Prospective virtual screening with Ultrafast Shape Recognition: the identification of novel inhibitors of arylamine N-acetyltransferases

There is currently a shortage of chemical molecules that can be used as bioactive probes to study molecular targets and potentially as starting points for drug discovery. One inexpensive way to address this problem is to use computational methods to screen a comprehensive database of small molecules to discover novel structures that could lead to alternative and better bioactive probes. Despite that pleasing logic the results have been somewhat mixed. Here we describe a virtual screening technique based on ligand–receptor shape complementarity, Ultrafast Shape Recognition (USR). USR is specifically applied to identify novel inhibitors of arylamine N-acetyltransferases by computationally screening almost 700 million molecular conformers in a time- and resource-efficient manner. A small number of the predicted active compounds were purchased and tested obtaining a confirmed hit rate of 40 per cent which is an outstanding result for a prospective virtual screening.     

Development of 3kA conduction cooled HTS current lead system

The research and development of superconducting magnet energy storage (SMES) system, a national project, began in 1999. One of the purposes of this project is investigation concerning the application of high-temperature superconducting (HTS) SMES. As a part of this project, the 3 kA class HTS small model coil was manufactured in order to verify the possibility of realizing conduction cooled HTS SMES. Therefore, it is important to develop the conduction cooled current lead system for applying this coil. We developed a kA class conduction cooled HTS current lead system. This current lead system consists of the copper current lead and the YBaCuO (YBCO) HTS current lead. The YBCO bulk manufactured by Nippon Steel Corporation was applied to the HTS current lead. The YBCO bulk keeps high critical current density (J_c > 10,000 A/cm²) in the magnetic field (1 T) at 77 K compared with Bi2223 superconductor. The experiment of this HTS current lead system was carried out, and rated current of 3000 A was achieved successfully.     

Optimization and characterization of tannic acid loaded niosomes for enhanced antibacterial and anti-biofilm activities

The purpose of this study was to prepare and characterize an optimized system of tannic acid-loaded niosomes as a potential carrier for antibacterial and anti-biofilm delivery. The niosomal formulation was optimized using response surface methodology (RSM). The effects of the molar ratio of surfactant to cholesterol, drug concentration, and molar ratio of Span 60 to Tween 60 on particle size and drug entrapment efficiency of the niosomal nanocarrier were studied. The optimized nanoparticles were characterized in terms of the morphology, in vitro release profile, and antibacterial properties. Moreover, Fourier-transform infrared spectroscopy (FTIR) and differential scanning calorimetry (DSC) techniques were utilized to investigate drug-excipient interactions. Antibacterial and anti-biofilm activities of free tannic acid and tannic acid-loaded niosome were investigated against selected pathogenic bacteria including Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus. Furthermore, the expression level of biofilm-associated genes was evaluated in selected pathogenic bacteria using Real-Time PCR. According to the results, the dependent variables (particle size and entrapment efficiency) were best fitted to the quadratic model. The particle size and entrapment efficiency of the best niosomal formulation were 89 nm and 82%, respectively. The in vitro release of the optimized formulation showed a controlled release profile. Release kinetics indicated a diffusion-based release of the drug. FTIR and DSC studies also confirmed the absence of drug-excipient interactions. The optimized formulation exhibited higher antibacterial effects as compared with the free drug solution. Moreover, the time-kill assay of the encapsulated drug revealed a slow and controlled inhibition of bacterial growth for 72 h while the free drug was used up in the first hours. Moreover, tannic acid-loaded niosome reduced biofilm formation capacity in selected strains and down-regulated the biofilm gene expression as compared to free tannic acid.The optimized formulation containing tannic acid can be a promising candidate for designing a new delivery system for this antibacterial and anti-biofilm agent.     

