plantMASST - Community-driven chemotaxonomic digitization of plants.

Understanding the distribution of hundreds of thousands of plant metabolites across the plant kingdom presents a challenge. To address this, we curated publicly available LC-MS/MS data from 19,075 plant extracts and developed the plantMASST reference database encompassing 246 botanical families, 1,469 genera, and 2,793 species. This taxonomically focused database facilitates the exploration of plant-derived molecules using tandem mass spectrometry (MS/MS) spectra. This tool will aid in drug discovery, biosynthesis, (chemo)taxonomy, and the evolutionary ecology of herbivore interactions.

DeepSAT: Learning Molecular Structures from Nuclear Magnetic Resonance Data.

The identification of molecular structure is essential for understanding chemical diversity and for developing drug leads from small molecules. Nevertheless, the structure elucidation of small molecules by Nuclear Magnetic Resonance (NMR) experiments is often a long and non-trivial process that relies on years of training. To achieve this process efficiently, several spectral databases have been established to retrieve reference NMR spectra. However, the number of reference NMR spectra available is limited and has mostly facilitated annotation of commercially available derivatives. Here, we introduce DeepSAT, a neural network-based structure annotation and scaffold prediction system that directly extracts the chemical features associated with molecular structures from their NMR spectra. Using only the 1H-13C HSQC spectrum, DeepSAT identifies related known compounds and thus efficiently assists in the identification of molecular structures. DeepSAT is expected to accelerate chemical and biomedical research by accelerating the identification of molecular structures.

Adenosine Deaminase Inhibitory Activity of Medicinal Plants: Boost the Production of Cordycepin in Cordyceps militaris.

Cordycepin, also known as 3'-deoxyadenosine, is a major active ingredient of Cordyceps militaris with diverse pharmacological effects. Due to its limited supply, many attempts have been conducted to enhance the cordycepin content. As part of this study, eight medicinal plants were supplemented with cultivation substrates of Cordyceps to increase the cordycepin content. Cordyceps cultivated on brown rice supplemented with Mori Folium, Curcumae Rhizoma, Saururi Herba, and Angelicae Gigantis Radix exhibited increased cordycepin content compared to a brown rice control. Among them, the addition of 25% Mori Folium increased the cordycepin content up to 4 times. Adenosine deaminase (ADA) modulates the deamination of adenosine and deoxyadenosine, and the inhibitors have therapeutic potential with anti-proliferative and anti-inflammatory properties. As ADA is also known to be involved in converting cordycepin to 3'-deoxyinosine, the inhibitory activity of medicinal plants on ADA was measured by spectrophotometric analysis using cordycepin as a substrate. As expected, Mori Folium, Curcumae Rhizoma, Saururi Herba, and Angelicae Gigas Radix strongly inhibited ADA activity. Molecular docking analysis also showed the correlation between ADA and the major components of these medicinal plants. Conclusively, our research suggests a new strategy of using medicinal plants to enhance cordycepin production in C. militaris.

Alpha-Glucosidase Inhibitory Activity of Saponins Isolated from Vernonia gratiosa Hance.

Species belonging to the Vernonia (Asteraceae), the largest genus in the tribe Vernonieae (consisting of about 1,000 species), are widely used in food and medicine. These plants are rich sources of bioactive sesquiterpene lactones and steroid saponins, likely including many as yet undiscovered chemical components. A phytochemical investigation resulted in the separation of three new stigmastane-type steroidal saponins (1 - 3), designated as vernogratiosides A-C, from whole plants of V. gratiosa. Their structures were elucidated based on infrared spectroscopy (IR), one-dimensional (1D) and two-dimensional nuclear magnetic resonance (2D NMR), high-resolution electrospray ionization mass spectrometry (HR-ESI-MS), and electronic circular dichroism analyses (ECD), as well as chemical reactivity. Molecular docking analysis of representative saponins with α-glucosidase inhibitory activity was performed. Additionally, the intended substances were tested for their ability to inhibit α-glucosidase activity in a laboratory setting. The results suggested that stigmastane-type steroidal saponins from V. gratiosa are promising candidate antidiabetic agents.

Anti-α-glucosidase and anti-oxidative isoflavonoids from the immature fruits of Maclura tricuspidata.

