Antibody-based technologies for target discovery

Antibodies have proven to be exquisite investigation tools in the field of life sciences. They also constitute one of the oldest and most successful biological products for diagnostics and therapeutics. This review investigates the current use of antibodies in target discovery. To address this topic in a larger context, established and emerging technologies that are expected to contribute to target discovery will first be examined. These technologies include: mass spectroscopic analysis of proteins, protein-protein interaction and other network analysis approaches, as well as protein and antibody arrays. The potential of antibody engineering and the ANTIBIOMIX technology will then be discussed; antibody therapeutics, however, will not be examined.     

From research to regulated: challenges in transferring methods

The current decade has seen an evolution in biomarker research, with a breakthrough from traditional single analyte studies to simultaneous multiple analyte technologies, aided by the progressive development of research tools and the discovery of many novel biomarkers. It is foreseeable that the application of such technologies will have an integral role in clinical studies for establishing biomarker profiles of disease status and prognosis. However, the transfer of such complex procedures to a regulated environment presents many obstacles. Here, we discuss some of these applied technologies and the validation approaches we have taken as an academic unit to prove their suitability and appropriateness for clinical application. We discuss the advantages and limitations for such end point assays in early Phase clinical trials.     

Computational and artificial intelligence-based methods for antibody development

Due to their high target specificity and binding affinity, therapeutic antibodies are currently the largest class of biotherapeutics. The traditional largely empirical antibody development process is, while mature and robust, cumbersome and has significant limitations. Substantial recent advances in computational and artificial intelligence (AI) technologies are now starting to overcome many of these limitations and are increasingly integrated into development pipelines. Here, we provide an overview of AI methods relevant for antibody development, including databases, computational predictors of antibody properties and structure, and computational antibody design methods with an emphasis on machine learning (ML) models, and the design of complementarity-determining region (CDR) loops, antibody structural components critical for binding.     

Drug target identification and quantitative proteomics

The emerging technologies in proteomic analysis provide great opportunity for the discovery of novel therapeutic drug targets for unmet medical needs through delivering of key information on protein expression, post-translational modifications and protein–protein interactions. This review presents a summary of current quantitative proteomic concepts and mass spectrometric technologies, which enable the acceleration of target discovery. Examples of the strategies and current technologies in the target identification/validation process are provided to illustrate the successful application of proteomics in target identification, in particular for monoclonal antibody therapies. Current bottlenecks and future directions of proteomic studies for target and biomarker identification are also discussed to better facilitate the application of this technology.     

Soft- and hard-lipid nanoparticles: a novel approach to lymphatic drug delivery

With the current advance in nanotechnology, the development has accelerated of a number of nanoparticle-type drugs such as nano-emulsions, lipid emulsions, liposomes, and cell therapeutics. With these developments, attempts are being made to apply these new drugs to healing many intractable diseases related to antibody production, autoimmune disorders, cancer, and organ transplantation in both clinical and nonclinical trials. Drug delivery to the lymphatic system is indispensable for treating these diseases, but the core technologies related to the in vivo distribution characteristics and lymphatic delivery evaluation of these particle-type drugs have not yet been established. Additionally, the core technologies for setting up the pharmacotherapeutic aspects such as their usage and dosages in the development of new drugs do not meet the needs of the market. Therefore, it is necessary to consider dividing these particle-type drugs into soft-lipid nanoparticles that can change size in the process of body distribution and hard-lipid nanoparticles whose surfaces are hardened and whose sizes do not easily change in vivo; these soft- and hard-lipid nanoparticles likely possess different biodistribution characteristics including delivery to the lymphatic system. In this review, we summarize the different types, advantages, limitations, possible remedies, and body distribution characteristics of soft- and hard-lipid nanoparticles based on their administration routes. We also emphasize that it will be necessary to fully understand the differences in distribution between these soft- and hard-lipid nanoparticle-type drugs and to establish pharmacokinetic models for their more ideal lymphatic delivery.     

