Computational assessment and in vitro test of phytochemicals of Usnea aciculifera as potential inhibitors of Escherichia coli efflux pump AcrB

Author:
Phan T.-V., Tuong L.-T., Nguyen V.-T.-V., Vo C.-V.T., Tran T.-D., Le M.-T., Nguyen B.G.D., Tran V.-T., Vu T.-T. & Thai K.-M.
Year:
2025
Journal:
Journal of Biomolecular Structure and Dynamics
Pages:
43(3): 1316–1328
Url:
https://doi.org/10.1080/07391102.2023.2291547
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Lichens produce secondary metabolites that have many pharmaceutical activities such as antimicrobial, antioxidant, antiviral, anticancer, antigenotoxic, anti-inflammatory, analgesic and antipyretic activities. However, there is limited research on their efflux pump inhibitory activities. Twelve phytochemicals were isolated from Usnea aciculifera, and their activity of AcrAB-TolC efflux pump inhibition was evaluated. Four potential compounds, which are diffractaic acid (2), 80 -O- methylstictic acid (5), 3-hydroxy-4-(methoxycarbonyl)-2,5-dimethylphenyl 2,4-dimethoxy-3,6-dimethylbenzoate (8) and 3-hydroxy-4-(methoxycarbonyl)-2,5-dimethylphenyl 2-hydroxy-4-methoxy-3,6-dimethylbenzoate (9), were found by virtual screening using pharmacophore and 2D-QSAR model. Compound 8 exhibited AcrB inhibition activity in vitro with an accumulation H33342 percentage compared with untreated control of 202% at a concentration of 50 mM and increased the antibacterial activity of levofloxacin by four-fold at a concentration of 200 mM. By molecular docking and molecular dynamics (MD) simulation, the binding affinity of depside and depsidone derivatives to AcrB was also clarified. Despite the poor docking score to the AcrB binding site, compound 8 was the most stable among the four complexes at 20 ns of MD simulation. The analysis of long MD at 100 ns indicated that compound 8 interacts strongly with the residues in the distal pocket, creating a stable complex with DGbind of 231.51 kcal.mol-1. According to the ADMETlab 2.0 web server’s predictions of pharmacokinetics and toxicities, compound 8 has the potential for drug development. Keywords: in silico; pump inhibitor; depside; molecular dynamics; accumulation assay; ADMET.
Id:
38304
Submitter:
zpalice
Post_time:
Wednesday, 04 June 2025 14:33