Current status and future prospects for ion-mobility mass spectrometry in the biopharmaceutical industry

Detailed characterization of protein reagents and biopharmaceuticals is key in defining successful drug discovery campaigns, aimed at bringing molecules through different discovery stages up to development and commercialization. There are many challenges in this process, with complex and detailed analyses playing paramount roles in modern industry.Mass spectrometry (MS) has become an essential tool for characterization of proteins ever since the onset of soft ionization techniques and has taken the lead in quality assessment of biopharmaceutical molecules, and protein reagents, used in the drug discovery pipeline. MS use spans from identification of correct sequences, to intact molecule analyses, protein complexes and more recently epitope and paratope identification.MS toolkits could be incredibly diverse and with ever evolving instrumentation, increasingly novel MS-based techniques are becoming indispensable tools in the biopharmaceutical industry. Here we discuss application of Ion Mobility MS (IMMS) in an industrial setting, and what the current applications and outlook are for making IMMS more mainstream.     

Aggregates in monoclonal antibody manufacturing processes

Monoclonal antibodies have proved to be a highly successful class of therapeutic products. Large-scale manufacturing of pharmaceutical antibodies is a complex activity that requires considerable effort in both process and analytical development. If a therapeutic protein cannot be stabilized adequately, it will lose partially or totally its therapeutic properties or even cause immunogenic reactions thus potentially further endangering the patients' health. The phenomenon of protein aggregation is a common issue that compromises the quality, safety, and efficacy of antibodies and can happen at different steps of the manufacturing process, including fermentation, purification, final formulation, and storage. Aggregate levels in drug substance and final drug product are a key factor when assessing quality attributes of the molecule, since aggregation might impact biological activity of the biopharmaceutical. In this review it is analyzed how aggregates are formed during monoclonal antibody industrial production, why they have to be removed and the manufacturing process steps that are designed to either minimize or remove aggregates in the final product.     

Immunogenicity of therapeutic proteins. Part 1: impact of product handling

The patents of first-generation biopharmaceutical proteins are expiring, creating opportunities for biosimilar products. Unlike conventional generic pharmaceuticals, the development of biosimilar products is far more complex and requires more than a simple demonstration of pharmacological bioequivalence to establish efficacy and safety. The main concern with biosimilar products, as for any therapeutic protein, is immunogenicity and with it the potential for serious clinical sequelae. In the absence of adequate predictors of immunogenicity outside the clinical trial setting, biosimilar products should be evaluated in the same way that any novel pharmaceutical is evaluated. Herein, the factors involved in breaking host tolerance following administration of a therapeutic protein are discussed. The impact of product handling on immunogenicity is considered in the context of some hard-fought lessons that have helped to shape the current era of biopharmaceutical manufacturing, packaging, distribution, storage, and quality assurance.     

无细胞蛋白表达体系研究进展及在生物制药领域中的应用

作为一种快速高效的体外蛋白合成手段,无细胞蛋白表达体系(Cell-free Protein Synthesis,CFPS)一直以来就被广泛应用于基础生物学领域的研究。与传统的基于细胞的体内表达体系相比,CFPS突破了细胞的生理限制,其可调控性强、对毒性蛋白的耐受力高,使得许多很难在体内合成的复杂蛋白在体外顺利表达。近年来随着研究人员不断对CFPS进行优化,通过简化制备工艺、开发价格低廉的能量再生系统、稳定底物供应、促进蛋白正确折叠等方式,成功研发出生产效率高、成本低廉、反应体积大的表达体系。凭借其高通量和大规模的蛋白表达优势,CFPS为解决生物制药领域中面临的难题提供了新的解决思路,并成功地应用于高通量药物筛选、大规模生产重组蛋白药物、个体化定制肿瘤疫苗等领域,显示出其在生物制药领域的重要应用潜力。     

重组单克隆抗体电荷异质性和工艺调控

重组单克隆抗体药物大多存在翻译后修饰且种类复杂多样,因此研发过程中的质量控制显得尤为重要。其中电荷异质性是关键质量属性,其可能影响生物制品的疗效,甚至有可能带来意想不到的副作用,从而影响药品的安全性和有效性,所以在单抗药物开发过程中需要重点关注并加以调控。单抗药物翻译后修饰是造成电荷异质性的主要原因,因此电荷异质性的控制是生物药物工艺开发的一个重要挑战。梳理了电荷异质性的表征方法,并且根据其分类对能够造成电荷异质性产生的蛋白翻译后修饰进行了总结,同时阐述了不同的电荷异质性对抗体类药物安全性及有效性的影响,最后总结了工艺开发中电荷异质性工艺调控策略的最新进展,以期给生物药物工艺开发及质量研究人员以启示。     

