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Biology term index: Related glossaries include Biologics
Chemistry
Drug
discovery & development Drug
discovery informatics Drug & disease
targets
active center:
The location in an enzyme
where the specific reaction takes place. IUPAC Bioinorganic
agonist(s):
An endogenous substance or a drug that can interact with a receptor
and initiate a physiological or a pharmacological response
characteristic of that receptor (contraction, relaxation, secretion,
enzyme activation, etc.) IUPAC Medicinal Chemistry]
Contrast with antagonist(s).
analog:
A drug whose structure is related to that of another drug but whose
chemical and biological properties may be quite different. IUPAC
Medicinal Chemistry
antagonist:
A drug or a compound that opposes the physiological effects of
another. At the receptor level, it is a chemical entity that opposes
the receptor- associated responses normally induced by another
bioactive agent. IUPAC Medicinal Chemistry
Compare agonist. Related term: selective
modulators
antigens:
Substances that are recognized by the immune system and induce an
immune reaction. MeSH
antisense: Many scientists are still confused by the terms ‘sense’ and antisense’
when referring to DNA because the terminology has changed over the years.
Because there are good logical threads that allow one to rationalize how
each strand could be designated as the sense strand of DNA, the terms become
intrinsically confusing…It became apparent that Richard Moldwin’s rmoldwin@midway.uchicago.edu
proposal is probably the best solution to the problem. ..that the terminology
for the strands of DNA with respect to transcription should therefore be
formalized and the use of sense strand for DNA be avoided in future literature.
One strand of DNA acts as the template for transcription and the other
does not. When referring to DNA, the terms should be "transcribed strand"… and
"non- transcribed strand"… The term antisense would be best reserved for
RNA...Whether the members’ decision will be taken seriously and whether
it will be come the existing standard remains to be seen. Methods and reagents.
Is there any sense in antisense terminology?
Hengen PN1. Trends
Biochem Sci. 1996 Apr;21(4):153-4.
https://www.ncbi.nlm.nih.gov/pubmed/8701474 Is this a moot point by now?
Molecular biologists describing DNA sequences or referring to one of
the two strands of double- stranded DNA frequently use complementary pairs
of terms, such as coding/ non- coding, sense/ nonsense or transcribing/ non-
transcribing.
Unfortunately none of these pairs is defined in a universally accepted
way…Of the three pairs of terms mentioned, NC- IUB and JCBN believe coding/
non- coding
to be preferable. Moreover, as the word 'coding' refers to the relationship
between nucleic acids and proteins, rather than the mere transcription
of DNA into RNA, it is logical to call the strand with the mRNA sequence
the coding strand, as in the first example. When DNA sequences are described
by giving the sequence of only one strand, this is usually the strand with
the same sequence as the RNA (messenger, ribosomal, transfer, etc.) and
should therefore be called the coding strand. [JCBN/ NC- IUB Newsletter,
Joint Commission on Biological Nomenclature and Nomenclature Commission
of IUB, 1989] http://www.chem.qmw.ac.uk/iubmb/newsletter/misc/DNA.html
antisense DNA:
DNA that is complementary to the sense strand. (The sense strand has the same sequence as the mRNA transcript. The antisense strand is the template for mRNA synthesis.) Synthetic antisense DNAs are used to hybridize to complementary sequences in target RNAs or DNAs to effect the functioning of specific genes for investigative or therapeutic purposes.
MeSH, 1991
antisense oligonucleotides:
Short fragments of DNA or RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.
MeSH, 1991 Related
terms antisense, antisense DNA, antisense
RNA, morpholinos
aptamer: Oligonucleotide
which displays specific binding to a protein or
other target, often selected by an iterative cycle of affinity-
based enrichment. A synthetic, specially- designed oligonucleotide
with the ability to recognize and bind a protein ligand molecule or
molecules with high affinity and specificity.
Narrower terms: photoaptamers, Functional
genomics Protein
technologies peptide
aptamer; Genomic
technologies
SELEX, spielgemers
Aptamers are
included in the IUPAC, Electrochemical nucleic acid based
biosensors http://www.iupac.org/publications/pac/pdf/2010/pdf/8205x1161.pdf
binding
affinity: the strength of
the binding interaction between a single biomolecule (e.g. protein
or DNA) to its ligand/binding partner (e.g. drug or inhibitor).
