Aggregation Time Machine: A Platform for the Prediction and Optimization of Long-Term Antibody Stability Using Short-Term Kinetic Analysis

Predicting the Long-Term Stability of Biologics with Short-Term Data

Understanding the long-term stability of biologics is crucial to ensure safe, effective, and cost-efficient life-saving therapeutics. Current industry and regulatory practices require arduous real-time data collection over three years; thus, reducing this bottleneck while still ensuring product quality would enhance the speed of medicine to patients. We developed a parallel-pathway kinetic model, combined with Monte Carlo simulations for prediction intervals, to predict the long-term (2+ years) stability of biotherapeutic critical quality attributes (aggregates, fragments, charge variants, purity, and potency) with short-term (3-6 months) data from intended, accelerated, and stressed temperatures. We rigorously validated the model with 18 biotherapeutic drug products, composed of IgG1 and IgG4 monoclonal antibodies, antibody-drug conjugates, dual protein coformulations, and a fusion protein, including high concentration (≥100 mg/mL) formulations, in liquid and lyophilized presentations. For each drug product, we accurately predicted the long-term trends of multiple quality attributes using just 6 months of data. Further, we demonstrated superior stability prediction via our methods compared with industry-standard linear regression methods. The robust and repeatable results of this work across an unprecedented suite of 18 biotherapeutic compounds suggest that kinetic models with Monte Carlo simulation can predict the long-term stability of biologics with short-term data.

Dynamic optimization of an integrated cultivation-aggregation model for mAb production

Due to their proteinaceous structure, monoclonal antibodies (mAbs) are susceptible to irreversible aggregation, with harmful consequences on drug efficacy and patient safety. To mitigate this risk in modern biopharmaceutical processes, it is critical to comply with current good manufacturing practices (cGMP) and pursue operating strategies minimizing irreversible aggregation whilst also maximizing mAb throughput. These conflicting objectives are targeted in this study by formulating and analyzing an integrated dynamic model accounting for both cultivation and aggregation of mAbs from a Chinese Hamster Ovary (CHO) cell line. Two manipulated dynamic variables are considered here in simulation studies: firstly temperature manipulation within a batch reactor, and secondly feed flow manipulation within a series of isothermal fed-batch reactors. Following this, dynamic optimization investigations have been conducted, firstly with the single objective of maximizing mAb throughput and secondly with multiple (two) objectives of maximizing mAb throughput while also minimizing irreversible aggregate content, simultaneously. The study provides key insight into tradeoffs of how simultaneous temperature and feed flowrate manipulation affects mAb throughput and aggregation inside bioreactors.

Designing Robust Monoclonal Antibody Drug Products: Pitfalls of Simplistic Approaches for Stability Prediction

Thermal stability attributes including unfolding onset (Tonset) and mid-point (Tm) are often utilized for efficient development of monoclonal antibody (mAb) products during lead selection and formulation screening workflows. An assumption of direct correlation between thermal and kinetic physical stability underpins this basic approach. While literature reports have substantiated this general approach under specific conditions, clear exceptions have been highlighted alongside. Herein, a set of mAbs formulated under diverse solution conditions to generate a broad array of thermal and kinetic stability profiles were systematically analyzed. Sequence modifications in the Fc region were purposefully engineered to generate a set of low-melting mAbs. A diverse set of excipients were subsequently utilized and shown to modulate the Tm over a wide range. While a general correlation between high Tm and low aggregation rate was observed under accelerated conditions, the predictive utility of Tm under relevant product storage conditions was inadequate at best. Critically, Tm data did not correlate with long-term aggregation rates under refrigerated or room temperature conditions. Even under accelerated conditions, Tm appeared to be a poor predictor of aggregation once it exceeded the solution storage temperature (40°C) by ∼15°C, similar to conditions routinely encountered in the development of canonical mAbs (Tm > 60°C). Pitfalls of simplistic correlative approaches are discussed in the context of practical biologics product development.

Biophysical Principles Emerging from Experiments on Protein-Protein Association and Aggregation

Protein-protein association and aggregation are fundamental processes that play critical roles in various biological phenomena, from cellular signaling to disease progression. Understanding the underlying biophysical principles governing these processes is crucial for elucidating their mechanisms and developing strategies for therapeutic intervention. In this review, we provide an overview of recent experimental studies focused on protein-protein association and aggregation. We explore the key biophysical factors that influence these processes, including protein structure, conformational dynamics, and intermolecular interactions. We discuss the effects of environmental conditions such as temperature, pH and related buffer-specific effects, and ionic strength and related ion-specific effects on protein aggregation. The effects of polymer crowders and sugars are also addressed. We list the techniques used to study aggregation. We analyze emerging trends and challenges in the field, including the development of computational models and the integration of multidisciplinary approaches for a comprehensive understanding of protein-protein association and aggregation.

