Fig. 10 Orientation compound 2e docking pose (thick cylinders) with respect to residues of the catalytic triad (thin cylinders).
Molecular modeling analysis for this compound manifested its orientation inside the active site cavity and its effective binding interactions to the residues lining the active site channel, which coincided with its in vitro activity.
We next carried out simultaneous quasi-Newton optimization of the compound rigid body orientation and the sidechain torsion angles, and in some cases, the torsion angles of the compound and the backbone torsion angles in the binding site, using the complete Rosetta energy function.
In addition, the polarizabilities of an organic compound with different orientations on the surface are also obtained.
Docking study of the synthesized compounds showed similar orientation as celecoxib within the active site of COX-2 enzyme and similar ability to emerge deeply in the additional pocket and binding with Arg513 and His90 the key amino acids responsible for selectivity.
Ureas do not seem to offer any advantage over amides, moreover both amide orientations (compound 10 vs 14) are tolerated and offer advantage in terms of physiochemical properties (e.g., improved solubility).
Assuming that compounds 11 and 13 adopt a similar scaffold orientation as compound 4, the para-substituents of 11 and 13 would point into a region outside the predicted pocket, without any protein atoms as interaction partners (Figure S4D).
Figure 5b shows the docking orientation of compound q5, which is stabilized by the hydrogen bond interaction between one of the hydroxyphenyl OH of compound q5 forms hydrogen bond with side chain oxygen and backbone HN of Glu357.
A new method based upon the Lorentz-Lorenz equation is deduced for the calculation of surface packing density of an adsorbed organic compound with a certain orientation on an electrode surface from ellipsometric data.
By comparison of docked pose orientation of all compounds, it was deduced that compound 2 (Figure 6b) has a better orientation than compounds 1, and 4 7.
By means of Ts/(Ts+Tm), MPI−1, 4-/1-MDBT and total concentration of carbazole compounds, the oil filling orientation in Yakela and Yuqi areas were from NEE to SWW and NW to SE, respectively.
