Proteomics: recent applications and new technologies

Interest in proteomics as a tool for drug development and a myriad of other applications continues to expand at a rapid rate. Proteomic analyses have recently been conducted on tissues, biofluids, subcellular components and enzymatic pathways as well as various disease and toxicological states, in both animal models and man. In addition, several recent studies have attempted to integrate proteomics data with genomics and/or metabonomics data in a systems biology approach. The translation of proteomic technology and bioinformatics tools to clinical samples, such as in the areas of disease and toxicity biomarkers, represents one of the major opportunities and challenges facing this field. An ongoing challenge in proteomics continues to be the analysis of the serum proteome due to the vast number and complexity of proteins estimated to be present in this biofluid. Aside from the removal of the most abundant proteins, a number of interesting approaches have recently been suggested that may help reduce the overall complexity of serum analysis. In keeping with the increasing interest in applications of proteomics, the tools available for proteomic analyses continue to improve and expand. For example, enhanced tools (such as software and labeling procedures) continue to be developed for the analysis of 2D gels and protein quantification. In addition, activity-based probes are now being used to tag, enrich and isolate distinct sets of proteins based on enzymatic activity. One of the most active areas of development involves microarrays. Antibody-based microarrays have recently been released as commercial products while numerous additional capture agents (e.g. aptamers) and many additional types of microarrays are being explored.     

Proteomics: an holistic analysis of nature's proteins.

Proteomics has matured to a technology platform way beyond two-dimensional gel electrophoresis, delivering on its promise to identify structure, function and cellular localization of all proteins expressed in a cell at a given time. Major achievements in the past year include mapping the proteome of human and microbial cells, improvements in two-dimensional gel electrophoresis and mass spectrometric analysis, and the development of protein arrays and biochips.     

Novel delivery technologies for protein and peptide therapeutics

The protein and peptide therapeutics have become an important class of drugs due to advancement in molecular biology and recombinant technology. There are more than 100 biopharmaceutical products approved and generating revenue of more than 56 billion US dollars. A safe, effective and patient friendly delivery of these agents is the key to commercial success. Currently, most of therapeutic proteins are administered by the parenteral route which has many drawbacks. Various delivery strategies and specialized companies have evolved over the past few years to improve delivery of proteins and peptides. Polymeric depot and PEGylation technologies have overcome some of the issues associated with parenteral delivery. A considerable research has been focused on non-invasive routes such as pulmonary, per oral and transdermal for delivery of proteins and peptides, in order to increase patient compliance yet their delivery via non-invasive routes remains challenge due to their poor absorption and enzymatic instability. Pulmonary route has shown some success evidenced by recent FDA approval of inhalable insulin. Development of an oral dosage form for protein therapeutics is still the most desirable one but with greater challenge. This review presents the issues of delivery of proteins and peptides, current and potential formulation technologies to improve delivery and current market trends.     

Recent advances in technologies for analyzing protein kinases

Most cellular events are regulated by protein phosphorylation mediated by protein kinases, whose malfunction is involved in the etiology of various disorders. The elucidation of the biochemical properties of the protein phosphorylation reaction will lead not only to a better understanding of the signal transduction mechanism, but also to developing new therapeutic agents. In this review, we briefly summarize the technologies to detect or characterize protein kinases with special emphasis on recently developed and/or commercially available techniques.     

Progress of small molecules for targeted protein degradation: PROTACs and other technologies

Recent years have witnessed the rapid development of targeted protein degradation (TPD), especially proteolysis targeting chimeras. These degraders have manifested many advantages over small molecule inhibitors. To date, a huge number of degraders have been excavated against over 70 disease-related targets. In particular, degraders against estrogen receptor and androgen receptor have crowded into phase II clinical trial. TPD technologies largely expand the scope of druggable targets, and provide powerful tools for addressing intractable problems that can not be tackled by traditional small molecule inhibitors. In this review, we mainly focus on the structures and biological activities of small molecule degraders as well as the elucidation of mechanisms of emerging TPD technologies. We also propose the challenges that exist in the TPD field at present.     

