Survey of marine natural product structure revisions: a synergy of spectroscopy and chemical synthesis

Ether-Diol Ambiguity: An Inconspicuous Issue in the Structure Elucidation of Oxygenated Natural Products

Tertiary and allylic hydroxyl groups readily eliminate water during positive ion mode mass spectrometry and may show similar NMR spectra to their corresponding ethers. In a routine structure elucidation workflow, these factors can cause researchers to incorrectly assign diol moieties as ethers or vice versa, leading to inaccurate chemical structures. After facing this problem during our work on oxygenated sesquiterpenoids from a Fusarium sp. fungal strain, we became aware of this challenging issue. We examined the literature for oxygenated natural products bearing these functional groups, and with the aid of density functional calculations of NMR chemical shifts, we now report the structures of 15 natural products that should be revised. We further establish that derivatizing sub-micromolar amounts of alcohols to their sulfates can be used to distinguish these from their corresponding ethers using liquid chromatography negative ion mode mass spectrometry. Finally, we isolated lignoren/cyclonerodiol from the Fusarium sp. culture extract and supported its revised identity as cyclonerodiol using this sulfation approach. Our results suggest that ether-diol ambiguity could be a prevalent issue affecting the structure elucidation of oxygenated natural products and highlight the importance of using complementary techniques, such as sulfation with LC-(-)-ESI-MS or density functional calculations of NMR chemical shifts.

Liquid-jet photoemission spectroscopy as a structural tool: site-specific acid-base chemistry of vitamin C

Liquid-jet photoemission spectroscopy (LJ-PES) directly probes the electronic structure of solutes and solvents. It also emerges as a novel tool to explore chemical structure in aqueous solutions, yet the scope of the approach has to be examined. Here, we present a pH-dependent liquid-jet photoelectron spectroscopic investigation of ascorbic acid (vitamin C). We combine core-level photoelectron spectroscopy and ab initio calculations, allowing us to site-specifically explore the acid-base chemistry of the biomolecule. For the first time, we demonstrate the capability of the method to simultaneously assign two deprotonation sites within the molecule. We show that a large change in chemical shift appears even for atoms distant several bonds from the chemically modified group. Furthermore, we present a highly efficient and accurate computational protocol based on a single structure using the maximum-overlap method for modeling core-level photoelectron spectra in aqueous environments. This work poses a broader question: to what extent can LJ-PES complement established structural techniques such as nuclear magnetic resonance? Answering this question is highly relevant in view of the large number of incorrect molecular structures published.

HSQC Spectra Simulation and Matching for Molecular Identification

In the pursuit of improved compound identification and database search tasks, this study explores heteronuclear single quantum coherence (HSQC) spectra simulation and matching methodologies. HSQC spectra serve as unique molecular fingerprints, enabling a valuable balance of data collection time and information richness. We conducted a comprehensive evaluation of the following four HSQC simulation techniques: ACD/Labs (ACD), MestReNova (MNova), Gaussian NMR calculations (DFT), and a graph-based neural network (ML). For the latter two techniques, we developed a reconstruction logic to combine proton and carbon 1D spectra into HSQC spectra. The methodology involved the implementation of three peak-matching strategies (minimum-sum, Euclidean-distance, and Hungarian distance) combined with three padding strategies (zero-padding, peak-truncated, and nearest-neighbor double assignment). We found that coupling these strategies with a robust simulation technique facilitates the accurate identification of correct molecules from similar analogues (regio- and stereoisomers) and allows for fast and accurate large database searches. Furthermore, we demonstrated the efficacy of the best-performing methodology by rectifying the structures of a set of previously misidentified molecules. This research indicates that effective HSQC spectral simulation and matching methodologies significantly facilitate molecular structure elucidation. Furthermore, we offer a Google Colab notebook for researchers to use our methods on their own data (https://github.com/AstraZeneca/hsqc_structure_elucidation.git).

