# Identification of Some Glutamic Acid Derivatives with Biological Potential by Computational Methods
## 2 Results and Discussion
### Characterisation of the \"Lead\" Compounds
Phosphinothricin, a GS inhibitor, shows the closest similarity (86.9%) to compound 4 Db6, as scored by SwissSimilarity (Score = 0.869) [148]. The comparison was made to identify the most probable binding site in the enzyme structure [149]. The study was conducted using SwissDock [150; 151; 152], PatchDock [136; 153; 154], and AutoDockVina 1.1.2 [155; 155]. In a study evaluating a crystalline structure of GS inhibited by phosphinothricin, the inhibitor molecule preferentially binds to the enzyme in the D subunit's active site. Phosphinothricin occupies the glutamate pocket and stabilises the Glu327 residue in a position that prevents glutamate from entering the active site [149]. This crystal structure (PDB code: 1 FPY) was observed using the Mol* Viewer web app of RCSB PDB [142; 156]. The preference for the D subunit was also confirmed by results obtained using the PatchDock app, which estimated the most probable binding site for the 4 Db6 compound [136; 153; 154]. The top 10 best solutions are shown in Table 13. Figure 4 illustrates the first best result generated. \begin{table}
\begin{tabular}{r c c c c} \hline \hline
**No.** & **ID Code** & **Rat IP LD50 Classification** & **Rat IV LD50 Classification** & **Rat OC LD50 Classification** \\ \hline
1 & 1 Aa7 & Non-Toxic in AD & Non-Toxic in AD & Non-Toxic in AD & Non-Toxic in AD \\
2 & 1 Aa8 & Non-Toxic in AD & Non-Toxic in AD & Class 5 in AD & Non-Toxic in AD \\
3 & 2 Ba2 & Class 5 in AD & Non-Toxic in AD & Class 4 in AD & Class 5 in AD \\
4 & 2 Ba5 & Class 4 in AD & Non-Toxic in AD & Class 4 in AD & Class 5 out of AD \\
5 & 2 Ba6 & Class 4 in AD & Class 5 in AD & Class 4 in AD & Class 4 in AD \\
6 & 3 Aa3 & Class 4 in AD & Class 5 in AD & Class 5 in AD & Class 5 in AD \\
7 & 3 Aa5 & Class 5 in AD & Class 5 in AD & Class 5 out of AD & Class 5 in AD \\
8 & 4 Da11 & Class 5 out of AD & Class 5 in AD & Class 5 in AD & Class 4 in AD \\
9 & 4 Db6 & Class 4 out of AD & Class 4 in AD & Class 4 out of AD & Class 3 in AD \\ \hline \hline \end{tabular}
\end{table} 
Table 11: Acute toxicity in rodents. Classification of Chemicals according to the OECD Project [138]. \begin{table}
\begin{tabular}{r c c c} \hline \hline
**Step** & **Time (fs)** & **Potential Energy (J)** & **Kinetic Energy (J)** \\ \hline
0 & 0.0 & 341.630730 & 86.279577 \\
100 & 0.1 & 335.578989 & 92.292502 \\
200 & 0.2 & 351.037095 & 77.385248 \\
300 & 0.3 & 333.800802 & 94.478719 \\
400 & 0.4 & 353.520040 & 74.902008 \\
500 & 0.5 & 363.225563 & 65.233746 \\
600 & 0.6 & 365.055252 & 63.321001 \\
700 & 0.7 & 359.244207 & 69.127817 \\
800 & 0.8 & 333.6010201 & 95.326086 \\
900 & 0.9 & 336.605457 & 91.597157 \\
1000 & 1 & 362.614614 & 65.517278 \\ \hline \hline \end{tabular}
\end{table} 
Table 12: Molecular dynamics simulation results for compound 4 Db6 [144]. However, the selected derivative does not bind to the active site. Thus, these derivatives will probably not show inhibitory activity towards the enzyme. Molecular docking was performed using SwissDock [134; 150; 152] and AutoDockVina 1.1.2 [151; 155] to increase the accuracy of the study. For PPQ, SwissDock found 257 conformations. The most probable binding site was chosen according to the conformation with the lowest energy, having \(\Delta\)G = \(-\)10.43 kcal/mol and a FullFitness value of \(-\)2192.23 kcal/mol [150; 152; 157]. The FullFitness parameter for a cluster is calculated using the average of 30% of the most favourable energies of its elements to lower the risk of inhibition of the entire cluster by some complexes. This energy is represented by the sum of the system's total energy and a solvation term [158]. For example, for compound 4 Db6, SwissDock found 160 conformations. By comparing the PPQ binding site with the sites of the 160 conformations, we consider that clusters 1, 6 and 33 could bind to the same site in a relatively similar way (Table 14).