Validation of Model of Cytochrome P450 2D6: An in Silico Tool for Predicting Metabolism and Inhibition

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Validation of Model of Cytochrome P450 2D6 An
in Silico Tool for PredictingMetabolism and
Inhibition

• Carol A. Kemp, Jack U. Flanagan, Annamaria J. van
  Eldik, Jean-Didier Marechal, C. Roland Wolf,
  Gordon C. K. Roberts, Mark J. I. Paine Michael
  J. Sutcliffe
• J. Med. Chem. 2004

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Cytochrome P450 (Cyp450)

• Group of oxidative enzymes
• Exits in all lineages
• Membrane protein (ER, mitochondria)
• Metabolite thousands of endogenous and exogenous
  compounds

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Importance of Cyp 2D6

• Oxidation of gt50 drugs

• Inhibited by drugs

Analgesics (pain killers)
Quinidine (heart rhythm disturbance)
Cytochrome P450 2D6
Beta Blockers (cardiovascular diseases)
fluoxertine (depression)
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Research Goals

• Previous work
• HM docking
• position metabolism site above heme
• Typical (basic nitrogen) substrates
• Screening a database for CYP2D6 inhibitors
• Can 3D method improve over 2D approach
• Asses model accuracy

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Comparative Modeling of 2D6
Bacterial P450
Mammalian P450

• FSSP Fold classification Secondary Structure
  Alignment (DALI)

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Model Validation

• Does a sequence fit a structure ?
• Buried area
• side chain buried with polar atoms
• Secondary structure

Errat non covalently pairs interactions ( CC,
CN, CO, NN, NO, OO ) 9 residue sliding window
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Screened Available Databases

• Docking Software GOLD 2.0
• Genetic algorithm
• Full ligand flexibility partial protein
  flexibility
• Energy functions partly based on conformational
  and non-bonded contact information from the CSD

• Ekins
• ( 21 compounds )

Strobl (30 compounds )
12 ring systems r2 0.56
1 ring system r2 0.36
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Creating an Additional Dataset

• NCI database
• (compounds tested for treating cancer)
• Weight Ekins Strobl datasets
• lt 4 Ring Systems
• Availability
• 33 Compunds

Basic Nitrogen Aromatic Group
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Consistency with known inhibition measurements
AMMC demethylase
Cyp450 2D6
Small Molecule
Inhibition
Inhibition
Ekins / Strobl
AMMC
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Predicting inhibition using Docking
Cutoffs IC50 lt 10 µM inhibitor -30 kJ/mol
predicted inhibitor Predictions 13 correct
7 false positives
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Questions for discussion

• Is the method applicable for large scale database
  scanning ?
• (7 min CPU on a one processor Silicon Graphics
  R14)
• Can substrate affinity be predicted with the same
  accuracy ?
• Are positions reliable enough for predicting
  drug-drug interactions ?

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Thank you for your attention