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

Energy minimization

Visualizing molecules

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

Partial charges on histamine

Partial charges on protonated histamine

Effect of delocalized charge

Molecular electrostatic potentials (MEPs)

Conformational analysis

Molecular Dynamics

Structure Comparison (2D)

Structure Comparison (3D)

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

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

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

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

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

DOCK

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

Bump filter Reject conformations which involve bad steric interactions

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

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

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

Potential energy probe to find binding site

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

Thymidylate synthase

Inhibitors similar to substrate or cofactor cofactor

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

De novo design of Thymidylate synthase inhibitor

Intended vs. actual interactions

Revised structure

Binding interactions of new structure

Modified inhibitor