Combination of omics, bioinformatics, molecular docking, and experimental validation to elucidate the hepatoprotective effects, mechanisms, and active compounds of Shandougen.

Omics, bioinformatics, molecular docking, and experimental validation were used to elucidate the hepatoprotective effects, mechanisms, and active compounds of Shandougen (SDG) based on the biolabel-led research pattern. Integrated omics were used to explore the biolabels of SDG intervention in liver tissue. Subsequently, bioinformatics and molecular docking were applied to topologically analyze its therapeutic effects, mechanisms, and active compounds based on biolabels. Finally, an animal model was used to verify the biolabel analysis results. Omics, bioinformatics, and molecular docking revealed that SDG may exert therapeutic effects on liver diseases in the multicompound and multitarget synergistic modes, especially liver cirrhosis. In the validation experiment, SDG and its active compounds (betulinic acid and gallic acid) significantly improved the liver histopathological damage in the CCl4-induced liver cirrhosis model. Meanwhile, they also produced significant inhibitory effects on the focal adhesion pathway (integrin alpha-1, myosin regulatory light chain 2, laminin subunit gamma-1, etc.) and alleviated the associated pathological processes: focal adhesion (focal adhesion kinase 1)-extracellular matrix (collagen alpha-1(IV) chain, collagen alpha-1(VI) chain, and collagen alpha-2(VI) chain) dysfunction, carcinogenesis (alpha-fetoprotein, NH3, and acetylcholinesterase), inflammation (tumor necrosis factor alpha, interleukin-1 [IL-1], IL-6, and IL-10), and oxidative stress (reactive oxygen species, malonaldehyde, and superoxide dismutase). This study provides new evidence and insights for the hepatoprotective effects, mechanisms, and active compounds of SDG.

Flavonoids From the Aerial Parts of Sophora tonkinensis and Their Potential Anti-Inflammatory Activities.

Four undescribed prenylated flavonoids, sophoratones A-D (1-4), and 17 known flavonoids, were obtained from the aerial parts of Sophora tonkinensis. Their structures with absolute configurations were elucidated by detailed interpretation of NMR spectroscopy, mass spectrometry, and ECD calculations. Meanwhile, the ability of these compounds to inhibit the release of nitric oxide (NO) by a lipopolysaccharide induced mouse in RAW 264.7 cells was assayed. The results indicated that some compounds exhibited clear inhibitory effects, with IC50 ranging from 19.91±1.08 to 35.72±2.92 µM. These results suggest that prenylated flavonoids from the aerial parts of S. tonkinensis could potentially be used as a latent source of anti-inflammatory agents.

Three new flavonoids from the roots of Sophora tonkinensis.

Three new flavonoids including two isoflavanones sophortones A and B (1 and 2), and one chalcone sophortone C (3) were isolated from the roots of Sophora tonkinensis. Their structures were established by UV, IR, HRESIMS, and NMR data. The absolute configurations of 1 and 2 were determined by electronic circular dichroism (ECD) calculations.

Three new quinolizidine alkaloids from the roots of Sophora tonkinensis.

Three new quinolizidine alkaloids (1 - 3), including one new naturally isoflavone and cytisine polymer (3), along with 6 known ones were isolated from the ethanol extract of Sophora tonkinensis Gagnep. Their structures were elucidated by comprehensive spectroscopic data analysis (IR, UV, HRESIMS, 1D and 2D NMR), combined with ECD calculations. The antifungal activity against Phytophythora capsica, Botrytis cinerea, Gibberella zeae, and Alternaria alternata of the compounds was evaluated in a mycelial inhibition assay. Biological tests indicated that compound 3 exhibited strong antifungal activity against P. capsica with EC50 values of 17.7 µg/ml.

Isolation and Characterization of Antimicrobial Metabolites from the Sophora tonkinensis-Associated Fungus Penicillium sp. GDGJ-N37.