The composition of a plant, together with its efficacy, vary depending on its maturity and plant parts. In this study, the chemical constituents of immature fruits of Maclura tricuspidata (Moraceae) were investigated together with their anti-diabetic and antioxidant effects. A total of 34 compounds were isolated from the immature fruits of M. tricuspidata using various chromatographic methods. Structure elucidation using extensive spectroscopic analysis led to the characterization of isolated compounds as isoflavonoids with prenyl substituents. Among them, macluraisoflavones A-O were first isolated from nature. The anti-diabetic and antioxidant activity of the isolated compounds were also suggested by α-glucosidase inhibitory activity and DPPH radical scavenging activity, respectively. In particular, macluraisoflavone I, an isoflavonoid with 2,2-dimethylpyran and 2-hydroperoxy-3-methylbut-3-enyl moieties, showed potent α-glucosidase inhibitory activity and DPPH radical scavenging activity. Further molecular docking analysis suggested hydrogen bond and alkyl interactions between α-glucosidase and macluraisoflavone I. Therefore, the immature fruits of M. tricuspidata can be used as an important natural product with antioxidant and anti-diabetic properties.

Aromatic Constituents from the Leaves of Actinidia arguta with Antioxidant and α-Glucosidase Inhibitory Activity.

As the leaf of Actinidia arguta has shown antioxidant activity, a study was conducted to identify the active ingredients. Forty-eight compounds were isolated from the leaves of A. arguta through various chromatographic techniques. Further characterization of the structures on the basis of 1D and 2D NMR and MS data identified several aromatic compounds, including phenylpropanoid derivatives, phenolics, coumarins, flavonoids and lignans. Among them, five compounds were newly reported, naturally occurring, and named argutosides A-D (1-4), which consist of phenylpropanoid glycosides that are conjugated with a phenolic moiety, and argutoside E (5), which is a coumarin glycoside that is conjugated with a phenylpropanoid unit. The isolated compounds showed good antioxidant and α-glucosidase inhibitory activity with differences in activity depending on the structures. Molecular docking analysis demonstrated the interaction between the hydroxyl and carbonyl groups of compounds 1 and 5 with α-glucosidase. Taken together, the leaves of A. arguta are rich in aromatic compounds with diverse structures. Therefore, the leaves of A. arguta and their aromatic components might be beneficial for oxidative stress and glucose-related diseases.

Lignans from Machilus thunbergii as Thymic Stromal Lymphopoietin Inhibitors.

Thymic stromal lymphopoietin (TSLP) plays an important role in the pathophysiology of various allergic diseases that are mediated by T helper cell type-2 (Th2) responses, including asthma and atopic dermatitis. The primary focus of this study was the identification of potent inhibitors of the TSLP signaling pathway for potential therapeutic use. The 80% methanol extract of Machilus thunbergii bark significantly inhibited the signal transducer and activator of transcription 5 (STAT5) phosphorylation in human mast cell (HMC)-1 cells. Through activity-guided isolation, three lignans (1-3) were obtained and identified as (+)-galbelgin (1), meso-dihydroguaiaretic acid (2), and machilin A (3). Among them, two lignans (1 and 2) significantly inhibited STAT5 phosphorylation and TSLP/TSLPR interaction, as determined by ELISA. Our results indicated that lignans isolated from M. thunbergii are a promising resource for the treatment of allergic diseases.

Anti-diabetic potential of Masclura tricuspidata leaves: Prenylated isoflavonoids with α-glucosidase inhibitory and anti-glycation activity.

Investigation of chemical constituents of Masclura tricuspidata leaves resulted in the isolation of 47 isoflavonoids possessing prenyl groups with different numbers and structures. Among them, sixteen compounds named cudracusisoflavones A-P (1-16) were first isolated from nature. The isoflavonoids isolated from M. tricuspidata leaves showed anti-diabetic effects as measured by inhibition on α-glucosidase activity and advanced glycation end-products (AGEs) formations. Especially, cudracusisoflavone L (12), a new compound, together with gancaonin M (27), erysenegalensein E (41) and millewanin G (44) showed strong α-glucosidase inhibition with IC50 values <10.0 µM. In addition, cudracusisoflavones A (1), D (4), M (13) and N (14), together with known prenylated isoflavonoids efficiently inhibited methylglyoxal (MGO)- or glyoxal (GO)-induced AGE formations. Structure activity relationship together with molecular docking analysis suggested the importance of hydroxy group and linear type of prenyl moiety for α-glucosidase inhibition. Conclusively, diverse prenylated isoflavonoids in M. tricuspidata leaves might ameliorate glycotoxicity-induced metabolic diseases.

In Vitro and In Silico Studies of Soluble Epoxide Hydrolase Inhibitors from the Roots of Lycopus lucidus.

Soluble epoxide hydrolase (sEH) is an enzyme that is considered a potential therapeutic target in human cardiovascular disease. Triterpenes (1-4) and phenylpropanoids (5-10) were isolated from Lycopus lucidus to obtain sEH inhibitors through various chromatographic purificationtechniques. The isolated compounds were evaluated for their inhibitory activity against sEH, and methyl rosmarinate (7), martynoside (8), dimethyl lithospermate (9) and 9″ methyl lithospermate (10) showed remarkable inhibitory activity, with the IC50 values ranging from 10.6 ± 3.2 to 35.7 ± 2.1 µM. Kinetic analysis of these compounds revealed that 7, 9 and 10 were competitive inhibitors bound to the active site, and 8 was the preferred mixed type inhibitor for allosteric sites. Additionally, molecular modeling has identified interacting catalytic residues and bindings between sEH and inhibitors. The results suggest that these compounds are potential candidates that can be used for further development in the prevention and treatment for cardiovascular risk.

