Crystal structure of an antiviral ankyrin targeting the HIV-1 capsid and molecular modeling of the ankyrin-capsid complex

Ankyrins are cellular repeat proteins, which can be genetically modified to randomize amino-acid residues located at defined positions in each repeat unit, and thus create a potential binding surface adaptable to macromolecular ligands. From a phage-display library of artificial ankyrins, we have isolated Ank^GAG1D4, a trimodular ankyrin which binds to the HIV-1 capsid protein N-terminal domain (NTD^CA) and has an antiviral effect at the late steps of the virus life cycle. In this study, the determinants of the Ank^GAG1D4-NTD^CA interaction were analyzed using peptide scanning in competition ELISA, capsid mutagenesis, ankyrin crystallography and molecular modeling. We determined the Ank^GAG1D4 structure at 2.2 Å resolution, and used the crystal structure in molecular docking with a homology model of HIV-1 capsid. Our results indicated that NTD^CA alpha-helices H1 and H7 could mediate the formation of the capsid-Ank^GAG1D4 binary complex, but the interaction involving H7 was predicted to be more stable than with H1. Arginine-18 (R18) in H1, and R132 and R143 in H7 were found to be the key players of the Ank^GAG1D4-NTD^CA interaction. This was confirmed by R-to-A mutagenesis of NTD^CA, and by sequence analysis of trimodular ankyrins negative for capsid binding. In Ank^GAG1D4, major interactors common to H1 and H7 were found to be S45, Y56, R89, K122 and K123. Collectively, our ankyrin-capsid binding analysis implied a significant degree of flexibility within the NTD^CA domain of the HIV-1 capsid protein, and provided some clues for the design of new antivirals targeting the capsid protein and viral assembly.     

Water‐Assisted Nitrile Oxide Cycloadditions: Synthesis of Isoxazoles and Stereoselective Syntheses of Isoxazolines and 1,2,4‐Oxadiazoles

Conventional methods generate nitrile oxides from oxime halides in organic solvents under basic conditions. However, the present work revealed that water‐assisted generation of nitrile oxides proceeds under mild acidic conditions (pH 4–5). Cycloadditions of nitrile oxides with alkynes and alkenes easily occurred in water without using catalysts, thus yielding isoxazoles and isoxazolines, respectively, with excellent stereoselectivity toward five‐ and six‐membered cyclic alkenes. A double stereoselective cycloaddition of two units of a nitrile oxide with cyclohexene was also achieved, thus yielding 1,2,4‐oxadiazole derivatives having a unique hybrid isoxazoline‐oxadiazole skeleton. Enantiomerically pure isoxazolines were prepared from monoterpenes with a ring strain. In one case, the isoxazoline with a butterfly‐like structure was simply prepared, and it might be used as a ligand in asymmetric catalysis.     

Alpha-Glucosidase Inhibitory Assay-Screened Isolation and Molecular Docking Model from Bauhinia pulla Active Compounds

The aim of this research was to establish the constituents of Bauhinia pulla as anti-diabetic agents. A phytochemistry analysis was conducted by chromatographic and spectroscopic techniques. The alpha-glucosidase inhibitory assay screening resulted in the isolation of eight known compounds of quercetin, quercitrin, luteolin, 5-deoxyluteolin, 4-methyl ether isoliquiritigenin, 3,2′,4′-trihydroxy-4-methoxychalcone, stigmasterol and β-sitosterol. Ethanol leaf extracts showed potential effects, which led to a strong inhibitory activity of isolated quercetin at 138.95 µg/mL and 5.41 µg/mL of IC₅₀, respectively. The docking confirmed that flavonoids and chalcones had the same potential binding sites and responsibilities for their activity. This study was the first report of Bauhinia pulla chemical constituents and its alpha-glucosidase inhibition.     

Depsides and depsidones from the soil-derived fungus Aspergillus unguis PSU-RSPG204

Three new depsides, aspergisides A-C, and one new depsidone, aspergisidone, were isolated from the soil-derived fungus Aspergillus unguis PSU-RSPG204 together with one phthalide derivative and 11 depsidones including emeguisin A, aspersidone and folipastatin. The structures were determined by spectroscopic evidence. Aspersidone and emeguisin A showed remarkably antibacterial activity against Staphylococcus aureus and methicillin-resistance S. aureus with equal MIC values of 0.5?μg/mL. Emeguisin A, which displayed the highest activity with 87.06% inhibition of human colon carcinoma (HCT-116) cell viability, decreased numbers of live cells/numbers of dead cells in a dose-dependent manner with the IC₅₀ values of 34.8–84.7?μM in a 3D culture model depending on durations of incubation. In addition, folipastatin dose-dependently inhibited forskolin-stimulated chloride secretion in human intestinal epithelial (T84) cells with an IC₅₀ value of 0.5?μM. These depsidones were considered to be inactive against noncancerous Vero Cells with the IC₅₀ values of >10?μM.     

