Characterization of yeast mutant strains for starter culture in Arabica coffee fermentation.

Arabica coffee is the most popular and best-selling type of coffee. During coffee fermentation, microorganisms are essential for the production of metabolites and volatile compounds that affect coffee flavor quality. This work aimed to study the mutation, selection, and characterization of the Wickerhamomyces anomalus strain YWP1-3 as a starter culture to enhance the flavor quality of Arabica coffee. The results revealed that six mutants could produce relatively high levels of the pectinase enzyme on pectin agar media and exhibited high activity levels, ranging from 332.35 to 415.88 U/ml in mucilage broth. Strains UV22-2, UV22-3, UV41-1 and UV32-1 displayed higher levels of amylase activity than did the wild type. The UV22-2 and UV22-3 mutants exhibited the highest pectin degradation indices of 49.22% and 45.97%, respectively, and displayed significantly enhanced growth rates in nitrogen yeast base media supplemented with various sugars; thus, these mutants were evaluated for their ability to serve as a starter for fermentation of Arabica coffee. The cupping scores of coffees derived from UV22-2 and UV22-3 were 83.5 ± 1.5 and 82.0 ± 2.14, respectively. The volatile compounds in the roasted coffee fermented by UV22-2 were analyzed by GC‒MS, which revealed higher levels of furfuryl alcohol and furfuryl acetate than did the other samples. These findings suggested that UV22-2 could be an influential starter culture for Arabica coffee fermentation.

Influence of Different Extraction Methods on the Changes in Bioactive Compound Composition and Antioxidant Properties of Solid-State Fermented Coffee Husk Extracts.

In brewing coffee, a huge amount of food waste is generated; that waste, coffee husks in particular, should be comprehensively exploited. They offer a rich source of bioactive compounds such as caffeine, chlorogenic acid, and trigonelline. The aim of this study was to investigate the effects of extraction methods on the bioactive compounds and antioxidant activity of such waste. Coffee husks in this study were fermented with S. cerevisiae based on a solid-state fermentation technique. The study method included ethanolic or water extraction with varied controllable factors, i.e., temperature (60, 100°C) and extraction technique. Bioactive contents were investigated with the Folin-Ciocalteu assay and 1H-NMR spectroscopy. The antioxidant activity was investigated with DPPH and FRAP assays. Results show that yields were the highest in the extract of fermented coffee husks at 100°C. The highest levels of bioactive contents (total trigonelline content at 3.59% and antioxidant activity at 23.35% (DPPH) and 25.9% (FRAP)) were found in the ethanolic extract of fermented coffee husks at 60°C. The bioactive content and bioactivity, including antioxidant activity, depended on different raw materials, preparation methods, and extraction conditions. This study illustrates the potential for using food waste such as coffee husks as a sustainable source of bioactive compounds or bioactive extracts.

13-Butoxyberberine Bromide Inhibits Migration and Invasion in Skin Cancer A431 Cells.

Cancer metastasis is the primary cause of cancer morbidity and mortality. Anti-metastasis mechanism of skin cancer by 13-butoxyberberine bromide, a novel berberine derivative, has not yet been reported. This study investigated the effects of 13-butoxyberberine bromide on migration and invasion of skin cancer A431 cells. The cytotoxicity of 13-butoxyberberine bromide was determined by MTT assay. The effect of 13-butoxyberberine bromide on cell migration and invasion were examined using a wound-healing assay, transwell migration assay, and transwell invasion assay, respectively. The cell adhesion ability was determined by an adhesion assay. Protein expressions that play important roles in cancer migration and invasion were evaluated by Western blot analysis. The results showed that 13-butoxyberberine bromide effectively inhibited cell migration, invasion, and adhesion in A431 cells. Interestingly, 13-butoxyberberine bromide was more effective for cell migration inhibition than berberine. In addition, 13-butoxyberberine bromide showed anti-migration and anti-invasion effects by down-regulated MMP-2 and MMP-9 expression and up-regulated TIMP-1 and TIMP-2 expression in A431 cells. Moreover, pretreatment with 13-butoxyberberine bromide significantly inhibited EGF-induced cell migration and p-EGFR, ERK, p-ERK, STAT3, and p-STAT3 expressions in A431 cells at lower concentrations when compared with the berberine. These findings indicated that 13-butoxyberberine bromide could be further developed as an anticancer agent.

New approach for screening of microorganisms from Arabica coffee processing for their ability to improve Arabica coffee flavor.