Target identification and validation in drug discovery: the role of proteomics

Proteomics, the study of cellular protein expression, is an evolving technology platform that has the potential to identify novel proteins involved in key biological processes in the cell that may serve as potential drug targets. While proteomics has considerable theoretical promise, individual cells/tissues have the potential to generate many millions of proteins while the current analytical technologies that involve the use of time-consuming two dimensional gel electrophoresis (2DIGE) and various mass spectrometry (MS) techniques are unable to handle complex biological samples without multiple high-resolution purification steps to reduce their complexity. This can significantly limit the speed of data generation and replication and requires the use of bioinformatic algorithms to reconstitute the parent proteome, a process that does not always result in a reproducible outcome. In addition, membrane bound proteins, e.g., receptors and ion channels, that are the targets of many existing drugs, are not amenable to study due, in part, to limitations in current proteomic techniques and also to these being present in low abundance and thus disproportionally represented in proteome profiles. Subproteomes with reduced complexity have been used to generate data related to specific, hypothesis-driven questions regarding target identification, protein-interaction networks and signaling pathways. However progress to date, with the exception of diagnostic proteomics in the field of cancer, has been exceedingly slow with an inability to put such studies in the context of a larger proteome, limiting the value of the information. Additionally the pathway for target validation (which can be more accurately described at the preclinical level as target confidence building) remains unclear. It is important that the ability to measure and interrogate proteomes matches expectations, avoiding a repetition of the disappointment and subsequent skepticism that accompanied what proved to be unrealistic expectations for the rapid contribution of data based on the genome maps, to biomedical research.     

Identification of genes for a complex trait: examples from hypertension

Essential hypertension (EH) affects approximately 20% of the adult population, and has a multifactorial origin arising from an interaction between susceptibility genes and environmental factors. Several strategies and methods have been used to identify hypertension susceptibility genes. This review is thought to highlight current strategies for a better understanding of their limitations and strengths in a complex trait like EH. Linkage analysis is less effective at identifying common variants with modest effects typical for complex traits, and has therefore proved to be largely unsuccessful in EH. No candidate gene was assessed by a human linkage study so far. Possible redesigns of the linkage approach for complex diseases may include larger sample sizes and dense marker maps. Genetic association studies may be an effective approach to the problems posed by complex traits. With the explosion of genotyping technologies, genome-wide association studies have become feasible, and small-scale association studies have become plentiful. The different types of association studies are reviewed and issues that are important to consider when interpreting association studies of complex traits are discussed. Properly defined phenotypes, large enough sample cohorts to achieve sufficient statistical power, carefully matched samples to avoid population stratification are all integral parts of a high-quality association study. Multiple testing often results in false-positive results by chance, and inconclusive results may arise from ignoring linkage disequilibrium of the tested polymorphism, an effect avoidable by haplotype analysis. A new evolutionary development of the candidate gene approach is introduced which will extent traditional association study settings gaining better understanding of complex diseases like hypertension and might give better chances to evaluate association studies for their functional relevance.     

Analytical tools for characterizing biopharmaceuticals and the implications for biosimilars

Biologics such as monoclonal antibodies are much more complex than small-molecule drugs, which raises challenging questions for the development and regulatory evaluation of follow-on versions of such biopharmaceutical products (also known as biosimilars) and their clinical use once patent protection for the pioneering biologic has expired. With the recent introduction of regulatory pathways for follow-on versions of complex biologics, the role of analytical technologies in comparing biosimilars with the corresponding reference product is attracting substantial interest in establishing the development requirements for biosimilars. Here, we discuss the current state of the art in analytical technologies to assess three characteristics of protein biopharmaceuticals that regulatory authorities have identified as being important in development strategies for biosimilars: post-translational modifications, three-dimensional structures and protein aggregation.     

靶向多次跨膜蛋白的抗体药物研究进展

多次跨膜蛋白作为连接细胞膜内外环境的重要渠道,参与多种信号的传导,调控细胞对外界刺激的响应。许多人类疾病都与多次跨膜蛋白功能异常密切相关,使它们成为理想的药物作用靶点。相较于以小分子和多肽为主导的现有治疗方式,基于抗体的药物具有特异性强等优势,为调控多次跨膜蛋白的功能提供了新的路径。然而,针对多次跨膜蛋白进行抗体药物研发也面临诸多挑战,其结构的复杂性产生了例如表位可及性、蛋白表达困难和蛋白动态构象等独特障碍,需要创新性策略来推动相应的抗体药物研发。对多次跨膜蛋白因复杂结构为抗体药物开发所带来的挑战进行探讨,以及对近年来为克服这些障碍所发展的新方法进行介绍,并且系统性总结目前在研的针对多次跨膜蛋白的抗体类药物。相信随着该领域的发展,从靶向多次跨膜蛋白的抗体药物研究中获得的见解不仅对改进治疗干预措施,而且对推进更广泛的药物研究创新具     

