Computation assisted chemical study of photo-induced late-stage skeleton transformation of marine natural products towards new scaffolds with biological functions

Quan Xu Ye-Qing Du Pan-Pan Chen Yili Sun Ze-Nan Yang Hui Zhang Bencan Tang Hong Wang Jia Li Yue-Wei Guo Xu-Wen Li

Citation:  Quan Xu, Ye-Qing Du, Pan-Pan Chen, Yili Sun, Ze-Nan Yang, Hui Zhang, Bencan Tang, Hong Wang, Jia Li, Yue-Wei Guo, Xu-Wen Li. Computation assisted chemical study of photo-induced late-stage skeleton transformation of marine natural products towards new scaffolds with biological functions[J]. Chinese Chemical Letters, 2025, 36(5): 110141. doi: 10.1016/j.cclet.2024.110141 shu

Computation assisted chemical study of photo-induced late-stage skeleton transformation of marine natural products towards new scaffolds with biological functions

English

  • Late-stage skeleton transformation (LSST) of natural products, especially those with biological activities, is an effective strategy for constructing valuable derivatives compared to stepwise synthetic approaches. In recent years, selective C-H activation and bio-catalysis strategies have developed rapidly, enabling efficient late-stage editing of natural products [17]. Such skeleton transformation often undergoes the breaking and reorganization of bonds, sometimes involving complex cascade reactions [8]. It is worth mentioning that although the LSST strategies for natural products are fascinating organic transformation process, the relevant strategies are limited [9].

    Photochemical reaction can offer unique opportunities to achieve fast and efficient skeleton transformation of natural products by unlocking site-specific reactivities under generally mild reaction conditions [10]. Undoubtedly, the use of photochemical reaction is a powerful strategy that allows the transformation between two highly different natural product skeletons in a single step. To our knowledge, although some meaningful derivatives have been obtained by photochemical reaction of natural products in recent years [9, [11], [12]], there are still some issues need to be addressed on the photochemical study of natural products. This is mainly due to the complex structure of natural products, which leads to the multiple possible photoreaction sites [9,1315]. Therefore, it is important to understand the reaction mechanism for further prediction of possible products.

    Polycyclic furanobutenolide-derived norcembrane diterpenoids are a small class of marine natural products with multiple remoted stereogenic centers in their macrocyclic ring and a wide range of biological activities, mainly isolated from soft corals of the genus Sinularia [1619]. These bioactive metabolites have attracted extensive interests for total syntheses in recent years [2022]. In our previous investigation of the chemical composition of Hainan soft coral Sinularia sp., norcembrane diterpenoid yonarolide (1) was found to be easily converted into yonarolide A (2), featuring an unprecedented 5/6/4/4/7 pentacyclic ring skeleton, through a [2+2] photocycloaddition reaction under sunlight (Fig. 1) [23]. As a continuation of our previous work, we further investigated the chemical composition of Hainan soft coral Sinularia sp., and five polycyclic furanobutenolide-derived norditerpenoids were obtained, including 5-epi-sinuleptolide (3) [24], sinuleptolide (4) [24], 10-epi-gyrosanolide E (5) [23], norcembrene 5 (6) [23], and sinulin D (7) (Fig. 2) [23,25].

    Figure 1

    Figure 1.  Our previous work on [2+2] photoreaction from 1 to 2.

    Figure 2

    Figure 2.  Late-stage skeleton transformation of compound 3 and the structures of compounds 38 in this study.

    Herein, inspired by our previous study of the photoreaction of 1 via a [2+2] photocycloaddition towards 2 (Fig. 1), we report the LSST of 3 to 4 by a Norrish type I reaction, along with the acquisition of a novel product 8 with new 4,14-dioxabicyclo[10.2.1]pentadecane scaffold (Fig. 2), the reaction mechanism study by deuterium experiment and detailed density functional theory (DFT) calculation, as well as the substrate scope examination leading to the late-stage modification of these intriguing natural products and the configuration revision of sinulin D (7).

