Dynamics simulation and in vitro studies of betulinic acid derivative with liver X receptor

Abstract

Molecular dynamics simulation of the dominant conformational conjugate was performed for 40 ns and 100 ns via Amber software based on molecular docking by Sybyl software. Because the RMSD and RMSF of 100 ns MD simulation were higher than that of 40 ns MD simulation, the 40 ns was reasonable and credible for MD simulation. The binding free energy and decomposition free energy of the two systems of betulinic acid, com3 with liver X receptor was calculated by the MM_GBSA and MM_PBSA methods, respectively. The results showed that the two systems reached equilibrium and convergence at 20 ns, both stable at about 2 Å, and exhibited low volatility in the range of amino acid 270 to 370 (RMSF <1 Å). The binding energy of com3 (ΔGbind = −68.02 kcal/mol by the MM_GBSA method or −55.50 kcal/mol by the MM_PBSA method) with the liver X receptor was lower than that of betulinic acid (ΔGbind = −55.70 kcal/mol or −42.73 kcal/mol) respectively, and van der Waals force was the most important main driving force, which was consistent with molecular docking and previous experiments. Hydrophobic groups and aromatic rings can be introduced appropriately in structure optimization to increase the van der Waals force and π-π accumulation effect of betulinic acid and liver X receptor, which is conducive to binding and thereby increasing antitumor activity. The clone formation assay and results of western blotting indicated that BA derivative com3 exposure inhibited cell proliferation may relate to the regulation of the AKT/mTOR pathway in 7721 cells. This study clarifies the dynamic interaction mode and potential mechanism of betulinic acid and its derivatives with the liver X receptor, which provides a new idea for the rapid screening of liver X receptor agonists from traditional Chinese medicines. Communicated by Ramaswamy H. Sarma