Frontiers in Bioactive Compounds: At the Crossroads between Nutrition and Pharmacology E-Book
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- Herausgeber: Bentham Science Publishers
- Kategorie: Fachliteratur
- Serie: Frontiers in Bioactive Compounds
- Sprache: Englisch
This volume presents different aspects related to bioactive compounds, starting with their natural state in raw sources, physicochemical characterization and employment in pharmacy and medicine. The volume is divided into three parts. The first part describes the chemicals structure of bioactive compounds from different natural sources such as olive oils, wines, and medicinal plants. Special attention has been given to identifying the bioactive composition within variations of these natural sources (for example, extra virgin, ordinary or lampante olive oils). The second part of the volume presents the principal methods used for detecting, identifying and quantifying bioactive compounds. Emphasis is given to the use of different types of sensors or biosensors, and multisensor systems in combination with analytical techniques. The final part explains the principal methods for protection of bioactive compounds and the implication of bioactive compounds in pharmacy. This volume is a useful guide for novice researchers interested in learning research methods to study bioactive compounds.
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Veröffentlichungsjahr: 2017
Ähnliche
Frontiers in Bioactive Compounds
(Volume 2)
(At the Crossroads Between
Nutrition and Pharmacology)
Editors
M. Victorina Aguilar
&
Cristina Otero
BENTHAM SCIENCE PUBLISHERS LTD.
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FOREWORD
Nutrition is the science that deals with the role of nutrients and other substances in food in relation to growth, development, metabolism and function, often in the context of health and disease. Pharmacology is the science of the study of drug action; a drug is a molecule which has a biochemical or physiological effect within an organism. Typically, in the context of pharmacology, the molecule (i.e., the drug) is used to treat, cure, prevent, or diagnose a disease or to promote well-being and is referred to as a medicine. It is important to note that many drugs are natural substances or derivatives of natural substances. It is immediately evident that there is likely to be some overlap between nutrition and pharmacology, since both are concerned with molecules that exert biochemical and physiological effects within the organism. However, in modern times, neither the teaching nor the scientific practice of nutrition and pharmacology have been considered to have much in common, and they exist quite separately from one another. This is different from earlier times, where the boundaries between these two academic disciplines were not clear and indeed may not have even existed. For example, many foods, food extracts and food-based potions have been used in traditional medicine to prevent and treat diseases and to promote well-being; this practice continues today in many, perhaps most, non-Western cultures. In other words, food can be medicine (i.e., a drug) and medicine can be food. Fortunately, the artificial barrier between nutrition and pharmacology is once more being removed. The pharmaceutical industry is becoming increasingly interested in food components as functional agents that have potential as drugs, while the food industry and nutrition scientists are expected to mainly adopt the practices of pharmacology and the pharmaceutical industry as part of their normal research and development activities.
This blurring of the boundaries is likely to become greater over the next years, and will certainly increase the chances of new discoveries being made by both the food and pharmaceutical industries and of translating those discoveries into new products, new claims, new preventative strategies and new treatments for human disease. In the contexts of these changing research and regulatory environments “At the Crossroads Between Nutrition and Pharmacology” is a timely offering. It brings together a series of articles dealing with bioavailability and bioactivity of a range of natural substances found in foods, suggesting that these nutritional substances have properties that will make them useful in health maintenance, disease prevention and, in some cases, disease treatment. The disease contexts being considered include those that pose an ever increasing threat to the global population, including diabetes, metabolic syndrome and cardiovascular disease. Thus, the contents of this book are extremely relevant, making it the most welcome addition.
Dr. Philip C. Calder Faculty of Medicine University of Southampton, Southampton United KingdomPREFACE I
This is the first volume of this eBook series entitled “Bioactive compounds: at the frontier between Nutrition and Pharmacology”. Functional Foods are emerging in the modern food industry. But their potential for preventive and therapeutic treatments must be safely determined. This way the field of Nutrition will be transformed into a knowledge-based science for the development of Functional Food products. This eBook presents the state-of-the art and most recent advances in the computational design of Functional Food products, their sources, detection, analysis, extraction or synthesis and their different biological effects. The book presents the most important and recent advances in chemistry, technology and health research of products with potential use as drugs, nutraceuticals, functional food ingredients, or cosmetics. This volume will be a great value to students, clinicians, nutritionists R&D scientists and food companies.
In Chapter 1, Younesi discusses the need of following the path of drug discovery and development to obtain new functional foods by the modern nutraceutical industry. He describes the potential of recent advances made by pharmaceutical stakeholders to evaluate the effects of bioactive compounds on human health. Targets identification for drugs and nutraceuticals are revised. Evidence-based modeling of the mode of action of functional ingredients influencing Alzheimer’s disease is presented as an example. The author describes how the fundamentals of systems biology and in silico target identification can be applied to the field of nutrition in support of the development of new functional food products.
