Identification of four new agr quorum sensing-interfering cyclodepsipeptides from a marine Photobacterium

Article abstract of DOI:10.3390/md11125051

During our search for new natural products from the marine environment, we discovered a wide range of cyclic peptides from a marine Photobacterium, closely related to P. halotolerans. The chemical fingerprint of the bacterium showed primarily non-ribosomal peptide synthetase (NRPS)-like compounds, including the known pyrrothine antibiotic holomycin and a wide range of peptides, from diketopiperazines to cyclodepsipeptides of 500-900 Da. Purification of components from the pellet fraction led to the isolation and structure elucidation of four new cyclodepsipeptides, ngercheumicin F, G, H, and I. The ngercheumicins interfered with expression of virulence genes known to be controlled by the agr quorum sensing system of Staphylococcus aureus, although to a lesser extent than the previously described solonamides from the same strain of Photobacterium.

Full text of DOI:10.3390/md11125051

Mar. Drugs 2013, 11, 5051-5062; doi:10.3390/md11125051
OPEN ACCESS
marine drugs
ISSN 1660-3397
www.mdpi.com/journal/marinedrugs
Article
Identification of Four New agr Quorum Sensing-Interfering
Cyclodepsipeptides from a Marine Photobacterium
Louise Kjaerulff 1, Anita Nielsen 2, Maria Mansson 3, Lone Gram 3, Thomas O. Larsen 3,
Hanne Ingmer 2,* and Charlotte H. Gotfredsen 1,*
1
Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark;
E-Mail: lokja@kemi.dtu.dk
2
Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of
Copenhagen, DK-1870 Frederiksberg C, Denmark; E-Mail: anini@sund.ku.dk
3
Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby,
Denmark; E-Mails: maj@bio.dtu.dk (M.M.); gram@bio.dtu.dk (L.G); tol@bio.dtu.dk (T.O.L.)
* Authors to whom correspondence should be addressed;
E-Mails: hi@sund.ku.dk (H.I.); chg@kemi.dtu.dk (C.H.G.); Tel.: +45-3533-2773 (H.I.);
Fax: +45-3533-2755 (H.I.); Tel.: +45-4525-2148 (C.H.G.); Fax: +45-4593-3968 (C.H.G.).
Received: 8 October 2013; in revised form: 21 November 2013 / Accepted: 2 December 2013 /
Published: 12 December 2013
Abstract: During our search for new natural products from the marine environment, we
discovered a wide range of cyclic peptides from a marine Photobacterium, closely related
to P. halotolerans. The chemical fingerprint of the bacterium showed primarily
non-ribosomal peptide synthetase (NRPS)-like compounds, including the known
pyrrothine antibiotic holomycin and a wide range of peptides, from diketopiperazines to
cyclodepsipeptides of 500–900 Da. Purification of components from the pellet fraction led
to the isolation and structure elucidation of four new cyclodepsipeptides, ngercheumicin F,
G, H, and I. The ngercheumicins interfered with expression of virulence genes known to be
controlled by the agr quorum sensing system of Staphylococcus aureus, although to a
lesser extent than the previously described solonamides from the same strain
of Photobacterium.
Keywords: Photobacterium; depsipeptide; structure elucidation; quorum sensing;
antivirulence; agr

Mar. Drugs 2013, 11
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1. Introduction
The marine environment is a rich and vastly underexplored resource in many aspects. Most of the
Earth’s surface is covered by water, inhabited by an incredible diversity of species, many of which
have yet to be discovered. Microbial species are an important source for marine chemodiversity and it
is believed that marine microorganisms will provide valuable drug candidates in the future [1,2]. There
are however certain challenges with respect to sampling and culturing, and the usually low yields of
metabolites can hamper full structural characterization and biological explorations.