Chemical investigation of Penicillium sp. GDGJ-N37, a Sophora tonkinensis-associated fungus, yielded two new azaphilone derivatives, N-isoamylsclerotiorinamine (1) and 7-methoxyl-N-isoamylsclerotiorinamine (2), and four known azaphilones (3-6), together with two new chromone derivatives, penithochromones X and Y (7 and 8). Their structures were elucidated based on spectroscopic data, CD spectrum, and semi-synthesis. Sclerotioramine (3) showed significant antibacterial activities against B. subtilis and S. dysentery, and it also showed most potent anti-plant pathogenic fungi activities against P. theae, C. miyabeanus, and E. turcicum.

Complete Genome Sequence of Bacillus velezensis TH-1, a Candidate Biocontrol Bacterium from China.

Bacillus velezensis TH-1 is a plant growth-promoting rhizobacteria with biocontrol potential that was isolated from the rhizosphere of Sophora tonkinensis Radix. Our previous results showed that strain TH-1 demonstrated effective biocontrol activity against root rot of Sophora tonkinensis Radix and bacterial wilt of ginger. Currently, only a few whole-genome sequences of biocontrol strains isolated from the rhizosphere of medicinal plants are available. We report, here, the complete genome sequence of B. velezensis TH-1. The size of TH-1 genome is 3,929,846 bp that consists of 3,900 genes with a total GC content of 46.48%. The strain TH-1 genome has 3,661 coding genes, 86 transfer RNAs, 27 ribosomal RNAs, and 16 small RNAs. Moreover, we identified nine gene clusters coding for the biosynthesis of antimicrobial compounds. The genomic information of TH-1 will provide resources for the study of biological control mechanisms and plant-microbe interactions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Matrine-producing endophytic fungus Galactomyces candidum TRP-7: screening, identification, and fermentation conditions optimization for Matrine production.

Matrine (MA) is an alkaloid extracted from the root of genus Sophora with various pharmacological activities. Production of MA by endophytic fungi offers an alternative challenge to reduce the massive consumption to meet the increasing demand of MA. In the current study, the positive strains with MA producing ability were screened from endophytic fungal isolated from the root of Sophora tonkinensis Gagnep. Chromatographic analyses verified the identity of the produced MA. Among these fungi, Galactomyces candidum strain TRP-7 was the most valuable strain for MA production with the initial yield 8.26 mg L-1. The MA production was efficiently maximized up to 17.57 mg L-1 of fermentation broth, after optimization of eight process parameters using Plackett-Burman and Box-Behnken designs. The statistical optimization resulted in a 1.127 times increase in MA production as compared to the initial yield of TRP-7. This is the first report to isolate endophytic fungi with MA-producing activity from S. tonkinensis Gagnep., and to identify an endophytic fungus G. candidum TRP-7 as a new promising start strain for a higher MA yield.

Omics combined with network pharmacology reveal the neuroprotective mechanism of Sophora tonkinensis based on the biolabel research pattern: The treatment of Parkinson's disease against oxidative stress and neuroexcitatory toxicity.

Based on the biolabel research pattern, omics and network pharmacology were used for exploring the neuroprotection of Sophora tonkinensis (ST) in the treatment of brain diseases. Multi-omics were applied to investigate biolabels for ST intervention in brain tissue. Based on biolabels, the therapeutic potential, mechanism and material basis of ST for treating brain diseases were topologically analyzed by network pharmacology. A Parkinson's disease (PD) mouse model was used to validate biolabel analysis results. Four proteins and three metabolites were involved in two key pathways (alanine, aspartate and glutamate metabolism and arginine biosynthesis) and considered as biolabels. Network pharmacology showed that ST has the potential to treat some brain diseases, especially PD. Eight compounds (including caffeic acid, gallic acid and cinnamic acid) may serve as the material basis of ST treating brain diseases via the mediation of three biolabels. In the PD model, ST and its active compounds (caffeic acid and gallic acid) may protect dopaminergic neurons (maximum recovery rate for dopamine, 49.5%) from oxidative stress (E3 ubiquitin-protein ligase parkin, reactive oxygen species, nitric oxide, etc.) and neuroexcitatory toxicity (glutamate dehydrogenase, glutamine, glutamic acid, etc.). These findings indicated that omics and network pharmacology may contribute to the achievement of the objectives of this study based on the biolabel research pattern.