The most recent developments for the extraction, identification and quantification of bioactive peptides in foods are described in Chapter 2 by Puchalska et al. More than 2600 bioactive peptides have been discovered. They are specific protein fragments with favorable effects on human health, and their different bioactivities are described. The general workflow for their identification is presented and an overview of the most modern strategies for their recovery from food protein hydrolysates is given. This chapter covers from the standard analytical and electrophoretic methods to new alternatives for the identification of bioactive peptides in complex food matrices. These methodologies are essential for safety evaluation, establishment of health claims, policy and regulations.
The concepts of bioavailability, bioaccessibility, bioactivity, bioefficiency and bioconversion of bioactive foods are clarified in Chapter 3. In vivo and in vitro methods for evaluating the bioactivity and bioavailability of foods are reviewed. Methods employed to provide scientific evidence on the effects of food structure, food composition, dietetic factors and food processing on bioactive foods, are described.
Sugar fatty acid esters are another class of promising bioactive compounds with bioactivities such as antimicrobial, antitumor and anti-insect activities. These biodegradable emulsifiers are used in pharmaceutical, cosmetic and food industries. Ye and Hayes describe the most important synthetic routes for obtaining these biocompatible non-ionic and biodegradable sugar esters in chapter 4. This Chapter is also an overview of the bioactive properties of these
sugar esters, including the comparison of the bioactive characteristics of sugar esters synthetized via chemical and enzymatic reactions.
Li et al. analyzes the bioactivities of arabinoxylans in relation to their molecular structure in Chapter 5. Arabinoxylans -present in cereals cell walls- have several health benefits as mediators of physiological and immunological processes. Various in vitro immunological tests are discussed. This chapter also relates the molecular features of arabinoxylans to the different extraction technologies used to obtain and study them.
Kumar in Chapter 6, describes the potential of indigenous medicinal foods, particularly the species of genus Dioscorea available in India as future functional foods. Some rural and tribal communities of wild Odisha base their subsistence on these foods, where they also play a critical role in their conventional medicine. Kumar studied the ethnobotanical values and bioactive compounds present in these tubers from the literature. Their potential as functional foods and for the formulation of new drugs is highlighted.
In Chapter 7, Mantello et al. describes the important role of Nutrigenomics to identify key cellular functions by specific genetic and epigenetic interactions with a nutrient or a food component. Novel features of new nutrigenomic driven action plan strategy to develop specific pharmacological treatments for the reduction or prevention of diseases are described. In this chapter, the case of fermented papaya is presented as an example of functional food, with the most recent rational and evidence-based biotechnological progress.
Chapter 8 reviews the most recent investigations on the anti-cancer properties of saponins as important bioactive components of medicinal plants, used in traditional medicine. The Examples of different plants, molecular and cellular mechanisms of their anti-tumor activities, and their prospective use to elaborate personalized nutrition are described.
Chapter 9 covers the most important advances on the study of the effect of a diet based on different bioactive foods on the prevention and treatment of Diabetes. The bioactive compounds and the Mediterranean Diet (rich in this compounds) affecting glucose meta- bolism are described by Menacho-Román et al.
In Chapter 10, Becerra-Fernández et al. describe the evidences of the antioxidants effects on cardiovascular diseases. They review cohort studies and randomized controlled trials that related the frequent consume of fruits and vegetables, and the intake of antioxidants supp- lements with the lower incidence of cardiovascular diseases.
In Chapter 11, Pen et al. reviews the most updated and relevant evidences of the beneficial effects of bioactive foods on metabolic syndrome, which is known as the coexisting metabolic disorder that increases an individual’s likelihood of developing type 2 diabetes, cardio- vascular disease and stroke, as well as other chronic diseases.
In Chapter 12, Brites gives a comprehensive review on Tauroursodeoxycholic acid and urso- and glycoursodeoxycholic acids with detergent properties for the treatment of hepatobiliary diseases, along with their mechanisms of action, their potential application in the prevention
and recovery of diseases associated to the central nervous system dysfunction and pathology, and neurodegenerative diseases.
In Chapter 13, Yartseva and Ivanenkov review the most recent studies showing the beneficial effects of some foods such as, natural phytochemicals in prostate cancer. This chapter describes the state of the art about the scientific studies focused on dietary polyphenols and analogs that have anticarcinogenic properties. Controversial results are discussed together with major issues of developing naturally occurring compounds into clinically used agents.
In Chapter 14, the readers will find a rigorous description beneficial and deleterious effects of methylxanthines (caffeine and others) present in many foods and beverages. Factors that play a role in methylxanthine effects and metabolism are analyzed. This chapter summarizes the physiological and toxicological effects of these bioactive food constituents.
Finally, in Chapter 15, the effects of different culinary methods used at present on bioactive food properties are described by García Viguera and Soler-Rivas. Positive and negative effects of traditional and the most modern technologies for food cooking or processing are presented and discussed.
The editors are grateful to the authors for their excellent contributions and to Bentham Science Publishers for making the publication of this eBook possible.
