The Advantage of Automatic Peer-Reviewing of 13C-NMR Reference Data Using the CSEARCH-Protocol

Antimicrobial Dihydroflavonols and Isoflavans Isolated from the Root Bark of Dalbergia gloveri

Three new dihydroflavonols, gloverinols A-C (1-3), a new flavon-3-ol, gloverinol D (4), two new isoflavans, gloveriflavan A (5) and B (6), and seven known compounds were isolated from the root bark of Dalbergia gloveri. The structures of the isolates were elucidated by using NMR, ECD, and HRESIMS data analyses. Among the isolated compounds, gloverinol B (2), gloveriflavan B (6), and 1-(2,4-dihydroxyphenyl)-3-hydroxy-3-(4-hydroxyphenyl)-1-propanone (10) were the most active against Staphylococcus aureus, with MIC values of 9.2, 18.4, and 14.2 μM, respectively.

SimpleNMR: An interactive graph network approach to aid constitutional isomer verification using standard 1D and 2D NMR experiments

Despite progress in computer automated solutions, constitutional isomer verification by NMR using one- and two-dimensional data sets is still, in the main, a manual, user-intensive activity that is challenging for a number of reasons. These include the problem of simultaneously keeping track of the information from a number of separate NMR experiments and the difficulty of another researcher subsequently verifying the assignments made without having to independently repeat the whole analysis. This paper describes a graphical interactive approach that overcomes some of these problems. By using concepts used to visualise graph networks, we have been able to represent the NMR data in a manner that highlights directly the link between the different NMR experiments and the molecule of interest. Furthermore, by making the graph networks interactive, a user can easily validate and correct the assignment and understand the decisions made in arriving at the solution. We have developed a usable proof-of-concept computer program, 'simpleNMR', written in Python to illustrate the ideas and approach.

Antiviral Rotenoids and Isoflavones Isolated from Millettia oblata ssp. teitensis

Three new (1-3) and six known rotenoids (5-10), along with three known isoflavones (11-13), were isolated from the leaves of Millettia oblata ssp. teitensis. A new glycosylated isoflavone (4), four known isoflavones (14-18), and one known chalcone (19) were isolated from the root wood extract of the same plant. The structures were elucidated by NMR and mass spectrometric analyses. The absolute configuration of the chiral compounds was established by a comparison of experimental ECD and VCD data with those calculated for the possible stereoisomers. This is the first report on the use of VCD to assign the absolute configuration of rotenoids. The crude leaves and root wood extracts displayed anti-RSV (human respiratory syncytial virus) activity with IC50 values of 0.7 and 3.4 μg/mL, respectively. Compounds 6, 8, 10, 11, and 14 showed anti-RSV activity with IC50 values of 0.4-10 μM, while compound 3 exhibited anti-HRV-2 (human rhinovirus 2) activity with an IC50 of 4.2 μM. Most of the compounds showed low cytotoxicity for laryngeal carcinoma (HEp-2) cells; however compounds 3, 11, and 14 exhibited low cytotoxicity also in primary lung fibroblasts. This is the first report on rotenoids showing antiviral activity against RSV and HRV viruses.

Structure Elucidation of Secondary Metabolites: Current Frontiers and Lingering Pitfalls

