Carpatamides A-C, cytotoxic arylamine derivatives from a marine-derived Streptomyces sp.

Three new acylated arylamine derivatives (1-3), carpatamides A-C, were isolated from a marine-derived Streptomyces sp. based on activity screening against non-small-cell lung cancer (NSCLC). The structures of 1-3 were established on the basis of comprehensive spectroscopic analyses and chemical methods. Compounds 1 and 3 showed moderate cytotoxicity against NSCLC cell lines HCC366, A549, and HCC44 with IC50 values ranging from 2.2 to 8.4 μM.

Examining the natural product profiles of underexploited organisms from the marine environment has become a research hotspot in drug discovery.[1] With more than 400 new compounds with cytotoxicity and antimicrobial activity isolated, such as abyssomycin C,[2] salinosporamide A,[3] discoipyrrole A, and marinomycin,[4] cultured marine actinomycetes have been a prolific resource of bioactive natural products.[5] This resource for natural products, combined with advancements in high-content phenotypic screening approaches, opens up tremendous possibilities for the discovery of biologically and structurally interesting compounds.[6] In order to identify molecules with selective activity against non-small-cell lung cancer (NSCLC), the most prevalent form of lung cancer, 6500 natural product fractions were screened against a panel of 17 comprehensively annotated NSCLC cell lines.[7] Analysis of the results from this screen revealed a series of natural product fractions that demonstrated selective activity against a subset of these lines at 5 μg/mL.

Herein we describe the isolation of metabolites from a cytotoxic fraction from a Streptomyces sp. (strain SNE-011). Analysis of the active fraction by LC-UV-MS showed it contained one main peak with the molecular weight of 347 and a UV profile suggestive of a substituted phenyl ring (Figure S1). Bioassay-guided chemical investigation resulted in the isolation of three new arylamine derivatives (1–3), which we have named carpatamides A–C. These compounds possess a novel amide structure consisting of an amino-phenylpropionic acid core and an unsaturated fatty acid chain. This aromatic substitution pattern has been previously encountered only in manumycin derivatives from Streptomyces parvulus,[8a,8b] although there are a large number of phenylpropionic acid-containing natural products reported.[8c−8f] Compounds 1 and 3 exhibited moderate cytotoxicity against non-small-cell lung cancer cell lines HCC366, A549, and HCC44, but no activity against H2122.

Marine-derived bacterium SNE-011 was isolated from a sediment sample collected from Kiawah Island, South Carolina, and isolated on a seawater-based humic acid medium. Analysis by 16S rRNA sequence revealed SNE-011 to be a Streptomyces sp. with closest identity (98%) to S. carpaticus. After identification of an active fraction in the library, a large-scale (10 L) shake fermentation was carried out to obtain sufficient material for full chemical and biological analysis of the metabolites. The excreted metabolites were collected using XAD-7-HP resin, and the resulting extract was purified by a combination of solvent/solvent extraction and reversed-phase flash chromatography to give fractions that showed cytotoxicity. Final purification by Sephadex LH-20 and gradient reversed-phase HPLC gave carpatamides A (1, 10.5 mg), B (2, 15.1 mg), and C (3, 2.0 mg).

