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Biopharmaceutical Assays & Screening glossary & taxonomy
Evolving  terminologies for Emerging Technologies
Comments? Questions? Revisions?
Mary Chitty MSLS
Last revised January 06, 2020

SCOPE NOTE One of the first steps in drug development and toxicity testing is creating test systems (assays) on which to evaluate the effects of chemical compounds on cellular, molecular or biochemical processes of interest. Investigators from the biomedical research community submit ideas for assays to NCATS scientists, who help enhance them for high-throughput small molecule screening. The results of these screens, called probes, can help researchers further explore protein and cell functions, biological processes, and effects of environmental chemicals that are relevant to human health and disease. In addition, these probes can become potential therapeutic candidates in the drug development pipeline.  National Center for Advancing Translational Sciences, NIH

Related glossaries include  Biologics: Antibodies & vaccines    Drug Discovery & development  Drug safety   Drug Targets   Regulatory
Chemistry Combinatorial libraries & synthesis  
Technologies:  Cell & tissue technologies   Labels, Signaling & Detection  MicroarraysMolecular Imaging
Chemistry term index   Drug discovery term index   Informatics term index   Technologies term index    Biology term index  

96, 384, 1536, 3456 well plates: See under microtiter/ microtitre plates 

adventitious agents: tests performed during vaccine manufacture are designed to detect possible contaminants, including viruses and bacteria that can be inadvertently introduced into the process stream. These unwanted pathogens are referred to as adventitious agents. A major potential source of adventitious agents is the cell substrates used to produce the vaccines. Cell substrates are the living cells of mammals, birds, or insects that serve as tiny biological factories used to make viral products. There are already many types of tests developed that can detect adventitious agents; however, some agents may escape detection by these tests due to limitations in test sensitivity and specificity. To address this issue we are also engaged in efforts to develop new, more sensitive and specific detection methods involving use of novel concentration and amplification techniques and high throughput genetic sequencing. FDA, CBER, New Ways to Improve Testing of Vaccines for Purity and Safety 2018

antibody assays:   include ELISAs, western blots, immunohistochemistry, immunocytochemistry, flow cytometry and FACs, immunoprecipitation, ELISPOT

assay A set of operations having the object of determining the value of a quantity. In analytical chemistry, this term is synonymous with measurement. IUPAC Compendium

Generically a bioassay where biological activity is derived; associated with a bioactive effector molecule. Within the screening discipline, an assay will probably be robust enough and have the capacity to enable testing of up to 10,000 samples, generally with limited chemical diversity. [The precise definition of the following terms varies widely between drug discovery companies. The meanings given here are aligned with the use of the terms within the lead discovery function at Glaxo Wellcome.  Martin J. Valler,  Darren Green  "Diversity screening versus focussed screening in drug discovery" Drug Discovery Today 5(7): July 2000] 

It could be argued that the rate-limiting factor in biology at the moment is not the speed of assays but devising the assays themselves; that is, establishing new and imaginative ways of measuring biological activity in vivo or in vitro and then using genetics or biochemistry to use the players - Kim Nasmyth ["Opinions on the potential of yeast biochemical genomics" in "The awesome power of yeast biochemical genomics" Trends in Genetics 16 (2): 49- 51 Feb. 2000  Narrower terms:  Enzyme- Linked Immunosorbent Assay ELISA, force assays, primary assays, secondary and tertiary assays; bioassay, cell assays, high content assays, homogeneous assays, immunoassay, quantitative assays, sandwich assay, single cell metabolism and enzyme assays, "smart" assays;  primary assays, secondary assays; Related terms: screening

assay validation: Experiments conducted to verify that the output measurements of the assay are consistently reflective of the activity against the target. Note: Results are compared internally over multiple runs and externally (when available) to existing literature parameters such as Kd, Ki, Km, or EC50. IUPAC Glossary of Biomolecular Screening

bead assays: See under multiplex assays

binding assays: Assay in which the specific physical association or interaction between two molecules (e.g., ligand–receptor, antibody–antigen, protein–protein, ligand–transport protein) is measured. Note: The assay can be homogeneous or heterogeneous, competitive or noncompetitive, and may be run at equilibrium or in kinetic mode. Appropriate assay controls and/or standard reagents are often needed to determine the specific binding in contrast to nonspecific adsorption processes. IUPAC Biomolecular Screening 

bioassay:  A procedure for determining the concentration or biological activity of a substance (e.g. vitamin, hormone, plant growth factor, antibiotic, enzyme) by measuring its effect on an organism or tissue compared with a standard preparation. IUPAC Medicinal Chemistry

A bioassay is a single step within a microarray experiment. There are 3 types of bioassays. A physical bioassay correspond to wet- lab microarray experimental step. A measured bioassay corresponds to a situation after feature extraction has been performed. A derived bioassay corresponds to data processing experimental steps. MGED "bioassay"

Bioassays for Biologics  Case Studies Demonstrating Successful Bioassay Development  May 7-8, 2020 • Boston, MA Program |  New therapeutic modalities, including cell & gene therapies, immunotherapies, and antibody therapies, continue to push the limit on bioassay development and implementation. New formats present challenges including determining what reference materials to use and how to validate the assay. Standards are advancing, but questions remain around the regulatory framework for assays.

