Drug Design: Optimising binding interactions

Question 1

What are lead compounds from the synthetic world?

Answer 1

• Combination of structure-based rational drug design and chemistry can be used for drug optimisation to produce binding interactions with target

Question 2

Why would this be needed?

Answer 2

• To increase activity and reduce dose levels

* To increase selectivity and reduce side effects

Question 3

What are the strategies of optimising binding interactions? (9)

Answer 3

• Vary alkyl substituents
• Vary aryl substituents
• Extension
• Chain extensions / contractions
• Ring expansions / contractions
• Ring variation
• Isosteres
• Simplification
• Rigidification

Question 4

What may alkyl groups in lead compounds do?

Answer 4

May interact with hydrophobic region in binding site
Varys length and bulk of group to optomize interaction
Also improves binding ability - increased methyl groups - improve hydrophobic interaction and improve binding affinity

Question 5

What else can varying length and bulk of alkyl groups do?

Answer 5

Introduce selectivity
- for example in adrenergic agents (ß-adrenoceptors over α-adrenoceptors)

Receptor 1 has a larger binding site – so both ligands can fit (large enough to accommodate both)
Receptor 2 binding site cannot fit the 2nd receptor – steric block

Question 6

Varying alkyl substituents - adrenoceptors

Answer 6

a-Adrenoceptor
• Smaller inside the active centre – less extended
• Adrenaline binds
b-Adrenoceptor
• Adrenaline can bind alpha OR beta – NON-SPECIFIC LIGAND
• Salbutamol – very bulky methyl groups which occupy extended section
• Steric flash – interaction is very thermodynamically unstable - SELECTIVE TO BETA

Question 7

What is an aryl group?

Answer 7

Functional group derived from a simple aromatic ring.

Substitute to incresse binding affinity

Question 8

What is extension?

Answer 8

Extra functional groups - to explore target binding site for further binding regions to achieve additional binding interactions - e.g. ACE INHIBITORS

Question 9

What is chain extension/contraction?

Answer 9

•Useful if a chain is present connecting two binding groups
•Vary length of chain to optimize interactions
Increase/decrease the chain length so it binds more strongly to binding regions

Question 10

Why is testing drug candidates required?

Answer 10

• Tests are required in order to find lead compounds and for drug optimisation
• Tests can be in vivo or in vitro
• A combination of tests is often used in research programmes

Question 11

What 2 factors need to be considered during testing?

Answer 11

sufficient activity against the desired target

minimal activity against any other targets to reduce off-target effect

Question 12

What are in vitro tests carried out on?

Answer 12

• In vitro tests are carried out on target molecules, whole cells, isolated tissues, or isolated organs
• Testing antibacterial agents on microbiological cultures is considered to be in vitro testing

Question 13

What are in vivo tests carried out on?

Answer 13

• In vivo tests are carried out on living systems such as animals or human volunteers
• The in vivo test for an antibacterial agent involves infecting a test animal with a bacterial strain, then administering the antibacterial agent to the animal to see whether it combats the infection

Question 14

What is an enzyme assay?

Answer 14

In vitro test
Test to evaluate the level of enzyme inhibition
To evaluate the mode of inhibition (e.g. competitive or non-commpetitive)
To measure IC50

Question 15

What is IC50?

Answer 15

Concentration of inhibitor in system which reduces activity of target enzyme by 50%

Question 16

During an enzyme assay, how can you tell if the inhibitor is efficient?

Answer 16

Compare with and without inhibitors present

If activity drops with inhibitor – then inhibitor is efficient

Question 17

What does IC50 correspond to ?

Answer 17

• IC50 corresponds to the concentration of inhibitor required to reduce enzyme activity by 50%
• The smaller the dose required to achieve the biological effect, the more potent the drug

Question 18

What is testing with receptors carried out on?

Answer 18

• Carried out on whole cells, tissue cultures, or isolated organs
*not easy to isolate membrane bound receptors as they’re usually integrated into the membrane

Question 19

Measurements in testing with receptors

Answer 19

• Affinity - strength with which compounds bind to a receptor
• Efficacy - measure of maximum biochemical effect resulting from binding of a compound to a receptor
• Potency - concentration of an agonist required to produce 50% of the maximum possible effect
• The smaller the dose required to achieve the biological effect, the more potent the agonist

Question 20

What do in vitro tests measure?

Answer 20

The interaction of a drug with the target
More suitable for routine testing than in vivo
• May also be used to test for pharmacokinetic properties of drug candidates (e.g. Caco-2 cell monolayer absorption models)
• Results are easier to rationalise - less factors involved

Question 21

What is high throughput screening?

Answer 21

Often an automated process
Is an in vitro testing
Carried out on small scale
• It can be carried out on large numbers of compounds in a short time
• It is designed to identify a drug lead within the large library of candidate molecules

Question 22

Limitations of in vitro tests

Answer 22

• Do NOT evaluate the ability of the drug to reach the target
• Does not demonstrate a physiological or clinical effect
• Does not identify possible side effects
• Does not identify effective prodrugs

Question 23

What do in vivo tests measure?

Answer 23

An observed physiological effect.
Measure a drugs ability to interact with its target and its ability to reach that target
Can identify possible side effects
• Rationalisation may be difficult due to the number of factors involved

Question 24

What is drug potency?

Answer 24

concentration of drug required to produce 50% of the maximum possible effect

Question 25

What is therapeutic ratio/index?

Answer 25

compares the dose level of a drug required to produce a desired effect in 50% of the test sample (ED50) versus the dose level that is lethal to 50% of the sample (LD50)