Synthesis of Molecularly Imprinted Polymers for Nevirapine by Dummy Template Imprinting Approach

Nevirapine (NVP) and its structurally related analogs including nicotinamide (NAM), benzamide (BZM) and benzophenone (BZP) were used as templates in the synthesis of molecularly imprinted polymers for NVP. Molecular modeling was used to estimate binding energy of the complex formation between methacrylic acid (MAA) monomer and the selected templates, while equilibrium binding studies were applied to evaluate the polymer binding efficiency. The data indicated that NAM is the best candidate to prepare MIPs for retaining NVP due to a relatively similar binding energy between the NVP–MAA and NAM–MAA complex. The NAM-imprinted polymer showed a high binding affinity and selectivity toward NVP. When the polymer was applied as a sorbent in solid-phase extraction of NVP from human plasma, high recovery and reproducibility were obtained.

     

Alpha-Glucosidase Inhibition and Molecular Docking of Isolated Compounds from Traditional Thai Medicinal Plant,Neuropeltis racemosa Wall.

Neuropeltis racemosa Wall. (Convolvulaceae) is wildly distributed in Asia. Its stem is used as the component in traditional Thai recipes for treatments of muscle rigidity, skin disorder, dysentery, and hypoglycemia. However, the chemical constituents and biological activities of N. racemosa have not been reported. From a screening assay, N. racemosa stem crude extract showed the potent effect on alpha-glucosidase inhibition at 2 mg/mL as 96.09%. The bioassay-guiding isolation led to 5 compounds that were identified by spectroscopic techniques as scopoletin (1), syringic acid (2), methyl 3-methyl-2-butenoate (3), N-trans-feruloyltyramine (4), and N-trans- coumaroyltyramine (5). Compounds 1, 4, and 5 exhibited an IC₅₀ of 110.97, 29.87, and 0.92 µg/mL, respectively, while the IC₅₀ of positive standard, acarbose was 272.72 µg/mL. Kinetic study showed that compound 1 performed as the mixed-type inhibition mechanism, whereas compounds 4 and 5 displayed the uncompetitive inhibition mechanism. The docking study provided the molecular understanding of isolated aromatic compounds (1, 2, 4 and 5) to alpha-glucosidase. Hence, this study would be the first report of isolated compounds and their anti-alpha-glucosidase activity with the mechanism of action from N. racemosa. Thus, these active compounds will be further studied to be the lead compounds among natural antidiabetic drugs.     

Structural and transport phenomena of urocanate-based proton carrier in sulfonated poly(ether ether ketone) membrane composite

Proton transport is one of crucial phenomena in electrolytic part highly considered to overcome a limit in fuel cell efficiency improvement. Proton conducting organic electrolyte was modeled and simulated at atomistic level of calculation by doping of butyl urocanate (C4U), a composite material with imidazole substructure, with sulfonated poly(ether ether ketone) (SPEEK) amorphous membrane at various working temperature. Molecular dynamics simulations were used to investigate structural and dynamics characteristic of C4U in the membrane comparing with the SPEEK-hydronium membrane model as a control. From simulations, thermal effect on water and proton carriers cluster surrounding the sulfonate groups was explored. At higher temperature, the more transport dynamics of C4U ions in SPEEK membranes were found than that of hydronium ions in the control system. Likewise, phase separation of hydrophobic and hydrophilic parts was taken into consideration here. A critical role of the enhancing proton conductivity by increasing the diffusion coefficient at temperature beyond C4U melting point in composite polymer membrane was emphasized. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 1625–1635     

Shifting from Hydrogen Bond Network to π–π Stacking: A Key Mechanism for Reversible Thermochromic Sulfonated Poly(Ether Ether Ketone)

Sulfonated poly(ether ether ketone) (SPEEK) thin film performs reversible thermochromic property by developing the color to be yellowish at the temperature above 190 °C. The detailed analyses based on temperature‐dependent techniques suggest the thermal treatment inducing the shifting of the hydrogen bond network between the sulfonated group and the hydrated water molecules to the π–π stacking among aromatic rings in SPEEK chains. Although it is general that the polymer chain packing is unfavorable at high temperature, the present work shows a good example that when the polymer chains can form specific molecular interaction, such as π–π stacking, even in harsh thermal treatment, a rearrangement will effectively occur, which leads to an external stimuli‐responsive property.