Electrospun cellulose acetate membrane for size separating and antibacterial screening of crude polysaccharides

This study aims to produce electrospun cellulose acetate (CA) membrane as the alternative supporting medium for a separation of crude polysaccharides by electrophoresis and a screening of their antibacterial activity. Among the tested conditions of fabrication, electrospun CA membrane at 57% porosity showed the best separation of each polysaccharide from the standard mixture and the crude extract of Aloe vera via electrophoresis. As compared with the commercial CA membrane, the produced electrospun CA membrane demonstrated more separated spots of polysaccharides. The antibacterial activity of the electrophoretic polysaccharide was also determined against Escherichia coli and Staphylococcus aureus as the inhibition zone after the bacterial culture agar was overlaid on the membrane and incubated for 24 h. The results of this study suggested the potential application of electrospun CA membrane combining with electrophoresis as a simple method for separating crude polysaccharides and screening for their antibacterial activity.Inspec keywords: electrospinning, polymers, antibacterial activity, microorganisms, electrophoresis, biomedical materials, porosityOther keywords: electrospun cellulose acetate membrane, size separating, antibacterial screening, crude polysaccharides, alternative supporting medium, electrophoresis, antibacterial activity, electrospun CA membrane, standard mixture, Aloe vera, electrophoretic polysaccharide, Escherichia coli, Staphylococcus aureus, bacterial culture agar     

Multianalyte single-cell analysis with multiple cell lines using a fiber-optic array

A single-cell drug screening method is described that produces rich single-cell data and discriminates between single-cell responses from clonal populations stimulated with different agonists. Ligand-induced receptor activation is commonly detected by observing intracellular Ca2+ oscillations using high-throughput screening (HTS) methods. In most cases, HTS results in an average signal from several cells and is not sensitive enough to enable the identification of population outliers or population variance. In order to obtain this information, many individual cells must be analyzed simultaneously. We have developed a novel system using a specialized fiber-optic platform and have combined it with statistical analysis, to simultaneously analyze the dynamics of Ca2+ oscillations in a large number of single cells. Mammalian cells ectopically expressing different human GPCR receptors were stimulated, and Ca2+ changes in numerous single cells were recorded over time using a fluorescent microscope and a CCD camera. We determined the percentage of live cells in a population responding to stimuli, the distribution of responses within a population of clonal cells, and the number of outliers. By employing principal component analysis and K-nearest neighbor modeling, we classified the time-resolved Ca2+ traces of single cells as a function of the stimulus type with high certainty for a population of cells. This method is potentially a powerful tool for identifying new drug targets or for investigating the single-cell behavior of an existing target or known receptor. The development of this single-cell drug screening method is presented, and fluorescent and statistical analyses of single-cell dynamic responses are discussed.     

Optimization of conduction-cooled Peltier current leads

A theoretical investigation for optimization of conduction-cooled Peltier current leads is undertaken. A Peltier current lead (PCL) is composed of a thermoelectric element (TE), a metallic lead and a high T_c superconductor (HTS) lead in the order of decreasing temperature. Mathematical expressions for the minimum heat flow per unit current crossing the TE-metal interface and that flowing from the metal lead to the joint of the metal and the HTS leads are obtained. It is shown that the temperature at the TE-metal interface possesses a unique optimal value that minimizes the heat flow to the joint. It is also shown that this optimal value depends on the material properties of the TE and the metallic lead but not the joint temperature nor electric current. Optimal geometric factors, viz. the ratio of the length to cross-sectional area, of both the TE and the metallic lead are obtained for various joint temperatures. A design procedure for optimizing PCLs is also proposed.     

Lab‐on‐a‐Chip‐Based High‐Throughput Screening of the Genotoxicity of Engineered Nanomaterials

The continuous increasing of engineered nanomaterials (ENMs) in our environment, their combinatorial diversity, and the associated genotoxic risks, highlight the urgent need to better define the possible toxicological effects of ENMs. In this context, we present a new high‐throughput screening (HTS) platform based on the cytokinesis‐block micronucleus (CBMN) assay, lab‐on‐chip cell sorting, and automated image analysis. This HTS platform has been successfully applied to the evaluation of the cytotoxic and genotoxic effects of silver nanoparticles (AgNPs) and silica nanoparticles (SiO₂NPs). In particular, our results demonstrate the high cyto‐ and genotoxicity induced by AgNPs and the biocompatibility of SiO₂NPs, in primary human lymphocytes. Moreover, our data reveal that the toxic effects are also dependent on size, surface coating, and surface charge. Most importantly, our HTS platform shows that AgNP‐induced genotoxicity is lymphocyte sub‐type dependent and is particularly pronounced in CD2+ and CD4+ cells.     

