The discovery of an anti-Candida xanthone with selective inhibition of Candida albicans GAPDH.

OBJECTIVES: This study aimed to discover novel antifungals targeting Candida albicans glyceraldehyde-3-phosphate dehydrogenase (CaGAPDH), have an insight into inhibitory mode, and provide evidence supporting CaGAPDH as a target for new antifungals. METHODS: Virtual screening was utilized to discover inhibitors of CaGAPDH. The inhibitory effect on cellular GAPDH was evaluated by determining the levels of ATP, NAD, NADH, etc., as well as examining GAPDH mRNA and protein expression. The role of GAPDH inhibition in C. albicans was supported by drug affinity responsive target stability and overexpression experiments. The mechanism of CaGAPDH inhibition was elucidated by Michaelis-Menten enzyme kinetics and site-specific mutagenesis based on docking. Chemical synthesis was used to produce an improved candidate. Different sources of GAPDH were used to evaluate inhibitory selectivity across species. In vitro and in vivo antifungal tests, along with anti-biofilm activity, were carried out to evaluate antifungal potential of GAPDH inhibitors. RESULTS: A natural xanthone was identified as the first competitive inhibitor of CaGAPDH. It demonstrated in vitro anti-C. albicans potential but also caused hemolysis. XP-W, a synthetic side-chain-optimized xanthone, demonstrated a better safety profile, exhibiting a 50-fold selectivity for CaGAPDH over human GAPDH. XP-W also exhibited potent anti-biofilm activity and displayed broad-spectrum anti-Candida activities in vitro and in vivo, including multi-azole-resistant C. albicans. CONCLUSIONS: These results demonstrate for the first time that CaGAPDH is a valuable target for antifungal drug discovery, and XP-W provides a promising lead.

Active ingredients Isorhamnetin of Croci Srigma inhibit stomach adenocarcinomas progression by MAPK/mTOR signaling pathway.

Gastric cancer (GC) remains the third leading cause of cancer-related mortality in the world, and ninety-five percent of GC are stomach adenocarcinomas (STAD). The active ingredients of Croci Stigma, such as Isorhamnetin, Crocin, Crocetin and Kaempferol, all have antitumor activity. However, their chemical and pharmacological profiles remain to be elusive. In this study, network pharmacology was used to characterize the action mechanism of Croci Stigma. All compounds were obtained from the traditional Chinese medicine systems pharmacology (TCMSP) database, and active ingredients were selected by their oral bioavailability and drug-likeness index. The targets of Croci Stigma active ingredients were obtained from the traditional Chinese medicine integrated database (TCMID), whereas the related genes of STAD were obtained from DisGeNET platform. Cytoscape was used to undertake visual analyses of the Drug Ingredients-Gene Symbols-Disease (I-G-D) network, and 2 core genes including MAPK14, ERBB3 were obtained, which are the predicted targets of isorhamnetin (IH) and quercetin, respectively. Data analysis from TCGA platform showed that MAPK14 and ERBB3 all upregulated in STAD patients, but only the effect of MAPK14 expression on STAD patients' survival was significant. Molecular docking showed that IH might affect the function of MAPK14 protein, and then the underlying action mechanisms of IH on STAD were experimentally validated using human gastric cancer cell line, HGC-27 cells. The results showed that IH can inhibit cell proliferation, migration, clonal formation, and arrest cell cycle, but promote the apoptosis of HGC-27 cells. qRT-PCR data demonstrated that IH downregulated the MAPK14 mRNA expression and EMT related genes. WB results showed that IH regulates MAPK/mTOR signaling pathway. These findings suggest that IH has the therapeutic potential for the treatment of STAD.

Structure of the Major G-Quadruplex in the Human EGFR Oncogene Promoter Adopts a Unique Folding Topology with a Distinctive Snap-Back Loop.

