Design and synthesis of novel hybrid benzamide–peptide histone deacetylase inhibitors

We designed and synthesized a series of novel hybrid histone deacetylase inhibitors based on conjugation of benzamide-type inhibitors with either linear or cyclic peptides. Linear tetrapeptides (compounds 13 and 14), cyclic tetrapeptides (compounds 1 and 11), and heptanediamide–peptide conjugates (compounds 10, 12, 15 and 16) were synthesized through on-resin solid-phase peptide synthesis (SPPS). All compounds were found to be moderate HDAC1 and HDAC3 inhibitors, with IC₅₀ values ranging from 1.3 μM to 532 μM. Interestingly, compound 15 showed 19-fold selectivity for HDAC3 versus HDAC1.     

Optimization of Hydrogels for Transdermal Delivery of Lisinopril by Box–Behnken Statistical Design

The aim of this study was to investigate the combined influence of three independent variables on the permeation kinetics of lisinopril from hydrogels for transdermal delivery. A three-factor, three-level Box–Behnken design was used to optimize the independent variables, Carbopol 971 P (X ₁), menthol (X ₂), and propylene glycol (X ₃). Fifteen batches were prepared and evaluated for responses as dependent variables. The dependent variables selected were cumulative amount permeated across rat abdominal skin in 24 h (Q ₂₄; Y ₁), flux (Y ₂), and lag time (Y ₃). Aloe juice has been first time investigated as vehicle for hydrogel preparation. The ex vivo permeation study was conducted using Franz diffusion cells. Mathematical equations and response surface plots were used to relate the dependent and independent variables. The regression equation generated for the cumulative permeation of LSP in 24 h (Q ₂₄) was Y ₁ = 1,443.3–602.59X ₁ + 93.24X ₂ + 91.75X ₃ − 18.95X ₁ X ₂ – 140.93X ₁ X ₃ – 4.43X ₂ X ₃ – 152.63X ₁ ² – 150.03X₂ ² − 213.9X ₃ ². The statistical validity of the polynomials was established, and optimized formulation factors were selected by feasibility and grid search. Validation of the optimization study with 15 confirmatory runs indicated high degree of prognostic ability of response surface methodology. The use of Box–Behnken design approach helped in identifying the critical formulation parameters in the transdermal delivery of lisinopril from hydrogels.     

When does invasive species removal lead to ecological recovery? Implications for management success

The primary goal of invasive species management is to eliminate or reduce populations of invasive species. Although management efforts are often motivated by broader goals such as to reduce the negative impacts of invasive species on ecosystems and society, there has been little assessment of the consistency between population-based (e.g., removing invaders) and broader goals (e.g., recovery of ecological systems) for invasive species management. To address this, we conducted a comprehensive review of studies (N = 151) that removed invasive species and assessed ecological recovery over time. We found positive or mixed outcomes in most cases, but 31% of the time ecological recovery did not occur or there were negative ecological outcomes, such as increases in non-target invasive species. Ecological recovery was more likely in areas with relatively little anthropogenic disturbance and few other invaders, and for the recovery of animal populations and communities compared to plant communities and ecosystem processes. Elements of management protocols, such as whether invaders were eradicated (completely removed) versus aggressively suppressed (≥90% removed), did not affect the likelihood of ecological recovery. Our findings highlight the importance of considering broader goals and unintended outcomes when designing and implementing invasive species management programs.     

Design,synthesis, antimicrobial activity and anti-HIV activity evaluation of novel hybrid quinazoline–triazine derivatives

Abstract

A series of novel hybrid quinazoline–triazine derivatives was designed and synthesized from cyanuric chloride and anthranilic acid through sequential reactions, which contain different pharmacophores like quinazoline and substituted diaryl triazine (DATA) linked with ethylene diamine. All the newly synthesized compounds were characterized by infrared, ¹H-NMR, ¹³C-NMR, MS and elemental analysis. Further, we evaluated the in vitro anti-HIV activity of the newly synthesized compounds against HIV-1 (III_B) and HIV-2 (ROD) viral strains and as well as in vitro antimicrobial activity against four bacteria (Staphylococcus aureus, Bacillus cereus, Pseudomonas aeruginosa, Klebsiella pneumoniae) and two fungi (Aspergillus clavatus, Candida albicans) using the paper agar streak dilution method. The bioassay results indicate that four compounds namely 7d, 7n, 7r and 7s could be considered as possible potential agents.     