Developing an approach based on the formation of YBa2Cu3O x -interlayer-YBa2Cu3O x epitaxial structures with high current-carrying ability

An approach based on the formation of YBa₂Cu₃O _x -interlayer-YBa₂Cu₃O _x multilayer epitaxial structures with high current-carrying ability is proposed. The use of interlayers representing simple cubic oxides (SrTiO₃ and CeO₂) allows the growth of crystal defects during the formation of a high-temperature superconductor (HTS) layer to be stopped. The phenomenon of current transfer through 10- to 50-nm-thick interlayers has been discovered. Using the proposed approach, it is possible to increase the current-carrying ability in proportion to the number of HTS layers in the structure. This in principle solves the problem of critical current-density degradation with increasing thickness of YBa₂Cu₃O _x layer.     

Synthesis, characterization and antimicrobial activity of conjugates based on fluoroquinolon-type antibiotics and gelatin

Different fluoroquinolon-type antibiotics were conjugated to gelatin with the aim to synthesize biomacromolecules with antimicrobial properties. The covalent linkage of the antibiotic was performed by a radical process involving the residues in the side chains of gelatin able to undergo oxidative modifications. The conjugation of antibiotic moieties onto the protein structure was confirmed by FT-IR, UV–Vis, fluorescence, and calorimetric analyses. Biocompatibility tests were performed on human bone marrow mesenchymal stromal cells and the antibacterial properties of bioactive polymers were investigated by appropriate tests against Klebsiella pneumoniae and Escherichia coli. With regard to the tests conducted in the presence of E. coli, a minimum inhibitory concentration (MIC) ranging from 0.05 to 0.40 μg mL^?1 was recorded, while in the presence of K. pneumoniae this concentration varies from 0.10 to 1.60 μg mL^?1. In all the conjugates, the drug moieties retain their biological activity and the MIC values are lower than the resistance parameters of fluoroquinolon-type antibiotics versus Enterobacteriacae. The collected data suggest a broad range of applications, from biomedical to pharmaceutical and food science for all conjugates.     

Cellular Assays with a Molecular Endpoint Measured by SAMDI Mass Spectrometry

Cell‐based, high‐throughput screening (HTS) assays are increasingly important tools used in drug discovery, but frequently rely on readouts of gene expression or phenotypic changes and require development of specialized, labeled reporters. Here a cell‐based, label‐free assay compatible with HTS is introduced that can report quantitatively on enzyme activities by measuring mass changes of substrates with matrix‐assisted laser desorption/ionization mass spectrometry. The assay uses self‐assembled monolayers to culture cells on arrays presenting substrates, which serve as reporters for a desired enzyme activity. Each spot of cells is treated with a compound, cultured and lysed, enabling endogenous enzymes to act on the immobilized peptide substrate. It is demonstrated that the assay can measure protein tyrosine phosphatase (PTP) activity from as few as five cells and a screen is described that identifies a compound that reduces PTP activity in cell lysates. This approach offers a valuable addition to the methods available for cell‐based screening.     

Design and fabrication of imidazolium ion-immobilized electrospun polyurethane membranes with antibacterial activity

By covalently immobilizing imidazolium ion onto molecular chain, functional polyurethane (PU) is fabricated and thus an effective way is initiated to prepare electrospun membranes with antibacterial activity. In the experiment, PUs containing imidazolium ion side group (Bmim-PUs) are synthesized through a two-step polymerization process. It includes prepolymerization of isophorone diisocyanate (IPDI) with polyester glycol and chain extension polymerization using imidazolium-based ionic diol (Bmim-OH). Then, the obtained Bmim-PUs are electrospun into fibrous membranes with a diameter of ~640 nm. After a careful assessment, antibacterial activities of electrospun membranes against Gram-positive Staphylococcus aureus and Gram-negative Escherichia coli are clearly exhibited. The antibacterial efficiency of Bmim-PUs on both bacteria species improves by 60% in comparison with PU without imidazolium ion. This research suggests a simple but effective methodology to design and fabricate ultrafine fibrous membrane with significant antibacterial activity. Moreover, the obtained fibrous membranes have widely potential applications in protective textiles, filtration, and biomedical engineering.     