Carpatamide A (1) was obtained as a yellow oil. Its molecular formula was assigned as C19H25NO5 on the basis of a molecular ion peak at m/z 348.1805 [M + H]+ observed by HRESIMS. Analysis of the 1D NMR data for 1 revealed two carbonyls, four quaternary carbons, seven methines (six olefinic or aromatic), three methylenes, and three methyls (one oxygenated) (Table 1). The 1H NMR spectrum showed four coupled signals at δH 6.16 (H-11, d, J = 14.9 Hz), 7.25 (H-12, dd, J = 14.9, 10.9 Hz), 6.26 (H-13, dd, J = 14.9, 10.6 Hz), and 6.15 (H-14, dt, J = 14.9, 7.2 Hz), due to a conjugated diene in the all E-configuration. The contiguous COSY correlations extending from H-11 through the H3-17 and H3-18 methyl groups, along with the HMBC correlations from H-12 to the C-10 carbonyl (δC 167.3), indicated the presence of a 7-methylocta-2,4-dienoic acid residue (Figure 1). The COSY correlation of H2-7 to H2-8 as well as HMBC correlations from H-3 to C-1 and C-5, H-6 to C-2 and C-4, H2-7 to C-3, C-5, and C-9, H2-8 to C-4, and 9-OCH3 to C-9 indicated the presence of a 1,2,4,5-tetrasubstituted benzene unit (Figure 1). COSY and HMBC correlations confirmed a methyl propionate residue was connected at C-4 (Figure 1). A combination of 13C NMR, examination of exchangeable protons, and chemical derivatization allowed us to determine C-1, C-2, and C-5 were substituted by −OH, −NHR, and −OH, respectively. In particular, the downfield 13C chemical shifts of C-1 (δC 149.7) and C-5 (δC 155.0) suggested oxygen substitution, while the shift of C-2 (δC 119.0) was indictive of −N-acyl substitution. In order to verify the 7-methylocta-2,4-dienoic acid residue was attached to the nitrogen at C-2, the HMBC spectrum was measured in DMSO-d6. HMBC correlations from an exchangeable proton (δH 9.50) to C-1, C-2, C-3, and C-10 were observed (Figure 1), thus verifying the assignment. Finally, to confirm the C-1 and C-5 −OH substitution, methylation of 1 was carried out using TMS-CHN2 to yield compound 1a (Scheme 1). The LC-MS analysis showed the presence of two new methyl groups (Figure S2), while NMR analysis gave 1H chemical shifts of two methoxy groups at δH 3.89 (1-OCHH3, s) and 3.85 (5-OCHH3, s) and HMBC correlations from 1-OCHH3 to C-1 and from 5-OCHH3 to C-5 (Figure 1).

Table 1

1D and 2D NMR Data of Compound 1a

no.	δCb	δH, mult. (J in Hz)b	δCc	δH, mult. (J in Hz)c	COSY	HMBC
1	149.7, C		147.9, C
2	119.0, C		117.0, C
3	125.4, CH	7.11, s	123.9, CH	7.20, s		1, 2, 4, 5, 7
4	119.7, C		117.8, C
5	155.0, C		152.9, C
6	105.1, CH	6.37, s	103.6, CH	6.37, s		1, 2, 4, 5
7	26.5, CH2	2.79, t (7.9)	25.1, CH2	2.65, t (7.7)	8	3, 4, 5, 8, 9
8	35.2, CH2	2.58, t (7.9)	33.8, CH2	2.49, t (7.7)	7	4, 7, 9
9	175.7, C		173.0, C
10	167.3, C		164.1, C
11	122.5, CH	6.16, d (14.9)	122.8, CH	6.27, d (15.0)	12	10, 12, 13
12	143.4, CH	7.25, dd (14.9, 10.9)	140.5, CH	7.12, dd (15.0, 10.9)	11, 13	10, 11, 13, 14
13	130.9, CH	6.26, dd (14.9, 10.6)	129.7, CH	6.22, dd (15.0, 10.9)	12, 14	11, 12, 14, 15
14	143.7, CH	6.15, dt (14.9, 7.2)	141.5, CH	6.14, dt (15.0, 7.3)	13, 15	12, 13, 15, 16
15	43.4, CH2	2.09, t (6.9)	41.7, CH2	2.04, t (7.0)	14, 16	13, 14, 16, 17, 18
16	29.5, CH	1.72, m	27.8, CH	1.68, m	15, 17, 18	14, 15, 17, 18
17	22.7, CH3	0.93, d (6.7)	22.2, CH3	0.88, d (6.7)	16	15, 16, 18
18	22.7, CH3	0.93, d (6.7)	22.2, CH3	0.88, d (6.7)	16	15, 16, 17
2-NH				9.50, s		1, 2, 3, 10
9-OCHH3	52.0, CH3	3.64, s	51.3, CH3	3.57, s		9

Spectra were recorded at 600 MHz for 1H and 100 MHz for 13C using the corresponding solvent residual signal as internal standard.