Bioassays ontology:  describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. 
See related biological assay

biochemical assays: Measure how compounds bind to targeted molecules (such as receptors) or how compounds inhibit enzyme activities.

biological assay: A method of measuring the effects of a biologically active substance using an intermediate in vivo or in vitro tissue or cell model under controlled conditions. It includes virulence studies in animal fetuses in utero, mouse convulsion bioassay of insulin, quantitation of tumor-initiator systems in mouse skin, calculation of potentiating effects of a hormonal factor in an isolated strip of contracting stomach muscle, etc. MeSH 1999 Annotation assays using living-matter intermediate; check text: not all "bioassays" are MeSH term BIOLOGICAL ASSAY

biomolecular screening:  The term "biomolecular screening" became widely used in the late 1980's to broadly describe a new and rapidly adopted process for lead identification in drug discovery.  This new process involved screening natural product extracts and/or amassed compound collections, typically from pharmaceutical companies, in a random, unbiased manner to identify novel modulators of biological targets ... The screens encompassed bioassays that could be cell-based or purely biochemical in nature, and the need to screen increasing numbers of samples as time progressed, fostered the development of many new assay formats. IUPAC Biomolecular Screening glossary

cell assays, cellular assays: Cell biology is also looking less traditional these days. Companies ... have developed live cell assays that fully automate sample handling and quantify cellular characteristics such as motility, proliferation and morphology. The ability to track the behavior of individual cells over time permits data gathering on functional behavior not available in any other kind of assay. This functional assay technology is amenable to high throughput analysis, and therefore can occupy a niche complementary to many proteomic technologies focused on identification of potential therapeutic targets. 

Can be used for drug screening ... some companies are using such assays to gain insights about target function.... assays [can also be used] to get detailed functional information   Related term: Microarrays: phenotypic microarray Narrower term: live cell assays

cell-based assays: are often used for screening collections of compounds to determine if the test molecules have effects on cell proliferation or show direct cytotoxic effects that eventually lead to cell death. Cell-based assays also are widely used for measuring receptor binding and a variety of signal transduction events that may involve the expression of genetic reporters, trafficking of cellular components, or monitoring organelle function. Regardless of the type of cell-based assay being used, it is important to know how many viable cells are remaining at the end of the experiment. There are a variety of assay methods that can be used to estimate the number of viable eukaryotic cells. This chapter will provide an overview of some of the major methods used in multi-well formats where data are recorded using a plate reader. … This chapter describes assays where data are recorded using a plate-reader; it does not cover assay methods designed for flow cytometry or high content imaging. Riss TL, Moravec RA, Niles AL, et al. Cell Viability Assays. 2013 May 1 [Updated 2016 Jul 1]. In: Sittampalam GS, Coussens NP, Brimacombe K, et al., editors. Assay Guidance Manual [Internet]. Bethesda (MD): Eli Lilly & Company and the National Center for Advancing Translational Sciences; 2004.  
Narrower term: high throughput cell based assays  Related terms: cell assays, cellular assays, cytotoxicity assay, chemotaxis assay, high-content screening assay.

competitive binding assay:  Molecular assay based on the competition between a ligand and a reference ligand for the same binding site on a receptor (e.g., antibody, transport protein). Note 1: Depending on the technology used to monitor the interaction, the reference ligand and/or the receptor can be labeled with a probe. Very rarely, and mostly outside the field of screening, neither is labeled and the interaction is assessed, for example, by mass determination of the complex. Note 2: Former definition of competition between labeled and non-labeled ligands is obsolete.  IUPAC Biomolecular Screening Glossary

competitive immunoassays: In a competitive immunoassay, the antigen in the unknown sample competes with labeled antigen to bind with antibodies. The amount of labeled antigen bound to the antibody site is then measured. In this method, the response will be inversely related to the concentration of antigen in the unknown. This is because the greater the response, the less antigen in the unknown was available to compete with the labeled antigen. Wikipedia  accessed Feb 25 2011  Broader term: immunoassay; Related term: competitive PCR

compound validation: A process to quickly determine whether a molecule identified in a screen or assay will eventually lead to a drug. If you look at the costs of developing compounds into drugs, the most costly failures result from toxicity or pharmacokinetic liabilities rather than from their failure to act on the target.  Related terms: Drug Targets

Conformation-Dependent Immunoassays CDI: A technique for detecting prions in tissue, developed in recent years by UCSF scientists, is significantly more sensitive than the diagnostic procedures currently used to detect the lethal particles in samples of brain tissue from patients, according to a study performed by a UCSF team.  Diagnosis of prions in patients should utilize novel strategy, conformation-dependent immunoassay  Medical News 22. February 2005 05:36 

counterscreen(s):  A screen performed in parallel with or after the primary screen. The assay used in the counter-screen is developed to identify compounds that have the potential to interfere with the assay used in the primary screen (the primary assay). Counter-screens can also be used to eliminate compounds that possess undesirable properties, for example, a counter-screen for cytotoxicity ().   Early Drug Discovery and Development Guidelines: For Academic Researchers, Collaborators, and Start-up Companies, published 2012 last updated 2016, Assay Guidance Manual NCBI Bookshelf

Screen in which test samples are assessed against a target for unwanted activity. Note: This target may or may not be structurally or functionally related to the intended target.  IUPAC Biomolecular Screening Glossary

