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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]

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): Have important potential for use in proteomics and molecular diagnostic applications. Allozymes are a form of catalytic RNA and/or DNA-based molecules whose ability to catalyze a reaction is modulated by their interaction with an effector molecule. Regulators of allozymes include a diverse range of compounds including proteins, nucleic acids, peptides, small molecules, and ions. Allozyme reactivity can be monitored by a variety of different methods, making these molecules useful sensors for both in vitro and in vivo applications. ["Ribozyme Pharmaceuticals and Archemix Enter Into a Proteomics and Molecular Diagnostics Strategic Alliance" Atlas Ventures News, May 9, 2001] http://www.atlasventure.com/news_content.asp?ne_id=204  Nature Biotechnology (19, 336-341)

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. 

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 binding site for a specific antigen (antigenic determinant or epitope). [IUPAC Bioinorganic]

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

Narrower terms recombinant antibodies; In-depth hybridoma, monoclonal antibodies, polyclonal antibodies. Related terms epitope In-depth immunogen, immunoglobulin; Assays, labels, signaling & detection glossary competitive immunoassay, immunoassay Microarrays glossary antibody microarray 

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

Related terms antibody, epitope

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 RNAi Functional genomics glossary; missense mutation, nonsense mutation Genetic variations glossary ribozymes Sequences DNA & beyond

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]

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]

An oligonucleotide that has a complementary sequence to a portion of, or to all of, an mRNA. Being complementary to a particular target mRNA, antisense oligonucleotides bind specifically to that mRNA; the proprietary chemical modifications made to the antisense molecules facilitate tight binding. When binding occurs, the ability of the mRNA to be read by the cell’s translational machinery is inhibited, and synthesis of the protein that it encodes is blocked. Unlike a gene knockout, this inhibition requires the continuous presence of the antisense molecule; thus, it is reversible. A great advantage of antisense technology is that researchers can design specific inhibitors of a gene of interest based only on knowledge of the gene sequence.  [CHI Target Validation]

Related terms  antisense, antisense DNA, antisense RNA.

antisense RNA: RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.   [MeSH]

RNA-like oligonucleotides that are complementary to a portion of a target mRNA molecule. More specifically, antisense oligonucleotides that are useful as reagents for target validation, or as drugs, are engineered molecules that differ from natural RNA but that have a base sequence that is recognized as being complementary to a very specific mRNA sequence. [CHI Target Validation]

Related terms  antisense, antisense DNA, antisense oligonucleotides.

aptamer: Oligonucleotide which displays specific binding to a protein or other target, often selected by an iterative cycle of affinity- based enrichment. Narrower term peptide aptamer Related term SELEX. [IUPAC Combinatorial Chemistry]

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] 

Related terms ligand; receptor mapping.

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

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 term enantiomer.

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. [CHI Proteomics]

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]

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] Broader term vaccines.

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]

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]

Enzymes chapter from MIT's Biology Hypertextbook http://esg-www.mit.edu:8001/esgbio/eb/ebdir.html

Related term substrate.

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] 

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.

epitope mapping: Maps, genomic & genetic

G-protein: One of a group of proteins involved in signal transduction - the intercellular or intracellular transfer of activation or inhibition signals through a so- called signaling pathway. within cells. [National Institute of General Medical Sciences (NIGMS)] 

Narrower terms: G- protein coupled receptor GPCR,  orphan G- protein coupled receptors

G-protein-coupled receptor GPCR: By far the most common targets of existing drugs: drugs that target these receptors account for 60% of pharmaceuticals on the market, with annual worldwide sales of more than $85 billion. [CHI Target Validation]

More than 350 currently marketed drugs act upon members of this receptor family. [CHI Functional Genomics]

Related term G protein, Narrower term orphan G-protein coupled receptors.

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]

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 glossary.

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] Related term receptor.

hybridoma: A hybrid cell line resulting from the fusion of a specific antibody- producing spleen cell (lymphocyte) with a myeloma cell, which has the growth characteristics of the myeloma component and the antibody- secreting characteristics of the lymphocyte, and will multiply to become a source of pure monoclonal antibody. [IUPAC Biotech]

immunogen: Å 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] 

Related term Gene definitions immunoglobulin genes

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

ligand: 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. [MeSH]

Molecules (e.g., drugs) that bind to active sites on proteins. [CHI Structural genomics]

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]  

Related terms binding site, lock and key: antibody- antigen, enzyme- substrate, or hormone- receptor reactions.

metabolism: In medicinal chemistry the term metabolism refers to the biotransformation of xenobiotics and particularly drugs. (See also Biotransformation; Xenobiotic). [IUPAC Medicinal Chemistry]

monoclonal antibodies MAbs: A single species of immunoglobulin molecules produced by culturing a single clone of a hybridoma cell. MAbs recognize only one chemical structure, i.e., they are directed against a single epitope of the antigenic substance used to raise the antibody. [IUPAC Biotech] 

Broader term antibody; Related terms cloning, hybridoma, polyclonal antibodies

naked DNA: See under DNA vaccines.

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.

peptide aptamer: Functional genomics glossary

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]

peptoid: A peptidomimetic that results from the oligomeric assembly of N-substituted glycines. [IUPAC Medicinal Chemistry]

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. [CHI Structural genomics]

pharmacophore generation: Drug discovery & development

polyclonal antibodies: A range of antibodies specific for many ‘sites’ of a single antigen. [Mucovax BV, Netherlands "Glossary" 2001] http://www.mucovax.nl/Glossary.htm

prodrug: 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]

rDNA: See recombinant DNA

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] Related terms ligand; receptor mapping Molecular modeling glossary

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 glossary

recombinant antibodies: The pipeline of therapeutic antibodies has been growing steadily, building on successful clinical trials particularly in cancer. This growth will certainly accelerate, as genomic companies with many novel targets seek to employ antibodies to modulate these targets. In addition, studies employing antibodies, or antibody mimics, are being ramped up as part of the explosive growth of proteomics. All of these trends place a tremendous emphasis on the development of new approaches for faster antibody development, improved methods of selection and optimization, alternatives for production, and evaluation for novel applications. Recombinant Antibodies April 24- 25, 2002, Cambridge, MA

recombinant DNA, rDNA: Biologically active DNA which has been formed by the in vitro joining of  segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected. [MeSH]

recombinant proteins:  Proteins prepared by recombinant DNA technology.  [MeSH] 

Related term genetic recombination Genetic variations glossary

recombinant therapeutics: See recombinant antibodies, recombinant proteins

recombination: See genetic recombination Genetic variations glossary

SELEX Systematic Evolution of Ligands by Exponential Enrichment: Process for identifying aptamers by iterative enrichment of  oligonucleotide mixtures with respect to their ability to bind a target.  [IUPAC COMBINATORIAL CHEMISTRY]

small molecules Drug Discovery & Development glossary

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 glossary

vaccine: An agent containing antigens produced from killed, attenuated or live pathogenic microorganisms, synthetic peptides or by recombinant organisms, used for stimulating the immune system of the recipient to produce specific antibodies providing active immunity and/or passive immunity in the progeny. [IUPAC Compendium] Narrower term DNA vaccine

Bibliography

Alpha glossary index

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