Computation-Assisted Structural Elucidation of Epoxyroussoeone and Epoxyroussoedione Isolated from Roussoella japanensis KT1651

Highly Functionalized Spirobisnaphthalenes from Roussoella sp. KT4147

Highly functionalized spirobisnaphthalenes, preussomerins N (1) and O (2), and simpler compounds, such as 2,3-α-epoxypalmarumycin CP18 (3), 3α-hydroxy-CJ-12,372 (4), and 16 known structurally related congeners, were isolated from a culture broth of Roussoella sp. KT4147. Structural analysis revealed that 1 was a dimer of preussomerin G (6), connected by a nitrogen atom, and 2 was a derivative of 6 with a macommelin substructure. Preussomerin N (1) was considered to be biosynthetically derived via the Michael-type 1,4-addition of ammonia to 6, followed by another Michael addition to another molecule of 6. Contrarily, 2 was suggested to be derived through an endo-Diels-Alder cycloaddition between a diene derived from the (E)-enol form of macommelinal via an ene-reaction and dienophile 6. Compounds 1 and 2 exhibited potent cytotoxicity against COLO-201 human colorectal cancer cells.

Enantioselective Synthesis of Spiro-oxiranes: An Asymmetric Addition/Aldol/Spirocyclization Domino Cascade

Enantioenriched spiro-oxiranes bearing three contiguous stereocenters were synthesized using a rhodium-catalyzed asymmetric addition/aldol/spirocyclization sequence. Starting from a linear substrate, the cascade enabled the formation of a spirocyclic framework in a single step. sp² - and sp-hybridized carbon nucleophiles were found to be competent initiators for this cascade, giving arylated or alkynylated products, respectively. Derivatization studies demonstrated the synthetic versatility of both the epoxide and the alkyne moieties of the products. DFT calculations were used to reconcile spectroscopic discrepancies observed between the solution- and solid-state structures of the products.

Computer Assisted Structure Elucidation (CASE): Current and future perspectives

The first efforts for the development of methods for Computer-Assisted Structure Elucidation (CASE) were published more than 50 years ago. CASE expert systems based on one-dimensional (1D) and two-dimensional (2D) Nuclear Magnetic Resonance (NMR) data have matured considerably by now. The structures of a great number of complex natural products have been elucidated and/or revised using such programs. In this article, we discuss the most likely directions in which CASE will evolve. We act on the premise that a synergistic interaction exists between CASE, new NMR experiments, and methods of computational chemistry, which are continuously being improved. The new developments in NMR experiments (long-range correlation experiments, pure-shift methods, coupling constants measurement and prediction, residual dipolar couplings [RDCs]), and residual chemical shift anisotropies [RCSAs], evolution of density functional theory (DFT), and machine learning algorithms will have an influence on CASE systems and vice versa. This is true also for new techniques for chemical analysis (Atomic Force Microscopy [AFM], "crystalline sponge" X-ray analysis, and micro-Electron Diffraction [micro-ED]), which will be used in combination with expert systems. We foresee that CASE will be utilized widely and become a routine tool for NMR spectroscopists and analysts in academic and industrial laboratories. We believe that the "golden age" of CASE is still in the future.

2-Oxaspiro[4.5]decane and α-pyrenocine derivatives from the endophytic fungus Roussoella sp. PSU-H51

One new 2-oxaspiro[4.5]decane, roussoellide, and one new α-pyrenocine, 2',3'-dihydropyrenocine A, together with nine known compounds including known arthropsolide A, and pyrenocines A and E, were obtained from the culture broth of the endophytic fungus Roussoella sp. Their structures were determined using spectroscopic data. The absolute configuration of known arthropsolide A was assigned on the basis of X-ray diffraction data using Cu Kα radiation. Known pyrenocine A displayed weak cytotoxic activity against breast cancer (MCF-7) cells with an IC₅₀ value of 27.1 µM and weak antifungal activity against Microsporum gypseum SH-MU-4 with an MIC value of 615.2 µM.