A marine Photobacterium was selected from 500 bacterial strains collected during a global marine
research cruise in 2006–2007 [3]. It was sampled from a mussel surface near the Solomon Islands and
this bacterial strain was singled out as particularly interesting because of a two-pronged inhibitory
effect of growth and quorum sensing (QS) in important human pathogens. The known pyrrothine
antibiotic holomycin was responsible for the growth inhibition of V. anguillarum and S. aureus [4],
while the solonamides were identified as the major contributors to the interference with agr quorum
sensing in S. aureus [5]. Inhibition of virulence factor production and activity has been suggested as a
new therapeutic approach suitable for antibiotic resistant pathogens [6]. In S. aureus, one of the
possible targets is the agr quorum sensing system that in response to autoinducing peptide (AIP)
accumulation at high cell densities induces expression of numerous extracellular toxins including hla
encoding α-hemolysin while repressing expression of surface factors such as the spa encoded
Protein A [7].
In this study, we report the identification of four cyclodepsipeptides in the 800–900 Da size range
from the cell-associated (pellet) fraction of this marine Photobacterium that modulate expression of
agr controlled virulence genes. The depsipeptides ngercheumicin F, G, H, and I are new additions to
the structural family that initially constituted ngercheumicin A and B [8]. Three other depsipeptides
ngercheumicin C, D, and E were isolated from the same bacterial strain as ngercheumicin A and B, but
they are structurally different. All ngercheumicins reported to date have been isolated from
Photobacterium spp. and a biological activity reported by Shizuri et al. for ngercheumicins A–E was
against infections by Pseudovibrio denitrificans [8]. Like the solonamides [5], the ngercheumicins are
16-membered macrocyclic depsipeptides with some structural resemblance to the AIPs of S. aureus.
Generally, AIPs consist of a cyclopentapeptide moiety cyclized through a cysteine residue by a
thiolactonization, and with an exocyclic peptide chain of variable length extended from the cysteine
residue in the N-terminal direction [9]. The exocyclic chain appears to be closely related to agonistic
activity as truncated AIPs are known to have antagonistic properties [10]. Structure-activity
relationship studies by Mayville et al. [11] indicated that adjacent Leu and Phe residues are required
for inhibitory activity; however, structural comparisons of 24 natural staphylococcal AIPs later showed
that they consistently have bulky, hydrophobic amino acid side chains in the C-terminus [12]. This
may instead be the structural requirement for activity.
Here, we describe the isolation and structure elucidation of the four new ngercheumicins and
discuss their role in QS.

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2. Results and Discussion
2.1. Isolation and Structure Elucidation of Ngercheumicins F–I
The pellet of the Photobacterium sp. was extracted with organic solvents (see Experimental
Section 3.2) and fractionated on a diol column. Mass spectrometric analysis revealed a series of
peptide-like analogues which display good ionization in ESI+ MS and end absorption in UV
spectroscopy. The fractions containing these analogues were pooled and subjected to further
purification, first on a smaller diol column and then by preparative reversed phase HPLC, which gave
four fractions of ngercheumicin F, G, H, and I, respectively. Ngercheumicins A and B were also
detected by LC-MS, but they were not purified in sufficient amounts for structural or biological
screening studies. The four new ngercheumicins were found to inhibit transcription of the regulatory
rnaIII in S. aureus, which is the effector molecule of the agr QS system (See Section 2.2 and
Supplementary Information).The ngercheumicins were isolated as white solids with the respective
exact masses (HR-ESI-TOF) and molecular formulae: Ngercheumicin F (m/z: [M + H]+ 853.5685,
calculated for C43H77N6O11 as 853.5650), ngercheumicin G (m/z: [M + H]+ 855.5907, calculated for
C43H79N6O11 as 855.5807), ngercheumicin H (m/z: [M + H]+ 881.6033, calculated for C45H81N6O11 as
881.5963), and ngercheumicin I (m/z: [M + H]+ 883.6255, calculated for C45H83N6O11 as 883.6120).