The purpose of this research was to isolate microorganisms from coffee fermentation processes and screen them for their potential to improve the flavor of Arabica coffee using a new approach that included pectin degradation ability and growth in mucilage broth. All of the studied microorganisms were isolated from 38 different samples of fresh coffee cherries, coffee mucilage and coffee pulp. A total of 262 microbial isolates were obtained and subjected to screening using pectinase screening agar medium for pectinolytic organisms. The results of the pectinase production test showed that 18 yeast isolates were found to produce pectinase that could degrade the pectin present in solid media. The sugar assimilation profiles and growth of selected strains in mucilage broth were studied. Therefore, 18 isolates from the selected yeasts were subjected to molecular identification by the use of 18S rRNA gene sequencing. The diversity of the yeast isolates was studied, and they were identified as Wickerhamomyces anomalus, Naganishia liquefaciens, Pichia kudriavzevii, Kazachstania naganishii and Kazachstania sp. Moreover, isolates SWU3YWP1-3, SWU3YSK9 and INFCY1-4 were used as a seed culture for Arabica coffee fermentation. The cupping sensory scores of the control (without yeast inoculation) and those inoculated with three isolated yeast strains that were determined by Q-Arabica Graders were 73.75, 84.75, 80.25 and 75.00, respectively. Unique flavors and aromas were detected. This is the first report of screening microorganisms from the Arabica coffee fermentation process by the combination of various properties with success in improving the quality of coffee beverage.

Enhancing Anticancer Potency of a 13-Substituted Berberine Derivative with Cationic Liposomes.

Cationic liposomal formulations of the telomeric G-quadruplex stabilizing ligand, 13-(2-naphthylmethoxy)berberine bromide (1), have been developed with the purpose of delivering 1 into the nucleus of cancer cells for potential telomere targeting. Berberine derivative 1 was encapsulated in various cationic lipids 2-4 by the thin film evaporation method; these lipids are cationic after amine protonation. The most appropriate liposomal berberine formulation was that of 1 and the cholesterol derived cationic lipid 4 in a weight ratio of 1 : 20 with 76.5% encapsulation efficiency of 1. Cellular uptake studies in the HeLa and HT-29 cancer cells lines showed that the liposomal berberine derivative uptake in the cells was higher and more stable than for berberine derivative 1 alone while free 1 was completely decomposed in the cells within 60 min exposure to the cells. Anticancer activity of the liposomal berberine derivative 1 based on 4 was greater than that for the free berberine derivative 1 in the MCF-7, HeLa and HT-29 cell line by 2.3-, 4.9- and 5.3-fold, respectively, and also, interestingly, superior to the anticancer drug doxorubicin against the HT29 cancer cell line.

Inhibitory effects on chondrosarcoma cell metastasis by Senna alata extract.

BACKGROUND: Senna alata L. Roxb or candle bush is a traditional medicinal plant with a wide range of biological activities including anti-inflammatory, antimicrobial and antifungal. Leaf extract of S. alata showed the anti-tumor activity in various cancer cell lines. In this study, we focused on the inhibitory mechanism of S. alata extract (SAE) on cancer metastasis including cell migration, cell invasion and signaling pathways in chondrosarcoma SW1353 cells. PURPOSE: This study aimed to evaluate the anti-metastatic mechanisms of Senna alata extract on chondrosarcoma SW1353 cells. METHODS: Screening for phytochemicals in biologically active fraction of SAE was analysed by 1H NMR spectroscopy. Cell viability and cytoxicity were determined by using MTT assay. Cell migration was observed by scratch wound healing and transwell migration assay. Cell invasion and cell adhesion assay were examined by Matrigel coated transwell chambers or plates. The expression of matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs), MAPKs and PI3K/Akt signaling pathways and NF-κB were detected by Western blot analysis. RESULTS: The SAE treatment at the sub-cytoxic and non-cytotoxic concentrations significantly inhibited cell migration, cell invasion and cell adhesion of SW1353 cells in a dose-dependent manner. The results from Western blot analysis showed decreased MMP-2 and MMP-9 expression, while increased TIMP-1 and TIMP-2 expression in SAE treated cells. Moreover, SAE suppressed phosphorylation of ERK1/2, p38 and Akt but decreased NF-κB transcription factor expression in SW1353 cells. CONCLUSION: These results revealed that SAE could reduce MMP-2 and MMP-9 expression by downregulation of NF-κB which is downstream of MAPKs and PI3K/Akt signaling pathway in SW1353 cells resulting in reduced cancer cell migration and invasion. Therefore, SAE may have the potential use as an alternative treatment of chondrosarcoma metastasis.