Binding affinity is typically measured and reported by the
equilibrium dissociation constant (KD), which is used to evaluate
and rank order strengths of bimolecular interactions. The smaller
the KD value, the greater the binding affinity of the ligand for its
target. The larger the KD value, the more weakly the target molecule
and ligand are attracted to and bind to one another. Binding
affinity is influenced by non-covalent intermolecular interactions
such as hydrogen bonding, electrostatic interactions, hydrophobic
and Van der Waals forces between the two molecules. In addition,
binding affinity between a ligand and its target molecule may be
affected by the presence of other molecules. There are many ways to
measure binding affinity and dissociation constants, such as ELISAs,
gel-shift assays, pull-down assays, equilibrium dialysis, analytical
ultracentrifugation, SPR, and spectroscopic assays. Isothermal
titration calorimetry (ITC) is
a direct, label-free analytical technique which measures the binding
affinity between any two molecules that interact with each other,
such as a protein and a ligand. Malvern Panalytical, Products
Measurement Type
https://www.malvernpanalytical.com/en/products/measurement-type/binding-affinity
binding, competitive: The interaction of two or
more substrates or ligands with the same binding site. The
displacement of one by the other is used in quantitative and
selective affinity measurements. MeSH 1973
binding site: A specific region (or atom) in a
molecular entity that is capable of entering into a stabilizing
interaction with another molecular entity. IUPAC Bioinorganic The
reactive parts of a macromolecule that directly participate in its
specific combination with another molecule. MeSH, 1968 Related
terms: ligand; receptor mapping. Narrower term: binding sites,
antibody
binding sites, antibody: Local surface sites on
antibodies which react with antigen determinant sites on antigens.
They are formed from parts of the variable regions of the Fab
fragment of the immunoglobulin. MeSH, 1973
chemical ligand studies: Use a more general set of
compounds [than chemical genomics] (often from combinatorial
libraries) to find new targets. Once the new targets are found, more
specific assays are done. In other words, with the chemical ligands
approach, one does blind screening of chemical libraries using
cellular assays. When one gets an interesting biological effect, one
uses the compound to find the target it modulates. [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
GlaxoWellcome. Martin J. Valler, Darren Green "Diversity
screening versus focussed screening in drug discovery" Drug
Discovery Today 5(7): July 2000
deorphanize: Identification of new ligands for
receptors.
drug leads: small molecule ligands DS Wishart
Identifying
putative drug targets and potential drug leads: starting points
for virtual screening and docking. Methods Mol Biol.
2008;443:333-51.
drug receptors: Proteins that bind specific drugs
with high affinity and trigger intracellular changes influencing the
behavior of cells. Drug receptors are generally thought to be
receptors for some endogenous substance not otherwise specified.
MeSH, 1968 Broader term: receptors
efficacy: Describes the relative intensity with
which agonists vary in the response they produce
even when they occupy the same number of
receptors and with the same affinity. Efficacy
is not synonymous to
intrinsic activity. The property that enables
drugs to produce responses. It is convenient to differentiate
the properties of drugs into two groups, those which cause them to
associate with the receptors (affinity) and those that produce
stimulus (Efficacy). This term is often used to characterize the
level of maximal responses induced by agonists. In fact, not all
agonists of a receptor are capable of inducing identical levels of
maximal responses. Maximal response depends on the efficiency of
receptor coupling, i.e., from the cascade of events, which, from the
binding of the drug to the receptor, leads to the observed
biological effect. IUPAC Medicinal Chemistry
efficacy (in receptor pharmacology) Extent to which
a compound activates a receptor to produce a response in an assay
under saturating conditions. Note 1: Usually compared to results
with the positive and negative assay controls. When the compound
produces a maximal signal that is 100 % of that of the positive
control, it is said to be a full agonist and has high efficacy. When
the effect plateaus with increasing concentration to reach an
intermediary level of activity, the compound is said to be a partial
agonist with lower efficacy. Note 2: Due to the common
overexpression of receptors in screening assays, it is not always
possible to detect differences in efficacy among full agonists. A
more accurate assessment of relative efficacy may require systems
with lower receptor expression where it is often found that one
agonist may show partial agonist character. See also partial
agonist. IUPAC Glossary of Biomolecular Screening
enzymes:
Macromolecules, mostly of protein nature, that function
as (bio) catalysts by increasing the reaction rates. In general, an enzyme
catalyses only one reaction type (reaction specificity) and operates on
only one type of substrate (substrate specificity). Substrate molecules
are attacked at the same site (regiospecificity) and only one or preferentially
one of the enantiomers or chiral substrates is attacked (stereospecificity).