Directed Evolution-Based Drug Discovery DNA Encoded Libraries and Other Diversity Oriented Platforms APRIL 9-10, 2019 San Diego CA Directed evolution approaches for drug discovery use genetic strategies (DNA-encoded, RNA-encoded or phage-based) to create very large but specific libraries of molecules whose amplification is driven by the target of interest. The theory was established decades ago but recently applications in early stage drug discovery have become more widespread. A few drug candidates arising from directed evolution campaigns are now in clinical trials. A bottleneck however of these diversity-oriented strategies is figuring out which hits to focus on from the many hits that are produced by these approaches.

diversity screening: The drivers behind the current ethos of large- scale diversity HTS are rooted in the desire to build an improved hit identification process, and are based on the simple model of testing everything. The key activity over the past five or so years has been scaling: taking the existing model and increasing capacity by application of technology. Martin J. Valler,  Darren Green  "Diversity screening versus focussed screening in drug discovery " Drug Discovery Today 5 (7) : July 2000 

end-point assay: (in biomolecular screening) Kinetic assay run for a set constant incubation time. Typically, at the end of the set incubation time, a reagent that stops the reaction is added to allow postponed measurement of the signal  IUPAC Biomolecular Screening Glossary   See also equilibrium assay, kinetic assay.

enzyme assays: Methods used to measure the relative activity of a specific enzyme or its concentration in solution. Typically an enzyme substrate is added to a buffer solution containing enzyme and the rate of conversion of substrate to product is measured under controlled conditions. Many classical enzymatic assay methods involve the use of synthetic colorimetric substrates and measuring the reaction rates using a spectrophotometer. MeSH 2010

Enzyme-Linked Immunosorbent Assay ELISA: An immunoassay utilizing an antibody labeled with an enzyme marker such as horseradish peroxidase. While either the enzyme or the antibody is bound to an immunosorbent substrate, they both retain their biologic activity; the change in enzyme activity as a result of the enzyme- antibody- antigen reaction is proportional to the concentration of the antigen and can be measured spectrophotometrically or with the naked eye. Many variations of the method have been developed. MeSH, 1986

(ELISA or EIA) Heterogeneous assay in which an antibody linked to an enzyme is used to detect the quantity of antigen present in a sample. Note: After binding of the enzyme-linked antibody to the antigen, either directly or indirectly via a second antibody, a subsequent reaction of the enzyme with a substrate yields a chromogenic or fluorogenic product that produces an amplified signal proportional to the concentration of the antigen.   IUPAC Biomolecular Screening Glossary

enzyme linked immunospot assay: A method of detection of the number of cells in a sample secreting a specific molecule. With this method a population of cells are plated over top of the immunosorbent substrate that captures the secreted molecules. MeSH 2011

equilibrium assay: Assay in which there is sufficient incubation time for the plateau phase of the signal to be reached and equilibrium has been established between the reactants. Note: At this point, the signal is time-independent. IUPAC Biomolecular Screening Glossary

focussed screening: Focussed screening is now well established as a successful hit generation strategy. With focussed screening, it should also be possible to use an assay that is more appropriate, rather than one that works well at a large scale.  Martin J. Valler,  Darren Green  "diversity screening versus focussed screening in drug discovery " Drug Discovery Today 5 (7): July 2000 

forward pharmacology: In the field of drug discovery, classical pharmacology,[1] also known as forward pharmacology,[2][3][4] or phenotypic drug discovery (PDD),[5] relies on phenotypic screening (screening in intact cells or whole organisms) of chemical libraries of synthetic small molecules, natural products or extracts to identify substances that have a desirable therapeutic effect. Using the techniques of medicinal chemistry, the potency, selectivity, and other properties of these screening hits are optimized to produce candidate drugs. Wikipedia accessed 2018 Feb 26

Fragment-Based Drug Discovery From Hits to Leads and Lessons Learned APRIL 9-10, 2019 san Diego CA  Program   Fragment-based drug discovery (FBDD) has proven to be a successful approach for finding new drug compounds, especially against difficult targets such as intracellular protein-protein interactions (PPIs). Quite a few drugs on the market today can trace their origins to hits from fragment-based library screening campaigns. Now that FBDD has been folded into many early drug discovery departments, questions such as how to merge hits arising from fragment-based screens with hits from traditional high throughput screening methods are more frequent. Plus, the challenge of growing fragment hits into drug leads still remains, especially when the fragment and target do not have co-crystal structures to guide ligand design.

functional bioassays:  Here, the concept of an array of 'functional' bioassays is presented which has ultimately been developed from the classical tool of mode of action diagnosis by symptoms. These bioassays are designed to differentiate between the distinct responses of the multiple organization units (plant, tissue, meristematic cell, organelle), developmental stages, types of metabolism (phototrophic, heterotrophic) and physiological processes in the plant organism. The response pattern to a herbicide can be viewed as the end result of changes induced in the molecular and biochemical process chain and should be diagnostic of its physiological mode of action.  K. Grossmann, What it takes to get a herbicide's mode of action. Physionomics, a classical approach in a new complexion, Pest Manag Sci.  Jan 20, 2005  Related term: physionomics 

heterogeneous assay: One or more assay components are present in solid phase at time detection. (e.g.: SPA, cells or IMAP). NIH Chemical Genomics Center Assay Guidance Glossary

High Content Analysis:
   June 20-21, 2018 Boston, MA Program |
High-Content Analysis

High-throughput screening (HTS), used for the en masse discovery of compounds that interact with molecular drug targets, provides many more hits than viable drug candidates. In the last decade, HCS (high-content screening), based largely on automated imaging technology, has come to provide a form of secondary screening in which hits can be tested efficiently for their effects on cells. Applications of HCS have diversified into what is now called HCA (high-content analysis), a more generalized term that covers areas such as target identification, pathway analysis, mechanism of action verification, and cell biology research in general. Focuses on the applications, technology and market aspects of high-content analysis (HCA)—a field that originated when automated microscopic imaging technology joined with the high-throughput screening paradigm that signified the birth of “industrialized drug discovery.”

