MOLECULAR DOCKING STUDIES OF BERBERINE DERIVATIVE AS NOVEL MULTITARGET PCSK9 AND HMGCR INHIBITORS

Hypercholesterolemia is a high risk for cardiovascular diseases, stroke, and mortality. Multitarget directed ligands (MTDLs) with dual inhibition of Proprotein Convertase Subtilisin/Kexin type 9 (PCSK9) and 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR) are the potential targets for the treatment of hyperlipidemia. In this work, a novel series of Berberine (BBR) derivatives was designed based on molecular docking to serve as MTDLs for PCSK9 and HMGCR. The binding energy of BBR derivatives was investigated, which confirmed that all the designed compounds showed better binding energy than the parent BBR for both enzymes. The effect of different benzenesulfonyl ring substituents was explored to improve the binding affinity. The obtained results indicated that there are significant differences in their interactions and mode of binding. All 24 designed compounds were identified as the potent multitarget inhibitors because the increase of hydrogen bond, hydrophobic and electrostatic interactions were observed. Among them, 12 could be selected as the best candidate for further study as potential multitarget PCSK9 and HMGCR inhibitors for anti-hypercholesterolemia. The obtained result suggested that the introduction of the nitro- group plays a vital role in the binding pose of the BBR derivative. Finally, in silico study confirmed that most of the compounds pass the drug likeliness properties

Additive effects on cotton dyeing with dye extract from achiote seeds

Cotton yarns have been pretreated with the additives, such as chitosan, microcrystalline chitosan, quaternized chitosan &aqueous extract from the fruit of Diospyros mollis Griff, as well as with the commercial formaldehyde-free cationic fixingagent (Sera® Fast C-NC) & alum (post-mordanting), and their dyeing fastness properties are studied. These treated cottonyarns are then dyed with the annatto dye extract from Bixa orellana L. (Achiote) seeds and tested for different propertiesincluding K/S value, light fastness, and wash fastness. Pre-treatment of cotton yarn with chitosan or microcrystallinechitosan solution (together with glyoxal cross-linking) or quaternized chitosan, or Sera® Fast C-NC before dyeing, shows abetter color depth (K/S) and improved wash fastness properties in comparison to yarn with alum post-mordanting and theuntreated cotton yarn. Improved light fastness is also obtained on inclusion of the anti-oxidant ascorbic acid in the posttreatmentprotocol. These additive treatments thus offer considerable potential for the improved annatto dyeing of cotton

Additive effects on cotton dyeing with dye extract from achiote seeds

466-474Cotton yarns have been pretreated with the additives, such as chitosan, microcrystalline chitosan, quaternized chitosan & aqueous extract from the fruit of Diospyros mollis Griff, as well as with the commercial formaldehyde-free cationic fixing agent (Sera® Fast C-NC) & alum (post-mordanting), and their dyeing fastness properties are studied. These treated cotton yarns are then dyed with the annatto dye extract from Bixa orellana L. (Achiote) seeds and tested for different properties including K/S value, light fastness, and wash fastness. Pre-treatment of cotton yarn with chitosan or microcrystalline chitosan solution (together with glyoxal cross-linking) or quaternized chitosan, or Sera® Fast C-NC before dyeing, shows a better color depth (K/S) and improved wash fastness properties in comparison to yarn with alum post-mordanting and the untreated cotton yarn. Improved light fastness is also obtained on inclusion of the anti-oxidant ascorbic acid in the post-treatment protocol. These additive treatments thus offer considerable potential for the improved annatto dyeing of cotton

A Potential of Mutant Yeast Strain for Improvement Arabica Coffee Fermentation Process

Arabica coffee is a worldwide popular beverage. Coffee fermentation is important process to enhance the coffee flavor quality. Microorganisms involved in the process are the main factor affecting coffee quality. This study aims to apply the new starter culture of Wickerhamomyces anomalus UV22-3, a UV mutant strain, for coffee fermentation and to improve arabica coffee beverage quality. The results showed that W. anomalus UV22-3 as a starter culture for coffee fermentation could enhance the coffee flavor quality compared to the control experiment (without inoculum). Fermented arabica coffee by strain UV22-3 showed a higher cupping score than wild type and a control condition with unique cupping notes. According to the flavor profile evaluated by Q-graders, the result of this sensory evaluation is 82. Microbial population in the fermentation broth was evaluated. The total yeast number was stable, while the total bacteria was higher after 24 h of strain UV22-3 fermentation. The pH value slightly decreased when the total dissolved solid increased. This research is one alternative to improve the quality of coffee in Thailand by using a novel yeast strain

Chemical Profiling and in vitro Testing for PCSK9 Inhibition of Coffee Cascara Extract

