Created by: Caty Chung, Nicolette Ross, Joan Glenny-Pescov, Jiaming Hu, Stephan Schurer*
Contact: Stephan Schurer stephan dot schurer at med dot miami dot edu
It is a measure of the number of dead cells in a culture well. We consider it as a subclass of 'percent inhibition', because cell death is induced by inhibition of vital cellular processes and percent cytotoxicity increases as the number of dead cells increases. It can be estimated in the compound treated wells in comparison to vehicle-treated control wells and is expressed as a percent. The compound treatment is preferably performed in a short window of time to avoid masking the effect due to cell proliferation. Compound cytotoxicity is an important parameter to measure when developing potential human therapeutics. Cytotoxicity is determined as a measure of radioisotope (3H thymidine or 51Cr) release, lactate dehydrogenase release from damaged cells, tetrazolium salt and alamar blue reduction, fluorescent dyes that selectively stain live or dead cells, and decrease in ATP content. ATP levels are detected using a luminescence based assay kit such as CellTiter-Glo (Promega). ATP values higher than controls indicate proliferation and cultures with ATP concentrations lower than controls indicate cytotoxicity. Percent cytotoxicity = 100-percent viability
They are used to express the binding interactions between labeled or unlabeled ligands with protein receptors and include Bmax, Kd, etc.
It is the amount of drug required to saturate a population of receptors and a measure of the number of receptors present in the sample. It is derived from Scatchard plot of binding data. It is analogous to Vmax in enzyme kinetics. The units of Bmax include cpm, sites/cell or fmol/mg. http://graphpad.com/curvefit/fitting_specific_binding_.htm
Kd – is the equilibrium dissociation constant for a drug. It describes the affinity between a ligand (L) (such as a drug) and a protein (P). Ligand-protein affinities are influenced by non-covalent intermolecular interactions between the two molecules such as hydrogen bonding, electrostatic interactions, hydrophobic and Van der Waals forces. Kd = ([P] [L]) / [PL] The dissociation constant has molar units (M), which corresponds to the concentration of ligand [L] at which the binding site on a particular protein is half occupied, i.e. the concentration of ligand, at which the concentration of protein with ligand bound [PL], equals the concentration of protein with no ligand bound [P]. The smaller the dissociation constant, the more tightly bound the ligand is, or the higher the affinity between ligand and protein. http://www.graphpad.com/curvefit/law_of_mass_action.htm
This refers to the effect of the perturbagen on the target of an assay, whether it brings about inhibition, activation, cytotoxicity, etc.
Percent increase or decrease of a predefined stimulus. Unit of Measure is always % when normalized to the dynamic range of the assay.
Data measuring the biological effect of a compound, e.g. % cell death, activation of reporter gene expression, inhibition of enzyme activity, etc.
In this assay, the binding of the ligand to a receptor is permanent and cannot be dissociated by changing the binding conditions such as buffer, salt concentration, etc.
In this assay, the interaction of the ligand with a receptor can be dissociated by changing the binding conditions, e.g. buffer, salt concentration, etc.
Increase of a predefined stimulus. Unit of Measure is always % when normalized to the dynamic range of the assay.
It is the toxic or cell-death inducing property of a perturbagen. Known cytotoxic agents mediate cell death commonly by necrosis, apoptosis, or autophagy. Cytotoxicity can be detected by measuring various aspects of the death process: e.g. membrane permeability, ATP concentration, DNA fragmentation, etc.
Reduction of a predefined stimulus. Unit of Measure is always % when normalized to the dynamic range of the assay.
Growth reduction of a predefined stimulus. Unit of Measure is always % when normalized to the dynamic range of the assay. As a measure of viable or proliferating cells, different researchers measure different parameters, namely, protein content (by sulforhodamine B staining followed by absorbance measurement), mitochondrial dehydrogenase activity (by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrasodium bromide, known as MTT staining followed by absorbance measurement), expression of proliferation associated antigens (by immunostaining for Ki-67), and ATP content (by using CellTiter-Glo reagent (Promega) followed by luminescence measurement.
% growth reduction of a predefined stimulus. Unit of Measure is always % when normalized to the dynamic range of the assay.
The concentration of a perturbagen used in an assay to elicit the biological effect or perturbation. This typically assumes uniform / equal distribution of the perturbagen / compound in the assay system (typically a screening well).