A current perspective on high-throughput polymer science

Recent years (2000–2003) have witnessed an upsurge in the application of combinatorial and high-throughput experimental methods to polymers. This review highlights the most recent developments in high-throughput polymer science, in order to put into perspective the articles selected for this special section of The Journal of Materials Science. This article begins by defining the unique challenges in polymer (and materials) high-throughput screening (HTS), with respect to other applications of combinatorial and high-throughput methods in drug discovery and catalyst development. Advances in the preparation of HTS libraries are then discussed, with a distinction made between libraries for synthetic investigation and libraries for formulation and characterization. Then, the recent applications of HTS to polymer analytical methods (for chemical characterization of synthetic libraries) and physical characterization methods (for formulation libraries) are presented.     

Development of Bi-2223 HTS tape and its application to coil and current leads

We are developing Bi-2223/Ag tapes with a high engineering critical current density by optimizing the powder-in-tube process and are studying its application to coil and current leads. We have fabricated 250 m-long tape and investigated optimized processing conditions to enhance engineering critical current density. More bubbling was found when the tape was heat-treated with a higher heating rate. Different kinds of superconducting joints were fabricated with multi-filamentary Bi-2223/Ag tapes, and 58% of retained I_c was achieved using the insertion of Bi-2223 core between two exposed tapes. Current decay property of the persistent mode HTS coil was investigated. Rapid current decay was observed when the operating current is in a flux-flow range. We could successfully fabricate a low heat leak type HTS current lead with Bi-2223/Ag–Au tapes by employing a stepped geometry. Using this lead, safe operation of 2 kA current transport was confirmed.     

Re-evaluation of the intercept temperature for HTS current leads based on practical and economical considerations

An optimization analysis was performed to determine the intercept temperature that minimizes the net room-temperature refrigeration requirements for a binary-type HTS current lead. Two types of HTS material systems were investigated: (1) Bi₂Sr₂Ca₁Cu₂O_x (2212) melt-cast-processed tube and (2) Bi₂Sr₂Ca₂Cu₃O_x (2223) Ag–Au alloyed powder-in-tube tape. An example analysis was performed on a conduction-cooled HTS current lead using a cryocooler. The presence of a safety lead and a background magnetic field strongly influences the optimum intercept temperature. In addition, an analysis was performed to determine the optimal intercept temperature based on economic considerations. In the economic analysis, the optimal intercept temperature is determined by minimizing the capital investment cost of the HTS current lead and its corresponding refrigeration system. It was the economic impact that the intercept temperature has on combined system cost that provided the motivation for this analysis and may be of interest for commercial applications.     

Recent Achievements on the Physics of High-T C Superconductor Josephson Junctions: Background, Perspectives and Inspiration

Coherent passage of Cooper pairs in a Josephson junction (JJ) above the liquid nitrogen temperature has been the first impressive revolutionary effect induced by high critical temperature superconductors (HTS) in the domain of the study of Josephson effect (JE). But this has been only the start. A d-wave order parameter has lead to significant novel insights in the physics of the JE turning into a device the notion of a π-junction. Spontaneous currents in a frustrated geometry, Andreev bound states, long-range proximity effect have rapidly become standard terms in the study of the JE, standing as a reference bench for conventional systems based on low critical temperature superconductors (LTS) and inspiring analogies for junctions based on novel superconductors discovered in the meantime. The extreme richness of the physics of HTS JJs has not been adequately supported by the expected impact in the applications, the main reason lying in the complexity of these materials and in the consequent unsatisfactory yield and reproducibility of the performances of the JJs within the required limits. The continuous progress in material science, and specifically in the realization of oxide multi-layers, and in nanotechnologies applied to superconductors, accompanied by the advances in a better understanding of the properties of HTS and of HTS devices, has as a matter of fact opened possible novel scenarios and interest in the field. We intend to give a brief overview on interesting new problems concerning HTS JJs of inspiration also for other systems. We also review some ideas and experimental techniques on macroscopic quantum decay phenomena occurring in Josephson structures. The attention is mainly addressed to intermediate levels of dissipation, which characterize a large majority of low critical current Josephson devices and are therefore an unavoidable consequence of nanotechnology applied more and more to Josephson devices.     