The terms HCS and HCA are sometimes used interchangeably, although purists reserve the former for screening of compound libraries and the latter for more generalized cell biology experiments. A common definition for the two terms encompasses the equipment and software for automated screening and analysis of cells for functional and structural changes resulting from some perturbation. Other definitions stress the multiplex nature of the analysis, which provides the richness of data that justifies the high-content designation. Yet others stress the quantitative nature of the approach; the fortuitous combination of automated microscopy, cytochemistry, and informatics; and access to subcellular information on phenotype, morphology, spatial distribution, and accumulation of proteins in cell compartment   Although applications of HCA are highly diverse, they are conveniently and adequately classified into cell signaling, cell and organism physiology, toxicology, and target identification and validation. HCS essentially originated with cell signaling studies, which are of key importance in both drug discovery and cell biology, since they follow the intracellular effects triggered by exogenous molecules on cell activities and functions  Insight Pharma Reports, High-Content Analysis: Technologies, Applications, and Market Dynamic, 2011

High content analysis (HCA) is the convergence between cell-based assays, high-resolution fluorescence imaging, automation and advanced image processing and analysis software. It has been widely adopted in the pharmaceutical and biotech industries for target identification and validation and as secondary screens to reveal potential toxicities or to elucidate a drug’s mechanism of action. In particular, HCA has made inroads into R&D applications where high throughput screening (HTS) has proven inadequate, such as measuring multiple biological pathways simultaneously, or revealing off-target drug effects. HCA has stepped into this void by demonstrating how particular proteins are affected by the application of a molecule to the cell line of interest.   Related/equivalent terms: high content assays,  high content screening, high content cellular analysis

high-content screening HCS: The area of High Content Screening is moving at a very rapid pace. It is hard to keep up. The purpose of this website is to provide a forum for those working in this field, a mechanism for exchange of information, an opportunity to develop educational tools and a facility to create training opportunities. Purdue Univ. Cytometry Laboratories    Related term:  high content analysis

High Throughput Screening HTS:  a method for scientific experimentation especially used in drug discovery and relevant to the fields of biology and chemistry [1][2]. Using robotics, data processing/control software, liquid handling devices, and sensitive detectors, high-throughput screening allows a researcher to quickly conduct millions of chemical, genetic, or pharmacological tests. Through this process one can rapidly identify active compounds, antibodies, or genes that modulate a particular biomolecular pathway. The results of these experiments provide starting points for drug design and for understanding the interaction or role of a particular biochemical process in biology.  Wikipedia accessed 2018 Feb 14

Process for rapid assessment of the activity of samples from a combinatorial library or other compound collection, often by running parallel assays in plates of 96 or more wells. IUPAC Combinatorial Chemistry

Traditionally describes the running of a large-scale assay campaign looking at the effects of a large number of compounds on a biological target.  
Broader term: screening   Narrower term: ultra high throughput screening Related terms: high content analysis, high content screening, throughput

high throughput screening assays: Rapid methods of measuring the effects of an agent in a biological or chemical assay. The assay usually involves some form of automation or a way to conduct multiple assays at the same time using sample arrays. MeSH 2010

hit:  Library component whose activity exceeds a predefined, statistically relevant threshold. IUPAC Combinatorial Chemistry

A molecule with robust dose­ response activity in a primary screen and known, confirmed structure. The output of most screening. [The precise definition of the following terms varies widely between drug discovery companies. The meanings given here are aligned with the use of the terms within the lead discovery function at Glaxo Wellcome.  Martin J. Valler,  Darren Green  "Diversity screening versus focussed screening in drug discovery" Drug Discovery Today 5(7): July 2000]   
Related terms: High Throughput Screening HTS, hit optimization library, lead discovery, screening. Narrower term: integrated hit identification, progressible hit

hit to lead: Reaching the next rung in hit-to-lead and lead optimization poses persistent challenges in the quest for successful drugs. As costs escalate, innovative approaches are needed to develop more efficient processes that lead to optimized compounds. Wikipedia Related term: lead optimization

homogeneous assay: All assay components exist in solution phase at the time of detection (e.g. none of the components are in beads or cells). Technically no component scatters light.  Glossary of Quantitative Biology Terms, 2012, 2014  

Performing homogenous assay, there should be no binding of the reaction components to the plate surface. Detection via different methods possible. In a competitive, homogeneous immunoassay, unlabeled analyte in a sample competes with labelled analyte to bind an antibody. The amount of labelled, unbound analyte is then measured. In theory, the more analyte in the sample, the more labelled analyte gets competed off and hence the amount of labelled, unbound analyte is proportional to the amount of analyte in the sample¹.