Measured in CD3OD.

Measured in DMSO-d6.

Figure 1

Key correlations for the structural assignment of 1, 3, and 1a.

Scheme 1

Methylation of 1 with TMS-CHN2

Carpatamide B (2) was nearly identical to 1 by 1H and 13C NMR, with the molecular formula determined to be C18H23NO5, indicating that a −CH3 of 1 was replaced by a −H. Analysis of the 1H and 13C NMR spectra revealed that the methoxy signals at δH/C 3.64/52.0 in compound 1 disappeared. Thus, compound 2 was determined to be the carboxylic acid analogue of 1.

The molecular formula of carpatamide C (3) was determined to be C18H23NO4 based on the HRESIMS peak at m/z 318.1701 [M + H]+, one oxygen atom less than 2. The 1H and 13C NMR spectra (Table S1) of 3 were very similar to those of 2, with the exception that an oxygenated quaternary carbon signal (δC 155.0) in compound 2 was replaced by a methine signal at δC/H 125.4/6.90 in compound 3. The 1H NMR signals at δH 7.49 (d, J = 1.9 Hz), 6.90 (dd, J = 8.2, 1.9 Hz), and 6.79 (d, J = 8.2 Hz) of compound 3 indicated a 1,2,4-trisubstituted benzene system. Furthermore, the COSY and HMBC correlations confirmed this structure (Figure 1).

Compounds 1–3 were evaluated for their cytotoxicity against four NSCLC cell lines (HCC366, A549, HCC44, and H2122). Compound 1 showed cytotoxicity against the cell lines HCC366 with an IC50 of 2.8 μM, A549 with an IC50 of 4.1 μM, and HCC44 with an IC50 of 8.4 μM. 1 showed no activity up to 24 μM against H2122. Compound 3 exhibited cytotoxicity against the HCC366 and A549 cell lines, with IC50 values of 2.2 and 3.7 μM, respectively. Compound 2 did not show significant cytotoxicity against any of the four cell lines tested. We believe that 2 does not show activity against cancer cell lines due to an inability to penetrate cells. It is plausible that the methyl ester of 1 acts as a prodrug and is cleaved in cells to give the active pharmacophore.

Experimental Section

General Experimental Procedures

UV spectra were recorded on a Shimadzu UV-1601 UV–vis spectrophotometer. 1H and 2D NMR spectroscopic data were recorded at 600 MHz in CD3OD or DMSO-d6 solution on a Varian System spectrometer. 13C NMR spectra were acquired at 100 MHz on a Varian System spectrometer. Chemical shifts were referenced to the corresponding solvent residual signal (3.31/49.00 in CD3OD, 2.50/39.52 in DMSO-d6). High-resolution ESI-TOF mass spectra were provided by The Scripps Research Institute, La Jolla, CA. Low-resolution LC/ESIMS data were measured using an Agilent 1200 series LC/MS system with a reversed-phase C18 column (Phenomenex Luna, 150 mm × 4.6 mm, 5 μm) at a flow rate of 0.7 mL/min. Preparative HPLC was performed on an Agilent 1200 series instrument with a DAD detector, using a C18 column (Phenomenex Luna, 250 × 10.0 mm, 5 μm). Sephadex LH-20 (GE Healthcare, Sweden) and ODS resin (50 mm, Merck) were used for column chromatography. Artificial seawater was used in microbial fermentations as described in previous references.[9]

