Homology modeling and molecular dynamics study on Schwanniomyces occidentalis alpha-amylase

With consumers growing increasingly aware of environmental issues, industries find enzymes as a reasonable alternative over physical conditions and chemical catalysts. Amylases are important hydrolase enzymes, which have been widely used in variety of industrial process such as pharmaceutical, food, and fermentation industries. Among amylases α-Amylase is in maximum demand due to its wide range of applications. The homology modeling study on Schwanniomyces occidentalis amylase (AMY1, UniProt identifier number: P19269) was performed by Modeller using Aspergillus oryzae (6TAA) as the template. The resulting structure was analyzed for validity and subjected to 14 ns of molecular dynamics (MD) simulation trough GROMACS. The validity of obtained model may represent that utilized OPLS force field is suitable for calcium-containing enzymes. DSSP secondary structure and contact map analysis represent the conservation of domain A TIM barrel feature together with calcium ion coordination sphere. Investigating the covariance matrix followed by principle component analyses for the first five eigenvectors of both trajectories indicate a little more flexibility for AMY1 structure. The electrostatic calculation for the final structures shows similar isoelectric point and superimposed buffering zone in the 5–8 pH range.     

Elemental analysis of herbal preparations for traditional medicines by neutron activation analysis with the k0 standardization method

Medicinal herb preparations prescribed for specific treatment purposes were purchased from markets and were analyzed by instrumental neutron activation analysis withk ₀ standardization. Then, 500–700 mg of each sample was pelletized under a pressure of six tones and irradiated together with monitors for a and neutron flux ratio determinations for about 6 h in a thermal flux of 2.29 x 10¹² n/cm²/s. The accuracy of the method was established by analyzing standard reference materials. Twenty-nine elements, Ag, As, Au, Ba, Br, Ca, Ce, Co, Cr, Cs, Eu, Fe, Hf, K, La, Mn, Mo, Na, Rb, Sb, Sc, Se, Sm, Sr, Th, U, Yb, and Zn, were measured in all the samples, and Hg was detected in some samples, with good accuracy and reproducibility. The concentration of elements determined was found to vary depending on the composition of the herbs used. Although the trend linking the element of the medicinal plants to its curative abilities could not be clearly determined, this study showed that the toxic elements found in the samples were below the levels prescribed by health regulations. Nevertheless, such data are important to understand the pharmacological action and the exact mechanisms of action and formation of active constituents for each medicinal plant and to decide the dosage of the herbs used in the final formulation.     

Current state and implications of research on biological effects of millimeter waves: A review of the literature

In recent years, research into biological and medical effects of millimeter waves (MMW) has expanded greatly. This paper analyzes general trends in the area and briefly reviews the most significant publications, proceeding from cell-free systems, dosimetry, and spectroscopy issues through cultured cells and isolated organs to animals and humans. The studies reviewed demonstrate effects of low-intensity MMW (10 mW/cm² and less) on cell growth and proliferation, activity of enzymes, state of cell genetic apparatus, function of excitable membranes, peripheral receptors, and other biological systems. In animals and humans, local MMW exposure stimulated tissue repair and regeneration, alleviated stress reactions, and facilitated recovery in a wide range of diseases (MMW therapy). Many reported MMW effects could not be readily explained by temperature changes during irradiation. The paper outlines some problems and uncertainties in the MMW research area, identifies tasks for future studies, and discusses possible implications for development of exposure safety criteria and guidelines. Bioelectromagnetics 19:393–413, 1998. © 1998 Wiley-Liss, Inc.     

Antibacterial properties of Apis dorsata honey against some bacterial pathogens

Now-a-days, different bioproducts are being used extensively for the welfare of mankind. However, for proper utility of any bioproduct, the exact biotechnological potential of that product should be explored. Honey is produced in almost every country on the planet. It has long been used as a medicinal agent in addition to its broader use as a popular food throughout the human history. It can be used to treat various diseases without causing any negative side effects. In the present study, the antibacterial potential of honey produced by A. dorsata was investigated at its variable concentrations (25, 50, 75 and 100 %) against four pathogenic bacterial species. The highest antimicrobial action was seen against E. coli at 100 % concentration of the honey while showing zone of inhibition of 37.5 ± 3.5 mm. However, the lowest antibacterial action was observed against E. faecalis. The overall order of growth inhibition by the honey at its 100 % concentration for the implicated bacterial species appeared as: E. coli ˃ P. aeruginosa ˃ S. aureus ˃ E. faecalis. The honey couldn’t show antibacterial action at its 25 % concentration. Our findings of the present study will be helpful for utility of the honey as an alternative medicine for curing different complications caused by microbial pathogens.     

