Molecular docking simulation
To demonstrate the molecular mechanism between rivaroxaban and CYP2J2,
molecular docking simulation was conducted using a CYP2J2 crystal
structure homology model. This
model
was constructed using the Clustal Omega webserver
(https://www.ebi.ac.uk/Tools/msa/clustalo/), as previously described
[19]. Docking simulation was performed using SYBYL (X-1.1). The 3D
structure of rivaroxaban was subjected to energy minimization with the
default Tripos force field parameters, and the Gasteiger-Hückel charges
were calculated for each compound. The Surflex-Dock mode was used to
generate binding conformations of rivaroxaban with CYP2J2, from which
the optimal conformations were determined by their empirical functions
TotalScore, ChemScore and CScore. In
addition, the PyMOL Molecular Graphics System, version 16.1.0.15350
(DeLano Scientific LLC) was used to visualize the docking results.