CoMSIA contour maps for TIs deriving from model CoMSIA-SDA.

<p>The amino acid residues located close to the binding pocket of thrombin are represented for comparing their position with the position of isopleths derived from the model. Compound <b>134</b> is shown inside the field. <b>(A)</b> Steric field: green isopleths indicate regions where bulky groups enhance the activity and yellow isopleths indicate regions where bulky groups disfavor the activity. <b>(B)</b>. HB donor field: cyan isopleths indicate regions where HB donors favor the activity, and purple isopleths indicate regions where HB donors disfavor the activity. <b>(C)</b> HB acceptor fields: magenta isopleths indicate regions where HB acceptors enhance the activity, and red isopleths indicate regions where HB acceptors decrease the activity.</p

Scatter plot of the experimental activities versus predicted activities for model CoMFA-SDA: (●) training set predictions (○) LOO cross-validated predictions (red ▲) test set predictions.

<p>Scatter plot of the experimental activities versus predicted activities for model CoMFA-SDA: (●) training set predictions (○) LOO cross-validated predictions (red ▲) test set predictions.</p

Structures of TIs.

<p>Structures of TIs.</p

Alignment of inhibitor docked structures on inhibitor X-ray reference structures, for the TI complexes.

<p><b>(A)</b> Compound <b>13</b> (PDB: 1T4U); <b>(B)</b> compound <b>24</b> (PDB: 1T4V); <b>(C)</b> compound <b>128</b> (PDB: 3C27), <b>(D)</b> compound <b>151</b> (PDB: 2R2M); <b>(E)</b> compound <b>165</b> (PDB: 3LDX). Crystal structures are represented in yellow, and docking results are represented in purple. Docking accuracy is reported by means of RMSD values.</p

Predicted MM-GBSA free energies (kcal/mol) and individual energy terms of the thrombin-inhibitor complexes for selected compounds.

<p>a Experimental ΔΔG was calculated using ΔG of compound <b>133</b> as reference.</p><p>Predicted MM-GBSA free energies (kcal/mol) and individual energy terms of the thrombin-inhibitor complexes for selected compounds.</p

Correlation between experimental ΔΔG (calculated from Ki values of compounds) and calculated ΔG values using MM-GBSA.

<p>Experimental ΔG was calculated from Ki values of compounds, and ΔΔG was calculated using ΔG of compound <b>133</b> as reference.</p

Time dependence of the RMSD for protein atoms from starting structures during equilibration process.

<p>RMSD for the studied systems are represented in colors indicated at the right.</p

Alignment of all docked structures within the thrombin binding site (docked ligands are in green stick representation in A-E).

<p><b>(A)</b> Full view of the binding site. <b>(B)</b> Subsite S₁, residues of the VSWGEGC motif are represented with white spheres, DACE motif is represented as an orange loop, Ser195 is represented with yellow sticks. <b>(C)</b> Subsite S₁, residues of the DACE motif are represented with orange spheres, VSWGEGC motif is represented as a white loop, Ser195 is represented with yellow sticks. <b>(D)</b> Subsite S₂, residues His57, Tyr61, and Trp64 are represented with violet spheres, and residues Trp215 and Gly216 from the VSWGEGC motif are represented with white spheres. <b>(E</b>, <b>F)</b> Subsite S₃, residues of the WRENL motif are represented with brown spheres, residues Trp215 and Glu217 from the VSWGEGC motif are represented with white spheres, and Ile174 is represented with yellow spheres. In f several compounds that have a P₁ moiety with two branches are represented: compounds with two hydrophobic branches are represented with green sticks, and compounds with one of the branches containing a polar group are represented with pink sticks.</p

Experimental and predicted thrombin inhibitory activities (log(10³/Ki) (nM)) using CoMSIA-SDA model.

<p>^a QSAR outliers.</p><p>^b test set compounds.</p><p>^c compounds selected for MM-GBSA calculations</p><p>Experimental and predicted thrombin inhibitory activities (log(10³/Ki) (nM)) using CoMSIA-SDA model.</p

Stepwise development of CoMSIA models by using SAMPLS and different field combinations.

<p>NC is the number of components from PLS analysis; R² is the square of the correlation coefficient; S is the standard deviation of the regression; F is the Fischer ratio; Q² and S_cv are the correlation coefficient and standard deviation of the leave-one-out (LOO) cross-validation, respectively. The best model is indicated in boldface.</p><p>Stepwise development of CoMSIA models by using SAMPLS and different field combinations.</p