Genomic biology & chemistry Map:  Finding guide to terms in these glossaries  Site Map
Related glossaries include Biomolecules, Drug discovery & development,  In silico & molecular Modeling 

active center: The location in an enzyme where the specific reaction takes place. [IUPAC Bioinorganic]

active site: See active center.

affinity: The tendency of a molecule to associate with another. The affinity of a drug is its ability to bind to its biological target (receptor, enzyme, transport system, etc.) For pharmacological receptors it can be thought of as the frequency with which the drug, when brought into the proximity of a receptor by diffusion, will reside at a position of minimum free energy within the force field of that receptor. [IUPAC Medicinal Chemistry]

A powerful method of protein purification in which a ligand is chemically attached to a solid support and used to absorb the relevant protein from solution. After washing to remove all other proteins, those bound tightly are eluted by adding soluble ligand or by changing the conditions to decrease the affinity of the protein for the bound ligand [ICN]

Related term/narrower?: antibody affinity

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).

allosteric ribozymes (allozymes): Sukeerthi Seetharaman et. al. "Immobilized RNA switches for the analysis of complex chemical and biological mixtures" Nature Biotechnology 19 (4): 336- 341, April 2001

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] Compare congener.

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

antibody: A protein (immunoglobulin) produced by the immune system of an organism in response to exposure to a foreign molecule (antigen) and characterized by its specific binding to a site of that molecule (antigenic determinant or epitope). [IUPAC Compendium] 

A protein, belonging to the class of immunoglobulins, designed to bind a specific antigen in order to remove it from the body. They are synthesised exclusively by B-lymphocytes, in millions of forms, each with a different amino acid sequence and a specific  for a specific antigen (antigenic determinant or epitope). [IUPAC Bioinorganic]

Immunoglobulin molecules having a specific amino acid sequence by virtue of which they interact only with the antigen that induced their synthesis in cells of the lymphoid series (especially PLASMA CELLS), or with an antigen closely related to it.  MeSH

Protecting Antibody IP Across Continents, Improving Selection and Libraries, Solving Antibody Problems: Aggregation, Glycosylation, and Delivery, Engineering for Optimum Performance and Yield, Emerging Technologies: The Next Generation, Applications and Case Studies  Antibodies Europe November 7-8, 2007 •  Vienna, Austria

Making and using antibodies, John Wagner's Logic of Molecular Approaches to Biological Problems (Cornell Univ. Graduate School of Medical Science, US ) has a section explaining what a powerful technology this is. http://www-users.med.cornell.edu/~jawagne/Antibody_Approaches.html
Antibody Resource Page, http://www.antibodyresource.com/index.html
Monoclonal Antibodies & Therapies, Nature, 2004 http://www.nature.com/focus/antibodies/ 

Narrower terms: domain antibodies, fully human antibodies, hybridoma, monoclonal antibodies, polyclonal antibodies, recombinant antibodies, therapeutic antibodies,. Need definitions for primary antibodies, secondary antibodies

Related terms: epitope, immunogen, immunoglobulin; Assays & screening competitive immunoassay, immunoassay; Microarrays antibody microarray 

antibody affinity: A measure of the binding strength between antibody and a simple hapten or antigen determinant. It depends on the closeness of stereochemical fit between antibody combining sites and antigen determinants, on the size of the area of contact between them, and on the distribution of charged and hydrophobic groups. It includes the concept of "avidity," which refers to the strength of the antigen- antibody bond after formation of reversible complexes. MeSH, 1979

antibody engineering: NFCR Center for Therapeutic Antibody Engineering Glossary , National Foundation for Cancer Research, Dana Farber Cancer Institute  http://research.dfci.harvard.edu/nfcr-ctae/research/tech_glossary.php 

antigen: A compound (protein, polysaccharide, microorganism, virus) foreign to the body that induces the production of specific antibodies. [IUPAC Bioinorganic] 

Related terms antibody, epitope

antigenic mimicry: See under molecular mimicry

antisense (molecule): An oligonucleotide or analog thereof that is complementary to a segment of RNA or DNA and that binds to it and inhibits its normal function. [IUPAC Medicinal Chemistry]

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. [PA Hengen, Is there any sense in antisense terminology? Trends in Biotechnology 21: 153-154 April 1996] 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  

Narrower terms: antisense DNA, antisense oligonucleotides, antisense RNA, Related terms: Genetic Manipulation & disruption RNAi; SNPs & other genetic variations missense mutation, nonsense mutation; Sequences DNA & beyond ribozymes