[IUPAC Compendium]
A substance (usually a protein) that speeds up, or catalyzes, a chemical
reaction without being permanently altered or consumed. [NIGMS]
Biological molecules that possess catalytic activity. They may occur
naturally or be synthetically created. Enzymes are usually proteins, however
catalytic RNA (RNA, CATALYTIC) and catalytic DNA (DNA, CATALYTIC) molecules have
also been identified. MeSH Related terms: substrate, Metabolic
engineering; Pharmacogenomics enzyme
kinetics Narrower term: immobilized enzymes
enzymes and
coenzymes: Biological catalysts and their
cofactors. MeSH 2004
epitope:
Any part of a molecule that acts as an
antigenic determinant. A macromolecule can contain many different
epitopes each capable of stimulating production of a different
specific antibody. IUPAC Glossary Biomolecular Screening
Sites on an antigen that interact with specific antibodies. MeSH,
1996
Sites involved
in noncovalent interactions. NS Greenspan and E Di Cera "Defining
epitope: It’s not as easy as it seems" Nature Biotechnology 17:936-
937 Oct. 1999 Related terms
antibody, antigen, hapten; Narrower terms: conformational epitopes
Wikipedia
http://en.wikipedia.org/wiki/Conformational_epitope
linear epitopes Wikipedia
http://en.wikipedia.org/wiki/Linear_epitope
Also known as discontinuous epitopes. Mimotopes Wikipedia
http://en.wikipedia.org/wiki/Mimotope
epitope mapping:
Maps, genomic & genetic
hapten:
A molecule (usually a small organic
molecule) which can be bound to an antigenic determinant/ epitope.
Usually they are too small to give a response of their own. They
become antigenic if they are coupled to a suitable macromolecule,
such as a protein. IUPAC Bioinorganic
Small antigenic determinants capable of eliciting an immune response
only when coupled to a carrier. Haptens bind to antibodies but by
themselves cannot elicit an antibody response. MeSH, 1965
homologue:
Used to describe a compound belonging to a series of
compounds differing from each other by a repeating unit, such as a methylene
group, a peptide residue, etc. IUPAC Medicinal Chemistry
This is different
from homolog/ homologue defined in the Functional
genomics
hormone:
A substance produced by endocrine glands, released in
very low concentration into the bloodstream, and which exerts regulatory
effects on specific organs or tissues distant from the site of secretion.
[IUPAC Medicinal Chemistry]
Chemical substances having a specific regulatory effect on the activity of a certain organ or organs. The term was originally applied to substances secreted by various endocrine glands and transported in the bloodstream to the target organs. It is sometimes extended to include those substances that are not produced by the endocrine glands but that have similar effects.
MeSH
Related term: receptor.
immobilized enzymes: Enzymes which are immobilized on or in a variety of
water- soluble or
water- insoluble matrices with little or no loss of their catalytic activity. Since they can be reused continuously, immobilized enzymes have found wide application in the industrial, medical and research fields.
MeSH, 1977
immunogen: A
substance that elicits a cellular immune response and/ or antibody
production (cf. antigen). IUPAC Compendium
inhibitors: A substance
that diminishes the rate of a chemical reaction. The process is
called inhibition. Inhibitors are sometimes called negative
catalysts but since the action of an inhibitor is fundamentally
different from that of a catalyst this terminology is discouraged.