Temperature-Controllable Liquid Crystalline Medium for Stereochemical Elucidation of Organic Compounds via Residual Chemical Shift Anisotropies

The configuration elucidation of organic molecules continues to pose significant challenges in studies involving stereochemistry. Nuclear magnetic resonance (NMR) techniques are powerful for obtaining such structural information. Anisotropic NMR techniques, such as measurement of residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs), complementing isotropic NMR parameters, provide relative configuration information. RCSAs provide valuable structural information, especially for nonprotonated carbons, yet have been severely underutilized due to the lack of an easily operational alignment medium capable of rapid transition from anisotropic to isotropic environments, especially in aqueous conditions. In this study, an oligopeptide-based alignment media (FK)4 is presented for RCSA measurements. Temperature variation manipulates the assembly of (FK)4, yielding tunable anisotropic and isotropic phases without the requirement of any special devices or time-consuming correction procedures during data analysis. Decent observed ΔΔRCSA values from sp3 carbons benefit the utilization of RCSA measurements in the structural elucidation of organic molecules highly composed with sp3 carbons. Moreover, the (FK)4 alignment medium is applicable for both RDC and RCSA measurements in one sample, further advancing the configuration analysis of molecules of interest.

Relative stereochemical determination of the C61-C83 fragment of symbiodinolide using a stereodivergent synthetic approach

Structural determination is required in the use of marine natural products to create novel drugs and drug leads in medicinal chemistry. Symbiodinolide, which is a polyol marine natural product with a molecular weight of 2860, increases the intracellular Ca2+ concentration and exhibits inhibitory activity against cyclooxygenase-1. Seventy percent of the structure of symbiodinolide has been stereochemically clarified. Herein, we report the elucidation of the relative configuration of the C61-C83 fragment, which is among the remaining thirty percent, using a stereodivergent synthetic strategy. We first assigned the relative configuration of the C61-C74 fragment. Two candidate diastereomers of the C61-C74 fragment were synthesized, and their NMR data were compared with those of the natural product, revealing the relative stereochemistry of this component. We then narrowed down the candidate compounds for the C69-C83 fragment from 16 possible diastereomers by analyzing the NMR data of the natural product, and we thus selected eight candidate diastereomers. Stereodivergent synthesis of the candidates for this fragment and comparison of the NMR data of the natural product and the eight synthetic products resulted in the relative stereostructural clarification of the C69-C83 fragment. These individually determined relative stereochemistries of the C61-C74 and C69-C83 fragments were connected via the common C69-C73 tetrahydropyran moiety of the fragments. Finally, the relative configuration of the C61-C83 fragment of symbiodinolide was determined. The stereodivergent synthetic approach used in this study can be extended to the stereochemical determination of other fragments of symbiodinolide.

Penicitone: Structural Reassignment of a Proposed Natural Product Acid Chloride

The proposed structure for the natural product penicitone, which contained a chemically improbable acid chloride functional group, was reassigned to a more probable structure using a combination of chemical knowledge, computer-assisted structure elucidation, and DFT methods.

Road Map Toward Computer-Guided Total Synthesis of Natural Products. The Dysiherbol A Case Study: What if Serendipity Hadn't Intervened?

We present a computational study inspired by the story of dysiherbol A, a natural product whose putative structure was found incorrect through synthesis by a completely fortuitous event. While the carbon connectivity and chemical environment between both structures remain similar, the real dysiherbol A has a different molecular weight than that reported for the natural product. Had the synthesis groups not been favored by fortune, it could be speculated that a substantial amount of time and effort would have been required to solve the structural puzzle. Within the realm of computer-guided total synthesis of natural products, the question arose whether a synthesis group could have in silico reassigned the structure before embarking on the experimental adventure. To address this query, we evaluated some state-of-the-art computational procedures based on their computational demand and ease of implementation for nonexpert users with basic skills in computational chemistry (including HOSE, CASCADE, ANN-PRA, ML-J-DP4, DP4, and DP4+). While discussing the strengths and limitations of these methods, this case study provides a roadmap of what could be done before venturing into complex and time-demanding total synthesis projects.

Enhancing Efficiency of Natural Product Structure Revision: Leveraging CASE and DFT over Total Synthesis

Natural products remain one of the major sources of coveted, biologically active compounds. Each isolated compound undergoes biological testing, and its structure is usually established using a set of spectroscopic techniques (NMR, MS, UV-IR, ECD, VCD, etc.). However, the number of erroneously determined structures remains noticeable. Structure revisions are very costly, as they usually require extensive use of spectroscopic data, computational chemistry, and total synthesis. The cost is particularly high when a biologically active compound is resynthesized and the product is inactive because its structure is wrong and remains unknown. In this paper, we propose using Computer-Assisted Structure Elucidation (CASE) and Density Functional Theory (DFT) methods as tools for preventive verification of the originally proposed structure, and elucidation of the correct structure if the original structure is deemed to be incorrect. We examined twelve real cases in which structure revisions of natural products were performed using total synthesis, and we showed that in each of these cases, time-consuming total synthesis could have been avoided if CASE and DFT had been applied. In all described cases, the correct structures were established within minutes of using the originally published NMR and MS data, which were sometimes incomplete or had typos.