Endpoint action correlation describes weather a low or high endpoint value corresponds to low or high activity. Specifically if the endpoint value is positively or inversely correlated with the action that corresponds to the endpoint and which is specified as 'mode of action'. For example 'percent control' can be positively correlated with enzyme activity (remaining activity) and inversely correlated with the mode of action (function) inhibition depending on how the signal is normalized.
Percent control is the response relative to a reference state, typically to a high control. For example it can describe (remaining) activity of a kinase (or e.g. kinase bound to substrate). Percent control could also quantify an inhibitory action depending on control and assay method.
The endpoint is a quantitive or qualitative interpretable standardized representation of a perturbation (a change from a defined reference state of a "closed" model system) that is measured by the bioassay. An endpoint consists of a series of data points, one for each perturbing agent (screened entity) tested the assay.
It can refer to the screening concentration (for example in a primary assay) or it can be a concentration at which the perturbagen mediates a defined response, such as IC50 or EC50. It always has one value and a concentration unit.
Reporting the extent / magnitude of the perturbation (induced by the perturbagen) such as percent inhibition. Response-type endpoints would typically be obtained from a single concentration perturbagen measurement.
The effective concentration of a perturbagen, which produces 50% of the maximal possible response, which could mean either activation (EC50) or inhibition (IC50) for that perturbagen.
The effective concentration of a cytotoxic compound, which produces 50% of the maximum possible cell death for that compound. Although the cytotoxic compound induces cell death, we define CC50 as subclass of IC50, because critical cellular processes are inhibited and CC50 is often used as a more specific description of IC50 for cell toxicity assays. Compound cytotoxicity is an important parameter to measure when developing potential human therapeutics. Cytotoxicity can be determined for example as a measure of radioisotope (3H thymidine or 51Cr) release, lactate dehydrogenase release from damaged cells, tetrazolium salt and alamar blue reduction, fluorescent dyes that selectively stain live or dead cells, or decrease in ATP content. ATP levels are detected using a luminescence based assay kit such as CellTiter-Glo (Promega). ATP values higher than controls (untreated cells) indicate proliferation and cultures with ATP concentrations lower than controls indicate cytotoxicity.
The effective concentration of an agonist, which produces 50% of the maximum possible response for that agonist.
The effective concentration of a growth inhibitor, which produces 50% of the maximum possible response for that inhibitor. GI50 is calculated from [(Ti-Tz)/(C-Tz)] x 100 = 50, where Tz is absorbance at time zero, Ti is absorbance in the presence of test drug, and C is absorbance in the control (untreated cells). As a measure of viable or proliferating cells, different researchers measure different parameters, namely, protein content (by sulforhodamine B staining followed by absorbance measurement), mitochondrial dehydrogenase activity (by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrasodium bromide, known as MTT staining followed by absorbance measurement), expression of proliferation associated antigens (by immunostaining for Ki-67), and ATP content (by using CellTiter-Glo reagent (Promega) followed by luminescence measurement).
The effective concentration of an inhibitor, which produces 50% of the maximum possible response for that inhibitor.
The effective concentration of an inhibitor, which produces 80% of the maximum possible response for that inhibitor.
Ki is the equilibrium inhibitor dissociation constant, the concentration of the competing inhibitor that results in binding to half the enzymes sites at equilibrium in the absence of substrate or other competitors. The Cheng and Prusoff equation: Ki - (IC50) / ( 1+ ([L]/Kd)) relates IC50 to Ki under conditions of competitive binding; Kd equilibrium dissociation constant of the (labeled) ligand, [L] ligand concentration. The Cheng and Prusoff equation: Ki - (IC50) / ( 1+ ([S]/Km)) relates IC50 to Ki under conditions of competitive inhibition; Ki equilibrium enzyme inhibitor dissociation constant; Km Michaelis-Menton constant, [S] substrate concentration.
It is the ratio of biological activity in the presence of an exogenous substance to that in its absence. The fold change is useful when comparing test compounds evaluated across multiple functional assays because varying levels of efficacy can be observed amongst the different or same reference agonists.