A Facile Synthesis of Self-Catalytic Hydrogel Films and Their Application as a Wound Dressing Material Coupled with Natural Active Compounds.

A simple and economical method for polyvinyl alcohol/polyvinylpyrrolidone/citric acid (PVA/PVP/CA) hydrogel preparation using microwave-assisted irradiation was presented. The synthesized hydrogels embedded with berberine or chlorogenic acid were investigated as a wound dressing agent. This study showed that the optimum condition for the hydrogel synthesis based on gel fraction and a degree of swelling values was 6:6:3% (w/v) of PVA/PVP/CA under 600 W at 120 °C for 3 min of microwave irradiation. Herbal active compounds, berberine and chlorogenic acid, were loaded onto the hydrogel (4% (w/v)), and both were able to inhibit the growth of Staphylococcus aureus. Additionally, the anti-inflammatory study revealed that 700 µg/mL berberine and 2500 µg/mL chlorogenic acid could inhibit protein degradation equivalent to a 200 µg/mL aspirin solution. The drug release study demonstrated that both compounds showed a more sustained release into PBS than water. The mechanism for the three-dimensional network formation based on esterification and the hydrogen-bonding interaction was also proposed. The ionic liquid-like structure of PVP-CA possibly played an important role in the cross-linking process. In addition, sodium bicarbonate applied to the synthesized hydrogel also had a significant effect in enhancing gel formation. The proposed approach showed a potential of the loaded hydrogels to protect wounds from infection and enhance the healing process.

A mechanism for the extension and unfolding of parallel telomeric G-quadruplexes by human telomerase at single-molecule resolution.

Telomeric G-quadruplexes (G4) were long believed to form a protective structure at telomeres, preventing their extension by the ribonucleoprotein telomerase. Contrary to this belief, we have previously demonstrated that parallel-stranded conformations of telomeric G4 can be extended by human and ciliate telomerase. However, a mechanistic understanding of the interaction of telomerase with structured DNA remained elusive. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) microscopy and bulk-phase enzymology to propose a mechanism for the resolution and extension of parallel G4 by telomerase. Binding is initiated by the RNA template of telomerase interacting with the G-quadruplex; nucleotide addition then proceeds to the end of the RNA template. It is only through the large conformational change of translocation following synthesis that the G-quadruplex structure is completely unfolded to a linear product. Surprisingly, parallel G4 stabilization with either small molecule ligands or by chemical modification does not always inhibit G4 unfolding and extension by telomerase. These data reveal that telomerase is a parallel G-quadruplex resolvase.

Tuning the chain length of new pyrene derivatives for site-selective photocleavage of avidin.

Rational design of photoreagents with systematic modifications of their structures can provide valuable information for a better understanding of the protein photocleavage mechanism by these reagents. Variation of the length of the linker connecting the photoactive moiety with the protein anchoring-group allowed us to investigate the control of the protein photocleavage site. A series of new photochemical reagents (PMA-1A, PMA-2A and PMA-3A) with increasing chain lengths is examined in the current study. Using avidin as a model system, we examined the interaction of these probes by UV-Vis, fluorescence spectroscopic methods, photocleavage and computational docking studies. Hypochromism of the absorption spectrum was observed for the binding of these new photochemical reagents with estimated binding constants (Kb) of 6.2 × 105, 6.7 × 105 and 4.6 × 105 M-1, respectively. No significant changes of Stern-Volmer quenching constant (Ksv) with Co(NH3)6Cl3 has been noted and the data indicated that the probes bind near the surface of the protein with sufficient exposure to the solvent. Photoexcitation of the probe-avidin complex, in the presence of Co(NH3)6Cl3, resulted in protein fragmentation, and the cleavage yield decreased with the increase in the linker length, and paralleled with the observed Ksv values. Amino acid sequencing of the photofragments indicated that avidin is cleaved between Thr77 and Val78, as a major cleavage site for all the three photoreagents. This site is proximate to the biotin binding site on avidin, and molecular docking studies indicated that the H-bonding interactions between the polar end-group of the photoreagents and hydrophilic amino acids of avidin were important in positioning the reagent on the protein. The major cleavage site, at residues 77-78, was within 5 Šof the pyrenyl moiety of the probe, and hence, molecular tuning of the linker provided a simple approach to position the photoreagent along the potential photocleavage site.

Photochemistry and mechanism of designed pyrenyl probe towards promoted cleavage of proteins.