Structural analysis of unusual alkaloids isolated from Narcissus pseudonarcissus cv. Carlton

Narciindole A, the first representative of Amaryllidaceae alkaloids with an indol-3-ylmethanone framework, was isolated from bulbs of Narcissus pseudonarcissus (L.) cv. Carlton, together with carltonine D and carltonine E, which share the same unusual structural motif as dimeric carltonine C (reported in 2020), exhibiting atropisomerism. Unambiguous structure elucidations have been achieved by NMR spectroscopy, HRMS, and comparison with literature data of related alkaloids. Furthermore, the chirality of known alkaloids with a galanthindole biaryl core was revised using optical rotation. Last, but not least, a biosynthetic pathway for dimeric carltonine-type alkaloids was proposed. Unfortunately, in terms of biological activity, the isolated alkaloids showed only moderate inhibition of human acetylcholinesterase and/or butyrylcholinesterase.

Attached Nitrogen Test by 13C-14N Solid-State NMR Spectroscopy for the Structure Determination of Heterocyclic Isomers

Differentiation of heterocyclic isomers by solution ¹H, ¹³C, and ¹⁵N NMR spectroscopy is often challenging due to similarities in their spectroscopic signatures. Here, ¹³C{¹⁴N} solid-state NMR spectroscopy experiments are shown to operate as an "attached nitrogen test", where heterocyclic isomers are easy to distinguish based on one-dimensional nitrogen-filtered ¹³C solid-state NMR. We anticipate that these NMR experiments will facilitate the assignment of heterocyclic isomers during synthesis and natural product discovery.

Reassignment of the structures of pestalopyrones A-D

Pestalopyrones A-D are four unusual tricyclic pyrone derivatives with flexible chiral structures, isolated from the endophytic fungus Pestalotiopsis neglecta S3. The full elucidation of their structures was a challenging task, and remained unsolved in the original article. Herein, the relative configurations of pestalopyrones A and pestalopyrones B were unambiguously assigned by detailed analyses on spectroscopic data and GIAO ¹³C NMR calculation method with sorted training sets (STS). The planar structures of pestalopyrones C and pestalopyrones D were revised by reinterpretation of their reported spectroscopic data, and then their relative configurations were deduced by STS GIAO ¹³C NMR calculation and NOE analysis. The absolute configurations of all the mentioned compounds were determined by the comparison of their experimental and calculated ECD curves.

NMR-Based Configurational Assignments of Natural Products: How Floating Chirality Distance Geometry Calculations Simplify Gambling with 2N-1 Diastereomers

Using NMR data, the assignment of the correct 3D configuration and conformation to unknown natural products is of pivotal importance in pharmaceutical and medicinal chemistry. In this report, we quantify the probability of configurational assignments to judge the quality of structural elucidations using Bayesian inference in combination with floating-chirality distance geometry simulations. Based on reference-free NOE/ROE data, residual dipolar couplings (RDCs), and residual quadrupolar couplings (RQCs) in various combinations, we demonstrate how the relative configurations of three natural compounds, namely, jatrohemiketal (1), artemisinin (2), and Taxol (3), can be unambiguously established without the necessity to carry out time-consuming DFT-based configurational and conformational analyses. Our results quantitatively describe how reliably molecular geometries can be inferred from experimental NMR data, thereby unequivocally unveiling remaining assignment ambiguities. The methodology presented here will dramatically reduce the risk of incorrect structural assignments based on the overinterpretation of incomplete data and DFT-based structure models in chemistry.

Pitfalls in the structural elucidation of small molecules. A critical analysis of a decade of structural misassignments of marine natural products

Covering: July 2010 to August 2021This article summarizes more than 200 cases of misassigned marine natural products reported between July 2010 and August 2021, sorting out errors according to the structural elements. Based on a comparative analysis of the original and the revised structures, major pitfalls still plaguing the structural elucidation of small molecules were identified, emphasizing the role of total synthesis, crystallography, as well as chemical- and biosynthetic logic to complement spectroscopic data. Distinct "trends" in natural product misassignment are evident between compounds of marine and plant origin, with an overall much lower incidence of "impossible" structures within misassigned marine natural products.

