An NMR fingerprint matching approach for the identification and structural re-evaluation ofPseudomonaslipopeptides

Abstract

Cyclic lipopeptides (CLiPs) are secondary metabolites secreted by a range of bacterial phyla. CLiPs display diverse structural variations in terms of the number of the amino acid residues, macrocycle size, amino acid identity and stereochemistry (e.g. D- vs. L-amino acids). Reports detailing the discovery of novel or already characterized CLiPs from new sources appear regularly in literature. However, in some cases, the lack of characterization detail threatens to cause considerable confusion, especially if configurational heterogeneity is present for one or more amino acids. The NMR fingerprint matching approach introduced in this work exploits the fact that the 1H and 13C NMR chemical shift fingerprint is sufficiently sensitive to differentiate the diastereomers of a particular CLiP even when they only differ in a single D/L configuration. This provides a means for a fast screening to determine whether an extracted CLiP has been reported before, by simply comparing the fingerprint of a novel CLiP with that of a reference CLiP. Even when the stereochemistry of a particular reference CLiP is unknown, the NMR fingerprint approach still allows to verify whether a CLiP from a novel source is identical to the reference. To facilitate this, we have made a publicly available knowledge base at https://www.rhizoclip.be, where we present an overview of published NMR fingerprint data of characterized CLiPs, together with literature data on the originally determined structures. The latter includes a description of the CLiPs original description, molecular mass, three dimensional structures (if available), and a summary of published antimicrobial activities. Moreover, a detailed protocol will be made available for researchers that wish to record NMR data of their newly extracted lipopeptides to compare them to the publicly available reference data.

Total Synthesis and Structure Correction of the Cyclic Lipodepsipeptide Orfamide A

“…These results emphasize once again the importance of total synthesis in natural products chemistry, especially when stereochemistry is concerned. [32] We have established a novel, robust, versatile, and high yielding synthetic route to CLPs by using a preformed ester bond in building block 14 and by suppressing O!N acyl migration during Fmoc deprotection. This methodology was implemented on solid support and is compatible with automated SPPS.…”

Complex electrostatic effects on the selectivity of membrane-permeabilizing cyclic lipopeptides

“…The cyclic lipopeptides viscosin and pseudodesmin A were extracted as previously described (18). The viscosin-E2K analog was obtained using the total synthesis approach developed for viscosin and other Pseudomonas lipopeptides as previously described (27,29). All cyclic lipopeptides were solubilized in DMSO and quantified by NMR spectroscopy (ERETIC methodology based on PULCON as described by Wider and Dreier (40)).…”

“…They possess an amphiphilic oligopeptide structure, which is partially cyclized via an ester bond, attached to a fatty acid moiety at its N terminus (2,(15)(16)(17)(18)(19)(20). Recent progress in the total synthesis of such CLiPs (21)(22)(23)(24)(25)(26)(27)(28)(29) allowed us to tackle the issue of electrostatic effects on lipid-CLiP-interactions by comparing the three almost identical CLiPs viscosin, pseudodesmin A, and viscosin-E2K (see Fig. 1 and section ''materials'' for details).…”

Nonribosomal Peptide Synthesis Definitely Working Out of the Rules

“…Another example lies within the maremycins biosynthetic pathway in Streptomyces sp., in which the A domain of MarQ adenylates with the same efficiency Cys and methyl-Cys, and to a lower extent Ser, allowing the production of major and minor compounds [ 30 ]. Detection of variants representing minor forms in mixtures will probably burst in the near future due to the availability of more sensitive methods and technologies for structural determination [ 31 ].…”