Rational Drug Design : HIV Integrase

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Rational Drug Design HIV Integrase
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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

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(No Transcript)
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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.
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de novo Ligand Design
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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
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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

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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

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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

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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

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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

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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

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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

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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

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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

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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 pKa5
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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
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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)

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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)

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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)

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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

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Results
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Results
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Ligand Design

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

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Ligand Design

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

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Ligand Design

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

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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

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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

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Site Mutations and Drug Resistance
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Problem with Protein Flexibility
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