations of opalescent biopharmaceuticals but have historically required the use of separate instrumentation.  The findings reported here address key knowledge gaps and provide opportunities for improving the efficiency and inter-laboratory comparability of opalescence measurements for biopharmaceuticals.

Characterization of Opalescence in low Volume Monoclonal Antibody Solutions Enabled by Microscale Nephelometry

Monoclonal antibody (mAb)-based drugs are often prone to unfavorable solution behaviors including high viscosity, opalescence, phase separation, and aggregation at the high concentrations needed to enable patient-centric subcutaneous dosage forms. Given that these can have a detrimental impact on manufacturability, stability, and delivery, approaches to identifying, monitoring, and controlling these behaviors during drug development are critical. Opalescence presents a significant challenge due to its relationship to liquid-liquid phase separation. Quantitative characterization of opalescence via turbidimetry is often restrictive due to large volume requirements (>2 mL) and alternative microscale approaches based on light transmittance (Eckhardt et al., J Pharm Sci Technol. 1994, 48: 64-70) may pose challenging with respect to accuracy. To address the need for accurate and quantitative microscale opalescence measurements, we have evaluated the use of a 'de-tuned' static light scattering detector which requires <10 μL sample per measurement. We show that tuning of the laser power to a range far below that of traditional light scattering measurements results in a stable detector response that can be accurately calibrated to the nephelometric turbidity unit (NTU) scale using appropriate standards. The calibrated detector signal yields NTU values for mAbs and other protein solutions that are comparable to a commercial turbidimeter. We used this microscale approach to characterize the opalescence of 48 commercial mAb drug products and found that the majority have opalescence below 15 NTU. However, in products with mAb concentrations greater than 75 mg/mL, a broad range of opalescence was observed, in a few cases greater than 20 NTU. These measurements as well as nephelometric characterization of several IgG1 and IgG4 mAbs across a broad pH range highlight subclass-specific tendencies toward opalescence in high concentration solutions.

Isolating and Analyzing Protein Containing Granules from Cells

Recent advancements in detection methods have made protein condensates, also called granules, a major area of study, but tools to characterize these assemblies need continued development to keep up with evolving paradigms. We have optimized a protocol to separate condensates from cells using chemical cross-linking followed by size-exclusion chromatography (SEC). After SEC fractionation, the samples can be characterized by a variety of approaches including enzyme-linked immunosorbent assay, dynamic light scattering, electron microscopy, and mass spectrometry. The protocol described here has been optimized for cultured mammalian cells and E. coli expressing recombinant proteins. Since the lysates are fractionated by size, this protocol can be modified to study other large protein assemblies, including the nuclear pore complex, and for other tissues or organisms. © 2021 Wiley Periodicals LLC. Basic Protocol 1: SEC separation of cross-linked mammalian cell lysates Alternate Protocol: Preparation of non-crosslinked mammalian cells Basic Protocol 2: SEC separation of E. coli lysate Support Protocol 1: Detecting protein of interest by ELISA Support Protocol 2: TCA precipitation of SEC fractions.

Suppression of Electrostatic Mediated Antibody Liquid-Liquid Phase Separation by Charged and Noncharged Preferentially Excluded Excipients

Isotonic concentrations of inert cosolutes or excipients are routinely used in protein therapeutic formulations to minimize physical instabilities including aggregation, particulation, and precipitation that are often manifested during drug substance/product manufacture and long-term storage. Despite their prevalent use within the biopharmaceutical industry, a more detailed understanding for how excipients modulate the specific protein-protein interactions responsible for these instabilities is still needed so that informed formulation decisions can be made at the earliest stages of development when protein supply and time are limited. In the present report, subisotonic concentrations of the five common formulation excipients, sucrose, proline, sorbitol, glycerol, arginine hydrochloride, and the denaturant urea, were studied for their effect on the room temperature liquid-liquid phase separation of a model monoclonal antibody (mAb-B). Although each excipient lowered the onset temperatures of mAb-B liquid-liquid phase separation to different extents, all six were found to be preferentially excluded from the native state monomer by vapor pressure osmometry, and no apparent correlations to the excipient dependence of mAb-B melting temperatures were observed. These results and those of the effects of solution pH, addition of salt, and impact of a small number of charge mutations were most consistent with a mechanism of local excipient accumulation, to an extent dependent on their type, with the specific residues that mediate mAb-B electrostatic protein-protein interactions. These findings suggest that selection of excipients on the basis of their interaction with the solvent exposed residues of the native state may at times be a more effective strategy for limiting protein-protein interactions at pharmaceutically relevant storage conditions than choosing those that are excluded from the residues of the native state interior.