EGFR tyrosine kinase inhibitors have made remarkable success in targeted cancer therapy. However, therapeutic resistance inevitably occurred and EGFR-targeting therapy has been demonstrated to have limited efficacy or utility in glioblastoma, colorectal cancer, and hepatocellular carcinoma. Therefore, there is a high demand for the development of new targets to inhibit EGFR signaling. Herein, we found that the EGFR oncogene proximal promoter sequence forms a unique type of snap-back loop containing G-quadruplex (G4), which can be targeted by small molecules. For the first time, we determined the NMR solution structure of this snap-back EGFR-G4, a three-tetrad-core, parallel-stranded G4 with naturally occurring flanking residues at both the 5'-end and 3'-end. The snap-back loop located at the 3'-end region forms a stable capping structure through two stacked G-triads connected by multiple potential hydrogen bonds. Notably, the flanking residues are consistently absent in reported snap-back G4s, raising the question of whether such structures truly exist under in vivo conditions. The resolved EGFR-G4 structure has eliminated the doubt and showed distinct structural features that distinguish it from the previously reported snap-back G4s, which lack the flanking residues. Furthermore, we found that the snap-back EGFR-G4 structure is highly stable and can form on an elongated DNA template to inhibit DNA polymerase. The unprecedented high-resolution EGFR-G4 structure has thus contributed a promising molecular target for developing alternative EGFR signaling inhibitors in cancer therapeutics. Meanwhile, the two stacked triads may provide an attractive site for specific small-molecule targeting.

Hybrids of ß-triketone and monoterpenoids from the peels of Callistemon viminalis.

Phytoconstituents of the peels of Callistemon viminalis has been investigated for the first time. As a result, two pair of diastereomers of hybrids of ß-triketone and α-phellandrene, named viminalisones A-B (1-2) and viminalisones CD (3-4), and three known analogues were obtained. Their structures and absolute configurations were elucidated through a combination of the analysis of their MS data, NMR spectra, single-crystal X-ray diffraction, and their experimental and calculated electronic circular dichroism (ECD) spectra. All isolates were evaluated for their antimicrobial activities against Botrytis cinerea and Cutibacterium acnes. Meroterpenoid 7 exhibited antibacterial activity against Botrytis cinerea with a MIC value of 0.256 mg/mL.

(±)-Pheharmines A-B, two pairs of racemic alkaloids with a morpholino[4,3,2-hi]ß-carboline core, from the roots of Peganum harmala.

Two pairs of unprecedented ß-carboline-phenylpropanoid heterogeneous alkaloids, (±)-pheharmines A-B (1-4), characterized by a morpholino[4,3,2-hi]ß-carboline core with two chiral centers, were isolated from the roots of Peganum harmala. The structures, including their absolute configurations, were identified using spectroscopic analyses and electronic circular dichroism (ECD) calculations. The biosynthetic hypothesis for the formation of pheharmines A-B was proposed. Compounds 1-4 exhibited moderate cytotoxic activities against HL-60 cell lines.

Structural insight into the bulge-containing KRAS oncogene promoter G-quadruplex bound to berberine and coptisine.

KRAS is one of the most highly mutated oncoproteins, which is overexpressed in various human cancers and implicated in poor survival. The G-quadruplex formed in KRAS oncogene promoter (KRAS-G4) is a transcriptional modulator and amenable to small molecule targeting. However, no available KRAS-G4-ligand complex structure has yet been determined, which seriously hinders the structure-based rational design of KRAS-G4 targeting drugs. In this study, we report the NMR solution structures of a bulge-containing KRAS-G4 bound to berberine and coptisine, respectively. The determined complex structure shows a 2:1 binding stoichiometry with each compound recruiting the adjacent flacking adenine residue to form a "quasi-triad plane" that stacks over the two external G-tetrads. The binding involves both π-stacking and electrostatic interactions. Moreover, berberine and coptisine significantly lowered the KRAS mRNA levels in cancer cells. Our study thus provides molecular details of ligand interactions with KRAS-G4 and is beneficial for the design of specific KRAS-G4-interactive drugs.

Oxidative Damage Induces a Vacancy G-Quadruplex That Binds Guanine Metabolites: Solution Structure of a cGMP Fill-in Vacancy G-Quadruplex in the Oxidized BLM Gene Promoter.