Small scale affinity purification and high sensitivity reversed phase nanoLC-MS N-glycan characterization of mAbs and fusion proteins

N-glycosylation is a complex post-translational modification with potential effects on the efficacy and safety of therapeutic proteins and known influence on the effector function of biopharmaceutical monoclonal antibodies (mAbs). Comprehensive characterization of N-glycosylation is therefore important in biopharmaceutical development. In early development, e.g. during pool or clone selection, however, only minute protein amounts of multiple samples are available for analytics. High sensitivity and high throughput methods are thus needed. An approach based on 96-well plate sample preparation and nanoLC-MS of 2- anthranilic acid or 2-aminobenzoic acid (AA) labeled N-glycans for the characterization of biopharmaceuticals in early development is reported here. With this approach, 192 samples can be processed simultaneously from complex matrices (e.g., cell culture supernatant) to purified 2-AA glycans, which are then analyzed by reversed phase nanoLC-MS. Attomolar sensitivity has been achieved by use of nanoelectrospray ionization, resulting in detailed glycan maps of mAbs and fusion proteins that are exemplarily shown in this work. Reproducibility, robustness and linearity of the approach are demonstrated, making use in a routine manner during pool or clone selection possible. Other potential fields of application, such as glycan biomarker discovery from serum samples, are also presented.     

Moss bioreactors producing improved biopharmaceuticals

Plants may serve as superior production systems for complex recombinant pharmaceuticals. Current strategies for improving plant-based systems include the development of large-scale production facilities as well as the optimisation of protein modifications. While post-translational modifications of plant proteins generally resemble those of mammalian proteins, certain plant-specific protein-linked sugars are immunogenic in humans, a fact that restricts the use of plants in biopharmaceutical production so far. The moss Physcomitrella patens was developed as a contained tissue culture system for recombinant protein production in photo-bioreactors. By targeted gene replacements, moss strains were created with non-immunogenic humanised glycan patterns. These were proven to be superior to currently used mammalian cell lines in producing antibodies with enhanced effectiveness.     

Small scale affinity purification and high sensitivity reversed phase nanoLC-MS N-glycan characterization of mAbs and fusion proteins

N-glycosylation is a complex post-translational modification with potential effects on the efficacy and safety of therapeutic proteins and known influence on the effector function of biopharmaceutical monoclonal antibodies (mAbs). Comprehensive characterization of N-glycosylation is therefore important in biopharmaceutical development. In early development, e.g. during pool or clone selection, however, only minute protein amounts of multiple samples are available for analytics. High sensitivity and high throughput methods are thus needed. An approach based on 96-well plate sample preparation and nanoLC-MS of 2- anthranilic acid or 2-aminobenzoic acid (AA) labeled N-glycans for the characterization of biopharmaceuticals in early development is reported here. With this approach, 192 samples can be processed simultaneously from complex matrices (e.g., cell culture supernatant) to purified 2-AA glycans, which are then analyzed by reversed phase nanoLC-MS. Attomolar sensitivity has been achieved by use of nanoelectrospray ionization, resulting in detailed glycan maps of mAbs and fusion proteins that are exemplarily shown in this work. Reproducibility, robustness and linearity of the approach are demonstrated, making use in a routine manner during pool or clone selection possible. Other potential fields of application, such as glycan biomarker discovery from serum samples, are also presented.     

In vitro-engineered non-antibody protein therapeutics

Antibodies have proved to be a valuable mode of therapy for numerous diseases, mainly owing to their high target binding affinity and specificity. Unfortunately, antibodies are also limited in several respects, chief amongst those being the extremely high cost of manufacture. Therefore, non-antibody binding proteins have long been sought after as alternative therapies. New binding protein scaffolds are constantly being designed or discovered with some already approved for human use by the FDA. This review focuses on protein scaffolds that are either already being used in humans or are currently being evaluated in clinical trials. Although not all are expected to be approved, the significant benefits ensure that these molecules will continue to be investigated and developed as therapeutic alternatives to antibodies. Based on the location of the amino acids that mediate ligand binding, we place all the protein scaffolds under clinical development into two general categories: scaffolds with ligand-binding residues located in exposed flexible loops, and those with the binding residues located in protein secondary structures, such as α-helices. Scaffolds that fall under the first category include adnectins, anticalins, avimers, Fynomers, Kunitz domains, and knottins, while those belonging to the second category include affibodies, β-hairpin mimetics, and designed ankyrin repeat proteins (DARPins). Most of these scaffolds are thermostable and can be easily produced in microorganisms or completely synthesized chemically. In addition, many of these scaffolds derive from human proteins and thus possess very low immunogenic potential. Additional advantages and limitations of these protein scaffolds as therapeutics compared to antibodies will be discussed.     

