Definitions of Commonly Used Technical Terms

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Absorbance

Absorbance is used for assays such as ELISA assays, protein and nucleic acid quantification or enzyme activity assays (i.e. in the MTT assay for cell viability). A light source illuminates the sample using a specific wavelength (selected by an optical filter, or a monochromator), and a light detector located on the other side of the well measures how much of the initial (100 %) light is transmitted through the sample: the amount of transmitted light will typically be related to the concentration of the molecule of interest.

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ADME

an acronym in pharmacokinetics and pharmacology for absorption, distribution, metabolism, and excretion, and describes the disposition of a pharmaceutical compound within an organism.

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Agonist

A drug that binds to and activates a receptor. Can be full, partial or inverse. A full agonist has high efficacy, producing a full response while occupying a relatively low proportion of receptors. A partial agonist has lower efficacy than a full agonist. It produces sub-maximal activation even when occupying the total receptor population, therefore cannot produce the maximal response, irrespective of the concentration applied. An inverse agonist produces an effect opposite to that of an agonist, yet binds to the same receptor binding-site as an agonist.

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Allosteric Modulator

A drug that binds to a receptor at a site distinct from the active site. Induces a conformational change in the receptor, which alters the affinity of the receptor for the endogenous ligand. Positive allosteric modulators increase the affinity, whilst negative allosteric modulators decrease the affinity.

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Antagonist

A drug that attenuates the effect of an agonist. Can be competitive or non-competitive, each of which can be reversible or irreversible. A competitive antagonist binds to the same site as the agonist but does not activate it, thus blocks the agonist’s action. A non-competitive antagonist binds to an allosteric (non-agonist) site on the receptor to prevent activation of the receptor. A reversible antagonist binds non-covalently to the receptor, therefore can be “washed out”. An irreversible antagonist binds covalently to the receptor and cannot be displaced by either competing ligands or washing.

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AUC

The area under the plasma (serum, or blood) concentration versus time curve.It is used in toxicology, biopharmaceutics and pharmacokinetics.

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BALB/c

an albino strain of laboratory mouse from which a number of common substrains are derived. BALB/c substrains are “particularly well known for the production of plasmacytomas on injection with mineral oil,” an important process for the production of monoclonal antibodies. They are also reported as having a “low mammary tumour incidence, but do develop other types of cancers in later life, most commonly reticular neoplasms, lung tumours, and renal tumours.

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B_max

The maximum amount of drug or radioligand, usually expressed as picomoles (pM) per mg protein, which can bind specifically to the receptors in a membrane preparation. Can be used to measure the density of the receptor site in a particular preparation.

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C57BL/6

C57BL/6 often referred to as “C57 black 6” or just “black 6” is a common inbred strain of lab mouse. Dark brown, nearly black, coat. Easily irritable temperament. They have a tendency to bite. The immune response of mice from the C57BL/6 strain distinguish it from other inbred strains like BALB/c.

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CYP

The cytochrome P450 superfamily. The function of most CYP enzymes is to catalyze the oxidation of organic substances. The most common reaction catalyzed by cytochromes P450 is a monooxygenase reaction. RH (organic substrate) + O₂ + 2H⁺ + 2e– → ROH + H₂O. CYP families in humans divided among 18 families of cytochrome P450 genes and 43 subfamilies.

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Cheng-Prusoff Equation

Used to determine the K_i value from an IC₅₀ value measured in a competition radioligand binding assay:Where [L] is the concentration of free radioligand, and K_d is the dissociation constant of the radioligand for the receptor.

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Desensitisation

A reduction in response to an agonist while it is continuously present at the receptor, or progressive decrease in response upon repeated exposure to an agonist.

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DMPK

(1) Drug Metabolism and Pharmacokinetics; (2) Dystrophia Myotonica Protein Kinase.

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EC₅₀

The molar concentration of an agonist that produces 50% of the maximum possible response for that agonist.

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ED₅₀

In vitro or in vivo dose of drug that produces 50% of its maximum response or effect.

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Efficacy

Describes the way that agonists vary in the response they produce when they occupy the same number of receptors. High efficacy agonists produce their maximal response while occupying a relatively low proportion of the total receptor population. Lower efficacy agonists do not activate receptors to the same degree and may not be able to produce the maximal response (see Agonist, Partial).

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ELISA

Enzyme-linked immunosorbent assay, also known as an enzyme immunoassay (EIA), is a biochemical technique used mainly in immunology to detect the presence of an antibody or an antigen in a sample.

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Ex vivo

Taking place outside a living organism.

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Fluorescence

a first optical system (excitation system) illuminates the sample using a specific wavelength (selected by an optical filter, or a monochromator). As a result of the illumination, the sample emits light (it fluoresces) and a second optical system (emission system) collects the emitted light, separates it from the excitation light (using a filter or monochromator system), and measures the signal using a light detector such as a photomultiplier tube (PMT). The advantages of fluorescence detection over absorbance detection are sensitivity, as well as application range, given the wide selection of fluorescent labels available today.

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Fluorescence polarization

the samples in the microplate are excited using polarized light (instead of non-polarized light in FI and TRF modes). Depending on the mobility of the fluorescent molecules found in the wells, the light emitted will either be polarized or not.

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Hit

a chemical compound that produces a result in a preliminary biochemical test indicating that the compound merits further study as part of a drug discovery project.

