Screening of hepatitis C NS5B polymerase inhibitors containing benzothiadiazine core: a steered molecular dynamics

Hepatic C virus (HCV) is a global health problem, resulting in liver cirrhosis and inflammation that can develop to hepatocellular carcinoma and fatality. The NS5B polymerase of HCV plays an important role in viral RNA replication process, making it an attractive therapeutic target for design and development of anti-HCV drugs. To search new potent compounds against the HCV NS5B polymerase, the molecular docking and the steered molecular dynamics (SMD) simulation techniques were performed. The potential potent inhibitors of the NS5B polymerase were screened out from the ZINC database using structural similarity search and molecular docking technique. Five top-hit compounds (the ZINC compounds 49888724, 49054741, 49777239, 49793673, and 49780355) were then studied by the SMD simulations based on the hypothesis that a high rupture force relates to a high binding efficiency. The results demonstrated that the ZINC compound 49888724 had a greater maximum rupture force, reflecting a good binding strength and inhibitory potency than known inhibitors and the rest four ZINC compounds. Therefore, our finding indicated that the ZINC compound 49888724 is a potential candidate to be a novel NS5B inhibitor for further design. Besides, the van der Waals interaction could be considered as the main contribution for stabilizing the NS5B-ligand complex.     

Theoretical guidance and experimental confirmation on catalytic tendency of M-CeO2 (M = Zr,Mn, Ru or Cu) for NH3-SCR of NO

Abstract

Herein, we demonstrate that the degrees of catalytic performance of M-CeO₂-based catalysts (M=Mn, Cu, Ru or Zr) for an ammonia selective catalytic reduction (NH₃-SCR) of nitric-oxide (NO) can be estimated using three theoretical terms; (i) an oxygen vacancy formation energy of a catalyst, (ii) an adsorption energy of NO and (iii) an adsorption energy of NH₃. Those terms predict the trend of the catalytic performance as the order; Mn–CeO₂ > Cu–CeO₂ > Ru–CeO₂ > Zr–CeO₂ > CeO₂. To verify the theoretical prediction, the catalysts were synthesized and tested their performances on the NH₃-SCR of NO reaction. The normalized NO conversion rates at low temperatures (100–200 °C) were measured for Mn–CeO₂, Cu–CeO₂, Ru–CeO₂, Zr–CeO₂ and CeO₂ as 2.61–7.46, 1.30–6.82, 0.73–3.02, 0.81–3.31 and 1.55–2.33 mol s^?1 m^?2, respectively. In addition, a concept of a structure-activity relationship analysis shows a strong relationship between theoretical and experimental results. Consequently, an application of predicting the catalytic performance of catalysts from theoretical calculations prior the catalyst synthesis is useful in catalyst design and screening that can reduce time and cost.     

Molecular Dynamics Simulation Reveals the Selective Binding of Human Leukocyte Antigen Alleles Associated with Beh?et's Disease

Behçet’s disease (BD), a multi-organ inflammatory disorder, is associated with the presence of the human leukocyte antigen (HLA) HLA-B*51 allele in many ethnic groups. The possible antigen involvement of the major histocompatibility complex class I chain related gene A transmembrane (MICA-TM) nonapeptide (AAAAAIFVI) has been reported in BD symptomatic patients. This peptide has also been detected in HLA-A*26:01 positive patients. To investigate the link of BD with these two specific HLA alleles, molecular dynamics (MD) simulations were applied on the MICA-TM nonapeptide binding to the two BD-associated HLA alleles in comparison with the two non-BD-associated HLA alleles (B*35:01 and A*11:01). The MD simulations were applied on the four HLA/MICA-TM peptide complexes in aqueous solution. As a result, stabilization for the incoming MICA-TM was found to be predominantly contributed from van der Waals interactions. The P2/P3 residue close to the N-terminal and the P9 residue at the C-terminal of the MICA-TM nonapeptide served as the anchor for the peptide accommodated at the binding groove of the BD associated HLAs. The MM/PBSA free energy calculation predicted a stronger binding of the HLA/peptide complexes for the BD-associated HLA alleles than for the non-BD-associated ones, with a ranked binding strength of B*51:01 > B*35:01 and A*26:01 > A*11:01. Thus, the HLAs associated with BD pathogenesis expose the binding efficiency with the MICA-TM nonapeptide tighter than the non-associated HLA alleles. In addition, the residues 70, 73, 99, 146, 147 and 159 of the two BD-associated HLAs provided the conserved interaction for the MICA-TM peptide binding.     

Optimization of simultaneously enzymatic fructo- and inulo-oligosaccharide production using co-substrates of sucrose and inulin from Jerusalem artichoke

Prebiotic substances are extracted from various plant materials or enzymatic hydrolysis of different substrates. The production of fructo-oligosaccharide (FOS) and inulo-oligosaccharide (IOS) was performed by applying two substrates, sucrose and inulin; oligosaccharide yields were maximized using central composite design to evaluate the parameters influencing oligosaccharide production. Inulin from Jerusalem artichoke (5–15% w/v), sucrose (50–70% w/v), and inulinase from Aspergillus niger (2–7 U/g) were used as variable parameters for optimization. Based on our results, the application of sucrose and inulin as co-substrates for oligosaccharide production through inulinase hydrolysis and synthesis is viable in comparative to a method using a single substrate. Maximum yields (674.82?mg/g substrate) were obtained with 5.95% of inulin, 59.87% of sucrose, and 5.68 U/g of inulinase, with an incubation period of 9?hr. The use of sucrose and inulin as co-substrates in the reaction simultaneously produced FOS and IOS from sucrose and inulin. Total conversion yield was approximately 67%. Our results support the high value-added production of oligosaccharides using Jerusalem artichoke, which is generally used as a substrate in prebiotics and/or bioethanol production.     