Design,recombinant expression,and antibacterial activity of a novel hybrid magainin–thanatin antimicrobial peptide

Antimicrobial peptides are small molecule polypeptides with biological activity, which can avoid the drug resistance. Magainin and thanatin are antimicrobial peptides with a broad spectrum of inhibitory microbes, and the core sequence of magainin is linked to a core sequence of thanatin. Here, the hybrid magainin–thanatin (MT) antimicrobial peptide was designed through bioinformatics analysis. The recombinant MT antimicrobial peptide was successfully expressed and purified in Escherichia coli BL21 (DE3). The molecular weight of the hybrid MT antimicrobial peptide was about 3.35?kDa. Moreover, the target protein indeed has an inhibitory effect on Staphylococcus aureus, E. coli DH5α, and Bacillus subtilis, with the minimum inhibitory concentrations 16.5, 20, and 9?μM, respectively. The rational designed hybrid MT antimicrobial peptide will hopefully provide large-scale fermentable antimicrobial peptides in the industrial production in the future.     

γ-Cyclodextrin–polyurethane copolymer adsorbent for selective removal of endotoxin from DNA solution

Copolymer particles for removal of endotoxins (lipopolysaccharides, LPSs) were prepared by suspension copolymerization of γ-cyclodextrin (CyD) and 1,6-hexamethylenediisocyanate. The LPS-removing activity of the copolymer particles was compared with that of poly(ε-lysine)-immobilized Cellufine (cationic adsorbent) or polystyrene particles (hydrophobic adsorbent) by a batch method. When DNA was present in solution with LPSs under physiological conditions (pH 6.0, ionic strength of μ = 0.05–0.8), LPS-removing activity of the cationic or hydrophobic adsorbent was unsatisfactory because both the DNA and the LPSs were adsorbed onto each adsorbent. By contrast, the copolymer particles with γ-CyD cavity (CyD content: 14–20 mol%) could selectively remove LPSs from a DNA solution (50 μg ml⁻¹, pH 6.0, and μ = 0.05–0.2) containing LPSs (15 EU ml⁻¹) without the adsorption of DNA. The residual concentration of LPSs in the treated DNA solution was below 0.1 EU ml⁻¹, and the recovery of DNA was 99%.     

Design and synthesis of a hybrid potentiator–corrector agonist of the cystic fibrosis mutant protein ΔF508-CFTR

A developing therapy of cystic fibrosis caused by the ΔF508 mutation in CFTR employs correction of defective CFTR chloride channel gating by a ‘potentiator’ and of defective CFTR protein folding by a ‘corrector’. Based on SAR data for phenylglycine-type potentiators and bithiazole correctors, we designed a hybrid molecule incorporating an enzymatic hydrolysable linker to deliver the potentiator (PG01) fragment 2 and the corrector (Corr-4a) fragment 13. The hybrid molecule 14 contained PG01-OH and Corr-4a–linker–CO₂H moieties, linked with an ethylene glycol spacer through an ester bond. The potentiator 2 and corrector 13 fragments (after cleavage) had low micromolar potency for restoration of ΔF508-CFTR channel gating and cellular processing, respectively. Cleavage of hybrid molecule 14 by intestinal enzymes under physiological conditions produced the active potentiator 2 and corrector fragments 13, providing proof-of-concept for small-molecule potentiator–corrector hybrids as a single drug therapy for CF caused by the ΔF508 mutation.     

Plant–bacteria interactions in the removal of pollutants

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Highlights► Rhizobacteria degrade a wide range of pollutants and efficiently colonize plant roots. ► Plants have an effect on the selection of their own rhizospheric microorganisms. ► Catabolic pathways can be induced by natural secondary plant products. ► Horizontal gene transfer has an important role in bioremediation. ► Manipulation of plant/microbe interactions could improve rhizoremediation outcomes.     

Application of physical–chemical and biological–chemical methods for heavy metals removal from acid mine drainage

Acid mine drainage (AMD) represents a serious environmental problem related to sulfide minerals and coal mining. High content of toxic metals and high acidity in AMD adversely affects surface water, groundwater and soil. The abandoned mine of the Smolník deposit in Slovakia is a typical example in this respect. The quality of AMD needs to be monitored and suitable treatment methods need to be developed.The aim of this paper was to demonstrate the technical feasibility of heavy metals removal from AMD using physical–chemical and biological–chemical methods. The base of the physical–chemical method was electrowinning. The principle of the biological–chemical method was the selective sequential precipitation (SSP) of metals with the application of hydrogen sulfide produced by sulfate-reducing bacteria and sodium hydroxide solution. Both the electrowinning and SSP processes decrease the content of heavy metals in AMD. The pre-treatment of AMD by chemical iron–aluminum precipitation (in the case of electrowinning tests) and chemical iron precipitation (in the case of SSP tests) improved the selectivity of the processes. A further aim of the work was the improvement of the SSP.During the electrochemical experiments, 99% Zn removal – under metallic form – and 94% Mn removal – under MnO₂ form – both with a high degree of purity, were achieved. The SSP process reached the selective precipitation of chosen metals with 99% efficiency – Fe, Al and Mn in the form of metal hydroxides, Cu and Zn as metal sulfides. The results achieved may be used for designing a process appropriate for the selective recovery of metals from the AMD discharged from the Smolník deposit.     