Recent Achievements in Total Synthesis for Integral Structural Revisions of Marine Natural Products

A great effort to discover new therapeutic ingredients is often initiated through the discovery of the existence of novel marine natural products. Since substances produced by the marine environment might be structurally more complex and unique than terrestrial natural products, there have been cases of misassignments of their structures despite the availability of modern spectroscopic and computational chemistry techniques. When it comes to refutation to erroneously or tentatively proposed structures empirical preparations through organic chemical synthesis has the greatest contribution along with close and sophiscated inspection of spectroscopic data. Herein, we analyzed the total synthetic studies that have decisively achieved in revelation of errors, ambiguities, or incompleteness of the isolated structures of marine natural products covering the period from 2018 to 2021.

Self-assembly of Helical Polymers and Oligomers to Create Liquid Crystalline Alignment for Anisotropic NMR Parameters

The measurement of anisotropic residual dipolar couplings (RDCs) parameters for the structure elucidation of organic molecules relies on suitable alignment media. Employment of self-assembled liquid crystalline systems to create anisotropic alignment can be an effective way to realize aligned samples and acquire RDCs. This Mini-review highlights the recent advances on amino acid-based helical polymers and supramolecular oligomers forming rigid, rod-like structures that aggregate into ordered liquid crystalline phases, including amino acid-based helical polyisocyanides, polyacetylenes, polypeptides, and oligopeptides assembled alignment media. The methodology for the determination of anisotropic liquid crystals was briefly discussed, and a summary of recent research progress in the enantiodifferentiation of helical polymers aligned media was followed. In addition, the self-assembled mechanism of oligopeptides and their RDCs structural analysis were also described. This article is protected by copyright. All rights reserved.

Synthesis of a novel naphthalenone endoperoxide and structural elucidation by nuclear magnetic resonance spectroscopy and theoretical calculation

Sesquiterpene lactones are found in plants of Asteraceae family, and endoperoxides are known for their antimalarial activity. Structural elucidation is a relevant aspect; however, it is not uncommon to find incorrect or incomplete structural assignments in the literature. Calculations based in quantum mechanics are frequently used to compute ¹ H and ¹³ C NMR chemical shifts, and after comparing with the experimental data, the correct structure is established from diverse candidates. Targeting the synthesis of bioactive compounds, we envisaged the synthesis of a novel endoperoxide from the natural sesquiterpene lactone α-santonin (2). Photochemical transformation of α-santonin (2) to mazdasantonin (4) followed by photooxidation catalyzed by rose bengal afforded the novel endoperoxide 5. This new endoperoxide contains five stereogenic centers and is analogous to the antimalarial agent artemisinin (1). The relative configuration of the stereogenic centers of the endoperoxide were established by nuclear magnetic resonance (NMR) analyses and confirmed by theoretical calculations. All approaches were in complete agreement, and the structure of mazdasantonin endoperoxide was established as (3S,3aS,5aS,8R,9bS)-3,6,6-trimethyl-3,3a,4,5,8,9b-hexahydro-2H-5a,8-epidioxynaphtho[1,2-b]furan-2,7(6H)-dione.

NMR-Based Configurational Assignments of Natural Products: Gibbs Sampling and Bayesian Inference Using Floating Chirality Distance Geometry Calculations

Floating chirality restrained distance geometry (fc-rDG) calculations are used to directly evolve structures from NMR data such as NOE-derived intramolecular distances or anisotropic residual dipolar couplings (RDCs). In contrast to evaluating pre-calculated structures against NMR restraints, multiple configurations (diastereomers) and conformations are generated automatically within the experimental limits. In this report, we show that the "unphysical" rDG pseudo energies defined from NMR violations bear statistical significance, which allows assigning probabilities to configurational assignments made that are fully compatible with the method of Bayesian inference. These "diastereomeric differentiabilities" then even become almost independent of the actual values of the force constants used to model the restraints originating from NOE or RDC data.