Characterization of Anti-Inflammatory and Antioxidant Constituents from Scutellaria baicalensis Using LC-MS Coupled with a Bioassay Method.

An effective and previously demonstrated screening method for active constituents in natural products using LC-MS coupled with a bioassay was reported in our earlier studies. With this, the current investigation attempted to identify bioactive constituents of Scutellaria baicalensis through LC-MS coupled with a bioassay. Peaks at broadly 17-20 and 24-25 min on the MS chromatogram displayed an inhibitory effect on NO production in lipopolysaccharide-induced BV2 microglia cells. Similarly, peaks at roughly 17-19 and 22 min showed antioxidant activity with an 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS)/2,2-diphenyl-1- picrylhydrazyl (DPPH) assay. For confirmation of LC-MS coupled with a bioassay, nine compounds (1-9) were isolated from an MeOH extract of S. baicalensis. As we predicted, compounds 1, 8, and 9 significantly reduced lipopolysaccharide (LPS)-induced NO production in BV2 cells. Likewise, compounds 5, 6, and 8 exhibited free radical-scavenging activities with the ABTS/DPPH assay. In addition, the structural similarity of the main components was confirmed by analyzing the total extract and EtOAc fractions through molecular networking. Overall, the results suggest that the method comprised of LC-MS coupled with a bioassay can effectively predict active compounds without an isolation process, and the results of molecular networking predicted that other components around the active compound node may also be active.

Characterization of α-glucosidase inhibitory constituents of the fruiting body of lion's mane mushroom (Hericium erinaceus).

ETHNOPHARMACOLOGICAL RELEVANCE: Hericium erinaceus, commonly called lion's mane mushroom, is an edible and medicinal mushroom that has been traditionally used for the treatment of metabolic disorders, gastrointestinal diseases and memory impairment. In this study, potential anti-hyperglycemic constituents were identified to support the traditional usage of H. erinaceus. MATERIALS AND METHODS: The components of H. erinaceus were purified using various column chromatography techniques. The structure of the separated compounds was determined based on spectroscopic data analysis, i.e., 1D and 2D NMR analysis. The anti-hyperglycemic activity of the isolated compounds was evaluated by measuring the inhibitory effects on α-glucosidase activity. Molecular docking analysis was also conducted for elucidation of α-glucosidase inhibitory activity of isolated compounds. RESULTS: Ten compounds including four new compounds, erinacenols A-D (1-4), were isolated from the fruiting bodies of H. erinaceus. Investigation of the anti-hyperglycemic effect of isolated compounds demonstrated that erinacenol D (4), 4-[3',7'-dimethyl-2',6'-octadienyl]-2-formyl-3-hydroxy-5-methyoxybenzylalcohol (6), hericene A (7), hericene D (8) and hericenone D (9) strongly inhibited α-glucosidase activity with IC50 values of <20 µM. The structure activity relationship suggested the importance of long side chain for α-glucosidase inhibitory activity. Further analysis by molecular docking demonstrated the interaction of α-glucosidase and isolated compounds, which supported the inhibitory activity of α-glucosidase. CONCLUSION: Our present study demonstrated the beneficial effect of H. erinaceus by characterization of α-glucosidase inhibitory compounds, including four new compounds. This approach can be valuable support for the traditional use of H. erinaceus for the treatment of diabetes and metabolic diseases, which needs to be clarified by further in-vivo study.

Phenylpropanoid-Conjugated Triterpenoids from the Leaves of Actinidia arguta and Their Inhibitory Activity on α-Glucosidase.

Actinidia arguta, commonly called hardy kiwifruit or kiwiberry, has cold-resistant properties and can be cultivated in Asia, including Korea. Seven new triterpenoids (2-4 and 8-11) along with eight known triterpenoids were isolated from the leaves of A. arguta through various chromatographic techniques. The new triterpenoids were defined as actiniargupenes A-C (2-4), actinidic acid derivatives with phenylpropanoid constituent units, dehydroisoactinidic acid (8), and actiniargupenes D-F (9-11), asiatic acid derivatives with phenylpropanoid substituents, on the basis of 1D and 2D NMR and MS data. Among the triterpenoids, those with a phenylpropanoid constituent unit showed inhibitory activity on α-glucosidase, which suggested the importance of the phenylpropanoid moiety. Molecular docking analysis demonstrated the interaction between the 4'-OH group of the phenylpropanoid moiety and α-glucosidase.