Aromatic diglycosides from Sophora tonkinensis and a multi-step conformer filtering procedure for TDDFT calculation of flexible glycoside.

Three previously undescribed aromatic diglycosides (1, 5, and 8) and six known analogs (2-4, 6, 7, and 9) were isolated from the roots and rhizomes of Sophora tonkinensis Gagnep. Their structures were elucidated by detailed spectroscopic analysis. The absolute configuration of compound 8 was determined by comparing the experimental and TDDFT calculated ECD spectra of 8 and aglycone 8a. Furthermore, a multistep conformer filtering procedure for TDDFT calculation of flexible glycoside was proposed, which afforded high accuracy with acceptable computing cost in determining the absolute configuration of glycosides using quantum calculated ECD.

Two new isoflavones from the roots of Sophora tonkinensis.

Two new isoflavones (1 and 2), as well as eight known ones were isolated from the roots of Sophora tonkinensis Gagnep. Compound 1 represents an unprecedented polymerization pattern constructed by isoflavone and cytisine. Their structures were elucidated by comprehensive spectroscopic data analysis, combined with ECD calculations. Compound 1 displayed significant anti-tobacco mosaic virus (TMV) activity compared with the positive control ningnanmycin. Moreover, compound 6 exhibited potent α-glucosidase inhibitory activity with IC50 value of 47.4 mg/L.

Systematic analysis of chemical profiles of Sophorae tonkinensis Radix et Rhizoma in vitro and in vivo using UPLC-Q-TOF-MSE.

Sophorae tonkinensis Radix et Rhizoma (S. tonkinensis) has been recorded as a 'poisonous' Chinese herbal medicine in Chinese Pharmacopoeia 2020. The clinical reaction reports of S. tonkinensis indicated its neurotoxicity; however, there still exists dispute about its toxic substances. At present, no report is available on the blood and brain prototype research of S. tonkinensis. Most studies focused on alkaloids and less on other compounds. Moreover, the constituents absorbed into the blood and brain have been rarely investigated so far. This study established a rapid and efficient qualitative analysis method using UPLC-Q-TOF-MSE to characterize the ingredients of S. tonkinensis and those entering into the rat's body after oral administration. A total of 91 compounds were identified in S. tonkinensis, of which 28 were confirmed by the standards. In addition, 30 and 19 prototypes were also first identified in the rat's blood and brain, respectively. It was found that most flavonoids, except alkaloids, were detected in the rat's body and distributed in the cerebrospinal fluid, suggesting that flavonoids may be one of the important toxic or effective substances of S. tonkinensis. This finding provides new clues and data for clarifying the toxicity or efficacy of this medicinal plant.

Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis.

BACKGROUND: Sophora tonkinensis Gagnep is a traditional Chinese medical plant that is mainly cultivated in southern China. Drought stress is one of the major abiotic stresses that negatively impacts S. tonkinensis growth. However, the molecular mechanisms governing the responses to drought stress in S. tonkinensis at the transcriptional and posttranscriptional levels are not well understood. RESULTS: To identify genes and miRNAs involved in drought stress responses in S. tonkinensis, both mRNA and small RNA sequencing was performed in root samples under control, mild drought, and severe drought conditions. mRNA sequencing revealed 66,476 unigenes, and the differentially expressed unigenes (DEGs) were associated with several key pathways, including phenylpropanoid biosynthesis, sugar metabolism, and quinolizidine alkaloid biosynthesis pathways. A total of 10 and 30 transcription factors (TFs) were identified among the DEGs under mild and severe drought stress, respectively. Moreover, small RNA sequencing revealed a total of 368 miRNAs, including 255 known miRNAs and 113 novel miRNAs. The differentially expressed miRNAs and their target genes were involved in the regulation of plant hormone signal transduction, the spliceosome, and ribosomes. Analysis of the regulatory network involved in the response to drought stress revealed 37 differentially expressed miRNA-mRNA pairs. CONCLUSION: This is the first study to simultaneously profile the expression patterns of mRNAs and miRNAs on a genome-wide scale to elucidate the molecular mechanisms of the drought stress responses of S. tonkinensis. Our results suggest that S. tonkinensis implements diverse mechanisms to modulate its responses to drought stress.

