Molecules 25 01108
Molecules 25 01108
Molecules 25 01108
net/publication/339627856
CITATIONS READS
12 307
6 authors, including:
All content following this page was uploaded by Qing Fang on 02 March 2020.
Abstract: Four compounds (1–4) were isolated from the extracts of Streptomyces sp. CT37 using
bioassay in conjunction with mass spectrometric molecular networking (MN) driven isolation. Their
complete structures were established by high-resolution electrospray ionization mass spectrometry
(HR-ESIMS), and 1D and 2D nuclear magnetic resonance (NMR) data. Legonimide 1 was identified
as a new alkaloid containing a rare linear imide motif in its structure, while compounds 2–4 were
already known and their structures were elucidated as 1H-indole-3-carbaldehyde, actinopolymorphol
B, (2R,3R)-1-phenylbutane-2,3-diol, respectively. The biosynthetic pathways of 1–4 were proposed
based on the reported biogenesis of indole alkaloids in literature. Bioactivity tests for 1 and 2 revealed
moderate growth inhibition activity against Candida albicans ATCC 10231 with MIC95 values of
21.54 µg/mL and 11.47 µg/mL, respectively.
Keywords: legonimide; indole alkaloids; imide; Streptomyces sp. CT37; natural products; antifungal
1. Introduction
Microbial natural products (NPs) encompass several chemical structures that constitute a treasure
trove of high-value molecules, such as antibiotics, anticancer and antioxidant drugs [1]. Streptomyces a
prominent resource for natural product discovery contributing up to 75% of present day clinically used
antibiotics [2,3]. As part of the efforts of our laboratory to investigate microbial NPs with antibiotic
bioactivity from under-investigated environments, we have studied several Streptomyces isolates from
soil samples collected in Legon, Ghana [4–14].
Recently, metabolomics guided microbial NPs discovery processes have been widely used for
the prediction of bioactive metabolite structures and prioritization of extracts for isolations [15,16].
The method offers a route to deliver qualitative and quantitative data analysis of chemical space for
the metabolites present in complex bacteria fermentation extracts [9]. A useful analytical technique
that has been integrated into the metabolomics-guided microbial NPs discovery is HR-ESIMS and
associated MS/MS fragmentation data. However, the complexity of HR-ESIMS/MS data prevents
manual annotation of the presence of metabolites in the extracts. As such, several computing-based
data mining tools have been applied; one of the widely used is the Molecular Networking (MN)
database [17–20]. The MN database is a web-based server that is extremely useful for dereplicating
natural product structures by comparing both experimental HR-ESIMS (MS/MS) spectra with the
database [17]. The method is useful for the effective dereplication and annotating of specialised
metabolite (SM) families and individual molecules.
The current study establishes mass spectrometric molecular networking (MN) in conjunction with
bioassay tests to guide isolation of the bioactive components from the Ghanaian isolate, Streptomyces sp.
CT37. The targeted isolation afforded four compounds: legonimide 1, 1H-indole-3-carbaldehyde 2,
actinopolymorphol B 3, and (2R,3R)-1-phenylbutane-2,3-diol 4.
Figure 1. Compounds 1–4 isolated from Streptomyces sp. CT37 ISP2 extract; compound 1 with correlation
spectroscopy (COSY) (—) and key heteronuclear multiple bond correlation (HMBC) (→) correlations.
Compound 1 was isolated as a pale yellow amorphous solid. The HR-ESIMS spectrum of 1
exhibited a prominent peak at m/z 293.1280 [M + H]+ corresponding to the molecular formula of
C18 H16 N2 O2 (calcd for C18 H17 N2 O2 + 293.1285, ∆ = −1.70 ppm) possessing 12 degrees of unsaturation.
