Cyan: (C=O–HN) amide carbonyl and Gln196. replace the natural stabilizing effect of the lipid bilayer and to avoid spurious movements of the TM helices.49 The detailed procedure followed for MD simulation is described in the experimental section. The average structures from your last 1 ns trajectory of MD simulation were minimized using OPLS-2005 forcefield. Again, a pressure constraint of 10 kcal/mol/?2 was maintained around the backbone of the protein to maintain the critical geometry of -helices. This protocol resulted in a significant increase in the binding site volume giving the processed model III. This model showed significant correlation with reported SAR information. However, it is still not able to explain the binding of larger ligands. vi. Refinement with compound 5 Model III was further processed by docking of the Y-shaped compound 5 followed by minimization and MD Estradiol dipropionate (17-Beta-Estradiol-3,17-Dipropionate) simulation. The presence of common pharmacophoric features allowed us to use the bound conformation of T-226296 in Model III as a reference for the docking of this branched compound. Docking was performed using the Platinum software by applying a distance constraint between the ligand basic nitrogen and Asp192 as well as a hydrogen bond constrain between the ligand urea carbonyl and Gln196 (as noticed with T-226296). As expected, the biphenyl moiety in this compound displayed steric clashes with the side chains of Estradiol dipropionate (17-Beta-Estradiol-3,17-Dipropionate) some binding site amino acid residues. This initial complex was minimized and then subjected to a 7 ns MD simulation using NVT ensemble at 300 K with moderate restraints of 10.0 kcal/mol/?2 around the backbone atoms to preserve the proper 3D fold. We believe that the 7 ns MD simulation was sufficient for the refinement of the model as the potential energy of the complex decreased steadily during the first 5 ns of the simulation, and then remained constant for the last 2 ns (Fig. 3). The producing complex was minimized to give the final processed model (Model IV). This model displayed desirable ligandCreceptor interactions (vide infra). The binding present of the branched compound 5 in the Model IV revealed the presence of crucial charge-assisted H-bonding conversation of Asp192 side chain carboxylate with the ligand basic nitrogen. The RMSD values Rabbit polyclonal to ODC1 for the backbone atoms as well as for all the heavy atoms, for Model II, Model III, and Model IV were calculated and outlined in Table 2. It was noticed that the transition from Model II (initial processed model) to Model III (T-226296 processed) caused more pronounced changes than the transition from Model Estradiol dipropionate (17-Beta-Estradiol-3,17-Dipropionate) III to Model IV (compound 5 processed). Changes in Model IV were observed mainly with the side chains of the binding site residues which were tilted outwards to accommodate the bulky compound 5. Open in a separate window Estradiol dipropionate (17-Beta-Estradiol-3,17-Dipropionate) Physique 3 Potential energy fluctuation of Compound 5 – Model III complex during the 7ns MD simulation. Table 2 RMSD comparison between BRho (1u19) and MCH-R1 models. = 300.035 1.082 K and 284010.59 1919.525 A3 for Model IV-compound 4 complex (system I), and = 299.967 1.092 K and 287979.72 1571.406 A3 for Model IV-compound 5 complex (system II). The energy profile of the two systems during the course of MD simulation is usually shown in physique 7. The total energy of system I decreased in the beginning for the first 8 ns, and then remained stable over the last 12 ns of simulation. Similarly, the total energy of system II decreased continuously until the 8th ns. Then, it stabilized between 8 and 14 ns before slightly decreasing and stabilizing until the end of simulation. Open in a separate window Physique 7 Total energy vs time plot during the production run (20 ns) of system I Estradiol dipropionate (17-Beta-Estradiol-3,17-Dipropionate) (a), and II (b). The RMSD of the backbone atoms can give information about the structural stability of the system under simulation. Figure 8 shows the RMSD values of the backbone of system I and system II, computed against the starting structures. In both systems, the RMSD of the backbone showed a significant stability over the course of MD simulation. It increased gradually until the 10th ns, and then stabilized for the rest of the simulation around 2.6 ?..