Quantitative and targeted proteomics-based identification and validation of drug efficacy biomarkers

Proteomics refers to the large-scale study of proteins, providing comprehensive and quantitative information on proteins in tissue, blood, and cell samples. In many studies, proteomics utilizes liquid chromatography-mass spectrometry. Proteomics has developed from a qualitative methodology of protein identification to a quantitative methodology for comparing protein expression, and it is currently classified into two distinct methodologies: quantitative and targeted proteomics. Quantitative proteomics comprehensively identifies proteins in samples, providing quantitative information on large-scale comparative profiles of protein expression. Targeted proteomics simultaneously quantifies only target proteins with high sensitivity and specificity. Therefore, in biomarker research, quantitative proteomics is used for the identification of biomarker candidates, and targeted proteomics is used for the validation of biomarkers. Understanding the specific characteristics of each method is important for conducting appropriate proteomics studies. In this review, we introduced the different characteristics and applications of quantitative and targeted proteomics, and then discussed the results of our recent proteomics studies that focused on the identification and validation of biomarkers of drug efficacy. These findings may enable us to predict the outcomes of cancer therapy and drug-drug interactions with antibiotics through changes in the intestinal microbiome.     

Implications of salivary proteomics in drug discovery and development: a focus on cancer drug discovery

Human saliva proteomics has proven to be a novel approach in the search for protein biomarkers for non-invasive detection of human cancers. This approach may also have implications within the process of anti-cancer drug discovery. Information from saliva proteomic measurements may contribute to the target discovery and validation, assessment of efficacy and toxicity of candidate drugs, identification of disease subgroups, and prediction of responses of individual patients. In this article, we aim to give a brief overview on human saliva proteome analysis, as well as its applications to cancer biomarker discovery. Potential applications of saliva proteomics in anticancer drug discovery and development will also be discussed.     

Mass spectrometry-based clinical proteomics

In recent years, mass spectrometry (MS) has been recognized as a 'Gold Standard' tool for the identification and analysis of individual proteins in expression proteomics studies. Moreover, MS has proven useful for the analysis of nucleic acids for single nucleotide polymorphism (SNP) genotyping purposes. With the increased usage of MS as a standard tool for life science applications and the advancement of MS instrumentation, sample preparation and bioinformatics, MS technology has entered novel screening and discovery application areas that are beyond the traditional protein identification and characterization applications. The areas of clinical diagnostics and predictive medicine are just two prime examples of these fields. Predictive markers or biomarkers for early diagnosis of diseases are of growing importance for the human healthcare community. The goal of using MS in clinical proteomics is to generate protein profiles (mass to charge [m/z] ratio versus signal intensity) from readily available body fluids like serum, saliva and urine to detect changes in protein levels that reflect changes in the disease states. Whereas the results originating from individual protein markers may be intriguing, data resulting from the analysis of complex, multiple biomarker patterns may be unequivocal. These biomarker patterns are hidden in complex mass spectra and are not always obvious to the human eye. Sophisticated bioinformatics algorithms have to be applied to determine these unique biomarker patterns. Here, we review the latest developments concerning the use of MS for the discovery of biomarker patterns and for the identification of individual biomarkers in the field of clinical proteomics applications.     

Gene expression profiling and therapeutic interventions in neurodegenerative diseases: a comprehensive study on potentiality and limits

INTRODUCTION: Neurodegenerative diseases are incurable debilitating disorders of the nervous system that affect approximately 30 million people worldwide. Despite profuse efforts attempting to define the molecular mechanisms underlying neurodegeneration, many aspects of these pathologies remain elusive. The novelty of their mechanisms represents a challenge to biology, to their related biomarkers identification and drug discovery. Because of their multifactorial aspects and complexity, gene expression analysis platforms have been extensively used to investigate altered pathways during degeneration and to identify potential biomarkers and drug targets. AREAS COVERED: This work offers an overview of the gene expression profiling studies carried out on Alzheimer's disease, Huntington's disease, Parkinson's disease and prion disease specimens. Therapeutic approaches are also discussed. EXPERT OPINION: Although many therapeutic approaches have been tested, some of them acting on several altered cellular pathways, no effective cures for these neurodegenerative diseases have been identified. Microarray technology must be associated with functional proteomics and physiology in an effort to identify specific and selective biomarkers and druggable targets, thus allowing the successful discovery of disease-modifying therapeutic treatments.     

