Conversion of sugarcane bagasse to carboxylic acids using a mixed culture of mesophilic microorganisms

Using the MixAlco process, biomass can be converted into carboxylic acids, which can be chemically converted into mixed alcohol fuels. This study focused on the use of countercurrent fermentation to anaerobically convert sugarcane bagasse and chicken manure to mixed carboxylic acids using a mixed culture of mesophilic microorganisms from terrestrial and marine sources. Bagasse was pretreated with lime to increase digestibility. The continuum particle distribution model (CPDM) simulated continuous fermentors based on data collected from batch experiments. This model saves considerable time in determining optimum operating conditions. For an 80% bagasse/20% chicken manure fermentation with terrestrial inoculum at a volatile solids loading rate (VSLR) of 7.36 g/(L of liquid·d) and a liquid residence time (LRT) of 8.88 d, total carboxylic acid productivity, total acid selectivity, and yield were 2.49 g/(L of liquid·d), 0.581 g of total acid/g of VS digested, and 0.338 g of total acid/g of VS fed, respectively, at a concentration of 18.7 g of total acid/L. At the same VSLR and LRT, fermentation with marine inoculum gave higher total acid productivity, total acid selectivity, and yield than fermentation with terrestrial inoculum. For an 80% bagasse/20% chicken manure fermentation with marine inoculum at a VSLR of 3.83 g/(L of liquid·d) and an LRT of 12.1 d, total carboxylic acid productivity, total acid selectivity, and yield were 1.38 g/(L of liquid·d), 0.667 g of total acid/g of VS digested, and 0.359 g of total acid/g of VS fed, respectively, at a concentration of 16.2 g of total acid/L.     

From BACE1 inhibitor to multifunctionality of tryptoline and tryptamine triazole derivatives for Alzheimer's disease

Efforts to discover new drugs for Alzheimer's disease emphasizing multiple targets was conducted seeking to inhibit amyloid oligomer formation and to prevent radical formation. The tryptoline and tryptamine cores of BACE1 inhibitors previously identified by virtual screening were modified in silico for additional modes of action. These core structures were readily linked to different side chains using 1,2,3-triazole rings as bridges by copper catalyzed azide-alkyne cycloaddition reactions. Three compounds among the sixteen designed compounds exerted multifunctional activities including β-secretase inhibitory action, anti-amyloid aggregation, metal chelating and antioxidant effects at micromolar levels. The neuroprotective effects of the multifunctional compounds 6h, 12c and 12h on Aβ???? induced neuronal cell death at 1 μM were significantly greater than those of the potent single target compound, BACE1 inhibitor IV and were comparable to curcumin. The observed synergistic effect resulting from the reduction of the Aβ???? neurotoxicity cascade substantiates the validity of our multifunctional strategy in drug discovery for Alzheimer's disease.     

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.

     

Characterization of fractionated asphaltenes by UV-vis and NMR self-diffusion spectroscopy

Asphaltenes have been fractionated by liquid/liquid extraction, yielding four subfractions. The characteristics of fractionated asphaltenes were studied with respect to solubility, aromaticity, heteroatom content, and diffusion behavior. It was observed that asphaltenes from the four subfractions showed variations in their tendency to flocculate and also distinct differences in aromaticity. Furthermore, NMR self-diffusion studies showed that the average diffusion coefficients varied for asphaltenes from the different subfractions. The results suggest a variation in average size and stability between asphaltenes, depending on what subfraction they belong to. The subfraction that consisted of asphaltenes with the largest average size and the highest aromaticity was also found to contain the asphaltenes that had the strongest tendency to flocculate.     