Guanine (G)-oxidation to 8-oxo-7,8-dihydroguanine (OG) by reactive oxygen species in genomic DNA has been implicated with various human diseases. G-quadruplex (G4)-forming sequences in gene promoters are highly susceptible to G-oxidation, which can subsequently cause gene activation. However, the underlying G4 structural changes that result from OG modifications remain poorly understood. Herein, we investigate the effect of G-oxidation on the BLM gene promoter G4. For the first time, we show that OG can induce a G-vacancy-containing G4 (vG4), which can be filled in and stabilized by guanine metabolites and derivatives. We determined the NMR solution structure of the cGMP-fill-in oxidized BLM promoter vG4. This is the first complex structure of an OG-induced vG4 from a human gene promoter sequence with a filled-in guanine metabolite. The high-resolution structure elucidates the structural features of the specific 5'-end cGMP-fill-in for the OG-induced vG4. Interestingly, the OG is removed from the G-core and becomes part of the 3'-end capping structure. A series of guanine metabolites and derivatives are evaluated for fill-in activity to the oxidation-induced vG4. Significantly, cellular guanine metabolites, such as cGMP and GTP, can bind and stabilize the OG-induced vG4, suggesting their potential regulatory role in response to oxidative damage in physiological and pathological processes. Our work thus provides exciting insights into how oxidative damage and cellular metabolites may work together through a G4-based epigenetic feature for gene regulation. Furthermore, the NMR structure can guide the rational design of small-molecule inhibitors that specifically target the oxidation-induced vG4s.

Solution Structure of Ternary Complex of Berberine Bound to a dGMP-Fill-In Vacancy G-Quadruplex Formed in the PDGFR-ß Promoter.

The G-quadruplexes (G4s) formed in the PDGFR-ß gene promoter are transcriptional modulators and amenable to small-molecule targeting. Berberine (BER), a clinically important natural isoquinoline alkaloid, has gained increasing attention due to its potential as anticancer drug. We previously showed that the PDGFR-ß gene promoter forms a unique vacancy G4 (vG4) that can be filled in and stabilized by guanine metabolites, such as dGMP. Herein, we report the high-resolution NMR structure of a ternary complex of berberine bound to the dGMP-fill-in PDGFR-ß vG4 in potassium solution. This is the first small-molecule complex structure of a fill-in vG4. This ternary complex has a 2:1:1 binding stoichiometry with a berberine molecule bound at each the 5'- and 3'-end of the 5'-dGMP-fill-in PDGFR-ß vG4. Each berberine recruits the adjacent adenine residue from the 5'- or 3'-flanking sequence to form a "quasi-triad plane" that covers the external G-tetrad of the fill-in vG4, respectively. Significantly, berberine covers and stabilizes the fill-in dGMP. The binding of berberine involves both π-stacking and electrostatic interactions, and the fill-in dGMP is covered and well-protected by berberine. The NMR structure can guide rational design of berberine analogues that target the PDGFR-ß vG4 or dGMP-fill-in vG4. Moreover, our structure provides a molecular basis for designing small-molecule guanine conjugates to target vG4s.

Chemical composition and antifungal activity of essential oil from Origanum vulgare against Botrytis cinerea.

In this study, the chemical composition of the essential oil (EO) of Origanum vulgare was characterized, and the antifungal activity of the EO and some individual components against Botrytis cinerea (Y-BC-1) was determined. Twenty-one components were identified by gas chromatography-mass spectrometry and gas chromatography-flame ionization detection, constituting 95.7% of the EO. The major components were methyleugenol (16.5%), myristicin (15.6%), carvacrol (15.0%), thymol (9.8%), apioline (9.4%), and (Z)-ß-farnesene (8.7%). B. cinerea in vitro mycelial growth and spore germination were strongly inhibited by the EO and two of its main components, thymol and carvacrol. In vivo vapor contact assays, the antifungal activity of the EO at 250 mg/L suppressed the decay of cherry tomatoes 96.39%. Moreover, thymol and carvacrol at 125 mg/L completely suppressed the gray mold. Thus, the EO of O. vulgare is a potentially nontoxic and ecofriendly botanical fungicide for postharvest control of gray mold.

Changes in soil water holding capacity and water availability following vegetation restoration on the Chinese Loess Plateau.

