Ligand expansion in ligand-based virtual screening using relevance feedback

Query expansion is the process of reformulating an original query to improve retrieval performance in information retrieval systems. Relevance feedback is one of the most useful query modification techniques in information retrieval systems. In this paper, we introduce query expansion into ligand-based virtual screening (LBVS) using the relevance feedback technique. In this approach, a few high-ranking molecules of unknown activity are filtered from the outputs of a Bayesian inference network based on a single ligand molecule to form a set of ligand molecules. This set of ligand molecules is used to form a new ligand molecule. Simulated virtual screening experiments with the MDL Drug Data Report and maximum unbiased validation data sets show that the use of ligand expansion provides a very simple way of improving the LBVS, especially when the active molecules being sought have a high degree of structural heterogeneity. However, the effectiveness of the ligand expansion is slightly less when structurally-homogeneous sets of actives are being sought.     

Synthesis and preliminary investigations of the siRNA delivery potential of novel, single-chain rigid cationic carotenoid lipids

The success of nucleic acid delivery requires the development of safe and efficient delivery vectors that overcome cellular barriers for effective transport. Herein we describe the synthesis of a series of novel, single-chain rigid cationic carotenoid lipids and a study of their preliminary in vitro siRNA delivery effectiveness and cellular toxicity. The efficiency of siRNA delivery by the single-chain lipid series was compared with that of known cationic lipid vectors, 3β-[N-(N',N'-dimethylaminoethane)carbamoyl]-cholesterol (DC-Chol) and 1,2-dimyristoyl-sn-glyceryl-3-phosphoethanolamine (EPC) as positive controls. All cationic lipids (controls and single-chain lipids) were co-formulated into liposomes with the neutral co-lipid, 1,2-dioleolyl-sn-glycerol-3-phosphoethanolamine (DOPE). Cationic lipid-siRNA complexes of varying (+/-) molar charge ratios were formulated for delivery into HR5-CL11 cells. Of the five single-chain carotenoid lipids investigated, lipids 1, 2, 3 and 5 displayed significant knockdown efficiency with HR5-CL11 cells. In addition, lipid 1 exhibited the lowest levels of cytotoxicity with cell viability greater than 80% at all (+/-) molar charge ratios studied. This novel, single-chain rigid carotenoid-based cationic lipid represents a new class of transfection vector with excellent cell tolerance, accompanied with encouraging siRNA delivery efficiency.     

Mixed biopolymer systems based on starch

A binary mixture of starch-starch or starch with other biopolymers such as protein and non-starch polysaccharides could provide a new approach in producing starch-based food products. In the context of food processing, a specific adjustment in the rheological properties plays an important role in regulating production processing and optimizing the applicability, stability, and sensory of the final food products. This review examines various biopolymer mixtures based on starch and the influence of their interaction on physicochemical and rheological properties of the starch-based foods. It is evident that the physicochemical and rheological characteristics of the biopolymers mixture are highly dependent on the type of starch and other biopolymers that make them up mixing ratios, mixing procedure and presence of other food ingredients in the mixture. Understanding these properties will lead to improve the formulation of starch-based foods and minimize the need to resort to chemically modified starch.     

Anti-angiogenic activity of Morinda citrifolia extracts and its chemical constituents

Morinda citrifolia L. has been used for the treatment of a wide variety of diseases, including cancer. This study was undertaken to evaluate the anti-angiogenic effect of M. citrifolia fruits and leaves. Anti-angiogenic activity was evaluated in?vivo using the chick chorioallantoic membrane assay. Bioactivity-guided fractionation and isolation were performed to identify the active constituent, and high-performance liquid chromatography analysis was then used to quantify the amount of this active constituent in the active extracts and fraction. The methanol extracts of fruits and leaves of M. citrifolia and the subsequent chloroform fraction of the fruit methanolic extract were found to have potential anti-angiogenic activity and were more potent compared to suramin. Scopoletin was identified as one of the chemical constituents that may be partly responsible for the anti-angiogenic activity of M. citrifolia fruits. The present findings further support the use of M. citrifolia in cancer or other pathological conditions related to angiogenesis.     

Applications of supercritical fluid extraction (SFE) of palm oil and oil from natural sources

Supercritical fluid extraction (SFE), which has received much interest in its use and further development for industrial applications, is a method that offers some advantages over conventional methods, especially for the palm oil industry. SC-CO? refers to supercritical fluid extraction (SFE) that uses carbon dioxide (CO?) as a solvent which is a nontoxic, inexpensive, nonflammable, and nonpolluting supercritical fluid solvent for the extraction of natural products. Almost 100% oil can be extracted and it is regarded as safe, with organic solvent-free extracts having superior organoleptic profiles. The palm oil industry is one of the major industries in Malaysia that provides a major contribution to the national income. Malaysia is the second largest palm oil and palm kernel oil producer in the World. This paper reviews advances in applications of supercritical carbon dioxide (SC-CO?) extraction of oils from natural sources, in particular palm oil, minor constituents in palm oil, producing fractionated, refined, bleached, and deodorized palm oil, palm kernel oil and purified fatty acid fractions commendable for downstream uses as in toiletries and confectionaries.     

