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
https://ncats.nih.gov/preclinical/drugdev/assay
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 Microarrays, Molecular
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
https://www.fda.gov/BiologicsBloodVaccines/ScienceResearch/BiologicsResearchAreas/ucm127314.htm
antibody assays:
https://www.abcam.com/protocols/antibody-methods-and-techniques
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] http://www2.uah.es/farmamol/Public/PDF_files/screening.pdf
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"
http://archive.fged.org/mged/Workgroups/MAGE/bioassay.html
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. http://bioassayontology.org/
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.
https://www.ncbi.nlm.nih.gov/books/NBK144065/
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 http://en.wikipedia.org/wiki/Immunoassay
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 http://www.news-medical.net/news/2005/02/22/7870.aspx
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 (1).
Early Drug Discovery and Development Guidelines: For
Academic Researchers, Collaborators, and Start-up Companies, published 2012 last
updated 2016, Assay Guidance Manual NCBI Bookshelf
https://www.ncbi.nlm.nih.gov/books/NBK92015/
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.
https://www.drugdiscoverychemistry.com/Directed-Evolution/
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 http://www2.uah.es/farmamol/Public/PDF_files/screening.pdf
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 http://www2.uah.es/farmamol/Public/PDF_files/screening.pdf
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
https://en.wikipedia.org/wiki/Classical_pharmacology
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. https://www.drugdiscoverychemistry.com/Fragment-Based-Drug-Discovery/
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
https://www.ncbi.nlm.nih.gov/pubmed/15662722 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-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 http://www.cyto.purdue.edu/HCS/
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
https://en.wikipedia.org/wiki/High-throughput_screening
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] http://www2.uah.es/farmamol/Public/PDF_files/screening.pdf
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
https://en.wikipedia.org/wiki/Hit_to_lead. 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
https://www.ncbi.nlm.nih.gov/books/NBK92002/
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.
https://www.wellplate.com/homogeneous-assays/
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 http://en.wikipedia.org/wiki/Immunoassay
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.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4526145/
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 assay. IUPAC 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] http://www2.uah.es/farmamol/Public/PDF_files/screening.pdf
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 http://www.iptonline.com/articles/public/IPTFIVE46NP.pdf
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
https://www.ncbi.nlm.nih.gov/pmc/articles/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 http://www.iupac.org/publications/pac/2004/pdf/7605x0991.pdf
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 screens. Related 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
https://en.wikipedia.org/wiki/Multiplex_(assay)
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 http://en.wikipedia.org/wiki/Immunoassay
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 http://www.nature.com/nrd/journal/v13/n8/full/nrd4366.html
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.
https://www.discoveryontarget.com/training-seminars/ts-4-detailed-agenda
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
http://www.nature.com/nrd/journal/v13/n8/full/nrd4366.html
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 http://grants1.nih.gov/grants/guide/rfa-files/RFA-HL-99-010.html
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
https://www.americanpharmaceuticalreview.com/Featured-Articles/169473-Potency-Testing-of-Biopharmaceutical-Products/
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). https://www.fda.gov/downloads/biologicsbloodvaccines/guidancecomplianceregulatoryinformation/guidances/cellularandgenetherapy/ucm243392.pdf
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] http://www2.uah.es/farmamol/Public/PDF_files/screening.pdf
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
https://en.wikipedia.org/wiki/Reverse_pharmacology
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
https://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/overview-elisa.html#2
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] http://www2.uah.es/farmamol/Public/PDF_files/screening.pdf
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
http://www.nature.com/nrd/journal/v13/n8/full/nrd4366.html
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
http://www.nature.com/scibx/journal/v5/n15/full/scibx.2012.380.html
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
https://www.ncbi.nlm.nih.gov/books/NBK92002/
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 http://en.wikipedia.org/wiki/Virtual_screening
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.
http://bioassayontology.org/
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
https://www.ncbi.nlm.nih.gov/books/NBK92002/
IUPAC Glossary of terms in Biomolecular Screening 2011 http://iupac.org/publications/pac/83/5/1129/
Nature: Drug screening
https://www.nature.com/subjects/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
https://www.ncbi.nlm.nih.gov/books/NBK53196
Chemistry conferences
http://www.healthtech.com/conferences/upcoming.aspx?s=CHM
How
to look for other unfamiliar terms
IUPAC
definitions are reprinted with the permission of the International Union of Pure
and Applied Chemistry.
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