The insight of in vitro and in silico studies on cholinesterase inhibitors from the roots of Cimicifuga dahurica (Turcz.) Maxim.

Cholinesterases (ChEs) are enzymes that break down neurotransmitters associated with cognitive function and memory. We isolated cinnamic acids (1 and 2), indolinones (3 and 4), and cycloartane triterpenoid derivatives (5-19) from the roots of Cimicifuga dahurica (Turcz.) Maxim. by chromatography. These compounds were evaluated for their inhibitory activity toward ChEs. Compound 1 was determined to have an IC50 value of 16.7 ± 1.9 µM, and to act as a competitive inhibitor of acetylcholinesterase (AChE). Compounds 3, 4 and 14 were found to be noncompetitive with IC50 values of 13.8 ± 1.5 and 6.5 ± 2.5 µM, and competitive with an IC50 value of 22.6 ± 0.4 µM, respectively, against butyrylcholinesterase (BuChE). Our molecular simulation suggested each key amino acid, Tyr337 of AChE and Asn228 of BuChE, which were corresponded with potential inhibitors 1, and 3 and 4, respectively. Compounds 1 and 4 were revealed to be promising compounds for inhibition of AChEs and BuChEs, respectively.

Cholinesterases inhibition studies of biological active compounds from the rhizomes of Alpinia officinarum Hance and in silico molecular dynamics.

Six diarylheptanoids (1-6) and two flavonoids (7 and 8) derived from Alpinia officinarum were evaluated for their ability to inhibit acetylcholinesterase. Compound 1 showed the highest degree of inhibition, with an IC50 of approximately 2 µM, followed by moderate degrees of inhibition by 2, 4 and 7, with IC50 values ranging from 20 to 40 µM. The remaining isolated compounds 3, 5, 6 and 8 had IC50 values greater than 50 µM. Enzyme kinetic studies showed that the compounds with high or moderate activity were competitive inhibitors, anchored to the active site of acetylcholinesterase. In particular, compounds 1 and 2 were docked at slightly different positions from those occupied by 4 and 7. Furthermore, molecular dynamics studies showed that compound 1 maintained its interactions with residues Thr74 and Phe295 throughout the simulation trajectory. Our findings suggest that compound 1 is a potential therapeutically relevant inhibitor of acetylcholinesterase.

Alkaloids from Tetrastigma hemsleyanum and Their Anti-Inflammatory Effects on LPS-Induced RAW264.7 Cells.

Alkaloids 1⁻10 were isolated from the aerial parts of Tetrastigma hemsleyanum (APTH) and obtained from species of the genus Tetrastigma for the first time. The chemical structures of the isolated compounds were identified by NMR, UV, and MS analyses. Their anti-inflammatory activities were investigated by measuring nitric oxide (NO) production in lipopolysaccharide (LPS)-induced RAW264.7 macrophages. Among all the isolates, compounds 6, 7 and 10 showed potent inhibitory activity against LPS-stimulated NO production in RAW264.7 cells (IC50: 31.9, 25.2 and 6.3 µM, respectively). Furthermore, APTH and S-(−)-trolline (10) inhibited induction of inflammatory cytokines or mediators such as interleukin-1ß (IL-1ß) and inducible nitric oxide synthase (iNOS) via suppression of nuclear factor κB (NF-κB) translocation into the nucleus. In addition, 10 suppressed extracellular signal-regulated protein kinase 1/2 (ERK1/2) mitogen-activated protein kinase (MAPK) phosphorylation in a dose-dependent manner. These results conclusively demonstrated that compound 10 displays anti-inflammatory activity via suppression of NF-κB activation and the ERK-MAPK signaling pathway in LPS-stimulated RAW264.7 cells.

Two new dammarane-type triterpene saponins from Korean red ginseng and their anti-inflammatory effects.

Panax ginseng has been the subject of extensive research on potential medicinal materials. The goal of this study was search the chemical constituents and biological activities of processed Panax ginseng, Korean red ginseng. Our efforts led to the isolation eleven compounds (1-11) including two new compounds 1 and 2 from Korean red ginseng using various chromatographic techniques. Chemical structures of isolated compounds were demonstrated by spectroscopic methods (1D-, 2D-NMR, and HR-ESI-MS). The anti-inflammatory effects of the compounds were investigated by inhibiting IL-6 and TNF-α secretion in LPS-activated RAW264.7 cells. Additionally, the effects of the compounds on the expression of COX-2 and iNOS were examined by Western blotting. Compound 1 significantly reduced the level of proinflammatory cytokines IL-6 and TNF-α secretion in LPS-activated RAW264.7 cells and the expression of COX-2 and iNOS inflammatory enzymes in the cells. These results suggested that compound 1, a new ginsenoside might useful in treatment of inflammation.