The 1 H nuclear magnetic resonance (NMR) spectrum in DMSO-d6 (Table 1) of 1 indicated the
presence of two exchangeable NH protons (δH 7.37, 10.96), two sp3 methylenes (δH 3.35, 3.46), nine
aromatic methines (δH 7.54, 7.34, 7.31, 7.28, 7.28, 7.21, 7.21, 7.06, and 7.02), and one sp2 methine
(δH 7.18). In addition to the signals corresponding to the above carbons, analysis of the 13 C NMR
and heteronuclear single quantum coherence (HSQC) spectra revealed the presence of six quaternary
carbons, including two carbonyls (δC 173.1, 172.3) and four aromatic groups (δC 136.6, 136.5, 127.3,
and 109.2).
Molecules 2020, 25, 1108 3 of 10
Thorough inspection of the 2D NMR spectra disclosed the presence of 4 substructures (A-D)
(Figure S3), including a 3H-subsituted indole, acetyl group (B), acetamide subunit (C), and one
monosubstituted aromatic ring (D) in the structure of 1. The monosubstituted phenyl group and
the ring in the indole moiety comprised two separate spin systems, H-14 through H-140 and H-4
through H-7, respectively, as indicated in the 1 H-1 H correlation spectroscopy (COSY) spectrum.
The heteronuclear multiple bond correlation (HMBC) from H-8 (δH 3.46) to the carbonyl carbon at C-9
(δC 173.1), and NH-10 (δH 7.37) to carbonyl C-11 (δC 172.3) and methylene carbon at C-12 (δC 42.0),
established the presence of the acetyl and acetamide subunits, respectively. The HMBC correlation
from H-12 (δH 3.35) to C-13 (δC 136.6) and C-14 (δC 128.1) established the connectivity of substructure C
to D at C-13. The cross peaks from H-8 to C-2 (δC 123.6), C-3 (δC 109.2), and C-4a (δC 127.3) confirmed
the connection of the indole subunit (substructure A) to the acetyl group (substructure B) at C-3.
The structure of 1 was further corroborated by the long-range HMBC correlation from NH-10 to C-4a
and C-12; thereby, the imide group flanked the 3H-substituted indole moiety and the monosubstituted
benzene ring (Figures S9–S11). Hence, the structure of 1 was elucidated representing a new alkaloid
containing a linear imide motif as N-(2-(1H-indol-3-yl)acetyl)-2-phenylacetamide and named as
legonimide in association with Legon, Ghana.
The free imide group in 1 can adopt three conformations: cis-trans, trans-trans and cis-cis [28]
(Figure S12). There was no HMBC correlation from NH-10 to C-8, while correlation was observed from
NH-10 to C-12 (Figure S13), suggesting that the imide motif in 1 is likely a cis-trans conformer. This
observation is in agreement with those reported for imide-containing natural products that the cis-trans
conformation is the most stable [29–32].
Compound 2 was identified as 1H-indole-3-carbaldehyde previously isolated from plants [33],
marine sponge [34], and several Streptomyces species [35,36] (Figures S14–S18, Table S4). Compound
3 was consistent with the reported data for actinopolymorphol B from actinopolymorpha rutilus [27]
(Figures S19–S23, Table S4). Compound 4 was 1-phenylbutane-2,3-diol found in several plants [37].
A threo isomer of 4 was previously isolated from a actinomycete Williamsia sp. MCCC 1A11233
(Figures S24–S28) [38]. The configuration of 4 was assigned upon careful comparison of the NMR data
with those reported for the four synthetic stereoisomers, two threo (2S,3R and 2R,3S) and two erythro
(2S,2S and 2R,3R) [26,37] (Table S5). The NMR data of 4 was consistent with the reported data for
threo isomers. Furthermore, comparison of the optical rotation of 4 with the synthetic stereoisomers
Molecules 2020, 25, 1108 4 of 10
pointed to (2R,3R)-1-phenylbutane-2,3-diol [26,37] (Tables S5 and S6). However, we could not exclude
the possibility that compound 4 could be a mixture of enantiomers.
3. Experimental
UK) to generate the total crude extract (6.1 g). All eight crude extracts were then subjected to disc
diffusion tests.
