Molecular Dynamics Simulation On Key Residue Mutations Of The S4 Pocket Of Coagulation Factor X

Coagulation is the stress response to trauma of blood system involving a series of enzymatic activations.The coagulation cascade is generally activated by intrinsic pathway or extrinsic pathway,and then proceeds into the common pathway at the activation of coagulation factor X(FX),which then activate thrombin.Thus the activated Factor X(FXa)is a key enzyme in blood coagulation and currently a hot target for anticoagulant design.Rivaroxaban(RIV)is a Direct Oral Anticoagulant(DOAC)targeting activated coagulation factor X(FXa).Its hydrophobic binding to the S4 pocket of FXa is critical to its high affinity and high specificity.In this study,the details of the dynamic interactions between Rivaroxaban and some key residues in the S4 pocket of factor Xa were analyzed by bioinformatics alignment,molecular dynamics simulation and binding free energy calculation.The results indicate that the disruption of the hydrophobic S4 pocket by mutations in the key residues directly lower the binding affinity of rivaroxaban to FXa.The hydrophobic effect of the Trp215 side chain is more important in the inhibitor binding,but the effect on the overall structure is relatively minor in the limited simulation.Although Tyr99 contributes less in the binding free energy,its mutation may result in an overall conformational change in the domain where the 99 loop is located,thereby affecting the binding specificity of the inhibitor or substrate.Besides,an unexpected alternative binding mode of S1'S1 was found relative stable in the F174 A mutant,which required dynamic motions of Gln192 and Gln61 to allow the morpholinone moiety of RIV to shift into the S1' pocket and form strong interactions.The different roles of key residues in the S4 pocket should be fully considered in the drug design of the direct inhibitor of factor Xa and the development of its antagonists.