## 3 Results
### In Silico Prediction of Mechanism by Molecular Docking Analysis
Each table column was colored with a three-color scheme gradient, ranging from red for the \(\Delta\)G value scored by the native ligand (used as control), through white for the midpoint interval, and to blue for the highest value (the structure with the lowest affinity), respectively. Thus, the columns of the target proteins where most of the compounds obtained good docking scores compared to the native ligands will be colored predominantly red (Figure 2). \begin{table}
\begin{tabular}{c c c c c c c c c c c c} \hline \hline  & **1N8Q** & **1 OG5** & **2 CDU** & **3 NRZ** & **1 JZQ** & **1K  
Concerning the set of proteins related to RGEO's antibacterial activity, our results show an increased affinity of the majority of docked molecules towards the DDI protein (2I80). DDI is an essential key enzyme involved in bacterial wall biosynthesis and an important drug target for developing new antibiotic agents. This enzyme is responsible for the formation of the dipeptide D-alanine: D-alanine, in a two-step reaction, sequentially by using D-alanine and ATP as substrates for the first reaction step and another D-alanine to complete the reaction [35]. The analyzed compounds were docked in an allosteric pocket adjacent to the D-Ala and ATP binding site. Of the docked compounds, various structures showed a good affinity towards DDI compared to the native ligand, in the range of 2.1 kcal/mol. These structures include monoterpenoids (\(\beta\)-Terpinyl acetate, \(-6.8\) kcal/mol; 4-Carene, \(-6.3\) kcal/mol), sesquiterpennes (Hexa-hydro-farnesol, \(-6.3\) kcal/mol; Elemol \(-6.3\) kcal/mol, \(\alpha\)-Eudesmol, \(-6.4\) kcal/mol), esters (Cyclopropancarboxylic acid, nonyl ester, \(-6.6\) kcal/mol; (2E)-2-Hexenyl benzoate, \(-6.9\) kcal/mol), and ketones (2-Tridecanone, \(-6.4\) kcal/mol; 4-(3,4-Methylenedioxyphenyl)-2-butanone, \(-7.1\) kcal/mol). These findings can be correlated with previous studies that have clearly shown that monoterpenes or terpene-rich EOs are bactericidal and induce bacterial wall disruption, causing the loss of essential nutrients [68, 69]. Additionally, based on the present computational data, the antibacterial effect of RGEO may be attributed more to the lower occuring components. \begin{table}
\begin{tabular}{c c c c c c c c c c c c c} \hline  & **1N8Q** & **1 OG5** & **2 CDU** & **3 NRZ** & **1 JZQ** & **1K2N** & **2 VEG** & **3 RAE** & **3 SRW** & **3 TTZ** & **3 UDI** & **2I80** \\ \cline{2-13}  & & \multicolumn{8}{c}{**Free Binding Energy AG (kcal/mol)**} \\ \hline
**19** & \(-2.5\) & \(-6.2\) & \(-6.3\) & \(-3\) & \(-5.8\) & \(-5.3\) & \(-4.8\)  
Compound 29 (4-(3,4-Methylenedioxyphenyl)-2-butanone) was recorded as the highest-scoring structure towards DDI. Binding analysis revealed a good accommodation of the structure in the protein binding pocket (Figure 3). The compound forms four hydrogen bonds (HBs) (Glu16, Leu95, Thr23, and Gly118), two hydrophobic interactions (Phe313, Leu94), and one S-Pi interaction with Met310. This binding pattern is highly similar to that of the native-ligand, which also forms three of the four HB mentioned above (Figure 3). Figure 2: Three-colored heat map (red-white-blue gradient) obtained after coloring each reordered column of the docking scores table in descending order, from red for the \(\Delta\)G value scored by the native ligand (control), through white for the midpoint interval, and to blue for the highest value (the structure with the lowest affinity). Terpenes, represent a varied structural group of naturally occurring compounds, with a wide range of pharmacological proprieties. Given their well-documented antioxidant potency, terpen were shown to induce significant protection against oxidative stress environments in the case of different types of diseases, such as neurodegenerative liver, cardiovascular and renal diseases, cancer, diabetes, and aging [70].