Predicting drug pharmacokinetic properties using molecular interaction fields and SIMCA

Abstract

We have developed a method that combines molecular interaction fields with soft independent modeling of class analogy (SIMCA) Wold:1977 to predict pharmacokinetic drug properties. Several additional considerations to those made in traditional QSAR are required in order to develop a successful QSPR strategy that is capable of accommodating the many complex factors that contribute to key pharmacokinetic properties such as ADME (absorption, distribution, metabolism, and excretion) and toxicology. An accurate prediction of oral bioavailability, for example, requires that absorption and first-pass hepatic elimination both be taken into consideration. To accomplish this, general properties of molecules must be related to their solubility and ability to penetrate biological membranes, and specific features must be related to their particular metabolic and toxicological profiles. Here we describe a method, which is applicable to structurally diverse data sets while utilizing as much detailed structural information as possible. We address the issue of the molecular alignment of a structurally diverse set of compounds using idiotropic field orientation (IFO), a generalization of inertial field orientation Clark:1998. We have developed a second flavor of this method, which directly incorporates electrostatics into the molecular alignment. Both variations of IFO produce a characteristic orientation for each structure and the corresponding molecular fields can then be analyzed using SIMCA. Models are presented for human intestinal absorption, blood-brain barrier penetration and bioavailability to demonstrate ways in which this tool can be used early in the drug development process to identify leads likely to exhibit poor pharmacokinetic behavior in pre-clinical studies, and we have explored the influence of conformation and molecular field type on the statistical properties of the models obtained.