Covering structural features such as functional groups, cyclic aliphatic compounds, and heterocycles found in organic compounds that are used as drugs – this medicinal chemistry glossary is the complete resource for your studies.

The first half of this extensive medicinal chemistry glossary will focus on some of the most important nomenclature that one comes across when studying medicinal chemistry. Indeed, many of the terms complement the study of clinical pharmacology as well; not least serving as a central resource for many sciences in this regard. The latter half of the medicinal chemistry glossary focuses on structural aspects of organic chemistry; a convenient revision resource for those studying sciences with a significant chemistry component.

Medicinal Chemistry Glossary

The following list explores some of the most common terminology employed in the language of medicinal chemistry.

S T U V W X Y Z #


Names of Structural Features



Ab initio (Latin: from the beginning) in chemistry means computational chemistry predictions or calculations solely based on quantum theory rather than experimental data.
Active Principle  The active principle is the compound(s) in the mixture that is responsible for that mixture’s biological activity.
ADME Abbreviation for Absorption, Distribution, Metabolism, Excretion.Sometimes referred to as ADMET or ADME-Tox to account for toxicity.
Adsorption In chemistry, often refers to situations where a molecule adheres to a surface.
Affinity Refers to a molecule’s tendency associate with another. Drug affinity refers to a drug’s ability to bind to a biological target.
Agonist A drug or an endogenous ligand that can bind to a receptor and elicit a biological response characteristic of the receptor. Note the existence of partial agonists, inverse agonists, and superagonists.
Allosteric A binding site is said to be allosteric if it’s a binding site other than the one used by the endogenous ligand.
Analogue A compound that is structurally related to another
Antagonist In pharmacology, antagonists are receptor ligands that bind to receptors without activating it.
Antibody-drug conjugates Drugs that are covalently linked to antibodies. One purpose is to enhance drug site-specificity.


Binding Region A region within the binding site that can interact with drugs through intramolecular interactions.
Binding Site Regions in a drug target where an endogenous ligand or drug can bind.
Bioavailability The fraction of an administered unchanged drug that reaches the blood supply.
Bioisostere Bioisosteres are chemical groups with similar physicochemical properties which give broadly similar biological properties to a compound.
Bioprecursor prodrug Prodrugs that are activated by oxidation or reduction processes rather than simple hydrolysis.
Biotransformation Chemical modifications done by an organism on chemical compounds.
Blood-Brain Barrier A highly selective permeability barrier that prevents many compounds from reaching the brain.


Calorimetry Experimental determination of heat changes arising from chemical or physical change.
Carrier-linked prodrug Prodrugs which contain the active compound linked to a removable carrier group. Removal is generally through hydrolysis.
ChemDraw A software package used to draw molecules.
Combinatorial Chemistry Combinatorial chemistry comprises of methods used to generate libraries of compounds with sizes ranging from hundreds to millions, in a single process.
Combinatorial Library Large collections of synthesised compounds generated through combinatorial chemistry.
Comparative Molecular Field Analysis (CoMFA) A 3D QSAR software
Computational Chemistry A branch of chemistry that specialises in using computers to help solve chemistry problems.
Conformational Blocker Groups introduced during drug design to prevent a molecule from adopting particular conformations.


De Novo Drug Design The use of molecular modelling software packages to design new drugs or lead compounds for binding sites.
Density Functional Theory (DFT) DFT computational approaches consider that the energy and other properties of a system can be computed from the electron density.
Desolvation The process by which solvent molecules disassociate from a species in solution. In medicinal chemistry, this usually refers to the removal of water molecules surrounding a biological target before the binding of a drug.
Dipole-dipole interactions Intermolecular interactions between two separate dipoles.
Docking In molecular modelling, docking refers to the process by which molecules fit into a binding site.
Drug Target In the simplest sense, drug targets are macromolecular biomolecules such as proteins whose activity can be altered by a pharmacologically active compound.


ELISA Short for enzyme-linked immunosorbent assay, an immunochemical test often employed in the biochemical sciences.
Enantiomer An enantiomer is either of a pair of molecules that are non-superposable mirror images of each other.
Energy Minimisation In molecular modelling, energy minimisations refer to operations carried out to detect a stable conformation for a molecule
Enzyme Large biological molecules (mostly proteins) that act as catalysts for a reaction.


FDA Short for Food and Drug Administration, an agency in the USA that is responsible for regulating vaccines, cosmetics, legal drugs, and food products.
First Pass Effect Refers to the extent by which orally administered drugs undergo biotransformation during its first passage through the liver and the intestines, reducing the concentration of the drug that reaches general circulation.
Functional Group In organic chemistry, refers to specific group of atoms within a molecule that are responsible for the characteristic chemical reactions of the molecule.


Gas Chromatography (GC) A common technique used in analytical chemistry that involves vapourisation, separation, and analysis of volatile compounds.
Genome An organism’s complete set of genetic information.
Global Energy Minimum  Important in molecular modelling, the global energy minimum refers to a molecule’s most stable conformation.