蛋白质组学:药理学研究的新动力

仅仅完成基因组的测序对于阐明生物学特性是远远不够的 ,蛋白质组学由于可大规模的研究基因在蛋白水平的表达而成为了基因组学研究的重要补充。由于几乎所有的药物都是通过蛋白质发挥作用 ,蛋白质组学在药物研究中已取得了广泛的应用 ,包括药理学中的药物作用靶点、毒理学机制以及耐药性研究等。     

Assessing cellular protein phosphorylation: high throughput drug discovery technologies

Changes in protein phosphorylation mediate much of cellular physiology. Perturbations in the activity of the kinases that catalyze these reactions underlie numerous human pathologies, including metabolic and inflammatory disorders and most notably, cancer. HTS techniques that determine the activity of protein kinases in vitro are useful in the development of small molecule kinase inhibitors, but do not address underlying mechanistic concerns or efficient in vivo targeting. Observing protein phosphorylation in cell lysates and fixed cells in a high throughput manner is fundamental to understanding the mechanism of action of lead molecules and whether they target signaling pathways of interest. Herein we discuss several higher throughput techniques to study cellular protein kinase signal transduction and the strategies for implementation in kinase drug discovery.     

Bioinspired tissue engineering: the great promise of protein delivery technologies

The concept of developing a tissue either in vitro or in vivo taking inspiration from physiological events has prompted toward the integration of molecular signals such as growth factors (GFs) in tissue engineering strategies with the aim to guide cell proliferation, differentiation and migration. After the first studies, the awareness emerged that a fine tuning of GF levels in the scaffold, when present, and at boundary with healthy tissue was needed to give successful results. Thus, the modality of GF presentation to cells has been recognized as a key fundamental in many tissue engineering applications and applied through different approaches. In this scenario the potential of particulate systems for GF delivery was promptly perceived as a mean to protect GFs during tissue regrowth and to offer adequate control over release rate. The use of tissue engineering constructs based on GF-loaded particles integrated in different scaffold types has impressively grown in recent years and led to significant advances in the field. Release of more than one GF at rates mimicking in vivo situation has become possible as well as to exert a fine control over GF spatial concentration by developing constructs with specific areas of bioactivities. However, if we consider the strategies for protein delivery currently applied in tissue engineering, it is soon realized that much more can be done. Thus, the aim here is to review some tissue engineering approaches involving the use of GFs by the point of view of delivery issues trying to highlight the remarkable impact that particulate systems can have in the next future.     

异烟肼致肝脏毒性的蛋白质组学分析

目的:应用蛋白质组学技术研究异烟肼致大鼠肝脏损伤时肝脏蛋白质表达谱的变化,为从分子水平上寻找毒性损伤标志物以及阐明异烟肼毒性机制奠定基础。方法:将Wistar大鼠随机分为生理盐水正常对照组和异烟肼组(400 mg.kg-1),分别连续灌胃14 d后处死大鼠,提取肝脏总蛋白,双向凝胶电泳分离蛋白质组成分,采用考马斯亮蓝R-250染色,经ImageMaster2D Platinum5.0软件分析比较两组图谱,并对差异蛋白斑点进行基质辅助激光解吸/电离飞行时间质谱(MALD-TOF-MS)分析鉴定。结果:发现11个差异有统计学意义的蛋白质点,鉴定出8个蛋白,其中,异烟肼处理组比对照组表达升高的蛋白质有鸟氨酸转氨酶、葡萄糖调节蛋白、乙醛脱氢酶和3α-羟甾类脱氢酶,比对照组表达降低的蛋白质有抗氧化酶B166、谷胱苷肽转硫酶、醛铜还原酶和碳酸酐酶。结论:异烟肼可能造成肝脏抗氧化系统和氧化应激异常,这对阐明异烟肼的肝损伤机制具有十分重要的作用。     

氯丙嗪致大鼠肝脏损伤的蛋白质组学研究*

目的:应用蛋白质组学技术研究氯丙嗪致大鼠肝脏损伤时肝脏蛋白质表达谱的变化,为从分子水平上阐明氯丙嗪毒性机制奠定基础。方法:18只雄性SD大鼠随机分成溶剂对照组、氯丙嗪37.5和75.0 mg.kg-1组,每组6只。单次给药,24 h后采集血液测定生化指标,之后处死大鼠,取肝脏做组织病理检查和提取肝脏总蛋白质。应用蛋白质组学技术分离和鉴定肝损伤大鼠与溶剂对照组大鼠之间的差异蛋白质。结果:发现9个差异有统计学意义的蛋白质点,鉴定出8个蛋白,其中,肝损伤大鼠组葡萄糖调节蛋白58、支链α-酮酸脱氢酶、儿茶酚邻位甲基转移酶、载脂蛋白A-I、碳酸酐酶3和过氧还蛋白Ⅰ表达下降,调钙素和微管蛋白表达上升。结论:氯丙嗪可能造成大鼠肝细胞钙离子浓度紊乱,肝脏抗氧化系统、能量代谢、胆固醇代谢等异常。     