Dr. Cristina Otero Director of Biocatalysis and Bioenergy laboratory Deparment of Biocatalysis, Institute of Catalysis and Petrochemistry, CSIC SpainPreface II
The Prevalence of chronic-degenerative diseases is increasing among the world’s population. Claiming 63% of all deaths worldwide, it is currently the world’s main killer. According to the World Economic Forum (2011), the total costs of these diseases were expected to rise upto $ 47 trillion by the year 2030.
Interventions to reduce disease risks (for example, diet) would constitute the most economic, affordable and sustainable key elements for effective primary prevention.
Since Hippocrates reported the aphorism “Let food be the medicine and medicine be the food”, there is strong evidence that reported links between diet and health. Healthy food actions are not only due to nutrients, but also to other constituents (bioactive compounds) with functional properties. These bioactive compounds are extranutritional constituents with beneficial effects and are typically present in small quantities in foods. They may promote optimal health. Actually, there are evidences of their effects on cancer, cardiometabolic syndrome, immunological system, nervous system, learning processes, sports performance. These evidences constitute new parts of the complex puzzle that is the Nutrition, in addition to demonstrating the permeability of the borderline between Nutrition and Pharmacology since these compounds can be used as drugs, nutraceuticals, functional food ingredients, or cosmetics. The relationship between bioactive food compounds and drugs is becoming closer. Moreover, bioactive products are considered as drug targets or physiological pumps and the technology traditionally used for drugs is being used to pioneer functional health ingredients from the bioactive compounds.
There are varied papers about bioactive compounds in which the most appropriate technological treatments (synthesis, concentration or purification from different natural sources, including food derivatives) are studied. Innovative ingredients and their healthy properties both in humans or animals are documented. Therefore, there are many areas of interest. Because of all of this, in this book, the first in a series, the latest knowledge on the different chemical or technological facets of bioactive compounds and their nutritional and pharmacological applications in prevention and treatment of different nosological entities are collected. The first volume of this eBook series is a compilation of several well written reviews on the state-of-the art developments in computational design of compounds with functional activity, sources, identification, analysis, technological treatments effect, or biological action. “Bioactive compounds: at the frontier between Nutrition and Pharmacology” focuses on this important area of chemical, technological and health research. This book will also be a valuable resource of information for professionals in this field that allows them to see the news of the topic and its potential for preventive and therapeutic application with safety, quality and efficacy.
This book has been possible by numerous co-authors for their collaboration to the task of synthesizing their knowledge on the subject in relatively concise chapters.
M. Victorina Aguilar Professor of Nutrition and Food Science Department of Biomedical Sciences Alcala University, 28871 Alcalá de Henares Madrid SpainPREFACE II
The Prevalence of chronic-degenerative diseases is increasing among the world’s population. Claiming 63% of all deaths worldwide, it is currently the world’s main killer. According to the World Economic Forum (2011), the total costs of these diseases were expected to rise upto $ 47 trillion by the year 2030.
Interventions to reduce disease risks (for example, diet) would constitute the most economic, affordable and sustainable key elements for effective primary prevention.
Since Hippocrates reported the aphorism “Let food be the medicine and medicine be the food”, there is strong evidence that reported links between diet and health. Healthy food actions are not only due to nutrients, but also to other constituents (bioactive compounds) with functional properties. These bioactive compounds are extranutritional constituents with beneficial effects and are typically present in small quantities in foods. They may promote optimal health. Actually, there are evidences of their effects on cancer, cardiometabolic syndrome, immunological system, nervous system, learning processes, sports performance. These evidences constitute new parts of the complex puzzle that is the Nutrition, in addition to demonstrating the permeability of the borderline between Nutrition and Pharmacology since these compounds can be used as drugs, nutraceuticals, functional food ingredients, or cosmetics. The relationship between bioactive food compounds and drugs is becoming closer. Moreover, bioactive products are considered as drug targets or physiological pumps and the technology traditionally used for drugs is being used to pioneer functional health ingredients from the bioactive compounds.
There are varied papers about bioactive compounds in which the most appropriate technological treatments (synthesis, concentration or purification from different natural sources, including food derivatives) are studied. Innovative ingredients and their healthy properties both in humans or animals are documented. Therefore, there are many areas of interest. Because of all of this, in this book, the first in a series, the latest knowledge on the different chemical or technological facets of bioactive compounds and their nutritional and pharmacological applications in prevention and treatment of different nosological entities are collected. The first volume of this eBook series is a compilation of several well written reviews on the state-of-the art developments in computational design of compounds with functional activity, sources, identification, analysis, technological treatments effect, or biological action. “Bioactive compounds: at the frontier between Nutrition and Pharmacology” focuses on this important area of chemical, technological and health research. This book will also be a valuable resource of information for professionals in this field that allows them to see the news of the topic and its potential for preventive and therapeutic application with safety, quality and efficacy.
