Alchemical approach performance in calculating the ligand-binding free energy.

Alchemical binding free energy calculations are one of the most accurate methods for estimating ligand-binding affinity. Assessing the accuracy of the approach over protein targets is one of the most interesting issues. The free energy difference of binding between a protein and a ligand was calculated via the alchemical approach. The alchemical approach exhibits satisfactory accuracy over four targets, including AmpC beta-lactamase (AmpC); glutamate receptor, ionotropic kainate 1 (GluK1); heat shock protein 90 (Hsp90); and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro). In particular, the correlation coefficients between calculated binding free energies and the respective experiments over four targets range from 0.56 to 0.86. The affinity computed via free energy perturbation (FEP) simulations is overestimated over the experimental value. Particularly, the electrostatic interaction free energy rules the binding process of ligands to AmpC and GluK1. However, the van der Waals (vdW) interaction free energy plays an important role in the ligand-binding processes of HSP90 and SARS-CoV-2 Mpro. The obtained results associate with the hydrophilic or hydrophobic properties of the ligands. This observation may enhance computer-aided drug design.

A Vulvovaginal Yeast Infection Caused by Cryptococcus victoriae in Vietnam: A Rare Case Report.

Cases of vulvovaginitis caused by Cryptococcus genus are exceedingly uncommon, with only a handful of instances having been described for this causative species. This report describes a rare case of vulvovaginitis suspected to be caused by Cryptococcus victoriae in a 58-year-old woman residing in an urban area of Hanoi city, Vietnam. The patient with a 10-year history of depression and type 2 diabetes mellitus was admitted to the hospital due to vulvar itching and vaginal discharge. Vaginal swabs confirmed the presence of a yeast infection by direct microscopic examination with 10% KOH and culture on CHROMagar Candida. The yeast was identified as C victoriae using genetic sequencing tools. The patient's treatment plan involved topical clotrimazole and a daily oral dose of 200 mg of itraconazole for 7 days. This comprehensive treatment approach resulted in the patient's full recovery. This is the first reported case of vulvovaginitis attributed to C victoriae in humans worldwide.

Anti-inflammatory and Antiphytopathogenic Fungal Activity of 2,3-seco-Tirucallane Triterpenoids Meliadubins A and B from Melia dubia Cav. Barks with ChemGPS-NP and In Silico Prediction.

Two new rearranged 2,3-seco-tirucallane triterpenoids, meliadubins A (1) and B (2), along with four known compounds, 3-6, were isolated from the barks of Melia dubia Cav. Compound 2 exhibited a significant inflammatory inhibition effect toward superoxide anion generation in human neutrophils (EC50 at 5.54 ± 0.36 µM). It bound to active sites of a human inducible nitric oxide synthase (3E7G) through interactions with the residues of GLU377 and PRO350, which may benefit in reducing the neutrophilic inflammation effect. The ChemGPS-NP interpretation combined with bioactivity assay and in silico prediction results suggested 2 to be an agent for targeting iNOS with different mechanisms as compared to a selected set of current approved drugs. Moreover, compounds 1 and 2 showed remarkable inhibition against the rice pathogenic fungus Magnaporthe oryzae in a dose-dependent manner with IC50 values of 137.20 ± 9.55 and 182.50 ± 18.27 µM, respectively. Both 1 and 2 displayed interactions with the residue of TYR223, a key active site of trihydroxynaphthalene reductase (1YBV). The interpretation of 1 and 2 in the ChemGPS-NP physical-chemical property space indicated that both compounds are quite different compared to all members of a selected set of reference compounds. In light of demonstrated biological activity and in silico prediction experiments, both compounds possibly exhibited activity against phytopathogenic fungi via a novel mode of action.

Chemical Composition Analysis and Antioxidant Activity of Coffea robusta Monofloral Honeys from Vietnam.

