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J Chem Inf Comput Sci. 2003 Jan-Feb;43(1):218-27.

Property distributions: differences between drugs, natural products, and molecules from combinatorial chemistry.

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  • 1SignalGene Inc., 335 Laird Road, Unit 2, Guelph, Ontario, N1G 4P7, Canada.


The differences between three different compound classes, natural products, molecules from combinatorial synthesis, and drug molecules, were investigated. The major structural differences between natural and combinatorial compounds originate mainly from properties introduced to make combinatorial synthesis more efficient. These include the number of chiral centers, the prevalence of aromatic rings, the introduction of complex ring systems, and the degree of the saturation of the molecule as well as the number and ratios of different heteroatoms. As drug molecules derive from both natural and synthetic sources, they cover a joint area in property space of natural and combinatorial compounds. A PCA-based scheme is presented that differentiates the three classes of compounds. It is suggested that by mimicking certain distribution properties of natural compounds, combinatorial products might be made that are substantially more diverse and have greater biological relevance.

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