Analysis of 1D and 2D nuclear magnetic resonance (NMR) spectroscopic data obtained for the four
compounds characterized the structures as cyclodepsipeptides consisting of six amino acids and a
3-hydroxy fatty acid (six NH signals and seven carbonyl resonances) (Figure 1). All four
ngercheumicins were elucidated as having identical amino acid sequences, consisting of three leucines,
two threonines, and one serine, as established by DQF-COSY, gHSQC, gHMBC, gH2BC, and
TOCSY 2D NMR spectroscopic analyses. The closure of the macrocyclic ring through an ester linkage
between the C-terminus and the hydroxyl group in one of the threonine residues was verified by the
low field chemical shift of the β-proton of Thr2 (H26, Table 1) and a HMBC correlation between H26
and the carbonyl (C1) of the C-terminal Leu1 residue (for HMBC and H2BC correlations, see
Supplementary Information). This formed a 16-membered macrocycle with an exocyclic chain
continuing in the N-terminal direction from Thr2, the chain constituting a Leu residue and a 3-hydroxy
fatty acid (Figure 1). The structural difference between the four analogues was found in the length and
saturation of the unbranched fatty acid chain. Ngercheumicin F and H each have one double bond in
the 3-hydroxy fatty acid chain, whereas the fatty acids in ngercheumicin G and I are fully saturated,
but with the same lengths as F and H, respectively. The previously isolated ngercheumicin A and B
have a similar relationship, but with 12-carbon long fatty acid chains [8], whereas ngercheumicin F
and H have fatty acid chains with 14 and 16 carbon atoms, respectively. The longer chains result in
increasing overlap of 1H and 13C resonances in the aliphatic regions on both sides of the double bond.
By thorough examination of HMBC and H2BC correlations in the chains, the structures of
ngercheumicin F and H were elucidated and assigned as shown in Figure 1 and Table 1, respectively.
The chemical shifts of ngercheumicin H were virtually symmetrical around the double bond because of
the long chain, whereas there was a slight shift in ngercheumicin F, which has a shorter alkyl chain.
The position of the double bond in ngercheumicin H was tentatively assigned based on the NMR data,
as the data left an ambiguity of a CH2-group between position 41 and 47 due to the high degree of

Mar. Drugs 2013, 11
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symmetry and the overlapping resonances that 2D NMR was unable to resolve. However, assuming a
correct assignment, a structural pattern emerged where ngercheumicin A, F, and H had their double
bonds positioned seven carbon atoms from the end of the fatty acid chain, also known as n-7 fatty
acids. Counting from the peptide-end of the fatty acid chain, the double bonds in ngercheumicin F and
H are thus situated further into the fatty acid chains.
Figure 1. Structures of ngercheumicin A, B, F, G, H, and I, where ngercheumicin A, F,
and H have an unsaturation (cis) in the unbranched alkyl chain, R.
1
13
Table 1. H and C NMR spectroscopic data (800 MHz, DMSO-d6) for ngercheumicins
F–I. More elaborate NMR tables can be found in the Supplementary Information.
Ngercheumicin F
Ngercheumicin G
δH (ppm) δC (ppm)
Ngercheumicin H
δH (ppm) δC (ppm)
Ngercheumicin I
δH (ppm) δC (ppm)
Position, Type δH (ppm)
δC (ppm)
Leu1
1—CO
−
4.37
170.8
51.1
40.4
24.5
22.3
22.5
−
−
170.8
−
170.8
−
170.8
2—CHα
3—CHβ
4—CHγ
5—CHδ,1
6—CHδ,2
7—NH
4.37
1.61, 1.55
1.49
51.1
40.4
24.5
22.3
22.5
−
4.37
1.62, 1.56
1.50
51.1
40.4
24.5
22.3
22.5
−
4.37
1.61, 1.56
1.49
51.1
40.4
24.5
22.3
22.5
−
1.62, 1.55
1.49
0.88
0.88
0.89
0.88
0.85
0.85
0.85
0.85
7.73
7.73
7.73
7.73
Leu2
8—CO
−
171.0
50.4
38.8
24.2
22.9
21.4
−
171.0
50.4
38.8
24.2
22.9
21.4
−
171.0
50.4
38.8
24.1
22.9
21.4
−
171.0
50.4
38.8
24.1
22.9
21.4
9—CHα
10—CHβ
11—CHγ
12—CHδ,1
13—CHδ,2
4.26
1.49
1.53
0.87
0.80
4.26
1.49
1.53
0.87
0.80
4.25
1.49
1.54
0.87
0.80
4.26
1.49
1.54
0.87
0.80

Mar. Drugs 2013, 11
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Table 1. Cont.
