Genome Mining and Molecular Networking Guided Discovery of Embleyamycins A–F, the Calcimycin-Type Polyethers from a Desert-Derived Embleya 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 Embleya genus was isolated. Genome sequencing and bioinformatic analysis of Embleya 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 N-methyltransferase gene. Guided by molecular networking, six new N-demethyl calcimycin analogs, embleyamycins A-F (1-6), were uncovered. Their planar structures and absolute configurations were elucidated through spectroscopic analysis, consideration of identical biosynthetic pathways, and quantum chemical calculations. Compounds 1-6 displayed significant antibacterial activities against a panel of Gram-positive pathogens, with MIC values ranging from 0.25 to 8 μg/mL. Notably, compounds 5 and 6 showed potent inhibitory activities against Candida albicans 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.