Predicting solution aggregation rates for therapeutic proteins: approaches and challenges

Non-native aggregation is a common concern during therapeutic protein product development and manufacturing, particularly for liquid dosage forms. Because aggregates are often net irreversible under the conditions that they form, controlling aggregate levels requires control of aggregation rates across a range of solution conditions. Rational design of product formulation(s) would therefore benefit greatly from methods to accurately predict aggregation rates. This article focuses on the principles underlying current rate-prediction approaches for non-native aggregation, the limitations and strengths of different approaches, and illustrative examples from the authors’ laboratories. The analysis highlights a number of reasons why accurate prediction of aggregation rates remains an outstanding challenge, and suggests some of the important areas for research to ultimately enable improved predictive capabilities in the future.     

Early Stages for Parkinson’s Development: α-Synuclein Misfolding and Aggregation

Misfolding and aggregation of proteins are common threads linking a number of important human health problems, including various neurodegenerative disorders such as Parkinson’s disease in particular. The first and perhaps most important elements in most neurodegenerative processes are misfolding and aggregation of specific proteins. Despite the crucial importance of protein misfolding and abnormal interactions, very little is currently known about the molecular mechanism underlying these processes. Factors that lead to protein misfolding and aggregation in vitro are poorly understood, in addition to the complexities involved in the formation of protein nanoparticles with different morphologies (e.g. nanopores and other species) in vivo. A clear understanding of the molecular mechanisms of misfolding and aggregation will facilitate rational approaches to prevent protein misfolding mediated pathologies. To accomplish this goal and to elucidate the mechanism of protein misfolding, we developed a novel nanotechnology tool capable of detecting protein misfolding. We applied single molecule probing technique to characterize misfolding and self-assembly of α-synuclein dimers, which is the very first step of the aggregation process. Using AFM force spectroscopy approach, we were able to detect protein misfolding via enhanced interprotein interaction. Moreover, such an important characteristic as the lifetime of dimers formed by misfolded α-synuclein was measured. These data suggest that compared to highly dynamic monomeric forms, α-synuclein dimers are practically static and thus can play a role of aggregation nuclei for the formation of aggregates. Importantly, two different dissociation channels were detected suggesting that aggregation process can follow different pathways. The application of these findings for understanding of the aggregation phenomenon and the development of the disease is discussed.     

Aggregation Pathway of Recombinant Human Keratinocyte Growth Factor and Its Stabilization

Recombinant human keratinocyte growth factor (rhKGF) is prone to aggregation at elevated temperatures. Its aggregation pathway is proposed to proceed initially with a conformational change which perhaps results from repulsion between positively charged residues in clusters forming heparin binding sites. Unfolding of the protein leads to formation of large soluble aggregates. These soluble aggregates then form disulfide cross-linked precipitates. Finally these precipitates are converted to scrambled disulfides and/or non-disulfide cross-linked precipitates. Stabilizers such as heparin, sulfated polysaccharides, anionic polymers and citrate can greatly decrease the rate of aggregation of rhKGF at elevated temperatures. These molecules may all act by reducing charge repulsion on the protein thus stabilizing the native conformation. EDTA, on the other hand, is found to inhibit disulfide formation in aggregates and has only a moderate stabilizing effect on rhKGF.     

Selective domain stabilization as a strategy to reduce human serum albumin-human granulocyte colony stimulating factor aggregation rate

Therapeutic proteins must be generally formulated to reduce unwanted aggregation. Fusion proteins, which comprise domains assembled from separate proteins, may require unique formulation strategies in order to maximize their stability. A fusion protein of human serum albumin (HSA) and human granulocyte colony stimulating factor (GCSF; HSA-GCSF) was used as a model to test the hypothesis that formulations that increase the thermodynamic conformational stability of the least stable domain of a fusion protein will stabilize the entire fusion protein against aggregation. Conformational stability of HSA-GCSF was modulated by addition of octanoic acid, which was previously shown to increase the conformational stability of HSA, the least stable domain. Contrary to our hypothesis, increased conformational stability of the HSA domain did not result in increased resistance to aggregation of HSA-GCSF. These results for HSA-GCSF were also compared with similar studies conducted previously on a therapeutic protein formed by the fusion of HSA and human growth hormone (hGH; HSA-hGH).     