Collection and Phylogenetic Analysis of Strain SNE-011

The actinomycete Streptomyces sp. SNE-011 was isolated from a marine sediment sample collected from South Carolina (32°35′10″ N, 80°07′31″ W). Bacterial spores were collected via stepwise centrifugation as follows: 2 g of sediment was dried over 24 h in an incubator at 35 °C, and the resulting sediment added to 10 mL of seawater (sH2O) containing 0.05% Tween 20. After vigorous vortexing for 10 min, the sediment was centrifuged at 2500 rpm for 5 min (4 °C). The supernatant was removed, transferred into a new tube, and centrifuged at 18 000 rpm for 25 min (4 °C), and the resulting spore pellet was collected. The resuspended spore pellet (4 mL of sH2O) was plated on a humic acid medium (humic acid 10 g, peptone 2 g, MgSO4 0.5 g, FeSO4 0.01 g, and agar 15 g, dissolved in 1 L of seawater), giving rise to individual colonies of SNE-011 after 2 weeks. Analysis of the 16S rRNA sequence of SNE-011 revealed 98% identity to Streptomyces carpaticus. The sequence is deposited in GenBank under accession no. KJ174292.

Cultivation and Extraction

Bacterium SNE-011 was cultured in 10 2.8 L Fernbach flasks each containing 1 L of a seawater-based medium (10 g starch, 4 g yeast extract, 2 g peptone, 1 g CaCO3, 40 mg Fe2(SO4)3·4H2O, 100 mg KBr) and shaken at 200 rpm at 27 °C. After 7 days of cultivation, sterilized XAD-7-HP resin (20 g/L) was added to adsorb the organic products, and the culture and resin were shaken at 200 rpm for 2 h. The resin was filtered through cheesecloth, washed with deionized water, and eluted with acetone. The acetone-soluble fraction was dried in vacuo to yield 7.9 g of extract.

Purification

The extract of strain SNE-011 (7.9 g) was partitioned with hexanes, CH2Cl2, EtOAc, and MeOH/H2O. The hexanes and the CH2Cl2 extracts were combined to give an extract (750 mg). This extract was fractionated by flash column chromatography on ODS (50 μm, 30 g), eluting with a step gradient of MeOH and H2O (10:90–100:0), and 12 fractions (Fr.1–Fr.12) were collected. Fraction 10 (25.1 mg) was purified by reversed-phase HPLC (Phenomenex Luna, C18, 250 × 10.0 mm, 2.5 mL/min, 5 μm) using a gradient solvent system from 30% to 100% CH3CN (0.1% formic acid) over 20 min to afford compounds 3 (2.0 mg, tR = 17.4 min) and 1 (10.5 mg, tR = 18.4 min). The EtOAc extract (480 mg) was separated by flash column chromatography on ODS (50 μm, 30 g), eluting with a step gradient of MeOH and H2O (10:90–100:0), to give 15 fractions (Fr.1–Fr.15). Fractions 12 (45.5 mg) and 13 (11.7 mg) were combined and then separated by Sephadex LH-20, eluting with MeOH, to give 12 fractions. The subfraction 12-6 (22.9 mg) was purified by reversed-phase HPLC (Phenomenex Luna, C18, 250 × 10.0 mm, 2.5 mL/min, 5 μm) using a gradient solvent system from 30% to 100% CH3CN (0.1% formic acid) over 20 min to yield compound 2 (15.1 mg, tR = 16.0 min).

Carpatamide A (1):

yellow oil; UV (MeOH) λmax (log ε) 266 (4.02), 315 (3.77) nm; 1H and 13C NMR, see Table 1; ESIMS m/z 346.1 [M – H]−; HRESIMS m/z 348.1805 [M + H]+ (calcd for C19H26NO5, 348.1805).

Carpatamide B (2):

yellow oil; UV (MeOH) λmax (log ε) 273 (4.19), 314 (3.86) nm; 1H and 13C NMR, see Table S1; ESIMS m/z 332.1 [M – H]−; HRESIMS m/z 334.1650 [M + H]+ (calcd for C18H24NO5, 334.1649).

Carpatamide C (3):

yellow oil; UV (MeOH) λmax (log ε) 272 (3.94), 305 (3.62) nm; 1H and 13C NMR, see Table S1; ESIMS m/z 316.2 [M – H]−; HRESIMS m/z 318.1701 [M + H]+ (calcd for C18H24NO4, 318.1700).

