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

Total Synthesis and Revision of Stereochemistry of a Natural Benzo[g]isochromene Stereodiad Isolated from Rubia philippinensis

This study presents a total synthesis and revision of the stereochemical configuration of the conformationally flexible natural product benzo[g]isochromene stereodiad alongside its diastereomeric counterparts. The highlights of the synthesis are the TiCl4-mediated diastereoselective aldol reaction, Pd-catalyzed lactonization, and Schmidt glycosidation. Our efforts using total synthesis disclosed herein proved that a previously assigned structure required revision.

Essentials in the acquisition, interpretation, and reporting of plant metabolite profiles

Plant metabolite profiling reveals the diversity of secondary or specialized metabolites in the plant kingdom with its hundreds of thousands of species. Specialized plant metabolites constitute a vast class of chemicals posing significant challenges in analytical chemistry. In order to be of maximum scientific relevance, reports dealing with these compounds and their source species must be transparent, make use of standards and reference materials, and be based on correctly and traceably identified plant material. Essential aspects in qualitative plant metabolite profiling include: (i) critical review of previous literature and a reasoned sampling strategy; (ii) transparent plant sampling with wild material documented by vouchers in public herbaria and, optimally, seed banks; (iii) if possible, inclusion of generally available reference plant material; (iv) transparent, documented state-of-the art chemical analysis, ideally including chemical reference standards; (v) testing for artefacts during preparative extraction and isolation, using gentle analytical methods; (vi) careful chemical data interpretation, avoiding over- and misinterpretation and taking into account phytochemical complexity when assigning identification confidence levels, and (vii) taking all previous scientific knowledge into account in reporting the scientific data. From the current stage of the phytochemical literature, selected comments and suggestions are given. In the past, proposed revisions of botanical taxonomy were sometimes based on metabolite profiles, but this approach ("chemosystematics" or "chemotaxonomy") is outdated due to the advent of DNA sequence-based phylogenies. In contrast, systematic comparisons of plant metabolite profiles in a known phylogenetic framework remain relevant. This approach, known as chemophenetics, allows characterizing species and clades based on their array of specialized metabolites, aids in deducing the evolution of biosynthetic pathways and coevolution, and can serve in identifying new sources of rare and economically interesting natural products.

Structural Revision of Tinotufolins from Tinospora crispa Leaves Guided by Empirical Rules and DFT Calculations

Clerodane diterpenes are a class of secondary metabolites that can be classified into four types according to the configuration of the H3-19/H-10-H3-17/H3-20 fragment, i.e., trans-cis (TC), trans-trans (TT), cis-cis (CC), and cis-trans (CT). Tinotufolins A-C and E (1a-3a and 5a), isolated from the leaves of Tinospora crispa, were previously elucidated as CT-type clerodanes; however, our established 13C NMR-based empirical rules and density functional theory calculations suggested that these clerodanes belong to the CC type. Therefore, tinotufolins A-F (1-6) were reisolated from the leaves of T. crispa, along with an undescribed compound 7 and known compounds 8-11, and their structures were established by extensive spectroscopic analyses. The structures of tinotufolins A-C and E were revised to CC-type 1-3 and 5, and undescribed compound 7 was established as a CC-type clerodane. The present study demonstrates that empirical rules and calculations can efficiently identify and revise erroneous structures in clerodane diterpenes.

Microbiome metabolite quantification methods enabling insights into human health and disease

Many of the health-associated impacts of the microbiome are mediated by its chemical activity, producing and modifying small molecules (metabolites). Thus, microbiome metabolite quantification has a central role in efforts to elucidate and measure microbiome function. In this review, we cover general considerations when designing experiments to quantify microbiome metabolites, including sample preparation, data acquisition and data processing, since these are critical to downstream data quality. We then discuss data analysis and experimental steps to demonstrate that a given metabolite feature is of microbial origin. We further discuss techniques used to quantify common microbial metabolites, including short-chain fatty acids (SCFA), secondary bile acids (BAs), tryptophan derivatives, N-acyl amides and trimethylamine N-oxide (TMAO). Lastly, we conclude with challenges and future directions for the field.