Therapeutic approaches against common structural features of toxic oligomers shared by multiple amyloidogenic proteins

Impaired proteostasis is one of the main features of all amyloid diseases, which are associated with the formation of insoluble aggregates from amyloidogenic proteins. The aggregation process can be caused by overproduction or poor clearance of these proteins. However, numerous reports suggest that amyloid oligomers are the most toxic species, rather than insoluble fibrillar material, in Alzheimer's, Parkinson's, and Prion diseases, among others. Although the exact protein that aggregates varies between amyloid disorders, they all share common structural features that can be used as therapeutic targets. In this review, we focus on therapeutic approaches against shared features of toxic oligomeric structures and future directions.     

Heterogeneous nucleation-controlled particulate formation of recombinant human platelet-activating factor acetylhydrolase in pharmaceutical formulation

Clinical lots of recombinant human platelet-activating factor acetylhydrolase (rhPAF-AH) were prepared in a lyophilized formulation. After reconstitution with sterile water for injection to form an aqueous solution (10 mM sodium citrate, 7.5 w/v% sucrose, and 0.1 w/v% Pluronic-F68, pH 6.5), a few visible, slowly growing particles formed consistently within hours at room temperature. To investigate the mechanism of this phenomenon, immediately after reconstitution, all protein aggregates and exogenous particles were removed by filtration. During 20 days incubation at room temperature, no visible aggregates formed in these filtered samples. In contrast, when nano-sized hydrophilic silica particles were added, they seeded rapid and extensive aggregation of rhPAF-AH. This effect was exacerbated in solutions containing a lower Pluronic-F68 concentration at 0.01%. Aggregation occurred even under conditions where rhPAF-AH adsorption was reversible, and induced no detectable changes to protein secondary and tertiary structures. Decreasing the extent (e.g., adding Pluronic-F68) or affinity (e.g., increasing solution pH) of rhPAF-AH adsorption on nano-sized silica particles was found to be effective at reducing aggregation. Accelerated aggregation was not observed when rhPAF-AH formulation was seeded with aggregated rhPAF-AH. These results show that rhPAF-AH aggregation proceeds through a heterogeneous nucleation-controlled mechanism, where exogenous particles present in solution serve as seeds on which rhPAF-AH adsorb, nucleate, and grow into large aggregates.     

Aggregation in protein-based biotherapeutics: computational studies and tools to identify aggregation-prone regions

Because of their large, complex, and conformationally heterogeneous structures, biotherapeutics are vulnerable to several physicochemical stresses faced during the various processing steps from production to administration. In particular, formation of protein aggregates is a major concern. The greatest risk with aggregates arises from their potential to give rise to immunogenic reactions. Hence, it is desirable to bring forward biotherapeutic drug candidates that show low propensity for aggregation and, thus, improved developability. Here, we present a comprehensive review of computational studies into the sequence and structural factors that underpin protein and peptide aggregation. A number of computational approaches have been applied including coarse grain models, atomistic molecular simulations, and bioinformatic approaches. These studies have focused on both the mechanism of aggregation and the identification of potential aggregation-prone sequence and structural motifs. We also survey the computational tools available to predict aggregation in therapeutic proteins. The findings communicated here provide insights that could be potentially useful in the rational design of therapeutic candidates with not only high potency and specificity but also improved stability and solubility. These sequence-structure-based approaches can be applied to both novel as well as follow-on biotherapeutics.     

Computational re-design of protein structures to improve solubility

ABSTRACT

Introduction: The rapid development of protein therapeutics is providing life-saving therapies for a wide range of human diseases. However, degradation reactions limit the quality and performance of these protein-based drugs. Among them, protein aggregation is the most common and one of the most challenging to prevent. Aggregation impacts biopharmaceutical development at every stage, from discovery to production and storage. In addition, regulators are highly concerned about the impact of protein aggregates on drug product safety.

Area covered: Herein, the authors review existing protein aggregation prediction approaches, with a special focus on four recently developed algorithms aimed to predict and improve solubility using three-dimensional protein coordinates: SAP, CamSol, Solubis and Aggrescan3D. Furthermore, they illustrate their potential to assist the design of solubility-improved proteins with a number of examples.

Expert opinion: Aggregation of protein-based drugs is, traditionally, addressed via wet lab experiments, using trial and error approaches that are expensive, difficult to perform and time-consuming. The structure-based in silico methods we describe here can predict accurately aggregation propensities, allowing researchers to work with pre-selected, well-behaved, protein candidates. These methods should contribute to the reduction of the time to the marketplace along with industrial costs and improve the safety of future therapeutic proteins.     