Adenosine Triphosphate-Induced Rapid Liquid-Liquid Phase Separation of a Model IgG1 mAb

Adenosine triphosphate (ATP) is amphiphilic in nature and has the characteristics of a hydrotrope because of the charged triphosphate moiety and the large aromatic ring located on each end of its structure. Previous studies revealed that ATP can effectively maintain the solubility and prevent liquid-liquid phase separation (LLPS) of some biological proteins. In this study, we assessed the impact of ATP on the stability of a model therapeutic IgG1 antibody (MA1) to evaluate its potential application in protein formulation design. In our system, ATP promotes rapid LLPS of MA1 and we demonstrate that the ATP-MA1 static interaction drives phase separation of MA1. The attractive protein-protein interaction increased exclusively in the presence of ATP but not in the presence of other ATP analogues, such as adenosine diphosphate, adenosine monophosphate, and adenine. Through an intrinsic fluorescence quenching study, we revealed that ATP bound to MA1 electrostatically and formed static interactions; furthermore, such static ATP-MA1 interactions significantly altered the surface property of the protein and the protein-protein interactions and subsequently induced LLPS of MA1. This ATP-induced LLPS could be effectively eliminated by Mg²⁺, which chelated with ATP and thus negated ATP-MA1 static interaction. Our results revealed the unique molecular mechanism of ATP-induced rapid LLPS of MA1.

Developability assessment for monoclonal antibody drug candidates: a case study

Various screening approaches are used by industry to evaluate development risks associated with discovery candidates. This process has become more complicated with biological therapeutics, a class dominated by monoclonal antibodies (mAb), and, increasingly, their derivative constructs. Effective early assessment for drug-like properties (DLP) can save time and costs by allowing a more complete consideration of issues that could impact the desired end result of a stable drug product. Here we report a case study of four IgG1 mAbs, with sequence variations in the variable domain region, screened as a set of possible drug candidates. Our comprehensive, tiered approach used a battery of analytical tools to assess molecular characteristics, conformational stability, colloidal stability, and short-term storage stability. While most DLP for the four candidates were developmentally acceptable and comparable, mAb-2 was associated with adverse colloidal properties. Further investigation of mAb-2 in an expanded pH range revealed a propensity for phase separation, indicating a need for the additional product development effort. Our results support that comprehensive DLP assessments in an expanded pH range are beneficial in identifying development options for promising molecules that show challenging stability trends. This adaptable approach may be especially useful in the development of increasingly complex antibody constructs.

Resolving Liquid-Liquid Phase Separation for a Peptide Fused Monoclonal Antibody by Formulation Optimization

Liquid-liquid phase separation (LLPS) of protein solutions has been usually related to strong protein-protein interactions (PPI) under certain conditions. For the first time, we observed the LLPS phenomenon for a novel protein modality, peptide-fused monoclonal antibody (pmAb). LLPS emerged within hours between pH 6.0 to 7.0 and disappeared when solution pH values decreased to pH 5.0 or lower. Negative values of interaction parameter (k_D) and close to zero values of zeta potential (ζ) were correlated to LLPS appearance. However, between pH 6.0 to 7.0, a strong electrostatic repulsion force was expected to potentially avoid LLPS based on the sequence predicted pI value, 8.35. Surprisingly, this is significantly away from experimentally determined pI, 6.25, which readily attributes the LLPS appearances of pmAb to the attenuated electrostatic repulsion force. Such discrepancy between experiment and prediction reminds the necessity of actual measurement for a complicated modality like pmAb. Furthermore, significant protein degradation took place upon thermal stress at pH 5.0 or lower. Therefore, the effects of pH and selected excipients on the thermal stability of pmAb were further assessed. A formulation consisting of arginine at pH 6.5 successfully prevented the appearance of LLPS and enhanced its thermal stability at 40 °C for pmAb. In conclusion, we have reported LLPS for a pmAb and successfully resolved the issue by optimizing formulation with aids from PPI characterization.

First-order nucleation and subsequent growth promote liquid-liquid phase separation of a model IgG1 mAb

