The marine environment, particularly with sponges, is a rich source of new bioactive metabolites—287 novel metabolites were isolated from marine sponges in 2008 [1]. The availability of biomass is a limiting factor for isolating marine natural products. The widespread isolation of typical microbial metabolites from sponges leads to the hypothesis that these metabolites are in fact the products of microbial metabolism [2]. The isolation of secondary metabolite-producing bacteria from sponges and of microbial secondary metabolism gene clusters from the metagenome of sponges has led to the general understanding that these metabolites are, in many cases, the products of microbial symbionts and are not derived from the microbial diet of sponges [3]. Thus, marine organism-associated microbes have been attracting increasing interest as potential sources of marine natural products in order to solve the supply shortage.

A number of reports have been published on the isolation of actinobacteria from marine organisms [4]. Screening bioactive substances from these marine-derived actinobacteria has yielded several new bioactive metabolites [5–8]. In our recent screening for new natural products, one novel deoxyuridine (1), along with two known nucleoside derivatives (2, 3), were isolated from Streptomyces microflavus strain No. HVG29 belonging to actinomycetes. To date, there have been no reports of deoxyuridine structures isolated from this species. We report herein the isolation and structure elucidation of 1–3.

The total ethyl acetate extract from 30 L of fermentation broth was partitioned between hexane and 9:1 MeOH–H₂O followed by diluting the aqueous layer to 3:2 MeOH–H₂O and solvent partitioning with EtOAc. The EtOAc fraction was subjected to further purification by gel permeation on Sephadex LH-20 to yield compounds 1–3 (Figure 1).

Compound 1 was obtained as a white powder, [α]²⁰_D +5.4° (c 0.39, MeOH). The IR spectrum possessed absorptions for hydroxyl groups (3394 cm⁻¹) and amide carbonyl groups (1693 cm⁻¹). The EIMS gave a molecular ion peak at m/z 284 [M]⁺, and the molecular formula C₁₂H₁₆N₂O₆ was determined by HRESIMS at m/z 307.0905 [M + Na]⁺ (calcd. for C₁₂H₁₆N₂O₆Na, 307.0906).

In the 1D NMR spectra, proton signals at δ_H 6.28 (1H, t, J = 7.0 Hz, H-2′), 2.22 (2H, m, H-3′), 3.90 (1H, q, J = 3.5 Hz, H-4′), 4.40 (1H, dt, J = 3.5, 5.9 Hz, H-5′), 3.79 (1H, dd, J = 3.2, 12.0 Hz, H-6′a), and 3.83 (1H, dd, J = 3.7, 12.0 Hz, H-6′b) and carbon resonances at δ_C 86.3 (CH, C-2′), 41.2 (CH₂, C-3′), 72.2 (CH, C-4′), 88.9 (CH, C-5′), and 62.9 (CH₂, C-6′) supported the presence of a pentose moiety in the molecule. The HMBC spectrum showed correlations from H-6′ to C-4′, from H-5′ to C-2′ and C-3′, from H-4′ to C-2′, from H-3′ to C-5′and C-2′, and from H-2′ to C-5′ and C-4′ (Figure 2). In addition, the correlations between H-2′/H₂-3′, H₂-3′/H-4′, H-4′/H-5′, and H-5′/H₂-6′ were observed in the ¹H-¹H COSY spectrum (Figure 2). The above NMR evidence established the presence of a 2′-deoxyribose moiety, which was supported by the similarity of the ¹H and ¹³C NMR data to those reported in the literatures for such a unit [9,10].

The remaining portion of 1 implied the elemental composition C₇H₇N₂O₃, and accounted for the remaining 5 degrees of unsaturation. In the 1D NMR spectra, proton signals at δ_H 7.81 (1H, s, H-6) and 1.88 (3H, s, H-7) and carbon resonances at δ_C 152.4 (C-2), 166.4 (C-4), 111.5(C-5), 138.2 (C-6), and 12.4 (C-7) evidenced the presence of a thymine moiety in the molecule. An acetyl group was supported by proton signal at δ_H 1.88 (3H, s, H-9) and carbon signals at δ_C 23.4 (C-9) and 179.2 (C-8). In combination with the chemical shifts of the corresponding carbons and the elemental composition, the acetyl group was assigned to N-3 of the thymine moiety, because only N-3 had a vacancy in the molecule. Meanwhile, HMBC long-range correlations from H-2′ to C-2 and C-6 (Figure 2), clearly located the 2′-desoxyribose moiety to N-1 of the 3-acetyl-5-methylthymine unit. Therefore, the structure of 1 was determined as 3-acetyl-5-methyl-2′-deoxyuridine.

The structures of known compounds 2 and 3 were confirmed by detailed NMR data comparison with those in literatures [11]. To the best of our knowledge, compound 1 is the first example of acetyl deoxyuridine from marine-derived actinomycetes to be isolated from the marine sponge Hymeniacidon perlevis.

In previous research into metabolites isolated from S. microflavus, many fattiviracin derivatives and actinomycin X2 have been elucidated [14]. The major product of these fattiviracin derivatives was fattiviracin FV-8, which consists of four glucose and two trihydroxy fatty acid residues [15–17]. Actinomycin X2 included a wide range of fatty acids (C10–C22), which have been isolated from Streptomyces nasri [18]. Compounds 1–3 represent the first examples of deoxyuridine structures isolated from S. microflavus which was associated with sponges.

The known compounds (2 and 3) were originally isolated from a marine sponge [11], Geodia barretti, and now, for the first time, from sponge-associated microorganisms. This finding strengthens the hypothesis that marine microbial symbionts are possibly the true producers or take part in the biosynthesis of some bioactive marine natural products isolated from the marine organism hosts.

These nucleosides may have potent biological or physiological effects. A series of nucleoside analogues were synthesized and exhibited potential antiviral activities against duck hepatitis B virus (DHBV) [19], herpes simplex virus type 1 and 2 (HSV-1 and HSV-2), and varicella zoster virus (VZV) [20–22]. All of those synthesized 2′-deoxyuridine analogues have special substituents on position C-5 of uridine moiety. However, there is no evaluation for the compound which has the substituents on position N-3 of uridine residue. Compounds 1 and 2 provide new thoughts of introducing functional groups on nucleoside structures for synthetic medical chemistry.