Diversity of Drug Molecules

The animal example shows that the degree of similarity of arbitrary objects depends very much on the observed properties. This trivial rule is also valid for the more compHcated problem of chemical structures. Indeed, the choice of appropriate structure properties is the essential problem involved in describing diversity. 

The most usual representation of an organic molecule is the two-dimensional structural formula. Therefore, similarity of molecules is looked at as similarity of the structural formulas. Two molecules are stated to be similar if the structural scaffolds are similar and the substitution patterns are similar. 

In dmg design, one must look at other properties of the molecules, and in this case the possibilities of interaction between the molecule and the biological target (e. g., an en2yme) are important. This interaction is influenced by the three-dimensional arrangement of hydrogen bond donor or acceptor groups, and of the polar or HpophiHc parts of a molecule (expressed as pharmacophores). From this point of view, two molecules are similar if they show similar pharmacophores and then they are assumed to show similar activities. 

Structure formula Some similarity between upper row 

Physico-chemical properties Similar pK -value (acids), more variation of lipophilicity 

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