Mapping property distributions of molecular surfaces: Algorithm and evaluation of a novel 3D quantitative structure-activity relationship technique

A novel molecular descriptor called MaP (mapping property distributions of molecular surfaces) is presented. It combines facile computation, translational and rotational invariance, and straightforward interpretability of the computed models. A three-step procedure is used to compute the MaP descriptor. First, an approximation to the molecular surface with equally distributed surface points is computed. Next, molecular properties are projected onto this surface. Finally, the distribution of surface properties is encoded into a translationally and rotationally invariant molecular descriptor that is based on radial distribution functions (distance-dependent count statistics). The calculated descriptor is correlated with biological data through chemometric regression techniques in combination with a variable selection. The latter is used to identify variables that are highly relevant for the model and hence for its interpretation. Three applications of the new descriptor are presented, each representing a different area of 3D-QSAR. For reasons of comparability, the new descriptor was tested on the steroid "benchmark" data set. Furthermore, a highly diverse data set with potentially eye-irritating compounds was studied, and third, a set of flexible structures with a modulating effect on the muscarinic M-2 receptor were studied. Not only were all models highly predictive but interpretation of the back-projected variables into the original molecular space led to biologically and chemically relevant conclusions.