Monofloral honey samples (Coffea robusta) from Vietnam were determined for their chemical compositions. This is the first report on the chemical composition and antioxidant activity of coffee honey from Vietnam. These samples were characterized by their high contents of total and reducing sugars, total phenolic contents, and total flavonoid contents. The contents of seven phenolic acids (PAs) were quantified by high performance liquid chromatography (HPLC) and analyzed with the assistance of principle component analysis (PCA) to differentiate the honey samples into groups. The hydroxymethylfurfural (HMF) (0.048-2.933 mg/kg) and free acid contents (20.326-31.163 meq/kg) of coffee honey were lower in Nepal, which reflected the freshness of the honey when conducting this survey. The coffee honey had total sugar and reducing sugar contents 831.711 g/kg and 697.903 g/kg, respectively. The high level of total phenolic (0.642 mg GAE/g) and flavonoid (0.0341 mg GE/g) contents of coffee honey contributed to their antioxidant activity of this honey sample. Among the coffee honey tested, the IC50 of DPPH radical-scavenging activities value was 1.134-17.031 mg/mL, while the IC50 of ABTS radical-scavenging activities value was 115.381-213.769 mg/mL. The phenolic acids composition analysis displayed that gallic acid appeared in high concentrations in all studied honey samples, ranging from 0.037-1.015 mg/kg, and ferulic acid content ranged from 0.193 to 0.276 mg/kg. The content of trigonelline and caffeine in coffee honey samples ranged from 0.314-2.399 mg/kg and 8.946-37.977 mg/kg. The data in this article highlight the relevance of coffee honey as a healthy substance.

Inhibition of α-Glucosidase, Acetylcholinesterase, and Nitric Oxide Production by Phytochemicals Isolated from Millettia speciosa-In Vitro and Molecular Docking Studies.

The phytochemical constituents from the roots of Millettia speciosa were investigated by chromatographic isolation, and their chemical structures were characterized using the MS and NMR spectroscopic methods. A total of 10 compounds, including six triterpenoids, two flavonoids, and two phenolic compounds, were identified from the roots of M. speciosa. Out of the isolated compounds, eight showed inhibitory effects on NO production in lipopolysaccharide (LPS)-stimulated RAW 264.7 cells, with IC50 values ranging from 43.9 to 449.5 µg/mL. Ursane-type triterpenes significantly suppressed NO production compared to the remaining compounds. In addition, these compounds also exhibited remarkable inhibitory effects on α-glucosidase. Among the tested compounds, 4, 5, and 10 exhibited excellent α-glucosidase inhibition, with IC50 values ranging from 1.1 to 2.2 µg/mL. Almost all of the test compounds showed little or no acetylcholinesterase inhibition, except for 5, which showed moderate anti-acetylcholinesterase activity in vitro. The molecular docking study of α-glucosidase inhibition by 3-5 and 10 was conducted to observe the interactions of these molecules with the enzyme. Compounds 4, 5, and 10 exhibited a better binding affinity toward the targeted receptor and the H-bond interactions located at the entrance of the enzyme active site pocket in comparison to those of 3 and the positive control acarbose. Our findings evidence the pharmacological potential of this species and suggest that the phytochemicals derived from the roots of M. speciosa may be promising lead molecules for further studies on the development of anti-inflammatory and anti-diabetes drugs.

Constituents from the Fruiting Bodies of Trametes cubensis and Trametes suaveolens in Vietnam and Their Anti-Inflammatory Bioactivity.

It is reported that various fungi have been used for medicine and edible foods. The tropical Trametes genus is popular and well-known in Vietnam for its health effects and bioactivities. In this study, the fruiting bodies of the edible fungi T. cubensis and T. suaveolens were collected in Vietnam. The preliminary bioactivity screening data indicated that the methanol extracts of the fruiting bodies of T. cubensis and T. suaveolens displayed significant inhibition of superoxide anion generation and elastase release in human neutrophils. Therefore, the isolation and characterization were performed on these two species by a combination of chromatographic methods and spectrometric analysis. In total, twenty-four compounds were identified, and among these (1-3) were characterized by 1D-, 2D-NMR, and HRMS analytical data. In addition, the anti-inflammatory potentials of some purified compounds were examined by the cellular model for the inhibition of superoxide anion generation and elastase release in human neutrophils. Among the isolated compounds, (5,14), and (19) displayed significant anti-inflammatory potential. As the results suggest, the extracts and isolated compounds from T. cubensis and T. suaveolens are potential candidates for the further development of new anti-inflammatory lead drugs or natural healthy foods.