TGI is total growth inhibition, which is the effective concentration of a growth inhibitor, which produces 0% relative growth for that inhibitor. Thus TGI signifies a cytostatic effect. tgi is calculated from [(Ti-Tz)/(C-Tz)] x 100 =0, where Ti = Tz and Tz is absorbance at time zero, Ti is absorbance in the presence of test drug, and C is absorbance in the control (untreated cells). As a measure of viable cells, different researchers measure different parameters, namely, protein content (by sulforhodamine B staining followed by absorbance measurement), mitochondrial dehydrogenase activity (by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrasodium bromide, known as MTT staining followed by absorbance measurement), and ATP content (by using CellTiter-Glo reagent (Promega) followed by luminescence measurement).
Absolute IC50 (calculated from the curve-fit function) is the concentration corresponding to exactly 50 percent inhibition. It is obtained from the curve fit function (back-calculated IC50) and can also be extrapolated. Commonly the relative IC50 is reported; however in cell proliferation assays absolute IC50 is often used. The absolute IC50 can be more reproducible.
The concentration of a test substance that produces an inhibitory effect corresponding to 50% of the activity of that particular substance (i.e. 50% of the difference between top and bottom of fitted curve). It can also be described as the concentration corresponding to the inflection point of the curve.
pIC50 is -log IC50, where IC50 is the effective concentration of an inhibitor, which produces 50% of the maximum possible response for that inhibitor.
Percent increase of a measureable response relative to some baseline. Unit of Measure is always % when normalized to the dynamic range of the assay. Percent activity measures the increased activity vs. an unperturbed state, i.e. percent activation := percent activity - 100; e.g. an agonist that results in twice the activity would have percent activity = 200 and percent activation = 100.
Percent decrease of a measureable response as a consequence of compound treatment. Unit of Measure is always % when normalized to the dynamic range of the assay. Percent inhibition is expressed relative to a positive control (which results in total inhibition).
It is a measure of living cells in a culture well. Unit of Measure is always % when normalized to the dynamic range of the assay. It can be estimated in the compound treated wells in comparison to vehicle-treated control wells and is expressed as a percent. Viability is determined by measuring tetrazolium salt and alamar blue reduction, staining with selective fluorescent dyes, or ATP content. ATP levels are detected using a luminescence based assay kit such as CellTiter-Glo (Promega). ATP values higher than controls indicate proliferation and cultures with ATP concentrations lower than controls indicates cytotoxicity. Percent viability = 100-percent cytotoxicity
signal increase corresponding to activation
Increase in perturbation (reported by the endpoint mode of action, activation) is correlated to increase in signal.
signal decrease corresponding to inhibition
Increase in perturbation (reported by the endpoint mode of action, inhibition) is correlated to decrease in signal.
50% increase of a predefined stimulus. Unit of Measure is always % when normalized to the dynamic range of the assay.
50% reduction of a predefined stimulus. Unit of Measure is always % when normalized to the dynamic range of the assay.
80% reduction of a predefined stimulus. Unit of Measure is always % when normalized to the dynamic range of the assay.
Assay has 50% living cells. Unit of Measure is always % when normalized to the dynamic range of the assay.
The ratio of biological activity in the presence of an exogenous substance to that in its absence. This result type is used exclusively with single point (screening concentration) assays.
The ratio of biological activity in the absence of an exogenous substance to that in its presence. This result type is used exclusively with single point (screening concentration) assays.
The B score is an analog of the Z score, but is more resistant to the presence of outliers and to differences in the measurement error distributions of the compounds. It is calculated by first computing a two-way median to account for row and column effects of the plate, which is then divided by their median absolute deviation to standardize for plate-to-plate variability.
Random and systematic error can induce either underestimation (false negatives) or overestimation (false positives) of measured signals. Z score indicates how many standard deviations an observation is above or below the mean. For calculating this, the average of the plate values is subtracted from individual raw values and the difference divided by the standard deviation estimated from all measurements of the plate.
Has curve fit parameters, curve fit method, properties like Hill coefficient, concentration range, and measurement repetition. It involves capturing the trend in the data by assigning a single function across the entire range. The goal of curve fitting is to find the parameter values that most closely match the data.
The Hill equation is commonly used to estimate the number of ligand molecules that are required to bind to a receptor to produce a functional effect. The Hill coefficient can be considered as an interaction coefficient, reflecting the extent of cooperativity among multiple ligand binding sites.
An assay based on the competition between a labeled and an unlabeled ligand in the reaction with a receptor binding agent (e.g. antibody, receptor, transport protein).
Non-competitive ligands interact with receptors at sites distinct from the competitive ligand binding pocket, conferring multiple modes of action.