image analysis/image processing: In the context of high- content screening, these efforts involve drawing conclusions from image- based data, typically from living cells that have been exposed to compounds of interest. Analyzing such images can be challenging for many reasons, including the transient nature of cellular events and the fact that image- processing algorithms are still not robust enough for certain important applications (e.g., pattern recognition). Related terms: Molecular Imaging

immunoassay: A ligand- binding assay that uses a specific antigen or antibody, capable of binding to the analyte, to identify and quantify substances. The antibody can be linked to a radiosotope (radioimmunoassay, RIA), or to an enzyme which catalyses an easily monitored reaction (enzyme- linked immunosorbent assay, ELISA), or to a highly fluorescent compound by which the location of an antigen can be visualized (immunofluorescence). IUPAC Compendium

An immunoassay is a biochemical test that measures the presence or concentration of a substance in solutions that frequently contain a complex mixture of substances. Analytes in biological liquids such as serum or urine are frequently assayed using immunoassay methods. Such assays are based on the unique ability of an antibody to bind with high specificity to one or a very limited group of molecules. Wikipedia  accessed Feb 25 2011   Narrower term: competitive immunoassay Related term: ELISA

immunometric assay: See sandwich assay

in vitro adventitious assay: Adventitious agent tests are routinely used to assess safety and purity of cell banks and biologics. The methods used have ensured that very few products have reached the market with viral contaminants, and in the cases where they have, the contaminants have not posed a risk to human health. The in vivo and in vitro assays currently in use were developed more than 50 years ago based on clinical diagnostics and originally were used to detect specific adventitious agents known to be possible contaminants in vaccines[1]. The Workshop on Microbial Agents in Animal Cell Substrates: Update on Testing and Methods held April 20-21, 2009, reinforced the findings of the earlier conference in 2004. In particular, the newer methods were coming closer to being introduced into routine testing or cell bank characterization. Despite a considerable number of in vivo tests having been performed over the past many years, it was reported at this conference that no adventitious agents were detected in this way that were not also detected using in vitro methods. While there remained reluctance to eliminate animal-based testing, there was recognition that given the “3 R's” policy to reduce, refine, or replace the use of animals in product safety testing, justification for use of the in vivo methods needs continued consideration.

Although there is some information available, the breadth and sensitivity of these assays have not been assessed systematically and publicly reported. With respect to the in vitro and in vivo adventitious agent tests, the Vaccine Cell Substrates 2004 meeting participants concluded that the sensitivity and breadth of existing tests are presumed from historical experience and should be evaluated systematically. The data obtained from this research would then be available to use as a baseline for comparison with newly emerging tests and for consideration of implementing the 3 R's with respect to in vivo testing. Gombold J, Karakasidis S, Niksa P, et al. Systematic Evaluation of In Vitro and In Vivo Adventitious Virus Assays for the Detection of Viral Contamination of Cell Banks and Biological Products. Vaccine. 2014;32(24):2916-2926. doi:10.1016/j.vaccine.2014.02.021.

Adventitious means of external origin, or not normally expected or found. 

kinetic assay: Assay in which the time dependence of the signal intensity is measured. Signal values are typically acquired at several time intervals in order to calculate kinetic parameters. Note: Kinetic assays are generally designed such that the change in signal with time is linear throughout the experiment. See also equilibrium assay, end-point assayIUPAC Biomolecular Screening Glossary

lead: A representative of a compound series with sufficient potential (as measured by potency, selectivity, pharmacokinetics, physicochemical properties, absence of toxicity and novelty) to progress to a full drug development programme.  [The precise definition of the following terms varies widely between drug discovery companies. The meanings given here are aligned with the use of the terms within the lead discovery function at Glaxo Wellcome.  Martin J. Valler,  Darren Green  "Diversity screening versus focussed screening in drug discovery " Drug Discovery Today 5(7): July 2000] Related term: hit

lead discovery: The process of identifying active new chemical entities, which by subsequent modification may be transformed into a clinically useful drug. [IUPAC Medicinal Chemistry] 
Related terms: drug discovery, hit, lead generation, lead discovery library, lead optimization, screen 

lead generation: Strategies developed to identify compounds which possess a desired but non- optimized biological activity. IUPAC Medicinal Chemistry  Related terms: drug development, hit, lead discovery, lead optimization

lead hopping:  The use of ChemSpace TM to identify topomeric shape similarity in non-analogues.  Tripos  Related terms:  Chemistry  scaffold hopping  Drug targets  target hopping

lead identification: Whatever the screening paradigm, the output of the hit discovery phase of a lead identification programme is a so-called ‘hit’ molecule, typically with a potency of 100 nM–5 µM at the drug target. A chemistry programme is initiated to improve the potency of this molecule.  Principles of early drug discovery JP Hughes, S Rees, SB Kalindjian, KL Philpott  Br J Pharmacol. 2011 Mar; 162(6): 1239–1249. doi: 10.1111/j.1476-5381.2010.01127.x PMCID: PMC3058157

lead-like: Intrinsically, lead-likeness and drug-likeness are the descriptors of potency and selectivity, but also absorption, distribution, metabolism, toxicity, and scalability. Until now, these parameters were optimized sequentially, but nowadays it is believed that these parameters should be optimized simultaneously. Thierry Langer, G Wolber, Virtual combinatorial chemistry and in silico screening, Pure and Applied Chemistry 76 (5): 991– 996 , 2004 

lead optimization: The synthetic modification of a biologically active compound, to fulfill all stereoelectronic, physicochemical, pharmacokinetic and toxicologic required for clinical usefulness. [IUPAC Medicinal Chemistry] 

Lead Optimization for Drug Metabolism and Safety April 12, 2019 San Diego, CA Program | The more chemists know about how the structure of a compound can possibly impact its drug-like properties, the faster they can optimize it for drug development. Lead compounds in drug discovery need to be optimized for both efficacy and safety. Unfortunately, some of the adverse events related to the compound do not surface until much later in development… will introduce chemists to some key concepts in biotransformation, drug metabolism, drug transport, and drug clearance using relevant case studies and research findings.