Coffee cascara is a by-product generated from coffee processing. It has been discarded as an agricultural waste.  In order to reduce the environmental problems caused by coffee processing, this study aimed to investigate the effect of fresh coffee cascara extract (CCE) on the inhibition of PCSK9 which is an enzyme that can increase low-density plasma lipoprotein (LDL) cholesterol by destructing LDL receptor.  Moreover, the CCE chemical profile was identified by the thin-layer chromatography (TLC) technique together with diffusion-ordered NMR spectroscopy (DOSY). The chemical profile analysis results showed that trigonelline, caffeine, and chlorogenic acid were present in CCE, and its PCSK9 inhibitory activity screening showed that CCE at concentrations of 0.25 and 0.50 mg/mL reduced the amount of PCSK9 by 72 and 78%, respectively.  These results revealed that coffee cascara provides novel applications in the nutraceutical industry

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

30 pags., 10 figs., 1 tab.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.Cancer Council NSW RG 11-07 Tracy M Bryan, Cancer Institute NSW Aaron Lavel Moye, Australian Research Council FL140100027 Antoine M van Oijen, Ernest and Piroska Major Foundation Scott B Cohen, Natural Sciences and Engineering Research Council of Canada, Masad J Damha Centre of Excellence for Innovation in Chemistry PERCH-CIC Siritron Samosorn Research Unit of Natural Products and Organic Synthesis for Drug Discovery NPOS 405/2560 Siritron Samosorn Cancer Council NSW RG 16-10 Tracy M Brya

Antimicrobial and Efflux Pump Inhibitory Activity of Caffeoylquinic Acids from Artemisia absinthium against Gram-Positive Pathogenic Bacteria

Background: Traditional antibiotics are increasingly suffering from the emergence of multidrug resistance amongst pathogenic bacteria leading to a range of novel approaches to control microbial infections being investigated as potential alternative treatments. One plausible antimicrobial alternative could be the combination of conventional antimicrobial agents/antibiotics with small molecules which block multidrug efflux systems known as efflux pump inhibitors. Bioassay-driven purification and structural determination of compounds from plant sources have yielded a number of pump inhibitors which acted against gram positive bacteria. Methodology/Principal Findings: In this study we report the identification and characterization of 4′,5′-O-dicaffeoylquinic acid (4′,5′-ODCQA) from Artemisia absinthium as a pump inhibitor with a potential of targeting efflux systems in a wide panel of Gram-positive human pathogenic bacteria. Separation and identification of phenolic compounds (chlorogenic acid, 3′,5′-ODCQA, 4′,5′-ODCQA) was based on hyphenated chromatographic techniques such as liquid chromatography with post column solid-phase extraction coupled with nuclear magnetic resonance spectroscopy and mass spectroscopy. Microbial susceptibility testing and potentiation of well know pump substrates revealed at least two active compounds; chlorogenic acid with weak antimicrobial activity and 4′,5′-ODCQA with pump inhibitory activity whereas 3′,5′-ODCQA was ineffective. These intitial findings were further validated with checkerboard, berberine accumulation efflux assays using efflux-related phenotypes and clinical isolates as well as molecular modeling methodology. Conclusions/Significance: These techniques facilitated the direct analysis of the active components from plant extracts, as well as dramatically reduced the time needed to analyze the compounds, without the need for prior isolation. The calculated energetics of the docking poses supported the biological information for the inhibitory capabilities of 4′,5′-ODCQA and furthermore contributed evidence that CQAs show a preferential binding to Major Facilitator Super family efflux systems, a key multidrug resistance determinant in gram-positive bacteria.National Institutes of Health (U.S.) (grant R01GM59903)National Institutes of Health (U.S.) (grant R01AI050875)Netherlands Organization for Scientific Research (VICI grant 700.56.442)Massachusetts Technology Transfer Center (MTTC)National Institutes of Health (U.S.) (grant 5U54MH084690-02