In contrast to a catalyst, an inhibitor may be consumed in the
course of a reaction. ... See also effector. [IUPAC Compendium]
Narrower term:
promiscuous inhibitors
ligand:
In inorganic chemistry the ligands are the atoms or groups of atoms
bound to the central atom (see also coordination). The root
of the word is sometimes converted into the verb to ligate, meaning to
coordinate as a ligand, and the derived participles, ligating and ligated…In
biochemistry the term ligand has been used more widely: if it is possible
or convenient to regard part of a polyatomic molecular entity as central,
then the atoms or groups or molecules bound to that part may be called
ligands. IUPAC Bioinorganic
Pharmacologists
traditionally divide ligands into agonists, which stimulate receptors, and
antagonists, which bind to receptors and block endogenous mediators. According
to the conventional view, the agonist fits into the receptor, like a key fits a
car's ignition, switching on the internal machinery. Antagonists fit the
ignition, but block endogenous transmitters. But recent studies suggest that
many receptors spontaneously activate internal machinery. In these cases, the
receptor is more akin to an accelerator. Mark Greener, Driving Changes in Ligand
Theory, The Scientist 18(15): 32, Aug. 2, 2004
A molecule that binds
to another molecule, used especially to refer to a small molecule that binds
specifically to a larger molecule, e.g., an antigen binding to an antibody, a
hormone or neurotransmitter binding to a receptor, or a substrate or allosteric
effector binding to an enzyme. Ligands are also molecules that donate or accept
a pair of electrons to form a coordinate covalent bond with the central metal
atom of a coordination complex. (From Dorland, 27th ed) MeSH 1974
Molecules (e.g., drugs) that bind to active sites on proteins. Particularly used of small molecules that bind to larger
molecules. Narrower term: protein ligand; Related terms:
antigen, binding site, enzyme- substrate, hormone- receptor reaction, lock and key
ligand binding:
The study of ligand binding is an essential step in
identifying receptor binding sites. There are several methods for
analysing ligand binding experiments. This laboratory offers the
opportunity to compare the most widely used. Ligand binding models
describe the interaction of one or more ligands with one or more binding
sites. Binding sites can be described by their behaviour as being
saturable or non-saturable. Saturable binding is also called specific
binding and non-saturable binding is also called non-specific binding.
Receptors have saturable binding sites and also express an effect. Models
for ligand binding are based on the law of mass action. Models can
describe the time course of binding (association and dissocation) but more
commonly binding is described at equilibrium. The driving force for
binding is the unbound ligand concentration but experimentally only total
ligand concentrations can be varied. Measurements of bound ligand can be
used to predict unbound ligand concentration (unbound=total-bound) but the
measurement error in the bound concentration will influence the predicted
unbound concentration. Ligand binding, Anita Sumpter, University of
Auckland, Dept of Pharmacology and Clinical Phamacology
http://holford.fmhs.auckland.ac.nz/teaching/medsci719/workshops/ligandbinding/
orphan
receptors: Receptor for
which no ligands have yet been identified.
Related terms: deorphan, deorphanize
peptide
receptors: Cell surface
receptors that bind peptide messengers with high affinity and
regulate intracellular signals which influence the behavior of
cells. MeSH, 1994
peptidomimetic: A compound
containing non- peptidic structural elements that is capable of
mimicking or antagonizing the biological action(s) of a natural
parent peptide. A peptidomimetic does no longer have classical
peptide characteristics such as enzymatically scissille peptidic
bonds. (See also peptoids). IUPAC Medicinal Chemistry
Related terms: -Omes
& -omics
peptidome, peptidomic
peptoid:
A peptidomimetic that results from the oligomeric assembly of
N-substituted glycines. IUPAC Medicinal Chemistry
pharmacophores: The
ensemble of steric and electronic features that is necessary to
ensure the optimal supramolecular interactions with a specific
biological target structure and to trigger (or to block) its
biological response. Does not represent a real molecule or a real
association of functional groups, but a purely abstract concept that
accounts for the common molecular interaction capacities of a group
of compounds towards their target structure. Can be considered as
the largest common denominator shared by a set of active molecules.