A critical review on the use of DP4+ in the structural elucidation of natural products: the good, the bad and the ugly. A practical guide

Covering: 2015 up to the end of 2020Even in the golden age of NMR, the number of natural products being incorrectly assigned is becoming larger every day. The use of quantum NMR calculations coupled with sophisticated data analysis provides ideal complementary tools to facilitate the elucidation process in challenging cases. Among the current computational methodologies to perform this task, the DP4+ probability is a popular and widely used method. This updated version of Goodman's DP4 synergistically combines NMR calculations at higher levels of theory with the Bayesian analysis of both scaled and unscaled data. Since its publication in late 2015, the use of DP4+ to solve controversial natural products has substantially grown, with several predictions being confirmed by total synthesis. To date, the structures of more than 200 natural products were determined with the aid of DP4+. However, all that glitters is not gold. Besides its intrinsic limitations, on many occasions it has been improperly used with potentially important consequences on the quality of the assignment. Herein we present a critical revision on how the scientific community has been using DP4+, exploring the strengths of the method and how to obtain optimal results from it. We also analyze the weaknesses of DP4+, and the paths to by-pass them to maximize the confidence in the structural elucidation.

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.

Nitro and Other Electron Withdrawing Group Activated Ruthenium Catalysts for Olefin Metathesis Reactions

Advanced applications of the Nobel Prize winning olefin metathesis reaction require user-friendly and highly universal catalysts. From many successful metathesis catalysts, which belong to the two distinct classes of Schrock and Grubbs-type catalysts, the subclass of chelating-benzylidene ruthenium complexes (so-called Hoveyda-Grubbs catalysts) additionally activated by electron-withdrawing groups (EWGs) provides a highly tunable platform. In the Review, the origin of the EWG-activation concept and selected applications of the resulting catalysts in target-oriented synthesis, medicinal chemistry, as well as in the preparation of fine-chemicals and in materials chemistry is discussed. Based on the examples, some suggestions for end-users regarding minimization of catalyst loading, selectivity control, and general optimization of the olefin metathesis reaction are provided.

Biogenesis-Guided Synthesis and Structural Revision of Sarocladione Enabled by Ruthenium-Catalyzed Endoperoxide Fragmentation

Sarocladione is the first 5,10:8,9-diseco-steroid with a 14-membered macrocyclic diketone framework to have been isolated from a natural source. Herein we report a biomimetic synthesis of sarocladione in only two or seven steps from inexpensive, commercially available ergosterol. The key feature of this synthesis was a novel ruthenium-catalyzed endoperoxide fragmentation, which transformed various saturated endoperoxides into olefinic diketones by cleavage of two C-C bonds. This synthesis allowed us to unambiguously determine the structure of sarocladione and provided experimental support for its revised biosynthetic origin. This work also vividly demonstrates that consideration of the biogenesis is a powerful tool for elucidating the structures of natural products.

Elucidating natural product structures using a robust measurement of carbon residual chemical shift anisotropy combined with DFT

Determination of configurations and conformations is an important step in the structural characterization of small molecules. Apart from utilizing isotropic J-couplings and nuclear overhauser effect (NOEs) measured in isotropic solution, anisotropic Nuclear Magnetic resonance (NMR) data such as residual dipolar couplings and residual chemical shift anisotropies (RCSAs) were also used to elucidate complex small molecule structures. Measuring RCSA has always been historically difficult due to the isotropic shift effect accompanied by molecular alignment and therefore only occasionally applied in a few examples. Here, we present a robust measurement of carbon RCSAs using a smaller gel-stretching device to determine the structures of a few small molecules. A systematic study on how different density functional theory computed anisotropies of the chemical shift anisotropy tensors impact RCSA data interpretation has also been discussed. We also discuss the effect of utilizing various carbons as reference nuclei for RCSA data extraction as well as the orientation behavior of estrone in orthogonal alignment media.

Synthesis-Driven Stereochemical Assignment of Marine Polycyclic Ether Natural Products

Marine polycyclic ether natural products have gained significant interest from the chemical community due to their impressively huge molecular architecture and diverse biological functions. The structure assignment of this class of extraordinarily complex natural products has mainly relied on NMR spectroscopic analysis. However, NMR spectroscopic analysis has its own limitations, including configurational assignment of stereogenic centers within conformationally flexible systems. Chemical shift deviation analysis of synthetic model compounds is a reliable means to assign the relative configuration of "difficult" stereogenic centers. The complete configurational assignment must be ultimately established through total synthesis. The aim of this review is to summarize the indispensable role of organic synthesis in stereochemical assignment of marine polycyclic ethers.

Total Synthesis and Structural Reassignment of Laingolide A

The asymmetric total synthesis of four diastereomers of laingolide A was achieved, which led to the unambiguous assignment of the stereochemistry of the natural product. The salient features of the convergent, fully stereocontrolled approach were a copper-catalysed stereospecific Kumada-type coupling, a Julia-Kocienski olefination and an RCM/alkene migration sequence to access the desired macrocyclic enamide.