This book has been possible by numerous co-authors for their collaboration to the task of synthesizing their knowledge on the subject in relatively concise chapters.
List of Contributors
From Pharma to Food: Mechanistic Target Identification for Bioactive Compounds Using Nutritional Systems Biology
INTRODUCTION
Avicenna and Rhazes, medieval Persian practitioners, were first to suggest the concept of “food as medicine” based on the use of natural products. This concept was transformed with the rise of drug development technologies so that the use of synthetic compounds in the form of supplements shadowed the concept of “food as medicine”. Now after more than two centuries, for two reasons, the concept of functional food and its role in health promotion has again gained momentum: firstly, the current paradigm with synthesized drugs in the pharma industry, i.e. “one size fits all”, has been seriously challenged by toxicity and unwanted effects of chemical compounds in the complex system of the human body (i.e. safety issue). Secondly, expensive and growing attrition rates in drug development pipelines plus the non-selective nature of chemical compounds (i.e. efficacy issues) together with the lack of theragnostic strategies for early diagnosis of and intervention in progressive chronic diseases like dementia or cancer has encouraged both pharmaceutical and food companies to bring the disease prevention and treatment using natural compounds into their business focus [1]. The term “reverse pharmacology” has been used to describe identification and evaluation of traditional recipes (e.g. herbal extracts) that have been used by ancient eastern societies for treatment of health problems for centuries. This process takes advantage of up-to-date, modern pharmacological techniques to convert those traditional recipes into health promoting products by following a target identification and clinical trial approach [2].
This emerging paradigm has generated both opportunities and challenges for the food industry. For instance, many countries have politically realized that prevention of chronic diseases through healthy life style including nutrition is a priority and this is a good opportunity for functional food businesses to step in. However, this is not a trivial task: the health and/or disease phenotype in humans results from complex interactions between biological molecules, environmental factors and disease-modifying entities. Hence, understanding how functional food ingredients are going to find their place in this complex picture is key to successful development of functional foods by the food industry. The food industry can benefit from expensive experiences that the pharma industry has accumulated during many years of heavy investment and scientific research in the area of “drug-like functional food” production. In contrast, addressing the complex biology of human health, which has been the focus of the pharmaceutical industry for long time, is considered as a new challenge posed to the food industry if the safety (side effects) and efficacy (mode-of-action) of the functional food products are to be shown for health claims. Regulatory authorities are gradually increasing the pressure on food businesses to cope with stringent health claim regulations. For example, from the perspective of the Food and Drug Administration (FDA), functional foods including food and beverage products with health claims do not belong to the food category but considered as drug and must meet safety and efficacy requirements of the FDA’s regulatory guidelines. Recently, several guidelines on scientific assessment of health claims have been published by the European Food Safety Authority (EFSA) has released guidelines on scientific assessment of health claims, which enforces food manufacturers to prove the quality, relevance and adequacy of scientific evidence supporting their health claims [3]. Perhaps, the most efficient solution for the food industry to keep up with the increasing amount of market demand and regulatory pressure is to attempt at bridging the technology gap with the pharmaceutical industry.
Technology Gap and the Role of Systems Biology
As mentioned above, the pharmaceutical industry has already established a sophisticated, strong technological infrastructure and scientific expertise in the area of drug discovery and development to deal with the complexities involved in human health and disease. However, it appears that the food industry lags behind such advancements when it comes to proving safety and efficacy of bioactive compounds in food products with health claims. It should be noted here that although drugs are different than nutrients, there are striking similarities between food and pharma pipelines (Fig. 1).
Perhaps the main reason behind such discrepancy are structural differences so that the pharmaceutical industry has gone through a gradual transformation from a manufacturing-based traditional business to a knowledge-based, modern industry whereas the food industry has still preserved its manufacture-based traditional pipeline. Today, the knowledge-based settings of the pharmaceutical industry are supported by advanced informatics platforms and computational methods to optimize the entire process of decision making for drug discovery and development. Knowledge-driven systems biology approaches are at the core of such platforms, driving knowledge and data management in support of time- and cost-effective decision-making [4]. The reason for this transformation in the pharmaceutical industry is the high level of risk associated with the expenses of developing new drugs: according to a new study, costs of development of a new drug has increased to 2.6 billion dollars, 145% increase from the previous estimate in 2003 [5]. Why is that? Perhaps the most compelling answer to this question is “the complex nature of human biology”. Complex interactions among a multitude of biological entities, from genes and proteins to metabolites, cells, tissues and organs in the human body make it difficult to understand how a drug or a bioactive compound interferes with health and disease processes. To permit understanding in the face of this complexity, we can consider the human body as a biological system with several components. The components of this system are interactive, their states change constantly and their behaviors depend on their context. For example, brain interacts with other organs through hormones but each interaction depends on the type of hormone and signals that it carries. Such complex interactions, both short-range and long-range interactions in the body, lead to emergence of novel properties and behaviors in the biological system of our body. For instance, when the balance between food intake and physical activity is perturbed, the risk of obesity and insulin resistance increases, in which condition cells in the human body cannot effectively use the insulin hormone. This condition causes diabetes type 2.