14—NH
L-allo-Thr1
15—CO
16—CHα
17—CHβ
17—OH
18—CHγ
19—NH
D-Ser
8.12
−
8.11
−
8.11
−
8.11
−
−
170.7
59.9
65.1
−
−
170.7
59.9
65.1
−
−
170.7
59.9
65.1
−
−
170.7
59.9
65.1
−
3.86
3.88
4.70
1.03
8.09
3.86
3.88
4.69
1.03
8.09
3.86
3.88
4.69
1.03
8.09
3.86
3.87
4.69
1.03
8.09
20.0
−
20.1
−
20.1
−
20.1
−
20—CO
21—CHα
22—CHβ
22—OH
23—NH
L-allo-Thr2
24—CO
25—CHα
26—CHβ
27—CHγ
28—NH
Leu3
−
170.0
54.5
61.6
−
−
170.0
54.6
61.5
−
−
170.0
54.5
61.5
−
−
170.0
54.5
61.5
−
4.38
3.54
4.86
7.53
4.38
3.54
4.86
7.53
4.38
3.54
4.86
7.53
4.38
3.54
4.86
7.53
−
−
−
−
−
168.4
56.2
69.6
17.0
−
168.4
56.2
69.6
17.0
−
168.4
56.2
69.6
16.9
−
168.4
56.2
69.6
17.0
4.40
5.35
1.10
8.40
4.39
5.34
1.10
8.39
4.39
5.34
1.10
8.39
4.39
5.35
1.10
8.39
29—CO
30—CHα
31—CHβ
32—CHγ
33—CHδ,1
34—CHδ,2
35—NH
Fatty acid
36—CO
37
−
173.1
51.7
40.3
24.2
22.6
21.9
−
−
173.2
51.8
40.2
24.2
22.6
21.9
−
−
173.1
51.8
40.2
24.2
22.6
21.9
−
−
173.2
51.8
40.2
24.2
22.6
21.9
−
4.37
1.48
1.62
0.92
0.87
8.20
4.37
1.48
1.62
0.92
0.87
8.20
4.37
1.48
1.62
0.91
0.87
8.20
4.37
1.48
1.63
0.92
0.87
8.20
−
~2.24
3.78
171.8
43.3
67.4
−
−
171.9
−
2.25, 2.22
3.78
171.9
43.4
67.5
−
−
2.25, 2.22
3.78
171.9
43.4
67.5
−
2.24, 2.22
3.77
43.4
67.5
−
38
38—OH
39
4.62
4.60
4.60
4.59
1.34, 1.30
1.42, 1.28
1.96
36.2
25.1
26.6
129.6
129.6
26.5
29.0
28.3
31.1
22.1
13.9
1.31
36.6
24.8
~29
~29
~29
~29
~29
29.1
31.3
22.1
13.9
1.32
36.6
24.8
~29
1.32
36.6
24.8
29.1
~29
~29
~29
~29
~29
~29
~29
31.3
22.1
13.9
40
1.34, 1.22
1.23
1.36, 1.23
~1.2
1.35, 1.22
1.23
41
42
5.31
~1.2
1.28
~29
~1.2
43
5.31
~1.2
1.97
26.6
129.6
129.6
26.6
~29
~1.2
44
1.96
~1.2
5.31
~1.2
45
1.28
~1.2
5.31
~1.2
46
1.24
1.21
1.97
~1.2
47
1.22
1.22
1.28
~1.2
48
1.25
1.25
1.25
28.2
31.1
22.0
13.9
~1.2
49
0.84
0.84
1.22
1.22
50
1.25
1.25
51
0.84
0.84

Mar. Drugs 2013, 11
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The resonances originating from the double bond were very close in chemical shift, leading to
1
severe second order effects in the H multiplet patterns. Due to the second order spin systems, it was
not possible to determine the size of the J coupling constant, however the total span of the multiplets at
5.31 ppm for both F and H was below 15 Hz, and assuming complete symmetry, a trans coupling
seemed unlikely. The chemical shifts for the allylic carbons at 26.5–26.6 ppm are also consistent with
cis configuration, as allylic carbons in trans fatty acids are about 5 ppm further downfield [13].
