Eda Altinöz

Turkey

Investigation of The Efflux Pump Inhibitory Potential of Hexacontane Against AcrB Protein by Molecular Docking and ADMET Analysis

Eda Altinöz1, Ilgaz Akata2, Ergin Murat Altuner1

1.Department of Biology, Faculty of Science, University of Kastamonu, Kastamonu, Turkey
2.Department of Biology, Faculty of Science, University of Ankara, Ankara, Turkey,

Abstract

Background

Reported that approximately 700,000 deaths occur worldwide each year due to bacterial resistance (García-Castro et al., 2023; Zhang et al., 2024). According to the World Health Organization report in early 2017, a list of antibiotic-resistant microorganisms was published, and this list includes the Enterobacteriaceae family, which is one of those considered highly pathogenic (Lamut et al., 2019; Zhang et al., 2024). Antibiotic resistance occurs after a complex process involving multiple mechanisms, and the efflux pump is only one of these mechanisms (Laws et al., 2022; Zhang et al., 2024). The RND efflux pump is also a mechanism from the superfamily class (Alt?nöz & Altuner, 2019; 2022; Alt?nöz et al., 2024). The RND efflux pump is an AcrAB-TolC complex protein containing AcrA, AcrB and TolC protein (Du et al., 2014; Szal et al., 2023; Alt?nöz et al., 2024). Efflux pump inhibitors can inactivate drug transport or can be used to restore the effectiveness of resistant antibiotics (Mahey et al., 2021; Zhang et al., 2024). However, their clinical use is not yet suitable due to toxicity (Duffey et al., 2024). In this study, the potential inhibitory property of the hexacontane (67.34%) component in the methanol extract of the macrofungus Fomes fomentarius against the AcrB protein (RND efflux pump) was investigated by molecular docking method, the binding relationship between the protein and ligand and in silico study and ADMET analysis.

Methods

According to the data obtained from GC/MS analysis, it was seen that the methanol extract of Fomes fomentarius contained 67.34% hexacontane component. Molecular docking application for this component was performed with Autodock 1.5.6 program. 3D crystal structure of the component was downloaded from protein database in .pdb format. 1OYE, 1T9U, 1T9X, 1T9V, 1T9Y, 2W1B, 3W9H and 4DX5 close monomers from AcrB protein structure belonging to MDR E. coli bacteria were downloaded from protein database and processed. Hexacontane component was downloaded from PubChem in .sdf format and converted to .pdb in Open Babel GUI program. Water and ligand residues were removed from the proteins to be used and molecular docking process was applied. Protein-ligand conformation of the obtained analysis results was created in Biovia Discovery Studio program.

Results

Fomes fomentarius methanol extract contains 67.34% hexacontane component. Although it is the major component, it does not provide the expected binding energy in molecular docking analysisThe binding energies of the component to total of 8 proteins are, from low to high, respectively: 4DX5: +0.07 kcal/mol-1, 1T9X: +1.89 kcal/mol-1, 3W9H: +2.80 kcal/mol-1, 1T9U: +2.85 kcal/mol-1, 2W1B: +3.10 kcal/mol-1, 1OYE: +3.12 kcal/mol-1, 1T9V: +3.26 kcal/mol-1, 1T9Y: +4.56 kcal/mol-1. According to in silico ADMET results: There is no drug similarity according to Lipinski, Ghose, Veber, Egan and Muegge. Absorption properties; there is human intestinal absorption and Caco-2 permeability. Distribution; it passes the blood-brain barrier penetration but cannot provide renal organic cation transport. Organ toxicity; acute oral toxicity classification III and herG inhibition is weak. There is no genomic toxicity AMES toxicity but it has a harmful effect in terms of carcinogenicity.

Conclusions

The presence of Hexacontane component in a high ratio (67.34%) in the methanol extract of Fomes fomentarius in a major ratio clearly suggested that there would be protein-ligand compatibility. However, when the molecular docking analysis results were examined, it was seen that the opposite was true. Thus, it was observed that the major component in high proportions did not exhibit proper binding because they did not have the desired level of binding energy as a result of molecular docking analysis. According to the ADMET analysis, it was understood that the desired level of compliance was not achieved.. This shows that although there was a major component in the extract, the component was insufficient to be a potential efflux pump inhibitor according to molecular docking analysis. Acknowledgment: The authors would like to thank the Kastamonu University Scientific Research Projects Coordination Department under the Grant No. KÜ-BAP01/2021-47 for the support.