molecules
Article
Natural Products from Singapore Soil-Derived
Streptomycetaceae Family and Evaluation of Their
Biological Activities
Elaine-Jinfeng Chin † , Kuan-Chieh Ching † , Zann Y. Tan, Mario Wibowo , Chung-Yan Leong ,
Lay-Kien Yang , Veronica W. P. Ng, Deborah C. S. Seow, Yoganathan Kanagasundaram * and Siew-Bee Ng *
Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and
Research (A*STAR), Singapore 138673, Singapore;
[email protected] (E.-J.C.);
[email protected] (K.-C.C.);
[email protected] (Z.Y.T.);
[email protected] (M.W.);
[email protected] (C.-Y.L.);
[email protected] (L.-K.Y.);
[email protected] (V.W.P.N.);
[email protected] (D.C.S.S.)
* Correspondence:
[email protected] (Y.K.);
[email protected] (S.-B.N.);
Tel.: +65-62792716 (Y.K.); +65-62792727 (S.-B.N.)
† These authors contributed equally to this work.
Citation: Chin, E.-J.; Ching, K.-C.;
Tan, Z.Y.; Wibowo, M.; Leong, C.-Y.;
Yang, L.-K.; Ng, V.W.P.; Seow, D.C.S.;
Kanagasundaram, Y.; Ng, S.-B.
Natural Products from Singapore
Soil-Derived Streptomycetaceae Family
Abstract: Natural products have long been used as a source of antimicrobial agents against various
microorganisms. Actinobacteria are a group of bacteria best known to produce a wide variety of bioactive secondary metabolites, including many antimicrobial agents. In this study, four actinobacterial
strains found in Singapore terrestrial soil were investigated as potential sources of new antimicrobial
compounds. Large-scale cultivation, chemical, and biological investigation led to the isolation of
a previously undescribed tetronomycin A (1) that demonstrated inhibitory activities against both
Gram-positive bacteria Staphylococcus aureus (SA) and methicillin-resistant Staphylococcus aureus
(MRSA) (i.e., MIC90 of 2–4 µM and MBC90 of 9–12 µM), and several known antimicrobial compounds,
namely nonactin, monactin, dinactin, 4E-deacetylchromomycin A3, chromomycin A2, soyasaponin II,
lysolipin I, tetronomycin, and naphthomevalin. Tetronomycin showed a two- to six-fold increase in
antibacterial activity (i.e., MIC90 and MBC90 of 1–2 µM) as compared to tetronomycin A (1), indicating
the presence of an oxy-methyl group at the C-27 position is important for antibacterial activity.
Keywords: actinobacteria; antimicrobial; Staphylococcus aureus; Streptomycetaceae; tetronomycin;
natural products
and Evaluation of Their Biological
Activities. Molecules 2023, 28, 5832.
https://doi.org/10.3390/
molecules28155832
Academic Editor: Céline Rivière
Received: 28 June 2023
Revised: 26 July 2023
Accepted: 26 July 2023
Published: 2 August 2023
Copyright: © 2023 by the authors.
Licensee MDPI, Basel, Switzerland.
This article is an open access article
distributed under the terms and
conditions of the Creative Commons
Attribution (CC BY) license (https://
creativecommons.org/licenses/by/
4.0/).
1. Introduction
Natural products have been significant in providing the groundwork for the development and advancement of antibiotics since ancient times. Since the discovery of penicillin
in 1928, antimicrobial agents linked to antibiotics were mainly isolated from natural sources,
such as plants and microorganisms [1,2]. Antimicrobial resistance has been one of the major
concerns worldwide. The proliferation of drug-resistant pathogens, which have developed
new mechanisms of resistance, poses an ongoing threat to our ability to combat common
infections due to antibiotics losing effectiveness. This has resulted in challenging-to-treat
infections that can lead to fatal outcomes. Thus, it is crucial to search for other potential
antimicrobial agents from natural sources such as actinobacteria [3,4]. Actinobacteria play
a pivotal role within the microbial community, as they are recognized as a vital source of
innovative bioactive compounds. Approximately 45% of bioactive compounds obtained
from microbes were produced by actinobacteria [5–7]. Given their extensive biotechnological applications, this group of microorganisms has consistently captivated the interest of
chemists, pharmaceutical companies, and various other researchers, making it a compelling
subject of study.
Molecules 2023, 28, 5832. https://doi.org/10.3390/molecules28155832
https://www.mdpi.com/journal/molecules
Molecules 2023, 28, 5832
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Our research team has been actively engaged in a continuous screening endeavor
aimed at identifying secondary metabolites derived from actinobacteria, which has the
potential to inhibit pathogenic microorganisms, such as Staphylococcus aureus (SA) and
methicillin-resistant Staphylococcus aureus (MRSA) [8,9]. Infections caused by these
pathogens are common in both community-acquired and hospital-acquired settings. Among
common staphylococcal bacteria, Staphylococcus aureus (SA) stands out as particularly dangerous. These Gram-positive, coccus-shaped (spherical) bacteria are not only responsible
for skin infections, but also pose a threat by causing pneumonia, cardiovascular related infections, osteomyelitis, and a range of potentially severe infections [10]. One of the reasons
why SA is a threat to the society is its ability to develop resistance to antibiotics. MRSA is a
well-known example of antibiotic-resistant SA that can be difficult to treat because of their
developed mechanisms to evade the effects of many antibiotics commonly used to treat bacterial infections. Actinobacterial-derived drugs have been instrumental in treating various
diseases such as microbial and protozoal infections, cancer, and severe inflammations [11].
The diversity and abundance of bioactive compounds produced by actinobacteria make
them a valuable resource for the exploration and advancement of drug discovery and
development. While there have been previous studies on actinomycetes-derived antibiotics, actinobacteria remains relatively under-explored in the context of Singapore soil.
Secondly, although antibiotics have been isolated from actinomycetes in the past, the threat
of antibiotic resistance continues to grow, necessitating the constant search for new agents.
By focusing on this specific microbial community, we contribute to the ongoing efforts to
address the challenges posed by antibiotic resistance and provide valuable insights into the
untapped resources of Singapore’s soil ecosystem [4,12].
The objective of our work, therefore, aims to discover new bioactive compounds from
actinobacteria strains isolated from Singapore soil with antimicrobial activity. As part
of our on-going screening campaign for new bioactive compounds, four actinobacterial
strains (A1099, A1174, A1301, and A2461) from our in-house Natural Organisms Library
isolated from terrestrial soil in Singapore were grown in five different liquid media [13].
In this study, we report the isolation and characterization of nine known and one new (1)
natural compounds from these four microbial strains, along with the evaluation of their
antimicrobial effect as well as their cytotoxicity against several cancer cell lines.
