Structural Revisions of Two Highly Aromatic Naphthoquinone-Derived Dimers Based on NMR Analysis, Computer-Assisted Structure Elucidation Methods, and Computations

Targeted isolation of isopentenyl flavonoids from Daphne giraldii Nitsche based on feature-based molecular networking and their cytotoxic activities

Isopentenyl flavonoids were important chemical components in Daphne giraldii Nitsche with significant cytotoxic activities against hepatocellular carcinoma cells in previous study. In this study, Feature-Based Molecular Networking was utilized to perform the targeted isolation of the phytochemical investigation of D. giraldii. As a result, five undescribed isopentenyl flavonoids (1, 2a/2b, 3, and 4) were isolated from D. giraldii. Their structures and configurations were established by comprehensive spectral analysis and comparing experimental ECD and calculated data. In addition, all isolated compounds were evaluated for cytotoxic activities against hepatocellular carcinoma HepG2 and Hep3B cell lines. Specifically, compound 2 exhibited significant cytotoxic activities with IC50 values of 11.63 ± 0.22 μM and 0.10 ± 0.02 μM, respectively.

Conformational Sampling in Computational Studies of Natural Products: Why Is It Important?

Conformational sampling is a vital component of a reliable computational chemistry investigation. With the aim of illustrating the importance of conformational sampling, and building awareness among new practitioners, we present a series of case studies that show how the quality and reliability of computational studies depend on undertaking a thorough conformer search. The examples are drawn from the most common types of research questions in natural products chemistry, but the fundamental principles apply more generally to computational studies of molecular structure and behavior in any field of chemistry.

Hydroxyl-Amide Alkaloids from Pepper Roots: Potential Sources of Natural Antioxidants and Tyrosinase Inhibitors

Pepper (Piper nigrum L.) is a widely used spice plant known for its fruits and roots, which serve as flavor enhancers in culinary applications and hold significant economic value. Despite the popularity of pepper fruits, their roots remain relatively understudied, with limited research conducted on their bioactive components. This study focused on discovering and separating the primary bioactive amide alkaloids found in pepper roots. The process involved using the antioxidant activity of crude fractions and the Global Natural Products Social Molecular Networking analysis platform. The process led to the discovery of 23 previously unknown hydroxyl-amide alkaloids. Notably, compounds 11, 12, and 14 showed excellent antioxidant activity, while compound 11 exhibited significant inhibitory effects on mushroom tyrosinase. Theoretical exploration of enzyme-ligand interactions was conducted through molecular docking and molecular dynamics simulation. The findings of this study highlight the potential of hydroxyl-amide alkaloids as antioxidant products and natural food preservatives in the pharmaceutical and food cosmetic industries.

Isolation of four new monoterpenes from Ailanthus altissima (mill.) Swingle and their enzyme inhibitory effects

A phytochemical study of the ethanol extract from Ailanthus altissima (Mill.) Swingle leaves resulted in the isolation of four new monoterpenoids (1-3, 5). The structures were elucidated using HRESIMS data, NMR spectroscopic data, quantum chemical calculations for NMR and ECD, and custom DP4+ probability analysis. Additionally, the absolute configuration of sugar was determined by acid hydrolysis. Compounds 1-4 are cyclogeraniane monocyclic monoterpenes, while compound 5 contains an acyclic mycrane monoterpenes skeleton. Anti-tyrosinase, anti-acetylcholinesterase, and anti-butyrylcholinesterase activities were tested. Compound 1 showed notable anti-acetylcholinesterase activity, and compound 3 exhibited significant inhibitory effects on anti-tyrosinase activity. Furthermore, the potential binding sites of compounds 1 and 3 were predicted by molecular docking.

Bioassay-Guided and DeepSAT-Driven Precise Mining of Monoterpenoid Coumarin Derivatives with Antifeedant Effects from the Leaves of Ailanthus altissima

Demand for the exploration of botanical pesticides continues to increase due to the detrimental effects of synthetic chemicals on human health and the environment and the development of resistance by pests. Under the guidance of a bioactivity-guided approach and HSQC-based DeepSAT, 16 coumarin derivatives were discovered from the leaves of Ailanthus altissima (Mill.) Swingle, including seven undescribed monoterpenoid coumarins, three undescribed monoterpenoid phenylpropanoids, and two new coumarin derivatives. The structure and configurations of these compounds were established and validated via extensive spectroscopic analysis, acetonide analysis, and quantum chemical calculations. Biologically, 5 exhibited significant antifeedant activity toward the Plutella xylostella. Moreover, tyrosinase being closely related to the growth and development of larva, the inhibitory potentials of 5 against tyrosinase was evaluated in vitro and in silico. The bioactivity evaluation results highlight the prospect of 5 as a novel category of botanical insecticide.