A new photochemical reagent, succinic acid-1(1-pyrene)methylamide (PMA-SUC), was developed to recognize the specific binding sites on model proteins, egg-white lysozyme and avidin. The interaction of the photochemical reagent with the proteins was studied by UV-Vis, fluorescence spectroscopic methods and docking description. PMA-SUC was found to bind to lysozyme and avidin with binding constants (Kb) of 2.4×105 and 6.7×105 (M-1), respectively. The fluorescence intensity of PMA-SUC decreased with increasing concentration of both proteins. Quenching of PMA-SUC fluorescence, in the absence and presence of the protein by an electron acceptor (Hexaamminecobalt(III) chloride, Co(NH3)6Cl3) showed no significant changes in the Ksv values (Stern-Volmer quenching constant), indicating that PMA-SUC bound to the hydrophilic sites or near the surface of the proteins. Irradiation of protein-PMA-SUC mixture, at 342nm for a period of time, in the presence of Co(NH3)6Cl3 as an electron acceptor, resulted in the cleavage of both proteins with high specificity. Binding mechanisms were studied using Molecular docking method. Molecular docking study indicated the position of PMA-SUC upon binding to the proteins by hydrogen bonding interaction with donor-acceptor within the distance of less than 5Å in the minimum of binding free energy. The docking results have supported the results obtained from the spectroscopic methods and cleavage studies.

ESI-MS Investigation of an Equilibrium between a Bimolecular Quadruplex DNA and a Duplex DNA/RNA Hybrid.

Electrospray ionization mass spectrometry (ESI-MS) conditions were optimized for simultaneous observation of a bimolecular qDNA and a Watson-Crick base-paired duplex DNA/RNA hybrid. The DNA sequence used was telomeric DNA, and the RNA contained the template for telomerase-mediated telomeric DNA synthesis. Addition of RNA to the quadruplex DNA (qDNA) resulted in formation of the duplex DNA/RNA hybrid. Melting profiles obtained using circular dichroism spectroscopy confirmed that the DNA/RNA hybrid exhibited greater thermal stability than the bimolecular qDNA in solution. Binding of a 13-substituted berberine (1) derivative to the bimolecular qDNA stabilized its structure as evidenced by an increase in its stability in the mass spectrometer, and an increase in its circular dichroism (CD) melting temperature of 10°C. The DNA/RNA hybrid did not bind the ligand extensively and its thermal stability was unchanged in the presence of (1). The qDNA-ligand complex resisted unfolding in the presence of excess RNA, limiting the formation of the DNA/RNA hybrid. Previously, it has been proposed that DNA secondary structures, such as qDNA, may be involved in the telomerase mechanism. DNA/RNA hybrid structures occur at the active site of telomerase. The results presented in the current work show that if telomeric DNA was folded into a qDNA structure, it is possible for a DNA/RNA hybrid to form as is required during template alignment. The discrimination of ligand (1) for binding to the bimolecular qDNA over the DNA/RNA hybrid positions it as a useful compound for probing the role(s), if any, of antiparallel qDNA in the telomerase mechanism.

Synthesis and structural characterization of 1-[2-(5-nitro-1H-indol-2-yl)phenyl]methylpyridinium chloride.

In the course of studies on hybrid antibacterials incorporating 2-aryl-5-nitro-1H-indole moieties as potential bacterial NorA efflux pump inhibitors, the compound 1-[2-(5-nitro-1H-indol-2-yl)phenyl]methylpyridinium chloride (2) was synthesized and structurally characterized. This pyridinium chloride salt crystallized in the monoclinic space group P2(1)/c with the following unit cell dimensions: a 10.274(3) Å, b 13.101(4) Å, c 13.439(4) Å, b 107.702(7)°, V 1723.2(9) ų, Z (f.u.) = 4; R1 = 0.048, and wR2 = 0.13. Of interest in the single crystal X-ray structure is the (intramolecular) disposition of the pyridinium plane over the indole heterocyclic residue [interplanar dihedral angle 17.91(4)°].

A mass spectrometric investigation of novel quadruplex DNA-selective berberine derivatives.

ESI mass spectrometry was used to assess the binding of 13-substituted, 5-nitro-2-phenylindolyl- and 2-naphthalenyl-based berberine derivatives to inter- and intramolecular G-quadruplex DNA molecules. In contrast with the parent berberine, the compounds showed selectivity for quadruplex over duplex DNA and stabilised the quadruplex structure. They represent a new class of quadruplex DNA-selective ligands.

Antibacterial activity of berberine-NorA pump inhibitor hybrids with a methylene ether linking group.