Structure Revision of Formyl Phloroglucinol Meroterpenoids: A Unified Approach Using NMR Fingerprinting and DFT NMR and ECD Analyses

NMR fingerprints are valuable tools for analyzing complex natural product mixtures and identifying incorrectly assigned structures in the literature. Our diagnostic NMR fingerprints for formyl phloroglucinol meroterpenoids revealed discrepancies in the structures reported for eucalyprobusal C (1a) and eucalypcamal K (2a). NMR fingerprinting PCA analyses identified 1a as an oxepine-diformyl phloroglucinol and 2a as an oxepine 3-acyl-1-formyl phloroglucinol, contrary to their initial assignments as pyrano-diformyl and pyrano 3-acyl-1-formyl phloroglucinols, respectively. Extensive reinterpretation of their reported one- and two-dimensional NMR data, coupled with GIAO DFT-calculated 1H and 13C NMR chemical shift and DP4+ analyses, supported the unequivocal reassignment of eucalyprobusal C to 1b and eucalypcamal K to 2b. The absolute configurations of the revised oxepine-containing phloroglucinol meroterpenoids were confirmed via the reinterpretation of their reported ROESY and NOESY NMR data, along with comparative TDDFT-calculated and experimental ECD spectra.

Nine New Antibacterial Diterpenes and Steroids from the South China Sea Soft Coral Lobophytum catalai Tixier-Durivault

Five new cembrane-type diterpenes, lobocalines A-E (1-5), and four new steroids, lobocaloids A-D (9-12), along with six known related compounds (6-8 and 13-15) were isolated from the Yalong Bay soft coral Lobophytum catalai Tixier-Durivault. The structures of the new compounds were elucidated by extensive spectroscopic analysis, NMR calculation with DP4+ analysis, time-dependent density functional theory-electronic circular dichroism (TDDFT-ECD) calculations, X-ray diffraction analyses and comparison with the reported spectroscopic data of known compounds. Further, with the aid of X-ray diffraction analysis, the structure of lobocrasol B (15) was firmly revised as 15a. In in vitro bioassays, compound 2 showed moderate antibacterial activities against fish pathogenic bacteria Streptococcus parauberis KSP28 and Phoyobacterium damselae FP2244 with minimum inhibitory concentration (MIC) values of 8.7 and 17.3 µg/mL, respectively. All the steroids exhibited antibacterial activities against the S. parauberis KSP28 with MIC values ranging from 12.3 to 53.6 µg/mL. Compounds 2, 7 and 14 have remarkable inhibitory effects on the hemolysin production of Staphylococcus aureus, while compounds 8-12 have medium inhibitory effects on the pyocyanin production in Pseudomonas aeruginosa.

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.

Four previously undescribed diketopiperazines from marine fungus Aspergillus puniceus FAHY0085 and their effects on liver X receptor α

Four previously undescribed diketopiperazine-type alkaloids including one oxepin-containing diketopiperazine-type alkaloid, oxepinamide L (1), three 4-quinazolinone alkaloids, puniceloids E-G (10-12), together with 12 known analogues, protuboxepin D (2), oxepinamides D-G, J-K and I (3-9), puniceloids B-D (13-15) and protubonine B (16), were isolated from the culture of the marine-derived fungus Aspergillus puniceus FAHY0085. The structures of the previously undescribed compounds were comprehensively elucidated by detailed interpretation of their NMR and HRESIMS data. Their absolute configurations were unambiguously determined by ROESY experiments, Marfey's method, calculated ECD experiments and single-crystal X-ray diffraction analysis. Compounds (3-4, 6-8, 14-15) were evaluated for their cytotoxic activity against HepG2, MCF-7, SW1116 and HeLa cells and compound 6 and 14 showed moderate cytotoxic activity against HeLa cells with IC50 49.61 ± 2.91 and 28.38 ± 1.57 μM, respectively. Compounds (1-8, 11-15) were screened for their transcriptional activation of liver X receptor α and compound 11 with known compounds 13-15 showed significant transcriptional activation of liver X receptor α with EC50 values in the range 2-50 μM.

Total Synthesis and Absolute Configuration Determination of the α-Glycosidase Inhibitor (3S,4R)-6-Acetyl-3-hydroxy-2,2-dimethylchroman-4-yl (Z)-2-Methylbut-2-enoate from Ageratina grandifolia

Herein, we report the first total synthesis of α-glycosidase inhibitor (3R, 4S)-6-acetyl-3-hydroxy-2,2-dimethylchroman-4-yl (Z)-2-methylbut-2-enoate as well as its enantiomer. Our synthesis confirms the chromane structure separately proposed by Navarro-Vazquez and Mata, on the basis of DFT computations. Furthermore, our synthesis allowed us to determine the absolute configuration of the natural compound as (3S, 4R) and not (3R, 4S).