2. Results and Discussion
2.1. Phylogenetic Analysis and Molecular Identification of Actinobacteria Isolates
A total of four actinobacterial strains isolated from terrestrial soil in Singapore were
molecularly identified via sequencing of the 16S rDNA gene region. This was followed
by a nucleotide BLAST search against the NCBI 16S rRNA database with the aligned 16S
rRNA gene sequences of A1099, A1174, A1301, and A2461. The neighbor-joining analysis
method using a bootstrapped analysis of 1000 replicates of four actinobacteria strains and
their closely related species from Genbank database was utilized to investigate their phylogenetic similarity (Figure 1). Our results revealed that strain A1099 shared 99.85% sequence
identity (E-value = 0.0) to Streptomyces badius with accession number MN966861.1; A1174
shared 99.34% sequence identity (E-value = 0.0) to Kitasatospora arboriphila with accession
number EU100404.1; A1301 shared 100% sequence identity (E-value = 0.0) to Streptomyces
chattanoogensis with accession number KM573812.1; and A2461 with 99.64% sequence
identity (E-value = 0.0) to Streptomyces aculeolatus with accession number MG190783.1.
The results show that they are strains from the family of Streptomycetaceae. In addition,
the genotypic and phenotypic characteristics of genera Streptomyces and Kitasatospora are
difficult to differentiate. They are known to be closely related as shown in the phylogenetic
tree in Figure 1 and looking morphologically similar (Figure 2). Morphologically, actinobacteria resemble fungi because of their elongated cells that branch into filaments or hyphae
(Figure 2). It is known that these hyphae can be distinguished from fungal hyphae based on
size with actinobacteria hyphae being smaller than fungal hyphae [14,15]. Previous studies
have shown that actinobacteria from the Streptomycetaceae family are exceptional antibiotic
Molecules 2023, 28, 5832
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producers. They are known to produce various bioactive compounds with antimicrobial
activities [16,17].
Figure 1. Phylogenetic tree showing the evolutionary relationship between strains A1099, A1174,
A1301, and A2461 and other type species of the family Streptomycetaceae. Neighbor-joining phylogenetic tree was constructed based on 16S rRNA gene sequence showing the relationship between
strains A1099, A1174, A1301, A2461 and representatives or related actinobacteria strains retrieved
from the GenBank with their respective accession numbers. Bootstrap values greater than 50% are
shown at the number on the branches nodes that were analyzed based on 1000 replicates. Bar, 0.01
substitutions per nucleotide position.
2.2. Preliminary Screening of Actinobacteria Isolates
Culture medium has a great effect not only on microbe growth, but also on metabolism.
Studies have shown that the carbon–nitrogen ratio, salinity, and presence of metal ions play
a regulatory role in determining the extent and pattern of secondary metabolite production.
Typically, culture media primarily consists of carbon and nitrogen sources. The carbon
source not only serves as the fundamental building block for biomass and provides energy
for microorganisms, but also supplies carbon units to produce secondary metabolites.
Similarly, the nitrogen source is essential for synthesizing vital proteins and nucleic acids
as well as providing nitrogen-containing units for secondary metabolites [18]. Hence,
microorganisms cultured in different medium composition can exhibit differently adapted
metabolism, which will produce differential biosynthesis of specialized metabolites.
Molecules 2023, 28, 5832
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Figure 2. Visual images of macroscopic plate image of strains (A) A1099, (B) A1174, (C) A1301,
and (D) A2461. Visual images of colony morphology (magnification: 200×) (E) A1099, (F) A1174,
(G) A1301, and (H) A2461. Gram staining of actinobacteria (magnification: 1000×) (I) A1099,
(J) A1174, (K) A1301, and (L) A2461.
In this study, 20 extracts were generated from the fermentation of the four actinobacterial strains in five different media. The extracts were tested for their inhibitory effects
against a series of microbial pathogens, including Klebsiella aerogenes (KA), Pseudomonas
aeruginosa (PA), Staphylococcus aureus (SA), Candida albicans (CA), and Aspergillus fumigatus
(AF). In addition, their cytotoxic activity towards the human lung carcinoma A549, pancreatic cancer MIA, and pancreatic cancer PANC-1 cell lines was evaluated. Antimicrobial
and cytotoxic primary screenings of the extracts derived from four actinobacterial strains
exhibited biological activities against at least one of the tested microbial pathogens or
cancer cell lines (Figure 3 and Table S1). The findings revealed noticeable variations in
the biological activities expressed by crude extracts derived from the same actinobacterial
strain when cultivated in different growth media. Previous studies have reported that
deliberate manipulation of different media substance is a tactic to identify a favorable
growth regime, which enhances the diversity of metabolites and the production of bioactive
secondary metabolites. This approach, commonly referred to as the OSMAC (one strain,
many compounds) approach, has been reported to yield promising results [19–21]. As
observed in the results shown in Figure 3 and Table S1 strain A1099 showed activity against
SA and CA when fermented in CA02LB, CA07LB, and CA08LB, whereas A1174 showed
activity against SA and A549 when fermented in CA08LB. As for A1301 in CA10LB, it
showed the most significant results with activity against three microbial pathogens—SA,
CA, AF—and three cancer cell lines—A549, MIA, PANC-1—while in CA07LB, the extract
was active against SA, CA, A549, MIA, PANC-1. Extracts generated in CA02LB was only
active against AF, whereas activity was only observed against SA in extracts from CA08LB
and CA09LB. Strain A2461 cultured in CA08LB and CA10LB exhibited activity against
Molecules 2023, 28, 5832
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SA. Further analysis of the primary bioassay screening showed that A1099 strain, when
fermented in CA08LB, exhibited the highest percentage of inhibition against SA and CA
compared to CA02LB and CA07LB (Table S1). For A2461 strain, antibacterial activity
against SA was more pronounced in terms of percentage of inhibition when fermented
in CA10LB in comparison with CA08LB (Table S1). Thus, CA08LB extract of A1099 and
CA10LB extract of A2461 were selected as the preferred extracts for further investigation.
CA08LB was selected as a preferred media to ferment strain A1174 because this was the
only extract that showed antibacterial activity against SA (Figure 3). In addition, strain
A1301 fermented in CA10LB was selected for further investigation due to its broad spectrum of antimicrobial activity against three microbial pathogens as well as cytotoxic activity
(Figure 3). From this study, CA08LB and CA10LB were found to be the optimal media
for production of bioactive compounds. Notably, these media contain relatively higher
amount of carbohydrates as compared to the others. Carbohydrates play a crucial role in
fermentation processes as a source of energy for microorganisms. During fermentation,
carbohydrates are broken down into simpler compounds, such as sugars, which are then
metabolized by microorganisms to produce various fermentation products, including alcohol, organic acids, and gases. Studies have shown that fermentation with high amount of
carbohydrate substance helped enhance production of bioactive compounds [22].