    To explore potantial new photo-products of polycyclic furanobutenolide-containing norditerpenoids, we first irradiated 3 in MeOH under 250 W long arc mercury lamp for 16 h, and a total of five products were obtained, with the yields shown in Table 1. Their structures were determined by 1D and 2D nuclear magnetic resonance (NMR) (the structure of 9 was determined by comparing 1H NMR with 8 and the structure of 11 was determined by comparing 1H NMR with 10). It is worth mentioning that 8 and 9 featuring a new 4,14-dioxabicyclo[10.2.1] pentadecane scaffold, which is a nice example of using the LSST strategy to obtain new natural products derivatives. In addition, we consider that in all photo-products, the Δ12 E/Z isomerization is due to the photoexcitation of Δ12, on the other hand, the photoexcitation of the C-6 carbonyl group lead to the C-5 chiral epimerization (products 4 and 11) and tetrahydrofuran ring opening (products 8 and 9 in methanol), which was consistent with the Norrish type I reaction. In fact, Norish type I cleavage occurs at the α-position of the excited carbonyl group, which generates acyl and alkyl radicals, followed by a series of reactions [26,27]. We next performed trapping experiment with 2,2,6,6-tetramethylpiperidinooxy (TEMPO) (Table S2 in Supporting information) and confirmed that our reaction involves radical intermediates, which is consistent with the feature of the Norrish type I reaction. Subsequently we investigated the effect of solvent on the reaction, dichloromethane (DCM) was shown to be more likely than MeCN to generate the Δ12 E/Z isomerization product 10, which was further confirmed by examining the product when the reaction underwent for 2 h (Fig. S1 in Supporting information). We also periodically monitored the 1H NMR spectra of the reaction when methanol and acetonitrile was used as the solvent (Figs. S2 and S3 in Supporting information). The gradual appearance process of each product within 16 h was visualized.

    Table 1

    Table 1.  The effects of solvent system on the reaction.a
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    To further investigate the generation mechanism of 8, we performed a deuterium experiment, and obtained a mixture of the deuterated products 12 and 13. By comparing the 1H NMR spetra of 12 and 13 with 8 (Fig. 3), the disappearance of H3–20 at 3.71 ppm (the chemical shift of H3–20 in 8) in 1H NMR confirmed that the methoxy group (CH3–20) in 8 was derived from the solvent methanol. In addition, the integral ratio of the H2–7 (chemical shift Ha-7: 2.46 ppm and Hb-7: 2.62 ppm) decreased from the original 2 to 1, which confirmed that the proton of methanol was transferred to one of the H2–7. Meanwhile, the integral ratio of Hb-7 and Ha-7 is 0.67 to 0.32 (2.32 includes the other two hydrogens), which means that the ratio of 12 to 13 is approximately 2 to 1. Furthermore, the 4 mass units more of 12 and 13 (407.1980 [M + Na]+) than that of 8 (381.1908 [M + H]+) in high resolution electrospray ionization mass spectroscopy (HR-ESI-MS) spectra confirmed that the H3–20 and H-7a (or H-7b) were involved in the conversion process. Therefore, we confirmed the formation of product 8 through a ketene intermediate [28].

    Figure 3

    Figure 3.  Deuterium experiment of Norrish type I reaction. The reaction was carried out under N2 protection with a 250 W long arc mercury lamp for 16 h in room temperature, methanol-d4 was used as solvent. 8 refers to purified compound 8.

    Based on the aforementioned experimental result, the isomerization process of 3 under irradiation was proposed (Fig. 4). In detail, the C-6 carbonyl group of 3 was excited under irradiation, and intersystem crossing (ISC) from 1n−π* to 3n−π*, followed by conformational relaxation to the stable excited state 3Int_1. Then 3Int_1 underwent α-cleavage to form acyl radicals and alkyl radicals by Norrish type I reaction to obtain diradical intermediate 3Int_2, with a Δ12 E/Z isomerization under irradiation at the same time. Subsequently, 3Int_1 could spontaneously release energy to form 3 and 10. 3Int_2 could undergo C-C rotation to become 3Int_3' easily, then 3Int_3' could be transformed into 4 and 11 through a diradical combination. Furthermore, diradical 3Int_2 underwent an internal hydrogen transfer to produce a ketene intermediate 1Int_4. 1Int_4 is with high reactivity, which could easily undergo an addition reaction with methanol, and then, the addition product of enol type would undergo keto-enol tautomerization to yield more stable esters 8 and 9.

    Figure 4

    Figure 4.  Proposed isomerization process of 3 under irradiation.

    To gain mechanistic insights into LSST of natural product 3, DFT and time-dependent DFT (TD-DFT) calculations were performed (Fig. 5) [29]. The TD-DFT calculations performed by using different functionals (M06–2X, B3LYP and CAM-B3LYP), and the excitation types of S1, T1 and T2 were by analyzed electron-hole analysis (Fig. 5A and Fig. S11 in Supporting information) [3032]. The results showed that Δ12 and C-6 carbonyl group can be easily excited, which means that they are the first or second triplet excited states, more likely to be obtained from S1 by ISC [33,34]. We consider that the excitation of Δ12 is responsible for the isomerization of the Δ12 of the photo-products, e.g., 9, 10 and 11, and we further investigated the condition after the C-6 carbonyl group excitation (Fig. 5B). The carbonyl group of 3Int_1 underwent α-cleavage to give 3Int_2, this process is controlled by transition structure 3TS_1 with free energy 2.7 kcal/mol above 3Int_1, in the transition state 3TS_1, the spin density was majorly shared by C5, C6, and O21. 3Int_3' and 3Int_2 can be converted quickly by 3Int_2', with activation barrier 6.7 kcal/mol. The radical of 3Int_3' attacks from the Si face to give 3Int_4'. When the two electrons in 3Int_4' spin in reverse to form open-shell singlet specie, the two radicals could directly combine and form 4. For the formation of product 8, the α hydrogen of the acyl radical in 3Int_2 was captured by the alkyl radical to form 3Int_3, the transition state 3TS_2 of this process is with a free energy of 18.7 kcal/mol higher than 3Int_2. In the transition state 3TS_2, the spin density was majorly shared by C5, C6, C7 and O21. Then, the formation of the ketene intermediate 1Int_4 was accomplished by the release of energy in 3Int_3. Finally, with the aid of methanol, 1Int_4 could be transformed into the thermodynamic product 8.

