What Is The Negative Binding Energy Of The Natural Compounds?

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According to the results discussed so far, including data presented in Figures 5, 6, and 7 and Tables 3 and 4, ZINC00936598, ZINC01020370, and ZINC00869973 compounds have the strongest linkage with the PR binding site residues among the natural compounds and all three compounds have more negative binding energy than the best-docked control drug (Levonorgestrel), in order to bind the PR binding cavity key residues. Furthermore, investigation of the interactions of these natural compounds reveals that whereas these compounds have the highest binding energy, PR binding site key residues that interact with these ligands were the same in all three cases reflecting the significant role of Glu23, Pro24, Asp25, Val26, Ile27, Gln53, Ser56, Val57,…show more content…
In total, according to the molecular docking results, 3 top ranked natural compounds (ZINC00936598, ZINC01020370, and ZINC00869973) give us promising results as potential PR inhibitors and are likely to have a noteworthy role in the treatment of breast cancer. 3.5 Molecular dynamic simulation studies In the present study, MD simulation was performed in two phases. In the first phase, in order to perform relaxation and investigation of the behavior of the PR structure, MD simulation was carried out for 100 ns. After exporting the simulated PR and performing screening and docking analysis, in order to inspect the stability and dynamic behavior of PR-ZINC00936598, PR-ZINC01020370, PR-ZINC00869973 and PR-Levonorgestrel complexes, MD simulation was conducted in the second phase for another 100 ns. In order to study the stability and conformational changes of the free PR and above-mentioned complexes during MD simulation, Root mean square deviation (RMSD) analysis was calculated (Karami, Jalali, & Mirzaie, 2017b) for backbone atoms of both structures (Figure 11). As shown in Figure 11, it can be said that all systems enjoy a level of the RMSD between 0.100 – 0.415 nm during 100 ns MD simulation. It is obvious that the RMSD of the free PR gradually rises in first 3 ns; afterward, no tangible rise was seen in the RMSD rate of the free PR until the end of the simulation,

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