Bacterial display in combinatorial protein engineering

Technologies for display of recombinant protein libraries are today essential tools in many research-intensive fields, such as in the drug discovery processes of biopharmaceutical development. Phage display is still the most widely used method, but alternative systems are available and are becoming increasingly popular. The most rapidly expanding of the alternative systems are the cell display-based technologies, offering innovative strategies for selection and characterization of affinity proteins. Most investigations have focused on eukaryotic yeast for display of protein libraries, but similar systems are also being developed using prokaryotic hosts. This review summarizes the field of bacterial surface display with a strong emphasis on library applications for generation of new affinity proteins. The main focus will be on the most recent progress of the work on primarily Escherichia coli, but also on studies using a recently developed system for display on Gram-positive Staphylococcus carnosus. In addition, general strategies for combinatorial protein engineering using cell display are discussed along with the latest developments of new methodologies with comparisons to mainly phage display technology.     

生物制药的现状和未来（二）：发展趋势与希望

随着基因组和蛋白质组研究的深入,越来越多的与人类疾病发展相关的靶标被确定,使得我们能够研发更精确的药物来防治这些疾病。这意味着生物制药将有更多机会获得突破性进展,最终将使更多更好的生物技术药物被批准上市。综述了生物制药发展的几个趋势,主要有:(1)哺乳动物细胞表达的产品将在相当长的时间内占统治地位;(2)治疗性抗体将会是生物制药领域第二次创新高潮;(3)越来越多分子量大、结构复杂的功能蛋白将被开发成生物技术药物,尤其是用于治疗遗传性疾病的药物;(4)对已批准上市的生物技术药物的化学修饰尤其是PEG化以改善药物性能;(5)通过某些药物的定点突变获得第二代新生物技术药物,如胰岛素、EPO和t-PA的突变体;(6)组织工程、细胞治疗和基因治疗充满了机遇和挑战。     

Harnessing phage and ribosome display for antibody optimisation

Therapeutic antibodies have become a major driving force for the biopharmaceutical industry; therefore, the discovery and development of safe and efficacious antibody leads have become competitive processes. Phage and ribosome display are ideal tools for the generation of such molecules and have already delivered an approved drug as well as a multitude of clinical candidates. Because they are capable of searching billions of antibody variants in tailored combinatorial libraries, they are particularly applicable to potency optimisation. In conjunction with targeted, random or semi-rational mutagenesis strategies, they deliver large panels of potent antibody leads. This review introduces the two technologies, compares them with respect to their use in antibody optimisation and highlights how they can be exploited for the successful and efficient generation of putative drug candidates.     

Current status and perspectives of biopharmaceutical drugs

Since the first approval of recombinant human insulin three decades ago, more than 150 biopharmaceutical drugs have been marketed, and some of them became blockbuster drugs in market size. The patent expiration of the oldest biopharmaceutical drugs resulted in the development of biosimilar drugs. However the short serum half-life of biopharmaceutical drugs incurs a frequent injection to maintain a target clinical outcome in patients. The other major critical concern of biopharmaceutical drugs is immunogenicity producing anti-drug antibodies. These antibodies may reduce clinical efficacy by neutralizing biological activity, and may not only cause a severe allergic reaction but also other serious adverse reactions by blocking endogenous proteins. In order to improve pharmaceutical properties and reduce immunogenicity, the next generation biobetter drugs were achieved by glycoengineering technology, pegylation technology and protein engineering technology. Other biobetter drugs having optimized binding sites were also generated by in vitro display technology. Many of those biobetter drugs have been developed and/or are under development, and come into the clinical field in the near future.     