Changes in land use type can lead to variations in soil water characteristics. The objective of this study was to identify the responses of soil water holding capacity (SWHC) and soil water availability (SWA) to land use type (grassland, shrubland and forestland). The soil water characteristic curve describes the relationship between gravimetric water content and soil suction. We measured the soil water characteristic parameters representing SWHC and SWA, which we derived from soil water characteristic curves, in the 0-50 cm soil layer at sites representing three land use types in the Ziwuling forest region, located in the central part of the Loess Plateau, China. Our results showed that the SWHC was higher at the woodland site than the grassland and shrubland, and there was no significant difference between the latter two sites, the trend of SWA was similar to the SWHC. From grassland to woodland, the soil physical properties in the 0-50 cm soil layer partially improved, BD was significantly higher at the grassland site than at the shrubland and woodland sites, the clay and silt contents decreased significantly from grassland to shrubland to woodland and sand content showed the opposite pattern, the soil porosity was higher in the shrubland and woodland than that in the grassland, the soil physical properties across the 0-50 cm soil layer improved. Soil texture, porosity and bulk density were the key factors affecting SWHC and SWA. The results of this study provide insight into the effects of vegetation restoration on local hydrological resources and can inform soil water management and land use planning on the Chinese Loess Plateau.

Microbial characteristics response to the soil quality of newly created farmland on the Loess Plateau.

Microbiome plays an important role in evaluating soil quality for sustainable agriculture. However, the suitability of biological indicators in reclaimed farmland is less understood. Using high-throughput sequencing, we evaluated the soil microbial community of the newly created farmland (NF) after reclamation with two local high-yield farmlands (slope farmland (SF), check-dam farmland (CF)) on the Loess Plateau. Soil enzyme activities and the amount of culturable microorganism were also quantified to assess the soil quality. Results showed that the microbial diversity, cultural microorganism abundance, and soil enzyme activities indicated poor soil quality in NF. The dominant bacterial phyla were Proteobacteria, Bacteroidetes, Acidobacteria, and Cyanobacteria. The abundance of Acidobacteria was significantly lower in NF (13.31%) than in SF (27.25%) and CF (27.91%). Soil enzyme activities had a significant correlation with the abundance of culturable microorganism, Proteobacteria and Bacteroidetes, soil organic matter, total nitrogen, cation exchange capacity, and pH, suggesting that soil microbes have driven the formation of nutrition and further mediated crop growth. Therefore, the application of bacterial fertilizers could be a potential way to improve the soil quality of reclaimed farmland for crop growth.

Potential health risk assessment of HFRs, PCBs, and OCPs in the Yellow River basin.

The concentrations of PBDEs, NBFRs, DP, PCBs, and OCPs were analyzed in water samples of the Yellow River Basin (YRB) and in soil and maize samples collected from basin irrigation areas to understand the status of POPs and associated health risks. The results showed: (1) the congeners of eight PBDEs and seven NBFRs were detected in 10 tributaries, with average concentrations of 1575 and 4288 pg. L-1. Thirty-three congeners of PCBs were detected, and the average concentration of PCB was 232 pg. L-1. Five HCHs were the primary congeners among twenty-three congeners of OCPs in the ten tributaries, accounting for 79% of the total. The average concentration of OCPs was 8287 pg. L-1. (2) Similar congeners of HFRs, PCBs, and OCPs were found in the trunk water. The ranking based on the HFR concentration was upstream > downstream > midstream, and that of the PCB and OCP concentration was downstream > upstream > midstream. (3) PCBs and OCPs in the trunk water of the YRB and in the soil and maize irrigated with river water pose potential carcinogenic and non-carcinogenic risks. The results indicate considerable organic pollution in the YRB, suggesting that national emission standards for POPs should be implemented soon.

Pegaharmols A-B, Axially Chiral ß-Carboline-quinazoline Dimers from the Roots of Peganum harmala.

Two nonbiaryl axially chiral ß-carboline-quinazoline dimers, pegaharmols A (1) and B (2), were isolated from the roots of Peganum harmala. Their planar structures were elucidated by the spectroscopic methods of high-resolution mass spectrometry and 1D and 2D nuclear magnetic resonance (NMR). The stereochemistry was established by a comparison between the experimental data of NMR and electronic circular dichroism and the computed data by quantum mechanical calculations. It is discovered for the first time that the ß-carboline at the C-8 position is bonded to the vasicine at the C-9 position. 1 exhibited moderate cytotoxic activity against HL-60 and A549 cell lines.

