Cancer is a complex and heterogeneous disease, not only at a genetic and biochemical level, but also at a tissue, organism, and population level. Multiple data streams, from reductionist biochemistry in vitro to high-throughput “-omics” from clinical material, have been generated with the h ...
Atherogenic lipids and chronic inflammation drive the development of cardiovascular disorders such as atherosclerosis. Many cardiovascular drugs target the liver which is involved in the formation of lipid and inflammatory risk factors. With robust systems biology tools and co ...
The immune system plays an important role in the development of personalized medicine for a variety of diseases including cancer, autoimmune diseases, and infectious diseases. Immunoinformatics, or computational immunology, is an emerging area that provides fundamental meth ...
Systems biology and pharmacogenomics are emerging and promising fields that will provide a thorough understanding of diseases and enable personalized therapy. However, one of the most significant obstacles in the practice of personalized medicine is the translation of scientif ...
Pharmacological agents and other perturbants of cellular homeostasis appear to nearly universally affect the activity of many genes, proteins, and signaling pathways. While this is due in part to nonspecificity of action of the drug or cellular stress, the large-scale self-regulatory ...
The extraction of regulatory networks and pathways from postgenomic data is important for drug �discovery and development, as the extracted pathways reveal how genes or proteins regulate each other. Following up on the seminal paper of Friedman et al. (J Comput Biol 7:601–620, 2000), Bayesian ...
Interactions among cellular constituents play a crucial role in overall cellular function and organization. These interactions can be viewed as being complementary to the usual “parts list” of genes and proteins and, in conjunction with the expression states of these parts, are key to a syst ...
Systems Biology approaches to drug discovery largely focus on the increasing understanding of intracellular and cellular circuits, by computational representation of a molecular system followed by parameter validation against experimental data. This chapter outlines a un ...
Stable isotope labeling with amino acids in cell culture (SILAC) has become increasingly popular as a quantitative proteomics (qProteomics) method. In combination with high-resolution mass spectrometry (MS) and new efficient algorithms for the analysis of quantitative MS data, S ...
Systems biology is essentially a proteomic and epigenetic exercise because the relatively condensed information of genomes unfolds on the level of proteins. The flexibility of cellular architectures is not only mediated by a dazzling number of proteinaceous species but moreover by ...
Studies of complex biological systems aimed at understanding their functions at a global level are the goals of systems biology. Proteomics, generally regarded as the comprehensive study of the expression of all the proteins at a particular time in different organs, tissues, and cell types is a ...
Inflammation is a complex, multiscale biological response to threats – both internal and external – to the body, which is also required for proper healing of injured tissue. In turn, damaged or dysfunctional tissue stimulates further inflammation. Despite continued advances in charac ...
Drug Discovery in modern times straddles three main periods. The first notable period can be traced to the nineteenth century where the basis of drug discovery relied on the serendipity of the medicinal chemists. The second period commenced around the early twentieth century when new drug str ...
Molecular recognition is mediated by three main factors: surface complementarity, thermodynamics, and associated physicochemical properties. These principles are responsible for ligand–target binding and therefore serve as the foundation for the design of new biologic ...
Macromolecular X-ray crystallography is an important and powerful technique in drug discovery, used by pharmaceutical companies in the discovery process of new medicines. The detailed analysis of crystal structures of protein–ligand complexes allows the study of the specific in ...
During the last decade, Virtual Screening (VS) has definitively established itself as an important part of the drug discovery and development process. VS involves the selection of likely drug candidates from large libraries of chemical structures by using computational methodolo ...
A critical step in the drug discovery process is the identification of high-affinity ligands for macromolecular targets, and, over the last 10 years, NMR spectroscopy has become a powerful tool in the pharmaceutical industry. Instrumental improvements in recent years have contribut ...
Solid Phase Organic Synthesis (SPOS) has become a powerful tool for the preparation of compound libraries used for screening efforts in Chemical Biology. While different types of screening libraries have become commercially available through several vendors, the elaboration of a h ...
The receptor concept is the primary theoretical basis for modern pharmacology. Drugs, hormones, neurotransmitters, toxin, and other biologically active substances are referred to as ligands. Ligands exert their actions by way of interaction with receptors/macromolecules. The ...
In the last few years, genomic tools have been incorporated in natural product approaches to drug discovery, including understanding mechanisms of action which cannot be elucidated from phenotypic screens such as cell viability assays. The characterization of perturbed biologi ...
