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Summary Receptor based drug design and computational models
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Drug design and mechanisms of drug action - 1st semester Includes bullet points, key diagrams and images
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Receptor Based Drug Design and Computational ModelsX-Ray Crystallography
Enzymes easier to work with than receptors
Solid state technique
Highly purified macromolecules are dehydrated to form crystals 0.05-0.5 mm
long
X-rays diffract and are detected
Position and intensity of diffraction allows the 3D structure of the protein to be
compared to the data base (PDB)
Biological NMR
Using N 15 and C 13
2D technique
Shifts show binding interactions
Solution state technique
Docking
Predicts the preferred orientation of a ligand when bound to a protein
Crystal structure taken from database and potential ligands added
Protein structure ideally comes from XRC than NMR
Rapid screening
De-Novo Design
Series of linked moieties (molecules divided up in sections)
Each moiety interacts at a given site
Take crystal structure with ligand bound
Identify main binding interactions and shape of binding site
Then remove the ligand from crystal structure
Identify structural motifs that could bind
Calculate distance between these and add core molecule
Fragment Based Ligand Design
Weak molecules with many minor interactions
Don’t fit in the receptor well
Use NMR and XRC
Optimise initial fragment to bind to adjacent regions of receptor
Fragment Linking
Take many different fragments
Assess efficacy at high concentrations to receptor
Identify 2 compounds that bind at different sites but close enough to bridge
Produce large high affinity compounds
Fragment Self Assembly
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