4. Conclusions
The bioassay and molecular network-assisted isolation afforded four alkaloids 1-4 from the
Ghanaian soil bacterium, Streptomyces sp. CT37. Their structures were deduced by analysis of the
HRESIMS, 1D, and 2D NMR. Legonimide 1 was identified as a new alkaloid bearing the imide motif in
its structure, while 2-4 were known and their structures were elucidated as 1H-indole-3-carbaldehyde,
3-hydroxy-4-(1H-indol-3-yl) butan-2-one, and (2R,3R)-1-phenylbutane-2,3-diol, respectively. Alkaloids
1 and 2 exhibited moderate inhibition against C. albicans ATCC 10,231 with MIC values of 21.54 µg/mL
and 11.47 µg/mL, respectively.
References
1. Ngo, L.T.; Okogun, J.I.; Folk, W.R. 21st Century natural product research and drug development and
traditional medicines. Nat. Prod. Rep. 2013, 30, 584–592. [CrossRef]
2. Mohana, N.C.; Rao, H.C.Y.; Rakshith, D.; Mithun, P.R.; Nuthan, B.R.; Satish, S. Omics based approach for
biodiscovery of microbial natural products in antibiotic resistance era. J. Genet. Eng. Biotechnol. 2018, 16, 1–8.
[CrossRef]
3. Hopwood, D.A. How do antibiotic-producing bacteria ensure their self-resistance before antibiotic
biosynthesis incapacitates them? Mol. Microbiol. 2007, 63, 937–940. [CrossRef] [PubMed]
4. Fang, Q.; Maglangit, F.; Wu, L.; Ebel, R.; Kyeremeh, K.; Andersen, J.H.; Annang, F.; Pérez-Moreno, G.;
Reyes, F.; Deng, H. Signalling and bioactive metabolites from Streptomyces sp. RK44. Molecules 2020, 25, 460.
[CrossRef] [PubMed]
5. Deng, H.; Ma, L.; Bandaranayaka, N.; Qin, Z.; Mann, G.; Kyeremeh, K.; Yu, Y.; Shepherd, T.; Naismith, J.H.;
O’Hagan, D. Identification of Fluorinases from Streptomyces sp MA37, Norcardia brasiliensis, and Actinoplanes
sp N902-109 by genome mining. ChemBioChem 2014, 15, 364–368. [CrossRef] [PubMed]
6. Maglangit, F.; Tong, M.H.; Jaspars, M.; Kyeremeh, K.; Deng, H. Legonoxamines A-B, two new hydroxamate
siderophores from the soil bacterium, Streptomyces sp. MA37. Tetrahedron Lett. 2019, 60, 75–79. [CrossRef]
7. Maglangit, F.; Fang, Q.; Leman, V.; Soldatou, S.; Ebel, R.; Kyeremeh, K.; Deng, H. Accramycin A, a new
aromatic polyketide, from the soil bacterium, Streptomyces sp. MA37. Molecules 2019, 24, 3384. [CrossRef]
8. Marmann, A.; Aly, A.H.; Lin, W.; Wang, B.; Proksch, P. Co-cultivation—A powerful emerging tool for
enhancing the chemical diversity of microorganisms. Mar. Drugs 2014, 12, 1043–1065. [CrossRef]
9. Tabudravu, J.N.; Pellissier, L.; Smith, A.J.; Subko, K.; Autreáu, C.; Feussner, K.; Hardy, D.; Butler, D.; Kidd, R.;
Milton, E.J.; et al. LC-HRMS-database screening metrics for rapid prioritization of samples to accelerate the
discovery of structurally new natural products. J. Nat. Prod. 2019, 82, 211–220. [CrossRef]
10. Su, L.; Zhang, R.; Kyeremeh, K.; Deng, Z.; Deng, H.; Yu, Y. Dissection of the neocarazostatin: A C4 alkyl side
chain biosynthesis by in vitro reconstitution. Org. Biomol. Chem. 2017, 3843–3848. [CrossRef] [PubMed]
11. Su, L.; Lv, M.; Kyeremeh, K.; Deng, Z.; Deng, H.; Yu, Y. A ThDP-dependent enzymatic carboligation reaction
involved in neocarazostatin a tricyclic carbazole formation. Org. Biomol. Chem. 2016, 14, 8679–8684.