Anti-tobacco mosaic virus (TMV) activity of chemical constituents from the seeds of Sophora tonkinensis.

Two new compounds, including one new arylbenzofuran (1) and one new pterocarpanoid (2), along with nine known ones, were isolated from the seeds of Sophora tonkinensis. The structures of the new compounds were elucidated based on a comprehensive spectroscopic data analysis. Compounds 2 and 3 exhibited good anti-tobacco mosaic virus (TMV) activities with the protective inhibition rate of 69.62% and 68.72% respectively, at concentration of 100 µg/ml.

First Report of Round Leaf Spot on Sophora tonkinensis Caused by Didymella glomerata in China.

The root of Sophora tonkinensis Gagnep is an important medicinal material in China. An unknown foliar disease, first observed In July 2018, occurred over 240 ha of S. tonkinensis (totally cultured 600 ha) in Guangxi, China, in December 2019. The initial symptoms on leaf were seen as small, tawny spots (0.5 to 1.5 mm in diam.). As the disease progressed, the lesions enlarged into grayish and dark brown concentric rings (5 to 10.0 mm in diam.) resulting in black protuberances in the center of the spots. Severe infections would adversely affect plant growth, and cut the production by 30-40%. Symptomatic leaves were sampled and the surface was sterilized with 75% ethanol for 30 s and then soaked in 0.1% HgCl2 for 2 min. After three washes with sterile distilled water, the samples were dried, placed aseptically onto potato dextrose agar (PDA) plates, and incubated at 28°C. Three days later, the isolates were placed on new PDA medium for subsequent purification and sporulation. The fungus, SDG-1, was recovered from 85% of the total 40 isolates. Its colonies were whitish initially and then became olive green 7 days after incubation at 28 °C. The pycnidias were globose to subglobose, initially brown and darken at maturity, 85 to 300 × 70 to 280 µm in size. The conidia were colorless, single-celled, rounded to ellipsoidal and 3.5 to 6.6 × 1.5 to 3.8 µm. The chlamydospores were multicellular and brick trellised, usually forming branched or unbranched chains, light to dark brown in color and measured 28.5 to 44.5 × 8.2 to 16.5 µm. The morphological characteristics were consistent with Didymella glomerata. The rDNA-ITS, ß-tubulin and actin of strain SDG-1 were PCR amplified, and the DNA sequencing results were almost 100% identical to those of D. glomerata, respectively (GenBank database accession numbers MN 435377, MN447333 and MN447334, respectively). The multi-locus phylogenetic analysis was carried out with the obtained sequences, which revealed that the isolates clustered within D. glomerata with the similarity of 100% (Fig.3). Therefore, based on the morphology and phylogenetic tree, strain SDG-1 was identified as D. glomerata. For pathogenicity tests, the S. tonkinensis was cultured for two years, and the conidial suspension of SDG-1 (1 × 106 conidia /mL) was prepared by harvesting conidia from a 10-day-old culture on PDA. Conidia were sprayed onto the healthy leaves of S. tonkinensis for co-culture, while the control group was sprayed with sterile distilled water. Each experiment was performed three times. All plants were covered with plastic bags for 3 days in order to maintain high humidity and cultured in a greenhouse at 28 °C with a 12-h/12-h light/dark cycle. The symptoms appeared 7 days after the leaves were inoculated with spores, which were identical to those observed in the field. The pathogenic fungus was re-isolated from the infected leaves and identified as previously described. The control leaves remained symptomless during the pathogenicity tests. According to the previous literature, D. glomerata is a plant pathogenic fungus with a wide host range, which can damage up to 100 species of woody and herbaceous plants (Aghapour et al. 2009, Lahoz et al. 2007). To our knowledge, this is the first report of D. glomerata causing round leaf spot on S. tonkinensis in China.

