MDN-0066

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General info

Original publicationCautain, 2015
Original sourcePseudomonas granadensis F-278,770T
Other known sources (non-putative)Pseudomonas azidae SWRI103 (De Roo, 2022)
Stereochemistry determined byMarfey’s analysis (only partially elucidated) (Cautain, 2015)
NMR fingerprint matching (De Roo, 2022)

Chemical properties

CAS
Molecular formulaC52H92N8O14
Molecular weight1053.4 g/mol
Mono-isotopic mass1052.6733 Da
Solubility 
CMCn.a.
Minimal surface tensionn.a.
3D conformationn.a.
NMR data available in literatureDMSO-d6 (Cautain, 2015)
DMF-d7 (De Roo, 2022)

Introduction

MDN-0066 is a cyclic lipodepsipeptide that belongs to the Bananamide group. It is produced by Pseudomonas granadensis F-278,770T, which is currently the only non-putative source of this CLiP. The producing bacterium was first described in the context of a high-throughput screening designed to search for new anticancer agents.

Biological activity

MDN-0066 shows antagonistic activity against Renal Cell Carcinoma (RCC) associated with the Von Hippel Lindau (VHL) syndrome, a rare hereditary disease characterized by an increasing risk to develop tumors. More specifically, MDN0066 is cytotoxic to VHL deficient RCC cells, inducing apoptosis below cytotoxic levels with IC50 values around 25 μM. When VHL expression is reintroduced in the same RCC cell line however, this compounds has no cytotoxic effect at these concentrations. Cell viability assays with other cancerous cell lines indicated that MND-0066 activity is higher in RCC without VHL than in all other tested cell lines. Thus, the compound shows an interesting selectivity towards cancerous cells.  Similar observations have been made for the CLiP xantholysin.

Chemical structure

The chemical structure of MDN-0066 was analyzed using tandem mass spectrometry and liquid state NMR spectroscopy. The stereochemistry of the individual amino acids was determined by Marfey’s analysis. However, the existence of peaks for both D and L-Leu residues in a proportion of 1:1 confirmed the presence of 2 Leu residues of each type and prevented the full assignment of the absolute configuration of the compound. Moreover, partial hydrolysis of the peptide followed by Marfey’s analysis of the fragments did not allow the assignment of the full configuration of the Leu amino acid residues. Subsequently, the stereochemistry of MDN-0066, originating from another bacterial source, was determined using NMR fingerprint matching and solid phase peptide synthesis. (De Roo, 2022). Moreover, by comparing the NMR fingerprints of the newly isolated MDN-0066 with those published for the original compound, it could be concluded that both compounds are indeed identical. The sequence of the compound is therefore 3R-OH C10:0 – D-Leu1 – D-Asp2 – D-aThr3 – L-Leu4 – D-Leu5 – D-Ser6 – L-Leu7 – L-Ile8 whereby the molecule is cyclised by means of an ester bond between the C-terminal carbonyl and the side chain hydroxyl moiety of D-aThr3.  

The structure of MDN-0066 is highly similar to that of other bananamide group members, such as bananamides 1-3 and bananamides D – G. The structure of MDN-0066 is the only CLiP within the Bananamide group of which the stereochemical make-up was elucidated.

Figure: Chemical structure of MDN-0066, including stereochemical make-up as determined by De Roo et al. (2022).
Figure: Schematic representation of the structure of MDN-0066.

NMR fingerprint data

Recently, it was established that the planar structure and stereochemistry of CLiPs can be assessed by simple comparison to a reference. (De Roo, 2022) More specifically, by matching NMR spectra of a CLiP from a newly isolated bacterial source with those of existing (reference) CLiPs, one can determine whether they are identical or not. A detailed explanation on what NMR fingerprint matching is, and how to use it, can be found here.

Below, we provide the reference NMR data of MDN-0066 in various formats. This data is recorded in DMF-d7 at room temperature, and can be used to asses similarities of newly isolated CLiPs to MDN-0066.

References

Cautain, et al. “Identification of the lipodepsipeptide MDN-0066, a novel inhibitor of VHL/HIF pathway produced by a new Pseudomonas species.” PLoS One10, 5 (2015): https://dx.doi.org/10.1371/journal.pone.0125221.

De Roo, et al. “An nuclear magnetic resonance fingerprint matching approach for the identification and structural re-evaluation of Pseudomonas lipopeptides.” Microbiology Spectrum (2022) https://dx.doi.org/doi:10.1128/spectrum.01261-22.

Previous Bananamides D – G