    Figure 5

    Figure 5.  (A) TD-DFT calculation the photoreactive site of compound 3 at the 6–311+G(d, p)/PCM(MeOH) level. (a) Excitation type of T1, (b) optimized T1, (c) excitation type of T2 and (d) optimized T2. (B) DFT calculated free energy surface for the C-5 chiral epimerization and H-abstraction process of 3 (at the (U)ωB97X-D/def2-TZVPP/PCM(MeOH)//(U)M06–2X/6–31G(d)/PCM(MeOH) level of theory).

    In addition, we noted that the Δ12 excitation of compound 3 may also generate [2+2] photo-products similar to compound 2, for which we also calculated the [2+2] photoreaction of compound 1 to 2 as well as compound 3 (Figs. S5–S9 in Supporting information). The results showed that for compound 1 to form 2, the energy barrier is only 11.1 kcal/mol. However, for compound 3 to form [2+2] photo-product, the only feasible way need to overcome a high energy barrier of 23.5 kcal/mol (see Fig. S9 for detail). On the other hand, the calculations also showed that for compound 3, the formation of [2+2] photo-product has a higher energy barrier compared to the Norrish type I products.

    With the clear mechanism of the reaction in hand, we expected to increase the chemical diversity of photochemical products 8 and 9, which are rare macrocyclic ethers. Therefore, the other four natural norditerpenoids 4, 5, 6, and 7 were employed in an attempt to explore the universality of this reaction (Fig. 6A). Compounds 46 yield the photochemical ethers 8, 14 and 15. The structures of 8, 14 and 15 were elucidated by 2D NMR spectroscopic data analysis. However, instead of the expected 16, 7 produced 15, whose structure was determined by X-ray diffraction analysis, indicating that the C-8 configuration of the original structure of 7 should be wrong. The X-ray diffraction analysis confirmed that the C-8 absolute configuration of 15 was R, which implied that 6 and 7 should be C-5 epimers. To further verify our hypothesis, quantum NMR calculation of 7 (revised) and 7 (original) was subjected to the GIAO method, at the mPW1PW91/6–31+G(d, p) level, with the PCM model in chloroform (Fig. 6B) [35,36]. The result indicated that the calculated NMR data of (1R*, 5R*, 8R*)-7 (revised) were consistent with the experimental data, with a correlation coefficient R2 = 0.9993 and DP4+ probability of 100% [3739]. Therefore, we proposed that the correct absolute configuration of sinulin D (7) should be 1R, 5R, 8R.

    Figure 6

    Figure 6.  (A) Scope of polycyclic furanobutenolide-containing norditerpenoids. All reaction details are described in Supporting information 1.3.5. (B) Parameters of the calculated chemical shifts of revised-7 and original-7.

    Glucagon-like peptide 1 (GLP-1) is a peptide hormone produced and secreted by intestinal L-cells, which lowering postprandial blood glucose by binding the GLP-1 receptor to stimulate the insulin secretion from beta cells. It is a currently popular target for the obesity and type diabetes related drug discovery [4043]. In this study, the stimulation of GLP-1 secretion by the compounds 1, 2, 10, 14, and 15 at 20 µmol/L was evaluated and compared to that of INT777, a Takeda G-protein-coupled receptor 5 (TGR5, a GPCR receptor) agonist. Among these five compounds 10 and 15 could stimulate GLP-1 secretion significantly with no cell toxicity, and dose-dependently (Fig. 7 and Fig. S13 in Supporting information). In the mechanism study, compounds 10 and 15 exhibited significant stimulation of GLP-1 secretion by increasing intracellular calcium concentration dependent on the protein kinase A (PKA) pathway (the details bioactivity results are described in Supporting information 1.7.3).

