Predicting adverse events accurately represents a significant challenge to both the pharmaceutical industry and academia, the reason being that our existing knowledge of biology, disease mechanisms (i.e. how a disease affects the healthy state of a human) and drug design is incomplete and sometimes incorrect. On top of that, the biological complexity and differences between living organisms is such that even if a treatment appears to work in the laboratory it may not work in humans.
The occurrence of an adverse event during a clinical trial is a significant event, not only because of the risk to humans but also from a financial point of view for the organization (usually a pharmaceutical company) sponsoring the development of the drug in question. As a result, a lot of effort is continuously invested in this area and there are a number of approaches to predicting adverse events including cell line assays, animal models and computer based in silico models.
In silico models are usually developed by extracting interactions and behaviors of biological systems either from the literature or from experimental data on a specific disease or biological system and integrating this information in some kind of a mathematical model that can be used to understand and predict the behavior of a drug in an organism. Another relatively recent method is based on mining the scientific literature and correlating evidence from seemingly unrelated drugs or medical conditions. If done correctly this type of analysis can offer quite good predictive accuracy and significant lead times which translates to lower cost and development times for new drugs.
While in silico methods aim to capture in depth the current knowledge of a biological system or a disease mechanism, they are still subject to the accuracy of that knowledge and may miss information that while seemingly unrelated, could in a multiply interconnected complex biological system prove highly relevant. This gap is addressed by the literature-based discovery approach which does not capture details to the same extent but compensates by offering complete coverage of the available knowledge from all potentially related fields.
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Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for in silico analyses of biological queries using mathematical and statistical techniques.
In vitro studies are performed with microorganisms, cells, or biological molecules outside their normal biological context. Colloquially called "test-tube experiments", these studies in biology and its subdisciplines are traditionally done in labware such as test tubes, flasks, Petri dishes, and microtiter plates. Studies conducted using components of an organism that have been isolated from their usual biological surroundings permit a more detailed or more convenient analysis than can be done with whole organisms; however, results obtained from in vitro experiments may not fully or accurately predict the effects on a whole organism. In contrast to in vitro experiments, in vivo studies are those conducted in living organisms, including humans, and whole plants.
Pharmacology is a branch of medicine, biology and pharmaceutical sciences concerned with drug or medication action, where a drug may be defined as any artificial, natural, or endogenous molecule which exerts a biochemical or physiological effect on the cell, tissue, organ, or organism. More specifically, it is the study of the interactions that occur between a living organism and chemicals that affect normal or abnormal biochemical function. If substances have medicinal properties, they are considered pharmaceuticals.
Toxicology is a scientific discipline, overlapping with biology, chemistry, pharmacology, and medicine, that involves the study of the adverse effects of chemical substances on living organisms and the practice of diagnosing and treating exposures to toxins and toxicants. The relationship between dose and its effects on the exposed organism is of high significance in toxicology. Factors that influence chemical toxicity include the dosage, duration of exposure, route of exposure, species, age, sex, and environment. Toxicologists are experts on poisons and poisoning. There is a movement for evidence-based toxicology as part of the larger movement towards evidence-based practices. Toxicology is currently contributing to the field of Cancer research, since some toxins can be used as drugs for killing tumor cells. One prime example of this is Ribosome Inactivating Proteins, tested in the treatment of Leukemia.
Pharmacodynamics (PD) is the study of the biochemical and physiologic effects of drugs. The effects can include those manifested within animals, microorganisms, or combinations of organisms.
An animal model is a living, non-human, often genetic-engineered animal used during the research and investigation of human disease, for the purpose of better understanding the disease process without the risk of harming a human. Although biological activity in an animal model does not ensure an effect in humans, many drugs, treatments and cures for human diseases are developed in part with the guidance of animal models. Animal models representing specific taxonomic groups in the research and study of developmental processes are also referred to as model organisms. There are three main types of animal models: Homologous, Isomorphic and Predictive. Homologous animals have the same causes, symptoms and treatment options as would humans who have the same disease. Isomorphic animals share the same symptoms and treatments, only. Predictive models are similar to a particular human disease in only a couple of aspects. However, these are useful in isolating and making predictions about mechanisms of a set of disease features.
Modelling biological systems is a significant task of systems biology and mathematical biology. Computational systems biology aims to develop and use efficient algorithms, data structures, visualization and communication tools with the goal of computer modelling of biological systems. It involves the use of computer simulations of biological systems, including cellular subsystems, to both analyze and visualize the complex connections of these cellular processes.
