Characterization by Empirical and Computational Methods of Dictyospiromide, an Intriguing Antioxidant Alkaloid from the Marine Alga Dictyota coriacea

ABSTRACT:

The challenging structural motif of dictyospiromide (1), a spirosuccinimide alkaloid with antioxidant properties that are associated with activation of the Nrf2/ARE signaling pathway, was assigned using contemporary NMR experiments complemented with anisotropic NMR, chiroptical, and computational methodologies. Anisotropic NMR parameters provided critical orthogonal verification of the configuration of the difficult to assign spiro carbon and the other stereogenic centers in 1.

Graphical Abstract

Recent advances in spectroanalytical techniques and computational methods have improved the accuracy and ability to make structure assignments for small molecules of unknown constitution. These advanced capabilities are particularly important in the structural definition of new natural products, which often contain novel molecular architecture and functional group arrays. NMR experiments utilizing newly developed pulse sequences have provided additional tools for structure elucidation,¹ while modifications in 2D data acquisition and processing such as nonuniform sampling (NUS) techniques increase both the resolution and sensitivity of these experiments.² In addition to conventional NMR approaches, anisotropy-based NMR measurements of residual dipolar coupling (RDC) and residual chemical shift anisotropy (RCSA) provide an orthogonal means to define and confirm both the structural framework and configuration of new compounds.³ Improved quantum mechanics based computational methods such as density functional theory (DFT) calculations of chemical shifts,⁴ coupling constants,⁵ chiroptical properties,⁶ and anisotropy parameters⁷ can be employed in combination with experimental spectroscopic measurements to define challenging structures that previously required an alternative approach such as X-ray analysis or synthesis.^3e,f

Marine brown algae of the genus Dictyota are a rich source of unusual diterpenes with diverse skeletons, many of which are biologically active.⁸ The potential of these metabolites as cytoprotectants against oxidative stress has generally not been evaluated, so specimens of Dictyota coriacea from the East China Sea were collected and analyzed. Fractionation of the EtOAc extract provided a diterpenoid metabolite with a unique carbon and nitrogen structural scaffold (Figure 1a) that was named dictyospiromide (1). Compound 1 had a molecular formula of C₂₂H₃₃NO₄ based on HRMS data, which required seven degrees of unsaturation. The ¹³C NMR spectrum displayed 22 carbon signals including two carbonyls and six additional sp² carbons, which indicated that 1 was bicyclic. Comprehensive 1D and 2D NMR analysis (see the Supporting Information for details) allowed assignment of a substituted 2-azaspiro[4.4]nonane-1,3-dione moiety for dictyospiromide (1), which represents a novel diterpenoid skeleton.

Figure 1.

(a) Structure of dictyospiromide (1) and (b) key NOEs.

The relative configurations at C-3, C-4, C-6, and C-10 in 1 were determined by NOESY analysis (Figure 1b). NOESY correlations between H-3/H₃-17, H-4/H₃-17, and 4-OH/H-10 suggested the 3S*,4R*,10R* configuration—the latter was also supported by an observed NOE between H-9/H-11a/b, while a correlation between H-7/H-3 was indicative of 6S*. The large coupling (12.0 Hz) between 4-OH (δ_H 3.79, d, J = 12.0 Hz) and H-4 implied that rotation around the C-4/O bond was restricted due to a hydrogen bond between 4-OH and the C-18 carbonyl. This required that C-18 and 4-OH were oriented on the same face of the cyclopentane ring in 1; thus, the relative configuration at C-2 was assigned as R*. The geometry of the exocyclic C-1/C-9 double bond was suggested to be E based on the deshielded chemical shift of H-9 (δ_H 7.33, s) and the absence of any NOE correlations between H-9/H-3, H-9/H-7, or H-9/H₃-20. With these data, it was possible to propose the constitution and configuration of 1, but a more rigorous analysis was needed.