Samples
Media
Antimicrobial1
KA
PA
SA
CA
Cytotoxicity2
AF
A549
MIA
PANC-1
CA02LB
CA07LB
A1099
A1174
A1301
A2461
CA08LB
CA09LB
CA10LB
CA02LB
CA07LB
CA08LB
CA09LB
CA10LB
CA02LB
CA07LB
CA08LB
CA09LB
CA10LB
CA02LB
CA07LB
CA08LB
CA09LB
CA10LB
Inhibition3
No Inhibition
1KA
= Klebsiella aerogenes, PA = Pseudomonas aeruginosa, SA = Staphylococcus aureus Rosenbach, CA = Candida
albicans and AF = Aspergillus fumigatus.
2A549 = human lung carcinoma cells, MIA = pancreatic cancer cells and PANC-1 = pancreatic cancer cells.
3Antimicrobial effect and cytotoxic activity (average growth inhibition ≥ 80%).
Figure 3. Antimicrobial and cytotoxicity primary screening results of 4 actinobacteria strains grown
in 5 different growth media.
Molecules 2023, 28, 5832
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2.3. Isolation and Structural Elucidation of Bioactive Compounds
Selected extracts from the 4 actinobacterial strains were subjected to large-scale bioassay guided fractionation. This study was performed not only to confirm the antimicrobial
activities of the active metabolites, but also to expand our in-house natural compounds
library [13]. Large-scale cultivation of 4 actinobacterial strains and purification of active
metabolites from their extracts led to the identification of numerous known metabolites as
summarized in Table 1. These known metabolites, namely nonactin, monactin, dinactin,
4E-deacetylchromomycin A3, chromomycin A2, soyasaponin II, lysolipin I, tetronomycin,
and naphthomevalin (Figure 4) were identified and characterized using high-resolution
mass spectroscopy (HRMS) and nuclear magnetic resonance (NMR) analyses and spectroscopic data comparison with the literature values [23–33]. In addition, one new natural
product, tetronomycin A (1), was also isolated from the extract derived from Streptomyces sp.
A2461 fermented in CA10LB (Table 1). Examples of structure elucidation of tetronomycin
and tetronomycin A (1) are presented below.
Table 1. Compounds identified by comparison of their NMR data with the literature values [23–33].
Strain
Media
Compounds Confirmation
Streptomyces sp. A1099
Kitasatospora sp. A1174
Streptomyces sp. A1301
Streptomyces sp. A2461
CA08LB
CA08LB
CA10LB
CA10LB
Nonactin, monactin, dinactin
4E-Deacetylchromomycin A3, chromomycin A2
Soyasaponin II, lysolipin I
Tetronomycin A (1), tetronomycin and naphthomevalin
Figure 4. Chemical structures of nonactin, monactin, dinactin, 4E-deacetylchromomycin A3, chromomycin A2, soyasaponin II, lysolipin I, tetronomycin, and naphthomevalin.
Molecules 2023, 28, 5832
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Tetronomycin was isolated as one of the bioactive compounds from the extract derived
from Streptomyces aculeolatus A2461 (Figure 5). The structure of tetronomycin consists of four
methyl, ten methylene, thirteen methine, and six non-protonated carbons was confirmed
through detailed analyses of the 1 H and 2D NMR spectra (Figures S7–S9). 1 H-1 H COSY
and HMBC correlations were deduced as shown in Figure 6 to establish the core skeleton of
tetronomycin. In addition, the identity of tetronomycin was also confirmed through comparing the 1 H NMR spectrum of tetronomycin in CDCl3 with literature data [23,24]. The assignment of the 13 C chemical shifts of tetronomycin was conducted based on correlations observed in HSQC and HMBC NMR spectra of tetronomycin (Table 2 and Figures S8 and S9).
Table 2. 1 H (400 MHz) NMR data of 1 and tetronomycin in (CD3 )2 CO.
1
13 C,
Pos.
1
2
3
4
4-CH2
5
6
6-Me
7
8
8-Me
9
10
11
12
13
14
14-CH2
15
16
16-Me
17
18
19
20
21
22
23
24
25
26
27
27-Me
27-OMe
Type 1
179.7, C
n.d., C
182.6, C
155.2, C
85.9, CH2
201.4, C
43.3, CH
8.6, CH3
48.5, CH
33.1, CH
20.0, CH3
36.3, CH2
25.9, CH2
35.4, CH2
36.4, CH
141.6, CH
132.5, C
56.5, CH2
91.7, CH
34.5, CH
18.2, CH3
32.6, CH2
32.1, CH2
80.0, CH
132.2, CH
135.4, CH
39.8, CH2
78.7, CH
32.3, CH2
26.8, CH2
82.2, CH
68.3, CH
16.5, CH3
-
Tetronomycin
1 H,
Mult. (J = Hz)
4.55, d (1.0); 4.93, d (1.0)
3.73, m
0.94, d (7.0)
1.83, m
1.48, m
1.14, m
1.08, m; 1.64, m
1.30, m; 1.59, m
1.01, m, 1.44, m
2.54, m
5.10, d (10.1)
3.83, m; 4.14, m
3.19, m
1.40, m
0.58, d (6.6)
1.23, m; 1.80, m
1.48, m; 1.61, m
3.80, m
5.57, dd (8.6, 15.1)
6.19, m
2.19, m; 2.39, m
4.10, m
1.58, m; 2.12, m
1.72, m; 1.92, m
4.03, m
3.82, m
0.97, d (6.3)
-
1
13 C,
Type 1
180.5, C
n.d., C
182.3, C
155.6, C
85.9, CH2
201.3, C
43.3, CH
9.0, CH3
48.5, CH
33.1, CH
20.1, CH3
36.1, CH2
25.9, CH2
35.7, CH2
36.5, CH
141.5, CH
n.d., C
56.5, CH2
91.7, CH
34.4, CH
18.3, CH3
32.7, CH2
32.0, CH2
80.0, CH
132.8, CH
n.d., CH
40.1, CH2
78.9, CH
32.2, CH2
27.7, CH2
80.7, CH
78.8, CH
11.1, CH3
57.0, CH3
1 H,
Mult. (J = Hz)
4.54, d (1.0); 4.93, d (1.0)
3.81, m
0.98, d (7.1)
1.81, m
1.45, m
1.14, m
1.06, m; 1.64, m
1.27, m; 1.58, m
1.00, m, 1.45, m
2.55, m
5.10, d (10.1)
3.84, m; 4.19, m
3.20, m
1.39, m
0.58, d (6.8)
1.22, m; 1.80, m
1.46, m; 1.60, m
3.79, m
5.54, dd (8.7, 15.6)
6.14, m
2.06, m; 2.38, m
4.11, m
1.60, m; 2.12, m
1.65, m; 1.96, m
4.15, m
3.37, dq (2.4, 6.4)
0.95, d (6.4)
3.33, s
Assignments based on HSQC and HMBC spectra, and comparison with the literature values of
tetronomycin [23,24]. Chemical shifts (δ) in ppm. n.d. = not determined.