Biofilm Inhibitory Abscisic Acid Derivatives from the Plant-Associated Dothideomycete Fungus, Roussoella sp

Roussoella species are well recorded from both monocotyledons and dicotyledons. As part of a research program to discover biologically active compounds from plant-associated Dothideomycetes in Thailand, the strain Roussoella sp. (MFLUCC 17-2059), which represents an undescribed species, was isolated from Clematis subumbellata Kurz, fermented in yeast-malt medium and explored for its secondary metabolite production. Bioassay-guided fractionation of the crude extract yielded the new abscisic acid derivative, roussoellenic acid (1), along with pestabacillin B (2), a related congener, and the cyclodipeptide, cyclo(S-Pro-S-Ile) (3). The structure of 1 was determined by 2D NMR spectroscopy and HR-ESIMS data analysis. Compounds 1 and 2 showed inhibitory activity on biofilm formation by Staphylococcus aureus. The biofilm formation of S. aureus was reduced to 34% at 16 µg/mL by roussoellenic acid (1), while pestabacillin B (2) only showed 36% inhibition at 256 µg/mL. In addition, compound 1 also had weak cytotoxic effects on L929 murine fibroblasts and human KB3-1 cancer cells.

Cyclohelminthols Y1-Y4 Metabolites Possessing Two Spirocyclopropanes in Their Structure

Cyclohelminthols Y1-Y4 (1-4) were isolated from the culture broth of Helminthosporium velutinum yone96. These compounds are diastereomers to each other featuring 3-azabicyclo[3.1.0]hexane-6-spirocyclopentane linked with a cyclopentanespirocyclopropane framework. Their planar structures were established via the comparison of their spectra with the simpler analogue cyclohelminthol X as well as analysis of their HMBC spectra. Although the proton-deficient core frameworks of 1-4 prevented us from obtaining configurational information via conventional NMR analysis, their total structures involving the relative and absolute configurations were established using density functional theory (DFT)-based molecular modeling calculations. The present study demonstrates the effectiveness of the comparison between the theoretical and experimental δ¹³C values for stereochemical analysis by focusing on the carbons that show relatively large δ¹³C deviations among the isomers. The G-ring of these molecules most likely originates from the cyclopropanation of the C6C7 double bond with the carbene equivalent 6 derived from cyclohelminthol IV (7), which was isolated from the same producer fungus. Preliminary biological experiments revealed the potent cytotoxicity of the (6 S)-isomers against COLO201 cells, whereas the (6 R)-isomers exhibited weak activity. The antifungal assay with Cochiobolus miyabeanus showed a slightly different profile.

Epoxynemanione A, nemanifuranones A-F, and nemanilactones A-C, from Nemania serpens, an endophytic fungus isolated from Riesling grapevines

Ten polyketide specialized metabolites, epoxynemanione A, nemanifuranones A-F, and nemanilactones A-C, were isolated from the culture filtrate of Nemania serpens (Pers.) Grey (1821), an endophytic fungus from a Riesling grapevine (Vitis vinifera) found in Canada's Niagara region. Additionally, four known metabolites 2-(hydroxymethyl)-3-methoxy-benzoic acid, phyllostine, 5-methylmellein and a nordammarane triterpenoid were isolated. A related known metabolite 2,3-dihydro-2-hydroxy-2,4-dimethyl-5-trans-propenylfuran-3-one has also been included for structural and biological comparison to the nemanifuranones. The latter was isolated from the culture filtrates of Mollisia nigrescens, an endophytic fungus from the leaves and stems of lowbush blueberry (Vaccinium angustifolium) found in the Acadian forest of Nova Scotia, Canada. Their structures were elucidated based on 1D and 2D NMR, HRESIMS measurements, X-ray crystallographic analysis of nemanifuranone A, the nordammarane triterpenoid and 2,3-dihydro-2-hydroxy-2,4-dimethyl-5-trans-propenylfuran-3-one compounds, and comparison of NOE and vicinal ¹H-¹H coupling constants to literature data for relative stereochemical assignments. Nemanifuranone A possesses a rare C2 hemiacetal and was active against both Gram-negative and Gram-positive bacteria.