A General Synthetic Method of 5-Carboranyluracil Nucleosides with Potential Antiviral Activity and use in Neutron Capture Therapy

Abstract

Previous biochemical and pharmacological studies indicated that 5-o-carboranyl-2′-deoxyuridine is a lead candidate for boron neutron capture therapy. This prompted the development of a rapid and stereoselective N ¹-glycosylation reaction of silylated 5-o-carboranyluracil with a variety of protected sugars. The key intermediate, 5-o-carboranyluracil (6), was prepared from 5-iodouracil in six steps. A novel coupling procedure of the 2,4-dimethoxy-5-ethynylpyrimidine (4) with decaborane without activator was used. Silylated 6 was coupled with a variety of carbohydrates under mild conditions to produce several carborane containing nucleosides. In each case, the stereochemistry and stereoselectivity of the glycosylation reaction was not affected by the presence of the carborane at the 5-position of the uracil and produced exclusively closo [closo-1,2-C₂B₁₀H₁₂ cage] nucleosides. This was confirmed by X-ray structure determination of racemic 5-carboranyl-2′,3′-dideoxy-3′-thiauridine. This compound demonstrated an anti-conformation with the oxathiolane ring in a pseudo C-2′-endo conformation. The toxicity profile of the new compounds and their precursors was determined in three cell culture systems, two of human origin (PBM and CEM cells) and one of monkey origin (Vero cells). The compounds were also evaluated for their potential antiviral activity against human immunodeficiency virus and herpes simplex virus in vitro. 5-o-Carboranyl-xylofuranosyluracil (12) demonstrated low toxicity in culture and in mice.     

A new species of Leptadenia (Apocynaceae) and two other new records from southwestern Saudi Arabia

Leptadenia jazanica Y. Masrahi from the province of Jazan, southwestern Saudi Arabia is described as a new species and illustrated. The species differs from the other known nearest species of the genus, Leptadenia pyrotechnica, by decumbent to scrambling habit of stems and persistent leaves. In the same province also two new records belonging to the genera Canavalia (Fabaceae) and Craterostigma (Scrophulariaceae) were collected; they were identified as Canavalia virosa (Roxb.) Wight & Arn. and Craterostigma plantagineum Hochst.     

The Extracellular δ-Domain is Essential for the Formation of CD81 Tetraspanin Webs

CD81 is a ubiquitously expressed member of the tetraspanin family. It forms large molecular platforms, so-called tetraspanin webs that play physiological roles in a variety of cellular functions and are involved in viral and parasite infections. We have investigated which part of the CD81 molecule is required for the formation of domains in the cell membranes of T-cells and hepatocytes. Surprisingly, we find that large CD81 platforms assemble via the short extracellular δ-domain, independent from a strong primary partner binding and from weak interactions mediated by palmitoylation. The δ-domain is also essential for the platforms to function during viral entry. We propose that, instead of stable binary interactions, CD81 interactions via the small δ-domain, possibly involving a dimerization step, play the key role in organizing CD81 into large tetraspanin webs and controlling its function.     

An Efficient Synthesis Of Acyclic N7- and N9-Adenine Nucleosides Via Alkylation With Secondary Carbon Electrophiles to Introduce Versatile Functional Groups At the C-1 Position of Acyclic Moiety

The introduction of versatile functional groups, allyl and ester, at the C-1 position of the acyclic chain in acyclic adenine nucleosides was achieved for the first time directly by alkylation of adenine and N⁶-protected adenine. Thus, the C-1′-substituted N⁹-adenine acyclic nucleoside, adenine-9-yl-pent-4-enoic acid ethyl ester (11), was prepared by direct alkylation of adenine with 2-bromopent-4-enoic acid ethyl ester (6), while the corresponding N⁷-regioisomer, 2-[6, (dimethylaminomethyleneamino)-purin-7-yl]-pent-4-enoic acid ethyl ester (10), was obtained in one step by the coupling of N,N-dimethyl-N′- (9H-purin-6-yl)-formamidine (9) with 2-bromopent-4-enoic acid ethyl ester (6). The functional groups, ester and allyl, were converted to the desired hydroxymethyl and hydroxyethyl groups, and subsequently to phosphonomethyl derivatives and corresponding pyrophosphorylphosphonates.