Preparative Purification of Total Flavonoids from Sophora tonkinensis Gagnep. by Macroporous Resin Column Chromatography and Comparative Analysis of Flavonoid Profiles by HPLC-PAD.

For the full development and utilization of Sophora tonkinensis Gagnep., this study was primarily intended to established a simple and efficient approach for the preparative purification of total flavonoids from S. tonkinensis by macroporous resin column chromatography (MRCC). The adsorption and desorption characteristics of the total flavonoids on ten macroporous resins were first studied, and AB-8 resin was chosen as the most suitable, and the adsorption data were best fitted to the pseudo-second-order kinetics model and Langmuir isotherm model. Furthermore, the technological parameters for the purification of the total flavonoids were optimized using column chromatography. After a sample one-step purification procedure, the content of the total flavonoids increased by about 4.76-fold from 12.14% to 57.82%, with a recovery yield of 84.93%. In addition, the comparative analysis of the flavonoid extracts before and after purification was performed by high-performance liquid chromatography coupled with photodiode-array detection (HPLC-PAD). The results showed that the contents of six major flavonoids in the purified product were all higher than before the purification. Therefore, the AB-8 MRCC established in this work was a promising method for the industrial-scale purification of the total flavonoids from S. tonkinensis.

[Studies on active aromatic constituents from rhizomes of Sophora tonkinensis].

Aromatic constituents from rhizomes of Sophora tonkinensis were purified by extensive chromatographic techniques including column chromatography over macroporous resin,MCI,silica gel,weak acid cation exchange resin,Sephadex LH-20,ODS,and semi-preparative HPLC. Twelve aromatic compounds were isolated and identified from the water aqueous extract of the rhizomes of S.tonkinensis. Their structures were elucidated as 4-( 3-hydroxypropyl) phenol( 1),( ±)-4-( 2-hydroxypropyl) phenol( 2),benzamide( 3),( ±)-3-( p-methoxyphenyl)-1,2-propanediol( 4),4-methoxybenzamide( 5),3-hydroxy-1-( 4-hydroxy-3-methoxyphenyl) propan-1-one( 6),tyrosol( 7),( ±)-2,3-dihydroxypropyl benzoate( 8),vanillin alcohol( 9),7,3'-dihydroxy-8,4'-dimethoxyisoflavone( 10),7,4'-dihydroxy-3'-methoxyisoflavone( 11),and 7,3'-dihydroxy-5'-methoxyisoflavone( 12). Compounds 1-9 were firstly isolated from the Sophora genus. Compounds 4,5,10 and 11 can remarkably protect Hep G2 cell against APAP-induced damage at the concentration of 10 µmol·L-1. Compounds 1-12 exhibited no significant activities on the assays of inhibition of LPS-induced NO production in RAW cell lines and NF-κB inhibition.

[Safety evaluation of Sophora tonkinensis and risk control].

The aim is to systemically review and evaluate the safety of Sophora tonkinensis from the literature on the herbal origin, toxicity record in modern literature and toxicological studies and publications in recent years. By systematic review and analysis, the results showed that its toxicity mainly involved the nervous system, the digestive system and the respiratory system, and respiratory failure may be the direct cause of death. The main symptoms included headache, dizziness, vomiting, nausea, abdominal pain, limbs weakness, palpitation, and chest distress; as well as pale complexion, limbs trembling, convulsions, chills, high heart rate, fall of blood pressure, shock, and respiratory failure to death in severe cases. High dose and long term medication may cause serious brain damage, especially in adolescents and children. The authors have proposed to use rationally under guidance of physician and strictly according to the dosage recommended by pharmacopoeia. The patients shall not be credulous about the folk prescriptions and test recipes to use it for,prevention of colds and treatment of sore throat at will. In addition, the researches on the conventional treatment methods for S. tonkinensis poisoning, the toxic substance basis, and toxicity mechanism shall be strengthened in further studies. These efforts will play important role in exerting the drug effect and avoiding side effect.