Drug-induced adverse events account for most drug recalls and delays experienced in gaining regulatory approvals. While improvements in pre-clinical screening and clinical trial design have helped with better detection and monitoring of such adverse events, the problem still persists and often goes unnoticed until the compound is further along in development and testing.  Related terms: hit to lead,  drug development;  Pharmacogenomics ADME, toxicogenomics; Drug discovery & development prototype  Narrower term: parallel optimization

lead prioritization: One of the major steps in lead prioritization is an assessment of compound binding to plasma proteins, because it affects both the pharmacokinetics and pharmacodynamics of the compound in vivo.  Development of a high throughput equilibrium dialysis method , Ilona Kariv, Hong Cao, Kevin R. Oldenburg, J. Pharm. Sci. 90( 5) : 580- 587, 200 DOI: 10.1002/1520-6017(200105)90:5<580::AID-JPS1014>3.0.CO%3B2-4   AAPS Pharmaceutica

lead validation: With no shortage of drug targets, increasing emphasis is being placed on lead validation. One key challenge is developing high throughput screensRelated term: target validation.

live cell assays:  Can be used to obtain functional information on a wide variety of cellular effects, including apoptosis, proliferation, differentiation, migration and protein secretion. Enables a better understanding of protein functionality in normal and diseased states. 

massively parallel: Many (assays or other procedures) at once.  Related term: Gene amplification & PCR multiplexing

measured bioassay: See under bioassay

microplate reader: Created from the tube spectrophotometer designs of the 1970s to save precious antibody samples. At first clumsy and inaccurate, absorbance microplate readers have evolved to pack unbelievable power and precision, replacing cuvette spectrophotometers for most multisample applications.1 Continuous improvement is enhancing the classic designs to embrace the world of high- throughput (HT) screening and to allow complete analytical automation.2 To handle the HT range (more than 10 microplates a day or 1,000 assays), many instruments now allow robotic handling of plates "stacked" in accessory plate handlers.  Jorge D. Cortese " Well Read: Technological improvements are pushing microplate readers into the 21st century's high-speed, computerized world" Scientist 14 (19): 24, Oct. 2, 2000

microtiter plate, microtitre plate: Sample holding device used in combinatorial chemistry and high throughput screening for cloning of PCR products and construction of cDNA libraries in expression vectors. Comes in 96, 384, 1536 and 3456- well formats. Related term: sample

multiplex assays:  In the biological sciences, a multiplex assay is a type of immunoassay that uses magnetic beads to simultaneously measure multiple analytes in a single experiment.[1] A multiplex assay is a derivative of an ELISA using beads for binding the capture antibody. Multiplex assays are much more common in research than in clinical settings.[2] In a multiplex assay, microspheres of designated colors are coated with a specific antibodies. The results can be read by flow cytometry because the beads are distinguishable by fluorescent signature.  Wikipedia accessed 2018 Aug 25

multiwell plate: See microtiter plate, microtitre plate.

non competitive immunoassays: In noncompetitive immunoassays, also referred to as the "sandwich assay," antigen in the unknown is bound to the antibody site, then labeled antibody is bound to the antigen. The amount of labeled antibody on the site is then measured. Unlike the competitive method, the results of the noncompetitive method will be directly proportional to the concentration of the antigen. This is because labeled antibody will not bind if the antigen is not present in the unknown sample. Wikipedia  accessed Feb 25 2011  Broader term: immunoassay

phenotypic assays: [phenotypic approaches (function-first, reverse chemical biology)] have the advantage of identifying drug leads and clinical candidates that are more likely to possess therapeutically relevant [molecular mechanisms of action] MMOAs. Phenotypic screening in cancer drug discovery — past, present and future John G. Moffat,  Joachim Rudolph & David Bailey Nature Reviews Drug Discovery 13, 588–602 (2014) doi:10.1038/nrd4366 Published online 18 July 2014

Phenotypic Screening September 18-19 2019 Boston MA Phenotypic drug discovery is experiencing a renaissance in the pharmaceutical industry, based on its successful track record in delivering first-in-class medicines. This approach offers the promise of delivering both novel targets and chemical matter modulating a disease phenotype of interest. Although phenotypic screening may appear at first sight to be similar to target-based screening, there are some significant differences between the two approaches. These need to be properly considered and addressed to ensure the greatest likelihood of success for phenotypic drug discovery programs.    

