Glossary of Terms Used in Medicinal Chemistry
(IUPAC Recommendations 1998)

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Continue from terms starting with A to H.


IND, Intrinsic activity, Inverse agonist, Isosteres, Latentiated drug See Drug Latentiation., Lead discovery, Lead generation, Lead optimization, Lipophilicity, Medicinal chemistry, Metabolism, Metabolite, Me-too drug, Molecular graphics, Molecular modeling, Mutagen, Mutual prodrug, NCE See New Chemical Entity., NDA, New Chemical Entity., Non-classical isostere See Bioisostere., Nucleic acid, Nucleoside, Nucleotide, Oligonucleotide, Oncogene, Orphan drug, Partial agonist, Pattern recognition, Peptidomimetic, Peptoid, Pfeiffer's rule, Pharmacokinetics, Pharmacophore (pharmacophoric pattern), Pharmacophoric descriptors, Placebo, Potency, Prodrug, QSAR See Quantitative Structure-Activity Relationships, Quantitative Structure-Activity Relationships (QSAR), Receptor, Receptor mapping, Second messenger, Site-specific delivery, Soft drug, SPC See Structure-property correlations, Structure-activity relationship (SAR), Structure-based design, Structure-property correlations (SPC), Systemic, Teratogen, Three-dimensional Quantitative Structure-Activity Relationship (3D-QSAR) , Topliss tree, Transition-state analog, Xenobiotic


Abbreviation for Investigational New Drug.

Intrinsic activity

Intrinsic activity is 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.

Inverse agonist

An inverse agonist is a drug which acts at the same receptor as that of an agonist, yet produces an opposite effect. Also called negative antagonists.


Isosteres are molecules or ions of similar size containing the same number of atoms and valence electrons, e.g., O2-, F-, Ne (See also Bioisostere).

Latentiated drug

See Drug Latentiation.

Lead discovery

Lead discovery is the process of identifying active new chemical entities, which by subsequent modification may be transformed into a clinically useful drug.

Lead generation

Lead generation is the term applied to strategies developed to identify compounds which possess a desired but non-optimized biological activity.

Lead optimization

Lead optimization is the synthetic modification of a biologically active compound, to fulfill all stereoelectronic, physicochemical, pharmacokinetic and toxicologic required for clinical usefulness.


Lipophilicity represents the affinity of a molecule or a moiety for a lipophilic environment. It is commonly measured by its distribution behaviour in a biphasic system, either liquid-liquid (e.g., partition coefficient in octan-1-ol/water) or solid/liquid (retention on reversed-phase high performance liquid chromatography (RP-HPLC) or thin-layer chromatography (TLC) system). (See also Hydrophobicity).

Medicinal chemistry

Medicinal chemistry is a chemistry-based discipline, also involving aspects of biological, medical and pharmaceutical sciences. It is concerned with the invention, discovery, design, identification and preparation of biologically active compounds, the study of their metabolism, the interpretation of their mode of action at the molecular level and the construction of structure-activity relationships.


The term metabolism comprises the entire physical and chemical processes involved in the maintenance and reproduction of life in which nutrients are broken down to generate energy and to give simpler molecules (catabolism) which by themselves may be used to form more complex molecules (anabolism).

In case of heterotrophic organisms, the energy evolving from catabolic processes is made available for use by the organism.

In medicinal chemistry the term metabolism refers to the biotransformation of xenobiotics and particularly drugs. (See also Biotransformation; Xenobiotic).


A metabolite is any intermediate or product resulting from metabolism.

Me-too drug

A me-too drug is a compound that is structurally very similar to already known drugs, with only minor pharmacological differences.

Molecular graphics**

Molecular graphics is the visualization and manipulation of three-dimensional representations of molecules on a graphical display device.

Molecular modeling**

Molecular modeling is a technique for the investigation of molecular structures and properties using computational chemistry and graphical visualization techniques in order to provide a plausible three-dimensional representation under a given set of circumstances.


A mutagen is an agent that causes a permanent heritable change (i.e., a mutation) into the DNA (deoxyribonucleic acid) of an organism.

Mutual prodrug

A mutual prodrug is the association in a unique molecule of two, usually synergistic, drugs attached to each other, one drug being the carrier for the other and vice versa.


See New Chemical Entity.


Abbreviation for New Drug Application.

New Chemical Entity

A new chemical entity (NCE) is a compound not previously described in the literature.

Non-classical isostere

Same meaning as Bioisostere.

Nucleic acid*

A nucleic acid is a macromolecule composed of linear sequences of nucleotides that perform several functions in living cells, e.g., the storage of genetic information and its transfer from one generation to the next DNA (deoxyribonucleic acid), the expression of this information in protein synthesis (mRNA, tRNA) and may act as functional components of subcellular units such as ribosomes (rRNA).