Therefore the double bonds in ngercheumicin F and H were assigned as cis.
Attempts to obtain absolute stereochemical assignment of the amino acids were done by Marfey’s
method, using existing methods for acid hydrolysis [14] and derivatization with Marfey’s reagent [15].
Complete stereochemical assignments were not obtained as Marfey’s method revealed the presence of
both L- and D-Leu, and unambiguous resolution of the hydroxyamino acids Ser and Thr is known to be
challenging [16]. Pure enantiomers of Leu, Ser and Thr were used to synthesise single diastereomers
with Marfey’s reagent for comparison with the Marfey’s derivatives of the hydrolysed ngercheumicins.
This also included allo-Thr. By comparison to the pure amino acid derivatives, L-Ser, D-Thr and
D-allo-Thr were dismissed. Therefore the configuration of the Ser residue was firmly assigned as
D-Ser. Although the peaks of L-Thr, D-Ser, and L-allo-Thr eluted within a narrow spectral window, the
elution order together with MS detection verified the presence of L-allo-Thr and no L-Thr. This was
supported by the size of the J coupling constant from Thr2 H26 to H25 and H27. The absolute
configuration of the three Leu residues was ambiguous, however both L- and D-Leu were present. Due
to the minute amounts available, (0.5–1.1 mg of each analogue) the configuration of the 3-hydroxy
fatty acid was not determined.
Organic synthesis could be a solution to the supply problem of these peptides, as synthesis of cyclic
peptides is often a relatively straightforward procedure. Many cyclic peptides from marine microbial
sources contain non-proteinogenic and D-amino acids as well as polyketide-derived structural motifs or
fatty acids [17], which is also the case for the solonamides and the ngercheumicins. Undoubtedly,
these traits complicate synthesis of both natural products and analogues. However, a study by
Molhoek et al. showed that cyclization of a peptide antibiotic and substitution of L- with D-amino acids
improved stability towards bacterial proteases (including those in S. aureus) and decreased cytotoxicity
while retaining the antibacterial activity [18]. The ngercheumicin macrocycle is closed through an
ester bond between the C-terminus and the side chain of a Thr residue. This is a common trait in
depsipeptides, and e.g., the cyclodepsipeptide plitidepsin [2], which is undergoing clinical trials for
treatment of several cancers, has this feature in common with the ngercheumicins.
2.2. Ngercheumicins Interfere with agr
Ngercheumicin F, G, H, and I were examined in the S. aureus lacZ reporter assays described by
Nielsen et al. [19] monitoring transcriptional activity of the hla, spa, and P3 (rnaIII) promotors. All
four ngercheumicins increased transcription of spa and reduced expression of hla and rnaIII, compared
to a solvent control (see Supplementary Information). The inverse effect of the ngercheumicins on spa
expression compared to rnaIII and hla indicates that the ngercheumicins interfere with agr activation.

Mar. Drugs 2013, 11
5057
To confirm these initial results, cultures of a highly virulent, community-acquired strain of
S. aureus USA300 were exposed to ngercheumicins F–I and RNAIII expression was monitored in
exponential and stationary growth phase by Northern blot analysis. Data confirmed that
ngercheumicins reduced expression of rnaIII and thus interfere with agr in CA-MRSA strain USA300.