The discipline of systems biology aims to understand normal and pathological physiology across multiple biological levels, from genes and proteins, molecular pathways and regulatory networks to cells, tissues, organs and the whole human body. Thus, in the pharmaceutical industry, systems biology methods are used to model and predict safety and efficacy of drugs across multiple scales of the human biology. This is usually done by integrating large datasets and heterogeneous data layers from both experimental and literature sources and the ultimate goal is to discover signaling pathways impacted by candidate drugs compounds so that the relation of observed compound effects to disease mechanism could be hypothesized and probable outcomes in the human body could be predicted [6] (Fig. 2).
The recognition that the effect of nutrition on health goes beyond epidemiological observation has led to a shift in studies towards research at the molecular and subcellular levels. Early attempts at understanding effects of nutrition on the human health at systems level were mostly focused on interactions of nutrients with our genes and proteins. It was within this framework that the concept of nutrigenomics emerged and evolved. The aim of nutrigenomics was to link genome research and molecular nutrition. However, thanks to advanced post-genomic technologies known as OMICs technologies, today an array of heterogeneous data can be generated across various biological scales from molecules to phenotypes, which allows us to combine all available information about effects of food on the human system. In classical systems biology methods, nutrition is considered as an external factor that interferes with the complex system of the human biology.
In this view, nutrition is different than pharmacology in that our diet is composed of various bioactive compounds that are constantly taken up by the body and unlike drugs, their effects cannot be prominently and immediately observed. With the introduction of novel concepts such as “functional food” and “health claims”, this paradigm has changed. Now food products that claim to have bioactive molecules that improve health or reduce the disease burden must have a proven record of scientific evidence for their claims. Although large companies in the food industry (e.g. Nestle) use high-throughput technologies to analyze compound profiles for food and feed, they have recently adopted the use of integrative systems biology methods to unravel complex mechanisms underlying health and disease. “Nutritional systems biology” has recently emerged as an independent branch of systems biology research in food science and considers nutritional attributes of the human life under dynamic conditions of growth and development (Fig. 3).
One of the first attempts at applying a systems nutrition strategy to food science was conducted by Bakker et al. (2010) [7]. In this work, a mixture of nutrients that were shown to have beneficial effects against inflammation, were administered in healthy obese men and then large-scale analyses on genes, proteins and metabolites in body fluids as well as adipose tissue were performed. It was observed that a number of biological processes including inflammation, oxidative stress and metabolic pathways were differentially expressed. However, this example clearly demonstrates that the concept of “nutritional systems biology” in the current food research is equivalent to nutrigenomics and a full-fledged systems biology strategy has yet to be employed. Indeed, it is only after application of the complete cycle of systems biology to nutrition research all the way from molecular biology to clinical trials that the data can be translated into health effects in the form of dietary product for consumers.
Given the importance of systems biology methods in nutrition studies and development of novel functional products, the author has proposed an integrative systems-based model for developing novel functional food products with substantiated health claims [8], which is briefly explained below.
Integrated Systems-based Development of Novel Functional Products
At present, health claims regulations for functional food products already exist in most developed countries but there is no universal regulations as a unique reference. The reason is that there are different views about health claims, so that local regulatory agencies have devised their standards and evaluation processes [9]. Due to these differences, food products that contain bioactive ingredients may not undergo strict evaluations similar to drugs in terms of claims and intended use, which may to production of food products that have variable quality and questionable claims. For example, according to FDA, within the period of 9 years recalls of food supplements from the market exceeded those of drugs [10]. However, food companies, particularly the big ones, are realizing that to survive the fierce competition in the market, they need to translate their innovative functional products into health claims and, for this, there is need to invest on substantiation of health claims to comply with the health claim regulatory requirements.
We propose that a successful strategy for health claim substantiation can be established on the basis of a systems biology foundation so that effects of food ingredients on biological and disease mechanisms can be scientifically explained. In this strategy, bioinformatics tools and systems biology methods are employed in the early phase of product design and development to produce computational models that are capable of predicting the success of the product. The proposed strategy, which is currently getting more popularity in the pharma sector, is based on integrating both published knowledge and experimental data into consolidated computational models. In this way, the mode of action of the bioactive ingredient at the molecular level can be supported by solid scientific evidence from the clinical studies (Fig. 4).
Among a few functional products that have successfully passed through the regulatory screening of EFSA in Europe, Fruitflow is an excellent example that paved the way for using the proposed integrated strategy with well-substantiated health claims. Based on experimental observations that tomato extract facilitates blood circulation and reduces the risk of platelet aggregation, Dutta-Roy and coworkers in 2001 identified potent platelet inhibitors in tomato seeds [11]. The point here to be emphasized is that molecular mechanism of platelet aggregation and pathways involved in blood clot were known before but it took about three decades that natural inhibitors of platelet were identified and extracted from tomato. This gap indicates that the existing knowledge published in the literature on platelet formation and their underlying molecular pathways could have been gathered and consolidated into a computational model that further validated by fresh experimental data with the aid of systems-based approaches so that the mode-of-action for Fruitflow would have been predicted much earlier and clinical trials could have been designed in a more informed and objective way.