Identification of sorbitol esterification of glutamic acid by LC-MS/MS in a monoclonal antibody stability assessment

The stability of monoclonal antibodies (mAbs) is vital for their therapeutic success. Sorbitol, a common mAb stabilizer used to prevent aggregation, was evaluated for any potential adverse effects on the chemical stability of mAb X. An LC-MS/MS based analysis focusing on the post-translational modifications (PTMs) of mAb X was conducted on samples that had undergone accelerated aging at 40°C. Along with PTMs that are known to affect mAbs' structure function and stability (such as deamidation and oxidation), a novel mAb PTM was discovered, the esterification of glutamic acid by sorbitol. Incubation of mAb X with a 1:1 ratio of unlabeled sorbitol and isotopically labeled sorbitol (13C6) further corroborated that the modification was the consequence of the esterification of glutamic acid by sorbitol. Levels of esterification varied across glutamic acid residues and correlated with incubation time and sorbitol concentration. After 4 weeks of accelerated stability with isotopically labeled sorbitol, it was found that 16% of the total mAb possesses an esterified glutamic acid. No esterification was observed at aspartic acid sites despite the free carboxylic acid side chain. This study unveils a unique modification of mAbs, emphasizing its potential significance for formulation and drug development.

Using Passive Microrheology to Measure the Evolution of the Rheological Properties of NIST mAb Formulations during Adsorption to the Air-Water Interface

The development of novel protein-based therapeutics, such as monoclonal antibodies (mAbs), is often limited due to challenges associated with maintaining the stability of these formulations during manufacturing, storage, and clinical administration. An undesirable consequence of the instability of protein therapeutics is the formation of protein particles. MAbs can adsorb to interfaces and have the potential to undergo partial unfolding as well as to form viscoelastic gels. Further, the viscoelastic properties may be correlated with their aggregation potential. In this work, a passive microrheology technique was used to correlate the evolution of surface adsorption with the evolution of surface rheology of the National Institute of Standards and Technology (NIST) mAb reference material (NIST mAb) and interface-induced subvisible protein particle formation. The evolution of the surface adsorption and interfacial shear rheological properties of the NIST mAb was recorded in four formulation conditions: two different buffers (histidine vs phosphate-buffered saline) and two different pHs (6.0 and 7.6). Our results together demonstrate the existence of multiple stages for both surface adsorption and surface rheology, characterized by an induction period that appears to be purely viscous, followed by a sharp increase in protein molecules at the interface when the film rheology is viscoelastic and ultimately a slowdown in the surface adsorption that corresponds to the formation of solid-like or glassy films at the interface. When the transitions between the different stages occurred, they were dependent on the buffer/pH of the formulations. The onset of these transitions can also be correlated to the number of protein particles formed at the interface. Finally, the addition of polysorbate 80, an FDA-approved surfactant used to mitigate protein particle formation, led to the interface being surfactant-dominated, and the resulting interface remained purely viscous.

Predicting Long-Term Stability of an Oral Delivered Antibody Drug Product with Accelerated Stability Assessment Program Modeling

The oral delivery of protein therapeutics offers numerous advantages for patients but also presents significant challenges in terms of development. Currently, there is limited knowledge available regarding the stability and shelf life of orally delivered protein therapeutics. In this study, a comprehensive assessment of the stability of an orally delivered solid dosage variable domain of heavy-chain antibody (VHH antibody) drug product was conducted. Four stability related quality attributes that undergo change as a result of thermal and humidity stress were identified. Subsequently, these attributes were modeled using an accelerated stability approach facilitated by ASAPprime software. To the best of our knowledge, this is the first time that this approach has been reported for an antibody drug product. We observed overall good model quality and accurate predictions regarding the protein stability during storage. Notably, we discovered that protein aggregation, formed through a degradation pathway, requires additional adjustments to the modeling method. In summary, the ASAP approach demonstrated promising results in predicting the stability of this complex solid-state protein formulation. This study sheds light on the stability and shelf life of orally delivered protein therapeutics, addressing an important knowledge gap in the field.