This definition discards a misuse often found in the medicinal
chemistry literature which consists of naming as pharmacophores
simple chemical functionalities such as guanidines, sulfonamides or
dihydroimidazoles (formerly imidazolines), or typical structural
skeletons such as flavones, phenothiazines, prostaglandins or
steroids. Pharmacophoric descriptors are used to define a
pharmacophore, including H- bonding, hydrophobic and electrostatic
interaction sites, defined by atoms, ring centers and virtual
points. IUPAC Medicinal Chemistry The ensemble of steric and
electronic factors which are necessary to insure supramolecular
interactions with a specific biological target structure. IUPAC
Combinatorial Chemistry
A template of chemical properties for an
active site of a protein - representing these properties’ spatial
relationship to one another - that theoretically defines a ligand
that would bind to that site. pharmacophore generation: A procedure
to extract the most important common structural features relevant
for a given biological activity from a series of molecules with a
similar mechanism of action. IUPAC Computational
paratope:
also called an antigen-binding site, is a part of an antibody which
recognizes and binds to an antigen.
It is a small region (of 5 to 10 amino
acids[citation
needed]) of the antibody's Fv
region, part of the fragment
antigen-binding (Fab region), and contains parts of the
antibody's heavy and light
chains.[1] Each
arm of the Y shape of an antibody monomer is tipped with a paratope,
which is a set of complementarity
determining regions. The part of the antigen to which the
paratope binds is called an epitope.
This can be mimicked by a mimotope. Wikipedia
accessed 2018 Nov 6
http://en.wiktionary.org/wiki/paratope
Related term: binding sites
prodrug:
Drugs that, once administered, must be chemically modified by
metabolic processes in order to become pharmaceutically active.
Any compound that undergoes
biotransformation
before exhibiting its pharmacological effects. Prodrugs
can thus be viewed as
drugs
containing specialized non- toxic protective groups used in a transient manner
to alter or to eliminate undesirable properties in the parent molecule. IUPAC
Medicinal Chemistry
promiscuous drugs:
We contend that an ideal drug may be one whose efficacy is based not
on the inhibition of a single target, but rather on the rebalancing
of the several proteins or events, that contribute to the etiology,
pathogeneses, and progression of diseases, i.e., in effect a
promiscuous drug.... Corollaries to this argument are that the
growing fervor for researching truly selective drugs may be
imprudent when considering the totality of responses; and that the
expensive screening techniques used to discover these, may be both
medically and financially inefficient. Promiscuous drugs compared to
selective drugs (promiscuity can be a virtue) Simon K Mencher and
Long G Wang, BMC Clinical Pharmacology 2005, 5:3
doi:10.1186/1472-6904-5-3
http://www.biomedcentral.com/1472-6904/5/3/abstract
Related term: selectivity
promiscuous inhibitors:
Nonspecific, seem to be hits in multiple high- throughput screening
(HTS) campaigns, but which turn out to be dead ends when attempts
are made to optimise their activity, a key problem in the field of
HTS. Peter Kirkpatrick, Won't get fooled again, Nature Reviews Drug
Discovery, 4(8): 630, August 2005 rotean ligands: The literature
contains few examples of ligands that seem to be able to both
promote and decrease activity at the same G-protein-coupled
receptors. Such 'protean ligands' — so- called after the mythical
character Proteus, who could adopt any shape he desired — have been
proposed to work by acting as agonists with low efficacy. They
thereby increase the activity of receptors that are basically silent
under resting conditions, but decrease the activity of receptors
that have high levels of ligand- independent, spontaneous (or
constitutive) activity. In this model, protean behaviour therefore
depends on having two populations of receptors with different levels
of spontaneous activity. Adam Smith, Adrenoceptor pharmacology: How
the ligand changed its spots Nature Reviews Drug Discovery 1, 569
Aug. 2002
https://www.nature.com/articles/nrd885
receptor:
A
protein
or a protein complex in or on a cell that specifically recognizes
and binds to a compound acting as a molecular messenger
(neurotransmitter, hormone, lymphokine, lectin, drug, etc.). In a
broader sense, the term receptor is often used as a synonym for any
specific (as opposed to non- specific such as binding to plasma
proteins) drug binding site, also including nucleic acids such as
DNA. IUPAC Computational