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This study aimed to explore the chemical composition of essential oil isolated from Origanum vulgare and investigated its allelopathic potential. The essential oil isolated by hydro-distillation from the whole plant of O. vulgare was analyzed by GC and GC-MS. Fourteen different components were identified, constituting 93.56% of the total area of peaks. The major components were methyleugenol (16.5%), myristicin (15.6%), carvacrol (15.0%), thymol (9.8%), and apioline (9.4%). We examined the inhibitory effects of essential oil on seed germination and seedling growth of wheat (Triticum aestivum), mung bean (Vigna radiata), and radish (Raphanus sativus). The results showed that essential oil of O. vulgare inhibited seed germination of all tested crops, with wheat being the most susceptible, followed by radish and mung bean. The inhibitory effects of essential oil on growth of the aboveground part of tested crops were greater than that of underground part. The inhibitory effects of essential oil on the seedling length of all tested crops increased in a dose-dependent manner, with the same pattern for radicle length of wheat and radish as well. Meanwhile, essential oil could stimulate radicle growth of V. radiata at low concentration, but inhibit the growth at high concentration. Our results confirmed the existence of allelochemicals in the essential oil of O. vulgare. However, what the compounds will be and how about their allelopathic mechanism needs further investigation.

PDGFR-ß Promoter Forms a Vacancy G-Quadruplex that Can Be Filled in by dGMP: Solution Structure and Molecular Recognition of Guanine Metabolites and Drugs.

Aberrant expression of PDGFR-ß is associated with a number of diseases. The G-quadruplexes (G4s) formed in PDGFR-ß gene promoter are transcriptional modulators and amenable to small molecule targeting. The major G4 formed in the PDGFR-ß gene promoter was previously shown to have a broken G-strand. Herein, we report that the PDGFR-ß gene promoter sequence forms a vacancy G-quadruplex (vG4) which can be filled in and stabilized by physiologically relevant guanine metabolites, such as dGMP, GMP, and cGMP, as well as guanine-derivative drugs. We determined the NMR structure of the dGMP-fill-in PDGFR-ß vG4 in K+ solution. This is the first structure of a guanine-metabolite-fill-in vG4 based on a human gene promoter sequence. Our structure and systematic analysis elucidate the contributions of Hoogsten hydrogen bonds, sugar, and phosphate moieties to the specific G-vacancy fill-in. Intriguingly, an equilibrium of 3'- and 5'-end vG4s is present in the PDGFR-ß promoter sequence, and dGMP favors the 5'-end fill-in. Guanine metabolites and drugs were tested and showed a conserved selectivity for the 5'-vacancy, except for cGMP. cGMP binds both the 3'- and 5'-end vG4s and forms two fill-in G4s with similar population. Significantly, guanine metabolites are involved in many physiological and pathological processes in human cells; thus, our results provide a structural basis to understand their potential regulatory functions by interaction with promoter vG4s. Moreover, the NMR structure can guide rational design of ligands that target the PDGFR-ß vG4.

Deep soil C and N pools in long-term fenced and overgrazed temperate grasslands in northwest China.

Fencing for grazing exclusion has been widely found to have an impact on grassland soil organic carbon (SOC) and total nitrogen (TN), but little is known about the impact of fenced grassland on the changes in deep soil carbon (C) and nitrogen (N) stocks in temperate grasslands. We studied the influence of 30 years fencing on vegetation and deep soil characteristics (0-500 cm) in the semi-arid grasslands of northern China. The results showed that fencing significantly increased the aboveground biomass (AGB), litter biomass (LB), total biomass, vegetation coverage and height, and soil water content and the SOC and TN in the deep soil. The belowground biomass (BGB) did not significantly differ between the fenced and grazed grassland. However, fencing significantly decreased the root/shoot ratio, forbs biomass, pH, and soil bulk density. Meanwhile, fencing has significantly increased the C and N stocks in the AGB and LB but not in the BGB. After 30 years of fencing, the C and N stocks significantly increased in the 0-500 cm soil layer. The accumulation of SOC mainly occurred in the deep layers (30-180 cm), and the accumulation of TN occurred in the soil layers of 0 to 60 cm and 160 to 500 cm. Our results indicate that fencing is an effective way to improve deep soil C and N stocks in temperate grassland of northwest China. There were large C and N stocks in the soil layers of 100 to 500 cm in the fenced grasslands, and their dynamics should not be ignored.

Indenoisoquinoline Topoisomerase Inhibitors Strongly Bind and Stabilize the MYC Promoter G-Quadruplex and Downregulate MYC.