Triterpenoids and steroids from the fruiting bodies of Hexagonia tenuis and their cytotoxicity.

One new triterpenoid, hexagonin F (1) was characterized from the fruiting bodies of Hexagonia tenuis with the assistance of spectroscopic and spectrometric analytical methods. In addition, two triterpenoids and two steroids were also identified by comparison of their physical and spectroscopic data with those reported. The purified compounds were examined for their cytotoxicity against five tumor cell lines, however, only weak cytotoxicity was demonstrated.

Alfa glucosidase inhibitory, anti inflammatory activities and a new furanocoumarin derivative of Ruellia tuberosa.

Rullia tuberosa L. is used for treatment of diabetes mellitus, anti-inflammation, etc. However, its hypoglycaemic and anti inflammatory activities has not been investigated so far. In the present study, the α-glucosidase inhibitory, anti inflammatory activities of the extract of this plant were investigated. Our results showed that the crude extract as well as ethyl acetate and methanol fractions showed α-glucosidase inhibitory activity with IC50 of 15.84, 4.73 and 8.27 µg/ml, respectively. In addition, the hexane and ethyl acetate fractions are capable of inhibiting LPS-induced NO production with IC50 of 17.41 and 23.95 µg/mL, respectively. From the ethyl acetate and methanol fractions, eight compounds, including isobargaptol 5-O-ß-D-glucopyranoside (1), syringaresinol (2), catechin (3), pulmatin (4), stigmast-4-en-3-on (4), verbascoside (5), hydroxymethylfurfural (6), rutin (7), and homoplantaginin (8) were extracted and isolated. Their chemical structures were elucidated by spectroscopic method including MS, 1 D and 2 D- NMR and comparison with the literature values.

Zoonotic diseases from birds to humans in Vietnam: possible diseases and their associated risk factors.

In recent decades, exceeding 60% of infectious cases in human beings are originated from pathogenic agents related to feral or companion animals. This figure continues to swiftly increase due to excessive exposure between human and contaminated hosts by means of applying unhygienic farming practices throughout society. In Asia countries-renowned for lax regulation towards animal-trading markets-have experienced tremendous outbreaks of zoonotic diseases every year. Meanwhile, various epidemic surges were first reported in the residential area of China-one of the largest distributor of all animal products on the planet. Some noticeable illnesses comprising of A/H5N1 or H7N9-known as avian influenza which transmitted from poultry and also wild birds-have caused inevitable disquiet among inhabitants. Indeed, poultry farming industry in China has witnessed dynamic evolution for the past two decades, both in quantity and degree of output per individual. Together with this pervasive expansion, zoonotic diseases from poultry have incessantly emerged as a latent threat to the surrounding residents in entire Asia and also European countries. Without strict exporting legislation, Vietnam is now facing the serious problem in terms of poultry distribution between the two countries' border. Even though several disease investigations have been conducted by many researchers, the disease epidemiology or transmission methods among people remained blurred and need to be further elucidated. In this paper, our aim is to provide a laconic review of common zoonotic diseases spread in Vietnam, outstanding cases and several factors predisposing to this alarming situation.

Chemical Constituents of the Leaves of Peltophorum pterocarpum and Their Bioactivity.

Two new sesquiterpenoids peltopterins A and B (compounds 1 and 2) and fifty-two known compounds were isolated from the methanol extract of P. pterocarpum and their chemical structures were established through spectroscopic and mass spectrometric analyses. The isolates 40, 43, 44, 47, 48, 51 and 52 exhibited potential inhibitory effects of superoxide anion generation or elastase release.