Molecular Dynamics Simulations in Designing DARPins as Phosphorylation-Specific Protein Binders of ERK2

Extracellular signal-regulated kinases 1 and 2 (ERK1/2) play key roles in promoting cell survival and proliferation through the phosphorylation of various substrates. Remarkable antitumour activity is found in many inhibitors that act upstream of the ERK pathway. However, drug-resistant tumour cells invariably emerge after their use due to the reactivation of ERK1/2 signalling. ERK1/2 inhibitors have shown clinical efficacy as a therapeutic strategy for the treatment of tumours with mitogen-activated protein kinase (MAPK) upstream target mutations. These inhibitors may be used as a possible strategy to overcome acquired resistance to MAPK inhibitors. Here, we report a class of repeat proteins—designed ankyrin repeat protein (DARPin) macromolecules targeting ERK2 as inhibitors. The structural basis of ERK2–DARPin interactions based on molecular dynamics (MD) simulations was studied. The information was then used to predict stabilizing mutations employing a web-based algorithm, MAESTRO. To evaluate whether these design strategies were successfully deployed, we performed all-atom, explicit-solvent molecular dynamics (MD) simulations. Two mutations, Ala → Asp and Ser → Leu, were found to perform better than the original sequence (DARPin E40) based on the associated energy and key residues involved in protein-protein interaction. MD simulations and analysis of the data obtained on these mutations supported our predictions.     

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     

Determination of Solubility Parameters of Ionic Liquids and Ionic Liquid/Solvent Mixtures from Intrinsic Viscosity

The total and partial solubility parameters (dispersion, polar and hydrogen‐bonding solubility parameters) of ten ionic liquids were determined. Intrinsic viscosity approaches were used that encompassed a one‐dimensional method (1D‐Method), and two different three‐dimensional methods (3D‐Method1 and 3D‐Method2). The effect of solvent type, the dimethylacetamide (DMA) fraction in the ionic liquid, and dissolution temperature on solubility parameters were also investigated. For all types of effect, both the 1D‐Method and 3D‐Method2 present the same trend in the total solubility parameter. The partial solubility parameters are influenced by the cation and anion of the ionic liquid. Considering the effect on partial solubility parameters of the solvent type in the ionic liquid, it was observed that in both 3D methods, the dispersion and polar parameters of a 1‐ethyl‐3‐methylimidazolium acetate/solvent (60:40 vol %) mixture tend to increase as the total solubility parameter of the solvent increases.     

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.     

Influence of metal cofactors and water on the catalytic mechanism of creatininase-creatinine in aqueous solution from molecular dynamics simulation and quantum study

The reaction mechanism of creatinine-creatininase binding to form creatine as a final product has been investigated by using a combined ab initio quantum mechanical/molecular mechanical approach and classical molecular dynamics (MD) simulations. In MD simulations, an X-ray crystal structure of the creatininase/creatinine was modified for creatininase/creatinine complexes and the MD simulations were run for free creatininase and creatinine in water. MD results reveal that two X-ray water molecules can be retained in the active site as catalytic water. The binding free energy from Molecular Mechanics Poisson-Boltzmann Surface Area calculation predicted the strong binding of creatinine with Zn²⁺, Asp45 and Glu183. Two step mechanisms via Mn²⁺/Zn²⁺ (as in X-ray structure) and Zn²⁺/Zn²⁺ were proposed for water adding step and ring opening step with two catalytic waters. The pathway using synchronous transit methods with local density approximations with PWC functional for the fragment in the active region were obtained. Preferable pathway Zn²⁺/Zn²⁺ was observed due to lower activation energy in water adding step. The calculated energy in the second step for both systems were comparable with the barrier of 26.03 and 24.44 kcal/mol for Mn²⁺/Zn²⁺ and Zn²⁺/Zn²⁺, respectively.     

Emetine regulates the alternative splicing of Bcl-x through a protein phosphatase 1-dependent mechanism

Exon 2 of the Bcl-x gene undergoes alternative splicing in which the Bcl-xS splice variant promotes apoptosis in contrast to the anti-apoptotic splice variant Bcl-xL. In this study, the regulation of the alternative splicing of pre-mRNA of Bcl-x was examined in response to emetine. Treatment of different types of cancer cells with emetine dihydrochloride downregulated the level of Bcl-xL mRNA with a concomitant increase in the mRNA level of Bcl-xS in a dose- and time-dependent manner. Pretreatment with calyculin A, an inhibitor of protein phosphatase 1 (PP1) and protein phosphatase 2A (PP2A), blocked emetine-induced alternative splicing in contrast to okadaic acid, a specific inhibitor of PP2A in cells, demonstrating a PP1-mediated mechanism. Our finding on the regulation of RNA splicing of members of the Bcl-2 family in response to emetine presents a potential target for cancer treatment.