Modelling interaction between ammonia and nitric oxide molecules and aquaporins

Aquaporin is a family of small membrane-proteins that are capable of transporting nano-sized materials. In the present paper, we investigate the structure of these channels and provide information about the mechanism of individual molecules being encapsulated into aquaglyceroporin (GlpF) and aquaporin-1 (AQP1) channels by calculating the potential energy. In particular, we presents a mathematical model to determine the total potential energy for the interaction of the ammonia and nitric oxide molecules and different aquaporin channels which we assume to have a symmetrical cylindrical structure. We propose to describe these interactions in two steps. Firstly, we model the nitrogen atom as a discrete point and secondly, we model the three hydrogen atoms on the surface of a sphere of a certain radius. Then, we find the total potential energy by summing these interactions. Next, by considering the nitric oxide molecule as two discrete atoms uniformly distributed interacting with GlpF and AQP1 channels then gathering all pairs of interaction to determine the potential energy. Our results show that the ammonia and nitric oxide molecules can be encapsulated into both GlpF and AQP1 channels.     

Identification of ligands that target the HCV-E2 binding site on CD81

Hepatitis C is a global health problem. While many drug companies have active R&D efforts to develop new drugs for treating Hepatitis C virus (HCV), most target the viral enzymes. The HCV glycoprotein E2 has been shown to play an essential role in hepatocyte invasion by binding to CD81 and other cell surface receptors. This paper describes the use of AutoDock to identify ligand binding sites on the large extracellular loop of the open conformation of CD81 and to perform virtual screening runs to identify sets of small molecule ligands predicted to bind to two of these sites. The best sites selected by AutoLigand were located in regions identified by mutational studies to be the site of E2 binding. Thirty-six ligands predicted by AutoDock to bind to these sites were subsequently tested experimentally to determine if they bound to CD81-LEL. Binding assays conducted using surface Plasmon resonance revealed that 26 out of 36 (72 %) of the ligands bound in vitro to the recombinant CD81-LEL protein. Competition experiments performed using dual polarization interferometry showed that one of the ligands predicted to bind to the large cleft between the C and D helices was also effective in blocking E2 binding to CD81-LEL.     

Two Unusual Carbohydrate Reactions: Nucleophilic Ring Opening of an Anhydrosugar and Reductive Elimination with Co‐occurring Hydrogenation

Treatment of the 1,6‐anhydrosugar epoxide 5 with a cyano‐Gilman cuprate [(CuCN (6 eq.), MeLi (12 eq.)] surprisingly led to the open chain rearranged (2S,3R)‐1,2‐dihydroxy‐3,6‐dimethylheptan‐4‐one (7), structurally confirmed by conversion to the corresponding diacetate 8. Another unusual reaction was found by hydrogenation of the 2‐tosyl‐1‐bromosugar 11, leading in one operation to the twofold deoxygenated chiral pyran derivative 14. This procedure might prove to be useful in the rapid deoxygenation of sugar derivatives.     

A New Approach for the C-Alkylation of Unsaturated Sugars Involving the Benzothiazol-2-Ylthio Leaving Group

ABSTRACT

The leaving ability of the benzothiazol-2-ylthio group was applied to the C-alkylation of a 2,3-enopyranoside model structure. Coordination of the organometallic reagent to the thio-heterocyclic moiety was responsible for a stereospecific syn conjugate alkyl attack.     

Synthesis and application of silica and calcium carbonate nanoparticles in the reduction of organics from refinery wastewater

Oil refinery is one of the fast growing industries across the globe and it is expected to progress in the near future. The worldwide increase in the generation of refinery wastewater along with strict environmental regulations in the discharge of industrial effluent, persistent efforts have been devoted to recycle and reuse the treated water. The wastewater from the refining operation leads to serious environmental threat to the ecosystem. Therefore, this study aimed to synthesize silica (SiO₂) and calcium carbonate nanoparticles (CaCO₃) in the reduction of organics from refinery wastewater. The synthesized nanoparticles were employed in the reduction of chemical oxygen demand (COD) from refinery wastewater by studying the influence of solution pH, contact time, dosage of nanoparticles and stirring speed on adsorption performance. From the batch experimental studies, the optimized processing conditions for the reduction of COD using SiO₂ nanoparticles are pH 4.0, dosage 0.5 g, stirring speed 125 rpm and 90 min stirring time, and the corresponding values for CaCO₃ nanoparticles are pH 8.0, dosage 0.4 g, stirring speed 100 rpm and 90 min stirring time. The study demonstrates that SiO₂ and CaCO₃ nanoparticles have a promising future in the reduction organics from refinery wastewater in different pH regimes.     

