## 3 Results and Discussion
### Molecular Docking Investigation
Although the RUT-GyrB-N complex had an even lower \(\Delta\)G\({}_{\text{int}}\) value of \(-9.01\) kcal/mol, this complex is unstable from a thermodynamic point of view. Considering the free energy of receptor-ligand dissociation (\(\Delta\)G\({}_{\text{diss}}\)) of 0 kcal/mol, the spontaneous detachment of the interacting molecules might be expected. Among all docking models, the complexes formed by GyrB-N with CLA and QUE were characterized by the widest interaction surfaces and the highest \(\Delta\)G\({}_{\text{diss}}\) values of 10.2 and 9.7 kcal/mol, respectively (Table 6), suggesting that external driving forces are needed for the detachment of the phenolic compounds out of their complexes with GyrB-N. The in silico observations indicated that CLA and RUT established non-bonded contacts with Thr\({}^{336}\), which is part of the QTK loop (Ser\({}^{334}\)-Lys\({}^{337}\)). Depending on the ATP before and after the hydrolysis stage, the QTK loop suffers an important spatial rearrangement, along with rigid-body motion of the transducer domain by 6-12\({}^{\circ}\) rotation with respect to the body of the ATPase domain [19]. Of particular interest is also the fact that, upon ATP hydrolysis, the Gln\({}^{335}\) and Thr\({}^{336}\) residues belonging to the QTK loops of the two subunits move closer together at the dimerization interface, resulting in a 7 A wider opening of the inter-subunit distance [25]. Considering CLA and RUT's contacts with Thr\({}^{336}\), these atomic-level events might occur upon ligand binding to the GyrB-N molecules. Furthermore, the QTK loop is in close contact with the ATP-binding region: a hydrogen bond connects the Gln\({}^{335}\) of the transducer domain to the Typ\({}^{26}\) of the ATPase domain, whereas a water molecule mediates the interaction of both Gln\({}^{335}\) and Lys\({}^{337}\) with the Glu\({}^{42}\)[25]. A detailed analysis at the atomic level allowed the identification of close hydrophobic contacts between the flavonoids considered as ligands in the docking study and the aromatic Phe\({}^{41}\) residue, which is located in the close vicinity of the interaction region between the transducer and ATPase domains. In addition, CLA's attachment to GyrB-N resulted in the burial of \(\sim\)40% of the Phe\({}^{41}\) surface initially exposed to the solvent. Therefore, the potential interference of CAT, QUE and CLA binding with the ability of GyrB-N to accurately fulfill its regular functions should be considered. Our observations agree with [PERSON] et al. [57], who reported that QUE is a competitive inhibitor of ATP binding to GyrB, impeding DNA supercoiling. The antibacterial activity of various flavonoids exerted through the inhibition of _E. coli_ DNA gyrase was also reported by [PERSON] et al. [58]. In fact, gyrase has been selected as an important target for antibacterial drugs [57; 58]. Another receptor protein considered in the molecular docking experiment was dispersion, an aggregative factor secreted to the bacterial surface [26]. Dispersin is encoded in the PAA virulence plasmid and is important for the adherence and colonization functions of enteroaggregative _E. coli_ ATCC 25922 [26; 59]. All phytochemicals considered in the in silico tests interacted firmly with the receptor protein, with at least two hydrogen bonds involved in the stabilization of the interface area in each studied case (Table 6). Among all molecular docking models, the complexes formed with QUE and RUT were characterized by the highest affinity (\(\Delta\)G\({}_{\rm int}\) of \(-6.08\) and \(-5.97\) kcal/mol, respectively), exhibiting also the highest thermodynamic stability (\(\Delta\)G\({}_{\rm diss}\) of \(9.2\) and \(9.8\) kcal/mol, respectively). The receptor-ligand interaction energy values are comparable to those reported by [PERSON] et al. [59] for the complexes formed by dispersin with carvacrol and cinnamaldehyde (binding energy of \(-5.17\) and \(-5.65\) kcal/mol, respectively).