High-Throughput Docking and Molecular Dynamics Simulations towards the Identification of Potential Inhibitors against Human Coagulation Factor XIIa

Abstract

Human coagulation factor XIIa (FXIIa) is a trypsin-like serine protease that is involved in pathologic thrombosis. As a potential target for designing safe anticoagulants, FXIIa has received a great deal of interest in recent years. In the present study, we employed virtual high-throughput screening of 500,064 compounds within Enamine database to acquire the most potential inhibitors of FXIIa. Subsequently, 18 compounds with significant binding energy (from -65.195 to -15.726 kcal/mol) were selected, and their ADMET properties were predicted to select representative inhibitors. Three compounds (Z1225120358, Z432246974, and Z146790068) exhibited excellent binding affinity and druggability. MD simulation for FXIIa-ligand complexes was carried out to reveal the stability and inhibition mechanism of these three compounds. Through the inhibition of activated factor XIIa assay, we tested the activity of five compounds Z1225120358, Z432246974, Z45287215, Z30974175, and Z146790068, with pIC50 values of 9.3∗10^-7, 3.0∗10^-5, 7.8∗10^-7, 8.7∗10^-7, and 1.3∗10^-6 M, respectively; the AMDET properties of Z45287215 and Z30974175 show not well but have better inhibition activity. We also found that compounds Z1225120358, Z45287215, Z30974175, and Z146790068 could be more inhibition of FXIIa than Z432246974. Collectively, compounds Z1225120358, Z45287215, Z30974175, and Z146790068 were anticipated to be promising drug candidates for inhibition of FXIIa.

Figure 1

Binding mode of Z1225120358 to the FXIIa. (a) Overall structure of FXIIa-Z1225120358 complex. Protein structure was shown in cartoon and ligand in sticks. Showing the binding site residue surface around the ligand. Displaying the H-bond donor (purple) and acceptor (green) area. (b) Interactions between Z1225120358 (sticks) and FXIIa residues (sticks). (c) 2D diagram of FXIIa interactions to compound Z1225120358.

Figure 2

Binding mode of Z432246974 to the FXIIa. (a) Overall structure of FXIIa-Z432246974 complex showing protein in cartoon model and ligand in stick. Showing the binding site residue surface around the ligand. Displaying the H-bond donor (purple) and acceptor (green) area. (b) Interactions of Z432246974 (sticks) to the FXIIa residues (sticks). (c) 2D diagram of FXIIa interactions to compound Z432246974.

Figure 3

Binding mode of Z432246974 to the FXIIa. (a) Overall structure of FXIIa-Z146790068 complex showing protein in cartoon model and ligand in stick. Showing the binding site residue surface around the ligand. Displaying the H-bond donor (purple) and acceptor (green) area. (b) Interaction of Z146790068 (stick) to the FXIIa residues (stick). (c) 2D diagram of FXIIa interaction to compound Z146790068.

Figure 4

Binding mode of Z45287215 to the FXIIa. (a) Overall structure of FXIIa-Z45287215 complex showing protein in cartoon model and ligand in stick. Showing the binding site residue surface around the ligand. Displaying the H-bond donor (purple) and acceptor (green) area. (b) Interaction of Z45287215 (stick) to the FXIIa residues (stick). (c) 2D diagram of FXIIa interaction to compound Z45287215.

Figure 5

RMSD values (a) and RMSF values (b) of FXIIa and its complexes with inhibitors as a function of time obtained for MD simulation.

Figure 6

Inhibition of activated factor XII (a-FXIIa) by five compounds Z1225120358, Z45287215, Z30974175, Z432246974, and Z146790068. Concentrations of these five compounds (10⁻⁸ M to 10⁻³ M) were incubated with 200 μM substrate peptide, and this was followed by addition of a-FXIIa; enzymatic activity was then monitored as described in Materials and Methods. pIC50 values were obtained by nonlinear regression (GraphPad Prism V8.0.2.263; log[inhibitor] versus response-variable slope algorithm with a bottom constraint). Error bars indicate the standard error (n = 3 independent observations).