Development of a chirality-sensitive flexibility descriptor for 3+3D-QSAR.

Multidimensional QSAR methodologies can be used to predict the active conformation encoded in the conformational preferences of molecules in an active series by utilizing conformational sampling. In the 3+3D-QSAR approach, the conformational free energy loss is modeled with internal coordinate-based flexibility descriptors. While the pharmacophore point pair distance descriptors introduced earlier proved useful in the construction of QSAR models and in the prediction of important features of the active conformation, they are inherently incapable of describing the chiral arrangement of the pharmacophores. As an improvement, a chirality-sensitive flexibility (CSF) descriptor is now introduced, which is based on the distance between a pharmacophore point and a plane defined by three pharmacophore points. The performance of the CSF descriptor was tested on two active series: 37 endomorphin analogues with opiate activity and 38 PGF2alpha analogues with antinidatory activity. The newly devised descriptor resulted in improved QSAR models in terms of both prediction accuracy and precision of the chiral geometric features of the predicted active conformations.