[CrossRef] [PubMed]
12. Rateb, M.E.; Zhai, Y.; Ehrner, E.; Rath, C.M.; Wang, X.; Tabudravu, J.; Ebel, R.; Bibb, M.; Kyeremeh, K.;
Dorrestein, P.C.; et al. Legonaridin, a new member of linaridin RiPP from a Ghanaian Streptomyces isolate.
Org. Biomol. Chem. 2015, 13, 9585–9592. [CrossRef] [PubMed]
13. Huang, S.; Tabudravu, J.; Elsayed, S.S.; Travert, J.; Peace, D.; Tong, M.H.; Kyeremeh, K.; Kelly, S.M.;
Trembleau, L.; Ebel, R.; et al. Discovery of a single monooxygenase that catalyzes carbamate formation
and ring contraction in the biosynthesis of the legonmycins. Angew. Chem. Int. Ed. 2015, 54, 12697–12701.
[CrossRef] [PubMed]
14. Maglangit, F.; Fang, Q.; Kyeremeh, K.; Sternberg, J.M.; Ebel, R.; Deng, H. Co-Culturing Approach Enables
Discovery and Biosynthesis of a Bioactive Indole Alkaloid Metabolite. Molecules 2020, 25, 256. [CrossRef]
15. Callahan, D.L.; Elliott, C.E.; Walker, J.M. Metabolomics Tools for Natural Product Discovery; Methods in Molecular
Biology 1055; HUMANA: Louisville, KY, USA, 2013; Volume 1055, ISBN 978-1-62703-576-7.
16. Cox, D.G.; Oh, J.; Keasling, A.; Colson, K.; Hamann, M.T. The utility of metabolomics in natural product and
biomarker characterization. Biochim. Biophys. Acta 2014, 1840, 3460–3474. [CrossRef]
17. Networking, S.M.; Wang, M.; Carver, J.J.; Phelan, V.V.; Sanchez, L.M.; Garg, N.; Peng, Y.; Nguyen, D.D.D.T.;
Watrous, J.; Kapono, C.A.; et al. Sharing and community curation of mass spectrometry data with global
natural products social molecular networking. Nat. Biotechnol. 2016, 34, 828–837.
18. Ernst, M.; Kang, K.B.; Caraballo-Rodríguez, A.M.; Nothias, L.-F.; Wandy, J.; Chen, C.; Wang, M.; Rogers, S.;
Medema, M.H.; Dorrestein, P.C.; et al. MolNetEnhancer: Enhanced molecular networks by integrating
metabolome mining and annotation tools. Metabolites 2019, 9, 144. [CrossRef]
19. Borges, R.M.; Taujale, R.; de Souza, J.S.; de Andrade Bezerra, T.; Silva, E.L.E.; Herzog, R.; Ponce, F.V.;
Wolfender, J.-L.; Edison, A.S. Dereplication of plant phenolics using a mass-spectrometry database
independent method. Phytochem. Anal. 2018, 29, 601–612. [CrossRef]
Molecules 2020, 25, 1108 9 of 10
20. Blaženović, I.; Kind, T.; Torbašinović, H.; Obrenović, S.; Mehta, S.S.; Tsugawa, H.; Wermuth, T.; Schauer, N.;
Jahn, M.; Biedendieck, R.; et al. Comprehensive comparison of in silico MS/MS fragmentation tools of the
CASMI contest: Database boosting is needed to achieve 93% accuracy. J. Cheminform. 2017, 9, 32. [CrossRef]
21. Bode, H.B.; Bethe, B.; Höfs, R.; Zeeck, A. Big effects from small changes: Possible ways to explore nature’s
chemical diversity. ChemBioChem 2002, 3, 619–627. [CrossRef]
