Rational Drug Design : HIV Integrase

1. Rational Drug Design : HIV Integrase

2. A process for drug design which bases the design of the drug upon the structure of its protein target. Structural mapping of the receptor (protein, P) active site Identification of ligands (L) of complementary shape and appropriate functionality Docking of the ligand to the receptor site - predicting a range of PL complexes with different DGPL values 4. Scoring i.e. ranking DGPL and correlating with experimentally determined properties such as IC50 values

4. The catalytic domainhas an RNaseH-type fold and belongs to the superfamily of polynucleotidyl transferases. The active site is comprised of two Asp residues and one Glu, in the typicalD,D(35)E motif, each of which is required for catalysis.

5. de novo Ligand Design

6. four criteria to conclude that integrase is theinhibitor target: 1. found to be active against recombinant integrase. 2. infected cells treated with the drug must show an accumulation of 2-LTR circles, resulting from the accumulation of viral cDNA and decreased HIV integration into host 3. integrase mutations must be found in drug-resistant viruses 4, the drug should be inactive in biochemical assays against recombinantintegrases bearing the mutations identified in the drug-resistant viruses DKAs DCQ acids; DCT acids PDP SQL Quinolone derived

7. Issues in Protein Setup • Crystal structure available for Integrase but : I. Limitations of crystal structure: • only catalytic domain • DNA binding not revealed • cystal structure vs. physiologically active structure II. Position of hydrogens undetermined III. Residues missing or ill-defined IV. Protonation of His undetermined V. Solvation

8. Issues in Protein Setup Crystal structure available for Integrase Catalytic Domain but : I. Crystal reveals trimeric structure II. Position of hydrogens undetermined III. Residues missing or ill-defined IV. Protonation of His undetermined V. Solvation

9. Issues in Protein Setup Crystal structure available for Integrase Catalytic Domain but : I. Crystal reveals trimeric structure II. Position of hydrogens undetermined III. Residues missing or ill-defined IV. Protonation of His undetermined V. Solvation

10. Issues in Protein Setup Crystal structure available for Integrase Catalytic Domain but : I. Crystal reveals trimeric structure II. Position of hydrogens undetermined III. Residues missing or ill-defined IV. Protonation of His undetermined V. Solvation

11. Issues in Protein Setup Crystal structure available for Integrase Catalytic Domain but : I. Crystal reveals trimeric structure II. Position of hydrogens undetermined III. Residues missing or ill-defined IV. Protonation of His undetermined V. Solvation

12. Issues in Protein Setup Crystal structure available for Integrase Catalytic Domain but : I. Crystal reveals trimeric structure II. Position of hydrogens undetermined III. Residues missing or ill-defined IV. Protonation of His undetermined V. Solvation

13. Issues in Ligand Design Crystal structure available for CITEP bound to catalytic core but : I. Position of hydrogens undetermined II. Tautomeric structures possible III. Influence of pH IV. Need to limit conformational flexibility based on experimental and theoretical crteria

14. Issues in Ligand Design Crystal structure available for CITEP bound to catalytic core but : I. Position of hydrogens undetermined II. Tautomeric structures possible III. Influence of pH IV. Need to limit conformational flexibility based on experimental and theoretical crteria

15. Issues in Ligand Design Crystal structure available for CITEP bound to catalytic core but : I. Position of hydrogens undetermined II. Tautomeric structures possible III. Influence of pH IV. Need to limit conformational flexibility based on experimental and theoretical crteria

16. Issues in Ligand Design Crystal structure available for CITEP bound to catalytic core but : I. Position of hydrogens undetermined II. Tautomeric structures possible III. Influence of pH IV. Need to limit conformational flexibility based on experimental and theoretical crteria Tetrazole pKa=5

17. Issues in Ligand Design Crystal structure available for CITEP bound to catalytic core but : I. Position of hydrogens undetermined II. Tautomeric structures possible III. Influence of pH IV. Need to limit conformational flexibility based on experimental and theoretical crteria Fixed and planar Based on HF/6-31G* calculations Limited to +/- 45 degrees

18. Issues in Docking The prediction of the ligand conformation and orientation within a targeted binding site involves: I. Positioning ligand and evaluating quality of binding II. Manually refining ligand position III. Energy minimization (electrostatic, steric, strain and h-bond)

19. Issues in Docking The prediction of the ligand conformation and orientation within a targeted binding site involves: I. Positioning ligand and evaluating quality of binding II. Manually refining ligand position III. Energy minimization (electrostatic, steric, strain and h-bond)

20. Issues in Docking The prediction of the ligand conformation and orientation within a targeted binding site involves: I. Positioning ligand and evaluating quality of binding II. Manually refining ligand position III. Energy minimization (electrostatic, steric, strain and h-bond)

21. Issues in Scoring The prediction of the optimum ligand conformation and orientation within a targeted binding site involves: I. Posing : Determining the fit of the ligand II. Conformational Searching III. Scoring and Ranking

22. Results

23. Results

24. Ligand Design Criterion for Ligand Selection: I. Theoretical and experimental structures II. Fill active site III. Conformational structures

25. Ligand Design Criterion for Ligand Selection: I. Theoretical and experimental structures II. Fill active site III. Conformational structures

26. Ligand Design Criterion for Ligand Selection: I. Theoretical and experimental structures II. Fill active site III. Conformational structures

27. Site Mutations and Drug Resistance The prediction of the affects of mutations within the binding site on the effects of the ligands involves: I. Identifying possible sights of mutations II. Determining effect of mutations

28. Site Mutations and Drug Resistance The prediction of the affects of mutations within the binding site on the effects of the ligands involves: I. Identifying possible sights of mutations II. Determining effect of mutations

29. Site Mutations and Drug Resistance

30. Problem with Protein Flexibility http://folding.stanford.edu/villin/S300x300.105.56.95.mpg