Monoterpenoid indole alkaloids from Melodinus axillaris W.T.Wang exhibit anti-inflammatory activities by inhibiting the NF-κB signaling pathways

ETHNOPHARMACOLOGICAL RELEVANCE

Melodinus axillaris W.T.Wang has been widely used as an important medicine in China. In the folk of China, its whole plant has been used for fractures, rheumatic heart disease, testitis, hernia, abdominal pain, and dyspepsia, etc. Despite its extensive use, there is a shortage of literature investigating the specific bioactive compounds and underlying mechanisms responsible for their anti-inflammatory effects. This knowledge gap serves as the primary impetus for conducting this study, which aims to shed light on the previously unexplored therapeutic potential of M. axillaris.

AIM OF THE STUDY

This study aims to investigate the material basis and potential mechanism of anti-inflammatory activity of M. axillaris.

MATERIALS AND METHODS

Compounds were isolated from the 95% ethanol extract of M. axillaris using a systematic phytochemical method. The structures were established by extensive spectroscopic analysis, including 1D and 2D NMR, HR-ESI-MS, ECD calculation, and DP4+ analysis. The anti-inflammatory activities of ethanol extract and compounds from M. axillaris were tested by an inflammation model of LPS-stimulated RAW264.7 cells in vitro. Western blot analysis was employed to evaluate the expressions of COX-2, iNOS, and NF-κB signaling pathways, aiming to elucidate the underlying mechanisms.

RESULTS

Eleven undescribed monoterpenoid indole alkaloids (MIAs), axillines A-K (1-11), along with thirteen known analogs were isolated from M. axillaris. Compound 1 was the first representative of vincadine alkaloid with unprecedented 6/5/9/6/6 skeletons. Compounds 1-11 and ethanol extract showed significant anti-inflammatory effects in vitro. Among them, compound 2 had the best activity of inhibiting NO release (IC50 = 3.7 ± 0.9 μM). Additionally, subsequent Western blot analysis revealed that 2 could significantly inhibit the up-regulation of NF-κB signaling pathways, iNOS, and COX-2 in LPS-stimulated RAW264.7 cells, thereby demonstrating its anti-inflammatory activity.

CONCLUSION

This study provides support for the traditional use of M. axillaris in terms of its anti-inflammatory properties and highlights the potential of MIAs as promising candidates for further development as anti-inflammatory drugs.

Two pairs of bioactive cyclohexene alkaloid enantiomers from the roots of Piper nigrum

Two pairs of cyclohexene amide alkaloid enantiomers were obtained from the root of Piper nigrum. Their plane structures were established by NMR and HRESIMS spectra. The absolute configurations of 1a/1b and 2a/2b were determined by the comparison between the experimental and calculated electronic circular dichroism (ECD) spectra. All identified compounds were tested for inhibitory effects on acetylcholinesterase (AChE) in vitro. Notably, compounds 1b and 2b showed strong inhibitory effects on AChE and the interaction between proteins and compounds was discussed by molecular docking studies.

Eight structurally diverse components with anti-acetylcholinesterase activity from Daphne bholua

Eight structurally diverse components, including six undescribed ones, (±)-daphuarin A (1a/1b), daphuarin B (2), daphuarin D-E (4-6), together with a pair of new natural products (±)-daphuarin C (3a/3b) were isolated from the herb of Daphne bholua Buch.-Ham. ex D. Don. Their planar structures were elucidated by extensive spectroscopic analyses. The configurations were established with the assistance of quantum chemical calculations, together with the Custom DP4+ method. The inhibitory potentials of all isolates against acetylcholinesterase were evaluated.