A simple method for the detection of insoluble aggregates in protein formulations

Low levels of insoluble aggregates in protein formulations can sometimes only be detected by visual inspection. To overcome the subjectivity and other limitations associated with visual inspection, a microscopic technique based on filtration/staining was developed. This method is a simple modification of the microscopic method listed in USP for particulate matter analysis and it provides two major advantages over the original method. First, particles are easier to see because of the staining. Second, this method is specific to protein aggregates so that it avoids interferences from other nonproteinaceous particles. In addition, this method does not have any restrictions on the rheological or optical properties of the samples. This method can be a useful tool in protein formulation development as demonstrated by its application in the evaluation of monoclonal antibody formulations.     

Aptamers: current challenges and future prospects

ABSTRACT

Introduction: Aptamers are oligonucleotide molecules raised in vitro from large combinatorial libraries of nucleic acids and developed to bind to targets with high affinity and specificity. Whereas novel target molecules are proposed for therapeutic intervention and diagnostic, aptamer technology has a great potential to become a source of lead compounds.

Areas covered: In this review, the authors address the current status of the technology and highlight the recent progress in aptamer-based technologies. They also discuss the current major technical limitations of aptamer technology and propose original solutions based on existing technologies that could result in a solid aptamer-discovery platform.

Expert opinion: Whereas aptamers have shown to bind to targets with similar affinities and specificities to those of antibodies, aptamers have several advantages that could outweigh antibody technology and open new opportunities for better medical and diagnostic solutions. However, the current status of the aptamer technology suffers from several technical limitations that slowdown the progression of novel aptamers into the clinic and makes the business around aptamers challenging.     

Current and future considerations for the new classes of biologicals.

PURPOSE: Key structural features of biologicals and their development are explained, and the fundamental distinctions between biological and chemical drugs in terms of their discovery, scale-up from research to commercial quantities, quality control, regulatory requirements, and potential for generic substitution are discussed. SUMMARY: Recent advances in biotechnology have accelerated the introduction of biological protein drugs into the marketplace, offering new treatment options and challenges for pharmacists. Because these drugs are produced in living systems and are structurally complex, they are more difficult to manufacture, purify, and evaluate than are traditional chemical drugs. The production of recombinant-DNA-based protein and monoclonal antibody drugs is explained, and the strengths and limitations in selecting one or another host system (i.e., bacteria, yeast, or mammalian cells) for making a given biological drug are explored. Subtle variations in production methods can lead to significant differences in product volume, potential viral or bacterial contamination, bioactivity, and toxicity. Like manufacturers, federal regulators face difficult new challenges because of the structural complexity and in vivo synthesis of biologicals. Pharmacists and regulators alike must determine when and if therapeutic interchange is relevant to biologicals. Because biologicals are so difficult to manufacture and test, noninnovator biologicals must be subject to more oversight than traditional generic drugs. CONCLUSION: Biologicals are complex agents whose production and properties present many considerations that are not associated with traditional chemical drugs.     

Protein interaction predictions from diverse sources

Protein-protein interactions play an important role in many cellular processes. The availability of a comprehensive and accurate list of protein interactions can facilitate drug target discovery. Recent advances in high-throughput experimental technologies have generated enormous amounts of data and provided valuable resources for studying protein interactions. However, these technologies suffer from high error rates because of their inherent limitations. Therefore, computational approaches capable of incorporating multiple data sources are needed to fully take advantage of the rapid accumulation of data. In this review, we focus on the computational methods that integrate multiple data sources by combining direct measurements on protein interactions from diverse organisms, and by integrating different types of indirect information from various genomic and proteomic approaches.     

An update on the clinical use of drug-coated balloons in percutaneous coronary interventions

ABSTRACT

Introduction: Drug-coated balloons (DCB) promise to deliver anti-proliferative drugs and prevent restenosis leaving nothing behind. Although, randomized clinical trials have demonstrated their efficacy for the treatment of in-stent restenosis, clinical evidence supporting their use in other coronary applications is still lacking.

Areas Covered: This review summarizes the development status of clinically available DCB technologies and provides an update on the current data for their coronary use.