Optimization of fermented Perilla frutescens seeds for enhancement of gamma-aminobutyric acid and bioactive compounds by Lactobacillus casei TISTR 1500

Abstract

Select LAB, including Lactobacillus fermentum TISTR 950, Lactobacillus plantarum TISTR 2265 and Lactobacillus casei TISTR 1500 were investigated for their ability to enhance GABA, TPC and the antioxidant activity of perilla seed juice. L. casei TISTR 1500 produced higher GABA and TPC contents and presented higher antioxidant activity than other strains. Furthermore, the optimal fermentation condition to perilla seeds inoculated with L. casei TISTR 1500 to improve the GABA, TPC and antioxidant activity was performed using 3³ full factorial design. The final optimal values for perilla fermentation was found at fermentation time of 4.82 days (4 days 19?h 40?min), initial substrate of 5% (w/v) and fermentation temperature of 30.07?°C. Under the optimal fermentation condition, an observed values of GABA, TPC, ABTS, DPPH and FRAP were 71.46 µg/g, 3175.00 µg GAE/g, 1991.40 µg TEAC/g, 9178.29 µg TEAC/g and 7753.34 µg TEAC/g, respectively, which was 3.3, 0.9, 2.9, 10.8 and 10.2 times higher than that of unfermented perilla seeds, and 2.1, 0.8, 0.9, 10 and 9.2 times of fermented perilla seeds before the optimization. These results may provide the foundation to further target in industrial application for the production of plant-based and develop functional perilla seed products containing GABA.

• Highlights

• Improved GABA, TPC and antioxidant contents were found using Lactobacillus casei TISTR 1500

• Full factorial design applied to optimize fermented perilla seeds by lactic acid fermentation

• The optimized conditions dramatically increased GABA and TPC contents

     

Treatability of cheese whey for single-cell protein production in nonsterile systems: Part I. Optimal condition for lactic acid fermentation using a microaerobic sequencing batch reactor (microaerobic SBR) with immobilized Lactobacillus plantarum TISTR 2265 and microbial communities

Cheese whey contains a high organic content and causes serious problems if it is released into the environment when untreated. This study aimed to investigate the optimum condition of lactic acid production using the microaerobic sequencing batch reactor (microaerobic SBR) in a nonsterile system. The high production of lactic acid was achieved by immobilized Lactobacillus plantarum TISTR 2265 to generate an acidic pH condition below 4.5 and then to support single-cell protein (SCP) production in the second aerobic sequencing batch reactor (aerobic SBR). A hydraulic retention time (HRT) of 4 days and a whey concentration of 80% feeding gave a high lactic acid yield of 12.58 g/L, chemical oxygen demand (COD) removal of 62.38%, and lactose utilization of 61.54%. The microbial communities in the nonsterile system were dominated by members of lactic acid bacteria, and it was shown that the inoculum remained in the system up to 330 days.     

Treatability of cheese whey for single-cell protein production in nonsterile systems: Part II. The application of aerobic sequencing batch reactor (aerobic SBR) to produce high biomass of Dioszegia sp. TISTR 5792

This study aimed to investigate the efficiency of an aerobic sequencing batch reactor (aerobic SBR) in a nonsterile system using the application of an experimental design via central composite design (CCD). The acidic whey obtained from lactic acid fermentation by immobilized Lactobacillus plantarum sp. TISTR 2265 was fed into the bioreactor of the aerobic SBR in an appropriate ratio between acidic whey and cheese whey to produce an acidic environment below 4.5 and then was used to support the growth of Dioszegia sp. TISTR 5792 by inhibiting bacterial contamination. At the optimal condition for a high yield of biomass production, the system was run with a hydraulic retention time (HRT) of 4 days, a solid retention time (SRT) of 8.22 days, and an acidic whey concentration of 80% feeding. The chemical oxygen demand (COD) decreased from 25,230 mg/L to 6,928 mg/L, which represented a COD removal of 72.15%. The yield of biomass production and lactose utilization by Dioszegia sp. TISTR 5792 were 13.14 g/L and 33.36%, respectively, with a long run of up to 180 cycles and the pH values of effluent were rose up to 8.32 without any pH adjustment.     

Decolorization of Reactive Red 159 by a consortium of photosynthetic bacteria using an anaerobic sequencing batch reactor (AnSBR)

This experiment aimed to decolorize Reactive Red 159 using a high potential of a consortium of purple nonsulfur bacteria (PNSB) with an application of response surface methodology through a central composite design in open system. The three factors of hydraulic retention time (HRT), sludge retention time (SRT) and dye concentration were applied to the design. The decolorization was operated in an anaerobic sequencing batch reactor until the system reached to a pseudosteady state for 30?cycles in each experiment. The optimal condition was 6,500?mg/L of Reactive Red 159 concentration with 20 days of SRT and 8 days of HRT, achieving dye effluent of 142.62?±?5.35?mg/L, decolorization rate of 264.54?±?7.13?mg/L/h and decolorization efficiency of 97.68?±?0.74%. The results revealed that PNSB efficiently decolorized the high concentration of Reactive Red 159 and they were a high potential of microorganisms for dyes contaminated wastewater treatment.