Phenotypic Screening

Phenotypic screening (A.K.A. classical pharmacology) has been historically used in drug discovery. While technological developments have made the prevalence of target-based screening more popular, statistical analysis shows that a disproportionate number of first-in-class drugs with novel mechanisms of action come from phenotypic screening.

phenotypic screens: looks at the effects, or phenotypes, that compounds induce in cells, tissues or whole organisms … Beginning in the 1980s, advances in molecular biology and genomics led to phenotypic screens largely being replaced by screens against defined targets implicated in disease. … some researchers have concluded that reductionist approaches such as target-based screening are useful but may also limit the breadth of new findings. Phenotypic screening, take two Kotz, J.SciBX 5(15); doi:10.1038/scibx.2012.380 Published online April 12 2012

The systematic classification and characterization of phenotypes is essential for ultimately mapping the genes responsible for normal and abnormal development and physiology. In any search for mutations or altered functional expression, identification depends on phenotypic screening and its ability to detect variation from normal. The challenge is to develop efficient, systematic and comprehensive phenotypic screening procedures and tools that will permit comparison between laboratories, temporally, and between different strains of mice. This is a necessary step before utilizing chemical or other mutagenesis methods to produce large numbers of mutant mice for the investigation of normal and abnormal development and physiology. ... a primary focus of this program is the development of high throughput phenotyping assays or tests that could efficiently, rapidly, and systematically be used to screen anywhere from 5,000 to 20,000 mice per year for alterations in cardiovascular, pulmonary, hematologic or sleep physiology. This could include, but not be limited to, biochemical surrogate markers, noninvasive imaging modalities, microarray analysis, or indicator screens. Another goal is to develop new phenotyping techniques or methods for heart, lung, blood, and sleep disorders that would accelerate the emergence of new concepts and improve our understanding of structural, metabolic, and functional relationships in cardiopulmonary, and blood systems.  Development of mouse phenotypic screens for heart, lung, and blood diseases, National Heart, Lung and Blood Institute, NIH, US, Apr. 13, 1999, Request for Application   Compare targeted based drug discovery, screens

potency assays: Potency determination refers to the quantitative measurement of the biological activity of a given product. Biological activity is a critical quality attribute; therefore, potency testing is an essential component of quality control. Various procedures, including animal-based assays, ligand and receptor binding assays, cell culture-based assays, or other biochemical assays (such as enzymatic assays), may be used for potency testing based on the mechanism of action of the product. This article provides a review of the more commonly adopted assays—specifically ligand and receptor binding and cell-based potency assays, as well as recent advancements in statistical analysis for potency determination and strategies for phase appropriate method development and validation. Potency Testing of Biopharmaceutical Products : November 26, 2014 Weihong Wang, PhD American Pharmaceutical Review

potency testing: Potency is defined as “the specific ability or capacity of the product, as indicated by appropriate laboratory tests or by adequately controlled clinical data obtained through the administration of the product in the manner intended, to effect a given result.” (21 CFR 600.3(s)). Strength6 is defined as “[t]he potency, that is, the therapeutic activity of the drug product as indicated by appropriate laboratory tests or by adequately developed and controlled clinical data. . . .” (21 CFR 210.3(b)(16)). Regulations require that “[t]ests for potency shall consist of either in vitro or in vivo tests, or both, which have been specifically designed for each product so as to indicate its potency in a manner adequate to satisfy the interpretation of potency given by the definition in § 600.3(s) of this chapter.” (21 CFR 610.10).

primary assay: Assays of drugs done on a single drug  target or small groups of targets 

primary screening:   Primary screening, which is higher throughput than secondary screening, typically seeks to identify which compounds bind to targets of interest, to what degree of affinity. In primary screens researchers may seek to determine what compounds bind to and inhibit targets of interest. 

progressible hit: A representative of a compound series with activity via an acceptable mechanism of action and some limited structure­ activity relationship. The precise definition of the following terms varies widely between drug discovery companies. The meanings given here are aligned with the use of the terms within the lead discovery function at Glaxo Wellcome.  Martin J. Valler,  Darren Green  Diversity screening versus focussed screening in drug discovery " Drug Discovery Today 5(7): July 2000]  Related term: Combinatorial libraries & synthesis  chemistry space

random screening: A staple of the pharmaceutical industry for many years. Now largely replaced by varying combination of combinatorial chemistry and/or rational drug design.  Related terms: diversity screening, focussed screening Broader terms: screen, screening

reverse pharmacology: also known as target-based drug discovery (TDD),[4] a hypothesis is first made that modulation of the activity of a specific protein target will have beneficial therapeutic effects. Screening of chemical libraries of small molecules is then used to identify compounds that bind with high affinity to the target. The hits from these screens are then used as starting points for drug discovery. This method became popular after the sequencing of the human genome which allowed rapid cloning and synthesis of large quantities of purified proteins. This method is the most widely used in drug discovery today.[5] Differently than the classical (forward) pharmacology, with the reverse pharmacology approach in vivo efficacy of identified active (lead) compounds is usually performed in the final drug discovery stages. Wikipedia accessed 2018 Feb 26

RNAi screening: RNA interference (RNAi) is being commonly used as a screening tool for identifying and validating potential drug targets, exploring cellular pathways, and for whole-genome screening studies. The screens developed, using both small interfering RNA (siRNA) and short hairpin (shRNA), are now fairly robust and sensitive and can be performed in a reliable and high-throughput fashion.      