δ
Figure 5. Chemical structures of 1 and tetronomycin.
Molecules 2023, 28, 5832
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Figure 6. Selected COSY and HMBC correlations for 1 and tetronomycin.
Tetronomycin A (1) (Figure 5) was isolated as a white amorphous powder. The
molecular formula was established as C33 H48 O8 based on HR-ESIMS analysis. The structure
of 1 was established based on NMR data comparison with those of tetronomycin. Following
the literature review, the 1 H NMR spectrum of 1 (Figure S3) was found to be similar to
that of tetronomycin except for the absence of a methoxy group in 1 [23,24]. Compound 1
was found to possess the same core structure as tetronomycin with the loss of a methyl
functional group on the oxy-methyl group at C-27 position as indicated by the missing
δ
there is a slight difference
proton singlet at δH 3.33 (Figure 5 and Table 2). In addition,
1
between the H chemical shifts of H-27 and H-26 in the 1 H NMR spectra of 1 and that
of tetronomycin. The chemical shift of H-27 shifted downfield, changing from δH 3.37
to δH 3.82 while the chemicalδ shift of δH-26 moved upfield, changing from δH 4.15 to
δ group caused a change in the chemical environment
δH 4.03. The loss ofδone methyl
around C-26 and C-27 positions and, thus, the change in their chemical shifts. In addition,
the core skeleton of tetronomycin A consists of a tetronic acid, a tetrahydrofuran, and a
tetrahydropyran fragments, which was established based on 1 H-1 H COSY and HMBC
correlations (Figures 6 and S4). Unfortunately, due to the low yield of compound 1, not all
13 C NMR shifts could be assigned from 13 C NMR experiment. Therefore, the 13 C NMR
chemical shifts were obtained from HSQC and HMBC spectra (Figures S5 and S6). The
structure of 1 was very similar with those of the known tetronomycin, suggesting they were
biosynthetically related. Thus, based on spectroscopic data comparison and biosynthetic
consideration, the relative configurations for 1 were proposed to be the same as those
in tetronomycin. Notably, the sign of optical rotation of 1 was the opposite to[α]that of
tetronomycin in this study ([α]23
D + 111, c 0.0003, MeOH), which was in accordance with
previously reported data [23]. Although a comparison of optical rotation signs of similar
structures had been used in many studies, it has been shown that the sign of the optical
rotation is an unreliable indicator of stereochemistry determination in natural products,
and the signs of the optical rotations of two compounds can be opposite regardless of their
identical configurations [34,35].
2.4. Chemical Structural Data of Tetronomycin A (1)
The UV spectra and HRESIMS spectra of 1 and 1D and 2D NMR spectra of tetronomycin and 1 are provided in Supplementary information,
Figures S1–S9.
[α]
23
1: White amorphous powders; [α] D -61 (c 0.001, MeOH); UV (MeCN/H2 O) λmax (%)
222 (100%), 296 (26%) nm; (+)-HRESIMS: m/z 595.3249 [M + Na]+ (calcd for C33 H48 NaO8 ,
595.3247); 1 H and 13 C NMR data, see Table 2.
2.5. Antimicrobial and Cytotoxic Activities of Compounds Isolated from the
4 Actinobacterial Strains
Tetronomycin A (1), tetronomycin and eight other known compounds isolated from
A1099, A1174, A1301, and A2461 were subjected to antimicrobial and cytotoxicity doseresponse testing against a panel of five microbial pathogens, K. aerogenes (KA), P. aeruginosa
(PA), S. aureus (SA), C. albicans (CA), and A. fumigatus (AF), and three cancer cell lines, A549,
MIA PaCa-2, and PANC-1. Table 3 shows the antimicrobial and cytotoxicity activities of
λ
Molecules 2023, 28, 5832
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the 8 known compounds from A1099, A1174, A1301, and A2461. Bioactivity testing results
showed that nonactin, monactin, and dinactin isolated from A1099 exhibited antimicrobial
activity towards the Gram-positive bacteria SA and antifungal activity against CA. These
compounds are from a family of naturally occurring cyclic ionophores known as the
macrotetrolide antibiotics [29,31]. Similarly, glycosylated tricyclic aureolic polyketides
4E-deacetylchromomycin A3 and chromomycin A2 isolated from A1174 exhibited activity
against SA, consistent with what was reported in the literature [36], and known compounds
lysolipin I and soyasaponin II isolated from A1301 showed activity against SA. Interestingly,
soyasaponin II demonstrated similar antimicrobial activity as chromomycin compounds
(i.e., MIC90 of 2–4 µM) and better antimicrobial activity than nonactin, monactin, and
dinactin. Soyasaponin II is a complex oleanane triterpenoid that was reported to have
hepatoprotective, antiviral (i.e., anti-herpes simplex virus activity), and cardiovascular
protective activity [37]. However, no antimicrobial activity against SA was previously
reported, even though a similar analog, soyasaponin I, was reported to exhibit antimicrobial
activity against E. coli. and CA [37]. Soyasaponins are a group of triterpenoids commonly
found on soybeans, which is part of CA10LB media component. This suggested that the
soyasaponin II isolated in this work was not produced by the actinobacterial strain but part
of the media component instead. In addition, lysolipin I also showed antifungal activity
against CA and AF. The most potent compound is lysolipin I as it showed sub-micromolar
antimicrobial activity against SA, CA, and AF (i.e., 0.01–0.9 µM) while naphthomevalin
did not exhibit any antibacterial activity, which is consistent with what was reported in the
literature [38]. In comparison with the respective positive controls tested, all compounds
isolated showed less potent activity except lysolipin I. No bioactivity was observed in these
compounds against Gram-negative bacteria (KA and PA) (Figure S10). In addition, the
eight known compounds exhibited cytotoxicity activity towards all three cancer cell lines
as shown in Table 3 and Figure S11. These bioactivity findings are consistent with reports
on the bioactivity of these known compounds [32,39,40]. However, the known compounds
of previous studies were isolated from different Streptomyces species not investigated in
this study. Streptomyces species have a vast genetic diversity, and each strain may possess
unique biosynthetic capabilities. As a result, different strains of Streptomyces can produce a
variety of secondary metabolites with similar or overlapping bioactivities.
Table 3. Biological activities of positive controls and 8 known compounds isolated from A1099CA08LB, A1174-CA08LB, A1301-CA10LB, A2461-CA10LB.