Computational Structural Revision of Elaeophorbate and Other Triterpenoids with the Help of NAPROC-13. A New Strategy for Structural Revision of Natural Products

A considerable number of natural products have been published in recent years with misassigned structure, even though they had been correctly elucidated in the past. The availability of databases containing revised structures can prevent the amplification of errors in structural elucidation. NAPROC-13, a dereplication tool based on the ¹³C chemical shift, has been used to search for substances that, possessing the same chemical shifts, have been described with different structures. The correct structure of these different structural proposals is verified by computational chemistry. This paper reports the structural revision of nine triterpenoids following this methodology.

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.

Absolute configuration of cyclopropanes and the structural revision of pyrones from Marine-derived fungus Stagonospora sp. SYSU-MS7888

Two new cyclopropane derivatives (1-2) and seven undescribed α-pyrone derivatives (3-9), along with one known congener (10) were obtained from the marine fungus Stagonospora sp. SYSU-MS7888, which was isolated from the South China Sea. Their planar structures were established through extensive spectroscopic analyses including 1D and 2D NMR and HR-ESIMS. The absolute configurations were identified on basis of the quantum chemical calculations of ECD and NMR, as well as the modified Mosher's method. It's particularly noteworthy that the tetrasubstituted furopyrans, chenopodolans A-F, possessing phytotoxicity and zootoxicity, were structural misassignments. The structures of chenopodolans featuring with furopyran skeleton were revised as common trisubstituted α-pyrones by computational chemistry, NMR spectroscopic method, and empirical rule. Compounds 1, 2, 7, and 9 showed significant anti-inflammatory activity with IC₅₀ values ranging from 3.6 to 22.8 μM, which is better than the positive control indomethacin (IC₅₀ = 26.5 ± 1.13 μM). This discovery holds potential for the development of new anti-inflammatory agents.

Natural sesquiterpene quinone/quinols: chemistry, biological activity, and synthesis

Covering: 2010 to 2021Sesquiterpene quinone/quinols (SQs) are characterized by a C15-sesquiterpenoid unit incorporating a C6-benzoquinone/quinol moiety. Numerous unprecedented carbon skeletons have been constructed with various connection patterns between the two parts. The potent anti-cancer, anti-inflammatory, anti-microbial, anti-viral, and fibrinolytic activities of SQs are associated with their diverse structures. The representative avarol has even entered the stage of clinical phase II research as an anti-HIV agent, and was developed as paramedic medicine against psoriasis. This review provides an overall summary of 558 new natural SQs discovered between 2010 and 2021, including seven groups and sixteen structure-type subgroups, which comprehensively recapitulates their chemical structures, spectral characteristics, source organisms, biological activities, synthesis, and biosynthesis, aiming to expand the application scope of this unique natural product resource.

Intramolecular O···H Hydrogen Bonding of Salicylic Acid: Further Insights from O 1s XPS and 1H NMR Spectra Using DFT Calculations

Intramolecular hydrogen bonding (HB) is a complex phenomenon that extends beyond a simple valence event, affecting the core electrons of a molecule. Salicylic acid (SA) and its conformers provide an excellent model compound for studying intramolecular HB as the proton donor (H) and acceptor (O) can be toggled by rotating the C-O and C-C bonds to form up to seven potential conformers through various HB. In this study, we computationally investigated intramolecular interactions in SA conformers with and without such HB, by examining their calculated O 1s core electron-binding energy (CEBE) and ¹H NMR chemical shifts validated using recent measurements. The quantum mechanically stable SA conformers are fully defined by three rotatable bonds in the compound, which are abstracted as SA(η₁η₂η₃) digital structures, where η_i = 0 if the η_i angles match the most stable SA conformer (000) and η_i = 1 otherwise. Our findings suggest that the stability is dominated by the appearance of the intergroup intramolecular HB of H_p···O (where O is in the carboxylic acid functional group and H_p is the phenolic proton in -OH_p), and η₃ serves as a switch of such HB. As a result, the (η₁η₂0) SA conformers containing such H_p···O HB are more stable than other SA conformers (η₁η₂1) without such the H_p···O HB. The present density functional theory calculations reveal that this H_p···O HB results in splitting of the O 1s CEBEs of two hydroxyl groups (-OH) by up to 1 eV and deshielding the H_p proton ¹H NMR (δH_p) up to 11.68 ppm for the (η₁η₂0) conformers. Without such H_p···O HB, the O 1s XPS binding energies of two -OH groups will be closely located in the same band, and the ¹H NMR chemical shift of the H_p atom will be as small as an 4.09 ppm SA conformer [SA-G(101)]. The present study indicates that the O 1s CEBE splitting between two -OH groups serves as an indicator of the presence of the H_p···O HB in SA conformers, which is also supported by the ¹H NMR results.