Design and analysis of a replicated server architecture for supporting IP–host mobility

Mobility support in IP networks requires servers to forward packets to mobile hosts and to maintain information pertaining to a mobile host's location in the network. In the mobile Internet Protocol (mobile-IP), location and packet forwarding functions are provided by servers referred to as home agents. These home agents may become the bottleneck when there are a large number of mobile hosts in the network. In this paper, we consider the design and analysis of a replicated server architecture in which multiple home agents are used to provide mobility support. In order to minimize the delay across the home agents, one of the key aspects is the design of load balancing schemes in which a home agent may transfer the control of a mobile host to another home agent in the same network. The methods for triggering the transfer and the policy for selecting the next home agent define various load balancing schemes which have different performance characteristics. In this paper, we design a protocol that forms the building block for implementing such load balancing schemes, and we then study the performance characteristics of three selection schemes, namely, random, round-robin, and join the shortest queue (JSQ), and three transfers policies, namely, timer-, counter- and threshold-based. The key results of this study are as follows: (1) The results show that both random and round-robin selection policies can yield modest load balancing gains, and that these gains increase when the traffic is more bursty (burstiness is defined as the ratio of the peak arrival rate to the mean arrival rate) as well as when there are more home agents. (2) The threshold-based transfer policy performs better than timer-based and counter-based policies, since in threshold-based policies transfers are made only when the queue is overloaded, unlike counter- and timer-based policies in which transfers can be made from an unloaded home agent to an overloaded home agent. This revised version was published online in August 2006 with corrections to the Cover Date.     

Dendritic cell–tumor cell hybrid vaccination for metastatic cancer

Dendritic cells are the most potent antigen-presenting cells, and the possibility of their use for cancer vaccination has renewed the interest in this therapeutic modality. Nevertheless, the ideal immunization protocol with these cells has not been described yet. In this paper we describe the preliminary results of a protocol using autologous tumor and allogeneic dendritic hybrid cell vaccination every 6 weeks, for metastatic melanoma and renal cell carcinoma (RCC) patients. Thirty-five patients were enrolled between March 2001 and March 2003. Though all patients included presented with large tumor burdens and progressive diseases, 71% of them experienced stability after vaccination, with durations up to 19 months. Among RCC patients 3/22 (14%) presented objective responses. The median time to progression was 4 months for melanoma and 5.7 months for RCC patients; no significant untoward effects were noted. Furthermore, immune function, as evaluated by cutaneous delayed-type hypersensitivity reactions to recall antigens and by peripheral blood proliferative responses to tumor-specific and nonspecific stimuli, presented a clear tendency to recover in vaccinated patients. These data indicate that dendritic cell–tumor cell hybrid vaccination affects the natural history of advanced cancer and provide support for its study in less advanced patients, who should, more likely, benefit even more from this approach.     

Design,characterization and expression of a novel hybrid peptides melittin (1–13)-LL37 (17–30)

Hybridizing of different antimicrobial peptides (AMPs) has been a common practice for obtaining novel hybrid AMPs with elevated antibacterial activity but minimized cytotoxicity. The hybrid peptides melittin (1-13)-LL37 (17-30) (M–L) combining the hydrophobic N-teriminal fragment of melittin (M) with the core antibacterial fragment of LL37 (L), was designed for the first time to explore its antibacterial activity and hemolytic activity against bacteria and sheep erythrocyte respectively. Results showed that M–L had an even more potent antibacterial activity against all indicator strains (especially gram-positive bacteria) than M and L, whereas didn’t exhibit hemolytic activity to sheep erythrocytes, implying M–L can be served as a potential therapeutic drug to substitute traditional antibiotics. However the high expense of biosynthesis limited its further research, therefore fusion expression of M–L was carried out in Escherichia coli (E. coli) for overproducing the hybrid peptide so as to solve the problem. The DNA sequence encoding M–L with preferred codons was cloned into the pET-SUMO vector for protein expression in E. coli BL21 (DE3). After IPTG induction, approximately 165 mg soluble fusion protein SUMO-M–L was recovered per liter supernatant of the fermentation ultrasonic lysate using Ni–NTA Sepharose column (92 % purity). And 23 mg recombinant M–L was obtained per liter culture after cleavage of SUMO protease and purification of Ni–NTA Sepharose column. In sum, this research not only supplied an effective approach for overproducing hybrid peptide M–L, but paved the way for its further exploration on pharmaceutical potential and medical importance.     