Isolation and characterization of seven neovibsane-type diterpenoids from Viburnum odoratissimum and their neuroblastoma cell protective effects

Seven undescribed neovibsane-type diterpenoids (1-7) were isolated from the leaves of Viburnum odoratissimum. Their planar structures and relative configurations were elucidated based on a combination of 1D and 2D NMR analysis. The absolute configurations were confirmed by Rh2(OCOCF3)4-induced ECD analysis and comparison of experimental and TDDFT-calculated ECD spectrum. Based on the empirical results of the ECD of in situ formed Rh-complexes, rapid determination of the absolute configuration of C-14 within vibsane-type diterpenoids was proposed. In addition, 3 exhibited a high neuroblastoma cell protective effect of 81.8 % at 50 μM (the control group showed a neuroblastoma cell protective effect of 56.2 % at 50 μM).

Target isolation of diverse sesquiterpenoid from the stems of Daphne genkwa based on molecular networking

Guiding by LC-MS/MS analysis and the Global Natural Products Social (GNPS) Molecular Networking, three undescribed sesquiterpenoids, stedapgens A-C, and two known analogues were discovered in the barks of Daphne genkwa Sieb. et Zucc. The structures were determined by analysis of their spectroscopic data and quantum-chemical calculations. All the isolated novel compounds were tested for their acetylcholinesterase inhibitory activities with IC50 = 0.754 ± 0.059, 0.696 ± 0.026, and 0.337 ± 0.023 μg/ml. Among them, stedapgen A displayed promising inhibitory activities against AChE, and the binding sites were predicted by molecular docking.

Expanded Application of Piper nigrum: Guided Isolation of Alkaloids with Inhibitory Activities of AChE/BuChE and Aβ Aggregation

Piper nigrum is a popular crop that can be used as seasoning or as an additive but its active ingredients also have an effect on the nervous system. Nineteen new amide alkaloids (1a/1b, 2-5, 6a/6b, 7, 8a/8b, 9, 10a/10b, 11a-11b, 12-14) were isolated from P. nigrum, guided by inhibitory activity of AChE and LC-MS/MS based on GNPS. The configurations were determined by extensive spectral analysis, Bulkiness rule, and NMR calculations. The inhibitory activities of AChE/BuChE and Aβ aggregation were tested, and the results showed compounds 2, 7, and 12 had significant inhibitory activities. These components were identified in the crude fraction and their relative quantities were tested, which suggested that compound 2 was the index component in the active site from P. nigrum.

Diterpenolignans and cephalotane diterpenoids from Cephalotaxus oliveri mast. with antitumor activity

Four undescribed naturally diterpenolignans, and two cephalotane diterpenoids, along with seven known compounds, including two pairs of enantiomers, were isolated from the twigs and leaves of Cephalotaxus oliveri Mast. Their structures were elucidated via spectroscopic data interpretation, chiral-phase HPLC analysis, NMR calculations, and electronic circular dichroism analysis. All the isolated compounds were evaluated for their cytotoxic activities against three kinds of human tumor cell lines. Among them, compound 8 exhibited the most potent activities against MCF-7, HepG2 and A549 cell lines with IC50 values of 2.83, 4.75 and 2.77 μM, respectively.

Phenolic constituents with antibacterial activity from Eleutherine bulbosa

Eleutherine bulbosa (Mill.) Urb. is a medicinal and edible plant with various benefits for humans and animals. In this work, four new phenolic constituents (1-4), along with six known phenolic compounds (5-10) were obtained from the red bulbs of E. bulbosa. Their structures with absolute configurations were characterized by extensive spectroscopic analysis, combined with HR-ESI-MS and quantum mechanical electronic circular dichroism (ECD). Compounds 1 and 2 are novel homologous and heterodimers, respectively, featuring an unusual spiro ring system. All isolated phenolic constituents were tested for their antibacterial effects. The results revealed four phenolic compounds 1-3 and 7 showed moderate antibacterial activity against Bacillus subtilis, Staphylococcus aureus and Escherichia coli with minimum inhibitory concentration (MIC) values ranging from 15.6 to 250.0 μg/mL.

Discovery of Michael reaction acceptors from the leaves of Ailanthus altissima by a modified tactic

Structural characteristics-guided investigation of Ailanthus altissima (Mill.) Swingle resulted in the isolation and identification of seven undescribed potential Michael reaction acceptors (1-7). Ailanlactone A (1) possesses an unusual 1,7-epoxy-11,12-seco quassinoid core. Ailanterpene B (6) was a rare guaianolide-type sesquiterpene with a 5/6/6/6-fused skeleton. Their structures were determined through extensive analysis of physiochemical and spectroscopic data, quantum chemical calculations, and single crystal X-ray crystallographic technology using Cu Kα radiation. The cytotoxic activities of isolates on HepG2 and Hep3B cells were evaluated in vitro. Encouragingly, ailanaltiolide K (4) showed significant cytotoxicity against Hep3B cells with IC50 values of 1.41 ± 0.21 μM, whose covalent binding mode was uncovered in silico.