Therefore, contribution of systems-based models to development of successful functional products can be mainly divided into two parts:
Model-based discovery of molecular targets and probably biomarkers associated with bioactive ingredients in the context of disease mechanism (target and biomarker discovery), andEvidence-based substantiation of functional ingredients effects through linking the ingredients mode of action of those ingredients to their expected health effects (mode-of-action analysis and efficacy/safety prediction).In the next section, I briefly touch on the application of systems nutrition to target identification and discovery of the mode-of-action of bioactive ingredients under disease condition.
Target Identification for Drugs
Target identification in drug development is a crucial step for follow-up medicinal chemistry studies. A target in the context of drug discovery can be defined as a disease- or health-associated protein that is functionally involved in the pathology of interest. Distinctions are typically made as to whether a target is ‘novel’, ‘established’, or ‘validated’. Briefly, novel targets are proposed targets with speculative involvement in the disease process and no clear indication of its clinical benefit whereas established targets are those with a good scientific support on functionality in both normal and disease states but unknown clinical benefit. In contrast, validated targets have shown a clear clinical benefit with a well-understood mechanism of action.
Specific biological hypotheses based on which targets are selected possess varying degrees of confidence, depending on the origin of those hypotheses. Given that targets have been historically identified on the basis of genetic studies or biological observations, Sams-Dodd from Boehringer Ingelheim Pharma (2005) divides targets into three classes: “physiological targets” that characterize physiological effects at the level of whole organism in animal models; “genetic targets” that represent genetic mutations; and “mechanistic targets” that represent receptors, enzymes, or other biological molecules and are linked to molecular mechanism [12]. Accordingly, genetic targets are specific to those diseases that arise from a genetic mutation or the increased disease risk by a single gene. Moreover, the gene or its product must be the main modulator of the disease at the time of intervention. These two conditions for genetic targets imply that multifactorial complex diseases that develop over time cannot be treated by such an approach. Instead, mechanistic targets go beyond the ‘single gene, single disease’ paradigm by engaging environmental factors in addition to causative biological components, and therefore, can be applied to multifactorial progressive diseases. Since mechanistic targets affect multiple molecular mechanisms, their validation is a complex task and depends on the availability of predictive models.
In general, there are three complementary approaches to target identification: biochemical methods, genetic interaction methods, and computational prediction methods [13]. Amongst these three methods, computational target identification methods have the advantage of the least bias compared to other methods because they rely on a combination of experimental data generated by others. A high-priority task for computational target identification methods is to address the issue of clinical efficacy; i.e. in the absence of clinical data, a model is required to integrate both the experimental data and expert knowledge in the context of the disease of interest so that ultimately the clinical efficacy of a target can be predicted in silico in the form of a set of relevant hypotheses. A success story in this regard is the instrumental role of computational data integration and model analysis in identification of Aurora kinase A as the key target of dimethylfasudil in acute megakaryoblastic leukemia. In this case, integrating transcriptomic and proteomic data led to generation of testable hypothesis, which identified relevant target of dimethylfasudil [14].
Normally, a research process starts with an exploration of the problem domain by collecting relevant data, information, and previous knowledge, which are often hidden in scientific publications. Accordingly, referring to the scientific literature is usually the first step towards drug target selection and validation process because it provides a valid and proper framework for drug target identification purposes. When merged with network-based disease models, the information extracted from text enhances the confidence about druggability of the candidate target(s). Moreover, it would be possible to generate informative profiles for each candidate target using information extracted from the text; i.e. literature-based annotation of target nodes on the network model of disease provides enormous insight about drug candidate efficacy and toxicity. Such profiles will be of high value for ranking or prioritizing target candidates. An “integrative disease modeling” approach takes advantage of the complementary nature of data-driven and knowledge-driven methods, combines them under a single framework, and produces knowledge-based, yet mechanistic disease models. The models generated by this approach represent either correlation or cause and effect relationships, depending on the type of associations between pairs of variables in the network model. The general strategy is depicted in Fig. (5).
The advantage of this hybrid approach, which combines data- and knowledge-driven strategies, is that it provides a unified framework for simultaneous identification and validation of potential target and biomarker candidates specific to the health context in silico.
It is important to distinguish between “targetability” and “druggability” features. While most of the studies have been focused on the druggability properties of the protein targets, less attention has been paid to the targetability properties of protein targets. This notion is supported by the fact that the primary target for 7% of approved drugs is not known and mode of action for 18% of approved drugs is not defined [15]. Druggability is defined as the ability of a target to be modulated by potent, small drug-like molecules, mostly reflects the structured-based physicochemical properties of the target in the binding site, and is used in the target validation phase. In contrast, there is no clear definition for targetability in the literature so far. Targetability can be defined as ‘the ability of a target to modify the path of disease or modulate disease-related phenotypes’. It is often used in the target identification phase.