Proteomics -- the protein expression technology to study connective tissue biology

During the formation of peribronchial fibrosis in asthma, remodeling of connective tissue is due to an increase in deposition of extracellular matrix components like that of specific types of collagens and proteoglycans. By taking bronchial biopsies, we were able to isolate cell cultures derived from asthmatic patients and healthy volunteers, which provides a good model system to study differences regarding cell morphology and key connective tissue proteins in the remodeling process. Proteomics, utilizing two-dimensional electrophoresis and modern image analysis systems have made it possible to study protein expression and regulation of proteins in biological systems. By using this powerful tool, it is possible to quantitatively study protein regulation and to obtain increased knowledge about the mechanism behind the inflammatory process and formation of peribronchial fibrosis. We have optimized a proteomic protocol enabling detailed investigation of the protein expression pattern in human lung cells. An increased expression pattern was obtained, whereby 20 protein spots could be detected by image analysis in the <45 kDa region. Out of these, specific regulations of four spots were found by quantitative image analysis and spots of interest were identified by MALDI TOF-MS. This protocol enables us to study 1000–2000 proteins simultaneously and the possibility to correlate protein expression to the physiological status of the cell culture investigated. We have found that two proteins, actin and tropomyosin, are increased in expression due to transforming growth factor-β stimulation. These proteins are correlated to the transformation of normal fibroblasts to myofibroblasts which are involved in the remodeling processes observed in asthma.     

Characterization of particles in protein solutions: reaching the limits of current technologies

Recent publications have emphasized the lack of characterization methods available for protein particles in a size range comprised between 0.1 and 10 μm and the potential risk of immunogenicity associated with such particles. In the present paper, we have investigated the performance of light obscuration, flow microscopy, and Coulter counter instruments for particle counting and sizing in protein formulations. We focused on particles 2-10 μm in diameter and studied the effect of silicon oil droplets originating from the barrel of pre-filled syringes, as well as the effect of high protein concentrations (up to 150 mg/ml) on the accuracy of particle characterization. Silicon oil was demonstrated to contribute significantly to the particle counts observed in pre-filled syringes. Inconsistent results were observed between different protein concentrations in the range 7.5-150 mg/ml for particles <10 μm studied by optical techniques (light obscuration and flow microscopy). However, the Coulter counter measurements were consistent across the same studied concentration range but required sufficient solution conductivity from the formulation buffer or excipients. Our results show that currently available technologies, while allowing comparisons between samples of a given protein at a fixed concentration, may be unable to measure particle numbers accurately in a variety of protein formulations, e.g., at high concentration in sugar-based formulations.     

专题演讲-W1毒理基因组学与蛋白质组学

Pharmacogenomics was established on the fact that certain genetic polymorphisms may cause significantly different responses among individuals exposed to a particular drug. Single nucleotide polymorphism （SNP） is the most common form of genetic polymorphism in human genome.     

Application of proteomic technologies to tumor analysis

The sequencing of the human genome has had an enormous impact on the proteomic analysis of cancer by providing a sequence-based framework for understanding the human proteome of tumor cells, tissues, and biological fluids. There is intense interest in applying proteomic technologies to uncover, at the protein level, processes involved in neoplastic transformation and new biomarkers that correlate with early diagnosis, as well as to accelerate the development of new therapeutic targets. To that effect, new technologies are being developed in order to meet the needs for the high throughput and high sensitivity that is required for cancer-related applications of proteomics. These innovative technologies have greatly enhanced our ability to separate and characterize complex protein mixtures, and have aided our ability to identify proteins with greater sensitivity, thereby providing the groundwork for future scientific breakthroughs and possibly providing impetus for the development of personalized cancer therapy.