Target based drug discovery

Question 1

Lessons learned : Chemical libraries

Answer 1

• Available synthetic libraries designed for eukaryotic targets do not contain many effective antibacterials
• Characteristics of antibiotics differ from those of drugs in other therapeutic sectors
• Antibiotics (natural ones also) do not follow the lipinski’s rule of five, on which libraries are based.

Question 2

Characteristics of antibiotics differ from those of drugs in other therapeutic sectors

Answer 2

• Structures more complex
• Higher serum concentrations are required
• Need to penetrate the bacterial cell enveloppe

Question 3

Go back to nature

Answer 3

• Look to competed species, new compounds produced by streptomyces sp.
• Soil : Low nutritions (screen soil bacteria)
• Explore new habitats for specialized metabolite producers.

Question 4

Metabolites

Answer 4

Products after verwerking of a substrate by bacteria

Like: ATP, aminoacids, glucose etc.

Question 5

How to get effective inhibitors

Answer 5

1. Select on targets on the outside: LPS/ membrane/ secreted proteins
2. Not only essential targets but also proteins important for virulence as potential target
3. Not only enzymes but also protein-protein interactions important
4. Find an inhibitor that target multiple targets
5. Invest more in analysing targets with unknown funciton

Question 6

Bacterial interactome

Answer 6

No proteins work alone in bacteria.

Find interaction inhibitors by In vitro screening and structure based design.

Question 7

Natural compounds are

Answer 7

• Structurally diverse
• More functionally complex
• Unique molecular architecture
• Higher antibacterial activity

Question 8

Conclusion from GSK approach

Answer 8

1. Using synthetic compound libraries against isolated bacterial targets was an unsuccessful strategy
2. Failed due to lack of chemical diversity at that time
3. Do not be too dogmatic on the properties a good target should have
4. Many targets can’t be readily inhibited
5. Targets can be essential in one species but not in another.
   Essentiality of targets should be validated in many different species and infection models.

Question 9

In discovery phase:
Target based discovery need:

And

In stead of target based screening.

Answer 9

Does antibiotic work? And in the body?

• Need a lot of compounds for targets for a few good outcomes
• Need more than two bacteria

Try whole cell screening:

• Try immediately on pathogens and observate
• Try to look in infection model in cell lines or animals.

Question 10

HTS:

Answer 10

High throughtput screening

• Lead identification (compound screening)
  Molecules hit from HTS > undergo limited optimization to identify lead compounds.

Question 11

Structure based design

Answer 11

Synthetic library (screen target) > Look to specific enzymic activity

Question 12

TBDD

Answer 12

Target based drug design: Used to find new drug for other diseases

1. Genome
2. Bioinformatics (target identification)
3. Experimental verification using molecular tools (target validation)
4. High throughtput screening (HTS): Lead identification/ compound selection by finding hits.
5. Medicinal chemistry (lead optimization)
6. Development compound

Question 13

Target validation

Answer 13

Are these targets truly relevant to the disease

Is it essential for growth?
Investigate with knock out

Question 14

Redundant

Answer 14

Genes can be redundant: Blocking one gene product will have no effect

Question 15

Target isolation bacterial

Answer 15

When you produce a prokaryoot target protein in a bacteria > Easy to purify

Question 16

Synthetic library:

SBDD

Answer 16

Screen isolated target > And look for specific enzymic activity

Question 17

Target identification

Answer 17

Characterize genes as candidates

Question 18

Lead identificaiton

Answer 18

Compound screening

Question 19

Lead optimization

Answer 19

Search for optimal efficcacy