Advances in DFT calculations and anisotropic NMR methods provided the means to orthogonally verify both the structure and relative stereochemistry of 1.^3,4 The ¹H and ¹³C chemical shifts of four isomers, a pair of diastereomers with different stereochemistry at the C-2 spiro carbon and the E/Z isomers of the 1-ene, i.e., 1E,2S (1a), 1Z,2S (1b), 1E,2R (1c), and 1Z,2R (1d), were calculated by DFT⁹ at the mPW1PW91/6–311+G(2d,p)//M06–2X/6–31+G(d,p) level of theory. The results (Table 1) indicated that the root-mean-square deviation (RMSD) and mean absolute error (MAE) values of the calculated ¹H chemical shifts of 1a, 1b, and 1c were very similar (0.16 and 0.12–0.13 ppm, respectively), while RMSD and MAE for 1d were significantly higher (0.33 and 0.21 ppm, respectively). Thus, on the basis of calculated ¹H chemical shifts, the stereochemistry remained ambiguous. Conversely, the RMSD and MAE of the calculated ¹³C chemical shifts gave better differentiating power, suggesting 1c as the best candidate, but the difference between the ¹³C RMSD of 1a and 1c (∼0.4 ppm) was not significant enough to draw an unambiguous conclusion. For a more rigorous chemical shift analysis DP4+ was utilized.¹⁰ Using only ¹H chemical shifts, the DP4+ analysis again afforded ambiguous results, but when ¹³C chemical shifts were incorporated the results clearly favored 1c as the correct isomer. However, the rather high ¹³C RMSD observed for all four isomers (1.91–2.65 ppm), coupled with the fact that both 1a and 1c have similar DP4+ probabilities when using only ¹H data, led us to conclude that stereochemical discrimination could not be considered definitive. Since DP4+ can sometimes produce false positives, we utilized anisotropic NMR methods to provide orthogonal confirmation of the stereochemistry at the spiro carbon and the exocyclic olefin.

Table 1.

Summary of DFT Chemical Shift RMSD and MAE Values Obtained for 1a–1d and DP4+ Probabilities for the Isomers

	1a: 1E,2S	1b: 1Z,2S	1c: 1E,2R	1d: 1Z,2R
1H RMSD (ppm)	0.16	0.16	0.16	0.33
1H MAE (ppm)	0.12	0.13	0.12	0.21
13C RMSD (ppm)	2.29	2.44	1.91	2.65
13C MAE (ppm)	1.74	1.74	1.34	1.93
DP4+ (1H) (%)	43.03	4.01	52.96	0
DP4+ (13C) (%)	0.06	0.06	99.88	0
DP4+ (1H + 13C) (%)	0.05	0	99.95	0

RCSA data can provide key stereochemical discrimination for quaternary carbons;¹¹ hence, the RCSA values of 1 were measured using PBLG [poly-γ-(benzyl-l-glutamate)] as the alignment medium,¹² and the chemical shift anisotropy tensors were calculated for all four isomers 1a, 1b, 1c, and 1d. Upon inspection of the 3D structures of the lowest energy conformers of each isomer (cutoff was set to ≥2% Boltzmann population) obtained from the DFT calculations, we observed that the core of the molecule was conformationally rigid, allowing a high degree of alignment among the selected superimposed conformers if the flexible side chains were not included in the analysis (Supporting Information). Thus, Q factors for each isomer were calculated using single tensor fitting of the experimental RCSA values of C-1–C-6, C-9–C-12, and C-17–C-20 vs the back-calculated RCSA values for the lowest energy conformer of each respective isomer. As illustrated in Figure 2, the lowest Q factor was obtained for isomer 1E,2R (1c) with a value of 0.097, followed by 1Z,2S (1b) with a Q factor of 0.138 (ratio 1b/1c = 1.423), 1E,2S (1a) with a Q factor of 0.196 (ratio 1a/1c = 2.021) and 1Z,2R (1d) with a Q factor of 0.234 (ratio 1d/1c = 2.412). These RCSA results further support that 1c is the correct structure for dictyospiromide, providing orthogonal evidence of the relative stereochemistry at the spiro carbon and the 1-ene double bond. The combined application of RCSA measurements, DFT chemical shift calculations, and analysis of proton coupling constant and NOE data provided consistent and complementary verification of the constitution and configuration of 1.

Figure 2.

Back-calculated vs experimentally measured ¹³C RCSA values for the (a) 1a, (b) 1b, (c) 1c, and (d) 1d isomers.