Development of novel DDS technologies for pharmacoproteomic-based drug discovery and development

With the success of the Human Genome Project, the focus of life science research has shifted to the functional and structural analyses of proteins, such as proteomics and structural genomics. These novel approaches to the analysis of proteins, including newly identified ones, are expected to help in the identification and development of protein therapies for various diseases. Thus pharmacoproteomic-based drug discovery currently has a very high profile. Nevertheless, the use of bioactive proteins in the clinical setting is not straightforward because in vivo these proteins have low stability and pleiotropic action. To promote pharmacoproteomic-based drug discovery and development, we have attempted to establish a system for creating functional mutant proteins (muteins) with the desired properties and to develop a site-specific bioconjugation system for further improving their therapeutic potency. These innovative protein-drug systems are discussed in this review.     

Metabolomic approaches in the discovery of potential urinary biomarkers of drug-induced liver injury (DILI)

Drug-induced liver injury (DILI) is a major safety issue during drug development, as well as the most common cause for the withdrawal of drugs from the pharmaceutical market. The identification of DILI biomarkers is a labor-intensive area. Conventional biomarkers are not specific and often only appear at significant levels when liver damage is substantial. Therefore, new biomarkers for early identification of hepatotoxicity during the drug discovery process are needed, thus resulting in lower development costs and safer drugs. In this sense, metabolomics has been increasingly playing an important role in the discovery of biomarkers of liver damage, although the characterization of the mechanisms of toxicity induced by xenobiotics remains a huge challenge. These new-generation biomarkers will offer obvious benefits for the pharmaceutical industry, regulatory agencies, as well as a personalized clinical follow-up of patients, upon validation and translation into clinical practice or approval for routine use. This review describes the current status of the metabolomics applied to the early diagnosis and prognosis of DILI and in the discovery of new potential urinary biomarkers of liver injury.     

Application of proteomic technologies in the drug development process

Proteins are the principal targets of drug discovery. Most large pharmaceutical companies now have a proteomics-oriented biotech or academic partner or have started their own proteomics division. Common applications of proteomics in the drug industry include target identification and validation, identification of efficacy and toxicity biomarkers from readily accessible biological fluids, and investigations into mechanisms of drug action or toxicity. Target identification and validation involves identifying proteins whose expression levels or activities change in disease states. These proteins may serve as potential therapeutic targets or may be used to classify patients for clinical trials. Proteomics technologies may also help identify protein-protein interactions that influence either the disease state or the proposed therapy. Efficacy biomarkers are used to assess whether target modulation has occurred. They are used for the characterization of disease models and to assess the effects and mechanism of action of lead candidates in animal models. Toxicity (safety) biomarkers are used to screen compounds in pre-clinical studies for target organ toxicities as well as later on in development during clinical trials. Complementary approaches such as metabolomics and genomics can be used in conjunction with proteomics throughout the drug development process to create more of a unified, systems biology approach.     

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.     

Proteomics as a tool in the pharmaceutical drug design process

Proteomics is a technology platform that is gaining widespread use in drug discovery and drug development programs. Defined as the protein complement of the genome, the proteome is a varied and dynamic repertoire of molecules that in many ways dictates the functional form that is taken by the genome. The importance of proteomics is a direct consequence of the central role that proteins play in establishing the biological phenotype of organisms in healthy and diseased states. Moreover, proteins constitute the vast majority of drug targets against which pharmaceutical drug design processes are initiated. By studying interrelationships between proteins that occur in health and disease and following drug treatment, proteomics contributes important insight that can be used to determine the pathophysiological basis for disease and to study the mechanistic basis for drug action and toxicity. Proteomics is also an effective means to identify biomarkers that have the potential to improve decision making surrounding drug efficacy and safety issues based on data derived from the study of key tissues and the discovery and appropriate utilization of biomarkers.     

Ariadne's ChemEffect and Pathway Studio knowledge base

Importance of the field: Drug discovery and development is a very complex and costly process. Understanding the detailed molecular mechanisms of a disease and drug actions can make it more efficient not only for new target discovery but also for lead prioritization, drug repositioning and development of biomarkers for drug efficacy and safety. Access to formalized knowledge about functions of proteins and small molecules is crucial for rationalization of the drug development process, and scientific publications are the main source of this knowledge. Protein knowledge networks capturing protein functions, protein–protein relations and organization of proteins in complex cellular sub-systems are making their way into modern drug discovery. Chemical networks representing multiple aspects of chemical functional information integrated into a protein systems biology network is even more advanced and promising paradigm.

Areas covered in this review: This review describes utilization of literature-derived protein and chemical functional knowledge bases in drug development.