Toxicogenomics is a subdiscipline of pharmacology that deals with the collection, interpretation, and storage of information about gene and protein activity within a particular cell or tissue of an organism in response to exposure to toxic substances. Toxicogenomics combines toxicology with genomics or other high-throughput molecular profiling technologies such as transcriptomics, proteomics and metabolomics. Toxicogenomics endeavors to elucidate the molecular mechanisms evolved in the expression of toxicity, and to derive molecular expression patterns that predict toxicity or the genetic susceptibility to it.
Metabolic network modelling, also known as metabolic network reconstruction or metabolic pathway analysis, allows for an in-depth insight into the molecular mechanisms of a particular organism. In particular, these models correlate the genome with molecular physiology. A reconstruction breaks down metabolic pathways into their respective reactions and enzymes, and analyzes them within the perspective of the entire network. In simplified terms, a reconstruction collects all of the relevant metabolic information of an organism and compiles it in a mathematical model. Validation and analysis of reconstructions can allow identification of key features of metabolism such as growth yield, resource distribution, network robustness, and gene essentiality. This knowledge can then be applied to create novel biotechnology.
Immunogenicity is the ability of a foreign substance, such as an antigen, to provoke an immune response in the body of a human or other animal. It may be wanted or unwanted:
Simcyp Limited is a research-based company which provides modelling and simulation software to the pharmaceutical industry for use during drug development. Simcyp is based in Sheffield, UK.
Safety pharmacology is a branch of pharmacology specialising in detecting and investigating potential undesirable pharmacodynamic effects of new chemical entities (NCEs) on physiological functions in relation to exposure in the therapeutic range and above.
Biosimulation is a computer-aided mathematical simulation of biological processes and systems and thus is an integral part of systems biology. Due to the complexity of biological systems simplified models are often used, which should only be as complex as necessary.
Phenotypic screening is a type of screening used in biological research and drug discovery to identify substances such as small molecules, peptides, or RNAi that alter the phenotype of a cell or an organism in a desired manner.
Translational bioinformatics (TBI) is an emerging field in the study of health informatics, focused on the convergence of molecular bioinformatics, biostatistics, statistical genetics and clinical informatics. Its focus is on applying informatics methodology to the increasing amount of biomedical and genomic data to formulate knowledge and medical tools, which can be utilized by scientists, clinicians, and patients. Furthermore, it involves applying biomedical research to improve human health through the use of computer-based information system. TBI employs data mining and analyzing biomedical informatics in order to generate clinical knowledge for application. Clinical knowledge includes finding similarities in patient populations, interpreting biological information to suggest therapy treatments and predict health outcomes.
In silico medicine is the application of in silico research to problems involving health and medicine. It is the direct use of computer simulation in the diagnosis, treatment, or prevention of a disease. More specifically, in silico medicine is characterized by modeling, simulation, and visualization of biological and medical processes in computers with the goal of simulating real biological processes in a virtual environment.
eTOX is a temporary consortium established in 2010 to share and use toxicology data. It is a pre-competitive collaboration which main goal is to create and distribute tools to predict drug side-effects based on pre-clinical experiments. Aims are a better in silico predictability of potential adverse events and a decrease of the use of animals in toxicological research. eTOX is funded by the Innovative Medicines Initiative (IMI).
In bioinformatics, a Gene Disease Database is a systematized collection of data, typically structured to model aspects of reality, in a way to comprehend the underlying mechanisms of complex diseases, by understanding multiple composite interactions between phenotype-genotype relationships and gene-disease mechanisms. Gene Disease Databases integrate human gene-disease associations from various expert curated databases and text mining derived associations including Mendelian, complex and environmental diseases.
An in silico clinical trial is an individualised computer simulation used in the development or regulatory evaluation of a medicinal product, device, or intervention. While completely simulated clinical trials are not feasible with current technology and understanding of biology, its development would be expected to have major benefits over current in vivo clinical trials, and research on it is being pursued.
Leon Aarons is an Australian pharmacist who researches and teaches in the areas of pharmacodynamics and pharmacokinetics. He lives in the United Kingdom and from 1976 has been a professor of pharmacometrics at the University of Manchester. In the interest of promoting the effective development of drugs, the main focus of his work is optimizing pharmacological models, the design of clinical studies, and data analysis and interpretation in the field of population pharmacokinetics. From 1985 to 2010 Aarons was an editor emeritus of the Journal of Pharmacokinetics and Pharmacodynamics and is a former executive editor of the British Journal of Clinical Pharmacology.
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