The authors regret the operational error that occurred during the molecular docking workflow. During the assignment of appropriate PDB entries for DNA gyrase proteins from E. coli and S. aureus, an operational error occurred: PDB entry 6F86, which represents E. coli DNA gyrase B in complex with a pyridine-3-carboxamide inhibitor, was mistakenly attributed to S. aureus. Conversely, the S. aureus gyrase–DNA–inhibitor complex, PDB 2XCS, was not correctly used in the original text. This was solely a labelling error and did not affect the molecular docking methodologies, data calculations, or the interpretation of results. The corrected text, table, and figure are provided below. All authors have reviewed and approved this erratum, which does not reflect any academic misconduct and does not alter the scientific conclusions of the study. Sub-chapter Correction: 3.7. Molecular docking [ …] The docking simulations utilized gentamicin as the positive control and were conducted on DNA gyrase enzymes from E. coli (PDB ID: 6F86) and S. aureus (PDB ID: 2XCS). All analyzed chemicals demonstrated consistent interactions with key amino acid residues within the active sites of both DNA gyrase enzymes. β-linalool looks to have the highest efficiency due to its OH group, which acts as a hydrogen donor, having an H-bond with Ala-47 and Lys-581 for DNA gyrase proteins, steering the ligand to achieve a stable complex with the receptor (Table 5). Also, docking ligand into the proteins pocket (6F86,2XCS) confirms the moderate, but stable interactions, thus the antimicrobial potential (Fig. 5). For S.aures DNA gyrase, the binding energies, ranging from −4.130 to −4.791 kcal/mol, indicated a strong affinity, particularly for limonene, which demonstrated almost half interactions value compared to those of gentamicin, while for E.coli DNA gyrase the docking scores vary between −4.989 and −5.465, with the best affinity registered for β-cis-ocimene and interactions comparable with gentamicin. These findings align with our in vitro findings, which demonstrated greater efficacy against E. coli than S. aureus. However, disparities may arise from the inability of in silico models to account for membrane permeability, chemical solubility and stability, bioavailability, or structural differences between Gram-negative and Gram-positive bacteria. Furthermore, in vitro findings demonstrate the influence of synergistic interactions among various components in the nano-emulsions, which are not fully represented by computer simulations (Xiao et al., 2024). However, the results for E. coli are comparable with those of gentamicin, resulting in a relevant antimicrobial activity Table Correction: [Table presented] Figure correction:[Figure presented] The authors would like to apologise for any inconvenience caused.
Corrigendum to “Citrus essential oils nano-emulsions: Antimicrobial and anti-inflammatory dual strategy against foodborne pathogens” [Food Bioscience 71 (2025) 107181]
Fucile, Mary;Statti, Giancarlo;Conforti, Filomena
2025-01-01
Abstract
The authors regret the operational error that occurred during the molecular docking workflow. During the assignment of appropriate PDB entries for DNA gyrase proteins from E. coli and S. aureus, an operational error occurred: PDB entry 6F86, which represents E. coli DNA gyrase B in complex with a pyridine-3-carboxamide inhibitor, was mistakenly attributed to S. aureus. Conversely, the S. aureus gyrase–DNA–inhibitor complex, PDB 2XCS, was not correctly used in the original text. This was solely a labelling error and did not affect the molecular docking methodologies, data calculations, or the interpretation of results. The corrected text, table, and figure are provided below. All authors have reviewed and approved this erratum, which does not reflect any academic misconduct and does not alter the scientific conclusions of the study. Sub-chapter Correction: 3.7. Molecular docking [ …] The docking simulations utilized gentamicin as the positive control and were conducted on DNA gyrase enzymes from E. coli (PDB ID: 6F86) and S. aureus (PDB ID: 2XCS). All analyzed chemicals demonstrated consistent interactions with key amino acid residues within the active sites of both DNA gyrase enzymes. β-linalool looks to have the highest efficiency due to its OH group, which acts as a hydrogen donor, having an H-bond with Ala-47 and Lys-581 for DNA gyrase proteins, steering the ligand to achieve a stable complex with the receptor (Table 5). Also, docking ligand into the proteins pocket (6F86,2XCS) confirms the moderate, but stable interactions, thus the antimicrobial potential (Fig. 5). For S.aures DNA gyrase, the binding energies, ranging from −4.130 to −4.791 kcal/mol, indicated a strong affinity, particularly for limonene, which demonstrated almost half interactions value compared to those of gentamicin, while for E.coli DNA gyrase the docking scores vary between −4.989 and −5.465, with the best affinity registered for β-cis-ocimene and interactions comparable with gentamicin. These findings align with our in vitro findings, which demonstrated greater efficacy against E. coli than S. aureus. However, disparities may arise from the inability of in silico models to account for membrane permeability, chemical solubility and stability, bioavailability, or structural differences between Gram-negative and Gram-positive bacteria. Furthermore, in vitro findings demonstrate the influence of synergistic interactions among various components in the nano-emulsions, which are not fully represented by computer simulations (Xiao et al., 2024). However, the results for E. coli are comparable with those of gentamicin, resulting in a relevant antimicrobial activity Table Correction: [Table presented] Figure correction:[Figure presented] The authors would like to apologise for any inconvenience caused.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.