MYC is one of the most important oncogenes and is overexpressed in the majority of cancers. G-Quadruplexes are noncanonical four-stranded DNA secondary structures that have emerged as attractive cancer-specific molecular targets for drug development. The G-quadruplex formed in the proximal promoter region of the MYC oncogene (MycG4) has been shown to be a transcriptional silencer that is amenable to small-molecule targeting for MYC suppression. Indenoisoquinolines are human topoisomerase I inhibitors in clinical testing with improved physicochemical and biological properties as compared to the clinically used camptothecin anticancer drugs topotecan and irinotecan. However, some indenoisoquinolines with potent anticancer activity do not exhibit strong topoisomerase I inhibition, suggesting a separate mechanism of action. Here, we report that anticancer indenoisoquinolines strongly bind and stabilize MycG4 and lower MYC expression levels in cancer cells, using various biochemical, biophysical, computer modeling, and cell-based methods. Significantly, a large number of active indenoisoquinolines cause strong MYC downregulation in cancer cells. Structure-activity relationships of MycG4 recognition by indenoisoquinolines are investigated. In addition, the analysis of indenoisoquinoline analogues for their MYC-inhibitory activity, topoisomerase I-inhibitory activity, and anticancer activity reveals a synergistic effect of MYC inhibition and topoisomerase I inhibition on anticancer activity. Therefore, this study uncovers a novel mechanism of action of indenoisoquinolines as a new family of drugs targeting the MYC promoter G-quadruplex for MYC suppression. Furthermore, the study suggests that dual targeting of MYC and topoisomerase I may serve as a novel strategy for anticancer drug development.

Racemic indole alkaloids from the seeds of Peganum harmala.

Five pairs of new 2-oxoindole alkaloids, (±)-peganumalines A-E (1-5), and a new indole alkaloid, peganumaline F (6), along with two known analogues, were isolated from the seeds of Peganum harmala. Their structures and absolute configurations were elucidated through spectroscopic analyses and quantum chemistry calculations. Notably, (±)-peganumalines A (1) represent a pair of rare 2-oxoindole dimeric alkaloid enantiomer with the hitherto unknown carbon skeleton. All isolates were tested for antiproliferative and antibacterial activities.

Cytotoxic quinazoline alkaloids from the seeds of Peganum harmala.

Seventeen quinazoline alkaloids and derivatives, containing two pairs of new epimers, named as (S)- and (R)-1-(2-aminobenzyl)-3-hydroxypyrrolidin-2-one ß-d-glucopyranosyl-(1 → 6)-ß-d-glucopyranoside (1, 2), (S)- and (R)-vasicinone ß-d-glucopyranosyl-(1 → 6)-ß-d-glucopyranoside (3, 4), and a new enantiomer (12b), together with six known ones (5-8, 10, and 12a), and three pairs of known enantiomers (9, 11, and 13), were isolated from the ethanol extracts of the seeds of Peganum harmala L.. Their structures including the absolute configuration were elucidated by using 1D and 2D NMR, and ECD calculation approaches. The cytotoxic activities of all isolated compounds were evaluated. 11 showed moderate cytotoxicity against PC-3 cells with an IC50 value of 15.41 µM.

Antiproliferative Dimeric Aporphinoid Alkaloids from the Roots of Thalictrum cultratum.

Inspired by the intriguing structures and bioactivities of dimeric alkaloids, 11 new thalifaberine-type aporphine-benzylisoquinoline alkaloids, thalicultratines A-K, a tetrahydroprotoberberine-aporphine alkaloid, thalicultratine L, and five known ones were isolated from the roots of Thalictrum cultratum. Their structures were defined on the basis of NMR and HRESIMS data. The antiproliferative activities of compounds 1-17 were evaluated against human leukemia HL-60 and prostate cancer PC-3 cells. Most alkaloids showed potent cytotoxicity against selected cancer cells. Preliminary SARs are discussed. The most active new compound (3), with an IC50 value of 1.06 µM against HL-60 cells, was selected for mechanism of action studies. The results revealed that compound 3 induced apoptosis and arrested the HL-60 cell cycle at the S phase with the loss of mitochondria membrane potential. The nuclear morphological Hoechst 33258 staining assay was also carried out, and the results confirmed apoptosis.