Rapid Approaches for Assignment of the Relative Configuration in 1-Oxygenated 1,2-Diarylpropan-3-ols by 1H NMR Spectroscopy

The structural elucidation of chiral molecules with more than one stereocenter is usually a tricky problem. In this paper, efficient ¹H NMR spectroscopic approaches for assigning the erythro and threo configurations of 1-oxygenated 1,2-diarylpropan-3-ols were developed. By analysis of the chemical shift differences of diastereotopic methylene H₂-3 (Δδ₃) in CDCl₃ or the chemical shift differences of H-1 and H-2 (Δδ_1,2) in methanol-d₄, deuterated dimethyl sulfoxide, and acetone-d₆, the configurations of 1-oxygenated 1,2-diarylpropan-3-ols can be rapidly and conveniently determined.

Total synthesis: the structural confirmation of natural products

This feature article highlights total synthesis as one of the reliable tools for the structural confirmation of natural products.

NMR Chemical Shift and Methylation of 4-Nitroimidazole: Experiment and Theory

Nitroimidazoles and derivatives are a class of active pharmaceutical ingredients (APIs) first introduced sixty years ago. As anti-infection agents, the structure–activity relationships of nitroimidazole compounds have been particularly difficult to study due to their low reduction potentials and unique electronic structures. In this study, we combine dynamic nuclear polarization (DNP)-enhanced solid-state (100K), solid-state (298K), and 1H-13C heteronuclear single quantum coherence (HSQC) solution-state NMR techniques (303K) with density functional theory (DFT) to study the 1H, 13C, and 15N chemical shifts of 4-nitroimidazole (4-NI) and 1-methyl-4-nitroimidazole (CH3-4NI). The 4-NI chemical shifts were observed at 119.4, 136.4, and 144.7ppm for 13C, and at 181.5, 237.4, and 363.0ppm for 15N. The measurements revealed that methylation (deprotonation) of the amino nitrogen N(1) of 4-NI had less effect (Δδ=−4.8ppm) on the N(1) chemical shift but was compensated by shielding of the N(3) (Δδ=11.6ppm) in CH3-4NI. The calculated chemical shifts using DFT for 4-NI and CH3-4NI agreed well with the experimental values (within 2%) for the imidazole carbons. However, larger discrepancies (up to 13%) were observed between the calculated and measured 15N NMR chemical shifts for the imidazole nitrogen atoms of both molecules, which indicate that effects such as imidazole ring resonant structures and molecular dynamics may also contribute to the nitrogen chemical environment.

Structure determination, correction, and disproof of marine macrolide natural products by chemical synthesis

Integration of chemical synthesis, NMR spectroscopy, and various analytical means is key to success in the structure elucidation of stereochemically complex marine macrolide natural products.

Total synthesis and complete configurational assignment of amphirionin-2

Amphirionin-2 is a linear polyketide metabolite that exhibits potent and selective cytotoxic activity against certain human cancer cell lines. We disclose herein the first total synthesis of amphirionin-2 and determination of its absolute configuration. Our synthesis featured an extensive use of cobalt-catalyzed Mukaiyama-type cyclization of γ-hydroxy olefins for stereoselective formation of all the tetrahydrofuran rings found in the natural product, and a late-stage Stille-type coupling for convergent assembly of the entire carbon backbone. Four candidate diastereomers of amphirionin-2 were synthesized in a unified, convergent manner, and their spectroscopic/chromatographic properties were compared with those of the authentic material. The present study culminated in the reassignment of the C5/C7 relative configuration, assignment of the C12/C18 relative configuration, and determination of the absolute configuration of amphirionin-2.

Total Synthesis and Structure Revision of (-)-Avicennone C

All four possible stereoisomers of the natural product (-)-avicennone C were synthesized using two different methods for ring closure. The absolute stereochemistry was elucidated unambiguously by comparison of the analytical data with those of the reported natural product and by single X-ray crystal diffraction of synthetic intermediates. The proposed structure needed to be revised with regard to the absolute configuration of the stereogenic center bearing the secondary hydroxyl group. The reported synthesis offers a flexible, selective, and efficient access to all possible stereoisomers and may be of value for the stereoselective synthesis of other epoxyquinone natural products.

