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Chapter 7 Classification of Chemical Compound Pharmacophore Structures

There is a staggeringly large number of chemical compounds that can be made; even when one considers only those hypothetical molecules that are “drug-like”, there are still probably on the order of 10 unique molecular structures. To date, only on the order of 10 compounds have been made and characterized. There is consequently no hope of producing the totality of known chemical compounds at any time in the future. However, many of the compounds that have been synthesized, as well as those that could be imagined in the size 10 set, are structurally close to each other and would be expected to interact with biological molecules such as enzymes (according to Fischer’s “lock & key” concept) in a similar fashion. One promising notion of structural similarity is the concept of a “pharmacophore”, where compounds matching the same pharmacophore often interact with biological molecules (enzymes, receptors, etc) in a similar way. For example, the pharmacophore fingerprint can provide valuable information in the search for novel active compounds, in the measure of diversity of a screening library, and of structure-activity relationships between these compounds. We are also particularly interested in classifying low molecular weight chemical compounds for drug discovery projects that can inhibit the action of an enzyme by lodging themselves within its active site. Since the geometry of these compounds must match the configuration of the receiving protein, the pharmacophore information could be used to improve the success rate. 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 centres. The corresponding groups under consideration are typically hydrogen bond acceptor (HACC), hydrogen bond donor (HDON), negative (NEG) and positive (POS) charges, and hydrophobic (HYD) groups. Other groups can easily be incorporated into the analysis. The centreto-centre distances have been estimated at between 2Å to 15Å, but again, other distance ranges can be easily