Perturbating Intramolecular Hydrogen Bonds through Substituent Effects or Non-Covalent Interactions

An analysis of the effects induced by F, Cl, and Br-substituents at the α-position of both, the hydroxyl or the amino group for a series of amino-alcohols, HOCH₂(CH₂)_nCH₂NH₂ (n = 0–5) on the strength and characteristics of their OH···N or NH···O intramolecular hydrogen bonds (IMHBs) was carried out through the use of high-level G4 ab initio calculations. For the parent unsubstituted amino-alcohols, it is found that the strength of the OH···N IMHB goes through a maximum for n = 2, as revealed by the use of appropriate isodesmic reactions, natural bond orbital (NBO) analysis and atoms in molecules (AIM), and non-covalent interaction (NCI) procedures. The corresponding infrared (IR) spectra also reflect the same trends. When the α-position to the hydroxyl group is substituted by halogen atoms, the OH···N IMHB significantly reinforces following the trend H < F < Cl < Br. Conversely, when the substitution takes place at the α-position with respect to the amino group, the result is a weakening of the OH···N IMHB. A totally different scenario is found when the amino-alcohols HOCH₂(CH₂)_nCH₂NH₂ (n = 0–3) interact with BeF₂. Although the presence of the beryllium derivative dramatically increases the strength of the IMHBs, the possibility for the beryllium atom to interact simultaneously with the O and the N atoms of the amino-alcohol leads to the global minimum of the potential energy surface, with the result that the IMHBs are replaced by two beryllium bonds.     

Malformin-A1 (MA1) Sensitizes Chemoresistant Ovarian Cancer Cells to Cisplatin-Induced Apoptosis

High-grade epithelial ovarian cancer is a fatal disease in women frequently associated with drug resistance and poor outcomes. We previously demonstrated that a marine-derived compound MalforminA1 (MA1) was cytotoxic for the breast cancer cell line MCF-7. In this study, we aimed to examine the effect of MA1 on human ovarian cancer cells. The potential cytotoxicity of MA1was tested on cisplatin-sensitive (A2780S) and cisplatin-resistant (A2780CP) ovarian cancer cell lines using AlamarBlue assay, Hoechst dye, flow cytometry, Western blot, and RT-qPCR. MA1 had higher cytotoxic activity on A2780S (IC50 = 0.23 µM) and A2780CP (IC50 = 0.34 µM) cell lines when compared to cisplatin (IC50 = 31.4 µM and 76.9 µM, respectively). Flow cytometry analysis confirmed the cytotoxic effect of MA1. The synergistic effect of the two drugs was obvious, since only 13% of A2780S and 7% of A2780CP cells remained alive after 24 h of treatment with both MA1 and cisplatin. Moreover, we examined the expression of bcl2, p53, caspase3/9 genes at RNA and protein levels using RT-qPCR and Western blot, respectively, to figure out the cell death mechanism induced by MA1. A significant down-regulation in bcl2 and p53 genes was observed in treated cells compared to non-treated cells (p < 0.05), suggesting that MA1 may not follow the canonical pathway to induce apoptosis in ovarian cancer cell lines. MalforminA1 showed promising anticancer activity by inducing cytotoxicity in cisplatin-sensitive and cisplatin-resistant cancer cell lines. Interestingly, a synergistic effect was observed when MA1 was combined with cisplatin, leading to it overcoming its resistance to cisplatin.     

Microwave photonic crystal on the slot transmission line with a ferroelectric film

A microwave electrically tunable photonic crystal based on a periodically width-modulated slot transmission line with a ferroelectric film is investigated for the first time. The dispersion and transmission characteristics of electromagnetic waves propagating in such a structure are calculated. The electric control over photonic crystal characteristics is simulated.     

Tuning protonation states of tripelennamine antihistamines by cucurbit[7]uril

The formation of host–guest complexes of cucurbit[7]uril (CB7) with the antihistamine drug tripelennamine (TRP) was studied by optical and NMR spectroscopy. The experimental and computational results are consistent with inclusion of a single TRP molecule in CB7. Addition of CB7 has tuned drug protonation states associated with (de)protonation of the ethyldimethylammonium and exocyclic nitrogens with an increase in the associated pK_a values by 1.5 and 2.5 units, respectively. The incorporation of antihistamines drugs such as TRP in cucurbiturils could be utilized for switching their capability for selective binding to histamine H₁‐receptors, in the future. Copyright © 2015 John Wiley & Sons, Ltd.     

Are bosonic replicas faulty?

Motivated by the ongoing discussion about a seeming asymmetry in the performance of fermionic and bosonic replicas, we present an exact, nonperturbative approach to both fermionic and bosonic zero-dimensional replica field theories belonging to the broadly interpreted beta=2 Dyson symmetry class. We then utilize the formalism developed to demonstrate that the bosonic replicas do correctly reproduce the microscopic spectral density in the QCD-inspired chiral Gaussian unitary ensemble. This disproves the myth that the bosonic replica field theories are intrinsically faulty.