What the reader will gain: Readers will gain an understanding of how integrated protein and chemical knowledge networks can be used for understanding and building the models of cellular events, disease mechanisms, and drug actions, finding biomarkers of drug efficacy and safety, as well as interpretation of high-throughput gene expression, proteomic and metabolomic experiments.

Take home message: Integrated literature-derived protein and chemical knowledge bases can rationalize many aspects of drug development process including drug repositioning and biomarker design.     

Quantitative Targeted Proteomics for Membrane Transporter Proteins: Method and Application

Although global proteomics has shown promise for discovery of many new proteins, biomarkers, protein modifications, and polymorphisms, targeted proteomics is emerging in the proteomics research field as a complement to untargeted shotgun proteomics, particularly when a determined set of low-abundance functional proteins need to be measured. The function and expression of proteins related to drug absorption, distribution, metabolism, and excretion (ADME) such as cytochrome P450 enzymes and membrane transporters are of great interest in biopharmaceutical research. Since the variation in ADME-related protein expression is known to be a major complicating factor encountered during in vitro–in vivo and in vivo–in vivo extrapolations (IVIVE), the accurate quantification of the ADME proteins in complex biological systems becomes a fundamental element in establishing IVIVE for pharmacokinetic predictions. In this review, we provide an overview of relevant methodologies followed by a summary of recent applications encompassing mass spectrometry-based targeted quantifications of membrane transporters.     

Bacterial proteomics and vaccine development

Until recently, the development of vaccines for use in humans relied on the response to attenuated or whole-cell preparations, or empirically selected antigens. The post-genomic era holds the possibility of rational design of novel vaccines for important human pathogens. The discovery and development of these new vaccines is likely to be accomplished through integrated proteomic strategies. Although most proteomic studies are based on two-dimensional gel electrophoresis (2D-PAGE) as a separation technique, new methods have been developed within the past two years that provide complementary information concerning microbial protein expression. The 2D-PAGE technique in combination with Western blotting has been successfully applied in the discovery of antigens from Helicobacter pylori, Chlamydia trachomatis and Borrelia garinii. Two-dimensional semi-preparative electrophoresis has provided complementary information regarding membrane protein expression in a strain of H. pylori. Through two-dimensional liquid chromatography-tandem mass spectrometry, the most comprehensive information to date regarding protein expression in yeast was obtained. This technique may shortly become an important tool in vaccinology. This review of the current state of bacterial proteomics as applied in vaccinology presents analytical techniques for protein separation, proteomics without gels, reverse vaccinology, and functional approaches to the identification of virulence proteins in microbes.     

Gene expression profiling and therapeutic interventions in neurodegenerative diseases: a comprehensive study on potentiality and limits

Introduction: Neurodegenerative diseases are incurable debilitating disorders of the nervous system that affect approximately 30 million people worldwide. Despite profuse efforts attempting to define the molecular mechanisms underlying neurodegeneration, many aspects of these pathologies remain elusive. The novelty of their mechanisms represents a challenge to biology, to their related biomarkers identification and drug discovery. Because of their multifactorial aspects and complexity, gene expression analysis platforms have been extensively used to investigate altered pathways during degeneration and to identify potential biomarkers and drug targets.

Areas covered: This work offers an overview of the gene expression profiling studies carried out on Alzheimer's disease, Huntington's disease, Parkinson's disease and prion disease specimens. Therapeutic approaches are also discussed.

Expert opinion: Although many therapeutic approaches have been tested, some of them acting on several altered cellular pathways, no effective cures for these neurodegenerative diseases have been identified. Microarray technology must be associated with functional proteomics and physiology in an effort to identify specific and selective biomarkers and druggable targets, thus allowing the successful discovery of disease-modifying therapeutic treatments.     

DDS and Me

With the success of the human genome project, the focus of life science research has shifted to the functional and structural analyses of proteins, such as proteomics and structural genomics. These analyses of proteins including newly identified proteins are expected to contribute to the identification of therapeutically applicable proteins for various diseases. Thus, pharmaco-proteomic-based drug discovery and development for protein therapies, including gene therapy, cell therapy, and vaccine therapy, is attracting current attention. However, there is clinical difficulty in using almost all bioactive proteins, because of their very low stability and pleiotropic actions in vivo. To promote pharmaco-proteomic-based drug discovery and development, we have attempted to develop drug delivery systems (DDSs), such as the protein-drug innovation system and the optimal cell therapeutic system. In this review, we introduce our original DDSs.     