Antimicrobial (µM) 1
Sample
Media
Compound
SA
Cytotoxicity (µM) 2
CA
AF
A549
MIA
PANC-1
MIC90
MBC90
MIC90
MFC90
MIC90
MFC90
IC50
IC50
IC50
A1099
CA08LB
Nonactin
Monactin
Dinactin
49.2
7.9
4.7
64.9
-
38.1
1.1
1.3
8.2
4.0
-
-
10.1
0.8
1.2
2.3
0.1
0.7
2.9
0.1
0.3
A1174
CA08LB
4E-Deacetylchromomycin A3
Chromomycin A2
2.9
3.1
13.4
3.8
-
-
-
-
1.7
0.3
1.9
0.5
3.0
0.4
A1301
CA10LB
Lysolipin I
Soyasaponin II
0.01
2.8
NT
2.4
0.1
-
NT
-
0.9
-
NT
-
0.1
2.1
0.2
3.1
0.3
2.1
A2461
CA10LB
-
-
-
-
3.7
6.4
9.0
0.1
0.2
0.5
1.7
0.6
0.2
0.8
Positive Controls
Naphthomevalin
-
-
Vancomycin hydrochloride
0.6
3.5
Amphotericin B
Puromycin
1
SA = Staphylococcus aureus Rosenbach, CA = Candida albicans, and AF = Aspergillus fumigatus. (–) Compounds
show no inhibition for MIC90 and MBC90 /MFC90. 2 A549 = human lung carcinoma cells, MIA = pancreatic cancer
cells, and PANC-1 = pancreatic cancer cells. NT indicates that compound of interest was not tested.
Previous studies have shown that tetronomycin exhibited potent antibacterial activity
against drug-resistant strains [24]. Thus, tetronomycin A (1) and tetronomycin isolated
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from A2461-CA10LB were subjected to additional screening to investigate their potential
activity against the drug-resistant bacteria MRSA (Table 4). Figures 7 and 8 show the
dose-response inhibition curves of the compounds and their IC90 values for SA and MRSA
as well as the IC50 values for the cytotoxicity against the three cancer cell lines, respectively.
As shown in Table 4, both 1 and tetronomycin showed potent antibacterial activities against
SA as well as MRSA. Tetronomycin was more potent (i.e., minimal inhibitory concentration
(MIC90 ) of 0.8 µM and minimal bactericidal concentration (MBC90 ) of 1.7 µM) against SA
than 1 (i.e., MIC90 of 2.2 µM and MBC90 of 9.2 µM). Similarly for MRSA, tetronomycin
(i.e., MIC90 of 0.9 µM and MBC90 of 2.1 µM) was more active compared to 1 (i.e., MIC90 of
3.9 µM and MBC90 of 11.8 µM). This two- to six-fold decrease in antibacterial activity was
observed in 1 as compared to tetronomycin when the oxy-methyl group at C-27 position was
changed to a hydroxy group. This may indicate the importance of oxy-methyl group as a
pharmacologically active group. In comparison with positive control, tetronomycin showed
similar bioactivity with vancomycin hydrochloride with one slightly higher bioactivity of
MBC 1.7 µM against SA. These two compounds were inactive against KA, PA, CA, and AF
(dose-response curves were shown in Figure S12).
Table 4. Biological activities of positive controls, tetronomycin A (1), and tetronomycin from A2491CA10LB.
μ
μ
Antimicrobial (µM) 1
Compounds
SA25923
μ
MRSA33591
μ
μ
μ
Cytotoxicity (µM) 2
μ
A549
μ
MIA
PANC-1
MIC90
MBC90
MIC90
MBC90
IC50
IC50
IC50
Tetronomycin A (1)
2.2
9.2
3.9
11.8
16.5
13.6
11.1
Tetronomycin
0.8
1.7
0.9
2.1
8.1
6.6
4.2
Vancomycin hydrochloride
0.6
3.5
0.6
2.0
Puromycin
0.6
1
μ
0.2
0.8
2
SA = Staphylococcus aureus Rosenbach, MRSA = Methicillin-resistant Staphylococcus aureus. A549 = human lung
carcinoma cells, MIA = pancreatic cancer cells, and PANC-1 = pancreatic cancer cells.
B
A
C
Figure 7. Dose response inhibition curves against Staphylococcus aureus Rosenbach (SA25923)
and methicillin-resistant Staphylococcus aureus subsp.
aureus Rosenbach (MRSA33591).
(A) Tetronomycin A (1), (B) Tetronomycin, and (C) Vancomycin hydrochloride.
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Figure 8. Dose response curves against A549 human lung carcinoma cells, and two pancreatic
cancer cell lines MIA PaCa-2 and PANC-1 cells. (A) Tetronomycin A (1), (B) Tetronomycin, and
(C) Puromycin.
Tetronomycin was first isolated from a cultured broth of Streptomyces sp. in 1982 [23].
It is a polycyclic polyether compound. Recently, Kimishima et al. reported the bioactivity of
tetronomycin and their semi-synthetic analogues [24]. The research group investigated acyl
derivatives of tetronomycin and other derivatives that did not possess an exo-methylene
group on the tetronic acid moiety. Acyl derivatives were reported to have similar antimicrobial activity profile as tetronomycin, but the derivatives exhibited less potent antimicrobial
activity than tetronomycin while the exo-methylene moiety in tetronomycin was crucial for
its antimicrobial activity. Interestingly, our A2461 Streptomyces aculeolatus produces tetronic
acid compounds (i.e., 1 and tetronomycin), which was not reported in the literature. On
the other hand, Streptomyces aculeolatus was reported to produce naphthoquinone derivatives, such as aculeolatins A-D and 2,5,7-trihydroxy-3, 6-dimethylnaphthalene-1,4-dione,
which shared similar core structures as one of our isolated compounds, naphthomevalin.
This strain was also reported to produce compounds that demonstrated antimalarial, antituberculosis, antibacterial, and weak cytotoxicity activities [41]. The findings of our study
not only serve to further demonstrate the actinobacteria as a prolific natural source for
antimicrobial drug discovery, but also significantly contribute to enriching the structural
diversity of microbial natural products. By identifying new bioactive compound from
actinobacteria strains isolated from Singapore soil, we expand the repertoire of potential antimicrobial agents and enhance our understanding of the wide range of structural
variations that microbial natural products can exhibit.
2.6. Effects of Growth Media on Production of Bioactive Compounds
To unravel the effects of growth media on actinobacteria for their potential to enhance
bioactive metabolite biosynthesis as well as bioactivity of the crude extracts, the abundance
of the isolated bioactive compounds produced by the four actinobacteria strains were
compared in different media as presented in Figure 9. From our primary screening results,
SA activity was only observed in A1174 fermented in CA08LB (Figure 3). This is consistent
with the abundance of bioactive compounds, 4E-deacetylchromomycin A3 (m/z 1141.5033)
and chromomycin A2 (m/z 1211.5472) found in extracts derived from different media.
These chromomycin analogues were only found in extract derived from A1174 fermented
in CA08LB but not found in extracts derived from other media (Figure 9B). In Figure 9C, a
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higher abundance of lysolipin I (m/z 598.1121) was observed in A1301 extract fermented in
CA10LB as compared to other media. This possibly led to a broader spectrum of antimicrobial activity against three pathogens, SA, CA, and AF observed in CA10LB extract (Figure 3).
