Glossary

Question 1

Ligand-based drug design

Answer 1

No structural information for biological target

Relies on knowledge of other molecules that bind to the target of interest

Question 2

QSAR

Answer 2

Quantitative Structure-Activity Relationship
The process of identifying and quantifying the physiochemical properties of a drug to determine if any correlate with its bioactivity

Question 3

Es

Answer 3

Taft’s steric factor

Question 4

MIC

Answer 4

Minimum Inhibitory Concentration

The lowest concentration of a chemical that prevents the visible growth of bacterium

Question 5

Antagonist

Answer 5

A drug that blocks the receptor - it binds to but doesn’t activate the receptor

Question 6

Pharmacophore

Answer 6

The steric and electronic features that are necessary in order to ensure optimal supramolecular interactions with a specific biological target and to trigger (or block) its biological response

Question 7

Structure-based drug design

Answer 7

Drug design based on knowledge of the 3D structure of the target

Question 8

Virtual screening

Answer 8

The use of computational methods to analyse large databases of compounds in order to identify a hit compound

Question 9

Molecular docking

Answer 9

Refers to a prediction of the binding mode of a compound to the active site
Also predicts the strength of association

Question 10

Supersaturation

Answer 10

A solution containing more dissolved material than could be dissolved by the solvent under normal conditions
e.g. by rapid cooling

Question 11

Non-covalent interactions

Answer 11

Relatively weak chemical bond that doesn’t involve sharing electrons
There are 4 main types in biological systems:
1. H-bonds
2. Ionic bonds
3. vdW interactions
4. Hydrophobic interactions

Question 12

Molecular mechanics

Answer 12

Uses classical (rather than quantum) mechanics to model molecular systems
The potential energy of the system is calculated as a function of nuclear coordinates (i.e. electrons are ignored)

Question 13

Force field

Answer 13

A collection of equations and parameter sets used to calculate the potential energy of a system of atoms in molecular mechanics

Question 14

Molecular dynamics

Answer 14

Computational technique where the time evolution of a set of atoms is followed

Question 15

Scoring function

Answer 15

A mathematical function to predict the binding affinity between 2 molecules after they have been docked

Question 16

IC50

Answer 16

Half maximal inhibitory concentration

A measure of the effectiveness of a substance in inhibiting a biological function

Question 17

Transition state analogue

Answer 17

Enzyme inhibitors which are designed to mimic the transition state of an enzyme-catalysed reaction

Question 18

Kinetic isotope effects

Answer 18

Change in reaction rate of a chemical reaction when one atom in the reactants is replaced by one of its isotopes