Ekins S, Bravi G, Wikel J H, Wrighton S A
Department of Drug Disposition, Lilly Research Laboratories, Eli Lilly and Co., Lilly Corporate Center, Indianapolis, Indiana, USA.
J Pharmacol Exp Ther. 1999 Oct;291(1):424-33.
To gain a better understanding of the active site of cytochrome P-450 (CYP) 3A4, a three-dimensional-quantitative structure activity relationship model was constructed using the structures and K(m (apparent)) values of 38 substrates of human liver microsomal CYP3A4. This pharmacophore was built using the program Catalyst and consisted of four features: two hydrogen bond acceptors, one hydrogen bond donor, and one hydrophobic region. The pharmacophore demonstrated a fit value (r) of observed and expected K(m(apparent)) value of 0.67. The validity of the CYP3A4 substrate model was tested by twice permuting (randomizing) the activity values and substrate structures. The results of this validation procedure indicated that the original model was a significant representation of the features required of CYP3A4 substrates. The second validation method used the Catalyst model to predict the K(m(apparent)) values of a test set of structurally diverse substrates for CYP3A4 not included in the 38 molecules used to build the model. Two fitting algorithms included in this software were examined: fast fit and best fit. The fast fitting method resulted in predictions for all 12 substrates that were within 1 log unit for the residual [i.e., the difference between predicted and observed K(m(apparent))]. In contrast, the best fit algorithm poorly predicted the K(m (apparent)) values (i.e., residual >1 log unit) of 4 of 12 substrates. 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 this activity. A Catalyst common features pharmacophore was also constructed from 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.
为了更好地理解细胞色素P - 450（CYP）3A4的活性位点，利用人肝微粒体CYP3A4的38种底物的结构和K(m（表观）)值构建了三维定量构效关系模型。该药效团使用Catalyst程序构建，由四个特征组成：两个氢键受体、一个氢键供体和一个疏水区域。该药效团的观测值与预期K(m（表观）)值的拟合值（r）为0.67。通过对活性值和底物结构进行两次置换（随机化）来测试CYP3A4底物模型的有效性。该验证程序的结果表明，原始模型是CYP3A4底物所需特征的显著代表。第二种验证方法是使用Catalyst模型预测用于构建模型的38个分子中未包含的一组结构多样的CYP3A4底物的K(m（表观）)值。研究了该软件中包含的两种拟合算法：快速拟合和最佳拟合。快速拟合方法对所有12种底物的预测结果与残余值（即预测的和观测的K(m（表观）)之间的差异）在1个对数单位以内。相比之下，最佳拟合算法对12种底物中的4种底物的K(m（表观）)值预测较差（即残余值>1个对数单位）。与最佳拟合函数的这些较差拟合表明，Catalyst中的快速拟合方法更能代表CYP3A4底物观测到的K(m（表观）)值，并能在计算机上对该活性进行良好的预测。还从初始CYP3A4模型的38个分子中已知能激活自身代谢的三个分子构建了一个Catalyst共同特征药效团。这表明CYP3A4的激活剂具有多个疏水区域，这些区域可能与活性位点中远离代谢位点的区域相对应。
