2. The lead compound
• A compound demonstrating a property likely to be therapeutically useful
• The level of activity and target selectivity are not crucial
• Used as the starting point for drug design and development
• Found by design (molecular modelling or NMR) or by screening compounds (natural or
synthetic)
• Need to identify a suitable test in order to find a lead compound
• Active principle - a compound that is isolated from a natural extract and which is
principally responsible for the extract’s pharmacological activity. Often used as a lead
compound.
3. Lead Compounds from a Variety of Sources
4. Natural Ligands
5. Existing Drugs
6. High Throughput Screening (HTS)
N
S
O
N
H
R
O
O
OH
Penicillin
O
OH
O
O
O
O
O
O
OH
O
O
O
O
H
NH
O
H
Taxol
N
H
N
N
N
O
O
S
N
O O
N Viagra
1. Chance Discovery
2. Natural Products
3. Clinical Observation
4. 4. Natural Ligands
O
H
O
H
OH
N
H
R
R=H adrenaline
R=Me noradrenaline
Catechol
bioisostere
(toxicity)
Increased size
(selectivity and duration)
Catechol
bioisostere
(toxicity)
Increased size
(selectivity and duration)
N
H
O
H
OH
N
H
O
O
H
Formoterol
AstraZeneca
O
H
OH
N
H
O
H
Salbutamol
GlaxoSmithKline
5. N
O
O
N
N
H
O
O
Cialis
Eli Lilly
N
H
N
N
N
O
O
S
N
O O
N
Levitra
Bayer
5. Existing Drugs
Also known as the “Me-Too” or “Me-Better” Approach
Issues: short duration
Multiple side effects and
incompatibility with other drugs
N
H
N
N
N
O
O
S
N
O O
N
Viagra
Pfizer
Fewer side effects and
incompatibility with other drugs
36h duration (“the weekend pill”)
BEWARE: Patent Issues!!
6. 6. High Throughput Screening (HTS)
• Validated, tractable targets
• target selection for HTS
• Industrialised process
• HTS assay technologies
and automation
• Chemical diversity
• sample selection for HTS
How?
“An industrialised process which brings together validated,
tractable targets and chemical diversity to rapidly identify
novel lead compounds for early phase drug discovery”
50-70% of new drug projects originate from a HTS
9. Drug Candidate
safety testing
Animal Studies
- relevant species
- transgenic KO/KI
mice
- conditional KOs
- agonists/antagonists
- antibodies
- antisense
- RNAi
Studies of
Disease Mechanisms
Human Studies
Phases I,II, III
Target
-receptor; -ion channel; -transporter;
-enzyme; - signalling molecule
Lead Search
-Develop assays (use of automation)
-Chemical diversity
-Highly iterative process
Molecular Studies
The Drug Discovery Process
Lead optimization
-selectivity
-efficacy in animal models
-tolerability: AEs mechanism-
based or structure-based?
-pharmacokinetics
-highly iterative process
Drug Approval
and Registration
Target selection &
validation
Discovery Development
15. CCE – Common Combinatorial Reactions
• Amide Coupling
R
3
O
H
O
N
R
2
H
R
1
N
R
2
R
1
R
3
O
+
HATU, Et3N
NMP
• Sulphonamide Formation
N
R
2
H
R
1
N
R
2
S
R
1
R
3
O O
S
Cl R
3
O O
+
Et3N
NMP
• Reductive Amination
N
R
2
H
R
1
N
R
2
R
1
R
3
H R
3
O
+
AcOH, NMP
Na(AcO)3BH
N N
N
N
O
N
N
+
PF6
-
N
O
HATU
NMP
20. Example 1: Inhibition of Stromelysin
Stromelysin is a zinc-dependent protease that is responsible for breaking down and
re-forming connective tissues, including collagen.