Narrower terms: amino acid receptors, cell surface receptors, drug
receptors, receptor mapping
In silico & Molecular modeling;
Related terms: ligand
recognition site:
1. A nucleotide sequence to which a protein
binds specifically. 2. An amino acid sequence in an antibody molecule to which
the specific antigen binds specifically. IUPAC Biotech recombination: See genetic recombination SNPs
& Genetic
variations
selectivity: describes a
drug's ability to affect a particular cell population in preference
to others. As part of the current state of art in the search for new
therapeutic agents, the property of selectivity is a mode of action
thought to have a high degree of desirability.... Selectivity is
generally a worthy property in a drug because a drug having high
selectivity may have a dramatic effect when there is a single agent
that can be targeted against the appropriate molecular-driver
involved in the pathogenesis of a disease. Promiscuous drugs
compared to selective drugs (promiscuity can be a virtue) Simon K
Mencher and Long G Wang, BMC Clinical Pharmacology 2005, 5:3
doi:10.1186/1472-6904-5-3
http://www.biomedcentral.com/1472-6904/5/3/abstract
Selectivity is the recommended term in
analytical chemistry to express the extent of interferences. To
avoid confusion, the use of the term specificity is to be
discouraged, as it is incorrect. A method is either specific or not.
Few, if any, methods are specific. 2. Definition of Selectivity
refers to the extent to which a method can determine particular
analytes in mixtures or matrices without interferences from other
components. Selectivity in analytica chemistry poster
https://old.iupac.org/projects/posters01/vessman01.pdf
The extent to which
a compound hits the intended drug target.
Related term: promiscuous drugs
solubility: The analytical composition of a saturated solution,
expressed in terms of the proportion of a designed solute in a designated
solvent is the solubility of that solute. The solubility may be expressed
as a concentration, molality, mole fraction, mole ratio, etc.
IUPAC Compendium 1997
Ability of a compound to dissolve.
Related terms: molality, molarity; Cheminformatics rule
of five specificity:
The terms selectivity or
specificity are in many cases used interchangeably. As specificity
is considered as an absolute term, it cannot be graded. IUPAC has
earlier stated that “specificity is the ultimate of selectivity”.
The desire to avoid the term specificity has been expressed as
“Sometimes the term specificity is used. This usage suggests that no
component other than the analyte contributes to the result. Hardly
any method is that specific (sic!) and, in general, the term should
be avoided”. Selectivity in analytica chemistry poster
https://old.iupac.org/projects/posters01/vessman01.pdf In the five
disciplines that eventually contributed to the formation of
molecular biology, ideas of specificity had widely different
standing and character. In microbiology, the relevance of
specificity in the present day sense awaited resolution of the long,
piecemeal shift of opinions about what sort of creatures micro-
organisms were....[Oswald Avery, Chargaff, Lwoff, Luria Delbruck,
Jacques Monod, Alice Audureau] Mendelian genetics itself had always
been highly specific, of course, and from very early the genetic
specificity - the map - was understood to form a strictly linear
array [Thomas Hunt Morgan, Boris Ephrussi, George Beadle, Edward
Tatum]... In physical chemistry, specificity was not abstract and
not linear, but concretely physical and three- dimensional [Pauling]
... Crystallography, in its way, was also permeated with specificity
[Edward Tyson Reichert, Amos Peaslee Brown, Felix Haurowitz] ...
Specificity in the present- day sense of unique molecular structures
was never a surprise to the crystallographers ... The fifth
discipline in the synthesis that formed molecular biology was
biochemistry. Yet the standard view of the rise of molecular biology
has somewhat taken for granted, for example, the radical sharpening
of ideas of specificity represented by Fritz Lipmann's elucidation
of the way energy is supplied to the steps of cellular reactions.
And it grievously undervalues the work of the two biochemists who
proved decisive in changing the way people thought about
specificity. The man who released the present day understanding of
molecular specificity in living processes was Frederick Sanger ...
the most general and profound [result of his methods] was that
proteins are entirely and uniquely specified. Horace Freeman Judson
Eighth Day if Creation, Cold Spring Harbor Laboratory Press, 1996
pp. 583- 585 100% specificity =
100% true negatives, 0% false negatives.