New cerebroside and chondrocyte proliferation activity of Caryota mitis L.

Caryota mitis L., a flowering plant, belongs to the family Arecaceae. In Vietnam, its fruits were used to treat joint pain. The present study was designed to investigate the phytochemicals and chondrocyte proliferation activity of C. mitis L. fruits on young human chondrocyte. The results showed that all of extracts (crude extract as well as n-hexane, chloroform, ethyl acetate and methanol fractions) were stimulated the growth of chondrocyte at 0.1 µg/mL; 0.01 µg/mL concentrations, of which the n-hexane and methanol fractions significantly increased the proliferation of chondrocyte by 30.75 and 24.42% at concentrations of 0.01 µg/mL, respectively. Repeated chromatography of the methanol fraction on silica gel, Sephadex LH-20 and ODS columns afforded a new cerebroside and eight known ones. Their structures were elucidated by analysis of spectral data and in comparison with the published reports.

Chemical constituents from the fruiting bodies of Phellinus igniarius.

A new tirucallane-type triterpenoid igniarine (1), and four known compounds meshimakobnol A (2), meshimakobnol B (3), ergosterol (4) and ergosterol peroxide (5), were purified from the methanol extracts of the fruiting bodies of Phellinus igniarius (DC. ex Fr.) Quél. The structure of 1 was elucidated using a combination of 1D and 2D NMR techniques and HR-ESI-MS analyses. In addition, the isolated compounds were examined for their cytotoxicity against several tumour cell lines and part of the tested compounds demonstrated weak cytotoxicity.

A new benzofuran derivative from the leaves of Ficus pumila L.

A new benzofuran derivative, pumiloside (1), together with seven known flavonoid glycosides, afzelin (2), astragalin (3), quercitrin (4), isoquercitrin (5), kaempferol 3-O-rutinoside (6), rutin (7) and kaempferol 3-O-sophoroside (8) were isolated from the leaves of Ficus pumila. Their structures were established by spectroscopic data and comparison with the literature values.

Characterization of Cyclodepsipeptides from the Mycelium of Isariajaponica from Vietnam.

A new cyclodepsipeptide, isarin (1), was isolated from the insect pathogenic fungus Isaria japonica Yasuda, together with one known compound, beauveriolide 1 (2). The structure of this new compound was characterized using a combination of spectroscopic and spectrometric analyses.

Occurrence, Human Intake and Biodegradation of Estrogen-Like Nonylphenols and Octylphenols.

BACKGROUND: Long-chain alkylphenols, such as nonylphenols and octylphenols, are man-made compounds with estrogen-like activity and considered to be endocrine disputing chemicals. They are known to influence sexual development and reproduction of humans and other animals, therefore cause health and ecological concerns. OBJECTIVE: This review aims to identify the key findings presented in recent scientific literature with respect to the presence of long-chain alkylphenols in food, intake by different populations and describe the metabolism by human and the mechanisms to disrupt the estrogenic activity of nonylphenols and octylphenols by bacteria and fungi in the environment. METHOD: The current knowledge related to the physicochemical properties, source, occurrence, toxic effects, level in foods, human intake, elimination and metabolism of long-chain alkylphenols was summarized. RESULTS: Long-chain alkylphenols have been detected in soil, surface and ground water, sediments, wastewater effluent, air and in most foods. The daily human intake of 4-nonylphenols and 4-octylphenols has been compared among different population. A comprehensive summary of the major degradation pathways and mechanism in bacteria, fungi, yeasts and vertebrates was described. CONCLUSION: The findings of this review revealed the wide distribution of long-chain alkylphenols in various environments and contamination in foods. Therefore, further investigation of long-term exposure is necessary to comprehensively evaluate the potential health risks to humans. The diverse biodegradation mechanisms can be used in the removal of these compounds before entering food chains. The review provides indication as to how it might be possible to reduce the adverse effects on human health from estrogen-like long-chain alkylphenols.

Chemical Constituents from the Fruiting Bodies of Hexagonia apiaria and Their Anti-inflammatory Activity.