On the other hand, SA activity was observed in extracts derived from A2461 grown in
CA08LB and CA10LB, but not in extracts grown in other media (Figure 3). Interestingly,
no SA activity was observed in the extract derived from A2461 grown in CA07LB even
though both tetronomycin (m/z 609.3408) and tetronomycin A (1) (m/z 595.3249) were
present. The observed bioactivity in the CA08LB and CA10LB extracts is likely due to a
higher abundance of tetronomycin in the CA08LB and CA10LB extracts compared to the
CA07LB extract (Figure 9D). Lastly, the activity observed in extracts derived from A1099
fermented in different media did not show any correlation with the abundance of nonactin
(m/z 737.4514), monactin (m/z 751.4650), and dinactin (m/z 765.4801) found in different
extracts (Figure 9A). Even though the abundance of these macrotetrolides were the highest
in CA10LB extract, no activity was observed as shown in Figure 3. However, CA08LB
extract was selected for further isolation and purification work because it showed the
highest percentage of inhibition against SA and CA in our primary screening results. This
finding further exemplified the OSMAC method as a promising strategy for diversification
of secondary metabolite production.
Figure 9. Comparison of relative abundance (peak area) of various bioactive compounds from the
four actinobacterial strains (A1099, A1174, A1301, and A2461) fermented in different media (CA02LB,
CA07LB, CA08LB, CA09LB, and CA10LB). (A) Streptomyces sp. A1099, (B) Kitasatospora sp. A1174,
(C) Streptomyces sp. A1301, (D) Streptomyces sp. A2461.
3. Materials and Methods
3.1. Molecular Identification and Phylogenetic Analysis of Actinobacteria Isolates
Actinobacteria strains used in this study were obtained from the Natural Product
Library, which were initially isolated from terrestrial soils in Singapore’s nature parks [13].
These strains were derived from soil samples collected at Singapore’s Bukit Batok Nature
Park and Kent Ridge Park and were isolated using two specific types of agar media. The
isolation media utilized were humic acid-vitamin agar and arginine-glycerol-salt agar.
Reference stock cultures stored at −80 ◦ C were
− revived and sub-cultured on Bennet’s Agar
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(Oxoid, Hampshire, UK), followed by incubation at 28 ◦ C for 24 h. Manufacturers’ protocol
from DNeasy PowerSoil Kit (Qiagen, Hilden, Germany) was followed and conducted to
isolate genomic DNA of strains of interest. The extracted DNA were quantified using
NanoDrop2000 spectrophotometer (ThermoFisher Scientific, San Diego, CA, USA). Amplification of 16S rDNA genes of interest were carried out using universal 16S primers 27F
(5′ —AGA GTT TGA TCC TGG CTC AG—3′ ) and 1492R (5′ —TAC GGY TAC CTT GTT
ACG ACT T—3′ ) [42,43]. The total PCR amplification reaction mixture of 20 µL consists of
2.0 µL of 10× PCR buffer with 20 mM MgCl2 , 2.0 µL of 2 mM dNTPs, 0.2 µL of Dream Taq
polymerase (ThermoFisher Scientific, Waltham, MA, USA), 1.0 µL of 10 µM of each primer,
and 1.0 µL of purified DNA templates. A negative control and non-template were included
in the run. The PCR amplifications were performed using Applied Biosystems ProFlex
Thermocycler (ThermoFisher Scientific, Waltham, MA, USA) with the following thermal
cycling profile conditions of initial denaturation at 95 ◦ C for 5 min; further denaturation of
30 cycles at 95 ◦ C for 30 s each; annealing at 60 ◦ C for 30 s; followed by initial extension at
72 ◦ C for 1 min and a final extension at 72 ◦ C for 5 min.
PCR products were electrophoresed on 1% agarose gels (1× TAE buffer, 1 g agarose
gel) stained with SYBR safe DNA gel stain (ThermoFisher Scientific, Waltham, MA, USA).
The agarose gels were visualized on a ChemiDoc™ MP Imaging System (Bio-Rad, Hercules, CA, USA). PCR products then underwent purification using MEGA quick-spin
total fragment DNA purification kit (iNtRON Biotechnology, Seongnam, Republic of Korea) following manufacturer’s instructions. Purified PCR products were then sent for
bi-directional sequencing services (1st BASE, Singapore) using the mentioned primer pair.
Alignment and analysis of the sequences was done using Benchling and BLAST [National
Center for Biotechnology Information (NCBI)]. The 4 actinobacteria strains were aligned
using ClustalW with the 16S rRNA regions of closely related strains retrieved from GenBank databases. The neighbor-joining tree algorithm method was utilized to determine
the genetic relationship between the strains. In order to construct the phylogenetic tree,
MEGA 11.0 software (Mega, PA, USA) was employed using a bootstrapped analysis of
1000 replicates [44]. DNA sequences of A1099, A1174, A1301, A2461 have been uploaded
to the GenBank database of NCBI under the accession number OR177839, OR177840,
OR177841, and OR177842 respectively.
3.2. Fermentation and Extraction of Actinobacterial Crude Extracts
Four actinobacterial strains were selected for extracts generation following phylogenetic analysis. A volume of 5 mL SV2 media (for 1 L, add 1 g calcium carbonate (SigmaAldrich, St. Louis, MO, USA), 15 g glucose (1st BASE, Singapore), 15 g glycerol (VWR,
Radnor, PA, USA), and 15 g soya peptone (Oxoid, Hampshire, UK), pH adjusted to 7.0)
was used to culture strains at 28 ◦ C for 3 days under constant agitation at 200 rpm to
generate a seed culture. The seed cultures were then inoculated in a 1:20 volume into five
in-house liquid media (CA02LB, CA07LB, CA08LB, CA09LB, and CA10LB) as shown in
Table 5. These media have been formulated and optimized by the Natural Product Library
group at SIFBI for actinobacteria secondary metabolites production. The cultures were
incubated for 9 days at 28 ◦ C in the dark with shaking at 200 rpm. Following incubation,
the cultures were lyophilized. The dried cultures underwent extraction using methanol
(MeOH) and were subsequently filtered through Whatman Grade 4 filter paper. MeOH
was then evaporated under reduced pressure to generate the crude extract.
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Table 5. Composition of the five media that were used in this study.
Media (per L)
Components
Lab-lemco, Oxoid LP0029
Cane molasses
Cottonseed flour
Glucose
Glycerol
Mannitol
Oatmeal
Soluble starch
Soybean meal
Yeast extract
CaCO3
KH2 PO4
Na2 HPO4 ·12H2 O
MgCl2 ·6H2 O
MgSO4 ·7H2 O
Trace salt sol 1
pH
CA02LB
CA07LB
CA08LB
CA09LB
CA10LB
20 g
20 g
7.5
15 g
30 g
5g
5g
5g
1g
Natural
20 g
25 g
15 g
40 g
8g
7.2
10 g
20 g
3g
4g
7.0
20 g
15 g
3g
2g
0.5 g
1 mL
7.2
1
Trace salt solution consists of 0.2 g each of FeSO4 ·7H2 O, MnCl2 ·4H2 O, ZnSO4 ·7H2 O, CuSO4 ·5H2 O, and
CoCl2 ·2H2 O in 100 mL.