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IC₅₀

In a functional assay, the molar concentration of an agonist or antagonist which produces 50% of its maximum possible inhibition. In a radioligand binding assay, the molar concentration of competing ligand which reduces the specific binding of a radioligand by 50%.

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ID₅₀

In vitro or in vivo dose of a drug that causes 50% of the maximum possible inhibition for that drug.

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K_B

The equilibrium dissociation constant for a competitive antagonist: the molar concentration that would occupy 50% of the receptors at equilibrium.

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K_D

The dissociation constant for a radiolabeled drug determined by saturation analysis. It is the molar concentration of radioligand which, at equilibrium, occupies 50% of the receptors.

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K_i

The inhibition constant for a ligand, which denotes the affinity of the ligand for a receptor. Measured using a radioligand competition binding assay, it is the molar concentration of the competing ligand that would occupy 50% of the receptors if no radioligand was present. It is calculated from the IC50 value using the Cheng-Prusoff equation.

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LC-MS

Liquid chromatography-mass spectrometry. an analytical chemistry technique that combines the physical separation capabilities of liquid chromatography (or HPLC) with the mass analysis capabilities of mass spectrometry. There are a lot of mass analyzers that can be used in LC/MS. Single Quadrupole, Triple Quadrupole, Ion Trap, TOF (time of Flight) and Quadrupole-time of flight (Q-TOF).

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Lead compound

(1) a compound that has been selected from a group of hit compounds based on qualities such as the intensity of the biochemical effect that occurs when the compound is present (efficacy), or the absence of coincidental effects (specificity); (2) a chemical compound that has pharmacological or biological activity and whose chemical structure is used as a starting point for chemical modifications in order to improve potency, selectivity, or pharmacokinetic parameters.

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Luminescence

The difference with fluorescence is that the light emitted by the samples is the result of a chemical or biochemical reaction (instead of being the result of excitation by light). Luminescence plate readers are simpler optically than fluorescence readers, as they don’t require a light source, just a light detector. Typically, the optical system consists in a light-tight reading chamber, and PMT detector measuring the light emitted by the samples during the reaction. Common applications include luciferase-based gene expression assays, as well as cell viability and cytotoxicity assays based on the luminescent detection of ATP.

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Nude mouse

a laboratory mouse from a strain with a genetic mutation that causes a deteriorated or absent thymus, resulting in an inhibited immune system due to a greatly reduced number of T cells. The genetic basis of the nude mouse mutation is a disruption of the FOXN1 gene. Most strains of nude mice are slightly “leaky” and do have a few T cells, especially as they age.

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Non-Specific Binding

The proportion of radioligand that is not displaced by other competitive ligands specific for the receptor. It can be binding to other receptors or proteins, partitioning into lipids or other things.

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Specific Binding

The proportion of radioligand that can be displaced by competitive ligands specific for the receptor.

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t_½

The biological half-life of a drug or radioligand in vitro or in vivo. In vitro, the t_½ of the effect of a drug is the time taken for the response to a drug to decline to half the original response. In radioligand binding, the t_½ can be used to measure the dissociation rate of a radioligand from its receptor, therefore it is the time taken for the amount of radioligand bound to the receptors to decline to half its original level. In vivo, t_½ refers to the metabolic half-life of a drug or radioligand, i.e. the time taken for the concentration of a drug in plasma to decline to half its original level.

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Time-of-flight mass spectrometry (TOFMS)

Time-of-flight mass spectrometry (TOFMS) is a method of mass spectrometry in which ions are accelerated by an electric field of known strength. This acceleration results in an ion having the same kinetic energy as any other ion that has the same charge. The velocity of the ion depends on the mass-to-charge ratio. The time that it subsequently takes for the particle to reach a detector at a known distance is measured. This time will depend on the mass-to-charge ratio of the particle (heavier particles reach lower speeds). From this time and the known experimental parameters one can find the mass-to-charge ratio of the ion.

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Time-resolved fluorescence (TRF)

relies on the use of very specific fluorescent molecules, called lanthanides, that have the unusual property of emitting over long periods of time (measured is milliseconds) after excitation, when most standard fluorescent dyes (e.g. fluorescein) emit within a few nanoseconds of being excited. As a result, it is possible to excite lanthanides using a pulsed light source (Xenon flash lamp or pulsed laser for example), and measure after the excitation pulse. This results in lower measurement backgrounds than in standard FI assays.

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Triple quadrupole mass spectrometer

a tandem mass spectrometer consisting of two quadrupole mass spectrometers in series, with a (non mass-resolving) radio frequency (RF) only quadrupole between them to act as a collision cell for collision-induced dissociation. The first (Q1) and third (Q3) quadrupoles serve as mass filters, whereas the middle (q2) quadrupole serves as a collision cell. This collision cell is an RF only quadrupole (non-mass filtering) using an inert gas such as Ar, He or N2 gas to provide collision-induced dissociation of a selected precursor ion that is selected in Q1. Subsequent fragments are passed through to Q3 where they may be filtered or scanned.

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XTT

(sodium 3´-[1-(phenylaminocarbonyl)- 3,4-tetrazolium]-bis (4-methoxy-6-nitro) benzene sulfonic acid hydrate).Colorimetric assay for the non-radioactive quantification of cell proliferation and viability. The assay is based on the cleavage of the yellow tetrazolium salt XTT to form an orange formazan dye by metabolic active cells.