RNA (ribonucleic acid) contains D-ribose, DNA contains 2-deoxy-D-ribose as the sugar component.


A nucleoside is a compound in which a purine or pyrimidine base is bound via a N-atom to C-1 replacing the hydroxy group of either 2-deoxy-D-ribose or of D-ribose, but without any phosphate groups. (See also nucleotide).

The common nucleosides in biological systems are adenosine, guanosine, cytidine, and uridine (which contain ribose) and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (which contain deoxyribose).


A nucleotide is a nucleoside in which the primary hydroxy group of either 2-deoxy-D-ribose or of D-ribose is esterified by orthophosphoric acid. (See also nucleoside).


An oligonucleotide is an oligomer resulting from a linear sequences of nucleotides.


An oncogene is a normal cellular gene which, when inappropriately expressed or mutated, can transform eukaryotic cells into tumour cells.

Orphan drug

An orphan drug is a drug for the treatment of a rare disease for which reasonable recovery of the sponsoring firm's research and development expenditure is not expected within a reasonable time. The term is also used to describe substances intended for such uses.

Partial agonist

A partial agonist is an agonist which is unable to induce maximal activation of a receptor population, regardless of the amount of drug applied (See also Intrinsic activity).

Pattern recognition**

Pattern recognition is the identification of patterns in large data sets using appropriate mathematical methodologies.


A peptidomimetic is 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).


A peptoid is a peptidomimetic that results from the oligomeric assembly of N-substituted glycines.

Pfeiffer's rule

Pfeiffer's rule states that in a series of chiral compounds the eudismic ratio increases with increasing potency of the eutomer.


Pharmacokinetics refers to the study of absorption, distribution, metabolism and excretion (ADME) of bioactive compounds in a higher organism. (See alsoDrug disposition).

Pharmacophore (pharmacophoric pattern)

A pharmacophore is 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.

A pharmacophore 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. The pharmacophore 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

Pharmacophoric descriptors are used to define a pharmacophore, including H-bonding, hydrophobic and electrostatic interaction sites, defined by atoms, ring centers and virtual points.


A placebo is an inert substance or dosage form which is identical in appearance, flavor and odour to the active substance or dosage form. It is used as a negative control in a bioassay or in a clinical study.


Potency is the dose of drug required to produce a specific effect of given intensity as compared to a standard reference.

Potency is a comparative rather than an absolute expression of drug activity. Drug potency depends on both affinity and efficacy. Thus, two agonists can be equipotent, but have different intrinsic efficacies with compensating differences in affinity.


A prodrug is 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 . (See also Double prodrug).


See Quantitative Structure-Activity Relationships.

Quantitative Structure-Activity Relationships (QSAR)**

Quantitative structure-activity relationships are mathematical relationships linking chemical structure and pharmacological activity in a quantitative manner for a series of compounds. Methods which can be used in QSAR include various regression and pattern recognition techniques.


A receptor is a molecule or a polymeric structure in or on a cell that specifically recognizes and binds a compound acting as a molecular messenger (neurotransmitter, hormone, lymphokine, lectin, drug, etc.).

Receptor mapping**

Receptor mapping is the technique used to describe the geometric and/or electronic features of a binding site when insufficient structural data for this receptor or enzyme are available. Generally the active site cavity is defined by comparing the superposition of active to that of inactive molecules.

Second messenger

A second messenger is an intracellular metabolite or ion increasing or decreasing as a response to the stimulation of receptors by agonists, considered as the "first messenger". This generic term usually does not prejudge the rank order of intracellular biochemical events.

Site-specific delivery

Site-specific delivery is an approach to target a drug to a specific tissue, using prodrugs or antibody recognition systems.

Soft drug

A soft drug is a compound that is degraded in vivo to predictable non-toxic and inactive metabolites, after having achieved its therapeutic role.


See Structure-property correlations.

Structure-activity relationship (SAR)

Structure-activity relationship is the relationship between chemical structure and pharmacological activity for a series of compounds.

Structure-based design**

Structure-based design is a drug design strategy based on the 3D structure of the target obtained by X-ray or NMR.

Structure-property correlations (SPC)**

Structure-property correlations refers to all statistical mathematical methods used to correlate any structural property to any other property (intrinsic, chemical or biological), using statistical regression and pattern recognition techniques.


Systemic means relating to or affecting the whole body.


A teratogen is a substance that produces a malformation in a foetus.

Three-dimensional Quantitative Structure-Activity Relationship (3D-QSAR)

A three-dimensional quantitative structure-activity relationship is the analysis of the quantitative relationship between the biological activity of a set of compounds and their spatial properties using statistical methods.

Topliss tree**

A Topliss tree is an operational scheme for analog design.

Transition-state analog

A transition-state analog is a compound that mimics the transition state of a substrate bound to an enzyme.


A xenobiotic is a compound foreign to an organism (xenos [greek] = foreign).

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