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

antisense RNA: RNA

aptamer: 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 peptide aptamer; Related terms: SELEX, spielgemers  

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

bioavailability: See biological availability

biological availability: The extent to which the active ingredient of a drug dosage form becomes available at the site of drug action or in a biological medium believed to reflect accessibility to a site of action. MeSH 1979  Also known as bioavailability.

biofilms: Are composed of populations or communities of microorganisms adhering to environmental surfaces. These microorganisms are usually encased in an extracellular polysaccharide that they themselves synthesize. Biofilms may be found on essentially any environmental surface in which sufficient moisture is present. [John Lennox, et. al., Biofilm Primer, Penn State Univ. Altoona, US ] http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/primer.html

May be involved in a number of human bacterial infections.

biotransformation: The chemical conversion of substances by living organisms or enzyme preparations. [IUPAC Medicinal Chemistry]

The chemical alteration of an exogenous substance by or in a biological system. The alteration may inactivate the compound or it may result in the production of an active metabolite of an inactive parent compound. The alteration may be either non- synthetic (OXIDATION- REDUCTION; HYDROLYSIS) or synthetic (glucuronide formation, sulfate conjugation, ACETYLATION; METHYLATION). This also includes metabolic detoxication and clearance. MeSH, 1970

CDR: Complementarity Determining Region [A CDR- Based Approach for Generating Fully Human Antibodies, CHI's GenomeLink 22.2

cancer vaccines: Cancer genomics

chiral: Having the property of chirality. As applied to a molecule the term has been used differently by different workers. Some apply it exclusively to the whole molecule, whereas others apply it to parts of a molecule. [IUPAC Compendium]

chirality: The geometric property of a rigid object (or spatial arrangement of points or atoms) of being non- superimposable on its mirror image; such an object has no symmetry elements of the second kind. [IUPAC Compendium] 

Related terms: enantiomer, handedness.

chromophore: That part of a molecular entity consisting of an atom or group of atoms in which the electronic transition responsible for a given spectral band is approximately located. [IUPAC Bioinorganic]

That part of a molecular entity consisting of an atom or group of atoms in which the electronic transition responsible for a given spectral band is approximately localized.  [IUPAC Photo]

chromophore assisted laser inactivation: Antibodies specific for the targeted protein, but not neutralizing, bring a reagent into proximity of the protein, and when activated by a laser, the reagent generates hydroxyl radicals that effectively inactivate the protein. 

conformers: Molecules with the same molecular structure (same number of atoms and same atoms are bonded within the molecule) but with a different 3-Dimension representation due to twisting of various internal bonds   [United Devices Cancer Project FAQs http://members.ud.com/projects/cancer/faq_chem.htm

Compare: de novo structure

congener: A substance literally con- (with) generated or synthesized by essentially the same synthetic chemical reactions and the same procedures. Analogs are substances that are analogous in some respect to the prototype agent in chemical structure.

Clearly congeners may be analogs or vice versa but not necessarily. The term congener, while most often a synonym for homologue, has become somewhat more diffuse in meaning so that the terms congener and analog are frequently used interchangeably in the literature. [IUPAC Medicinal Chemistry]

cytochrome P450 enzymes: The most important and well- studied group of drug- metabolizing enzymes, the cytochrome P450 enzymes (found in the liver) are responsible for the metabolism of a large number of pharmaceutical compounds. These enzymes function to detoxify xenobiotics (foreign molecules in the body, including drugs). The various genetic polymorphisms in cytochrome P450 can result in increased enzymatic activity, decreased enzymatic activity, or complete loss of enzyme activity. These changes can, in turn, lead to increased (or decreased) activation of pro- drugs, or to increased (or decreased) metabolism and excretion of drugs. 

cytoplasmic and nuclear receptors: Proteins in the cytoplasm or nucleus that specifically bind signaling molecules and trigger changes which influence the behavior of cells. The major groups are the steroid hormone receptors (RECEPTORS, STEROID), which usually are found in the cytoplasm, and the thyroid hormone receptors (RECEPTORS, THYROID HORMONE), which usually are found in the nucleus. Receptors, unlike enzymes, generally do not catalyze chemical changes in their ligands. MeSH, 1994

DNA vaccines: Recombinant DNA vectors encoding antigens administered for the prevention or treatment of disease. The host cells take up the DNA, express the antigen, and present it to the immune system in a manner similar to that which would occur during natural infection. This induces humoral and cellular immune responses against the encoded antigens. The vector is called naked DNA  because there is no need for complex formulations or delivery agents; the plasmid is injected in saline or other buffers. MeSH, 1997    Broader term: vaccines  Narrower term: naked DNA vaccines