At the ngercheumicin concentrations used in the culture samples for Northern blotting, there was a
minor down regulation of rnaIII by ngercheumicin G and H at 5 µg mL−1 (see Supplementary
Information). At 20 µg mL−1 (23 μM, see Figure 2), the rnaIII inhibiting effect was more pronounced
for ngercheumicin G and H, but also F showed activity here and appeared to have the highest rnaIII
inhibiting activity. Ngercheumicin I did not show any significant effect at either 5 or 20 µg mL−1.
Figure 2. Northern blot of ngercheumicin F, G, H and I treated S. aureus USA300 wt
(FPR3757) cells in stationary phase (OD600 = 3) at ngercheumicin concentration of
20 µg mL−1.
The ngercheumicins share structural traits with the AIPs of S. aureus. S. aureus strains express one
of a least four variants of AIPs and each variant induces agr expression in strains of the same type but
repress agr expression in strains of other types [20]. Interestingly, the ngercheumicins resemble the
type II and III AIPs, whereas the solonamides resemble type I and II the most [21]. All have
16-membered macrocyclic rings and flexible exocyclic chains (Figure 3). The AIPs have purely
peptidic exocyclic chains, whereas the depsipeptides all contain fatty acid chains, but both the AIPs
and the cyclodepsipeptides have variations in the length of the exocyclic chains, which perhaps relate
to receptor specificity. Looking at the amino acid sequence of the ngercheumicins (Figure 3) starting at
the C-terminus, the two Leu residues are also found in AIP-III, and the Thr-Ser sequence closely
resembles the Ser-Ser sequence in AIP-II. It should be noted that this comparison is made without
taking 3D configuration of the side chains into account, because only the 2D structures are known. It is
however clear that part of the backbone structure is highly homologous to the native AIPs of S. aureus.

Mar. Drugs 2013, 11
Figure 3. Schematic structures of S. aureus autoinducing peptides (AIPs) I–III, solonamide
5058
B and ngercheumicin G, with amino acid sequences and type of ring closure. AIP
structures are reproduced from [21]. AIP-IV also exists, where the aspartic acid (D) of
AIP-I is replaced by a tyrosine residue.
Little is known about peptide signaling in the marine environment and whether other groups of
peptide signal molecules exist there. It can be speculated that these depsipeptides interfere with QS
pathways present in the marine environment or even act as alternative quorum sensing molecules.
Existing QS systems include the N-acyl homoserine lactones in Gram-negative bacteria and the auto
inducing peptides in the Gram-positive staphylococci [22]. That ngercheumicins F–I were isolated in
low yields as intracellular metabolites, unlike the solonamides that were excreted in large amounts,
could mean that they do not act as intercellular signaling molecules in the natural environment and
therefore there could be an unexplored biological role for the ngercheumicins. Analyses of co-cultures
of this Photobacterium with naturally co-occurring or competitive strains could provide further insight
into the biological function of these compounds.
3. Experimental Section
3.1. Isolation and Identification of Strain s2753
Bacterial strain s2753 was isolated from a mussel surface collected in the tropical Pacific (9.1° S
156.8° E) during the Danish Galathea 3 expedition [3]. S2753 was assigned to the Vibrionaceae and
sequence similarity of household genes identified it as a Photobacterium halotolerans as previously
described [3–5].

Mar. Drugs 2013, 11
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3.2. Isolation and Structure Elucidation of Four New Ngercheumicins
S2753 was cultured in 10 L glass fermentors in 5 × 4 L SSS containing 0.4% glucose and 0.3%
casamino acids in (25 °C, 72 h, 100 rpm). The liquid culture was centrifuged (15 min, 3500 × g) to
isolate the pellet from the broth and Diaion HP20SS (12 g L−1) which was used to extract the bioactive
compounds holomycin and solonamides A–B as previously described [4,5]. The pellet was extracted
with 1 L 1:9 (v/v) MeOH/EtOAc (25 °C, 24 h, 100 rpm) and filtered off through a Watman 1 filter.