Antimicrobial and anti‐biofilm activities of Bi subnitrate and BiNPs produced by Delftia sp. SFG against clinical isolates of Staphylococcus aureus,Pseudomonas aeruginosa,and Proteus mirabilis

In the present study Delftia sp. Shakibaie, Forootanfar, and Ghazanfari (SFG), was applied for preparation of biogenic Bi nanoparticles (BiNPs) and antibacterial and anti‐biofilm activities of the purified BiNPs were investigated by microdilution and disc diffusion methods. Transmission electron micrographs showed that the produced nanostructures were spherical with a size range of 40–120 nm. The measured minimum inhibitory concentration of both the Bi subnitrate and BiNPs against three biofilms producing bacterial pathogens of Staphylococcus aureus, Pseudomonas aeruginosa, and Proteus mirabilis were found to be above 1280 µg/ml. Addition of BiNPs (1000 µg/disc) to antibiotic discs containing tobramycin, nalidixic acid, ceftriaxone, bacitracin, cefalexin, amoxicillin, and cefixime significantly increased the antibacterial effects against methicillin‐resistant S. aureus (MRSA) in comparison with Bi subnitrate (p  < 0.05). Furthermore, the biogenic BiNPs decreased the biofilm formation of S. aureus, P. aeruginosa, and P. mirabilis to 55, 85, and 15%, respectively. In comparison to Bi subnitrate, BiNPs indicated significant anti‐biofilm activity against P. aeruginosa (p  < 0.05) while the anti‐biofilm activity of BiNPs against S. aureus and P. mirabilis was similar to that of Bi subnitrate. To sum up, the attained results showed that combination of biogenic BiNPs with commonly used antibiotics relatively enhanced their antibacterial effects against MRSA.Inspec keywords: nanoparticles, bismuth, nanofabrication, antibacterial activity, microorganisms, biomedical materials, toxicology, nanomedicine, transmission electron microscopy, biochemistry, drugsOther keywords: Bi, size 40.0 nm to 120.0 nm, mass 1000.0 mug, Delftia sp. SFG, Staphylococcus aureus, antibiofilm mechanisms, antibiofilm effect, antibiofilm activity, Proteus mirabilis, Pseudomonas aeruginosa, purified biogenic BiNPs, antibacterial biofilm mechanisms, Bi subnitrate, antibacterial effects     

Preliminary study of anti-infective function of a copper-bearing stainless steel

In this study the copper (Cu)-bearing stainless steel was developed to reduce the incidence of implant-associated infections in clinical areas. A 317L austenitic stainless steel containing 4.5% Cu (317L-Cu SS) was designed and fabricated, and its anti-infective function was preliminarily studied both in vitro and in vivo by means of antibacterial test, confocal laser scanning microscope (CLSM) and scanning electron microscopy (SEM) observations, and animal implantation. The results indicated that the 317L-Cu SS possessed strong antibacterial rates against both Escherichia coli and Staphylococcus aureus, and showed anti-infective ability by inhibiting the formation of bacterial bio-film on surface of the steel due to the release of Cu ions from the steel surface. The microbiological and histological evaluations from animal implantation further proved that the 317L-Cu SS could obviously reduce the happening of bacterial infection, and is potential to be used as a new class of surgical implant material with anti-infective function.     