DNA Vaccine.com http://dnavaccine.com/

de novo structure: A de novo structure, or de novo derivative, is a molecule that has actually been altered slightly rather than just contorted. [United Devices Cancer Project FAQs ]http://members.ud.com/projects/cancer/faq_chem.htm

Compare: conformer

deorphanize: Identification of new ligands for receptors.

domain antibodies:  The smallest known antigen- binding fragments of antibodies, ranging from 11 kDa to 15 kDa. ... owing to their small size and inherent stability, can be formatted into larger molecules to create drugs with prolonged serum half- lives or other pharmacological activities. LJ Holt et. al, Domain Antibodies: Proteins for Therapy, Trends in Biotechnology, 21 (11): 484- 490, Nov. 2003

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]

See also definition in  IUPAC Provisional glossary Biomolecular Screening

Is this related to efficacy as required by the FDA for regulatory approval?

enantiomer: One of a pair of molecular entities that are mirror images of each other and non- superimposable. [IUPAC Bioinorganic] 

Also called optical isomers. Related terms: chirality, racemate.

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

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.

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 Compendium] 

See also definition in  IUPAC Provisional glossary Biomolecular Screening

The specific interaction between proteins is determined by only limited parts of the proteins involved. In general the epitope (interaction site) of a protein is composed of 7-30 amino acids. ... If an epitope is formed by a continuous stretch of amino acids sequence it is called a linear epitope. In about one third of all proteins the epitope is linear. However, in the majority of cases the epitope is composed of amino acids that are close in space, but can be located on different loops of the amino acid sequence. These epitopes are referred to as discontinuous epitopes. Our technology is very well suited to study and target linear epitopes, but also the more difficult to study, conformational epitopes   Epitopes, PepScan Systems  http://www.pepscan.nl/html/outframeset.html

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, discontinuous epitopes, linear epitopes, 

epitope mapping: Maps, genomic & genetic

G-protein-coupled receptors GPCRs: Drug targets .

Good Informatics Practices Guidance Document (GIP): A newly drafted comprehensive body of information of regulatory requirements in the form of existing (GLP, GMP, GCP and Part 11) and currently used standards compiled in one reference guide for an IT system of a life science or healthcare environment. http://www.lsit.org/initiatives/gip.php

GTP-binding proteins: Regulatory proteins that act as molecular switches. They control a wide range of biological processes including: receptor signaling, intracellular signal transduction pathways, and protein synthesis. Their activity is regulated by factors that control their ability to bind to and hydrolyze GTP to GDP. EC 3.6.1 MeSH, 1997  Is this different from G- proteins?

handedness: Chirality and handedness are concepts that apply to the structure of molecules. Chirality is defined by the lack of certain features of symmetry, which lead to an object not being superimposable on its mirror image. Handedness is a different phenomenon relating to the ability to classify chiral objects into right-handed and left-handed objects. All handed objects are chiral, but not all chiral objects are handed. In 1968 through 1970, Ruch and coworkers developed a theory of chirality that provided a mathematical basis for the handedness of chiral objects. Handed chiral objects are considered to be analogous to shoes, which are readily classified into right and left shoes regardless of the size, material, style, or other attributes of the shoes in question. Nonhanded chiral objects are considered to be analogous to potatoes, which have no symmetry because of their irregular patterns of "bumps" and "eyes," thereby meeting the lack of symmetry requirements for chirality. There is, however, no unambiguous way to classify a set of potatoes into "left" and "right" potatoes. RB King, Chirality and handedness: the Ruch "shoe-potato" dichotomy in the right- left classification problem, Annals of the  New York Academy of Sciences 988: 158- 170, May 2003

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.

hybridoma: Genetic manipulation & disruption

hydrophilicity: Pharmaceutical chemistry

hydrophobicity: Pharmaceutical chemistry

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

immunoglobulin Ig: A protein of the globulin- type found in serum or other body fluids that possesses antibody activity. An individual Ig molecule is built up from two light (L) and two heavy (H) polypeptide chains linked together by disulfide bonds. Igs are divided into five classes based on antigenic and structural differences in the H chains. [IUPAC Compendium] 