Neomacrophorin X, a [4.4.3]Propellane-Type Meroterpenoid from Trichoderma sp. 1212-03

Neomacrophorin X (1) was isolated from Trichoderma sp. 1212-03. Heteronuclear multiple bond correlation (HMBC) spectral analysis indicated a unique [4.4.3]propellane framework, which was verified by the ¹H and ¹³C chemical shift calculations based on density functional theory (DFT) and subsequent comparison with experimental data obtained in CDCl₃. The DFT-based electronic circular dichroism (ECD) calculations were effective in not only determining the absolute configuration but also confirming the relative structure. The predominant conformation of 1 was found to be solvent-dependent, with different conformations presenting different NMR and ECD profiles. Introduction of J-based analysis with a J-resolved HMBC aided in this investigation. This conformational alternation was reproduced by considering the solvation with the SM5.4 model in the calculation, although it was not sufficiently quantitative. Although the calculations without solvent effects suggested a conformer that satisfies the spectral profiles in CDCl₃, postcalculations with the SM5.4 solvation protocol stabilized the second major conformer, which reproduces the NMR and ECD profiles in polar solvents. Neomacrophorin X (1) is assumed to be biosynthesized by a coupling between the reduced form of anthraquinone and a neomacrophorin derivative. This hypothesis was supported experimentally by the isolation of pachybasin and chrysophanol, as well as acyclic premacrophorin (2), from the same fungus. Some biological properties of 1 are described.

Cyclohelminthol X, a Hexa-Substituted Spirocyclopropane from Helminthosporium velutinum yone96: Structural Elucidation, Electronic Circular Dichroism Analysis, and Biological Properties

Helminthosporium velutinum yone96 produces cyclohelminthol X (1), a unique hexa-substituted spirocyclopropane. Although its molecular formula and NMR spectral data resemble those of AD0157, being isolated from marine fungus Paraconiothyrium sp. HL-78-gCHSP3-B005, our detailed analyses disclosed a totally different structure. Chemical shift calculations and electronic circular dichroism spectral calculations were quite helpful to establish the structure, when those were performed based on density functional theory. The carbon framework of cyclohelminthols I-IV is found at the C1-C8 propenylcyclopentene substructure of 1. Thus, 1 is assumed to be biosynthesized by cyclopropanation between an oxidized form of cyclohelminthol IV and a succinic anhydride derivative 4. Cytotoxicity for two cancer cell lines and proteasome inhibition efficiency are measured.

Synergistic Combination of CASE Algorithms and DFT Chemical Shift Predictions: A Powerful Approach for Structure Elucidation, Verification, and Revision

Structure elucidation of complex natural products and new organic compounds remains a challenging problem. To support this endeavor, CASE (computer-assisted structure elucidation) expert systems were developed. These systems are capable of generating a set of all possible structures consistent with an ensemble of 2D NMR data followed by selection of the most probable structure on the basis of empirical NMR chemical shift prediction. However, in some cases, empirical chemical shift prediction is incapable of distinguishing the correct structure. Herein, we demonstrate for the first time that the combination of CASE and density functional theory (DFT) methods for NMR chemical shift prediction allows the determination of the correct structure even in difficult situations. An expert system, ACD/Structure Elucidator, was used for the CASE analysis. This approach has been tested on three challenging natural products: aquatolide, coniothyrione, and chiral epoxyroussoenone. This work has demonstrated that the proposed synergistic approach is an unbiased, reliable, and very efficient structure verification and de novo structure elucidation method that can be applied to difficult structural problems when other experimental methods would be difficult or impossible to use.