Alashanines A-C, Three Quinone-Terpenoid Alkaloids from Syringa pinnatifolia with Cytotoxic Potential by Activation of ERK

Three quinone-terpenoid alkaloids, alashanines A-C (1-3), possessing an unprecedented 6/6/6 tricyclic conjugated backbone and quinone-quinoline-fused characteristic, were isolated from the peeled stems of Syringa pinnatifolia. Their structures were elucidated by analysis of extensive spectroscopic data and quantum chemical calculations. A hypothesis of biosynthesis pathways for 1-3 was proposed on the basis of the potential precursor iridoid and benzoquinone. Compound 1 exhibited antibacterial activities against Bacillus subtilis and cytotoxicity against HepG2 and MCF-7 human cancer cell lines. The results of the cytotoxic mechanism revealed that compound 1 induced apoptosis of HepG2 cells through activation of ERK.

Rapid screening of diarylpentanoids from Daphne bholua

Fractionation motivated by biological activity screening and NMR characteristic signals analysis led to the isolation of seventeen diarylpentanoids from the whole plant of Daphne bholua Buch.-Ham. ex D. Don, among which nine compounds were undescribed. Their structures and stereochemistry were determined by comprehensive spectroscopic data, J-based configurational analysis, and quantum chemical calculations. The inhibitory potentials of all isolates against acetylcholinesterase were evaluated in vitro and in silico.

Two new iridoids and triterpenoid analogues from the leaves of Viburnum chingii and their anti-acetylcholinesterase activity

Two undescribed split-ring iridoids (1-2) with six known triterpenes (3-8) and one steride (9) were isolated from the Viburnum chingii. Compound 2 possessed an unprecedented split-ring iridoid skeleton formed by electrocyclic reaction and split ring. The structures and absolute configurations of the new iridoids were established by NMR, HRESIMS, and ECD calculations. All the isolated compounds were tested for AChE inhibitory activity. Biologically, 1, 2, 3, 4, and 7 displayed significant AChE effects compared to the positive control donepezil, and have also been subjected to molecular docking studies.

HSQC-based small molecule accurate recognition technology discovery of diverse cytotoxic sesquiterpenoids from Elephantopus tomentosus L. and structural revision of molephantins A and B

Elephantopus tomentosus L. is a perennial herb taxonomically belonging to the family Asteraceae, which has been used as a folk medicine for the treatment of hepatobiliary diseases. Sesquiterpenoids from this plant have broad biological activities, including anti-tumor, anti-inflammatory, and antibacterial effects. In this study, fifteen structurally diverse sesquiterpenoids comprised 11 germacrane-type and 4 eudesmane-type sesquiterpenoids were prioritized to isolated from Elephantopus tomentosus L. based on the HSQC-based Small Molecule Accurate Recognition Technology (SMART) strategy. Among them, ten sesquiterpenoids were previously unreported, and their structures were elucidated by spectroscopic data, computational methods, single-crystal X-ray diffraction crystallographic data or electronic circular dichroism calculations. In addition, the structures of two known sesquiterpenoids, molephantin A and B, which were reported to possess E-geometry for the Δ¹⁽¹⁰⁾ double bond, were revised by reanalyzing their spectroscopic and X-ray crystallographic data. Some sesquiterpenoids exhibited significant cytotoxic activities against Hep3B and HepG2 cell lines.

Isolation of cytotoxic daphnane-type and tigliane-type diterpenoids from Daphne genkwa using MetGem software

Guided by MetGem Molecular Networking, eight daphnane-type and tigliane-type diterpenoids including four undescribed compounds were isolated from Daphne genkwa.

Chouchunsteride A-D, four new steroids from the leaves of Ailanthus altissima (Mill.) Swingle

Four new steroids, chouchunsteride A-D (1-4), together with four known steroids (5-8), were isolated from the leaves of Ailanthus altissima (Mill.) Swingle. Their structures were elucidated based on spectroscopic data analysis, while the relative and absolute configurations were determined via acetonide analysis and quantum chemical ECD calculations. All isolated steroids were evaluated for their cytotoxic activity against two hepatoma carcinoma cell lines (HepG2, Hep3B). Among them, 1 exhibited the most potent cytotoxicity against HepG2 cells with an IC₅₀ value of 4.03 μM.