Biofabrication of broad range antibacterial and antibiofilm silver nanoparticles

Silver nanoparticles (AgNPs) were biosynthesized via a green route using ten different plants extracts (GNP1‐ Caryota urens, GNP2‐Pongamia glabra, GNP3‐ Hamelia patens, GNP4‐Thevetia peruviana, GNP5‐Calendula officinalis, GNP6‐Tectona grandis, GNP7‐Ficus petiolaris, GNP8‐ Ficus busking, GNP9‐ Juniper communis, GNP10‐Bauhinia purpurea). AgNPs were tested against drug resistant microbes and their biofilms. These nanoparticles (NPs) were characterised using UV‐vis spectroscopy, transmission electron microscope, Fourier transform infrared spectroscopy, X‐ray diffraction and Image J software. Most of the AgNPs were distributed over a range of 1 of 60 nm size. The results indicated that AgNPs were antibacterial in nature without differentiating between resistant or susceptible strains. Moreover, the effect was more prominent on Gram negative bacteria then Gram positive bacteria and fungus. AgNPs inhibited various classes of microbes with different concentration. It was also evident from the results that the origin or nature of extract did not affect the activity of the NPs. Protein and carbohydrate leakage assays confirmed that the cells lysis is one of the main mechanisms for the killing of microbes by green AgNPs. This study suggests that the action of AgNPs on microbial cells resulted into cell lysis and DNA damage. Excellent microbial biofilm inhibition was also seen by these green AgNPs. AgNPs have proved their candidature as a potential antibacterial and antibiofilm agent against MDR microbes.Inspec keywords: silver, nanoparticles, antibacterial activity, nanofabrication, microorganisms, ultraviolet spectra, visible spectra, transmission electron microscopy, Fourier transform infrared spectra, X‐ray diffraction, proteins, DNA, nanomedicine, biomedical materials, cellular biophysicsOther keywords: biofabrication, broad range antibacterial nanoparticles, antibiofilm silver nanoparticles, plant extract contribution, drug resistant microbes, UV‐vis spectroscopy, transmission electron microscope, Fourier transform infrared spectroscopy, X‐ray diffraction, Image J software, resistant strains, susceptible strains, Gram positive bacteria, fungus, protein leakage assays, carbohydrate leakage assays, cell lysis, DNA damage, Ag     

Bio‐fabrication of silver nanoparticles by Pseudomonas aeruginosa : optimisation and antibacterial activity against selected waterborne human pathogens

Multiple drug resistance and treatment of contaminated water has become a serious issue in past years. Silver nanoparticles (AgNPs), being bactericidal, non‐toxic, cheap and environment friendly behaviour, have drawn attention to overcome these problems. This study has been designed to synthesise AgNPs from Pseudomonas aeruginosa. AgNPs formation was confirmed by colour change and UV–vis spectroscopy. Furthermore, Fourier transform infrared spectroscopy peaks demonstrated the presence of capped proteins as reducing and stabilising agent. Transmission electron microscopy micrograph revealed spherical shape AgNPs with the size ranging between 10 and 20 nm. Antibacterial activity of AgNPs was evaluated against the most prevalent waterborne pathogens enterohaemorrhagic Escherichia coli and Salmonellae typhimurium. Moreover, the antibacterial activity of AgNPs was tested for the treatment of contaminated water which showed attenuation in bacterial load within 8 h as demonstrated by growth kinetics data. Furthermore, AgNPs did not exhibit haemolytic effects on human red blood cells (RBCs) even at 100 mg L⁻¹ concentration of AgNPs. The results herein suggest that AgNPs synthesised by P. aeruginosa under optimised conditions exhibit microbicidal property against waterborne pathogens and having no toxic effect on human RBCs. These AgNPs could be employed for treatment of contaminated water after process optimisation.Inspec keywords: silver, nanoparticles, nanobiotechnology, nanofabrication, microorganisms, antibacterial activity, water treatment, ultraviolet spectra, visible spectra, Fourier transform infrared spectra, transmission electron microscopy, blood, cellular biophysicsOther keywords: biofabrication, silver nanoparticles, Pseudomonas aeruginosa, optimisation, antibacterial activity, waterborne human pathogens, multiple drug resistance, contaminated water treatment, colour change, UV‐vis spectroscopy, Fourier transform infrared spectroscopy, capped proteins, reducing agent, stabilising agent, transmission electron microscopy micrograph, enterohaemorrhagic Escherichia coli, Salmonellae typhimurium, growth kinetics, human red blood cells, microbicidal property, process optimisation, Ag