Classification of Chemical Compound Pharmacophore Structures

Abstract

A pharmacophore is a structural abstraction of the interactions between various functional group types in a compound. They are described by a spatial representation of these groups as centres (or vertices) of geometrical polyhedra, together with pairwise distances between distances.

We provide an analysis that facilitates counting 3 and 4 centre pharmacophores, including a mathematical model for distance interval ratios, triangle and other inequality requirements for feasible triangles and tetrahedra, and symmetries.

Beside spatial symmetries and and distance similarities for each edge of the polyhedra, there does not appear to be any other relevant structural similarity feature between two pharmacophores that can be used to reduce the classification of a typical compound.