22. Shirling, E.B.; Gottlieb, D. Methods for characterization of streptomyces species. Int. J. Syst. Bacteriol. 1966,
16, 313–340. [CrossRef]
23. Mohimani, H.; Gurevich, A.; Shlemov, A.; Mikheenko, A.; Korobeynikov, A.; Cao, L.; Shcherbin, E.;
Nothias, L.-F.; Dorrestein, P.C.; Pevzner, P.A. Dereplication of microbial metabolites through database search
of mass spectra. Nat. Commun. 2018, 9, 4035. [CrossRef] [PubMed]
24. Santen, J.; Van, A.; Jacob, G.; Singh, A.L.; Aniebok, V.; Balunas, M.J.; Bunsko, D.; Neto, F.C.; Castaño-Espriu, L.;
Chang, C.; et al. The natural products atlas: An open access knowledge base for microbial natural products
discovery. ACS Cent. Sci. 2019, 5, 1824–1833. [CrossRef] [PubMed]
25. Sun, D.; Dong, W.; Li, X.; Zhang, H. Indole alkaloids from the roots of isatis ingigotica and their antiherpes
simplex virus type 2 (HSV-2) activity in vitro. Chem. Nat. Compd. 2010, 46, 763–766. [CrossRef]
26. Awano, K.I.; Yanai, T.; Watanabe, I.; Takagi, Y.; Kitahara, T.; Mori, K. Synthesis of all four possible stereoisomers
of 1-phenyl-2,3-butanediol and both enantiomers of 3-hydroxy-4-phenyl-2-butanone to determine the absolute
configuration of the natural constituents. Biosci. Biotechnol. Biochem. 1995, 59, 1251–1254. [CrossRef]
27. Huang, S.X.; Powell, E.; Rajski, S.R.; Zhao, L.X.; Jiang, C.L.; Duan, Y.; Xu, W.; Shen, B. Discovery and total
synthesis of a new estrogen receptor heterodimerizing actinopolymorphol A from actinopolymorpha rutilus.
Org. Lett. 2010, 12, 3525–3527. [CrossRef]
28. Parra, R.D.; Furukawa, M.; Gong, B.; Zeng, X.C. Energetics and cooperativity in three-center hydrogen
bonding interactions. I. diacetamide-X dimers (X=HCN, CH3 OH). J. Chem. Phys. 2001, 115, 6030–6035.
[CrossRef]
29. Hvoslef, J.; Tracy, M.L.; Nash, C.P. Interatomic distances and angles in four planar systems with adjacent
C–O and C–N bonds: Structures of pivalamide (I), dipivalamide (II),N-pivaloylpivalamidinium pyrosulfate
(III) and N-pivaloylpivalamidine (IV). Acta Crystallogr. Sect. C Cryst. Struct. Commun. 1986, 42, 353–360.
[CrossRef]
30. Hinterberger, S.; Hofer, O.; Greger, H. Synthesis and corrected structures of sulphur-containing amides from
glycosmis species: Sinharines, penimides, and illukumbins. Tetrahedron 1994, 50, 6279–6286. [CrossRef]
31. Cardoso-Martínez, F.; De La Rosa, J.M.; Díaz-Marrero, A.R.; Darias, J.; D’Croz, L.; Cerella, C.; Diederich, M.;
Cueto, M. Oximoaspergillimide, a fungal derivative from a marine isolate of Aspergillus sp. Eur. J. Org. Chem.
2015, 2015, 2256–2261. [CrossRef]
32. Karplus, M. Contact electron-spin coupling of nuclear magnetic moments. J. Chem. Phys. 1959, 30, 11–15.
[CrossRef]