Guided Isolation of An Uncommon Cembranoid Orthoester, Sarcotortin A, and Three Skeletal Diverse Terpenoids from the Hainan Soft Coral Sarcophyton tortuosum Based on Molecular Networking Strategy

Applying the emerging molecular networking strategy, an uncommon cembranoid orthoester, sarcotortin A (1), featuring a 3/14/8/5-fused scaffold, an unusual eunicellane-type diterpenoid, sarcotorolide A (2), and two new biscembranoids, ximaolides M and N (7 and 8), along with nine known terpenoids 3-6 and 9-13 were isolated from the Hainan soft coral Sarcophyton tortuosum. The structure and absolute configuration of all new compounds were established by a combination of spectroscopic data, X-ray diffraction analysis, and/or quantum chemical computational approaches. The plausible biogenetic relationship among these skeletally different terpenoids was proposed and discussed. In in vitro bioassay, new compound 7 exhibited a remarkable inhibitory activity against protein tyrosine phosphatases 1B (PTP1B) with the IC₅₀ value of 8.06 μM. In addition, compounds 4 and 10 displayed significant inhibitory effects on lipopolysaccharide (LPS)-induced inflammatory responses in RAW264.7 macrophages cells with the IC₅₀ values of 19.13 and 16.45 μM, respectively. Compound 9 showed interesting cytotoxicity against H1975, MDA-MB231, A549, and H1299 cancer cell lines with IC₅₀ values of 31.59, 34.96, 43.87, and 27.93 μM, respectively.

Future of computational molecular spectroscopy-from supporting interpretation to leading the innovation

Molecular spectroscopy measures transitions between discrete molecular energies which follow quantum mechanics. Structural information of a molecule is encoded in the spectra, which can be only decoded using quantum mechanics and therefore computational molecular spectroscopy becomes essential. In this review perspective, the role evolution of computational molecular spectroscopy has been discussed with several joint theory and experiment spectroscopic studies in the past decades, which includes rotational (microwave), vibrational and electronic spectroscopy (valence and core) of molecules. With the development in high resolution and computerized synchrotron sourced spectroscopy, spectral measurements and computational molecular spectroscopy need to be integrated for materials development. Contemporary computational molecular spectroscopy is, therefore, more than merely supporting interpretation but leading the innovation. Future development of molecular spectroscopy lies to identify the niche to integrate experimental and computational molecular spectroscopy. It also requires to engineer molecular spectroscopic databases that function according to the universal approaches of computing, such as those in a Turing machine, to be realized in a chemical and/or spectroscopic programable manner (digital twinning research) in the future.

Further undescribed cembranoids from South China Sea soft coral Sarcophyton ehrenbergi: Structural elucidation and biological evaluation

A detailed chemical investigation of the South China Sea soft coral Sarcophyton ehrenbergi has yield seven undescribed cembranoids, namely isoehrenbergol D and sarcoehrenolides F-K embodying a rare α,β-unsaturated-lactone moiety at C-6 to C-19, along with two known related compounds, ehrenbergol D and sarcoehrenolide A. Their structures and absolute configurations were unambiguously established in the light of extensive spectroscopic data analysis, modified Mosher's method, X-ray diffraction analysis, and quantum chemical computation method. In a bioassay for α-glucosidase inhibition, ehrenbergol D was evaluated as α-glucosidase inhibitor with an IC₅₀ value of 13.57 μM.

Computational Approaches to Enzyme Inhibition by Marine Natural Products in the Search for New Drugs

The exploration of biologically relevant chemical space for the discovery of small bioactive molecules present in marine organisms has led not only to important advances in certain therapeutic areas, but also to a better understanding of many life processes. The still largely untapped reservoir of countless metabolites that play biological roles in marine invertebrates and microorganisms opens new avenues and poses new challenges for research. Computational technologies provide the means to (i) organize chemical and biological information in easily searchable and hyperlinked databases and knowledgebases; (ii) carry out cheminformatic analyses on natural products; (iii) mine microbial genomes for known and cryptic biosynthetic pathways; (iv) explore global networks that connect active compounds to their targets (often including enzymes); (v) solve structures of ligands, targets, and their respective complexes using X-ray crystallography and NMR techniques, thus enabling virtual screening and structure-based drug design; and (vi) build molecular models to simulate ligand binding and understand mechanisms of action in atomic detail. Marine natural products are viewed today not only as potential drugs, but also as an invaluable source of chemical inspiration for the development of novel chemotypes to be used in chemical biology and medicinal chemistry research.

