| Summary: | Six new metabolites, including a pair of inseparable mixtures of secofumitremorgins A (<b>1a</b>) and B (<b>1b</b>), which differed in the configuration of the nitrogen atom, 29-hydroxyfumiquinazoline C (<b>6</b>), 10<i>R</i>-15-methylpseurotin A (<b>7</b>), 1,4,23-trihydroxy-hopane-22,30-diol (<b>10</b>), and sphingofungin I (<b>11</b>), together with six known compounds (<b>2</b>–<b>5</b> and <b>8</b>–<b>9</b>), were isolated and identified from the deep-sea sediment-derived fungus <i>Aspergillus fumigatus</i> SD-406. Their structures were determined by detailed spectroscopic analysis of NMR and MS data, chiral HPLC analysis of the acidic hydrolysate, X-ray crystallographic analysis, <i>J</i>-based configuration analysis, and quantum chemical calculations of ECD, OR, and NMR (with DP4+ probability analysis). Among the compounds, <b>1a</b>/<b>1b</b> represent a pair of novel scaffolds derived from indole diketopiperazine by cleavage of the amide bond following aromatization to give a pyridine ring. Compounds <b>1</b>, <b>4</b>, <b>6</b>, <b>7</b>, <b>10</b> and <b>11</b> showed inhibitory activities against pathogenic bacteria and plant pathogenic fungus, with MIC values ranging from 4 to 64 μg/mL.
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