It identifies whether the data has been normalized (by Z and Z' factors, signal to background, signal to noise, and coefficient of variance), or if it was an immediate readout obtained from a HTS assay.
Data can be normalized by Z and Z' factors, signal to background, signal to noise, and coefficient of variance. Plate based normalization is usually based on controls. In the absence of controls, the Z-score can be used to normalize the data by plate.
The readout obtained from a HTS assay which includes measurements from the positive and negative control wells in each plate. This is the data that needs to be processed.
Concepts describing the type of perturbagen interaction with the receptor.
The concentration of substrate at ½ Vmax, according to the Henri-Michaelis-Menten kinetic model.
The off-rate associated with the release of inhibitor from an enzyme-inhibitor complex.
The on-rate associated with the formation of an enzyme-inhibitor complex.
Turnover number representing the maximum number of substrate molecules converted to products per active site per unit time.
A competitive inhibitor binds only to free enzyme. Often this binding event occurs on the active site of the target, precisely where substrate also binds. It will raise the apparent KM value for its substrate with no change in the apparent Vmax value. As a result, competitive inhibition can be overcome, observed by an increase in the apparent KI value, at higher concentrations of substrate.
An uncompetitive inhibitor binds exclusively to the enzyme-substrate complex yielding an inactive enzyme-substrate-inhibitor complex. When encountered, the apparent Vmax value and the apparent KM value should both decrease.
A noncompetitive inhibitor binds equally well to both free enzyme and the enzyme-substrate complex. These binding events occur exclusively at a site distinct from the precise active site occupied by substrate. It will lower the apparent Vmax value, yet there is no effect on the apparent KM value for its substrate. Essentially, the KI of the inhibitor does not change as a function of the substrate concentration.
Describe kinetics of enzyme-catalyzed reactions. It includes the enzyme kinetic constants namely, Km and Vmax, which help to model the time course of disappearance of substrate and the production of product.
Partial inhibition results from the formation of an enzyme-substrate-inhibitor complex that can generate product with less efficiency than the enzyme-substrate complex.
An allosteric effector operates to enhance active site substrate affinity and/or catalysis. An allosteric inhibitor decreases activity by binding to an allosteric site, other than or in addition to the active site on the target. This interaction is characterized by a conformational change in the target enzyme that is required for inhibition.
In this type of inhibition, the population of free, soluble inhibitor is significantly depleted by the formation of the enzyme-inhibitor or enzyme-substrate-inhibitor complex. While tight-binding inhibitors can bind to the target enzyme in a competitive, noncompetitive, or uncompetitive manner with respect to substrate binding, they can display noncompetitive phenotypes.
Time-dependent inhibitors bind slowly to the enzyme on the time scale of enzymatic turnover, and thus display a change in initial velocity with time. This has the effect of slowing the observed onset of inhibition.
It is the trend of measured readout signal, whether it increases or decreases in perturbagen treated wells, as compared to the untreated or carrier-treated wells and the endpoint mode of action of an assay.
These experiments measure specific radioligand binding at equilibrium at various concentrations of the radioligand.
Tm is defined as the midpoint temperatuere of the protein unfolding transition. It is determined by generating a thermal denaturation curve for the target molecule and taking the midpoint temperature between folding and unfolding state of the protein. In nucleic acid thermodynamics, it is the temperature at which 50% of the DNA strands and its perfect complement are in duplex.
Raw or qualitative data are reported as endpoints in an assay, e.g., luminescence counts, fluorescence intensity, etc.
The types of endpoints that report changes in temperature as a measure of a biological reaction, e.g. tm.
Vmax is defined as the maximum initial velocity of an enzyme catalyzed reaction under the given conditions, and it is measured in units of quantity of substrate transformed per unit time for a given concentration of enzyme.
This endpoint type describes the bonding affinity between two molecules at equilibrium, e.g., drug-receptor interaction.
The perturbagen mediated 50% of cells to die in an assay.
The effective concentration of an agonist, which produces 30% of the maximum possible response for that agonist.
It is the term that describes an endpoint or result of a bioassay, which is deposited at PubChem.
A mathematical model / equation to which the data is fitted (using the curve fit method / algorithm).
The maximum response that can be achieved with the perturbagen as percentage of the positive control.