Although protein aggregation is commonly encountered during the manufacturing and storage of bio-therapeutics, the actual aggregation mechanism remains unclear, and little has been reported about the protein aggregation kinetics from time zero under particular solution conditions. In this study, we used real-time dynamic light scattering (DLS) to continuously monitor the time-dependent evolution of the Z-average hydrodynamic radius of a model IgG1 (JM2) immediately after the JM2 solution was subjected to various low temperatures (0-4 °C). We observed that JM2 aggregated to form nuclei first, and then it subsequently grew to small liquid droplets via a two-step, first-order, reversible process without causing irreversible structural changes: a slow first step defined as the "nucleation" step, wherein nuclei formed slowly until reaching a transitional time point (t_onset), and a much faster second step initiated after t_onset and the nucleus size of the protein increased rapidly, which eventually caused liquid droplet formation and liquid-liquid phase separation (LLPS). The "nucleation" rate constant (K_nucleation) and particle growth rate constant (K_growth), as well as t_onset, were found to be temperature, pH and concentration dependent. The aggregation of JM2 could be universally described by these two-step first-order kinetics: under conditions where JM2 aggregated very slowly, the second step was not observed within the experimental time scale, while under conditions where JM2 aggregated very rapidly, the first step could not be recorded. We believe that these three parameters, K_nucleation, K_growth, and t_onset, can be used to quantify and compare the aggregation kinetics of JM2 under different solution and temperature conditions and, furthermore, serve as a theoretical base to account for the key characteristics of the aggregation kinetics of JM2 and other protein therapeutics under conditions of interest.

On the Aggregation and Nucleation Mechanism of the Monoclonal Antibody Anti-CD20 Near Liquid-Liquid Phase Separation (LLPS)

The crystallization of Anti-CD20, a full-length monoclonal antibody, has been studied in the PEG400/Na2SO4/Water system near Liquid-Liquid Phase Separation (LLPS) conditions by both sitting-drop vapour diffusion and batch methods. In order to understand the Anti-CD20 crystallization propensity in the solvent system of different compositions, we investigated some measurable parameters, normally used to assess protein conformational and colloidal stability in solution, with the aim to understand the aggregation mechanism of this complex biomacromolecule. We propose that under crystallization conditions a minor population of specifically aggregated protein molecules are present. While this minor species hardly contributes to the measured average solution behaviour, it induces and promotes crystal formation. The existence of this minor species is the result of the LLPS occurring concomitantly under crystallization conditions.

A "Soft" and "Hard" Ionization Method for Comprehensive Studies of Molecules

Ambient mass spectrometry can be rapidly and directly effective for molecular studies, while there still seems to be a gap between two major groups of electrospray ionization (ESI)- and atmospheric pressure chemical ionization (APCI)-related techniques, for detection of moderately polar to polar and low polar to nonpolar molecules in a relatively low mass range, respectively. Here, an extensively applicable "soft" and "hard" ionization method, spray-dependent plasma mass spectrometry (SDP MS), was established for detecting various molecules with diverse polarities or molecular weights. By SDP MS, both fragment ions and intact molecular ions can be obtained. Significantly, cluster ions of aggregates in high mass range formed by weak molecular interactions can also be well recorded, much softer than traditional ESI MS. By filling the gap between ESI-based and APCI-based ionization techniques, SDP MS would enhance MS performance for comprehensive molecular studies and be extensively applicable in fields of organic synthesis, biological chemistry, medical chemistry, and clinical diagnosis.

Methods for Physical Characterization of Phase-Separated Bodies and Membrane-less Organelles

Membrane-less organelles are cellular structures which arise through the phenomenon of phase separation. This process enables compartmentalization of specific sets of macromolecules (e.g., proteins, nucleic acids), thereby regulating cellular processes by increasing local concentration, and modulating the structure and dynamics of their constituents. Understanding the connection between structure, material properties and function of membrane-less organelles requires inter-disciplinary approaches, which address length and timescales that span several orders of magnitude (e.g., Ångstroms to micrometer, picoseconds to hours). In this review, we discuss the wide variety of methods that have been applied to characterize the morphology, rheology, structure and dynamics of membrane-less organelles and their components, in vitro and in live cells.

A Novel Human-Like Collagen Hydrogel Scaffold with Porous Structure and Sponge-Like Properties

The aim of this research was to prepare a novel sponge-like porous hydrogel scaffold based on human-like collagen (HLC) that could be applied in cartilage tissue regeneration. In this study, bovine serum albumin (BSA) was used as a porogen to prepare the porous hydrogel, which had not been previously reported. Glutamine transaminase (TGase) was used as the cross-linker of the hydrogel, because it could catalyze the cross-linking of BSA. During the crosslinking process, BSA and HLC were mixed together, which affected the cross-linking of HLC. When the cross-linking was completed, the non-crosslinked section formed pores. The microstructure, porosity, swelling properties, and compressive properties of the hydrogel were studied. The results showed that the pore size of the hydrogel was between 100 and 300 μm, the porosity reached up to 93.43%, and the hydrogel had rapid water absorption and suitable mechanical properties. Finally, we applied the hydrogel to cartilage tissue engineering through in vitro and in vivo research. The in vitro cell experiments suggested that the hydrogel could promote the proliferation and adhesion of chondrocytes, and in vivo transplantation of the hydrogel could enhance the repair of cartilage. In general, the hydrogel is promising as a tissue engineering scaffold for cartilage.