Glycoproteins present in the blood (ANTIBODIES) and in other tissue. They are classified by structure and activity into five classes (IMMUNOGLOBULIN A; IMMUNOGLOBULIN D; IMMUNOGLOBULIN E; IMMUNOGLOBULIN G; IMMUNOGLOBULIN M).  MeSH, 1972

Related term: Gene categories immunoglobulin genes

immunotoxins:  Semi-synthetic conjugates of various toxic molecules, including radioactive isotopes and bacterial or plant toxins, with specific immune substances such as immunoglobulins, monoclonal antibodies, and antigens. The antitumor or antiviral immune substance carries the toxin to the tumor or infected cell where the toxin exerts its poisonous effect. MeSH, 1990

Broader term: antibodies

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

integrative biology: the ability to take data sources from a number of different places and integrate them to help us understand biological systems better.  David de Graaf in "Building Integrative Biology at Boehringer Ingelheim, BioIT World Jan-Feb 2009 http://www.bio-itworld.com/2009/1/05/de-graaf-at-boehringer-ingelheim.html 

Related terms: systems biology

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]

ion channels: Ion channels regulate many physiological functions and are targets for numerous drugs under investigation. Topics include case studies on the design of robust and reliable screening platforms, ion channels library design, initial studies with structure guided models, and specific case studies of novel antagonists.  Ion Channels: An emerging target for therapeutic development, Discovery on Target, Oct. 15-19, 2007, Boston MA

Enable ions to flow rapidly through membranes in a thermodynamically downhill direction after an electrical or chemical impulse. [IUPAC Bioinorganic]

Gated, ion-selective glycoproteins that traverse membranes. The stimulus for channel gating can be a membrane potential, drug, transmitter, cytoplasmic messenger, or a mechanical deformation. Ion channels which are integral parts of ionotropic neurotransmitter receptors are not included. MeSH, 1979

"Valves" on the cell membrane that allow ions to flow in and out of the cell membrane. Ion channels constitute a major class of targets for drug discovery and development.  CHA, Cambridge Healthtech Advisors Model Animal Systems: Emerging Applications and Commercial Opportunities in Drug Discovery and Development, report, 2004

Related term: Cell biology patch clamping 

kinases: see protein kinases

Related terms: protein kinase targets: See Protein categories protein kinase; Chemistry computational and medicinal chemistry integration 

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 http://www.the-scientist.com/yr2004/aug/research4_040802.html 

Molecules (e.g., drugs) that bind to active sites on proteins.

Particularly used of small molecules that bind to larger molecules.

Google = about 301,000 Aug. 13, 2002  about 1, 170,000 Dec. 3, 2003

Narrower term: protein ligand; Related terms: binding site, lock and key, antibody,  antigen, enzyme- substrate, hormone- receptor reactions.

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]

mechanism of action: Pharmacogenomics

medicinal biology, medicinal chemistry, medicinal systems biology: Chemistry & biology

metabolism, metabolite, metabolite profiling, metabonomics: Metabolic profiling

molality: The molal unit is not used nearly as frequently as the molar unit. A molality is the number of moles of solute dissolved in one kilogram of solvent. Be careful not to confuse molality and molarity. Molality is represented by a small "m," whereas molarity is represented by an upper case "M."  [Roberta Crowell Barbarlace "Molarity, Molality and Normality" Environmental Chemistry.com, 1995-2001] http://environmentalchemistry.com/yogi/chemistry/MolarityMolalityNormality.html

Related term: solubility

molarity: The molar unit is probably the most commonly used chemical unit of measurement. Molarity is the number of moles of a solute dissolved in a liter of solvent. [Roberta Crowell Barbarlace "Molarity, Molality and Normality" Environmental Chemistry.com, 1995- 2001] http://environmentalchemistry.com/yogi/chemistry/MolarityMolalityNormality.html

Related term: solubility

molecular breeding: Genetic manipulation & disruption

molecular mechanisms of action: Pharmacogenomics

monoclonal antibodies: Drug discovery & Development

morpholinos: http://www.macalester.edu/~montgomery/Morpholinos.html 
Broader term: antisense oligonucleotides

naked DNA: DNA

naked DNA vaccines: NIAID, NIH, Division of AIDS, Naked DNA Vaccines http://www.niaid.nih.gov/daids/vaccine/dna.htm 

NF-kappa B: Ubiquitous, inducible, nuclear transcriptional activator that binds to enhancer elements in many different cell types and is activated by pathogenic stimuli. The NF-kappa B complex is a heterodimer composed of two DNA- binding subunits: NF-kappa B1 and relA. MeSH, 1991

nuclear receptors: See under cytoplasmic and nuclear receptors . Related term: selective modulators

optical isomers: See under enantiomers

orphan G-protein-coupled receptors: GPCRs with unknown function.

orphan receptors: Receptor for which no ligands have yet been identified.