See also
Molecular Medicine
(analytical and clinical sensitivity and specificity).
substrate: A chemical species, the reaction of which with some
other chemical reagent is under observation (e. g. a compound that is transformed
under the influence of a catalyst). The term should be used with care.
Either the context or a specific statement should always make it clear
which chemical species in a reaction is considered the substrate. IUPAC
Compendium
How does this definition compare with substrate Microarrays
& protein arrays Related term enzyme.
substrate specificity:
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
MeSH, 1978
Bibliography
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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Pharmaceutical biology
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Evolving terminologies for emerging
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Suggestions? Comments? Questions?
Mary Chitty MSLS mchitty@healthtech.com
Last revised
January 14, 2020
Narrower terms: antisense DNA, antisense oligonucleotides,
antisense RNA,
Related terms: Biologics antisense therapy; RNAi; SNPs
& other genetic
variations missense mutation, nonsense mutation; Sequences
DNA & beyond ribozymes
Enzyme nomenclature list, IUPAC, 1992 print edition &
supplements http://www.chem.qmul.ac.uk/iubmb/enzyme/
See also Nomenclature Enzyme
nomenclature for more detailed explanation.
intrinsic
activity:
The maximal stimulatory response induced
by a compound in relation to that of a given reference compound (See
also partial agonist)
This term has evolved with common usage. It was introduced by Ariëns
as a proportionality factor between tissue response and
receptor
occupancy. The numerical value of intrinsic activity (alpha) could
range from unity (for full
agonists,
i.e., agonist inducing the tissue maximal response) to zero (for
antagonists),
the fractional values within this range denoting
partial agonists.
Ariëns' original definition equates the molecular nature of alpha to
maximal response only when response is a linear function of
receptor
occupancy. This function has been verified. Thus, intrinsic
activity, which is a
drug
and tissue parameter, cannot be used as a characteristic drug
parameter for classification of drugs or drug receptors. For this
purpose, a proportionality factor derived by null methods, namely,
relative
efficacy,
should be used. Finally, "intrinsic activity" should not be used
instead of "intrinsic efficacy". A "partial agonist" should be
termed "agonist with intermediate intrinsic efficacy" in a given
tissue. IUPAC Medicinal Chemistry
Related terms: Drug
discovery informatics drug design
Cheminformatics
molecular design; Targets binding site,
ligand design:
The design of ligands using structural information
about the target to which they should bind, often by attempting to maximize
the energy of the interaction. IUPAC Computational
permeability:
Ability of a compound to diffuse across
biological membranes. Related terms: bioavailability, biological availability
Related
term: molecular recognition. Drug
discovery & development
IUPAC International Union of Pure and Applied Chemistry, Glossary of Terms
used in Bioinorganic Chemistry, Recommendations, 1997. 450+ definitions.
https://www.ncbi.nlm.nih.gov/books/NBK16710/
IUPAC International Union of Pure and Applied Chemistry, Glossary of
Terms used in Biomolecular Screening 2011 http://iupac.org/publications/pac/83/5/1129/
IUPAC International Union of Pure and Applied
Chemistry, Compendium of Chemical Terminology: Recommendations, compiled
by Alan D. McNaught and Andrew Wilkinson, Blackwell Science, 2005-2017. "Gold
Book" http://goldbook.iupac.org/
IUPAC Inernational Union of Pure and Applied
Chemistry, Glossary of terms used in Computational Drug Design Part 1
https://www.degruyter.com/view/j/pac.1997.69.issue-5/pac199769051137/pac199769051137.xml
IUPAC International Union of Pure and Applied Chemistry, Glossary of Terms
used in Computational Drug Design, Part II
https://iupac.org/recommendation/glossary-of-terms-used-in-computational-drug-design-part-ii
IUPAC International Union of Pure and Applied
Chemistry, Glossary of Medicinal Chemistry, 1998. 100+ terms.
https://www.qmul.ac.uk/sbcs/iupac/medchem/
IUPAC Pharmaceutics 2009
https://www.iupac.org/publications/pac/81/5/0971/
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