Cytisine-type alkaloids and flavonoids from the rhizomes of Sophora tonkinensis.

A new cytisine-type alkaloid, (-)-N-hexanoylcytisine (1), and a new isoflavan, (3S, 4R)-4-hydroxy-7,4'-dimethoxyisoflavan 3'-O-ß-d-glucopyranoside (2), along with 10 known compounds, were isolated from the rhizomes of Sophora tonkinensis. Their structures were determined by spectroscopic methods, chemical evidence, and ECD data analysis. All of the isolates were evaluated for their cytotoxic activities against four human tumor cell lines.

[Bioactive quinolizidine alkaloids from Sophora tonkinensis].

Twelve quinolizidine alkaloids were isolated from Sophora tonkinensis by means of silica gel, preparative MPLC, and preparative HPLC. On analysis of NMR spectroscopic data, their structures were established as 3-(4-hydroxyphenyl)-4-(3-methoxy-4-hydroxyphenyl)-3,4-dehydroquinolizidine(1), lanatine A(2), cermizines C(3), senepodines G(4), senepodines H(5), jussiaeiines A(6), jussiaeiines B(7),(+)-5α-hydroxyoxysophocarpine(8),(-)-12ß-hydroxyoxysophocarpine(9),(-)-clathrotropine(10),(-)-cytisine(11), and (-)-N-methylcytisine(12), respectively. Compounds 1-7 were first isolated from Sophora L. plant. In the in vitro assays,the isolated compounds 1, 3, 6-10 exhibited potent activity against CVB3 with IC50 of 6.40, 3.25, 4.66, 3.21, 0.12, 0.23 and 1.60, and with selective index values(SI=TC50/IC50)of 12.0, 5.6, 13.0, 15.1, 50.1, 26.2, and 23.6, respectively. Compounds 1, 3, and 7 exhibited activity against staphylococcus aureus(ATCC 29213)with MICvalues of 8.0, 3.5, 6.0 g•L⁻¹, respectively. Compounds 1, 3, 7, and 12 exhibited activity against staphylococcus aureus(ATCC 33591)with MIC values of 18.0, 7.5, 8.0, 12.0 g•L⁻¹, respectively. Compounds 2, 6, 7 exhibited activity against Escherichia coli(ATCC 25922) with MIC values of 1.0, 3.2, 0.8 g•L⁻¹.

[Studies on chemical constituents of rhizomes of Sophora tonkinensis].

Thirteen compounds were isolated from the 95% aqueous EtOH extract of the rhizomes of Sophora tonkinensis by a combination of various chromatographic techniques including column chromatography over silica gel, Sphadex LH-20, MCI, ODS, and semi-preparative HPLC.Their structures were elucidated as 1-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-3-yl)ethanone(1), cyclo(Pro-Pro)(2), nicotinic acid(3), p-hydroxybenzonic acid(4), p-methoxybenzonic acid(5), 4-hydroxymethyl-2,6-dimethoxyphenol-1-O-ß-D-glucopyranoside(6), coniferin(7), syringin(8),(-)-secoisolariciresinol-4-O-ß-D-glucopyranoside(9),(-)-syringaresinol-4-O-ß-D-glucopyranoside(10),(-)-syringaresinol-4,4'-di-O-ß-D-glucopyranoside(11),(-)-pinoresinol-4,4'-di-O-ß-D-glucopyranoside(12), and(6S,9R)-roseoside(13) by their physicochemical properties and spectroscopic data.Compound 1 was a new naturalproduct, and compounds 2,5,6,9,10,12 and 13 were obtained from the Sophora genus for the first time.Compound 1 possessed moderate cytotoxic activity against A549 human tumor cell [IC50（23.05 ± 0.46）µmol•L⁻¹].