Setosol Structure Elucidation

February 28, 2025

by Mikhail Elyashberg, Leading Researcher, ACD/Labs

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Setosol

Okeke et al. [1] reported the isolation of a novel catechol, which they named setosol (1), from the fungus Pleiochaeta setosa. Its molecular formula of C₁₅H₁₆O₅ was determined from the ESI-MS spectrum.

1

Okeke et al. acknowledged that this structure was unique amongst natural products at that time. Indeed, such a ring system also appears to be unknown amongst synthetic compounds. In addition to its unprecedented ring system, setosol is also proposed to be an enol ether. Setosol was subsequently reported to be active against several fungal and bacterial strains. This compound was reisolated from Preussia isomera by Chen et al. who confirmed its anti-bacterial activity [2]. Setosol 1 has also been mentioned in a review without any further comment [3].

Having in mind the unusual properties mentioned of structure 1, Bates et al [4] performed its verification and subsequent revision to structure 2.

2

To verify structure 1, it was entered into Structure Elucidator Suite and the ¹³C chemical shifts were predicted using the incremental approach. The results are presented in Figure 1.

Figure 1. Results of ¹³C chemical shift prediction for the proposed structure of setosol. Each atom is colored to mark a difference between its experimental and calculated ¹³C chemical shifts. The green color represents a difference between 0 to 3 ppm, yellow >3 to 15 ppm, and red >15 ppm. The average deviation of predicted chemical shifts from experimental is denoted as d_I(¹³C). A maximum deviation is designated as max_d_I(¹³C).

The large d_I(¹³C) and max_d_I(¹³C) values clearly show that the proposed structure of setosol is incorrect. Though the authors[1] wrote that they used ¹H – ¹³C 2D NMR correlations for the structure elucidation, unfortunately, this information is absent from the article. If 2D NMR data were available as constraints, Structure Elucidator could be used for structure generation in standard mode. Therefore, to reveal a correct structure in a manageable timeframe, a molecular connectivity diagram containing the left (green) part of the benzene ring was created, leaving all the other atoms “free”, so all possible combinations can be explored.

Figure 2. The molecular connectivity diagram (MCD) of setosol. Hybridizations of carbon atoms are marked by corresponding colors: sp² – violet, sp³ – blue. Labels “ob” and “fb” are set to carbon atoms for which neighboring with heteroatom is either obligatory (ob) or forbidden (fb).

The structure generation was completed in 6 h 20 min, and 8,143,488 structures were produced from which 5783 remained after filtering and duplicate removal. The ¹³C NMR chemical shift predictions were performed for structures of the output file, and structures were ranked in increasing order of the average deviation value. The twelve top ranked structures are shown in Figure 3.

Figure 3. The twelve top ranked structures of the output file. ¹³C NMR chemical shift prediction was carried out using the HOSE code-based method, the neural networks, and the incremental approach. Average deviations of ¹³C NMR chemical shifts determined by these methods are denoted as d_A, d_N and d_I correspondingly. Each atom is colored to mark a difference between its experimental and calculated ¹³C NMR chemical shifts. The green color represents a difference between 0 to 3 ppm, yellow was >3 to 15 ppm, red > 15 ppm.

The top ranked structure #1 is compound 2, and its validity was confirmed by empirical DP4 probability calculations (see Figure 4) as well as by ¹³C chemical shift prediction using DFT based approach DU8 ML.

Figure 4. The three top ranked structures of the output file. The ¹³C NMR chemical shift prediction was carried out using the HOSE code-based method, the neural networks, and the incremental approach. Average deviations of ¹³C NMR chemical shifts determined by these methods are denoted as d_A, d_N and d_I correspondingly. Each atom is colored to mark a difference between its experimental and calculated ¹³C NMR chemical shifts. The green color represents a difference between 0 to 3 ppm, yellow was >3 to 15 ppm, red > 15 ppm. DP4_A(¹³C), DP4_N(¹³C) and DP4_I(¹³C) are the probability values that a given structure is correct.

It turned out that structure 2 corresponded to a known natural product, a biaryl ether, which was isolated earlier by several groups. Its structure was reliably established, and biological activity was studied. Comparison of NMR spectra of setosol with those corresponding to structure 2 confirmed the structure revision performed in the work. [1]

References

1. B. Okeke, M. Kaouadji, F. Seigle-Murandi, R. Steiman. (1994). Biosci, Biotech, Biochem., 58, 734-736.
2. H.-L. Chen, W.-T. Zhao, Q.-P. Liu, H.-Y. Chen, W. Zhao, D.-F. Yang, X.-L. Yang. (2020). Fitoterapia, 141, 104475.
3. Agudo-Jurado, F.; Reveglia, P.; Rubiales, D.; Evidente, A.; Barilli, E. (2023). Int. J. Mol. Sci., 24, 5116.
4. R. W. Bates, M. Elyashberg, A. G. Kutateladze, C. M. Williams. (2024). Eur. J. Org. Chem. e202400431. https://doi.org/10.1002/ejoc.202400431

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