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Background: Based on our previous work, we found that 10-methoxycanthin-6-one displayed potential antibacterial activity and quaternization was an available method for increasing the antibacterial activity. Here, we explored the antibacterial activity of quaternized 10-methoxy canthin-6-one derivatives. Methods and Results: Twenty-two new 3-<i>N</i>-benzylated 10-methoxy canthin-6-ones were designed and synthesized through quaternization reaction. The in vitro antibacterial activity against three bacteria was evaluated by the double dilution method. Moreover, the structure&#8211;activity relationships (SARs) were carefully summarized in order to guide the development of antibacterial canthin-6-one agents. Two highly active compounds (<b>6p</b> and <b>6t</b>) displayed 8-fold superiority (MIC = 3.91 &#181;g/mL) against agricultural pathogenic bacteria <i>R. solanacearum</i> and <i>P. syringae</i> compared to agrochemical streptomycin sulfate, and showed potential activity against <i>B. cereus</i>. Moreover, these two compounds exhibited good &#8220;drug-like&#8222; properties, low cytotoxicity, and no inhibition on seed germination. Conclusions: This work provides two new effective quaternized canthin-6-one derivatives as candidate bactericide, promoting the development of natural-sourced bactericides and preservatives.