Expert Opinion: Current generation DCB prevent restenosis by delivering paclitaxel particles on the surface of the vessel wall. Although clinically available technologies share a common mechanism of action, important differences in pharmacokinetic behavior and safety profiles do exist. Future technological improvements include the development of coatings displaying: high transfer efficiency; low particle embolization potential; and alternative drug formulations. Optimized balloon-based delivery systems and drug encapsulation technologies also promise to improve the technical limitations of current generation DCB. Although proving clinical superiority against DES may prove to be difficult in mainstream applications (i.e., de novo), new generation DCB technologies have the potential to achieve a strong position in the interventional field in clinical settings in which the efficacy of DES use is not proven or justified (i.e., bifurcations).     

Advances in bispecific biotherapeutics for the treatment of cancer

Conventional monoclonal antibody (mAb) therapeutics interfering with cellular signaling of their respective target antigens are frequently limited in their ability to induce significant anti-tumor activities when administered as single agents in patients with solid tumors. To overcome these limitations, several new technologies are being developed to empower biotherapeutics and to improve their anti-tumor activities, while maintaining their high tumor selectivity and superior safety profiles.The various efficacy enhancement technologies developed for mAbs can be divided broadly into two categories: First, technologies that improve the intrinsic anti-tumor activities of conventional immunoglobulin mAb formats, including the enhancement of effector cell functions and modulations of target binding properties, including interference with multiple signaling pathways. The second category of empowered biologics combines complementary anti-tumor modalities independent of the IgG format, including antibody drug conjugates (ADCs). In addition, bispecific compounds designed to recruit different subsets of inflammatory cells to the tumor environment, also belong to the mechanistic complementation strategy. This approach termed redirected immune cell killing, belongs to one the most promising new biotherapeutic platforms developed in oncology.Over 20 bispecific compounds are currently being developed pre-clinically, and several compounds are undergoing early stage clinical trials. In this report, we review the progress made in the development of bispecific biotherapeutics in the context of ADCs, redirected T- and B-cell killing and targeting of multiple signaling pathways. We also discuss the status of the clinical development of this class of compounds in oncology and the promises and challenges this field is currently facing.     

Proteomics in developmental toxicology

The objective of this presentation is to review the major proteomic technologies available to developmental toxicologists and, when possible, to provide examples of how various proteomic technologies have been used in developmental toxicology or toxicology in general. The field of proteomics is too broad for us to go into great depth about each technology, so we have attempted to provide brief overviews supplemented with many references that cover the subjects in more detail. Proteomics tools produce a global view of complex biological systems by examining complex protein mixtures using large-scale, high-throughput technologies. These technologies speed up the process of protein separation, quantification, and identification. As an important complement to genomics, proteomics allows for the examination of the entire complement of proteins in an organism, tissue, or cell-type. Current proteomics technologies not only identify protein expression, but also post-translational modifications and protein interactions. The field of proteomics is expanding rapidly to provide greater volume and quality of protein information to help understand the multifaceted nature of biological systems.     

Computational identification and analysis of G protein‐coupled receptor targets

The completion of the human genome sequence has provided a large pool of potential drug targets for disease therapy. G protein–coupled receptors (GPCRs), which are central to signaling networks that regulate basic cellular processes, represent the most important known class of therapeutic targets for multiple disease states. Bioinformatics approaches can be applied to facilitate the identification of novel GPCRs, understanding their physiological and pathological roles, and screening for drug discovery. The present review summarizes current bioinformatics approaches that can be used to identify and analyze GPCR targets. In addition, the limitations of these technologies with the intention of setting reasonable expectations are also discussed together with some potential avenues for GPCR research. Drug Dev. Res. 67:771–780, 2006. © 2007 Wiley‐Liss, Inc.     

Particle Engineering for Pulmonary Drug Delivery

With the rapidly growing popularity and sophistication of inhalation therapy, there is an increasing demand for tailor-made inhalable drug particles capable of affording the most efficient delivery to the lungs and the most optimal therapeutic outcomes. To cope with this formulation demand, a wide variety of novel particle technologies have emerged over the past decade. The present review is intended to provide a critical account of the current goals and technologies of particle engineering for the development of pulmonary drug delivery systems. These technologies cover traditional micronization and powder blending, controlled solvent crystallization, spray drying, spray freeze drying, particle formation from liquid dispersion systems, supercritical fluid processing and particle coating. The merits and limitations of these technologies are discussed with reference to their applications to specific drug and/or excipient materials. The regulatory requirements applicable to particulate inhalation products are also reviewed briefly.