Maximum inhibition of an antagonist or inhibitor (relative an efficacious positive control)
The maximum percent activation of an agonist
Percent activity is the response relative to an unperturbed state; in case of inhibition the interpretation is that of remaining activity, i.e. percent inhibition := 100 - percent activity.
IRI prefix change from BAO_02000 to BAO_00012 in January 2017
The percentage of cells in an assay that show the hallmarks of 'programmed cell death' or apoptosis, namely, membrane asymmetry, caspase activation, nuclear fragmentation, etc.
This represents the percentage of cells in a cell population that are in the M phase of the cell cycle. The cells in this phase can be detected using various markers, one of which is the characteristic phosphorylation of certain proteins that stain positive with MPM2 antibody.
'has marker' some (not ('DEVD-NucView 488' or 'LysoTracker Red' or 'Hoechst 33342'))
This represents the percentage of cells in a cell population that are preparing for cell division and that exist in either G1, S or G2 phases of the cell cycle. This is calculated by subtracting from the total cell number, the number of cells in the M phase, apoptotic and dead cells in an assay plate.
This represents the percentage of cells in a cell population that have undergone the S phase (completed DNA replication) in preparation for mitosis, as indicated by staining positive for EdU.
'has marker' some ('Hoechst 33342' and not ('DEVD-NucView 488' or 'LysoTracker Red') )
The percentage of cells in an assay that are no longer alive (viable), and show the characteristic features, such as staining with propidium iodide, blurry staining with DAPI, etc.
This represents the percentage of cells in a cell population that have undergone the DNA synthesis in the S phase as indicated by staining positive for EdU, but have not undergone the M phase as they stained negative for MDM2. In other words, these cells were arrested in the G2/M cell cycle check-points after treatment with the respective perturbagen in the assay.
This represents the percentage of cells in a cell population that have completed the mitotic cell cycle, and that have stained positive for both S phase (EdU) and M phase (MDM2) markers. In other words, these cells were not arrested in any of the cell cycle check-points after treatment with the respective perturbagen in the assay.
An endpoint defined by a length in time at which a desired effect or observation occurs.
Half-life of drug is the time taken for the concentration of the drug to decrease by half.
An endpoint defined an effect seen in animals at a particular dosage, typically defined as a ratio of treatment to animal mass (e.g., mg/kg).
The median lethal dose is the dose required to kill (produce lethality) in 50% of tested population.
An endpoint derived from calculus-based analysis of graphical measures.
The maximal concentration of a drug achieved following administration (maximum point of a concentration-time curve).
It is the area under the drug concentration-time curve (AUC) following a single dose or at steady state, and is expressed as weight*time/volume.
Slope is described as the ratio of the change in y-axis divided by the change in x-axis between two points on a line or a curve. m= y2-y1 / x2-x1
Endpoint values derived from an exponential growth curve, such as in a PCR reaction.
Crossing point- In an exponential amplification curve (i.e., qPCR amplification) the value in number of amplification cycles at which the signal enters log phase, as determined by the maximal second derivative of the curve.
Quantificatoin cycle; general term, whether defined by Cp or Ct, for the value of interest determined from an exponential amplification curve (such as number of cycles in a PCR reaction).
Crossing threshold; in an exponential amplification curve (i.e., qPCR amplification) the value in number of amplification cycles at which the signal crosses a defined threshold.
Endpoint values determined by a statistical measurement of the signal relative to the populations of signals observed.
The number of median absolute deviations outside the median of control or compound wells.
A measurement of an intrinsic property of a molecular entity.
Logarithm (log10) of the Distribution Coefficient, D, which is defined as the ratio of concentrations of a small molecule / drug distributed between octanol and water. LogD refers to the distribution of all forms of a compound between the two immiscible phases at equilibrium. It depends on pH of the aqueous phase, which is buffered to a specific value. A larger logD means the compound / drug is more hydrophobic (greasy) and a lower logD corresponds to better solubility in water.
Logarithm (log10) of the Partition Coefficient, P, which is defined as ratio of concentrations of a small molecule / drug distributed in octanol and water. LogP refers to the distribution of un-ionized (neutral species of) compound between the two immiscible phases at equilibrium; the pH is adjusted such that the major microspecies is the un-ionized form. A larger logP means the compound / drug is more hydrophobic (greasy) and a lower logP corresponds to better solubility in water.
pKa is the negative log10 of the acid dissociation constant (Ka) of a molecule. Ka is the equilibrium constant for dissociation of the protonated base (acid) into the free base and a proton (hydromium ion).
