Two new alkaloids, fumigatosides E (1) and F (2), and a new natural product, 3, 7-diketo-cephalosporin P1 (6) along with five known compounds (3–5, 7, 8) were isolated from deep-sea derived fungal Aspergillus fumigatus SCSIO 41012. Their structures were determined by extensive spectroscopic data analysis, including 1D, 2D nuclear magnetic resonance (NMR) and mass spectrometry (MS), and comparison between the calculated and experimental electronic circular dichroism (ECD) spectra. In addition, all compounds were tested for antibacterial and antifungal inhibitory activities. Compound 1 showed significant antifungal activity against Fusarium oxysporum f. sp. momordicae with MIC at 1.56 µg/mL. Compound 4 exhibited significant higher activity against S. aureus (16,339 and 29,213) with MIC values of 1.56 and 0.78 µg/mL, respectively, and compound 2 exhibited significant activity against A. baumanii ATCC 19606 with a MIC value of 6.25 µg/mL.

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