Molecular Dynamics Simulations Explore The Interactions Between Different Inhibitors And Xanthine Oxidase

Xanthine oxidase(XO)plays a key role in the induction of uric acid production,and the accumulation of uric acid in tissues and organs in the body is one of the main causes of hyperuricemia and gout.Hence,Xanthine oxidase has become a target protein for long-term treatment and prevention of gout and hyperuricemia,and its interaction with inhibitors has become a research hotspot.With the widespread use of Xanthine oxidase inhibitors(XOI)allopurinol,the number of related side effects is also increasing.Reference study has shown that puerarin,a natural drug with rich pharmacological properties obtained from the Kudzu root,has a good inhibitory effect on XO,and can reduce the level of serum uric acid and in a gentle way.In order to understand the effects of allopurinol and puerarin on the conformation of XO,and explore whether puerarin can be developed as a mild drug for the treatment of gout,three systems of XO,XO/allopurinol and XO/puerarin were analysed using 200 ns conventional molecular dynamics simulations.We found that allopurinol combined with XO,part of the helix in the secondary structure of the Phe798-Leu814 region became a loop,and part of the loop in the secondary structure of the Glu1065-Ser1075 region become a helix.At the same time,the movement direction and amplitude of the residue at the inhibitor binding pocket were also changed,indicating that the binding of allopurinol had a greater effect on XO.Then,when studying the effects of inhibitors on the spatial structure of XO,we found that after the combination of allopurinol and puerarin with XO,the distance between the active pocket residue Arg880 and Thr1010 was significantly reduced,and the distance between Glu802 and Thr1010 was significantly increased.MM-PBSA calculations suggested that allopurinol has stronger interaction with XO than puerarin,which might be the reason for the stronger inhibitory effect of allopurinol on XO.Subsequently,we used steered molecular dynamics(SMD)simulations to explore the dynamic process of the dissociation of inhibitors allopurinol and puerarin from XO.The tunnel analysis based on CAVER3.0 illustrated the shape of the tunnel was relatively regular,which was beneficial to the dissociation of the inhibitors.The steered molecular dynamics simulation results revealed that compared to puerarin,allopurinol needed more external force and longer time to escape from XO.In addition,Phe1009,Arg880,Ala1079,Val1011 and Thr1010 played important roles in maintaining the structural stability of the two compounds binding to XO,Phe649 and Phe1013 functioned as a gating role in the process of inhibitor dissociation,and His875 played a blocking role in inhibitors dissociation.Our results provided some theoretical clues for the study of the interactions between inhibitors and XO,and provided a theoretical basis for the development of mild gout drugs targeting XO in the future.