A chemical investigation of the fruiting bodies of Hexagonia apiaria resulted in the identification of nine compounds including five new triterpenoids, hexagonins A-E (1-5), along with four known compounds. The purified constituents were examined for their anti-inflammatory activity. Among the tested compounds, hexatenuin A displayed the most significant inhibition of superoxide anion generation and elastase release. These triterpenoids may have potentials as anti-inflammatory agents.

Characterization of fungal and bacterial components in gut/fecal microbiome.

The gut microbiota is a complex ecosystem that affects the development, nutritional status and immunological responses of the host. Prokaryotes and fungi in the community have the abilities to withstand the adverse conditions of high temperature, low oxygen etc. and to decompose complex organic molecules. The novel approaches of metagenomics and metaproteomics provide data that allow the detection of patterns of constancy or changes in time or under different conditions, such as different diets, disease condition and antibiotic therapy. These large-scale patterns can be correlated with certain health or disease conditions. From the organismic point of view, however, the species identity of the organisms and their interactions in the gut and how these interactions influence the prevention or development of disease are poorly known. The diversity and roles of fungi in animal feces appear to be better known than in human gut/feces. A combined compilation of the diverse methods applied towards prokaryotes and fungi in the gut/feces microbiome serves as a base for meeting the challenges of masses of large-scale datasets on the one hand and lack of substantial organismic understanding on the other. Starting from long-term monitoring and large-scale characterization of the composition of microbiome from systematic higher groups down to the genus level, microbial genomes and proteomes, particular key components with antimicrobial or immune functions can be selected and investigated in detail with respect to understanding of host-microbiota interaction, disease pathogenesis and developing diagnostic and therapeutic tools.

New schiartane-type triterpene from Kadsura heteroclita and their cytotoxic activities.

One new schiartane-type triterpene, heteroclitalactone N (1), and four known compounds (2-5), seco-coccinic acid F, dihydroguaiaretic acid, schizanrin F, and kadsuralignan B were isolated from the stems of Kadsura heteroclita. Their structures were determined by the combination of spectroscopic and chemical methods, including 1D-, 2D-NMR, and CD spectra as well as by comparing with the NMR data reported in the literature. The cytotoxic activities of all isolated compounds were evaluated on three human cancer cell lines. Compound 3 exhibited moderate to weak cytotoxic activities on three human cancer cell lines, OVCAR, HT-29, and A-549, with IC50 values ranging from 16.2 to 36.4 microM.

Multiple approaches to characterize the microbial community in a thermophilic anaerobic digester running on swine manure: a case study.

In this study, the first survey of microbial community in thermophilic anaerobic digester using swine manure as sole feedstock was performed by multiple approaches including denaturing gradient gel electrophoresis (DGGE), clone library and pyrosequencing techniques. The integrated analysis of 21 DGGE bands, 126 clones and 8506 pyrosequencing read sequences revealed that Clostridia from the phylum Firmicutes account for the most dominant Bacteria. In addition, our analysis also identified additional taxa that were missed by the previous researches, including members of the bacterial phyla Synergistetes, Planctomycetes, Armatimonadetes, Chloroflexi and Nitrospira which might also play a role in thermophilic anaerobic digester. Most archaeal 16S rRNA sequences could be assigned to the order Methanobacteriales instead of Methanomicrobiales comparing to previous studies. In addition, this study reported that the member of Methanothermobacter genus was firstly found in thermophilic anaerobic digester.

Draft Genome Sequence of Pseudomonas nitroreducens Strain TX1, Which Degrades Nonionic Surfactants and Estrogen-Like Alkylphenols.

Pseudomonas nitroreducens TX1 ATCC PTA-6168 was isolated from rice field drainage in Taiwan. The bacterium is of special interest because of its capability to use nonionic surfactants (alkylphenol polyethoxylates) and estrogen-like compounds (4-t-octylphenol and 4-nonylphenol) as a sole carbon source. This is the first report on the genome sequence of P. nitroreducens.