Genome Mining and Molecular Networking Guided Discovery of Embleyamycins A–F, the Calcimycin-Type Polyethers from a Desert-Derived <i>Embleya</i> sp. L77

In our continuous bioprospecting for novel species and antibiotics from desert-derived actinomycetes on the Qinghai-Tibet Plateau, China, a strain, L77, affiliated with the rare <i>Embleya</i> genus was isolated. Genome sequencing and bioinformatic analysis of <i>Embleya</i> sp. L77 revealed that it was a putative new species in actinomycete with the potential to produce new calcimycin analogs, as it possessed calcimycin biosynthetic gene clusters (BGCs) but lacked the key <i>N</i>-methyltransferase gene. Guided by molecular networking, six new <i>N</i>-demethyl calcimycin analogs, embleyamycins A-F (<b>1</b>-<b>6</b>), were uncovered. Their planar structures and absolute configurations were elucidated through spectroscopic analysis, consideration of identical biosynthetic pathways, and quantum chemical calculations. Compounds <b>1</b>-<b>6</b> displayed significant antibacterial activities against a panel of Gram-positive pathogens, with MIC values ranging from 0.25 to 8 μg/mL. Notably, compounds <b>5</b> and <b>6</b> showed potent inhibitory activities against <i>Candida albicans</i> ATCC 10231, with MICs as low as ≤0.0625 μg/mL. These findings expand the chemical diversity of the important calcimycin family and highlight that an integrated strategy of genome mining and MS/MS-based molecular networking can effectively facilitate the dereplication of known compounds and accelerate the discovery of new analogs.