Drug discovery in the context of Classical pharmacology

Studies that are in vivo (Latin for "within the living"; often not italicized in English) are those in which the effects of various biological entities are tested on whole, living organisms or cells, usually animals, including humans, and plants, as opposed to a tissue extract or dead organism.

Examples of investigations in vivo include: the pathogenesis of disease by comparing the effects of bacterial infection with the effects of purified bacterial toxins; the development of non-antibiotics, antiviral drugs, and new drugs generally; and new surgical procedures. Consequently, animal testing and clinical trials are major elements of in vivo research. In vivo testing is often employed over in vitro because it is better suited for observing the overall effects of an experiment on a living subject. In drug discovery, for example, verification of efficacy in vivo is crucial, because in vitro assays can sometimes yield misleading results with drug candidate molecules that are irrelevant in vivo (e.g., because such molecules cannot reach their site of in vivo action, for example as a result of rapid catabolism in the liver).

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. Phenotypic screening must be followed up with identification (sometimes referred to as target deconvolution) and validation, often through the use of chemoproteomics, to identify the mechanisms through which a phenotypic hit works.

Alkaloids are a broad class of naturally occurring organic compounds that contain at least one nitrogen atom. Some synthetic compounds of similar structure may also be termed alkaloids.

Alkaloids are produced by a large variety of organisms including bacteria, fungi, plants, and animals. They can be purified from crude extracts of these organisms by acid-base extraction, or solvent extractions followed by silica-gel column chromatography. Alkaloids have a wide range of pharmacological activities including antimalarial (e.g. quinine), antiasthma (e.g. ephedrine), anticancer (e.g. homoharringtonine), cholinomimetic (e.g. galantamine), vasodilatory (e.g. vincamine), antiarrhythmic (e.g. quinidine), analgesic (e.g. morphine), antibacterial (e.g. chelerythrine), and antihyperglycemic activities (e.g. berberine). Many have found use in traditional or modern medicine, or as starting points for drug discovery. Other alkaloids possess psychotropic (e.g. psilocin) and stimulant activities (e.g. cocaine, caffeine, nicotine, theobromine), and have been used in entheogenic rituals or as recreational drugs. Alkaloids can be toxic (e.g. atropine, tubocurarine). Although alkaloids act on a diversity of metabolic systems in humans and other animals, they almost uniformly evoke a bitter taste.

The disk diffusion test (also known as the agar diffusion test, Kirby–Bauer test, disc-diffusion antibiotic susceptibility test, disc-diffusion antibiotic sensitivity test and KB test) is a culture-based microbiology assay used in diagnostic and drug discovery laboratories. In diagnostic labs, the assay is used to determine the susceptibility of bacteria isolated from a patient's infection to clinically approved antibiotics. This allows physicians to prescribe the most appropriate antibiotic treatment. In drug discovery labs, especially bioprospecting labs, the assay is used to screen biological material (e.g. plant extracts, bacterial fermentation broths) and drug candidates for antibacterial activity. When bioprospecting, the assay can be performed with paired strains of bacteria to achieve dereplication and provisionally identify antibacterial mechanism of action.

In diagnostic laboratories, the test is performed by inoculating the surface of an agar plate with bacteria isolated from a patient's infection. Antibiotic-containing paper disks are then applied to the agar and the plate is incubated. If an antibiotic stops the bacteria from growing or kills the bacteria, there will be an area around the disk where the bacteria have not grown enough to be visible. This is called a zone of inhibition. The susceptibility of the bacterial isolate to each antibiotic can then be semi-quantified by comparing the size of these zones of inhibition to databases of information on known antibiotic-susceptible, moderately susceptible and resistant bacteria. In this way, it is possible to identify the most appropriate antibiotic for treating a patient's infection. Although the disk diffusion test cannot be used to differentiate bacteriostatic and bactericidal activity, it is less cumbersome than other susceptibility test methods such as broth dilution.

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Sanford Burnham Prebys is an American nonprofit biomedical research institute located in La Jolla, California, conducting biomedical and translational research, including stem cell and drug discovery studies. It operates a National Cancer Institute-designated Cancer Center and conducts genomics research.

Drug development is the process of bringing a new pharmaceutical drug to the market once a lead compound has been identified through the process of drug discovery. It includes preclinical research on microorganisms and animals, filing for regulatory status, such as via the United States Food and Drug Administration for an investigational new drug to initiate clinical trials on humans, and may include the step of obtaining regulatory approval with a new drug application to market the drug. The entire process—from concept through preclinical testing in the laboratory to clinical trial development, including Phase I–III trials—to approved vaccine or drug typically takes more than a decade.

Pharmacognosy is the study of crude drugs obtained from medicinal plants, animals, fungi, and other natural sources. The American Society of Pharmacognosy defines pharmacognosy as "the study of the physical, chemical, biochemical, and biological properties of drugs, drug substances, or potential drugs or drug substances of natural origin as well as the search for new drugs from natural sources".

Ergosterol (ergosta-5,7,22-trien-3β-ol) is a mycosterol found in cell membranes of fungi and protozoa, serving many of the same functions that cholesterol serves in animal cells. Because many fungi and protozoa cannot survive without ergosterol, the enzymes that synthesize it have become important targets for drug discovery. In human nutrition, ergosterol is a provitamin form of vitamin D₂; exposure to ultraviolet (UV) light causes a chemical reaction that produces vitamin D₂.

Transdifferentiation, also known as lineage reprogramming, is the process in which one mature somatic cell is transformed into another mature somatic cell without undergoing an intermediate pluripotent state or progenitor cell type.(a process where one type of fully developed body cell changes directly into another type of body cell, without the cell turning into a stem cell first) It is a type of metaplasia, which includes all cell fate switches, including the interconversion of stem cells.(it's considered as a form of metaplasia, which refers to any change from one kind of cell to another, including changes involving stem cells.) Current uses of transdifferentiation include disease modeling and drug discovery and in the future may include gene therapy and regenerative medicine.(transdifferentiation is currently used in areas like understanding diseases, testing new drugs, and possibly future treatments such as gene therapy and tissue repair). The term 'transdifferentiation' was originally coined by Selman and Kafatos in 1974 to describe a change in cell properties as cuticle-producing cells became salt-secreting cells in silk moths undergoing metamorphosis.

In pharmacokinetics, a compartment is a defined volume of body fluids, typically of the human body, but also those of other animals with multiple organ systems. The meaning in this area of study is different from the concept of anatomic compartments, which are bounded by fasciae, the sheath of fibrous tissue that enclose mammalian organs. Instead, the concept focuses on broad types of fluidic systems. This analysis is used in attempts to mathematically describe distribution of small molecules throughout organisms with multiple compartments. Various multi-compartment models can be used in the areas of pharmacokinetics and pharmacology, in the support of efforts in drug discovery, and in environmental science.

In humans and related organisms, there are five major body compartments: the blood plasma, interstitial fluids, fat tissues, intracellular fluids, and transcellular fluids, the latter of which includes fluids in the pleural (peritoneal) cavity. The relative percents of body mass of these are included in the pie chart above.