Structure determination of the bioactive depsipeptide xenobactin from Xenorhabdus sp. PB30.3

Abstract

A new hexadepsipeptide called xenobactin (1) was isolated from Xenorhabdus sp. PB30.3. Structure elucidation was performed after isolation by extensive 1D- and 2D-NMR experiments. To determine the absolute configuration of the amino acids, modifications of the advanced Marfey's method were applied avoiding racemization and additionally allowing the stereochemical assignment of tryptophan. Moreover, the three dimensional structure was modeled by ROE derived constraints and molecular dynamics runs. The major conformation was verified by comparison of the modeled and experimentally predicted hydrogen bonds. Moreover, bioactivity testing of 1 revealed good antiprotozoal activity against Plasmodium falciparum and a specific antibiotic activity against the Gram positive bacterium Micrococcus luteus, whereas no cytotoxicity could be observed.