DNA gyrase-inhibitory antimicrobial anthraquinone from the endophytic Sordariomycetes fungus Diaporthe perseae

Fungi of the order Diaporthales are prolific sources of antimicrobial secondary metabolites. In this paper, we describe antimicrobial and antituberculosis anthraquinones (AQs) from Diaporthe perseae, an endophytic fungus isolated and identified from the endemic Philippine medicinal plant Uvaria alba (Annonaceae). Large-scale rice fermentation of D. perseae yielded an ethyl acetate extract which was subjected to a series of chromatographic purification to yield three compounds. Spectroscopic analyses allowed the identification of the anthraquinone compounds citreorosein (1), skyrin (2), and rugulosin A (3). AQs 1 and 3 showed broad-spectrum against Gram-positive bacteria (Micrococcus luteus, Bacillus subtilis, and Staphylococcus aureus) (MIC = 1.0–2.0 µg/mL), however only 3 demonstrated strong inhibition against Gram-negative bacterial strains (Escherichia coli, Pseudomonas aeruginosa, and Chromobacterium violaceum) and non-TB mycobacteria (Mycobacterium smegmatis) (MIC = 8.25–66.0 µg/mL). AQ 3 also exhibited inhibition against both M. tuberculosis (Mtb) H37Rv (Microplate Alamar Blue Assay; MABA MIC = 29.2 µg/mL) and its non-replicating persistent strain (Low-Oxygen Recovery Assay; LORA MIC = 30.3 µg/mL). To explore the potential mechanism of 3, DNA supercoiling assay was performed. Thus, rugulosin A (3) displayed inhibition of Mtb. DNA gyrase, an enzyme necessary for genomic replication via ATP-dependent DNA relaxation mechanisms. Molecular docking and molecular dynamics revealed strong, stable binding affinity of 3 (BE = -9.5 kcal/mol) and its tautomer 4 (BE = -9.6 kcal/mol) within the active pocket of the MtbDNA gyrase. Overall, rugulosin A (3) represents a promising antibiotic prototype with in vitro and in silico activity against M. tuberculosis, and identifies DNA gyrase as therapeutic target for anthraquinone antimycobacterials.