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Cytosine-Type Nucleosides from Marine-Derived Streptomyces Rochei 06CM016

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Cytosine-Type Nucleosides from Marine-Derived Streptomyces Rochei 06CM016 The Journal of Antibiotics (2016) 69, 51–56 & 2016 Japan Antibiotics Research Association All rights reserved 0021-8820/16 www.nature.com/ja ORIGINAL ARTICLE Cytosine-type nucleosides from marine-derived Streptomyces rochei 06CM016 Semiha Çetinel Aksoy1, Ataç Uzel1 and Erdal Bedir2 Rocheicoside A (3), a nucleoside analog possessing a novel 5-(hydroxymethyl)-5-methylimidazolidin-4-one substructure, was isolated from marine-derived actinomycete Streptomyces rochei 06CM016, together with a new (4) and three known compounds. Structures of the new metabolites were elucidated by one-dimensional (1H and 13C) and 2D NMR (COSY, HMQC and HMBC) and HR-TOF-MS analyses. All the metabolites exhibited significant antimicrobial activity. A plausible mechanism was proposed for compound 3’s formation from amicetin. The Journal of Antibiotics (2016) 69, 51–56; doi:10.1038/ja.2015.72; published online 1 July 2015 INTRODUCTION RESULTS AND DISCUSSION Antibiotics are natural compounds produced by microorganisms The isolation process performed using the sediment sample resulted in as secondary metabolites to kill or inhibit other microorganisms. acquiring a bioactive mesophilic actinomycete 06CM016. The isolate As their first discovery in the middle of the twentieth century, showed antibacterial activity against Escherichia coli (17 mm) and they had an important role in the treatment of infectious diseases. MRSA (22 mm), and antifungal activity against Candida albicans Up to now, pharmaceutical industry has primarily targeted (37 mm). Sequencing using primers 27F and 1492R revealed that drugs from soil organisms, and of the antibiotics in clinical use, the isolate was a member of Streptomyces genus. When the molecular fi most are of bacterial or fungal origin. Among the bacteria, identi cation evaluated with the phenotypical results (data not fi Actinobacteria are particularly noteworthy, as they produce shown), the isolate was identi ed as Streptomyces rochei. After large- antibiotics such as streptomycin, neomycin, chloramphenicol, scale fermentation, 1.92 g of EtOAc extract was acquired. Bioassay- fi chlortetracycline and erithyromycin.1,2 Members of Actinomycetes, guided fractionation using the extract led to the isolation of ve – especially Streptomyces, are fruitful organisms, producing ~ 80% of the compounds (1 5), of which 1 (plicacetin), 2 (norplicacetin) and 5 3,4 were identified as cytosine-type nucleoside derivatives, by comparison antibiotics. 14–17 The acquired resistance of pathogen microorganisms due to their of their spectral data with those previously reported (Figure 1). The high resolution time of flight mass spectrum (HR-TOF-MS) of high mutation rates, toxic effects of some known antibiotics on 3 ½½a25 ¼ 5:7(c 0.0035, MeOH)] gave molecular ions of m/z 631.3123 human health and the existence of naturally resistant bacteria D [(+) mode] and 629.2387 [(− ) mode], attributed to [M+H]+ and require the discovery of novel antibiotics.5,6 As antibiotic discovery [M − H]−, respectively. Together with the 13CNMRdata,accurate efforts result in identified secondary metabolite frameworks with mass data supported a molecular formula of C H N O .Initial known mode of actions, recently, the researchers have started to 30 42 6 9 inspection of the one-dimensional NMR spectra (1H, 13C and DEPT) focus on microorganisms living in extreme conditions, namely also suggested a cytosine derivative, similar with compounds 1 and 2. 2,7,8 ocean and ocean bottoms, to discover novel chemical entities. 1H NMR spectrum of 3 exhibited a tertiary and two secondary It is thought that these novel compounds in general are produced up-field methyl groups (δ 1.10, 1.16 and 1.27, respectively), a tertiary as response to stress conditions.9 This research line led to the lower field methyl group (δ2.38, 6H) attributable to a N(CH3)2 unit, a discovery of many new microbial species producing bioactive para-disubstituted aromatic ring (δ 7.79, 2H, d, J = 8.8 Hz; δ 8.07, 2H, compounds.10,11 Recent studies have revealed that unusual marine d, J = 8.8 Hz) and two vinyl protons (δ 7.34, 1H, d, J = 7.6 Hz; δ 8.16, Actinomycetes are good candidates for the discovery of new natural 1H, d, J = 7.6 Hz; Table 1). The chemical shifts of the latter protons products.12 are typical of the CH(5) and CH(6) resonances of a cytosine unit.18–20 As part of our ongoing studies,13 the aim of this study was to On the basis of the HMQC connectivity, this assumption was discover new antimicrobial molecules from marine Actinomycetes substantiated, which indicated characteristic C-5 and C-6 signals at living in unexplored areas of Mediterranean Sea. 97.1 and 145.7 p.p.m., respectively. 