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An endophytic fungus <i>Arthrinium arundinis</i> TE-3 was isolated and purified from the fresh leaves of cultivated tobacco (<i>Nicotiana tabacum</i> L.). Chemical investigation on this fungal strain afforded three new prenylated diphenyl ethers (<b>1</b>&#8315;<b>3</b>) as well as three known analogues (<b>4</b>&#8315;<b>6</b>). Structure elucidation of the isolated compounds was carried out by analysis of 1D and 2D nuclear magnetic resonance (NMR) and high-resolution electrospray ionization mass spectroscopy (HRESIMS) spectra, as well as by comparison of those data with literature data. The absolute configuration of the stereogenic center at C-8 in <b>1</b> was assigned by comparison of the experimental and calculated ECD spectra. Compounds <b>1</b> and <b>2</b> showed selective antifungal activity against <i>Mucor hiemalis</i> with minimum inhibitory concentration (MIC) values of 8 and 4 &#956;g/mL, respectively. Compounds <b>5</b> and <b>6</b> exhibited inhibitory activity against <i>Alteraria alternata</i> with an MIC value of 8 &#956;g/mL. In the cytotoxic assay, <b>2</b>, <b>5</b>, and <b>6</b> displayed moderate in vitro cytotoxicity against the human monocytic cell line (THP-1 cell line), with IC₅₀ values of 40.2, 28.3, and 25.9 &#956;M, respectively. This study indicated that endophytic fungi possess great potential for exploring new bioactive secondary metabolites.