Application of anaerobic–aerobic sequential treatment system to real textile wastewater for color and COD removal

A sequential anaerobic packed column reactor and an activated sludge unit was operated continuously for treatment of a textile industry wastewater, in Izmir, Turkey. Metal sponges were used as support material in anaerobic unit and pre-activated textile dyestuff biodegrading PDW facultative anaerobic bacterial culture was immobilized on the support particles. Effects of hydraulic retention times in anaerobic unit (θ_H anaerobic = 12–72 h) and initial COD concentration (COD₀ = 3000 ± 200 mg/L and 800 ± 100 mg/L) at θ_H anaerobic = 24 h on color and COD removal performance of the system were investigated. The results indicated that over 85% decolorization and about 90% COD removal efficiency can be obtained up to θ_H anaerobic = 48 h but higher retention times causes decreasing in decolorization efficiency. Operating the system with real wastewater without adding any nutrients at θ_H anaerobic = 24 h resulted in over 60% improvement in color removal in studied wastewater compared to existing treatment plant.     

Design of novel lead molecules against RhoG protein as cancer target – a computational study

Cancer is a class of diseases characterized by uncontrolled cell growth. Every year more than 2 million people are affected by the disease. Rho family proteins are actively involved in cytoskeleton regulation. Over-expression of Rho family proteins show oncogenic activity and promote cancer progression. In the present work RhoG protein is considered as novel target of cancer. It is a member of Rho family and Rac subfamily protein, which plays pivotal role in regulation of microtubule formation, cell migration and contributes in cancer progression. In order to understand the binding interaction between RhoG protein and the DH domain of Ephexin-4 protein, the 3D structure of RhoG was evaluated and Molecular Dynamic Simulations was performed to stabilize the structure. The 3D structure of RhoG protein was validated and active site identified using standard computational protocols. Protein–protein docking of RhoG with Ephexin-4 was done to understand binding interactions and the active site structure. Virtual screening was carried out with ligand databases against the active site of RhoG protein. The efficiency of virtual screening is analysed with enrichment factor and area under curve values. The binding free energy of docked complexes was calculated using prime MM-GBSA module. The SASA, FOSA, FISA, PISA and PSA values of ligands were carried out. New ligands with high docking score, glide energy and acceptable ADME properties were prioritized as potential inhibitors of RhoG protein.     

Simultaneous biological removal of nitrogen–sulfur–carbon: Recent advances and challenges

Biological removal of carbon, nitrogen and sulfur is drawing increasing research interest in search for an efficient and cost-effective wastewater treatment. While extensive work on separate removal of nitrogen and sulfur is well documented, investigation on simultaneous denitrifying sulfide removal has only been reported recently. Most of the work on denitrifying sulfide removal has been focusing on bioreactor performance, loading and operating conditions. Nonetheless, underlying principles elucidating the biochemical reactions and the mechanisms of the microbial degradation are yet to be established. In addition, unstable denitrifying sulfide removal which is a major operating problem that hinders practical application of the process, is yet to be resolved. This paper provides a review on the state-of-the-art development of simultaneous biological removal of sulfur, nitrogen and carbon. Research on bioreactor operation and performance, reactor configurations, mechanisms and modeling work including the use of mass balance analysis and artificial neural networks is delineated. An in-depth discussion on the microbial community and functional consortium is also provided. Challenges and future work on simultaneous biological removal of nitrogen–sulfur–carbon are also outlined.     

Ionic liquid-based in situ product removal design exemplified for an acetone–butanol–ethanol fermentation

Selecting an appropriate separation technique is essential for the application of in situ product removal (ISPR) technology in biological processes. In this work, a three-stage systematic design method is proposed as a guide to integrate ionic liquid (IL)-based separation techniques into ISPR. This design method combines the selection of a suitable ISPR processing scheme, the optimal design of an IL-based liquid–liquid extraction (LLE) system followed by process simulation and evaluation. As a proof of concept, results for a conventional acetone–butanol–ethanol fermentation are presented (40,000 ton/year butanol production). In this application, ILs tetradecyl(trihexyl)phosphonium tetracyanoborate ([TDPh][TCB]) and tetraoctylammonium 2-methyl-1-naphthoate ([TOA] [MNaph]) are identified as the optimal solvents from computer-aided IL design (CAILD) method and reported experimental data, respectively. The dynamic simulation results for the fermentation process show that, the productivity of IL-based in situ (fed-batch) process and in situ (batch) process is around 2.7 and 1.8fold that of base case. Additionally, the IL-based in situ (fed-batch) process and in situ (batch) process also have significant energy savings (79.6% and 77.6%) when compared to the base case.     

Global dynamic modes of peristaltic-ciliary flow of a Phan–Thien–Tanner hybrid nanofluid model

Biomechanics and Modeling in Mechanobiology - In this paper, the tools of dynamical systems theory are applied to examine the streamline patterns and their local and global bifurcations for...