Three-dimensional-quantitative structure activity relationship analysis ofcytochrome P-450 3A4 substrates

To gain a better understanding of the active site of cytochrome P-450 (CYP) 3A4, a three-dimensional-quantitative structure activity relationship mode l was constructed using the structures and K-m(apparent) values of 38 subst rates of human liver microsomal CYP3A4. This pharmacophore was built using the program Catalyst and consisted of four features: two hydrogen bond acce ptors, one hydrogen bond donor, and one hydrophobic region. The pharmacopho re demonstrated a fit value (r) of observed and expected K-m(apparent) valu e of 0.67. The validity of the CYP3A4 substrate model was tested by twice p ermuting (randomizing) the activity values and substrate structures. The re sults of this validation procedure indicated that the original model was a significant representation of the features required of CYP3A4 substrates. T he second validation method used the Catalyst model to predict the K-m(appa rent) values of a test set of structurally diverse substrates for CYP3A4 no t included in the 38 molecules used to build the model. Two fitting algorit hms included in this software were examined: fast fit and best fit. The fas t fitting method resulted in predictions for all 12 substrates that were wi thin 1 log unit for the residual [i.e., the difference between predicted an d observed K-m(apparent)]. In contrast, the best fit algorithm poorly predi cted the K-m(apparent) values (i. e., residual.1 log unit) of 4 of 12 subst rates. These poor fits with the best fit function suggest that the fast fit method within Catalyst is more representative of the observed K-m(apparent ) values for CYP3A4 substrates and enables good in silico prediction of thi s activity. A Catalyst common features pharmacophore was also constructed f rom three molecules known to activate their own metabolism included in the 38 molecules of the initial CYP3A4 model. This demonstrated that activators of CYP3A4 possess multiple hydrophobic regions that might correspond with a region in the active site away from the metabolic site.