23. Library for the Protein kinase inhibitor
N
H
NOCH3
O
N OCH3
O
N OCH3
OH
N OCH3
S
N OCH3
N OCH3
OH
OH
N
N
OCH3
Cl
O
N OCH3
Cl
Cl
N OCH3
N OCH3
OH
N
S N
O
O
N
OCH3
O
N OCH3
OH
1
2
3 4
5
6
9 10
7
8
11 12
D.J.Maly, I.C.Choong and J.A, Ellman,Proc.Natl.Acad.Sci.USA,2000,97,2419-2424
Example 3. Protein kinase inhibitor
24. Library for the Protein kinase inhibitor
D.J.Maly, I.C.Choong and J.A, Ellman,Proc.Natl.Acad.Sci.USA,2000,97,2419-2424
Ki =41µM
N
H
NOCH3
O
N OCH3
O
N OCH3
OH
N OCH3
S
N OCH3
N OCH3
OH
OH
N
N
OCH3
Cl
O
N OCH3
Cl
Cl
N OCH3
N OCH3
OH
N
S N
O
O
N
OCH3
O
N OCH3
OH
1
2
3 4
5
6
9 10
7
8
11 12
25. Library of protein kinase inhibitor
D.J.Maly, I.C.Choong and J.A, Ellman,Proc.Natl.Acad.Sci.USA,2000,97,2419-2424
F
F
F
F
F
N OCH3
O
Br
Br
O
N OCH3
N
OH
N OCH3
N
N OCH3
O
N OCH3
HO
HO
N OCH3
O
O
O
N OCH3
S
N OCH3
N OCH3
S
N
OCH3
H3CO
C6H5H2CO
N
OCH3
N
OCH3
16
17
18 19
20
13
14 15
21 22 23 24
Ki= 40M
26. Fragment-Based Design : Protein Kinase Inhibition
D.J.Maly, I.C.Choong and J.A, Ellman,Proc.Natl.Acad.Sci.USA,2000,97,2419-2424
Compound IC50µM
C-Src Fyn Lyn Lck
[7] 41± 5 >1000 >1000 >1000
[16] 40± 16 64± 50 400± 170 >500
[7,16] 0.064± 0.038 5.0± 2.4 13 ± 2.4 >250
N
N OCH3
N
N
O
N
O
HO
OH
OH
OH
N
H3CO
7 16
27. Entry
1
2
3
4
6
7
8
Compound
7,16, n=2
Linker c-Src IC50, M
(CH2)n
7,16, n=3
7,16, n=4
7,16, n=5
7,16, n=6
7,16, cis
7,16, trans (1R,2R)
(CH2)n
(CH2)n
(CH2)n
(CH2)n
0.0640.038
1.10.2
6.53.0
6.50.8
5.32.1
1.20.6
0.620.02
N
N N
O
HO
OH
O
linker
Correlation of linker structure with IC50 values for c-Src Inhibition
29. 3. Virtual Screening
Lipinski’s rule screening
Pharmacophore screening
ADMET based screening
Docking, consensus scoring,
visual inspection
Schematic illustration virtual screening strategy
Hit Compound
IC50 prediction, in silico ADME
prediction, in silico toxicity
prediction (TOPKAT)
30. 2D/3D Substructure Searching
Selection of compounds based on
chemical similarity to known active
compounds using some similarity
measure
a. Compound similarity
32. Filtering Hits to Lead Compounds
1.Pharmacodynamics and Pharmacokinetics
2. Biological Assays
3. Lipinski’s Rules and Related Indices
4. Etc.
33. Classic medicinal chemistry
Improve the classic properties of
o Potency
o Selectivity
o Toxic side effect
o Pharmacokinetic
Computer-Aided Drug Discovery:
o Docking,
o 2D-, 3D-, 4D- QSAR
o 3D-QSAR Pharmacophore
o Dynamic simulation
o The drug discovery pipeline
o ADMET profiling
o TOXICITY Profiling
Leads Optimization
34. Structure-based
know receptor,
don’t known ligands
There are two major types of drug design. The first is referred to as Structure-based
drug design and the second, Ligand-based drug design
What will be happy in there???
Ligand-based
don’t know receptor,
known ligands
Protein/ligand interactions
structure/biophysics
docking Statistical analysis (eq. QSAR) of
what group(s) are important for
biological activity
Structure modeling
(Homology/experimental X-
ray/NMR/neutron)
Get a structure