Post on 05-Jan-2016
Rational Drug Design : HIV Integrase
A process for drug design which bases the design of the drug upon the structure of its protein target.
1. Structural mapping of the receptor (protein, P) active site
2. Identification of ligands (L) of complementary shape and appropriate functionality
3. Docking of the ligand to the receptor site - predicting a range of PL complexes with different GPL values
4. Scoring i.e. ranking GPL and correlating with experimentally determined properties such as IC50 values
In the first step of the integration process, two nucleotides are removed fromeach 3’-end of the viral DNA. This reaction exposes the terminal 3’-hydroxylgroup that is to be joined to target DNA (Fig. 1B). In the second step, DNAstrand transfer, a pair of processed viral DNA ends is inserted into thetarget DNA (Fig. 1C). Integrase is responsible for 3’-processing and DNAstrand transfer, but the latter repair steps are likely to be carried out bycellular enzymes.
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.
de novo Ligand Design
DCQ acids; DCT acids
DKAs
Quinolone derived
PDP SQL
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 host3. integrase mutations must be found in drug-resistant viruses4, the drug should be inactive in biochemical assays against recombinantintegrases bearing the mutations identified in the drug-resistant viruses
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 structureII. Position of hydrogens undetermined III. Residues missing or ill-definedIV. Protonation of His undeterminedV. Solvation
Issues in Protein Setup
Crystal structure available for Integrase Catalytic Domain but :
I. Crystal reveals trimeric structureII. Position of hydrogens undetermined III. Residues missing or ill-definedIV. Protonation of His undeterminedV. Solvation
Issues in Protein Setup
Crystal structure available for Integrase Catalytic Domain but :
I. Crystal reveals trimeric structureII. Position of hydrogens undetermined III. Residues missing or ill-definedIV. Protonation of His undeterminedV. Solvation
Issues in Protein Setup
Crystal structure available for Integrase Catalytic Domain but :
I. Crystal reveals trimeric structureII. Position of hydrogens undetermined III. Residues missing or ill-definedIV. Protonation of His undeterminedV. Solvation
Issues in Protein Setup
Crystal structure available for Integrase Catalytic Domain but :
I. Crystal reveals trimeric structureII. Position of hydrogens undetermined III. Residues missing or ill-definedIV. Protonation of His undeterminedV. Solvation
Issues in Protein Setup
Crystal structure available for Integrase Catalytic Domain but :
I. Crystal reveals trimeric structureII. Position of hydrogens undetermined III. Residues missing or ill-definedIV. Protonation of His undeterminedV. Solvation
Issues in Ligand Design
Crystal structure available for CITEP bound to catalytic core but :
I. Position of hydrogens undeterminedII. Tautomeric structures possibleIII. Influence of pHIV. Need to limit conformational flexibility based
on experimental and theoretical crteria
Issues in Ligand Design
Crystal structure available for CITEP bound to catalytic core but :
I. Position of hydrogens undeterminedII. Tautomeric structures possibleIII. Influence of pHIV. Need to limit conformational flexibility based
on experimental and theoretical crteria
Issues in Ligand Design
Crystal structure available for CITEP bound to catalytic core but :
I. Position of hydrogens undeterminedII. Tautomeric structures possibleIII. Influence of pHIV. Need to limit conformational flexibility based
on experimental and theoretical crteria
Issues in Ligand Design
Crystal structure available for CITEP bound to catalytic core but :
I. Position of hydrogens undeterminedII. Tautomeric structures possibleIII. Influence of pHIV. Need to limit conformational flexibility based
on experimental and theoretical crteria
Tetrazole pKa=5
Issues in Ligand Design
Crystal structure available for CITEP bound to catalytic core but :
I. Position of hydrogens undeterminedII. Tautomeric structures possibleIII. Influence of pHIV. Need to limit conformational flexibility based
on experimental and theoretical crteria
Fixed and planar
Based on HF/6-31G* calculationsLimited to +/- 45 degrees
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)
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)
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)
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 ligandII. Conformational SearchingIII. Scoring and Ranking
Results
Results
Criterion for Ligand Selection:
I. Theoretical and experimental structuresII. Fill active siteIII. Conformational structures
Ligand Design
Criterion for Ligand Selection:
I. Theoretical and experimental structuresII. Fill active siteIII. Conformational structures
Ligand Design
Criterion for Ligand Selection:
I. Theoretical and experimental structuresII. Fill active siteIII. Conformational structures
Ligand Design
The prediction of the affects of mutations within thebinding site on the effects of the ligands involves:
I. Identifying possible sights of mutationsII. Determining effect of mutations
Site Mutations and Drug Resistance
The prediction of the affects of mutations within thebinding site on the effects of the ligands involves:
I. Identifying possible sights of mutationsII. Determining effect of mutations
Site Mutations and Drug Resistance
Site Mutations and Drug Resistance
Problem with Protein Flexibility
http://folding.stanford.edu/villin/S300x300.105.56.95.mpg