Production of FMDV virus-like particles by a SUMO fusion protein approach in Escherichia coli

Virus-like particles (VLPs) are formed by the self-assembly of envelope and/or capsid proteins from many viruses. Some VLPs have been proven successful as vaccines, and others have recently found applications as carriers for foreign antigens or as scaffolds in nanoparticle biotechnology. However, production of VLP was usually impeded due to low water-solubility of recombinant virus capsid proteins. Previous studies revealed that virus capsid and envelope proteins were often posttranslationally modified by SUMO in vivo, leading into a hypothesis that SUMO modification might be a common mechanism for virus proteins to retain water-solubility or prevent improper self-aggregation before virus assembly. We then propose a simple approach to produce VLPs of viruses, e.g., foot-and-mouth disease virus (FMDV). An improved SUMO fusion protein system we developed recently was applied to the simultaneous expression of three capsid proteins of FMDV in E. coli. The three SUMO fusion proteins formed a stable heterotrimeric complex. Proteolytic removal of SUMO moieties from the ternary complexes resulted in VLPs with size and shape resembling the authentic FMDV. The method described here can also apply to produce capsid/envelope protein complexes or VLPs of other disease-causing viruses.     

Ribosomally-synthesised cyclic peptides from plants as drug leads and pharmaceutical scaffolds

Owing to their exceptional stability and favourable pharmacokinetic properties, plant-derived cyclic peptides have recently attracted significant attention in the field of peptide-based drug design. This article describes the three major classes of ribosomally-synthesised plant peptides – the cyclotides, the PawS-derived peptides and the orbitides – and reviews their applications as leads or scaffolds in drug design. These ribosomally-produced peptides have a range of biological activities, including anti-HIV, cytotoxic and immunomodulatory activity. In addition, recent interest has focused on their use as scaffolds to stabilise bioactive peptide sequences, thereby enhancing their biopharmaceutical properties. There are now more than 30 published papers on such ‘grafting’ applications, most of which have been reported only in the last few years, and several such studies have reported in vivo activity of orally delivered cyclic peptides. In this article, we describe approaches to the synthesis of cyclic peptides and their pharmaceutically-grafted derivatives as well as outlining their biosynthetic routes. Finally, we describe possible bioproduction routes for pharmaceutically active cyclic peptides, involving plants and plant suspension cultures.     

Evaluation of the influenza A replicon for transient expression of recombinant proteins in mammalian cells

Recombinant protein expression in mammalian cells has become a very important technique over the last twenty years. It is mainly used for production of complex proteins for biopharmaceutical applications. Transient recombinant protein expression is a possible strategy to produce high quality material for preclinical trials within days. Viral replicon based expression systems have been established over the years and are ideal for transient protein expression. In this study we describe the evaluation of an influenza A replicon for the expression of recombinant proteins. We investigated transfection and expression levels in HEK-293 cells with EGFP and firefly luciferase as reporter proteins. Furthermore, we studied the influence of different influenza non-coding regions and temperature optima for protein expression as well. Additionally, we exploited the viral replication machinery for the expression of an antiviral protein, the human monoclonal anti-HIV-gp41 antibody 3D6. Finally we could demonstrate that the expression of a single secreted protein, an antibody light chain, by the influenza replicon, resulted in fivefold higher expression levels compared to the usually used CMV promoter based expression. We emphasize that the influenza A replicon system is feasible for high level expression of complex proteins in mammalian cells.     

用于筛选人工结合蛋白的骨架蛋白

抗体作为最著名的天然结合蛋白,因其具有与抗原特异结合的特性,近100多年以来无论在生物技术领域,还是在疾病的诊断及治疗方面,都发挥着广泛而重要的作用。但是抗体自身固有的局限性也在很大程度上限制了它的应用,而人工结合蛋白既具有抗体的特点,又兼具更多优势:分子更小;稳定性更高;能在大肠杆菌中高产量、高可溶性表达;易于修饰;能够达到高亲合力和高特异性;并且与抗体没有知识产权的冲突,因此被称为理想的"新一代抗体"。人工结合蛋白是从基因改造构建而成的骨架蛋白库中针对特定的靶分子筛选而得的。从骨架蛋白的概念和设计,骨架蛋白的分类,应用骨架蛋白筛选人工结合蛋白的技术以及人工结合蛋白的应用和前景等方面进行总结概述。     

蛋白质骨架库的构建及其在功能蛋白质设计中的应用

利用活性位点嫁接设计新的功能蛋白质的方法需要功能模体和蛋白质骨架两种构件。出于活性位点嫁接的需要,我们构建了一个蛋白质骨架库,且提供搜索与功能模体相配骨架的工具及其评估方法。并用两个活性位点的嫁接进行了检验。