    Figure 7

    Figure 7.  Effects of compounds 1, 2, 10, 14, and 15 on GLP-1 secretion in STC-1 cells. Left: effect of 1, 2, 10, 14, and 15 on GLP-1 secretion at 20 µmol/L STC-1 cells. Right: proposed mechanism for 10 and 15-stimulated secretion of GLP-1, drawn by Figdraw. The results are presented in the form of mean ± SEM (n = 3). The t-test was used to analyze the significance. P < 0.05, **P < 0.01, ***P < 0.001 vs. DMSO group. BAPTA-AM, a membrane permeable Ca2+ chelator; H89, a PKA inhibitor.

    In summary, inspired by our previous study of the photoreaction of 1 via a [2+2] photocycloaddition towards 2, we conducted a photo-induced late-stage skeleton transformation of the co-occurring compound 3 towards compounds 8 and 9 with new 4,14-dioxabicyclo[10.2.1]pentadecane skeleton. The biomimetic conversion of 3 to 4 was achieved meanwhile. A Norrish type I reaction mechanism was proposed based on the deuterium experiments and further confirmed by the DFT calculations. Subsequently, a substrate scope examination produced new skeleton derivatives 14 and 15, and further confirmed that the correct absolute configuration of 7 is 1R, 5R, 8R. All these findings not only enlarged the chemical space, but also gave us a clue for obtaining more new derivatives of bioactive natural products. Intriguingly, compounds 10 and 15 were found to stimulate the intracellular calcium and promote GLP-1 secretion in the PKA-dependent pathway, which could inspire the discovery of new metabolic disease-related drug leads from marine sources. The present work forms the first paradigm for efficient construction photo-induced late-stage skeleton transformation strategy of complex natural products through combination of quataum chemistry calculation and experimental validation, which will give a perspective for efficient LSST of interesting natural products towards new bioactive compounds.

    The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

    Quan Xu: Writing – original draft. Ye-Qing Du: Validation, Data curation. Pan-Pan Chen: Validation. Yili Sun: Validation. Ze-Nan Yang: Investigation. Hui Zhang: Data curation. Bencan Tang: Software. Hong Wang: Methodology. Jia Li: Funding acquisition. Yue-Wei Guo: Funding acquisition. Xu-Wen Li: Funding acquisition.

    We sincerely appreciate Prof. K. N. Houk at University of California and Dr. Yike Zou at Lawrence Livermore National Laboratory for the helpful suggestions and comments on our manuscript. We are grateful of the National Key Research and Development Program of China (Nos. 2021YFF0502400, 2022YFC2804100), the Natural Science Foundation of China (Nos. 82022069, 81991521, 42076099, 22171153, 81903682), Shandong Laboratory Program (No. SYS202205), Ningbo Natural Science Foundation Programme (No. 2022J171), the CAS Youth Interdisciplinary Team, and Taishan Scholars Program (Nos. tstp0648, tsqn202312302).

    Supplementary material associated with this article can be found, in the online version, at doi:10.1016/j.cclet.2024.110141.


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  • Figure 1  Our previous work on [2+2] photoreaction from 1 to 2.

    Figure 2  Late-stage skeleton transformation of compound 3 and the structures of compounds 38 in this study.

    Figure 3  Deuterium experiment of Norrish type I reaction. The reaction was carried out under N2 protection with a 250 W long arc mercury lamp for 16 h in room temperature, methanol-d4 was used as solvent. 8 refers to purified compound 8.

    Figure 4  Proposed isomerization process of 3 under irradiation.

    Figure 5  (A) TD-DFT calculation the photoreactive site of compound 3 at the 6–311+G(d, p)/PCM(MeOH) level. (a) Excitation type of T1, (b) optimized T1, (c) excitation type of T2 and (d) optimized T2. (B) DFT calculated free energy surface for the C-5 chiral epimerization and H-abstraction process of 3 (at the (U)ωB97X-D/def2-TZVPP/PCM(MeOH)//(U)M06–2X/6–31G(d)/PCM(MeOH) level of theory).

    Figure 6  (A) Scope of polycyclic furanobutenolide-containing norditerpenoids. All reaction details are described in Supporting information 1.3.5. (B) Parameters of the calculated chemical shifts of revised-7 and original-7.

    Figure 7  Effects of compounds 1, 2, 10, 14, and 15 on GLP-1 secretion in STC-1 cells. Left: effect of 1, 2, 10, 14, and 15 on GLP-1 secretion at 20 µmol/L STC-1 cells. Right: proposed mechanism for 10 and 15-stimulated secretion of GLP-1, drawn by Figdraw. The results are presented in the form of mean ± SEM (n = 3). The t-test was used to analyze the significance. P < 0.05, **P < 0.01, ***P < 0.001 vs. DMSO group. BAPTA-AM, a membrane permeable Ca2+ chelator; H89, a PKA inhibitor.

    Table 1.  The effects of solvent system on the reaction.a

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