Methylation of 1 with TMS-CH2N2

To a solution of 1 (1.0 mg) in MeOH (0.5 mL) was added 200 μL of TMS-CHN2 (2.0 M in Et2O) until a yellow color persisted upon addition. After allowing it to stir for 1 h, solvent was removed via a stream of N2, and the reaction mixture was analyzed via LC/MS (Figure S2). The reaction product was purified by reversed-phase HPLC (Phenomenex Luna, C18, 250 × 10.0 mm, 2.5 mL/min, 5 μm) using a gradient solvent system (solvents: A H2O + 0.1% formic acid; B CH3CN + 0.1% formic acid; gradient: 0 min, 30% B; 20 min, 100% B; 25 min, 100% B) to yield compound 1a (0.9 mg, tR = 22.0 min, 83% yield). Compound 1a, yellow oil; 1H NMR (600 MHz, CD3OD) δ 7.71 (s, 1H, H-3), 7.21 (dd, J = 14.9, 10.7 Hz, 1H, H-12), 6.65 (s, 1H, H-6), 6.26 (dd, J = 15.1, 10.9 Hz, 1H, H-13), 6.19 (d, J = 15.0 Hz, 1H, H-11), 6.15 (dt, J = 15.1, 7.3 Hz, 1H, H-14), 3.89 (s, 3H, 1-OCHH3), 3.85 (s, 3H, 5-OCHH3), 3.65 (s, 3H, 9-OCHH3), 2.83 (t, J = 7.7 Hz, 2H, H-7), 2.55 (t, J = 7.7 Hz, 2H, H-8), 2.09 (t, J = 7.0 Hz, 2H, H-15), 1.73 (m, 1H, H-16), 0.94 (d, J = 6.7 Hz, 6H, H-17/18); 13C NMR (100 MHz, CD3OD) δ 175.5 (C, C-9), 167.2 (C, C-10), 156.5 (C, C-5), 151.7 (C, C-1), 143.2 (CH, C-14), 142.9 (CH, C-12), 131.0 (CH, C-13), 125.6 (CH, C-3), 122.3 (CH, C-11), 121.1 (C, C-4), 120.5 (C, C-2), 96.6 (CH, C-6), 56.5 (CH3, 1-OCHH3), 56.2 (CH3, 5-OCHH3), 52.0 (CH3, 9-OCHH3), 43.4 (CH2, C-15), 35.3 (CH2, C-8), 29.6 (CH, C-16), 26.6 (CH2, C-7), 22.7 (2 × CH3, C-17/18); ESIMS m/z 374.2 [M – H]−.

Cytotoxicity Assays

Cell lines were cultured in 10 cm dishes (Corning, Inc.) in NSCLC cell-culture medium: RPMI/l-glutamine medium (Invitrogen, Inc.), 1000 U/mL penicillin (Invitrogen, Inc.), 1 mg/mL streptomycin (Invitrogen, Inc.), and 5% fetal bovine serum (Atlanta Biologicals, Inc.). Cell lines were grown in a humidified environment in the presence of 5% CO2 at 37 °C. For cell viability assays, HCC366, A549, HCC44, and H2122 cells (60 μL) were plated individually at a density of 1200, 750, and 500 cells/well, respectively, in 384-well microtiter assay plates (Bio-one; Greiner, Inc.). After incubating the assay plates overnight under the growth conditions described above, purified compounds were dissolved and diluted in DMSO and subsequently added to each plate with final compound concentrations ranging from 50 μM to 1 nM and a final DMSO concentration of 0.5%. After an incubation of 96 h under growth conditions, Cell Titer Glo reagent (Promega, Inc.) was added to each well (10 mL of a 1:2 dilution in NSCLC culture medium) and mixed. Plates were incubated for 10 min at room temperature, and luminescence was determined for each well using an Envision multimodal plate reader (PerkinElmer, Inc.). Relative luminescence units were normalized to the untreated control wells (cells plus DMSO only). Data were analyzed using the Assay Analyzer and Condoseo modules of the Screener Software Suite (GeneData, Inc.) as described previously.[10]