A comparison of crystallographic and DFT optimized geometries on two taxane diterpenoids and docking studies with phospholipase A2

Structure optimization of two taxane diterpenoids I and II has been carried out using GAUSSIAN03 program with B3LYP/6-31G** basis set. The structures were fully optimized without any geometric constraints. Coordinates found in crystallographic study were used as input to the GAUSSIAN. The results show that the conformations of taxoid cores are almost same as were observed from crystallography, while the conformations of the substituents are slightly different. Thus, taxoid cores are robust enough to maintain their conformations in gaseous state while the conformations of substituents may vary depending upon the reaction condition. To understand the mode of binding, the docking studies of both compounds have been carried out with Russell's viper phospholipase A(2) (vPLA2) as target using induced fit docking. The docking results show that regarding the interactions and energy for indomethacin binding with vPLA2, compound I shows the best results.