Effect of Azide Preservative on Thermomechanical Aggregation of Purified Reference Protein Materials

Protein aggregation can affect the quality of protein-based therapeutics. Attempting to unravel factors influencing protein aggregation involves systematic studies. These studies often include sodium azide or similar preservatives in the aggregation buffer. This work shows effects of azide on aggregation of two highly purified reference proteins, both a bovine serum albumin (BSA) as well as a monoclonal antibody (NISTmAb). The proteins were aggregated by thermomechanical stress, consisting of simultaneous heating of the solution with gentle agitation. Protein aggregates were characterized by asymmetric flow field flow fractionation (AF⁴) with light scattering measurements along with quantification by UV spectroscopy, revealing strong time-dependent generation of aggregated protein and an increase in aggregate molar mass. Gel electrophoresis was used to probe the reversibility of the aggregation and demonstrated complete reversibility for the NISTmAb, but not so for the BSA. Kinetic fitting to a commonly implemented nucleated polymerization model was also employed to provide mechanistic details into the kinetic process. The model suggests that the aggregation of the NISTmAb proceeds via nucleated growth and aggregate-aggregate condensation in a way that is dependent on the concentration (and presence) of the azide anion. This work overall implicates azide preservatives as having demonstrable effects on thermomechanical stress and aggregation of proteins undergoing systematic aggregation and stability studies.     

A false paradise - mixed blessings in the protein universe: the amyloid as a new challenge in drug development

Significant advances in therapeutic applications of proteins and peptides have brought new challenges in the field of drug development. Ordered protein aggregation known as amyloid formation has recently emerged as a universal phenomenon due to extensive research in protein folding and amyloid diseases. The amyloid represents a new generic structure characterized by cross-beta-sheet formation in its core, which implies that any polypeptide can adopt this conformation under amyloid-prone conditions. Some widely-used biopharmaceuticals such as insulin, glucagon, amylin and calcitonin have been shown to form amyloids and this list may be significantly extended upon further research. Compared to soluble precursor proteins and amorphous aggregates amyloids gain new properties such as remarkable stability and protease resistance, polymorphism, self-propagation via seeding and cross-seeding, cytotoxicity and induced immunogenicity. Some of them can be hazardous in biopharmaceutical applications. The causes of amyloid aggregation and strategies for its prevention are reviewed here. They utilize the current knowledge of amyloid properties, structure-based design principles and protein chemistry. Once these challenges are met, they will ultimately lead to safer and surer pharmaceuticals.     

Laser-induced breakdown detection of temperature-ramp generated aggregates of therapeutic monoclonal antibody

The detection and characterization of protein aggregation is essential during development and quality control of therapeutic proteins, as aggregates are typically inactive and may trigger anti-drug-antibody formation in patients. Especially large multi-domain molecules, such as the important class of therapeutic monoclonal antibodies (mAbs), can form various aggregates that differ in size and morphology. Although particle analysis advanced over the recent years, new techniques and orthogonal methods are highly valued. To our knowledge, the physical principle of laser-induced breakdown detection (LIBD) was not yet applied to sense aggregates in therapeutic protein formulations. We established a LIBD setup to monitor the temperature-induced aggregation of a mAb. The obtained temperature of aggregation was in good agreement with the results from previously published temperature-ramped turbidity and dynamic light scattering measurements. This study demonstrates the promising applicability of LIBD to investigate aggregates from therapeutic proteins. The technique is also adaptive to online detection and size determination, and offers interesting opportunities for morphologic characterization of protein particles and impurities, which will be part of future studies.     

Recent structural and computational insights into conformational diseases

Protein aggregation correlates with the development of several deleterious human disorders such as Alzheimer's disease, Parkinson's disease, prion-associated transmissible spongiform encephalopathies and type II diabetes. The polypeptides involved in these disorders may be globular proteins with a defined 3D-structure or natively unfolded proteins in their soluble conformations. In either case, proteins associated with these pathogeneses all aggregate into amyloid fibrils sharing a common structure, in which beta-strands of polypeptide chains are perpendicular to the fibril axis. Because of the prominence of amyloid deposits in many of these diseases, much effort has gone into elucidating the structural basis of protein aggregation. A number of recent experimental and theoretical studies have significantly increased our understanding of the process. On the one hand, solid-state NMR, X-ray crystallography and single molecule methods have provided us with the first high-resolution 3D structures of amyloids, showing that they exhibit conformational plasticity and are able to adopt different stable tertiary folds. On the other hand, several computational approaches have identified regions prone to aggregation in disease-linked polypeptides, predicted the differential aggregation propensities of their genetic variants and simulated the early, crucial steps in protein self-assembly. This review summarizes these findings and their therapeutic relevance, as by uncovering specific structural or sequential targets they may provide us with a means to tackle the debilitating diseases linked to protein aggregation.     