Related terms: deorphan, deorphanize

paratope: Wikipedia http://en.wiktionary.org/wiki/paratope 
Related term: binding sites, antibody  MeSH

pathways: Metabolic profiling

peptide aptamers: Genetic manipulation & disruption

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]

permeability:  Ability of a compound to diffuse across biological membranes.
"Reducing the investment made in likely drug development failure" CHI's Genome Link 15.1  http://www.healthtech.com/newsarticles/issue15_1.asp Christopher  Lipinski talks about improving permeability.

Related terms: bioavailability, biological availability

pharmacophore: 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] 

photoaptamers: Aptamers that incorporate a brominated deoxyuridine (BrdU) in place of the thymidine (T) normally found in DNA. A photoaptamer recognizes both the complex shape and charge distribution of its protein target and the presence of specific amino acid residues at specific sites. 

Related term: spiegelmer; Broader term: aptamers

polyclonal antibodies: Genetic manipulation & disruption

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 

protean 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  http://www.nature.com/cgi-taf/Gateway.taf?g=5&file=/
drugdisc/res_high/articles/nrd885.html&filetype=&_UserReference=

protein kinases: Have become key targets for therapy of various diseases, especially in oncology. New developments in inhibiting the catalytic function of kinases, as well as emerging promising technologies, expand the possibilities of kinases for drug development. Enabling rational drug design, furthering target identification, developing selective and also multitargeted kinase inhibitors are only a few of the pharmaceutical drug development strategies. Due to the growing research and emerging technology available, the limiting factor is not the amount of data that can be obtained but rather the quality of the data, validation and the associated costs. Protein Kinase Targets  June 4-6, 2007 • Boston, MA

rDNA: See recombinant DNA

RNAi RNA interference: Genetic Manipulation & Disruption

racemate: An equimolar mixture of a pair of enantiomers. It does not exhibit optical activity. The chemical name or formula of a racemate is distinguished from those of the enantiomers by the prefix (±)- or rac- (or racem-) or by the symbols RS and SR. [IUPAC Compendium]  

Related term: enantiomer

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:  Cell biology 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]  

Related term: molecular recognition. Drug discovery & development

recombinant antibodies: Drug targets 

recombinant DNA, rDNA, recombinant proteins, recombinant therapeutics:: Genetic manipulation & disruption

recombinant therapeutics: See recombinant antibodies, recombinant proteins

recombination: See genetic recombination SNPs & Genetic variations

reverse vaccinology: Today, the possibility of using genomic information allows us to study vaccine development in silico, without the need of cultivating the pathogen. This approach, which we have named 'reverse vaccinology', reduces the time required for the identification of candidate vaccines and provides new solutions for those vaccines which have been difficult or impossible to develop. Rappuoli R. Reverse vaccinology, a genome- based approach to vaccine development, Vaccine. 19 (17-19) 2688- 2691, Mar 21, 2001

ribosome display, SELEX Systematic Evolution of Ligands by Exponential Enrichment: Genetic manipulation & disruption

selectivity: The word 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

Related term: promiscuous drugs

small molecule therapeutics, small molecules Drug Discovery & Development

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.

"Reducing the investment made in likely drug development failure" CHI's Genome Link 15.1  http://www.healthtech.com/newsarticles/issue15_1.asp Christopher  Lipinski talks about improving solubility.

Related terms:  molality, molarity; Cheminformatics rule of five

spiegelmer: The chiral inversions or mirror images of aptamers. 

Related term: photoaptamer; Broader term: aptamers

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]  Related term enzyme.

How does this definition compare with substrate Microarrays & protein arrays

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

systems biology: Manipulation & disruption

therapeutic antibodies:  While all of the therapeutic antibodies to reach the market to date are murine, chimeric, or humanized antibodies, several companies are developing fully human monoclonal antibodies.  An alternate approach is to isolate fully human variable domains from phage libraries, and then convert these into monoclonal antibodies. 

Related terms: fully humanized antibodies, monoclonal antibodies

Toll- like receptors TLRs: See under DNA CpG DNA 

vaccine: Drug discovery & development

Bibliography
IUPAC Computational
IUPAC Provisional glossary Biomolecular Screening 2008

Alpha glossary index

How to look for other unfamiliar  terms

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