W8.3_Moleuclar Kinetics of CYP450 Mechanism

Question 1

How is the rate of oxidation in CYP450 metabolism affected? Define K(d) and its implication when binding affinity is strong. Relate energetics to the binding of ligands.

Answer 1

• Rate of oxidation: determined by oxidation reaction and concentration of drug-CYP complex
• K(d): dissociation constant of drug binding to CYP (≈protein-ligand interactions)
• Protein(aq) + Ligand(aq) ⇌ Protein-ligand complex(aq)
• K(d)=[P][L]/[PL] moldm^-3
• ∴ When [L]=K(d), [P]=[PL] (when ligand is in significant excess and [L]=K(d), P will be 50% occupied)
• Stronger binding causes lower concentration required to achieve 50% occupancy
• Binding of ligand to protein must be energetically favoured (∆G must be -ve, ∆G=∆H-T∆S)

Question 2

Discuss the unfavourable and favourable enthalpic and entropic effects when a ligand binds to a protein in a hydrated setting.

Answer 2

Unfavourable enthalpic
- Loss of ligand-water/ protein-water bonding interactions
- Energetic changes in protein/ligand
Favourable enthalpic
- Formation of bonding interactions with protein
Entropic
Unfavourable entropic
- Loss of conformational flexibility in protein/ ligand
Favourable entropic
- Desolvation of ligands (return of bound water to bulk state)

Question 3

Compare and explain how the lipophilicity of drug compounds effect the specificity of ligand-protein interactions.

Answer 3

Lipophilic ligands:
- Less formation of bonding interactions with protein
- Less loss of ligand-water bonding interactions and much more desolvation of ligands
- ∴ Bind through entropic effects predominantly -> low specificity of ligand-protein interactions -> can bind to any proteins
Hydrophilic ligands:
- More loss of ligand-water bonding interactions and loss of conformational flexibility in ligand
- More formation of bonding interactions with protein and desolvation of ligands
- ∴ Bind through bonding interactions predominantly -> ligand have to fix very nicely to repay desolvation cost -> highly specific binding to small subsets of proteins

Question 4

Relate the lipophilicity of drugs to excretion. Explain how drug metabolism is usually predicted and how it relates to the uncommon situation of multiple phase 1 metabolisms acting on the same drug compound.

Answer 4

• Most important factor: lipophilic drugs are more likely to be rapidly cleared
• Once bound, molecule must be reactive and driven by chemical environment of the drug
• ∵ Drugs have different affinity for metabolic enzymes, where lipophilicity is the best predictor
• ∴ Metabolism creates more polar form that are less likely to form -> multiple phase 1 not likely

Question 5

Explain the ways to reduce metabolism through altering the chemical strucutre of drug compounds (4).

Answer 5

• Introduce groups at susceptible sites to block the reaction (change C-H environment into C-CH3 environment) to increase metabolic stability and drug half-life
• Introduce fluorine (C-H -> C-F) to block metabolic sites (stop CYP-mediated metabolism through H abstraction)
• Reduce lipophilicity to reduce clearance (as in drugs with logD>3, blocking metabolism at susceptible positions would just move the site of metabolism to another part of molecule)
• Bioisosteres: changing chemical structure of drug by shifting the position of metabolically susceptible group but behave similarly in biological environment (unrecognisable to metabolic enzyme but still recognisable by target)