sandwich assay: The most powerful ELISA assay format is the sandwich assay. This type of capture assay is called a “sandwich” assay because the analyte to be measured is bound between two primary antibodies – the capture antibody and the detection antibody. The sandwich format is used because it is sensitive and robust.  ELISA formats, Thermo Fisher Scientific

screen: An optimized, streamlined assay format with characterized robustness to diverse chemical types and conditions such that testing of 10,000 samples is both feasible and cost effective. The spectrum of low- throughput screening (10,000­ 50,000 assay points) medium- throughput screening (50,000­100,000 data points) and high- throughput screening (100,000­ 500,000 data points) can be defined. The scale of implementation of a given screen is greatly influenced by format, application of technology (e.g. automation), time and resource constraints. [The precise definition of the[se] terms varies widely between drug discovery companies. The meanings given here are aligned with the use of the terms within the lead discovery function at GlaxoWellcome.  Martin J. Valler,  Darren Green  "Diversity screening versus focussed screening in drug discovery " Drug Discovery Today 5(7): July 2000] 

screening: Pharmacological or toxicological screening consists of a specified set of procedures to which a series of  compounds is subjected to characterize pharmacological and toxicological properties and to establish dose- effect and dose- response relationships. IUPAC Toxicology

While drug screening is often talked about in the context of achieving hits, it is useful to note that the Oxford English Dictionary definition of screening specifies that this is "esp. for the detection of unwanted attributes or objects".  Narrower terms: diversity screening, focussed screening, HTS High Throughput Screening, synthetic lethal screening, Ultra High Throughput Screening UHTS; Drug targets target screening  Not the same as screening in Molecular Medicine Related terms: assay, I.R. Thermography 

secondary assays (and tertiary assays): Undertaken after primary screening has identified "hit" compounds against drug  targets, are more complicated - and time-consuming - tests of a drug and include ADME/Tox (absorption, distribution, metabolism, excretion/toxicology) studies (e.g., done on mice or rats). Test a drug against more than one target, complicated and time- consuming, so they have not been considered practical for use in very early drug development.... . The secondary and tertiary assays tell you more biology. ...Typically, secondary and tertiary assays are more comprehensive, but they also take longer, and they are more complex and less reproducible. 

secondary screening:  Secondary screening, which is lower throughput than primary screening, seeks to provide more detailed information about compounds than just their binding affinity. For example, secondary screens may shed light on mechanism of action and other parameters. As the primary screening technologies are becoming increasingly automated and high-throughput, the drug discovery bottleneck is shifting downstream towards secondary screening and lead optimization. This is the area where researchers had the most experience with High Content Screening. The high-content cellular information on lead specificity, bioavailability, and ADME/Tox allows researchers to prioritize leads with more confidence and impact the bottom line by reducing late- stage attrition.

small molecule screening:  The basic goal of small- molecule screening is the identification of chemically 'interesting' starting points for elaboration towards a drug. A number of innovative approaches for pursuing this goal have evolved, and the right approach is dictated by the target class being pursued and the capabilities of the organization involved. A recent trend in high- throughput screening has been to place less emphasis on the number of data points that can be produced, and to focus instead on the quality of the data obtained.  Walters WP, Namchuk M., Designing screens: how to make your hits a hit. Nature Reviews Drug Discovery 2003 Apr;2(4): 259- 266 

target-based drug discovery: [target-first, forward chemical biology]  is not an intrinsically inferior approach but … is more likely to fail if target modulation is prioritized at the expense of understanding the most desirable MMOAs. These mechanisms can best be demonstrated by functional and phenotypic assays. Phenotypic screening in cancer drug discovery — past, present and future John G. Moffat,  Joachim Rudolph & David Bailey Nature Reviews Drug Discovery 13, 588–602 (2014) doi:10.1038/nrd4366 Published online 18 July 2014

target-based screens. measure the effect of compounds on a purified target protein via in vitro assays. … Over the last decade, however, some drug developers have questioned whether an over-reliance on genetic approaches to validating targets for subsequent target-based drug discovery has resulted in reduced success in discovering first-in-class medicines. Phenotypic screening, take two Kotz, J. SciBX 5(15); doi:10.1038/scibx.2012.380 Published online April 12 2012  Compare targeted based assays, screens

tertiary assays: See secondary assays (and tertiary assays)

throughput: Output or production, rate at which something can be processed.  

Ultra High Throughput Screening (uHTS) : A screening rate of  100,000 assays per day. IUPAC Combinatorial Chemistry

Greater than 500,000 compounds screened per screen. Glossary Quantitative Biology

Narrower term: cell- based uHTS; Broader term: High Throughput Screening HTS 

virtual screening: Selection of compounds by evaluating their desirability in a computational model. Also termed in silico screening. IUPAC Combinatorial Chemistry
Wikipedia   Narrower terms: grid based virtual screening, high throughput virtual screening  Related terms: docking; Pharmaceutical biology ligands, receptors; Combinatorial libraries & synthesis 

Assays Resources
BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.
Glossary of Quantitative Biology Terms Assay Guidance Manual Viswanath Devanarayan, Barry D. Sawyer, Chahrzad Montrose, Dwayne Johnson, David P. Greenen, Sitta Sittampalam, Terry Riss, and Lisa Minor. Published 2012, last updated 2014
IUPAC Glossary of terms in Biomolecular Screening 2011
Nature: Drug screening
Sittampalam GS, Coussens NP, Brimacombe K, et al., editors. Assay Guidance Manual [Internet]. Bethesda (MD): Eli Lilly & Company and the National Center for Advancing Translational Sciences; 2004

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IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.

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