Phytochemical analysis, cytotoxic activity and constituents-activity relationships of the leaves of Cinnamomum iners (Reinw. ex Blume-Lauraceae)

The leaves of Cinnamomum iners (Reinw. ex Blume-Lauraceae) have been refluxed successively with chloroform and alcohol to get chloroform extract and alcoholic extract. Both the extracts have been assayed for cytotoxicity against human colorectal tumour cells. The chloroform extract exhibited significant cytotoxicity with IC(50) 31?μg mL(-1) (p??200?μg mL(-1). The chloroform extract has been further proceeded for chemical analysis by GC-TOFMS and 178 components were identified including acids, amines, amides, aldehydes, alcohols, esters, benzene derivatives, bicyclic compounds, terpenes, hydrocarbons, naphthalene derivatives, furan derivatives, azulenes, etc. Nine components representing 51.73% of the total chloroform extract were detected as major components. Caryophyllene (14.41%) and Eicosanoic acid ethyl ester (12.17%) are the most prominent components of the chloroform extract. β-Caryophyllene (14.41%) as most abundant compound supports potent cytotoxicity as shown by chloroform extract.     

The molecular basis of the adsorption of xylans on cellulose surface

In order to model the adsorption of xylan on cellulose, we have simulated, at the atomic level, the gas phase adsorption of small xylan fragments having 5 skeletal β (1 → 4) xylosyl residues (X₅), using molecular dynamics simulations. A first regime was considered, corresponding to a low surface coverage, with the adsorption of isolated X₅ in various initial orientations. In this regime, the simulation indicated that X₅ moved toward extended conformations, some of them being helical, with the possibility of either 2₁ or left-handed 3₁ helices. During the simulation, the X₅ fragments became preferentially oriented, parallel or anti parallel with respect to the cellulose chain axis. Substitution of the X₅ backbone by either GlcA and/or Araf side chains had no major influence on either the conformation or the efficiency of the interaction. However, the presence of side chains favored orientations of the X₅ backbone inclined with respect to the cellulose chain axis. In a second regime corresponding to monolayer coverage, the geometrical features of the adsorption of the xylan fragments on cellulose was roughly the same as that in the individual coverage situation. In this case, the monolayer became equilibrated at 0.14 g of xylan fragments for each g of cellulose, a figure that compared favourably with the values obtained in experimental adsorption of xylan on bacterial cellulose.     

Hydrolysis of Native and Heat-Treated Starches at Sub-Gelatinization Temperature Using Granular Starch Hydrolyzing Enzyme

The effect of heat treatment below the gelatinization temperature on the susceptibility of corn, mung bean, sago, and potato starches towards granular starch hydrolysis (35°C) was investigated. Starches were hydrolyzed in granular state and after heat treatment (50°C for 30 min) by using granular starch hydrolyzing enzyme for 24 h. Hydrolyzed heat-treated starches showed a significant increase in the percentage of dextrose equivalent compared to native starches, respectively, with corn 53% to 56%, mung bean 36% to 47%, sago 15% to 26%, and potato 12% to 15%. Scanning electron microscopy micrographs showed the presence of more porous granules and surface erosion in heat-treated starch compared to native starch. X-ray analysis showed no changes but with sharper peaks for all the starches, suggested that hydrolysis occurred on the amorphous region. The amylose content and swelling power of heat-treated starches was markedly altered after hydrolysis. Evidently, this enzyme was able to hydrolyze granular starches and heat treatment before hydrolysis significantly increased the degree of hydrolysis.     

Combination of developed in-house method and application of Eichrom Sr resin to determine the radioactivity of <Superscript>90</Superscript>Sr in environmental sample

A method is described for the determination of ⁹⁰Sr in environmental samples using combination of developed in-house method, Eichrom Sr resin and Beta Counter. Strontium was efficiently, rapidly and simply separated from Ca and other interfering matrix components by Eichrom Sr resin. All the results in general showed good accuracy, high precision, reliable and in good agreement between these two measured and certified value of SRM (i.e. IAEA-375, IAEA-326, IAEA-152 and IAEA-414). As a whole, the procedure described in this work notably improves conventional methods in particular concerning the time needed, sample volume, safer and others. Thus, the introduced method was successfully performed and will be applied to actual sample for the determination of ⁹⁰Sr in different environmental materials such as soil, sediments, milk, biological sample, water etc.     

Optical band gap and conductivity measurements of polypyrrole-chitosan composite thin films

Electrical conductivity and optical properties of polypyrrole-chitosan（PPy-CHI） conducting polymer composites have been investigated to determine the optical transition characteristics and energy band gap of composite films.The two electrode method and I-V characteristic technique were used to measure the conductivity of the PPy-CHI thin films,and the optical band gap was obtained from their ultraviolet absorption edges.Depending upon experimental parameter,the optical band gap（E_g） was found within 1.30-2.32 eV as estimated from optical absorption data.The band gap of the composite films decreased as the CHI content increased.The room temperature electrical conductivity of PPy-CHI thin films was found in the range of 5.84×10^-7-15.25×10^-7 S·cm^-1 depending on the chitosan content.The thermogravimetry analysis（TGA） showed that the CHI can improve the thermal stability of PPy-CHI composite films.