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PTPN1 in PDB view
Structure of target protein
receptor
Preparation of a computational
model for in-silico analysis
Docking and analysis
database
Ligand
optimization
Ligand
Lead molecule
Hindu College of Pharmacy, Guntur A.P
1/31/2015
2
Receptor Structure
REQUIREMENT
A Model Receptor
Known
REQUIREMENT
Lead Compound and
derivatives with biological
data
Unknown
Analog Based
Drug Design
Structure Based
Drug Design
Homology Modeling
Receptor Mapping
QSAR
Docking
Molecular Dynamics
Simulations
Quantum
Mechanical
(BRABO)
Rigid Docking
FlexiDock
PCA
ANN
Simulated Annealing
Monte Carlo
Simulations
Quantum
Mechanics for
Alignment
SINGLE MOLECULE
CoMFA
CoMSIA
GA
Quantum
Mechanical
Descriptors
SYBYL, INSIGHT II, CERIUS2, MOE, AMBER (CDAC), DOCK, AUTODOCK
BURGER’S “MEDICINAL CHEMISTRY
ANDofDRUG
DISCOVERY”,
JHON WILEY
AND SONS PUBLICATION, LONDON,SIXTH
EDITION, 2009
3
1/31/2015
Hindu College
Pharmacy,
Guntur A.P
Compound databases,
Microbial broths,
Plants extracts,
Combinatorial Libraries
Target Enzyme
(or) Receptor
Random screening
synthesis
Lead molecule
Receptor-Ligand
Complex
3D QSAR
Docking
Linking or
Binding
3D ligand
Databases
3D structure by
Crystallography,
NMR, electron
microscopy (or)
Homology Modeling
Testing
Redesign
to improve
affinity,
specificity etc.
BURGER’S “MEDICINAL CHEMISTRY
ANDofDRUG
DISCOVERY”,
JHON WILEY
AND SONS PUBLICATION, LONDON,SIXTH
EDITION, 2009
4
1/31/2015
Hindu College
Pharmacy,
Guntur A.P
1. Obtain target protein
2. Preparation of protein
3. Identification of receptor pocket
4. Preparation of compound database
5. Docking
6. Analysis
7. Ligand optimization
8. Re-evaluation
9. Identification of lead molecule
Hindu College of Pharmacy, Guntur A.P
1/31/2015
5
Hindu College of Pharmacy, Guntur A.P
1/31/2015
6