Site-Specific Structural Changes in Long-Term-Stressed Monoclonal Antibody Revealed with DEPC Covalent-Labeling and Quantitative Mass Spectrometry

Studies of structural changes in mAbs under forced stress and storage conditions are essential for the recognition of degradation hotspots, which can be further remodeled to improve the stability of the respective protein. Herein, we used diethyl pyrocarbonate (DEPC)-based covalent labeling mass spectrometry (CL-MS) to assess structural changes in a model mAb (SILuMAb). Structural changes in the heat-stressed mAb samples were confirmed at specific amino acid positions from the DEPC label mass seen in the fragment ion mass spectrum. The degree of structural change was also quantified by increased or decreased DEPC labeling at specific sites; an increase or decrease indicated an unfolded or aggregated state of the mAb, respectively. Strikingly, for heat-stressed SILuMAb samples, an aggregation-prone area was identified in the CDR region. In the case of longterm stress, the structural consequences for SILuMAb samples stored for up to two years at 2-8 °C were studied with SEC-UV and DEPC-based CL-MS. While SEC-UV analysis only indicated fragmentation of SILuMAb, DEPC-based CL-MS analysis further pinpointed the finding to structural disturbances of disulfide bonds at specific cysteines. This emphasized the utility of DEPC CL-MS for studying disulfide rearrangement. Taken together, our data suggests that DEPC CL-MS can complement more technically challenging methods in the evaluation of the structural stability of mAbs.

Discovery of ABBV-154, an anti-TNF Glucocorticoid Receptor Modulator Immunology Antibody-Drug Conjugate (iADC)

Stable attachment of drug-linkers to the antibody is a critical requirement, and for maleimide conjugation to cysteine, it is achieved by ring hydrolysis of the succinimide ring. During ADC profiling in our in-house property screening funnel, we discovered that the succinimide ring open form is in equilibrium with the ring closed succinimide. Bromoacetamide (BrAc) was identified as the optimal replacement, as it affords stable attachment of the drug-linker to the antibody while completely removing the undesired ring open-closed equilibrium. Additionally, BrAc also offers multiple benefits over maleimide, especially with respect to homogeneity of the ADC structure. In combination with a short, hydrophilic linker and phosphate prodrug on the payload, this afforded a stable ADC (ABBV-154) with the desired properties to enable long-term stability to facilitate subcutaneous self-administration.

Optimization of Drug-Linker to Enable Long-term Storage of Antibody-Drug Conjugate for Subcutaneous Dosing

To facilitate subcutaneous dosing, biotherapeutics need to exhibit properties that enable high-concentration formulation and long-term stability in the formulation buffer. For antibody-drug conjugates (ADCs), the introduction of drug-linkers can lead to increased hydrophobicity and higher levels of aggregation, which are both detrimental to the properties required for subcutaneous dosing. Herein we show how the physicochemical properties of ADCs could be controlled through the drug-linker chemistry in combination with prodrug chemistry of the payload, and how optimization of these combinations could afford ADCs with significantly improved solution stability. Key to achieving this optimization is the use of an accelerated stress test performed in a minimal formulation buffer.

A universal tool for stability predictions of biotherapeutics, vaccines and in vitro diagnostic products

It is of particular interest for biopharmaceutical companies developing and distributing fragile biomolecules to warrant the stability and activity of their products during long-term storage and shipment. In accordance with quality by design principles, advanced kinetic modeling (AKM) has been successfully used to predict long-term product shelf-life and relies on data from short-term accelerated stability studies that are used to generate Arrhenius-based kinetic models that can, in turn, be exploited for stability forecasts. The AKM methodology was evaluated through a cross-company perspective on stability modeling for key stability indicating attributes of different types of biotherapeutics, vaccines and biomolecules combined in in vitro diagnostic kits. It is demonstrated that stability predictions up to 3 years for products maintained under recommended storage conditions (2-8 °C) or for products that have experienced temperature excursions outside the cold-chain show excellent agreement with experimental real-time data, thus confirming AKM as a universal and reliable tool for stability predictions for a wide range of product types.