3.3. Biological Assays
The 20 extracts generated from the fermentation of the 4 strains in 5 media were
first subjected through a primary screening campaign. These extracts were screened for
anti-microbial activity against selected bacterial and fungal strains, which were Klebsiella
aerogenes, KA (ATCC® 13048™); Pseudomonas aeruginosa, PA (ATCC® 9027™); Staphylococcus aureus Rosenbach, SA (ATCC® 25923™); Candida albicans, CA (ATCC® 10231™), and
Aspergillus fumigatus, AF (ATCC® 46645™). Primary screening for the cytotoxic effects
of the extracts was also done on A549 human lung carcinoma cells (ATCC® CCL-185™)
and two pancreatic cancer cell lines, which were MIA PaCa-2 (ATCC® CCL-1420™) and
PANC-1 cells (ATCC® CCL-1469™). Primary screening was performed in triplicate at a
single concentration of 100 µg/mL to determine its percentage of inhibition activity of
crude extracts. The criteria of active hits were antimicrobial effect and cytotoxic activity
with an average growth inhibition ≥ 80%. Following a bioactivity-guided primary testing
strategy for compound isolation, selected active hits from extracts with desired bioactivity
were then subjected to scale-up fermentation for isolation of active compounds.
Dose-response testing of the isolated compounds for the antimicrobial and cytotoxicity
testing was performed in triplicates using a sixteen-point, 2-fold serial dilution assay
format with a starting assay concentration of 100 µM. For the anti-microbial bioassays,
a modified version of the microbroth dilution method established in alignment with the
Clinical Laboratory Standards Institute (CLSI) guidelines was performed to investigate
the minimum inhibition concentration (MIC) and the minimum bactericidal/fungicidal
concentration (MBC/MFC) of the isolated compounds. Bacterial MIC testing was done by
incubating the isolated compounds with 5.5 × 105 cfu/mL of bacterial cells at 37 ◦ C for 24 h.
For fungal MIC testing against CA the compounds were incubated with 2.5 × 103 cfu/mL
and incubated at 25 ◦ C for 48 h. Whereas for MIC testing against AF, the compounds were
incubated with the fungal cells seeded at a concentration of 2.5 × 104 spores/mL, followed
by incubation at 25 ◦ C for 72 h. OD600 absorbance readings of the cultures were performed
after incubation to determine the inhibitory effect of the compounds on the microbes. To
further study the potential bactericidal and fungicidal effects of the compounds, 5 µL
of the treated culture was inoculated into freshly dispensed media in microtiter plates.
The microtiter plates were then incubated using the same condition for the respective
microbes, followed by OD600 measurement. Vancomycin hydrochloride and amphotericin
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B (Sigma-Aldrich, St. Louis, MO, USA) were utilized as the standard inhibitor controls for
the antibacterial and antifungal assays, respectively. The isolated compounds were also
subjected to cytotoxicity testing against human carcinoma cell lines. The human carcinoma
cells were seeded at a density of 3.3 × 104 cells/mL, followed by treatment with the
compounds at 37 ◦ C for 72 h under 5% CO2 condition. PrestoBlue™ cell viability reagent
(ThermoFisher Scientific, Waltham, MA, USA) was used for quantification of cytotoxic
effects via fluorescence reading at an emission of 590 nm and an excitation of 560 nm.
Puromycin (Sigma-Aldrich, St. Louis, MO, USA) were used as the standard inhibitor
controls for the cytotoxicity assays. Bioassay results were analysed using GraphPad Prism 8
software (GraphPad, San Diego, CA, USA) to determine the respective IC50 and IC90 values.
3.4. Natural Product Extraction, Compound Isolation, and Structure Elucidation
The 4 actinobacterial strains underwent large scale fermentation of 4 L in their respective selected media of interest, which were CA08LB and CA10LB. Following incubation, the cultures were lyophilized. The dried cultures were extracted with MeOH
and filtered through filter paper (Whatman Grade 4). This was followed by removal
of MeOH in vacuo to obtain the crude extracts from strains A1099 (weight of 10.20 g),
A1174 (weight of 15.03 g), A1301 (weight of 6.36 g), and A2461 (weight of 0.98 g). A volume of 2.5 mL MeOH was added to each of the extracts to generate a saturated solution
of extract. The saturated solution was then subjected to C18 reversed-phase preparative
HPLC purification. Solvent A was water + 0.1% formic acid, solvent B was acetonitrile
+ 0.1% formic acid, and flow rate was 30–52 mL/min. These conditions were the same
for purification of compounds from all 4 extracts. For A1099, the extract was fractionated
by the following condition (gradient conditions: isocratic condition of 15% B for 5 min,
30 mL/min; followed by linear increment of flow rate to 52 mL/min over 5 min; 15–42%
B over 28 min, 52 mL/min; 42–100% B over 24 min; and isocratic condition of 100% B
for 10 min) to give 19.8 mg of nonactin, 20.5 mg of monactin, and 47.8 mg of dinactin.
For A1174, the extract was fractionated by the following condition (gradient conditions:
isocratic condition of 25% B for 5 min, 30 mL/min; followed by linear increment of flow
rate to 52 mL/min over 5 min; 25–60% B over 42 min, 52 mL/min; 60–100% B over 10 min;
and isocratic condition of 100% B for 10 min) to give 3.6 mg of 4E-deacetylchromomycin A3
and 5.0 mg of chromomycin A2. For A1301, the extract was fractionated by the following
condition (gradient conditions: isocratic condition of 15% B for 5 min, 30 mL/min; followed
by linear increment of flow rate to 52 mL/min over 5 min; 15–32% B over 15 min, 52
mL/min; 32–65% B over 35 min; 65–100% B over 2 min; and isocratic condition of 100% B
for 10 min) to give 0.8 mg of soyasaponin II and 2.4 mg of lysolipin I. For A2461, the extract
was fractionated by the following condition (gradient conditions: isocratic condition of
20% B for 5 min, 30 mL/min; followed by linear increment of flow rate to 52 mL/min over
5 min; 20–45% B over 10 min, 52 mL/min; 45–85% B over 40 min; 85–100% B over 2 min;
and isocratic condition of 100% B for 10 min) to give 0.8 mg of 1, 1.0 mg of tetronomycin,
and 0.8 mg of naphthomevalin. Known metabolites, namely nonactin, monactin, dinactin,
4E-deacetylchromomycin A3, chromomycin A2, soyasaponin II, lysolipin I, tetronomycin,
and naphthomevalin were confirmed by comparison of NMR and ESI-HRMS data with the
literature values [23–31].