Nowadays, the concept of targetability is being transformed from a ‘target-based’ paradigm into ‘pathway-based’ paradigm, where network subgraphs and pathways emerge as targetable entities. Rising attrition rates of new compounds in the past decade, which was highest (62%) during phase II, indicates the lack of efficacy and reflects the low predictive capacity of target-based drug discoveries. Advantages of the pathway-based approach over the target-based approach are manifold:
the hypothesis behind a target’s mechanism of action in the context of the disease can be disproved (i.e. what if manipulation of target X fails to modify the disease process Y);the functional output of the target pathway can be predicted and linked to clinically relevant outcomes; andpositive therapeutic off-target effects of approved or pipeline drugs can be predicted.Several studies have previously shown the effectiveness of using pathways as therapeutic targets in neurobiology. For example, measurement of hippocampal neurogenesis pathway by high-throughput screening for approved drugs on mouse models showed that cholesterol lowering drugs can predict the stimulatory effect of these drugs on the adult neurogenesis pathway in animal models. In another study by the same group, lipopolysaccharide-induced microglia proliferation pathway in the rat brain was subjected to HTS analysis and drugs were found that ameliorated clinical symptoms in the mouse models of Parkinson’s disease.
Target Identification for Nutraceuticals
The human body is considered as an integrated, interconnected, complex system. This complex system is perturbed by any environmental input including nutritional ingredients, and as a result, the body generates a physiological response to this input. Understanding the way bioactive compounds affect the physiology of human body under both healthy and disease states can help us discover, design and formulate health promoting products (nutraceutical, functional food, dietary supplement) that produce desired health effects. Foods and medicinal plants contain various biochemical compounds including phenols and flavonoids that affect various physiological processes in our body. These compounds convey their effects through interaction with particular targets such as proteins or metabolites. For instance, flavonoids are used in folk medicine to treat disorders related to thyroid hormone because they are active anti-thyroid ingredients. However, to identify molecular targets of these flavonoids, a synthetic flavonoid compound has been produced and tested by in vitro experiments as well as in vivo studies in animal models. By this means, three targets were identified in the network of thyroid hormone signaling and their safety was also evaluated: thyroperoxidase, transthyretin, and deiodinase [16]. In another study, comparative genomics methods and molecular modeling techniques were used to identify the targets in E.coli for 19 antibacterial flavonoids; overall 5 targets were discovered and validated in silico [17].
Unfortunately, the mode-of-action of many food ingredients at the mechanistic level is not known. This requires a sound understanding of health and disease mechanisms at the molecular level and the way bioactive ingredients intervene with these mechanisms. Moreover, mode-of-action of nutrients at the molecular level is often disconnected from its effects at the disease or health level (i.e. phenotype level). Thus, systems nutrition methods can be used to explain mode-of-action of bioactive compounds at the molecular level and connect this molecular mechanism to the expected health outcome.
With a good knowledge about the mode-of-action of the candidate ingredient and how it is going to alter cellular pathways, we will be also able to predict efficacy and safety profile of that particular ingredient. Consequently, knowing how effectively a new bioactive ingredient is going to improve health of the human population is essential for reducing the risk of failure in clinical trials and increasing rate of success at the post-marketing level. Demonstrating the biological efficacy of bioactive compounds is critical for the clinical success and approval of any nutraceutical (functional food, dietary supplement) product. This requirement can be investigated by systems-based integrative approaches that model mechanistic relations between disease pathways and health outcomes. In the following, I demonstrate how such a systems-based approach can be applied to explain the mode-of-action of several functional diets in the contexts of neurotrophin pathway.
Evidence-based Modeling of Mode-of-action for Functional Ingredients Influencing Alzheimer’s Disease
There is a growing body of evidence that support the links between reduced levels of neurotrophic factors and increased risk of Alzheimer’s disease (AD). From these findings a hypothesis can be derived that if functional ingredients can rescue the affected neurotrophin pathway (by compensating for the reduced concentrations of BDNF) and cognitive abilities may improve in AD patients.
