On the possible structural differencies between molecules present in natural extracts and the synthetic ones

Discrepancies are observed in biological activity of the same molecule present in natural substrates and those extracted from the phytocomplex or produced by synthesis. In the last two cases a lower activity is sometimes observed, e.g. as described for quercetin and hypericin in St. John's wort, artemisin in Artemisia annua, VitaminC and Flavonols in Citrus. This behavior can be ascribed to synergism with other molecular species, but a further hypothesis can be considered, i.e. that the different activity could originate from a different conformation of the active compound in the biological substrate, due to interactions with other molecular species and/or with oligoelements. The drug-receptor interaction is responsible for biological activity and consequently it is related to the drug conformation, which would be highly specific in the natural substrate. In the case of synthetic products the spatial structure at the lowest internal energy is expected to be different to that of the same molecule present in the natural substrate; however, molecular dynamics indicates that there is a non-zero probability that it assumes the right conformation for the interaction with the receptor site. This aspect could explain the partial maintenance of biological activity and give account for its lowering with respect to that of the natural product.