Percent purity is the ratio of mass of pure compound to the actual mass of the available/vendor supplied compound, multiplied by 100. The majority of compounds and elemental substances are only available with a larger or smaller amount of impurities, which contribute to the mass of the impure compound.
apical‑to‑basolateral permeability (A > B)
Measurement of compound transport across a polarized epithelial monolayer from the apical to the basolateral side, typically reported as Papp (cm/s)
basolateral‑to‑apical permeability (B > A)
Measurement of compound transport across a polarized epithelial monolayer from the basolateral to the apical side, typically reported as Papp (cm/s)
The ability of a chemical substance to dissolve in a solid, liquid, or gaseous solvent to form a homogeneous solution. The solubility of a given substance is dependent on the solvent used, as well as on temperature and pressure.
An endpoint defined by a set of measurements from a multiparametric assay. The set of measurements may be aggregated to an overall profile score, weighting each measurment in the profile relative to a desired outcome.
The effective concentration of an inhibitor, which produces 90% of the maximum possible response for that inhibitor.
It is 50% lethal concentration (the concentration that kills 50% of treated cells).
The lowest concentration of an inhibitor (antimicrobial agent) required to inhibit the growth of a microorganism.
It is a measure of the amount of radioligand that binds to its receptor in a competitive binding assay. It is the ratio of the bound to the total bound, where bound refers to the reading obtained from a binding reaction involving radioligand, receptor and a cold competitor ligand, while total bound is the reading obtained in the absence of any added competitor.
In a purification assay, percent recovery is the ratio of mass of the entity obtained after the affinity purification to the mass of the unpurified entity originally added in the assay, multiplied by 100.
signal decrease corresponding to activation
Increase in perturbation (reported by the endpoint mode of action, activation) is correlated to decrease in signal.
signal increase corresponding to inhibition
Increase in perturbation (reported by the endpoint mode of action, inhibition) is correlated to increase in signal.
pEC50 is -logEC50, where EC50 is the effective concentration of an agonist, which produces 50% of the maximum possible response for that agonist.
90% reduction of a predefined stimulus. Unit of Measure is always % when normalized to the dynamic range of the assay.
Measured / detected concentration of the perturbagen / compound in the assay or a subsystem (locally) in the assay. For example measured absolute concentration in the brain. This is in contrast to screening concentration, which is the (final assumed) concentration of a compound added to the assay.
Clearance is defined as the volume of plasma cleared of a drug over a specified time period.
The time taken for the concentration of the drug in a particular tissue or blood plasma to decrease by half.
The time taken for the concentration of the drug in an in-vitro system (e.g., liver microsomes) to decrease by half.
The area under the drug concentration-time curve following an oral dose.
The area under the drug concentration-time curve following an intravenous dose.
Clearance of the drug due to renal excretion.
Clearance of the drug due to hepatic enzyme activity and biliary excretion.
The ability of a chemical substance to dissolve in water.
apparent permeability coefficient (Papp)
A rate measure of how quickly a compound crosses a biological or artificial membrane, expressed in centimeters per second (cm/s), calculated from the transport rate normalized to membrane area and donor concentration
The concentration of compound that elicits an extension of circadian period length by 5 hours.
The compound concentration at which the fitted curve passes activity threshold 1000.
The compound concentration at which the fitted curve passes activity threshold 10.
The compound concentration at which the fitted curve passes activity threshold 26.
The compound concentration at which the fitted curve passes activity threshold 35.
The compound concentration at which the fitted curve passes activity threshold 40.
The compound concentration at which the fitted curve passes activity threshold 500.
The compound concentration whereupon perceived activity reaches the maximum value observed (with a positive control).
The compound concentration whereupon perceived activity (change in Tm) reaches the maximum value observed (with a positive control).
The agonist concentration whereupon perceived activity reaches the maximum value observed (with a positive control).
The compound concentration whereupon perceived activity (fold increase) reaches the maximum value observed (with a positive control).
The compound concentration whereupon perceived activity (percent inhibition) reaches the maximum value observed (with a positive control).
Small molecule that can bind to sites other than the receptor active site and affect activity of the receptor.
The lowest concentration of an antimicrobial agent required to inhibit the growth of 50% of organisms.