Neurotrophins and their receptors have already shown promising results for the treatment of neurological diseases. They constitute an important family of growth factors that initiate a series of signaling cascades on the surface of neurons, thereby the survival, development, and function of neurons through “neurotrophin signaling pathway” [18]. The most widely expressed member of the neurotrophin growth factor family in the human brain is BDNF, which binds to NTRK2 receptors and triggers the neurotrophin signaling. Accumulated evidence suggest that BDNF exerts broad neuroprotective effects in animal models of Alzheimer’s disease [19]. For example, it has been shown that infusion of BDNF in rat and mouse reverses cognitive decline and restores memory [20]. However, neurotrophin proteins cannot be directly administered as therapeutic agents for treatment because of their poor stability in serum, negligible oral bioavailability, and the pleiotropic effects; most importantly, neurotrophins do not have the ability to cross the blood-brain barrier and penetrate the brain [21]. Therefore, alternative strategies are needed to take advantage of therapeutic potential of neurotrophins. Here, I describe a systems biology strategy that was used step by step to find nutritional ingredients that can mimic the effect of neurotrophins and boost the outcome of the neurotrophin pathway:
In the first step, published knowledge in the biomedical literature as well as curated pathway information in pathway databases were scanned to identify and extract useful pieces of information that describe BDNF signaling in both normal and disease states. Out of this information, two cause-and-effect models of BDNF signaling for the two states, i.e. normal state and Alzheimer’s disease state, were constructed. The unperturbed BDNF pathway representing the non-disease state was reconstructed from the neurotrophin pathway, which can be found in the KEGG database. When looking into this pathway, it can be seen that a part of this pathway represents downstream signaling by BDNF- NTRK2 interaction through a variety of intracellular signaling cascades so that it transmits positive signals like enhanced survival and growth of neurons. The perturbed BDNF signaling pathway representing the disease state under AD conditions was constructed by keyword search within the abstracts of biomedical publications in PubMed database using the following query: Alzheimer’s disease AND BDNF AND neurotrophin signaling pathway ; (accessed 16.07.2014). In total, 29 abstracts were retrieved and then these abstracts were manually checked for their relevance to impaired BDNF signaling under AD conditions as well as useful information content that can be coded into the model. As a result, out of 29 abstracts, 6 publications were qualified (PMIDs: 11438587, 16187222, 9106250, 21460223, 21647938, 23599427). Finally, we extracted cause-and-effect statements from these abstracts and used those statements to derive triples and build the model. Thus, behind all interactions in this model there are scientific evidence harvested from the literature.In the second step, we performed a “differential model analysis” between the two non-disease and disease states by aligning the two models. The resultant differential model that represents BDNF mode-of-action was further validated using the “biomarker-guided validation” approach. In this approach, we extracted published information explaining the potential biomarker activity (i.e. expression) of BDNF and NTRK2, manually checked them and highlighted them in the differential model.In the third step, we collected scientific evidence explaining the effect of various functional diets on BDNF levels and BDNF-related biological processes or outcomes was harvested from biomedical literature using an advanced semantic search engine. The following query was formulated and used for search in the literature: ((Human Genes/Proteins:“BDNF”) AND MeSH Disease:“Alzheimer Disease”) AND (NDD:“Diet”). We checked retrieved documents manually and extracted cause-and-effect information was extracted. We then compared this information was then compared to the mechanistic model of BDNF mode-of-action and used them to substantiate the mode-of-action model.The analysis of the differential model (i.e. BDNF-normal vs. BDNF-disease) resulted in a mechanistic mode-of-action model that represented mode-of-action for the effector BDNF signaling pathway through NTRK2 receptor in neurons (Fig. 6).
The model revealed possible existence of an amyloid-mediated neurotrophin switch mechanism by which the amyloid-beta protein competitively blocks BDNF-NTRK2 downstream signaling under Alzheimer’s disease conditions. At the same time, amyloid-beta promotes neuronal death via cross-linking NGFR receptor with NTRK1 and suppressing the cell survival pathway of PI3K/Akt signaling, thereby “switching” the entire pathway from its normal state with neuroprotective estate to the disease state with a strong push towards neuron apoptosis. The next step was to validate this hypothesis. We used measured (expressed) biomarkers under disease conditions as well as empirical data obtained from experimentation of BDNF mimetics in animal models to validate the switch mechanism. The validation results using biomarker evidence for BDNF and NTRK2 receptor are summarized in Table 1. As shown in this table, there are several studies that confirm the hypothesis that BDNF and its receptor NTRK2 are downregulated in the hippocampus and cortex of Alzheimer´s patients.
However, we can further substantiated the biomarker evidence using the results from translational studies which have tested BDNF synthetic agonists and reported positive effects on the neural survival pathway. A list of such BDNF agonists is shown in Table 2 where it lists studies with BDNF agonists that experimentally showed to reverse memory impairment in mouse AD models. Based on those results summarized in Table 2, we can hypothesize that any functional ingredient with BDNF boosting properties of BDNF may be able to revert the neural apoptosis to the neurons back to the neuron survival pathway.
Our literature mining approach led to identification of several functional diets that have shown agonistic effects on the BDNF signaling pathway (Table 3). These effects are exerted through enhanced levels of BDNF and subsequently, activating the BDNF pro-survival pathway is induced, which leads to similar observations that have been made with BDNF mimetics in animal models. As summarized in Table 3, several diets demonstrate both positive (agonistic) and negative (antagonistic) effects on the BDNF signaling pathway.