Development of berberine-based derivatives as novel antimicrobial agents

Multidrug resistance (MDR) mediated by a drug efflux mechanism is one of the major drug resistance problems not only in bacteria but also in other microorganisms. NorA MDR efflux protein is a well characterized and major efflux pump in the pathogenic Gram-positive bacterium, Staphylococcus aureus. It contributes to the resistance to berberine and ciprofloxacin antibiotics by extrusion of these drugs from the cells of S. aureus. In order to overcome this type of drug resistance by dual action agents incorporating efflux pump inhibitor properties and antibacterial activity, a variety of new, aryl group-substituted 2-aryl-5-nitro-1H-indole efflux pump inhibitors were synthesized. In the synthesis of these 2-aryl-5-nitro-1H-indoles, a new procedure for the N-acylation of indoles was developed based on DCC/DMAP coupling with carboxylic acids. This method was particularly effective with 5-nitro-1H-indole. The activity of these indole derivatives as inhibitors of the NorA MDR pump in S. aureus was assessed. It was found that some of the 2-aryl-5-nitro-1H-indole derivatives potentiated the activity of the antibacterial agents berberine and ciprofloxacin against the resistant strain, K2361, of S. aureus. The new 2-aryl-5-nitro-1H-indole inhibitors were particularly effective in potentiating the antibacterial activity of berberine. The compound [4-benzyloxy-2-(5-nitro-1H-2-yl)-phenyl]-methanol (43) was the most potent NorA pump inhibitor found in this work. A number of dual action antibacterial agents were designed and synthesized. These included dual action prodrugs, in which the MDR pump inhibitor and berberine were attached in the same molecule with enzymatically cleavable linkages (ester or amide groups), and dual action drugs with a non-cleavable linkage (methylene group). In the synthesis of the dual action agents, a direct new approach to 13-substituted berberine derivatives was found. This approach involved alkylation of 8-allyldihydroberberine followed by the elimination of propene. The antimicrobial activity of these indole-berberine compounds was assessed against a variety of pathogenic microorganisms. One of the dual action drugs, 9,10-dimethoxy-13-[2-(5-nitro-1H-indol-2-yl)benzyl]-5,6-dihydrobenzo[g]-1,3-benzodioxolo[5,6-a]quinolizinium bromide (64), was a potent antimicrobial agent at a clinically viable concentration against various bacteria in vitro, including Staphylococcus aureus K2361, Enterococcus faecalis V583, and Salmonella enterica Serovar Typhimurium SL1344R2. This compound also had good activity against the protozoan, Plasmodium falciparum K1 (in vitro). In the case of the dual action prodrugs, the amide prodrugs were more active than the ester prodrugs against the Gram-positive bacterium S. aureus and vice versa against the Gram-negative bacterium S. enterica Serovar Typhimurium. However, minimum inhibitory concentrations for all the dual action drugs and dual action prodrugs were near or at clinically useful concentrations (ca. 1��g/mL or less) as antibacterial agents against S. enterica Serovar Typhimurium SL1344R2, and they showed 400- to 1600-fold higher activity than the parent antibacterial agent berberine. The design principle of having in the one molecule an MDR inhibitor moiety and an antibacterial moiety was established as a viable one, which potentially could be extended to other types of antimicrobial agents

Morphological changes of a small reef island on a platform reef

This study examines: i) the morphological evolution of a small sand cay on a platform reef over past millennia; ii) changes in its shoreline over past decades; and ii) contemporary characteristics of waves on the reef platform. The study site is Warraber Island located on a platform reef in Torres Strait, Australia. The study is based upon: i) detailed radiocarbon dating; ii) 3-D morphological reconstruction using a DTM; and iii) field measurement of island topography, waves and wind. Temporal patterns of evolution were assessed based on radiocarbon dating on both bulk samples and on specific components. Bulk radiocarbon ages are indicated to be unreliable for the determination of time of sand deposition. However, ages from shells provide a more appropriate indication of time of deposition of sand in this reef setting. Shell ages imply the continual accretion of the island over the past 3,000 years with a long-term rate of accumulation of approximately 900 m3/y. Successive stages of accretion, and episodic progradation are indicated by prominent beach ridges. Variations in island shore position over shorter time scales were examined based on island shape over the past 40 years (1966-2004). Significant change of island shape has occurred only on the southwestern and northeastern ends, rotating in a clockwise direction; the island appears to have undergone net accretion on the northeastern end and erosion on the southwestern end. Wind climate and medium-term wind patterns were reconstructed. The E-SSE winds, especially ESE and SE winds, have been dominant with winds from the WNNW sector subordinate. The influence of sunspot periodicity and ENSO on the wind patterns is not discernible but the initiation of solar magnetic cycle was found to coincide with times of the low magnitude of wind effect. Wave conditions on the reef platform were examined based on the spectra of waves that were measured at a location close to the windward reef rim and five locations around the island. Development of spectral components and saturating conditions were also investigated. Wave characteristics were normally tidally modulated and related to the local wind system. In addition to incident wind wave components generated off the reef, incident short-period wave and infragravity wave components generated on the reef were prominent around the island. Combinations of these three components generate higher and shorter waves on the windward side of the island, and smaller and longer waves on the leeward side of the island. These wave characteristics can initiate movement of sediment around the island and on the island beach. Probable wave conditions in relation to topographical development over the period of island evolution are discussed based on the contemporary wave conditions on the reef platform. Wind climate and associated patterns of waves and sediment transport are major influences on island shape in response to seasonal influence. Changing wind patterns and wave conditions in relation to nearby reefs, and human activities on the island were examined to identify probable causes of change in island shape over the past 40 years. Over the coming decades, the island is likely to be maintained by the transport of sediment already on the reef flat to the island. Further adjustments of the island morphology are anticipated due to changes in climate and sea level. However, even if there is a gradual rise in sea level, sediment supply to the island is still anticipated because of the greater capacity of waves to entrain and transport sediment, presently abundant on the reef flat