Protein quality control in Alzheimer's disease: a fatal saviour

Aggregation of Abeta plays a key role in the pathogenesis of Alzheimer's disease. Although the highly structured Abeta aggregates (fibrils) have long been thought to be the toxic form of Abeta, recent evidence suggests that smaller, soluble intermediates in Abeta aggregation are the real culprit. Because these oligomeric aggregates are already formed in the secretory pathway, this raises another issue: Is intra- or extracellular Abeta involved in the pathogenic cascade? Because aggregated proteins are very toxic, cells have developed quality control responses to deal with such proteins. A prime site for quality culum. Here, aberrant proteins are recognized and can be targeted for degradation to the cytosolic quality control system. In addition, there is accumulating evidence for quality control in other subcellular compartments in the cell. All quality control mechanisms are initially protective, but will become destructive after prolonged accumulation of aggregated proteins. This is enhanced by decreased efficiency of these systems during aging and therefore, these responses may play an important role in the pathogenesis of Alzheimer's disease. In this review, we will discuss the role of protein quality control in the neurotoxicity of Abeta.     

Holographic Characterization of Protein Aggregates in the Presence of Silicone Oil and Surfactants

Characterizing protein aggregates in the presence of silicone oil is a long standing challenge for the pharmaceutical industry. Silicone oil is often used as a lubricant in devices that deliver and store therapeutic protein products and has been linked to protein aggregation, which can compromise a drug’s effectiveness or cause autoimmune responses in patients. Most traditional technologies cannot quantitatively distinguish protein aggregates and silicone oil in their native formulations for sizes less than 5 μm. We use holographic video microscopy to study protein aggregation to demonstrate its capability to quantitatively distinguish protein aggregates and silicone oil in the presence of varying amounts of the surfactants SDS and polysorbate 80 in the size range of 0.5-10 μm without the need for dilution or special sample preparation. We show that SDS denatures proteins and stabilizes silicone oil. We also show that polysorbate 80 may limit protein aggregate formation if it is added to an IgG solution before introducing silicone oil.     

Microfluidic Approaches for the Characterization of Therapeutic Proteins

In the last decades, the pharmaceutical market has experienced an increase in the number of therapeutic proteins. The high activity and selectivity of these macromolecules is often achieved at the expense of complex structures, which exhibit several biophysical properties that must be carefully controlled and optimized for the successful development of these drugs as well as for guaranteeing their quality and safety. This need has motivated the application of a variety of biophysical techniques to analyze properties of therapeutic proteins and protein solutions including interactions, aggregation, solubility, viscosity, and thermal stability. After briefly summarizing currently available experimental approaches, we highlight the emerging possibilities offered by advances in microfluidic technology for the analysis of therapeutic proteins during manufacturing and formulation.     

Lead-induced attenuation in the aggregation of acetylcholine receptors during the neuromuscular junction formation

Lead (Pb2+) toxicity is more common in children and is associated with cognitive deficits, which may reflect lead-induced changes in central synaptic development and function. Aside from neurotoxicity, lead exposure may also impact mature neuromuscular junction (NMJ) and cause muscle weakness. NMJ is known as a peripheral cholinergic synapse and its signaling cascades responsible for development are similar to those for the central synapses. However, the effect of lead exposure on the formation of NMJ in mammals is unclear. In the present study, a NG108-15/C2C12 coculture model was used to measure the acetylcholine receptor (AChR) aggregates formed on the myotubes which was an early hallmark for the NMJ formation. AChR aggregates were identified by alpha-bungarotoxin under fluorescent microscope. Single dose of lead acetate with final concentrations at 10(-3), 10(-1), or 10 microM was applied to dishes at the beginning of coculturing. Following 3-day exposure, although NG108-15 cells could extend long neurites to nearby myotubes, obvious dose-dependent attenuation in AChR aggregation was shown. The averaged area of an AChR aggregate, the averaged number of AChR aggregates per myotube, and the total area of AChR aggregates per myotube were all significantly decreased. In addition, the distribution percentages of various sizes of AChR aggregates showed that almost half of the AChR aggregates were formed with a size of 2-5 microm2 regardless of lead exposure. After treating 10 microM of lead acetate, significantly more AChR aggregates ranged from 2 to 20 microm2 were formed and significantly less AChR aggregates larger than 20 microm2 were formed. These results indicated that lead exposure reduced the extent of AChR aggregation concerning both the size and number of AChR aggregates and large AChR aggregates could hardly be formed after acute high-level lead exposure. No significant change was found in the total amount of AChRs on the myotubes after lead exposure, which indicated that the attenuation of AChR aggregation was not caused by reducing the synthesis of AChRs but by remaining dispersed pattern of AChRs on the myotubes. These data suggest that lead exposure exerts detrimental effects on the formation of NMJ.     

