Molecular modeling reveals the inhibition mechanism and binding mode of ursolic acid to TLR4-MD2

In the previous literature, it was reported that ursolic acid, a natural compound, can potently inhibit nuclear factor-kB by inhibiting the binding of LPS to the TLR4-MD2 complex. In this work, the inhibition mechanism of ursolic acid towards the TLR4-MD2 complex was explored using molecular dynamics simulations and binding free energy calculations. Molecular dynamics simulations revealed that ursolic acid can bind to the active pocket in MD2, which is the binding region of substrate lipopolysaccharide. These results indicated that residues Ile52, Leu78, Ile80, Phe121, and Tyr131 play a key role in the binding of ursolic acid with TLR4-MD2 based on energy decomposition analysis and binding energy calculations. Due to the coordination of ursolic acid to the substrate binding region, the binding of lipopolysaccharide with TLR4-MD2 was restricted, leading to a reduction of activity for TLR4-MD2. Furthermore, through simulation trajectory analysis of TLR4-MD2- ursolic acid, we found that the ring structure diameter of TLR4 in the TLR4-MD2- ursolic acid complex system is significantly less than that of TLR4 in the TLR4-MD2 and TLR4-MD2-lipopolysaccharide complex systems. This result implies that the conformation of TLR4 was changed by the binding of ursolic acid to TLR4-MD2, which decreased the activity of TLR4-MD2. On the basis of these simulation results, it was confirmed that ursolic acid may inhibit the activity of TLR4-MD2 by coordinating to the substrate binding region and by influencing the conformation of TLR4.