Structural Investigation of Aaptourinamine by a Novel Module-Assembly-Based Calculation

Natural products have various and complicated structures, which is still a challenge for elucidating these compounds, especially for those lacking two-dimensional nuclear magnetic resonance (2D NMR) correlations mainly caused by high C/H ratios or proton-deficient and multiple heteroatoms through the conventional structural analytical methods. We reported a novel module-assembly calculation method named Dooerafa, which included constructing the meta-structures by a grafting method based on the crucial and the limited 2D NMR correlations, ring-contraction strategy based on mechanic force field and quantum chemical theory, and self-assemble calculation in Python programming for shaping up the structural candidates along with DFT-GIAO calculation. This new method, verified by a known alkaloid spiroreticulatine with the structure determined by X-ray diffraction, was performed for the structural elucidation of aaptourinamine isolated from marine sponge Aaptos suberitoides, showing us a brand new scaffold of imidazo [4,5,1-ij]pyrrolo [3,2-f]quinolin-7(8H)-one, which has a biosynthetic relationship with the bioactive and structurally unique aaptamine alkaloid.

Stellerasespenes A‒E: Sesquiterpenoids from Stellera chamaejasme and their anti-neuroinflammatory effects

Five undescribed sesquiterpenoids stellerasespenes A‒E and four reported congeners were isolated from the roots of Stellera chamaejasme. The structures were elucidated by comprehensive spectroscopic analyses together with X-ray single crystal diffraction and theoretical calculations. The structure of holosericin B was revised. All the isolated compounds were evaluated for NO production in murine microglial BV2 cells induced by LPS. Stellerasespene A showed better inhibitory activity than the positive control minocycline, inhibiting NO production and overexpression of pro-inflammatory cytokine IL-1β in LPS-activated BV2 cells.

MS/MS-based molecular networking accelerated discovery of germacrane-type sesquiterpene lactones from Elephantopus scaber L

Assisted by an MS/MS-based molecular networking guided strategy, six undescribed germacrane-type sesquiterpene lactones, namely scaberxones A-F, along with a known analog were obtained and characterized from Elephantopus scaber L. Their structures were unequivocally assigned by detailed spectroscopic analyses, NMR and ECD spectral calculations, and computer-assisted structure elucidation (CASE), complemented with single-crystal X-ray diffraction. All compounds were measured for their production of nitric oxide (NO) levels in lipopolysaccharide (LPS)-induced BV-2 microglial cells to assess their anti-neuroinflammatory activity. Scaberxone F showed the most potent inhibition of NO production at a concentration of 10 μM.

(±)-Usphenethylones A-C, three pairs of heterodimeric polyketide enantiomers from Aspergillus ustus 3.3904

Three pairs of new heterodimeric polyketide enantiomers, (±)-usphenethylones A-C (1-3), were isolated from the culture extract of Aspergillus ustus 3.3904. Compounds 1-3 present two heterodimerization patterns by a phenylethyl unit connected to an α-pyrone moiety, of which usphenethylones A-B (1-2) feature a 2,6,18-trioxa-tetracyclo-[8.8.0.03,8.011,16]octadecane core and usphenethylone C (3) possesses a 2-phenyl-3,4-dihydro-pyrano[4,3-b]pyran-5-one scaffold. The structures of (±)-1-3 were elucidated based on spectroscopic data analyses, and their absolute configurations were determined by single-crystal X-ray diffraction analysis and ECD calculation. Plausible biosynthetic pathways for 1-3 were proposed. Compounds (+)-3 and (-)-3 exhibited moderate inhibitory effects against ConA-induced T cell and LPS-induced B cell proliferation.

Characteristic guaiane sesquiterpenes from Daphne penicillata and ECD/NMR-based assignment of C-1 configuration

40 compounds including the first C17 homo-guaiane sesquiterpene (1) were isolated from Daphne penicillata and an efficient method using ECD/NMR strategy to access the C-1 configuration of characteristic guaiane sesquiterpenes has been developed.

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A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as asporychalasin from Aspergillus oryzae.