Analytical methods allow for the structure determination of submilligram quantities of complex secondary metabolites. This has been driven in large part by advances in NMR spectroscopic capabilities, including access to high-field magnets equipped with cryogenic probes. Experimental NMR spectroscopy may now be complemented by remarkably accurate carbon-13 NMR calculations using state-of-the-art DFT software packages. Additionally, microED analysis stands to have a profound effect on structure elucidation by providing X-ray-like images of microcrystalline samples of analytes. Nonetheless, lingering pitfalls in structure elucidation remain, particularly for isolates that are unstable or highly oxidized. In this Account, we discuss three projects from our laboratory that highlight nonoverlapping challenges to the field, with implications for chemical, synthetic, and mechanism of action studies. We first discuss the lomaiviticins, complex unsaturated polyketide natural products disclosed in 2001. The original structures were derived from NMR, HRMS, UV-vis, and IR analysis. Owing to the synthetic challenges presented by their structures and the absence of X-ray crystallographic data, the structure assignments remained untested for nearly two decades. In 2021, the Nelson group at Caltech carried out microED analysis of (-)-lomaiviticin C, leading to the startling discovery that the original structure assignment of the lomaiviticins was incorrect. Acquisition of higher-field (800 MHz 1H, cold probe) NMR data as well as DFT calculations provided insights into the basis for the original misassignment and lent further support to the new structure identified by microED. Reanalysis of the 2001 data set reveals that the two structure assignments are nearly indistinguishable, underscoring the limitations of NMR-based characterization. We then discuss the structure elucidation of colibactin, a complex, nonisolable microbiome metabolite implicated in colorectal cancer. The colibactin biosynthetic gene cluster was detected in 2006, but owing to colibactin's instability and low levels of production, it could not be isolated or characterized. We used a combination of chemical synthesis, mechanism of action studies, and biosynthetic analysis to identify the substructures in colibactin. These studies, coupled with isotope labeling and tandem MS analysis of colibactin-derived DNA interstrand cross-links, ultimately led to a structure assignment for the metabolite. We then discuss the ocimicides, plant secondary metabolites that were studied as agents against drug-resistant P. falciparum. We synthesized the core structure of the ocimicides and found significant discrepancies between our experimental NMR spectroscopic data and that reported for the natural products. We determined the theoretical carbon-13 NMR shifts for 32 diastereomers of the ocimicides. These studies indicated that a revision of the connectivity of the metabolites is likely needed. We end with some thoughts on the frontiers of secondary metabolite structure determination. As modern NMR computational methods are straightforward to execute, we advocate for their systematic use in validating the assignments of novel secondary metabolites.

Deazaflavin cofactor boosts earthworms Henlea bioluminescence

The bioluminescence of Siberian earthworms Henlea sp. was found to be enhanced by two low molecular weight activators, termed ActH and ActS, found in the hot extracts. The fluorescence emission maximum of the activators matches the bioluminescence spectrum that peaks at 464 nm. We purified 4.3 and 8.8 micrograms of ActH and ActS from 200 worms and explored them using orbitrap HRMS with deep fragmentation and 1D/2D NMR equipped with cryoprobes. Their chemical structures were ascertained using chemical shift prediction services, structure elucidation software and database searches. ActH was identified as the riboflavin analoge archaeal cofactor F0, namely 7,8-didemethyl-8-hydroxy-5-deazariboflavin. ActS is a novel compound, namely ActH sulfated at the 3' ribityl hydroxyl. We designed and implemented a new four step synthesis strategy forActH that outperformed previous synthetic approaches. The synthetic ActH was identical to the natural one and activated Henlea sp. bioluminescence. The bioluminescence enhancement factor X was measured at different ActH concentrations and the Michaelis constant K_m = 0.22 ± 0.01 μM was obtained by nonlinear regression. At an excess of synthetic ActH, the factor X was saturated at X_max = 33.3 ± 0.5, thus opening an avenue to further characterisation of the Henlea sp. bioluminescence system. ActH did not produce bioluminescence without the luciferin with an as yet unknown chemical structure. We propose that ActH and the novel sulfated deazariboflavin ActS either emit the light of the Henlea sp. bioluminescence and/or accept hydride(s) donor upon luciferin oxidation.

NMR-Based Chromatography Readouts: Indispensable Tools to “Translate” Analytical Features into Molecular Structures

Gaining structural information is a must to allow the unequivocal structural characterization of analytes from natural sources. In liquid state, NMR spectroscopy is almost the only possible alternative to HPLC-MS and hyphenating the effluent of an analyte separation device to the probe head of an NMR spectrometer has therefore been pursued for more than three decades. The purpose of this review article was to demonstrate that, while it is possible to use mass spectrometry and similar methods to differentiate, group, and often assign the differentiating variables to entities that can be recognized as single molecules, the structural characterization of these putative biomarkers usually requires the use of NMR spectroscopy.

