1. Molecular mechanics Classical physics, treats atoms as spheres Calculations are rapid, even for large molecules Useful for studying conformations Cannot calculate electronic properties

2. Energy minimization

3. Visualizing molecules

4. Quantum Mechanics Considers interactions between electrons and neutrons Can calculate electronic properties Slower calculations than molecular mechanics Ab initio vs. semi-empirical

5. Partial charges on histamine

6. Partial charges on protonated histamine

7. Effect of delocalized charge

8. Molecular electrostatic potentials (MEPs)

9. Conformational analysis

10. Molecular Dynamics

11. Structure Comparison (2D)

12. Structure Comparison (3D)

13. Identifying the active conformation of ligand X-ray crystallography Cambridge Structural Database Protein Data Bank Comparing biological activity of non- rigid ligands with various rigid ligands

14. 3D Pharmacophore Identification X-ray crystal structure of protein-ligand complex (from PDB) Comparison of active compounds (when target structure is unknown) Automated identification of pharmacophores

15. Generate range of conformers For each conformer, define set of pharmacophore triangles Another structure is analyzed Pharmacophore triangles compared to those for previous structures

16. Pharmacophore plot Use pharmacophore triangles common to all active compounds x,y,z correspond to lengths of three sides of triangles Graphing allows identification of distinct pharmacophores Omit triangles involving non-essential binding groups

17. Docking procedures X-ray crystal structure of target protein with binding region highlighted Place ligand within active site with different orientations to identify best orientation Simplest approach—treat ligand and target as non-flexible

18. DOCK

19. ChemX: Analyzing potential binding centers Compare ligand pharmacophores to those in binding site

20. Bump filter Reject conformations which involve bad steric interactions

21. Constructing protein model Need primary amino acid sequence Compare to other proteins Need X-ray structure of related protein Arrange new protein to match sequences similar to known protein Determine structure of connecting sequences by comparison to proteins in databases or with loops

22. Model protein Side chains added in energetically favorable conformations Energy minimization Structure refined with molecular dynamics Use this model protein to analyze potential ligands

23. Constructing binding site when protein structure is unknown Range of structurally diverse compounds with varying activities Align molecules to match up pharmacophores Potential energy grid with probes to measure interaction energies

24. Potential energy probe to find binding site

25. De novo design In theory, design drug for target given structure of binding site In reality, design good lead compound Used to get drugs unlike natural substrates to minimize side effects

26. Thymidylate synthase

27. Inhibitors similar to substrate or cofactor cofactor

28. CB3717 binding to thymidylate synthase active site Create empty binding site from X-ray crystal structure of protein plus inhibitor Found hydrophobic area near where pteridine group is bound

29. De novo design of Thymidylate synthase inhibitor

30. Intended vs. actual interactions

31. Revised structure

32. Binding interactions of new structure

33. Modified inhibitor