It is the dose that produces an effect in 50% of the tested population, or the dose required to produce half-maximal response.
The time required for a drug to reach maximum concentration in plasma (Cmax) following administration.
The negative logarithm (log10) of the molar concentration of antagonist which requires the agonist concentration to be doubled in order to achieve the original response.
In the disk diffusion susceptibility test, the zone of inhibition is the clear area surrounding an antimicrobial disk where bacterial growth is inhibited, usually measured as a diameter. The diameter of the zone of inhibition is proportional to the susceptibility of the organism tested.
Volume of Distribution is defined as the theoretical volume in which the total drug administered would need to be distributed to produce the concentration that is observed in plasma. Measured as the total amount of drug in the body divided by the concentration of drug in the plasma.
The theoretical volume in which the total drug administered would need to be distributed to produce the concentration that is observed in plasma at steady state i.e when the rate of change of amount of drug in the body is zero. VdSS is proportional to the amount of drug in the body versus the plasma concentration of the drug at steady state (pseudo-equilibrium).
Bioavailability is a subcategory of absorption and is the fraction (or %) of unchanged drug that reaches the systemic circulation, thereby accessing the site of action. It is usually determined as the ratio of AUC(oral)/AUC(iv).
The effective concentration of an inhibitor, which produces 20% of the maximum possible response for that inhibitor.
The effective concentration of an inhibitor, which produces 25% of the maximum possible response for that inhibitor.
The effective concentration of an inhibitor, which produces 30% of the maximum possible response for that inhibitor.
fragments per kilobase of exon per million mapped reads
The concentration of compound required to kill 50% of a cell population (i.e., 50% inhibitory concentration in a cytotoxicity assay).
50% Tissue Culture Infective Dose (TCID50) is the measure of infectious virus titer. This endpoint dilution assay quantifies the amount of virus required to kill 50% of infected hosts or to produce a cytopathic effect in 50% of inoculated tissue culture cells.
Any result reported as a simple binary assessment, such as 'active/ inactive', 'true/ false', etc.
The Transfluor assay employs a a beta-arrestin-GFP fusion protein to detect activation of GPCRs: Upon ligand binding the GPCR, cytosolic arrestin-GFP quickly translocates to the cell membrane and then to endocytic vesicles, where it 'clusters' and can be detected by fluorescent image analysis. (Developed / commercialized by Norak, then Molecular Devices)
perturbagen / positive control ratio endpoint
The property values are divided by the average value for the positive control wells and multiplied by 100: X' = 100*(X/PosAvg)
Maximum induction effect (dimensionless)
This is a measurement of how strongly a chemical species attenuates light at a given wavelength. Common units are L/(mol*cm).
The fraction of compound that does not bind to substrate (e.x. plasma proteins)
A ratio endpoint is the relative relation between two quantitative results (a/b)
The ratio of the concentration of molecule in whole blood (i.e. contains both red blood cells and plasma) to the concentration of molecule in plasma, namely CB/CP.
A categorical endpoint is any result that can take one of a limited number of possible values.
Branch of endpoints reported by electrical measurements.
https://github.com/Scientist328455 https://github.com/BioAssayOntology/BAO/issues/62
Electrical current density is a measure of the density of flow of electric charge; it is the electric current per unit area of cross section. Electric current density is a vector-valued quantity.
The fraction of the bioavailable dose which has been metabolized.
Kp values are defined as the ratio of total concentration of compound in the tissue to total concentration of compound in the plasma at steady state.
A physiological endpoint is a response from either an isolated tissue or organ (i.e. smooth muscle contraction, urine output ) that also serves as an observed enpoint for a bioassay.
Opioid Drug Ontology (ODO) (https://opioiddrugontology.github.io/) - Nicolette Ross (https://orcid.org/0000-0002-4677-2140)
[DefinitionUpdate: BAO v 2.8.15 (May 2025)] [NodeCreation: BAO v 2.8.13 (March 2025)]
Ratio of functional bias calculated for a test agonist compound/the measured functional bias of a reference agonist compound allowing for normalization within a single assay (parameter: ΔLog τ/KA).
The bias factor, defined as 10ˆΔΔLogτ/KA(assay1-assay2), quantifies the difference in relative agonist activity between two assays. A higher bias factor indicates a greater distinction in the agonist's performance across the two assays relative to the reference agonist.