Conjugation of the NorA substrate berberine and the NorA inhibitor 5-nitro-2-phenyl-1H-indole via a methylene ether linking group gave the 13-substituted berberine-NorA inhibitor hybrid, 3. A series of simpler arylmethyl ether hybrid structures were also synthesized. The hybrid 3 showed excellent antibacterial activity (MIC Staphylococcus aureus, 1.7 microM), which was over 382-fold more active than the parent antibacterial berberine, against this bacterium. This compound was also shown to block the NorA efflux pump in S. aureus.

Hetisine-type diterpenoid alkaloids from the Bhutanese medicinal plant Aconitum orochryseum.

Investigation of Aconitum orochryseum, a Bhutanese traditional medicine ("gSo-ba Rig-pa") plant locally known as "Bong-kar", resulted in the isolation of three new hetisine-type diterpenoid alkaloids, named orochrine (1), 2-O-acetylorochrine (2), and 2-O-acetyl-7alpha-hydroxyorochrine (3), together with the previously reported alkaloids atisinium chloride (4) and virescenine (5). The structures of the new alkaloids were elucidated by spectroscopic data analysis.

Dual action-based approaches to antibacterial agents.

This review collates and analyses recent work done on dual action approaches to tackling the mounting health problem of resistance by human pathogenic bacteria to antibacterial agents. In particular the areas reviewed include the use of two drugs in combination, dual action prodrugs, and dual action drugs (or hybrid drugs).

Selectivity of an indolyl berberine derivative for tetrameric G-quadruplex DNA.

Negative ion electrospray ionization mass spectrometry (ESI-MS) was used to compare the binding affinities and stoichiometries of the alkaloid berberine, a 13-substituted indolyl berberine derivative, SS14, and the chemotherapeutic agent, daunomycin, for 16-mer double-stranded (ds) DNA (D1 and D2) and for an 8-mer tetrameric quadruplex, Q1 (d(TTGGGGGT)(4)). Under the experimental conditions presented here, ESI mass spectra of Q1 showed that the major ions were from Q1 with three ammonium ions bound in the structure. Ions from Q1 with four ammonium ions were of lower abundance. In agreement with other work, there were multiple binding sites on the dsDNA and the quadruplex for daunomycin and berberine. The binding of SS14 to both dsDNA and Q1 was less extensive. Although the binding affinity of SS14 for Q1 was modest, this compound showed a clear preference for Q1 DNA over D1 or D2 DNA. Berberine and daunomycin bound with greater affinity to both types of DNA secondary structure, with the former showing a slight preference for Q1 over D1 while the latter showed a slight preference for D1 over Q1. While at least five berberine molecules bound to Q1, this quadruplex could accommodate only two SS14 molecules. These investigations show that SS14 is a promising lead compound for drugs that may selectively bind quadruplex over duplex DNA.

Conjugating berberine to a multidrug efflux pump inhibitor creates an effective antimicrobial.

In bacteria, multidrug-resistance pumps (MDRs) confer resistance to chemically unrelated amphipathic toxins. A major challenge in developing efficacious antibiotics is identifying antimicrobial compounds that are not rapidly pumped out of bacterial cells. The plant antimicrobial berberine, the active component of the medicinal plants echinacea and golden seal, is a cation that is readily extruded by bacterial MDRs, thereby rendering it relatively ineffective as a therapeutic agent. However, inhibition of MDR efflux causes a substantial increase in berberine antimicrobial activity, suggesting that berberine and potentially many other compounds could be more efficacious if an effective MDR pump inhibitor could be identified. Here we show that covalently linking berberine to INF 55 , an inhibitor of Major Facilitator MDRs, results in a highly effective antimicrobial that readily accumulates in bacteria. The hybrid molecule showed good efficacy in a Caenorhabditis elegans model of enterococcal infection, curing worms of the pathogen.

Synthesis of functionalized 2-aryl-5-nitro-1H-indoles and their activity as bacterial NorA efflux pump inhibitors.

In order to develop structure-activity relationships and to provide access to antibacterial agents for dual action studies, a variety of aryl group-substituted 2-aryl-5-nitro-1H-indoles were synthesized and the activity of the compounds assessed as inhibitors of the NorA multidrug resistance pump in the bacterium Staphylococcus aureus. The NorA protein from the major facilitator superfamily of efflux pumps confers resistance to a variety of structurally dissimilar antimicrobials such as norfloxacin, ethidium bromide, berberine and acriflavin. The compound [4-benzyloxy-2-(5-nitro-1H-2-yl)-phenyl]-methanol was the most potent pump inhibitor.