3.5 Molecular docking studies
Molecular docking studies were carried out by AutoDock 4.2 in order to
predict the preferred binding state as well as the binding site of the
thymol, carvacrol, beta-elemene, trans-caryophyllene, germacrene-D,
spathulenol, and 5alpha-pregnane compounds (as well-known
allelochemicals of amaranth) with PsbA and PsbS proteins. These
compounds are highly bound to these proteins. According to the results
(Table 5), the 5alpha-pregnane compound with more negative binding
energy as well as its lower inhibition constants compared to other
compounds indicates a more stable and better binding to PsbA and PsbS
encoded proteins. After the 5alpha-pregnane, the trans-caryophyllene,
germacrene-D, spathulenol, beta-elmenene, thymol, and carvacrol
compounds were placed in next rank, respectively. The site effect and
amino acids involved in the binding of these compounds are shown in
Figure 2 to 8.