Forwards and backwards - synthesis of Laurencia natural products using a biomimetic and retrobiomimetic strategy incorporating structural reassignment of laurefurenynes C-F

Laurefurenynes C-F are four natural products isolated from Laurencia species whose structures were originally determined on the basis of extensive nuclear magnetic resonance experiments. On the basis of a proposed biogenesis, involving a tricyclic oxonium ion as a key intermediate, we have reassigned the structures of these four natural products and synthesized the four reassigned structures using a biomimetic approach demonstrating that they are the actual structures of the natural products. In addition, we have developed a synthesis of the enantiomers of the natural products laurencin and deacetyllaurencin from the enantiomer of (E)-laurefucin using an unusual retrobiomimetic strategy. All of these syntheses have been enabled by the use of tricyclic oxonium ions as pivotal synthetic intermediates.

Route exploration and synthesis of the reported pyridone-based PDI inhibitor STK076545

The enzyme protein disulfide isomerase (PDI) is essential for the correct folding of proteins and the activation of certain cell surface receptors, and is a promising target for the treatment of cancer and thrombotic conditions. A previous high-throughput screen identified the commercial compound STK076545 as a promising PDI inhibitor. To confirm its activity and support further biological studies, a resynthesis was pursued of the reported β-keto-amide with an N-alkylated pyridone at the α-position. Numerous conventional approaches were complicated by undesired fragmentations or rearrangements. However, a successful 5-step synthetic route was achieved using an aldol reaction with an α-pyridone allyl ester as a key step. An X-ray crystal structure of the final compound confirmed that the reported structure of STK076545 was achieved, however its lack of PDI activity and inconsistent spectral data suggest that the commercial structure was misassigned.

Magnetically Induced Alignment of Natural Products for Stereochemical Structure Determination via NMR

Anisotropic NMR has gained increasing popularity to determine the structure and specifically the configuration of small, flexible, non-crystallizable molecules. However, it suffers from the necessity to dissolve the analyte in special media such as liquid crystals or polymer gels. Generally, small degrees of alignment are also caused by an anisotropic magnetic susceptibility of the molecule, for example, induced by aromatic moieties. For this mechanism, the alignment can be predicted via density functional theory. Here we show that both residual dipolar couplings and residual chemical shift anisotropies can be acquired from natural products without special sample preparation using magnetically induced alignment. On the two examples of the novel natural product gymnochrome G and the alkaloid strychnine, these data, together with the predicted alignment, yield the correct configuration with high certainty.

Relative configuration of micrograms of natural compounds using proton residual chemical shift anisotropy

3D molecular structure determination is a challenge for organic compounds or natural products available in minute amounts. Proton/proton and proton/carbon correlations yield the constitution. J couplings and NOEs oftentimes supported by one-bond ¹H,¹³C residual dipolar couplings (RDCs) or by ¹³C residual chemical shift anisotropies (RCSAs) provide the relative configuration. However, these RDCs or carbon RCSAs rely on 1% natural abundance of ¹³C preventing their use for compounds available only in quantities of a few 10’s of µgs. By contrast, ¹H RCSAs provide similar information on spatial orientation of structural moieties within a molecule, while using the abundant ¹H spin. Herein, ¹H RCSAs are accurately measured using constrained aligning gels or liquid crystals and applied to the 3D structural determination of molecules with varying complexities. Even more, deuterated alignment media allow the elucidation of the relative configuration of around 35 µg of a briarane compound isolated from Briareum asbestinum.

Determination of 3D molecular structures remains challenging for natural products or organic compounds available in minute amounts. Here, the authors determine the structure of complex molecules, including few micrograms of briarane B-3 isolated from Briareum asbestinums, through measurement of ¹H residual chemical shift anisotropy.

EBC-232 and 323: A Structural Conundrum Necessitating Unification of Five In Silico Prediction and Elucidation Methods

Structurally unique halimanes EBC-232 and EBC-323, isolated from the Australian rainforest plant Croton insularis, proved considerably difficult to elucidate. The two diastereomers, which consist an unusual oxo-6,7-spiro ring system fused to a dihydrofuran, were solved by unification and consultation of five in silico NMR elucidation and prediction methods [i.e., ACDLabs, olefin strain energy (OSE), DP4, DU8+ and TD DFT CD]. Structure elucidation challenges of this nature are prime test case examples for empowering future AI learning in structure elucidation.