Improved activity and stability of lysozyme at the water/CH2Cl2 interface: enzyme unfolding and aggregation and its prevention by polyols

Protein inactivation and aggregation at the water/CH2Cl2 interface is one of the most detrimental events hindering the encapsulation of structurally unperturbed proteins into poly(lactide-co-glycolide) (PLG) microspheres for their clinical application as sustained release dosage forms. We have investigated the inactivation and aggregation of the model protein hen egg-white lysozyme at this interface and devised methods to prevent both events. When lysozyme was exposed to a large water/CH2Cl2 interface achieved by homogenization, lysozyme aggregation occurred. Fourier-transform infrared (FTIR) spectroscopic data demonstrated that the aggregates formed contained intermolecular beta-sheets. The aggregates were of a noncovalent nature because they slowly dissolved in D2O and the IR spectral bands typical for the intermolecular beta-sheets disappeared at approximately 1617 and 1690 cm(-1). The observed loss in specific enzyme activity of soluble lysozyme was caused by the irreversible formation of an unfolded lysozyme species, which was found to be monomeric, and was able to leave the water/CH2Cl2 interface and accumulate in the aqueous phase. Polyols were, in a concentration dependent fashion, efficient in ameliorating lysozyme unfolding and aggregation. However, prevention of lysozyme aggregation and activity loss in the various samples were unrelated. Thus, polyols must work by more than one mechanism preventing the two events. For the first time, an excipient effect on the conformational stability of lysozyme has been excluded from contributing to the prevention of lysozyme unfolding and aggregation.     

Effects of formulation development methods on the stability of model protein pharmaceuticals embedded in solid lipid matrices

This study was conducted to investigate the influence of formulation development methods on the stability (secondary structure, aggregation, and biological activity) of protein drugs embedded in lipid matrices. Catalase, horseradish peroxidase, and α-chymotrypsin were employed as model proteins, while Precirol® AT05 (glyceryl palmitostearate) was used as lipid matrix. Protein-loaded lipid matrices were prepared using melting and mixing and wet granulation methods. Attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy, size exclusion chromatography (SEC) and biological activity analyses were performed. ATR FT-IR analysis indicated significant interference of the lipid with the protein amide-I band, which was eliminated using spectral subtraction. Wet granulation method induced more changes in protein secondary structure compared to melting and mixing method. SEC analysis gave evidence of protein aggregation for catalase upon adopting the wet granulation method. The biological activity of catalase was found to reduce significantly than other two proteins upon using wet granulation method, which might be ascribed to both secondary structure alterations and the formation of aggregates. Horseradish peroxidase and α-chymotrypsin did not form any soluble aggregates. In conclusion, melting and mixing method emerged as a better incorporation method compared to wet granulation because of better stability shown by the formulated proteins.     

Tissue transglutaminase: a novel pharmacological target in preventing toxic protein aggregation in neurodegenerative diseases

Alzheimer's disease, Parkinson's disease and Huntington's disease are neurodegenerative diseases, characterized by the accumulation and deposition of neurotoxic protein aggregates. The capacity of specific proteins to self-interact and form neurotoxic aggregates seems to be a common underlying mechanism leading to pathology in these neurodegenerative diseases. This process might be initiated and/or accelerated by proteins that interact with these aggregating proteins. The transglutaminase (TG) family of proteins are calcium-dependent enzymes that catalyze the formation of covalent ε-(γ-glutamyl)lysine isopeptide bonds, which can result in both intra- and intermolecular cross-links. Intramolecular cross-links might modify self-interacting proteins, and make them more prone to aggregate. In addition, intermolecular cross-links could link self-aggregating proteins and thereby initiate and/or stimulate the aggregation process. So far, increased levels and activity of tissue transglutaminase (tTG), the best characterized member of the TG family, have been observed in many neurodegenerative diseases, and the self-interacting proteins, characteristic of Alzheimer's disease, Parkinson's disease and Huntington's disease, are known substrates of tTG. Here, we focus on the role of tTG in the initiation of the aggregation process of self-interacting proteins in these diseases, and promote the notion that tTG might be an attractive novel target for treatment of neurodegenerative diseases.