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1,4-Naphthoquinones have antibacterial activity and are a promising new class of compound that can be used to treat bacterial infections. The goal was to improve effective antibacterial agents; therefore, we synthesized a new class of naphthoquinone hybrids, which contain phenylamino-phenylthio moieties as significant counterparts. Compound <b>4</b> was modified as a substituted aryl amide moiety, which enhanced the antibacterial activity of earlier compounds <b>3</b> and <b>4</b>. In this study, five bacterial strains <i>Staphylococcus aureus</i> (<i>S. aureus</i>), <i>Listeria monocytogenes</i> (<i>L. monocytogenes</i>), <i>Escherichia coli</i> (<i>E. coli</i>), <i>Pseudomonas aeruginosa</i> (<i>P. aeruginosa</i>) and <i>Klebsiella pneumoniae</i> (<i>K. pneumoniae</i>) were used to evaluate the antibacterial potency of synthesized naphthoquinones using the minimal inhibitory concentration (MIC) method. Most of the studied naphthoquinones demonstrated major antibacterial activity with a MIC of 15.6 &#181;g/mL&#8211;500 &#181;g/mL. Selected compounds (<b>5a</b>, <b>5f</b> and <b>5x</b>) were studied for the mode of action, using intracellular ROS generation, determination of apoptosis by the Annexin V-FITC/PI assay, a bactericidal kinetic study and in silico molecular modelling. Additionally, the redox potentials of the specified compounds were confirmed by cyclic voltammetry (CV).