The pellet extract was concentrated on a rotary evaporator and absorbed onto 5 g Isolute diol (Biotage,
Uppsala, Sweden) for dry loading onto a 50 g SNAP column packed with Isolute diol and eluted on an
Isolera automated flash system (Biotage, Uppsala, Sweden) using solvents ranging from heptane,
dichloromethane, EtOAc to pure MeOH (30 mL min−1, 72 min). A total of 33 fractions were collected
and subjected to LC-UV/MS. Fractions 7 to 10 (dichloromethane/EtOAc) were pooled and absorbed
onto 1.5 g Isolute diol and further fractionated on a 10 g diol column run by gravity with heptanes,
dichloromethane, EtOAc and MeOH as above. This yielded 10 fractions (again subjected to
LC-UV/MS) of which fractions 6 and 7 (10%–30% MeOH in EtOAc) were purified on a Luna II
column (5 μm C18, 250 × 10 mm ID, Phenomenex) in a Gilson 322 liquid chromatograph with a
215 liquid handler/injector (BioLab, Risskov, Denmark) going from 70% to 100% aqueous MeCN,
20 mM formic acid, over 10 min followed by 6 min isocratic elution. This yielded 12 fractions of
which pure compounds were obtained directly: Ngercheumicin F (0.5 mg), Ngercheumicin G (1.0 mg),
Ngercheumicin H (0.5 mg), and Ngercheumicin I (1.1 mg). Selected chromatograms are available in
the Supplementary Information.
LC-UV/MS analyses were performed on an Agilent 1100 HPLC system with a diode array detector
coupled to an LCT TOF mass spectrometer (Micromass, Manchester, UK) using a Z-spray ESI source.
Separation was performed at 40 °C with a Luna II C18 column (50 × 2 mm ID, 3 μm, Phenomenex,
Torrance, CA, USA), applying a linear gradient of 15%–100% aqueous MeCN, 20 mM formic acid
(LC-MS-grade), over 20 minutes at a flow rate of 0.3 mL/min. MS experiments were performed in
ESI+ with a data acquisition range of m/z 100–2000. Accurate masses of ammonium adducts were
measured for Ngercheumicin F (m/z: [M + NH4]+ 870.5979, calculated for C43H80N7O11 as 870.5916),
ngercheumicin G (m/z: [M + NH4]+ 872.6206, calculated for C43H82N7O11 as 872.6072),
ngercheumicin H (m/z: [M + NH4]+ 898.6359, calculated for C45H84N7O11 as 898.6229), and
ngercheumicin I (m/z: [M + NH4]+ 900.6450, calculated for C45H86N7O11 as 900.6385). The [M + H]+
adducts were reported in Section 2.1.
To solve the absolute configuration of the amino acids Marfey’s method was applied: 100 μg of
each cyclodepsipeptide was subjected to acid hydrolysis (200 μL 6 M HCl, 110 °C, 20 h), redissolved
in 50 μL water and added 20 μL 1 M aqueous NaHCO3, then derivatised with 100 μL 1% w/v
Marfey’s reagent in acetone (1-fluoro-2,4-dinitrophenyl-5-L-alanine amide, FDAA, Sigma-Aldrich,
St. Louis, MO, USA) at 40 °C for 1 h as described by Bonnard et al. [15]. The reaction mixtures were
neutralised with 10 μL 2 M aqueous HCl and diluted with 820 μL MeOH. Pure amino acid standards
were derivatised by the same procedure using 50 μL 50 mM aqueous amino acid solution. Ultra-high
performance liquid chromatography-diode array (UHPLC-DAD) separation and detection of the amino
acid derivatives was done on a Dionex RSLC Ultimate 3000 (Dionex, Sunnyvale, CA, USA) equipped
with a diode array detector. The separation was done in a Kinetex C18 column (150 × 2.10 mm,

Mar. Drugs 2013, 11
5060
2.6 μm, Phenomenex) at 60 °C with a flow rate of 0.8 mL min−1 using two different linear gradient
methods. Method A included all L- and D-amino acids in the structure, whereas method B was run with
shallow gradient and included L- and D-allo-Thr but not L- and D-Leu. This was an attempt to
distinguish derivatives of D-Ser, L-Thr and L-allo-Thr which had very similar chromatographic
properties on the column.