1Ege University, Department of Biology, Basic and Industrial Microbiology Section, Izmir, Turkey and 2Ege University, Department of Bioengineering, Izmir, Turkey Correspondence: Dr SÇ Aksoy, Ege University, Department of Biology, Basic and Industrial Microbiology Section, Bornova, Izmir 35100, Turkey. E-mail: [email protected] or Professor Dr E Bedir, Ege University, Department of Bioengineering, Bornova, Izmir 35100, Turkey. E-mail: [email protected] Received 12 February 2015; revised 27 April 2015; accepted 7 May 2015; published online 1 July 2015 Cytosine-type nucleosides from S. rochei SÇ Aksoy et al 52 Figure 1 Structures of 1–5. In addition, 1HNMRspectrumof3 displayed typical signals for electron donating amino group of p-amino benzoic acid, possibly an two sugar units, namely amicetose and amosamine as in 1 and 2.16–20 amide functionality. The two major spin systems of the disaccharidic part were deduced After exclusion of the above-mentioned parts, the remaining side from the COSY spectrum starting from the well resolved anomeric chain of the molecule had the formula C5H9N2O2. On the basis of the protons (Figure 2). The H-1′ resonance of amicetose (δ 5.73) showed comprehensive examination of one-dimensional and 2D NMR data of cross peaks with two methylene protons (H-2′: δ 1.73 and 2.07), 3, and the comparison of these data with those of related metabolites, which, in turn, coupled with H2-3′ (δ 1.50 and 2.29). H2-3′ exhibited well-known cytosine-type antibiotics, namely amicetin, bamicetin 16,19,20–22 correlation with H-4′ (δ 3.36), whereas the latter proton showed cross and oxamicetin, it was inferred that a framework derived α peaks with H-5′ (δ 3.65), which coupled with an up-field methyl from -methylserine was connected to the benzoyl unit via an amide δ signal at δ 1.16 (H -6′). In a similar manner, the spin system of bond. Four of the left over carbons at 176.9, 66.2, 65.6, 19.3 (C-16 3 13 amosamine moiety could be traced from the low-field H-1″ (δ 4.81) to (s), C-19 (t), C-17 (s), and C-20 (q), respectively) in the CNMR δ H -6″ (1.27; Table 1). The use of HMQC spectrum of 3 allowed the spectrum, a singlet methyl at 1.10 (H3-20) and two methylene 3 δ = 1 assignment of the carbon signals ascribable to the saccharides, which protons at 3.32 and 3.62 (each d, J 5.6 Hz, H2-19) in the HNMR spectrum were evident for the integration of the aforementioned also verified the presence of inner amicetose and terminal amosamine amino-acid moiety. Furthermore, in the HMBC spectrum, long-range moieties. The absolute configurations of these deoxy sugars were correlations between C-16/C-17 and H -20/H -19 substantiated our suggested to be D based on the same biosynthetic origin as in 1, 2 and 3 2 assumption. The remaining NMR signals indicated an isolated 5. This assumption was substantiated by carrying out acidic hydrolysis methylene group (H -21: δ 4.73, 4.85, each d, J = 7.6 Hz; C-21: on compound 3. 2 δ 63.1, t), secured by the COSY and HMQC spectra. One of the two The interfragment relationship deduced from the HMBC spectrum unsaturation numbers calculated for the side chain was readily helped us to locate the O-andN-glycosidic linkages, shown in accounted for the amide carbonyl at δ 176.9, suggestive of a δ Figure 2. Thus, the anomeric proton of the amosamine unit ( 4.81) cyclization. Thus, incorporation of the remaining carbon should ′ δ displayed a long-range correlation to C-4 of amicetose ( 73.6), afford a ring system. In this case, there are two possibilities, either – 3 – whereas the anomeric carbon of the latter sugar showed a J C H N–CH –N– or –N–CH –O– bridges. In case of the latter (oxazolidine δ 2 2 heteronuclear correlation with H-6 of cytosine moiety ( 8.16). ring), C-21 was supposed to be resonated around 80–85 p.p.m. in the δ – Moreover, the methyl signal observed at 2.38 (6H) was readily 13CNMRspectrum.23 25 However, the observed carbon data (δ 63.1) assigned to C-4″-[N(CH ) ] on the basis of a long-range connectivity 26 3 2 was entirely compatible with –N–CH2–N– connection, referring a to C-4″ (δ 70.5). 5-(hydroxymethyl)-5-methylimidazolidin-4-one skeleton. The stereo- The combined use of COSY, HMQC and HMBC spectra also chemistry of C-17 was assigned by a combination of 2D NOESY data permitted the complete assignment of the aromatic ring (Table 1, and molecular modeling studies performed on 3.Inregardtothe Figure 2) as p-substituted benzoyl extending from cytosine moiety. absolute configuration of C-17, the minimum energy conformations The proton chemical shift of H-11(13) was notably deshielded of R and S stereoisomers were calculated with a three-dimensional compared with those in compound 1 (δ 7.79 and 6.57, respectively), computer-generated model.
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