3.5. General Chemistry Experimental Procedures
Several instruments were used to characterize the chemical properties of the compounds; for example, P-2000 digital polarimeter (JASCO) was used to measure the specific
rotations of the compounds and Bruker DRX-400 NMR spectrometer with 5-mm BBI (1H,
G-COSY, multiplicity-edited G-HSQC, and G-HMBC spectra) probe heads equipped with
z-gradients and Cryoprobe was utilized to collect NMR spectra of the compounds. The
1 H chemical shifts were referenced to the residual solvent peaks for CDCl at δ 7.26 ppm
3
H
and (CD3 )2 CO at δH 2.05 and δC 29.8 ppm, respectively. C18 reversed-phase preparative
HPLC purification was conducted using Agilent 1260 Infinity Preparative-Scale LC/MS
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Purification System coupled to Agilent 6130B single quadrupole mass spectrometer with
Agilent 5 Prep C18 column (100 × 30 mm, 5 µm). HPLC-MS analyses were conducted
using Agilent UHPLC 1290 Infinity coupled to Agilent 6540 accurate-mass quadrupole
time-of-flight (QTOF) mass spectrometer and an ESI source. Gradient elution that starts
from 98% water with 0.1% formic acid to 100% acetonitrile with 0.1% formic acid over
8.6 min along with an Acquity UPLC BEH C18 (2.1 × 50 mm, 1.7 µm) column at a flow rate
of 0.5 mL/min was used. The operating parameters for QTOF were the same as previously
reported [45].
4. Conclusions
A series of actinobacterial strains were isolated from a soil sample collected in Singapore and were found to produce several known antimicrobial compounds, namely
nonactin, monactin, dinactin, 4E-deacetylchromomycin A3, chromomycin A2, soyasaponin
II, lysolipin I, tetronomycin, and naphthomevalin and a newly discovered tetronomycin
A derivative (1) that exhibited antibacterial activity against SA and MRSA, with MIC90
values ranging from 2 to 4 µM and MBC90 values ranging from 9 to 12 µM. In addition, this
study showed the importance of an oxy-methyl group at C-27 position of tetronomycin for
antibacterial activity. This report also further demonstrated actinobacteria as a potential
natural source for antimicrobial drug discovery and provided better understanding on
tetronomycins as potent antibacterial agents. In addition, the findings also demonstrated
OSMAC method as a possible strategy to enhance the production of a diverse bioactive
secondary metabolites in actinobacteria.
The discovery of antimicrobial compounds in this study warrants future investigation
into the specific biochemical interactions through which a substance produces its pharmacological effect (mechanism of action studies). Moreover, the discovery of tetronomycin A
(1) could lead to medicinal chemistry research to generate compounds libraries for structure activity relationships (SAR) and chemical biology studies, owing to the presence of
the secondary hydroxy moiety at C-27 (i.e., incorporating ester or carbamate moieties).
However, the relatively low yield of pure compounds obtained in this study could be the
limiting factor for future works. Thus, larger scale isolation studies would be necessary to
obtain higher quantity of compounds.
Supplementary Materials: The following supporting information can be downloaded at: https:
//www.mdpi.com/article/10.3390/molecules28155832/s1. Figure S1. UV spectrum for 1. Figure S2.
(+)-HRESIMS spectrum for 1. Figure S3. 1 H NMR spectrum ((CD3 )2 CO, 400 MHz) of 1. Figure S4.
COSY spectrum of 1. Figure S5. HSQC spectrum of 1. Figure S6. HMBC spectrum of 1. Figure S7. 1 H
NMR spectrum ((CD3 )2 CO, 400 MHz) of tetronomycin. Figure S8. HSQC spectrum of tetronomycin.
Figure S9. HMBC spectrum of tetronomycin. Figure S10. Dose response curve against Staphylococcus
aureus Rosenbach (SA25923), Klebsiella aerogenes (EA13048), Pseudomonas aeruginosa (PA9027), Candida
albicans (CA10231) and Aspergillus fumigatus (AF46645). (A) Nonactin, (B) Monactin, (C) Dinactin,
(D) 4E-Deacetylchromomycin A3, (E) Chromomycin A2, (F) Lysolipin I, (G) Soyasaponin II, and
(H) Naphthomevalin. Figure S11. Dose response curve against A549 human lung carcinoma cells,
and two pancreatic cancer cell lines MIA PaCa-2 and PANC-1 cells. (A) Nonactin, (B) Monactin, (C)
Dinactin, (D) 4E-Deacetylchromomycin A3, (E) Chromomycin A2, (F) Lysolipin I, (G) Soyasaponin II,
and (H) Naphthomevalin. Figure S12. Dose response curve against Klebsiella aerogenes (EA13048),
Pseudomonas aeruginosa (PA9027), Candida albicans (CA10231), and Aspergillus fumigatus (AF46645).
(A) 1 and (B) Tetronomycin. Table S1. Antimicrobial and cytotoxicity primary screening results of 4
actinobacteria strains grown in 5 different growth media.
Author Contributions: Conceptualization, E.-J.C. and K.-C.C.; methodology, E.-J.C., K.-C.C., Z.Y.T.,
M.W., C.-Y.L., L.-K.Y., V.W.P.N. and D.C.S.S.; and investigation, E.-J.C., K.-C.C., Z.Y.T., M.W., C.-Y.L.,
L.-K.Y., V.W.P.N. and D.C.S.S.; writing—original draft preparation, E.-J.C. and K.-C.C.; writing—
review and editing, E.-J.C., K.-C.C., Z.Y.T., M.W., C.-Y.L., L.-K.Y., V.W.P.N., D.C.S.S., S.-B.N. and
Y.K.; visualization, E.-J.C., K.-C.C., Z.Y.T., M.W., C.-Y.L. and V.W.P.N.; supervision, S.-B.N. and Y.K.;
project administration, S.-B.N. and Y.K. All authors have read and agreed to the published version
of the manuscript.
Molecules 2023, 28, 5832
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Funding: This work was financially supported by Natural Product Research Laboratory Biomedical Research Council of A*STAR (Agency for Science, Technology, and Research) Transition Fund
(H16/99/b0/004), National Research Foundation Singapore (NRF-CRP19-2017-05), and Singapore
Institute of Food and Biotechnology Innovation core fund.
Institutional Review Board Statement: Not applicable.
Informed Consent Statement: Not applicable.
Data Availability Statement: The data supporting the finding in this study are contained within the
article or Supplementary Materials.
Acknowledgments: The authors would like to express their sincere appreciation to A*STAR Singapore, National Research Foundation Singapore, and Singapore Institute of Food and Biotechnology
Innovation for the fundings.
Conflicts of Interest: The authors declare no conflict of interest.
Sample Availability: Samples of the compounds are not available from the authors.
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