Method A: From 8% to 15% aqueous MeCN, 0.65 mM TFA, over 22 min followed by an increase
from 15% to 100% for 8.5 min. Retention times for the FDAA-amino acid derivatives were: L-Ser
(4.21 min), L-Thr (5.46 min), D-Ser (5.56 min), D-Thr (12.38 min), L-Leu (25.23 min), D-Leu
(26.00 min). Unreacted FDAA eluted at 11.0 min.
Method B: From 8% to 10% aqueous MeCN, 0.65 mM TFA, over 25 min followed by an increase
from 10% to 100% over 5.5 min. Retention times for the FDAA-amino acid derivatives were: L-Ser
(4.46 min), L-Thr (5.90 min), D-Ser (5.97 min), L-allo-Thr (6.15 min), D-allo-Thr (10.28 min), D-Thr
(15.82 min). Unreacted FDAA eluted at 10.4 min.
NMR spectra were recorded on a Bruker Avance 800 MHz spectrometer equipped with a 5 mm TCI
Cryoprobe using standard pulse sequences. The NMR data used for the structural assignments were
1
13
acquired in DMSO-d6 (δH 2.49 ppm and δC 39.5 ppm). H and C NMR spectra are available in the
Supplementary Information.
3.3. Antivirulence Activity Testing and Northern Blotting
The S. aureus lacZ reporter assays were performed as described by Nielsen et al. [19].
Ngercheumicin F, G, H, and I were dissolved in DMSO, and DMSO and H2O was included as negative
controls in the assay. Pictures were taken after 11, 13 and 34 h of incubation for the rnaIII-, hla- and
spa-reporter strains respectively (Supplementary Information).
RNA for Northern blotting was purified from USA300 (FPR3757) samples from cultures grown in
100 mL Erlenmeyer flasks containing 10 mL Tryptone Soya Broth (TSB, Oxoid, Greve, Denmark)
shaking vigorously (200 rpm) in a water bath at 37 °C. Ngercheumicins (5 µg mL−1 and 20 µg mL−1)
and DMSO (control) were added at OD600 = 0.4, and samples were taken at OD600 = 0.8 and 3.0.
Northern blotting was performed as previously described [5] using an RNAIII-probe constructed using
primer rnaIII forward (5′-GGG GAT CAC AGA GAT GTG ATG-3′), and rnaIII reverse (5′-GGG
CAT AGC ACT GAG TCC AAG G-3′)(TAG Copenhagen A/S, Frederiksberg, Denmark).
4. Conclusions
Four new ngercheumicins were isolated on the mg-scale and their structure elucidated; however
complete stereochemical assignments were not obtained. Although 20 L of bacterial culture was
extracted, low isolated yields restricted the possibilities in both the structure elucidation and in the
assessment of biological properties. Ngercheumicins were found to inhibit transcription of the
regulatory rnaIII in S. aureus, the effector molecule of the agr QS system. These findings will aid in
the future work to understand quorum sensing in bacteria, as more structural knowledge about QS
inhibitors is valuable in the design of novel inhibitors. The cyclodepsipeptides isolated from this
marine Photobacterium have some resemblance to the AIPs of S. aureus, and it can be speculated as to
whether these molecules are a new class of peptide signaling molecules in the marine environment.

Mar. Drugs 2013, 11
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Acknowledgments
We gratefully thank the Danish Instrument Center for NMR Spectroscopy of Biological
Macromolecules for NMR time on the 800 MHz. Funding from the Danish Council for Strategic
Research (DSF) is acknowledged. The present work was carried out as part of the Galathea 3
expedition under the auspices of the Danish Expedition Foundation and this is Galathea 3
contribution P103.
Conflicts of Interest
The authors declare no conflict of interest.
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