Half-Life In terms of pharmacology, drug half-life refers to the time taken for a drug’s plasma concentration to fall by half. In terms of nuclear chemistry, half-life refers to the time taken for a radioisotope to fall to half its original value.
Hansch Analysis In QSAR, Hansch analysis expresses biological activity using electronic, hydrophobic, and steric parameters.
Hard Drug In medicinal chemistry, hard drugs refer to compounds that are generally nonmetabolisable.
Heteroatom In terms of organic compounds, heteroatoms are any atoms that are not carbon or hydrogen.
Heterocycle Cyclic organic compounds that contain at least two different elements in the ring system.
High Performance Liquid Chromatography (HPLC) A form of liquid chromatography used in analytical chemistry used to separate, identify, and quantify the components of a mixture.
High Throughput Screening An automated method of performing large amounts of in vitro experiments.
Hydrogen Bond Attractive interactions involving two groups: one containing an electron-deficient hydrogen covalently bonded to an electronegative atom and one containing an electron-rich heteroatom.
Hydrogen Bond Acceptor (HBA) The functional group that contains the electron-rich heteroatom and is the recipient of the hydrogen bond.
Hydrogen Bond Donor (HBD) The functional group that contains the electron-deficient hydrogen covalently bonded to an electronegative atom.
Hydrophilic Refers to molecules or groups that are polar and are capable of forming strong hydrogen bonds with water.
Hydrophobic Refers to non-polar molecules that have little affinity for water.


Induced Dipole Interactions A charge or a dipole can induce a dipole in another molecule. Induced dipole interactions refer to interactions between a charge or a dipole and an induced dipole.
In silico Refers to experiments and/or studies performed with a computer.
Infrared Spectroscopy Spectroscopic technique that deals with the infrared region of the electromagnetic spectrum. Used during the characterisation of molecules.
Intermolecular interactions  Interactions that occur between molecules.
Intramolecular interactions Interactions that occur within a molecule.
In vitro Refers to experiments and/or studies performed with isolated macromolecules, cells, or tissue samples.
In vivo Refers to experiments and/or studies performed with live animals or humans.
Ion-dipole Interactions Intermolecular interactions between a charged species and a dipole.
Ionic Interactions Often refers to attractive interactions between oppositely charged ions.
IUPAC Short for International Union of Pure and Applied Chemistry.


Joule A derived unit of energy, work, or amount of heat in the International System of Units.


Kelvin A unit of measurement for temperature. Uses absolute zero as its null point.


Lead Discovery The process of discovering and identifying chemical entities that could serve as a starting point for the development of a clinically useful drug.
Lead Compound Compounds that could serve as a starting point for the development of a clinically useful drug.
Lead Optimisation Drug design techniques employed on lead compounds to improve pharmacokinetic and pharmacodynamic profiles.
Ligand In medicinal chemistry, ligands refer to molecules that are able to bind to a binding site. In coordination chemistry, ligands are ions, molecules, or functional groups that bind to a central metal atom, forming a coordination complex.
Lipinski’s Rule of Five A set of rules that are obeyed by many orally active drugs. Often used as a guide during drug design. Not all orally active drugs obey the rule.
Lipophilic A compound is said to be lipophilic if it has high solubility in fat.


Macromolecule Large molecules with relatively high molecular weights typically generated through polymerisation of smaller subunits.
Medicinal Chemistry A branch of chemistry that incorporates aspects of organic chemistry, physical chemistry, computational chemistry, analytical chemistry, pharmacology, and the biological sciences to design, develop, and synthesise drugs.
Me-too Drugs Drugs that are structurally related to existing drugs. Me-too drugs are often developed by rival pharmaceutical companies in order to gain a foothold in the same area of the market.
Metabolic Blockers Chemical groups added to a drug that slow down or block metabolism at that part of the drug.
Molecular Modelling Comprises of techniques used to investigate molecular structures and their properties using computational chemistry
MSDS Short for Material Safety Data Sheet.
Mutual Prodrug A prodrug that consists of two generally synergistic drugs attached to each other.


Nanoparticle Particles with sizes ranging from 1 – 100 nanometres
New Chemical Entity (NCE) A compound that has not been previously described in the scientific literature.
Nuclear Magnetic Resonance Spectroscopy (NMR) An analytical technique that takes advantage of the magnetic properties of certain nuclei. 1H NMR and 13C NMR are useful analytical techniques.


Organic Synthesis A branch of chemical synthesis that focuses on the synthesis of organic molecules.
Organometallic Chemistry A branch of chemistry that mainly studies the chemistry of compounds that contain Carbon-Metal bonds.
Orphan Drug Pharmaceutical agents that are used to treat rare medical conditions.


Pharmacodynamics The study of the processes by which ligands interact with their binding site and the biochemical and physiological changes associated with the ligand. In simple terms, it is the study of what the drug does to the body.
Pharmacokinetics The study of the fate of the drug administered to a living organism. Pharmacokinetics involves the study of a compound’s ADME properties. In simple terms, it is the study of what the body does to the drug.
Pharmacopoeia An official documentation which details the analytical procedures, effects and directions of use of medicinal substances.
Pharmacophore A description of the main molecular features necessary for biological activity and their relative positions in space. Sometimes referred to as the minimum structure required to elicit a biological response.
Phases of Drug Action The three phases of drug action are the pharmaceutical phase, pharmacokinetic phase, and the pharmacodynamic phase.
Pi-Pi (p-p) interactions Attractive non-covalent interactions that arise between aromatic rings
Prodrug Inactive derivatives of active drug molecules that are converted to parent drug molecules in the body.


