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Four new indolyl diketopiperazines, aspamides A–E (<b>1</b>–<b>4</b>) and two new diketopiperazines, aspamides F–G (<b>5–6</b>), along with 11 known diketopiperazines and intermediates were isolated from the solid culture of <i>Aspergillus</i> <i>versicolor</i>, which is an endophyte with the sea crab (<i>Chiromantes haematocheir</i>). Further chiral high-performance liquid chromatography resolution gave enantiomers (+)- and (−)-<b>4</b>, respectively. The structures and absolute configurations of compounds <b>1</b>–<b>6</b> were determined by the comprehensive analyses of nuclear magnetic resonance (NMR), high-resolution mass spectrometry (HR-MS), and electronic circular dichroism (ECD) calculation. All isolated compounds were selected for the virtual screening on the coronavirus 3-chymoretpsin-like protease (Mpro) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), and the docking scores of compounds <b>1</b>–<b>2</b>, <b>5</b>, <b>6</b>, <b>8</b> and <b>17</b> were top among all screened molecules, may be helpful in fighting with Corona Virus Disease-19 (COVID-19) after further studies.