## 3 Results and Discussion
### Molecular Docking Investigation  
The antibiotic resistance of microorganisms is related to oxidative stress, making the identification of bioactive molecules with both antioxidant and antibacterial properties very appealing [55; 56]. Therefore, further in silico investigations were carried out to test the abilities of the major compounds with antioxidant activity found in the BC extract to form complexes with selected protein models from _S. aureus_ and _E. coli_. The molecular models of all favorably docked complexes (Figure 3) were further characterized in terms of the contacts established between the two interacting molecules, affinity and thermodynamic stability (Table 6). Figure 3: Superposition of the molecular complexes formed between targeted B subunit of DNA gyrase (**a**) and dispersin (**b**) from _Escherichia coli_ or tyrosyl-tRNA synthetase (**c**) and DNA gyrase (**d**) from _Staphylococcus aureus_ and bioactive compounds prevailing in the black chokeberry extract: catechchin (blue), chlorogenic acid (red), quercetin (green) and rutin (orange). The protein models used as receptors in the docking procedure are represented in silver in new cartoon style, while the ligands are represented in Van der Waals style and DNA fragments (**d**) in violet in licorice style. The images were prepared with the VMD 1.9.3 software. \begin{table}
\begin{tabular}{l c c c c} \hline \hline  & \multicolumn{4}{c}{**Complexes formed between GyrB-N and**} \\ \cline{2-5}  & CAT & CLA & QUE & RUT \\ \hline \(\Delta\)Gint, kcal/mol & \(-7.22\) & \(-7.04\) & \(-7.26\) & \(-9.01\) \\ \(\Delta\)Gdiss, kcal/mol & \(0.0\) & \(10.2\) & \(9.7\) & \(0.0\) \\ Interaction surface, Å2 & \(68.6\) & \(68.8\) & \(97.3\) & \(48.9\) \\ \hline \multirow{3}{*}{Interfacing residues} & Phe41, Glu193, Tyr267, & Phe41, Ile186, Lys189, & His38, Phe41, Arg190, & His38, Phe41, Ile186, \\  & Cys268, Phe269, & Arg190, Glu193, & Ile266, Pro274, & Lys189, Arg190, Pro274, \\  & Pro274, Gln275, Arg276 & Pro274, Thr336 & Gln275, Arg276 & Arg276, Thr336 \\ \hline \hline \end{tabular}
\end{table} 
Table 6: Details of the interactions established within the molecular complexes formed between the targeted B subunit of DNA gyrase (GyrB-N) and dispersin proteins from _Escherichia coli_ or tyrosyl-tRNA synthetase (TyrRS) and DNA gyrase from _Staphylococcus aureus_ and bioactive compounds prevailing in the black chokeberry extract: catechchin (CAT), chlorogenic acid (CLA), quercetin (QUE) and rutin (RUT). Regarding _E. coli_, the proteins used as receptors in the molecular docking procedure were the N-terminal fragment of the B subunit of DNA gyrase (GyrB-N) (Figure 3a), which  
is a prototype of the type II DNA topoisomerase, and the dispersin molecule (Figure 3b), which plays an important role in the adherence and colonization functions of enteroag-gregative _E. coli_. GyrB-N includes the ATPase and transducer domains of DNA gyrase and is fully functional as a dimer. The enzyme uses the free energy released through ATP hydrolysis to introduce negative supercoils into double-stranded DNA molecules, therefore playing an important role in the three-dimensional orientation of double-stranded DNA [25]. The dimer of the GyrB-N model used in this study exhibits a 20 A large hole in the central zone, which is meant to accommodate double-stranded DNA [25]. GyrB-N is able to hydrolyze ATP only in dimeric form, in the presence of double-stranded DNA. Previous studies have reported GyrB-N as an important binding target for antibacterial activity [57; 58]. Careful analysis of the GyrB-N docking models indicated that all investigated ligands were in close contact with residues of both the ATPase domain (residues 1-220) and transducer domain (residues 221-392). The results presented in Table 6 suggest that CAT, CLA and QUE exerted comparable affinity towards the GyrB-N molecule, with the free energy of interaction (\(\Delta\)G\({}_{\text{int}}\)) ranging between \(-7.26\) and \(-7.04\) kcal/mol.