Total Syntheses of Nominal and Actual Prorocentin

The dinoflagellate-derived polyether prorocentin is a co-metabolite of the archetypical serine/threonine phosphatase inhibitor okadaic acid. Whereas a structural relationship cannot be missed and a biosynthetic link was proposed, it is currently unknown whether there is any parallel in the bioactivity profile of these natural products. However, it was insinuated in the past that the structure assigned to prorocentin might need to be revised. Indeed, re-examination of the published spectra cast doubts as to the constitution of the fused/spirotricyclic BCD-ring system in the core. To clarify this issue, a flexible synthesis blueprint was devised that allowed us to obtain the originally proposed structure as well as the most plausible amended structure. The key to success was late-stage gold-catalyzed spirocyclization reactions that furnished the isomeric central segments with excellent selectivity. The lexicon of catalytic transformations used to make the required cyclization precursors comprised a titanium-mediated ester methylenation/metathesis cascade, a rare example of a gold-catalyzed allylic substitution, and chain extensions via organocatalytic asymmetric aldehyde propargylation. A wing sector to be attached to the isomeric cores was obtained by Krische allylation, followed by a superbly selective cobalt-catalyzed oxidative cyclization of the resulting di-unsaturated alcohol with the formation of a 2,5-trans-disubstituted tetrahydrofuran; the remaining terminal alkene was elaborated into an appropriate handle for fragment coupling by platinum-catalyzed asymmetric diboration/oxidation. The assembly of the different building blocks to the envisaged isomeric target compounds proved that the structure of prorocentin needs to be revised as disclosed herein.

Chemistry and bioactivity of secondary metabolites from South China Sea marine fauna and flora: recent research advances and perspective

Marine organisms often produce a variety of metabolites with unique structures and diverse biological activities that enable them to survive and struggle in the extremely challenging environment. During the last two decades, our group devoted great effort to the discovery of pharmaceutically interesting lead compounds from South China Sea marine plants and invertebrates. We discovered numerous marine secondary metabolites spanning a wide range of structural classes, various biosynthetic origins and various aspects of biological activities. In a series of reviews, we have summarized the bioactive natural products isolated from Chinese marine flora and fauna found during 2000-2012. The present review provides an updated summary covering our latest research progress and development in the last decade (2012-2022) highlighting the discovery of over 400 novel marine secondary metabolites with promising bioactivities from South China Sea marine organisms.

New flexible cembrane-type macrocyclic diterpenes as TNF-α inhibitors from the South China Sea soft coral Sarcophyton mililatensis

A further study on the rarely reported soft coral Sarcophyton mililatensis disclosed five new flexible cembrane-type macrocyclic diterpenes sarcomililatols C-G (1-5) and two known analogues 6 and 7. The structures and absolute configurations of natural macrocyclic compounds 1-6 were established by the extensive spectroscopic analysis, X-ray diffraction analysis, time-dependent density functional theory/electronic circular dichroism (TDDFT ECD) calculations, chemical reaction, and modified Mosher's method. In the bioassays, the macrocyclic diterpene 2 exhibited potent TNF-α inhibition (IC₅₀ = 6.1 μmol/L), which was better than the positive control dexamethasone (IC₅₀ = 8.7 μmol/L), and no obvious cytotoxicity against RAW264.7 cells with CC₅₀ values over 50 μmol/L, indicating natural macrocyclic compound 2 could be served as a model compound to develop a new and prospective chemotype of an anti-inflammatory lead compound or drug candidate.

Polyoxygenated cembranoids from the South China Sea soft coral Sarcophyton boettgeri and their stereochemistry

Four new polyoxygenated cembranoids, namely sarcoboettgerol A (1), 12-epi-humilisin D (2), sarcoboettgerol B (3), and sarcoboettgerol C (4), together with one known related analogue, humilisin D (5), were isolated and characterized from the soft coral Sarcophyton boettgeri collected off Ximao island, Hainan Province, China. The structures and absolute configurations of the new compounds were determined by extensive spectroscopic data analyses, Cu kα single crystal X-ray diffraction analysis, and TDDFT-ECD calculations. A plausible biogenetic relationship of 3 and 4 was proposed.