Descriptors from a Pharmacophore Model

Most important for a probable drug molecule is its capability to interact with a biological target (e. g., an enzyme or receptor). Not all atoms of a molecule are able to build up these interactions. Therefore, the substructures of the molecule can be divided into two classes  

Groups with target interaction (i.e., hydrogen bond acceptors, hydrogen bond donors, positively charged centers, aromatic rings, hydrophobic centers) are the pharmacophore centers [66]. 

Spacer fragments that are necessary to bring the functional groups into a correct relative orientation. 

The pharmacophore is defined as the critical geometric arrangement of molecular fragments required for binding [67] (Fig. 9). Pharmacophore descriptors are derived by analyzing distances between pairs or triples of pharmacophore centers [20, 68-70]. 

Pharmacophore centers can be used instead of atoms to describe a molecular structure. PCs derived from a three-dimensional structure include the direction of interaction, and are vectors. 

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