Different Roles of Some Key Residues in the S4 Pocket of Coagulation Factor Xa for Rivaroxaban Binding †

doi:10.7503/cjcu20190261

Abstract

Abstract:

The details of the dynamic interaction between rivaroxaban and some key residues in the S4 pocket of Coagulation factor X(FXa) were analyzed by bioinformatics alignment, molecular dynamics simulation and binding free energy calculation. The results indicated that the disruption of the hydrophobic S4 pocket caused 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 time of simulations. 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. The different roles of key residues in the S4 pocket should be fully considered in the drug design of the direct inhibitor of FXa and the development of its antagonists.

Key words: Coagulation factor Xa, Rivaroxaban, S4 pocket, Molecular dynamics simulation, Binding free energy

CLC Number:

O641

TrendMD:

QU Siying, XU Qin. Different Roles of Some Key Residues in the S4 Pocket of Coagulation Factor Xa for Rivaroxaban Binding ^†[J]. Chem. J. Chinese Universities, 2019, 40(9): 1918.

Figures/Tables 8

Fig.1 Model of RIV binding to FXa Based on PDB structure 2W26, RIV is shown by sticks in green, the key residues Tyr99, Phe174, Trp215 and Asp189 are shown by sticks in cyan, while the backbone of FXa is shown by cartoon.

Fig.2 Sequence alignment of the serine protease domain and conservation analysis of residues around the S4 pockets among homologous coagulation factors Surrounding the S4 pocket, the critical residues of 99 loop, 170 loop and 215 strand are framed in red, green and blue, respectively. The corresponding conservation analyses are shown on the right with the residues labeled by Chymotrypsin numbering.

Fig.3 Superposition of the S4 pockets of homologous coagulation factors The backbone of FX is shown as tube and colored by secondary structure, with the residues shown by balls and sticks and colored in magenta. In comparison, the residues and backbones of other coagulation factors are shown by lines and colored in orange for FⅡ, yellow for FⅦ, brown for FⅨ, green for FⅪ and blue for FⅫ.

Fig.4 Water molecules around S4 pockets with WT(A), Y99A(B) and W215A(C) RIV is shown by CPK in green; the key residues Tyr99, Phe174, Trp215 and Asp189 are shown by CPK in cyan; the backbone of FXa is shown by cartoon.

Species	E/(kJ·mol^-1)
Species	Wild type	Y99A	W215A
van der Waals energy	-188.141±13.438	-145.748±21.088	-108.356±19.709
Electrostatic energy	-52.079±15.698	-39.173±31.740	-22.613±25.232
Polar solvation energy	175.618±22.205	127.588±42.215	89.180±38.211
SASA energy	-20.516±1.214	-14.328±2.153	-12.718±1.969
Binding energy	-85.119±15.624	-71.660±21.972	-54.507±20.198

Fig.5 Swing of Trp215 side chain in Y99A mutant The side chain of Trp215 swings from the bottom of S4 pocket(A) to the entry of S1 pocket(B). RIV is shown by sticks in green, the key residues Tyr99, Phe174, Trp215 and Asp189 are shown by sticks in cyan, while the backbone of FXa is shown by cartoon in cyan.

Residue	E/(kJ·mol^-1)
Residue	Wild type	Y99A	W215A
Y/A99	-5.088±0.292	0.016±0.015	-0.609±0.189
W/A215	-9.990±0.259	-6.101±0.204	0.216±0.072

Fig.6 RMSD(A) and RMSF(B) of backbone atoms

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