Marine compounds targeting the PI3K/Akt signaling pathway in cancer therapy

Cancer is a disease characterized by overproliferation, including that due to transformation, apoptosis disorders, proliferation, invasion, angiogenesis and metastasis, and is one of the deadliest diseases. Currently, conservative chemotherapy is used for cancer treatment due to a lack of effective drugs. The PI3K/Akt signaling pathway plays a very essential role in the pathogenesis of many cancers, and abnormal activation of this pathway leads to abnormal expression of a series of downstream proteins, which ultimately results in the excessive proliferation of cancer cells. Therefore, the PI3K/Akt signaling pathway is a critical target in cancer treatment. Marine drugs have attracted much attention in recent years, and studies have found that many extracts from oceanic animals, plants and microorganisms or their metabolites exert antitumor effects, including antiproliferative effects or the induction of cell cycle arrest, apoptosis or autophagy. However, most anticancer targets and the mechanisms of marine compounds remain unclear. The great potential of the development of marine drugs provides a new direction for cancer treatment. This review focuses on marine compounds that target the PI3K/Akt signaling pathway for the prevention and treatment of cancer and provides comprehensive information for those interested in research on marine drugs.

Structure reassignment of two triterpenes with CASE algorithms and DFT chemical shift predictions

Two triterpenes (14S,17S,20S,24R)-25-hydroxy-14,17-cyclo-20,24-epoxy-malabarican-3-one (CEM, 1a) and (14S,17S,20S,24R)-20,24,25-trihydroxy-14,17-cyclomalabarican-3-one (CM, 2a) with a cyclobutane ring were reported, which have the same NMR data as ocotillone (1b) and gardaubryone C (2b), respectively. An incorrect structure might be reported. Therefore, the structure reanalysis of these triterpenes was achieved by CASE algorithm and DFT chemical shift predictions, and the results showed that the structures of CEM and CM might be incorrect. To further verify the structure of compound 1, the HMBC, ¹H-¹H COSY and HSQC-TOCSY spectra were employed. Herein, we revised the structure of CEM and CM, and our study also showed that CASE algorithm and DFT chemical shift predictions can hold the post of effective structure reassignment method.

Misassigned Polyoxygenated Sterols and Reassignments of Their Structures

This review will summarize the authors’ studies on the reassignments of structures of 9 natural polyoxygenated sterols (24 S)-24-ethylcholest-8-ene-3β,5α,6β,7α-tetrol (1), (24 S)-24-ethylcholest-8(14)-ene-3β,5α,6β,7α-tetrol (2), (22 E)-24-methylcholesta-8(14),22-diene-3β,5α,6β,7α-tetrol (3), 5β,6β-epoxy-(22 E)-ergosta-8,22-diene-3β,7β-diol (4), (22 E)-ergosta-7,22-diene-3β,5α,6β,9α,14α-pentol (5), 3β,5α,6β,8β,14α-pentahydroxy-(22 E)-ergost-22-en-7-one (6), 5β,6β-epoxy-24-methylenecholesta-8,24(28)-diene-3β,7α,11α-triol (7), 6β-acetoxy-(22 E)-10α-ergosta-7,22-diene-3β,5α-diol (8), and 8α,9α-epoxy-(22 E)-ergosta-6,22-diene-3β,5α,14α-triol (9). The structures of 1 to 9 have been reassigned as (24 S)-5α,6α-epoxy-24-ethylcholest-8-ene-3β,7α-diol (16), (24 S)-5α,6α-epoxy-24-ethylcholest-8(14)-ene-3β,7α-diol (17), 5α,6α-epoxy-(22 E)-ergosta-8(14),22-diene-3β,7α-diol (13), 5α,6α-epoxy-(22 E)-ergosta-8,22-diene-3β,7α-diol (12), (22 E)-ergosta-7,22-diene-3β,5α,6β,9α,14β-pentol (25), 5α,6α;8α,14α-diepoxy-3β-hydroxy-(22 E)-ergost-22-en-7-one (18), 5α,6α-epoxyergosta-8,24(28)-diene-3β,7α,11α-triol (21), 6β-acetoxy-(22 E)-ergosta-7,22-diene-3β,5α-diol (26), and 8α,14α-epoxy-(22 E)-ergosta-6,22-diene-3β,5α,9α-triol (28), respectively, from the results of careful reexamination of the published1H and13C NMR spectral data.

Vibrational optical activity for structural characterization of natural products

This review presents the recent progress towards elucidating the structures of chiral natural products and applications using vibrational optical activity (VOA) spectroscopy.