The absolute configuration at C-4 was determined by in situ generation of a metal-complexed auxiliary chromophore after addition of Rh₂(OCOCF₃)₄ to a CHCl₃ solution of 1 and measurement of the induced CD (ICD) spectrum. The sign of the E band (350 nm) in the ICD spectrum is indicative of the absolute configuration of secondary alcohols by applying Snatzke’s bulkiness rule;¹³ thus, the negative Cotton effect observed at 350 nm (Supporting Information) was in agreement with a 4R configuration. With these findings in hand, the absolute configurations at C-2, C-3, C-6, and C-10 were established as R, S, S, and R, respectively. Support for this assignment was provided by comparison of the experimentally recorded ECD spectrum of dictyospiromide (1) with DFT-calculated ECD spectra at the B3LYP/def2-TZVP level of theory for the four isomers of 1 [1a (1E,2S), 1b (1Z,2S), 1c (1E,2R), and 1d (1Z,2R)]. The measured ECD spectrum of 1 was very similar to the calculated spectrum for 1c (Figure 3).

Figure 3.

ECD spectrum of dictyospiromide (1) and calculated ECD spectra of four possible configurations 1a (1E, 2S), 1b (1Z, 2S), 1c (1E, 2R), and 1d (1Z, 2R).

Cells in aerobic environments have to contend with reactive oxygen species (ROS) and the resultant oxidative damage they produce, so numerous oxidative stress response mechanisms have evolved, including the production of antioxidant secondary metabolites. The cytoprotective effect of dictyospiromide (1) against H₂O₂-induced oxidative damage and toxicity in neuron-like PC12 cells was evaluated, and cell survival following treatment with 1 increased in a dose-dependent manner (Figure 4a). This was coupled with a reduction in H₂O₂-induced lactate dehydrogenase (LDH) production in cells treated with 1 at a concentration as low as 0.5 μM (Figure 4b). Release of LDH is an index of cell injury; thus, 1 is a potent cytoprotectant with antioxidant properties. Compound 1 was also investigated for activation of the Nrf2/ARE signaling pathway, which regulates the expression of genes involved in cellular antioxidant defense and is recognized as an important mediator of neuroprotection. The effect of 1 on nuclear translocation of Nrf2 was assessed, and both 1 (2 μM) and the positive control tert-butylhydroquinone (TBHQ, 2 μM) significantly enhanced accumulation of Nrf2 in the nucleus (Figure 4c), suggesting that 1 is a potent Nrf2 activator. In a Western blot assay for up-regulation of heme oxygenase-1 (HO-1) expression, an antioxidant protein regulated by Nrf2, 1 promoted HO-1 production in a dose-dependent manner comparable to that of TBHQ (Figure 4d). Nrf2 siRNA was applied to investigate if the antioxidant effect of 1 in PC12 cells is dependent on Nrf2. Cell viability in the control siRNA group (si Con) was increased by 1, while the cytoprotection was reversed by knockdown of Nrf2 (Figure 4e), indicating that Nrf2 contributes to the antioxidant effect of 1. Finally, the role of HO-1 in the cytoprotective effect of 1 was investigated using the HO-1 inhibitor zinc protoporphyrin (ZnPP). Cytoprotection provided by 1 was partially suppressed when 1 and the maximum noncytotoxic concentration of ZnPP were applied together, implying that HO-1 contributes to the antioxidant activity of 1 (Figure 4f). Thus, dictyospiromide (1) demonstrated a cytoprotective antioxidant effect in PC12 cells that involved activation of the Nrf2/ARE signaling pathway and enhanced expression of HO-1.

Figure 4.

Dictyospiromide (1) protects PC12 cells from oxidative damage by activating the Nrf2 signaling pathway. (a) 1 increased cell survival in a H₂O₂ damage model. TBHQ (2 μM) was used as the positive control. (b) 1 decreased LDH production after treatment with H₂O₂. (c) 1 induced Nrf2 nuclear translocation in cells stained with DAPI (blue) and Nrf2 antibody (red). (d) 1 up-regulated the expression of HO-1 protein in PC12 cells. (e) Down-regulation of Nrf2 expression by siRNA decreased the cytoprotective effect of 1. (f) Pretreatment with HO-1 inhibitor ZnPP suppressed the cytoprotective effects of 1.

In summary, combined application of contemporary spectroscopic and computational methods allowed unambiguous assignment of the constitution and configuration of the novel marine alkaloid dictyospiromide (1). Anisotropic NMR experiments provided orthogonal evidence for defining the stereochemistry of the difficult to define spiro ring junction and exocyclic olefin. Dictyospiromide (1) showed potent cytoprotective and antioxidant properties associated with activated Nrf2/ARE signaling, so its novel molecular scaffold could serve as a lead structure for the development of neuroprotective agents that reduce cellular oxidative stress.