33. Yu, L.; Liu, J.; Yu, L.; Chen, L.; Qiu, F. Chemical constituents of seed oil leavings of xanthoceras sorbifolia.
Chem. Nat. Compd. 2018, 54, 769–771. [CrossRef]
34. Netz, N.; Opatz, T. Marine indole alkaloids. Mar. Drugs 2015, 13, 4814–4914. [CrossRef] [PubMed]
35. Yang, S.W.; Cordell, G.A. Metabolism studies of indole derivatives using a staurosporine producer,
Streptomyces staurosporeus. J. Nat. Prod. 1997, 60, 44–48. [CrossRef] [PubMed]
36. Lacret, R.; Oves-Costales, D.; Gómez, C.; Díaz, C.; De La Cruz, M.; Pérez-Victoria, I.; Vicente, F.; Genilloud, O.;
Reyes, F. New ikarugamycin derivatives with antifungal and antibacterial properties from streptomyces
zhaozhouensis. Mar. Drugs 2015, 13, 128–140. [CrossRef]
37. Cartus, A.T.; Stegmüller, S.; Simson, N.; Wahl, A.; Neef, S.; Kelm, H.; Schrenk, D. Hepatic metabolism of
carcinogenic β-asarone. Chem. Res. Toxicol. 2015, 28, 1760–1773. [CrossRef]
38. Xie, C.L.; Niu, S.W.; Zhou, T.T.; Zhang, G.Y.; Yang, Q.; Yang, X.W. Chemical constituents and chemotaxonomic
study on the marine actinomycete Williamsia sp. MCCC 1A11233. Biochem. Syst. Ecol. 2016, 67, 129–133.
[CrossRef]
39. Böttcher, C.; Chapman, A.; Fellermeier, F.; Choudhary, M.; Scheel, D.; Glawischnig, E. The biosynthetic
pathway of indole-3-carbaldehyde and indole-3-carboxylic acid derivatives in arabidopsis. Plant Physiol.
2014, 165, 841–853. [CrossRef]
Molecules 2020, 25, 1108 10 of 10
40. Khan, A.R.; Park, G.S.; Asaf, S.; Hong, S.J.; Jung, B.K.; Shin, J.H. Complete genome analysis of Serratia
marcescens RSC-14: A plant growth-promoting bacterium that alleviates cadmium stress in host plants.
PLoS ONE 2017, 12, 1–17. [CrossRef]
41. Zhang, L.S.; Davies, S.S. Microbial metabolism of dietary components to bioactive metabolites: Opportunities
for new therapeutic interventions. Genome Med. 2016, 8, 46. [CrossRef]
42. Hudzicki, J. Kirby-bauer disk diffusion susceptibility test protocol author information. Am. Soc. Microbiol.
2009, 1–23.
43. Kessner, D.; Chambers, M.; Burke, R.; Agus, D.; Mallick, P. ProteoWizard: Open source software for rapid
proteomics tools development. Bioinformatics 2008, 24, 2534–2536. [CrossRef] [PubMed]
44. Nothias, L.F.; Petras, D.; Schmid, R.; Dührkop, K.; Rainer, J.; Sarvepalli, A.; Protsyuk, I.; Ernst, M.; Tsugawa, H.
Feature-based molecular networking in the GNPS analysis environment. BiorXiv 2019, 812404.
45. Pluskal, T.; Castillo, S.; Villar-briones, A.; Orešič, M.; Ore, M. MZmine 2: Modular framework for processing,
visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinform. 2010, 11, 395.
[CrossRef] [PubMed]
46. Horai, H.; Arita, M.; Kanaya, S.; Nihei, Y.; Ikeda, T.; Suwa, K.; Ojima, Y.; Tanaka, K.; Tanaka, S.; Aoshima, K.;
et al. MassBank: A public repository for sharing mass spectral data for life sciences. J. Mass Spectrom. 2010,
45, 703–714. [CrossRef]
47. Carpenter, D.E.; Karen Anderson Diane Citron, C.M.; JoAnn Dzink-Fox, B.L.; Meredith Hackel, M.;
Jenkins, S.G.; Cindy Knapp, F.; Laura Koeth, M.; Audrey Schuetz, M.N.; Hannah Wexler, D. Methods for
Antimicrobial Susceptibility Testing of Anaerobic Bacteria; Clinical and Laboratory Standards Institute: Wayne,
PA, USA, 2018; pp. 11–19.
© 2020 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 (http://creativecommons.org/licenses/by/4.0/).