Accelerating therapeutic protein design with computational approaches toward the clinical stage

Therapeutic protein, represented by antibodies, is of increasing interest in human medicine. However, clinical translation of therapeutic protein is still largely hindered by different aspects of developability, including affinity and selectivity, stability and aggregation prevention, solubility and viscosity reduction, and deimmunization. Conventional optimization of the developability with widely used methods, like display technologies and library screening approaches, is a time and cost-intensive endeavor, and the efficiency in finding suitable solutions is still not enough to meet clinical needs. In recent years, the accelerated advancement of computational methodologies has ushered in a transformative era in the field of therapeutic protein design. Owing to their remarkable capabilities in feature extraction and modeling, the integration of cutting-edge computational strategies with conventional techniques presents a promising avenue to accelerate the progression of therapeutic protein design and optimization toward clinical implementation. Here, we compared the differences between therapeutic protein and small molecules in developability and provided an overview of the computational approaches applicable to the design or optimization of therapeutic protein in several developability issues.

High concentration formulation developability approaches and considerations

The growing need for biologics to be administered subcutaneously and ocularly, coupled with certain indications requiring high doses, has resulted in an increase in drug substance (DS) and drug product (DP) protein concentrations. With this increase, more emphasis must be placed on identifying critical physico-chemical liabilities during drug development, including protein aggregation, precipitation, opalescence, particle formation, and high viscosity. Depending on the molecule, liabilities, and administration route, different formulation strategies can be used to overcome these challenges. However, due to the high material requirements, identifying optimal conditions can be slow, costly, and often prevent therapeutics from moving rapidly into the clinic/market. In order to accelerate and derisk development, new experimental and in-silico methods have emerged that can predict high concentration liabilities. Here, we review the challenges in developing high concentration formulations, the advances that have been made in establishing low mass and high-throughput predictive analytics, and advances in in-silico tools and algorithms aimed at identifying risks and understanding high concentration protein behavior.

Insights into ultra-low affinity lipase-antibody noncovalent complex binding mechanisms

Detection of host cell protein (HCP) impurities is critical to ensuring that recombinant drug products, including monoclonal antibodies (mAbs), are safe. Mechanistic characterization as to how HCPs persist in drug products is important to refining downstream processing. It has been hypothesized that weak lipase-mAb interactions enable HCP lipases to evade drug purification processes. Here, we apply state-of-the-art methods to establish lipase-mAb binding mechanisms. First, the mass spectrometry (MS) approach of fast photochemical oxidation of proteins was used to elucidate putative binding regions. The CH1 domain was identified as a conserved interaction site for IgG1 and IgG4 mAbs against the HCPs phospholipase B-like protein (PLBL2) and lysosomal phospholipase A2 (LPLA2). Rationally designed mutations in the CH1 domain of the IgG4 mAb caused a 3- to 70-fold K_D reduction against PLBL2 by surface plasmon resonance (SPR). LPLA2-IgG4 mutant complexes, undetected by SPR and studied using native MS collisional dissociation experiments, also showed significant complex disruption, from 16% to 100%. Native MS and ion mobility (IM) determined complex stoichiometries for four lipase-IgG4 complexes and directly interrogated the enrichment of specific lipase glycoforms. Confirmed with time-course and exoglycosidase experiments, deglycosylated lipases prevented binding, and low-molecular-weight glycoforms promoted binding, to mAbs. This work demonstrates the value of integrated biophysical approaches to characterize micromolar affinity complexes. It is the first in-depth structural report of lipase-mAb binding, finding roles for the CH1 domain and lipase glycosylation in mediating binding. The structural insights gained offer new approaches for the bioengineering of cells or mAbs to reduce HCP impurity levels.Abbreviations: CAN, Acetonitrile; AMAC, Ammonium acetate; BFGS, Broyden-Fletcher-Goldfarb-Shanno; CHO, Chinese Hamster Ovary; K_D, Dissociation constant; DTT, Dithiothreitol; ELISA, Enzyme-linked immunosorbent assay; FPOP, Fast photochemical oxidation of proteins; FA, Formic acid; F(ab'), Fragment antibodies; HCP, Host cell protein; IgG, Immunoglobulin; IM, Ion mobility; LOD, Lower limit of detection; LPLA2, Lysosomal phospholipase A2; Man, Mannose; MS, Mass spectrometry; MeOH, Methanol; MST, Microscale thermophoresis; mAbs, Monoclonal antibodies; PPT1, Palmitoyl protein thioesterase; ppm, Parts per million; PLBL2, Phospholipase B-like protein; PLD3, Phospholipase D3; PS-20, Polysorbate-20; SP, Sphingomyelin phosphodiesterase; SPR, Surface plasmon resonance; TFA, Trifluoroacetic acid.