4a-methyl-dodecahydro-1H-pyrrolo[3,4-b]quinoline-6-one produced by Endophytic Fungi Aspergillus niger E12 obtained from Dodonaea viscosa Plant Leaves as a Novel Antibacterial Compound

Endophytic fungi were isolated from forty plant leaf samples from Gudiyam forest. The potent antibacterial strain Aspergillus niger E12 isolated from the plant Dodonaea viscosa showed maximal antibacterial activity against all the test organisms, viz., Staphylococcus aureus, Bacillus coagulans, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The production of the antibacterial compound was optimized using the yeast extract sucrose medium (2% YES) using response surface methodology (RSM). For the production, the optimal parameters were carbon/nitrogen (C:N) ratio, 9:1; temperature, 25 °C; pH, 5.7; incubation time, 240 h; and rpm, 30. A zone of inhibition of 19.33 mm was observed as maximal bioactivity against Pseudomonas aeruginosa. The antibacterial compound was purified by extraction with ethyl acetate, activity-guided fractionation, and preparative high-performance liquid chromatography (HPLC), gas chromatography-mass spectrometry (GC-MS), Fourier transform infrared (FTIR) spectroscopy, and nuclear magnetic resonance (NMR) studies showed that the Aspergillus niger E12 bioactive substance is 4a-methyl-dodecahydro-1H-pyrrolo [3,4-b] quinoline-6-one.

Sampling CASE Application for the Quality Control of Published Natural Product Structures

Structure elucidation with NMR correlation data is dicey, as there is no way to tell how ambiguous the data set is and how reliably it will define a constitution. Many different software tools for computer assisted structure elucidation (CASE) have become available over the past decades, all of which could ensure a better quality of the elucidation process, but their use is still not common. Since 2011, WebCocon has integrated the possibility to generate theoretical NMR correlation data, starting from an existing structural proposal, allowing this theoretical data then to be used for CASE. Now, WebCocon can also read the recently presented NMReDATA format, allowing for uncomplicated access to CASE with experimental data. With these capabilities, WebCocon presents itself as an easily accessible Web-Tool for the quality control of proposed new natural products. Results of this application to several molecules from literature are shown and demonstrate how CASE can contribute to improve the reliability of Structure elucidation with NMR correlation data.

Ecological and Pharmacological Activities of Polybrominated Diphenyl Ethers (PBDEs) from the Indonesian Marine Sponge Lamellodysidea herbacea

Two known Polybrominated Diphenyl Ethers (PBDEs), 3,4,5-tribromo-2-(2′,4′-dibromophenoxy)phenol (1d) and 3,4,5,6-tetrabromo-2-(2′,4′-dibromophenoxy)phenol (2b), were isolated from the Indonesian marine sponge Lamellodysidea herbacea. The structure was confirmed using ¹³C chemical shift average deviation and was compared to the predicted structures and recorded chemical shifts in previous studies. We found a wide range of bioactivities from the organic crude extract, such as (1) a strong deterrence against the generalist pufferfish Canthigaster solandri, (2) potent inhibition against environmental and human pathogenic bacterial and fungal strains, and (3) the inhibition of the Hepatitis C Virus (HCV). The addition of a bromine atom into the A-ring of compound 2b resulted in higher fish feeding deterrence compared to compound 1d. On the contrary, compound 2b showed only more potent inhibition against the Gram-negative bacteria Rhodotorula glutinis (MIC 2.1 μg/mL), while compound 1d showed more powerful inhibition against the other human pathogenic bacteria and fungi. The first report of a chemical defense by compounds 1d and 2b against fish feeding and environmental relevant bacteria, especially pathogenic bacteria, might be one reason for the widespread occurrence of the shallow water sponge Lamellodysidea herbacea in Indonesia and the Indo-Pacific.

Taxonomy-Focused Natural Product Databases for Carbon-13 NMR-Based Dereplication

The recent revival of the study of organic natural products as renewable sources of medicinal drugs, cosmetics, dyes, and materials motivated the creation of general purpose structural databases. Dereplication, the efficient identification of already reported compounds, relies on the grouping of structural, taxonomic and spectroscopic databases that focus on a particular taxon (species, genus, family, order, etc.). A set of freely available python scripts, CNMR_Predict, is proposed for the quick supplementation of taxon oriented search results from the naturaL prOducTs occUrrences database (LOTUS, lotus.naturalproducts.net) with predicted carbon-13 nuclear magnetic resonance data from the ACD/Labs CNMR predictor and DB software (acdlabs.com) to provide easily searchable databases. The database construction process is illustrated using Brassica rapa as a taxon example.