Qualitative Analysis In analytical chemistry, quantitative analysis is the determination of the presence or absence of a substance in a sample.
Quantitative Analysis In analytical chemistry, quantitative analysis is the determination of the concentration of a substance in a sample.
Quantitative Structure-Activity Relationships (QSAR) Expresses the biological activity of a set of compounds as a function of physicochemical and/or structural parameters.


Racemic A mixture is said to be racemic if the mixture contains equivalent amounts of the left and right-handed enantiomers of a molecule that is chiral.
Radiopharmaceuticals Medicinal compounds that contain a radioactive nuclide.
Rational Drug Design The design of drugs to specifically work for their respective targets.
Receptor Proteins which ligands can bind to and elicit a biological response.
Retrosynthesis In synthetic organic chemistry, is a problem-solving technique used to transform a typically more complex target molecule into simpler, commercially available precursor structures.
Rigidification Drug design technique used to restrict free rotation about rotatable bonds.


Site-specific Drug Delivery Comprises of methods of delivering pharmaceutical agents at higher concentrations to the desired part of the body
Simplification Drug design technique used when the lead compound is structurally complex. The use of simpler analogues eases synthesis.
Soft Drug Drugs that undergo biotransformations in vivo to metabolites that are generally inactive and non-toxic.
Stereochemistry A branch of chemistry that is concerned with the study of the relationship between chemical properties and the spatial arrangement of atoms and molecules in a compound.
Steric Shield In drug design, steric shields are bulky groups added to metabolically vulnerable parts of the drug in order to slow down metabolism.
Structure-Activity Relationships (SAR) SAR studies explore the relationship between a molecule’s biological activity and the three dimensional structure of the molecule.


Thin Layer Chromatography (TLC) An analytical, separatory technique based on the differing affinities of the constituents of the mixture for the stationary phase.
Transition State Analogue In medicinal chemistry, transition state analogues are compounds that are designed to mimic an enzyme-catalysed reaction’s transition state. Can be used to inhibit an enzyme,


Ultraviolet–visible Spectroscopy (UV-Vis) An absorption spectroscopy technique that uses the ultraviolet-visible regions of the electromagnetic spectrum.


van der Waals interactions Refers to weak intermolecular interactions between transient dipoles usually in hydrophobic regions of molecules.


Withdrawal Symptoms A group of symptoms associated with sudden decrease of or cessation of intake of drugs.


Xenobiotic A compound is said to be xenobiotic if it is foreign to an organism.
X-ray Crystallography A scientific tool used to determine the 3D arrangement of atoms in a crystal using the X-rays.


Yield In chemical synthesis, yield refers to the amount of product obtained at the end of a chemical reaction.


Zwitterion A chemical entity that contains both anionic and cationic groups.


3D QSAR Three-Dimensional quantitative structure-activity relationships are QSAR studies which analyses the biological activities of a series of compounds with respect to their spatial properties using statistical methods.

For the equivalent clinical pharmacology glossary, check out the following link:
Common Terms in Pharmacology

Names of Structural Features in Medicinal Chemistry

Familiarising yourself with the language used in the chemical sciences can help avoid confusion when reading about topics in medicinal chemistry. This next section of our comprehensive medicinal chemistry glossary will show some (and by no means all) of the names and the structures of functional groups, cyclic aliphatic rings, organoheteroatoms, and heterocycles. A lot of the structural features shown below are common to small organic drug molecules. Note that R groups are often used as a generic placeholder for alkyl or sometimes aryl groups.

Simple Acyclic Aliphatic Hydrocarbons

Simple Acyclic Aliphatic Hydrocarbons

Haloalkanes (alkyl halides)

Haloalkanes (alkyl halides)

Simple Organooxygen

Simple Organooxygen

Simple Organonitrogen

Medicinal Chemistry Glossary

Some Groups Containing the Carbonyl Functional Group

Carbonyl Functional Group









Cyclic Aliphatic Hydrocarbons

Cyclic Aliphatic Hydrocarbons

Aromatic Hydrocarbons

Aromatic Hydrocarbons



With enough practice, naming and pointing out the structural features and functional groups of molecules becomes second nature in medicinal chemistry. Try to use this medicinal chemistry glossary as a convenient revision – tying up loose ends whenever you need to refresh your memory. In addition, you should practice using and identifying many of these structures, particularly when it comes to real drug examples. Below, you will find the neurotransmitter serotonin – try to identify all the structural features of this molecule.


medicinal chemistry glossary

The structure of the anti-cancer compound, paclitaxel (Taxol) is shown below. Although it may seem like a daunting task, it is not difficult to point out and name the main features of paclitaxel. Can you point out the key structural features and functional groups of paclitaxel?


That’s about it for our medicinal chemistry glossary. If you would like to explore related articles in this area, check out the following link for more.