Beyond the genome--SMi Conference 27-28 January 2003, London,UK

Over a decade of astonishing developments, genomics and proteomics have promised a fundamentally new approach to drug discovery. Although there has been an undeniable increase in the range of potential targets available, this has not led to an increased output of the drug discovery pipeline into the clinic. With tighter markets and increasing competition, the major pharmaceutical companies are under intense pressure to achieve rapid, concrete delivery of those early promises, but there remain acute problems in the genes-to-drugs pipeline. This meeting showcased a range of novel approaches from proteomics and bioinformatics to address these problems. A common theme in the range of proteomics offerings was the prioritization of potential novel targets on the basis of their accessibility to drugs and their functional link to disease phenotypes. Informatics and in silico offerings also concentrated on fast, accurate, drug-focused workflows built on large integrative databases and novel data-mined algorithms.     

Pharmacoproteomic approach by quantitative targeted proteomics

Omics analyses provided many candidates for drug targets and biomarkers. However, these analyses have not contributed to drug development efficiently because of top-down omics analyses. To solve this problem, we have recently developed quantitative targeted proteomics with multiplexed-multiple reaction monitoring (multiplexed-MRM) method, which enables us to perform bottom-up proteomics. In this method, the target proteins for quantification are selected prior to analysis based on the knowledge related to interesting phenomena. Target peptides for quantification are selected only from sequence information, so time-consuming procedures such as antibody preparation and protein purification are unnecessary. In this review, we introduce the technical features of multiplexed-MRM method as novel protein quantification method, and summarize its advantages with reference to recently reported results, including species differences, in vitro-to-in vivo reconstruction and personalized chemotherapy. This novel simultaneous protein quantification method overcomes problems of antibody-based quantification and would open new drug research based of protein as "Pharmacoproteomics".     

Functional genomics to new drug targets

The completion of the sequencing of the human genome, and those of other organisms, is expected to lead to many potential new drug targets in various diseases, and it is predicted that novel therapeutic agents will be developed against such targets. The role of functional genomics in modern drug discovery is to prioritize these targets and to translate that knowledge into rational and reliable drug discovery. Here, we describe the field of functional genomics and review approaches that have been applied to drug discovery, including RNA profiling, proteomics, antisense and RNA interference, model organisms and high-throughput, genome-wide overexpression or knockdowns, and outline the future directions that are likely to yield new drug targets from genomics.     

Comparative chemical proteomics: simultaneous identification of disease-specific protein targets and their small molecule-binding partners, suitable as drug candidates

The simultaneous identification of disease-specific protein targets and their small molecule binding partners, suitable as drug candidates, could radically reduce the timeline and costs of drug discovery and development. Comparative chemical proteomics provides a novel approach to achieve this goal through rapid detection of overexpressed proteins in diseased samples by the application of small molecule microarrays. The interacting small molecules enables direct affinity-based isolation and identification of the proteins. In the present paper we report comparative chemical proteomics studies on melanocytes and melanoma cell-lines, which led to the identification of 3 overexpressed proteins (e.g. -tubulin) together with their small molecule binding partner.     

Biomarkers in drug discovery and development: from target identification through drug marketing

Biomarkers of disease play an important role in medicine and have begun to assume a greater role in drug discovery and development. The challenge for biomarkers is to allow earlier, more robust drug safety and efficacy measurements. Their role in drug development will continue to grow for the foreseeable future. For biomarkers to assume their rightful role, greater understanding of the mechanism of disease progression and therapeutic intervention is needed. In addition, greater understanding of the requirements for biomarker selection and validation, biomarker assay method validation and application, and clinical endpoint validation and application is needed. Biomarkers need to be taken into account while the therapeutic target is still being identified and the concept is being formulated. Biomarkers need to be incorporated into a continuous cycle that takes what is learned from the discovery and development of one series of biomarkers and translates it into the next series of biomarkers. Optimum biomarker development and application will require a team approach because of the multifaceted nature of biomarker selection, validation, and application, using such techniques as pharmacoepidemiology, pharmacogenetics, pharmacogenomics, and functional proteomics; bioanalytical method development and validation; disease process and therapeutic intervention assessments; and pharmacokinetic/pharmacodynamic modeling and simulation to improve and refine drug development. The potential for biomarkers in medicine and drug development will be limited by the least effective component of the processes. The team approach will minimize the potential for the least effective component to be fatal to the rest of the process. As scientific/regulatory foundations for biomarkers in medicine and drug development begin to be established, successes and applications will need to be effectively communicated with all of the stakeholders, including not only internal and external drug developers and regulators but also the medical community, to ensure that biomarkers are totally integrated into drug discovery and development as well as the practice of medicine.