Covalent immobilization of tyrosinase on magnetic multi-walled carbon nanotubes for inhibitor screening

The inhibition of tyrosinase is considered to be a common therapeutic strategy for some hyperpigmentation disorders. Screening of tyrosinase inhibitors is of great significance to the treatment of pigmentation diseases. In this study, tyrosinase was covalently immobilized on magnetic multi-walled carbon nanotubes for the first time, and the immobilized tyrosinase was applied for ligand fishing of tyrosinase inhibitors from complex medicinal plants. The immobilized tyrosinase was characterized by transmission electron microscopy, atomic force microscopy, Fourier-transform infrared spectroscopy, vibrating sample magnetometry, and thermo-gravimetric analyzer, which indicated that tyrosinase was immobilized onto magnetic multi-walled carbon nanotubes. The immobilized tyrosinase showed better thermal stability and reusability than the free one. The ligand was fished out from Radix Paeoniae Alba and identified as 1,2,3,4,6-pentagalloylglucose by ultra-performance liquid chromatography-quadrupole time-of-flight high-resolution mass spectrometry. 1,2,3,4,6-pentagalloylglucose was found to be a tyrosinase inhibitor with similar half maximal inhibitory concentration values of 57.13 ± 0.91 μM compared to kojic acid (41.96 ± 0.78 μM). This work not only established a new method for screening tyrosinase inhibitors but also holds considerable potential for exploring the new medicinal value of medicinal plants.     

A novel highly flexible,simple, rapid and low-cost fabrication tool for paper-based microfluidic devices (μPADs) using technical drawing pens and in-house formulated aqueous inks

Paper-based microfluidic devices (μPADs) are capable of achieving rapid quantitative measurements of a variety of analytes inexpensively. μPADs rely on patterning hydrophilic-hydrophobic regions on a sheet of paper in order to create capillary channels within impermeable fluidic brakes on the paper. Here, we present a novel, highly flexible and low-cost fabrication method using a desktop digital craft plotter/cutter and technical drawing pens with tip size of 0.5 mm. The pens were used with either commercial black permanent ink for drawing fluidic brakes, or with specialty in-house formulated aqueous inks. With the permanent marker ink it was possible to create barriers on paper rapidly and in a variety of designs in a highly flexible manner. For instance, a design featuring eight reservoirs can be produced within 10 s for each μPAD with a consistent line width of brakes (%RSD < 1.5). Further, we investigated the optimal viscosity range of in-house formulated inks controlled with additions of poly(ethylene glycol). The viscosity was measured by capillary electrophoresis and the optimal viscosity was in the range of ∼3–6 mPa s. A functional test of these μPADs was conducted by the screening of antioxidant activity. Colorimetric measurements of flavonoid, phenolic compounds and DPPH free radical scavenging activity were carried out on μPADs. The results can be detected by the naked eye and simply quantified by using a camera phone and image analysis software. The fabrication method using technical drawing pens provides flexibility in the use of in-house formulated inks, short fabrication time, simplicity and low cost.     

In-situ nanoelectrospray for high-throughput screening of enzymes and real-time monitoring of reactions

The in-situ and high-throughput evaluation of enzymes and real-time monitoring of enzyme catalyzed reactions in liquid phase is quite significant in the catalysis industry. In-situ nanoelectrospray, the direct sampling and ionization method for mass spectrometry, has been applied for high-throughput evaluation of enzymes, as well as the on-line monitoring of reactions. Simply inserting a capillary into a liquid system with high-voltage applied, analytes in liquid reaction system can be directly ionized at the capillary tip with small volume consumption. With no sample pre-treatment or injection procedure, different analytes such as saccharides, amino acids, alkaloids, peptides and proteins can be rapidly and directly extracted from liquid phase and ionized at the capillary tip. Taking irreversible transesterification reaction of vinyl acetate and ethanol as an example, this technique has been used for the high-throughput evaluation of enzymes, fast optimizations, as well as real-time monitoring of reaction catalyzed by different enzymes. In addition, it is even softer than traditional electrospray ionization. The present method can also be used for the monitoring of other homogenous and heterogeneous reactions in liquid phases, which will show potentials in the catalysis industry.     

SPOT‐Ligand: Fast and effective structure‐based virtual screening by binding homology search according to ligand and receptor similarity

Structure‐based virtual screening usually involves docking of a library of chemical compounds onto the functional pocket of the target receptor so as to discover novel classes of ligands. However, the overall success rate remains low and screening a large library is computationally intensive. An alternative to this “ab initio” approach is virtual screening by binding homology search. In this approach, potential ligands are predicted based on similar interaction pairs (similarity in receptors and ligands). SPOT‐Ligand is an approach that integrates ligand similarity by Tanimoto coefficient and receptor similarity by protein structure alignment program SPalign. The method was found to yield a consistent performance in DUD and DUD‐E docking benchmarks even if model structures were employed. It improves over docking methods (DOCK6 and AUTODOCK Vina) and has a performance comparable to or better than other binding‐homology methods (FINDsite and PoLi) with higher computational efficiency. The server is available at http://sparks-lab.org . © 2016 Wiley Periodicals, Inc.     

Flexible CDOCKER: Development and application of a pseudo‐explicit structure‐based docking method within CHARMM

Protein‐ligand docking is a commonly used method for lead identification and refinement. While traditional structure‐based docking methods represent the receptor as a rigid body, recent developments have been moving toward the inclusion of protein flexibility. Proteins exist in an interconverting ensemble of conformational states, but effectively and efficiently searching the conformational space available to both the receptor and ligand remains a well‐appreciated computational challenge. To this end, we have developed the Flexible CDOCKER method as an extension of the family of complete docking solutions available within CHARMM. This method integrates atomically detailed side chain flexibility with grid‐based docking methods, maintaining efficiency while allowing the protein and ligand configurations to explore their conformational space simultaneously. This is in contrast to existing approaches that use induced‐fit like sampling, such as Glide or Autodock, where the protein or the ligand space is sampled independently in an iterative fashion. Presented here are developments to the CHARMM docking methodology to incorporate receptor flexibility and improvements to the sampling protocol as demonstrated with re‐docking trials on a subset of the CCDC/Astex set. These developments within CDOCKER achieve docking accuracy competitive with or exceeding the performance of other widely utilized docking programs. © 2015 Wiley Periodicals, Inc.     

molSimplify: A toolkit for automating discovery in inorganic chemistry

We present an automated, open source toolkit for the first‐principles screening and discovery of new inorganic molecules and intermolecular complexes. Challenges remain in the automatic generation of candidate inorganic molecule structures due to the high variability in coordination and bonding, which we overcome through a divide‐and‐conquer tactic that flexibly combines force‐field preoptimization of organic fragments with alignment to first‐principles‐trained metal‐ligand distances. Exploration of chemical space is enabled through random generation of ligands and intermolecular complexes from large chemical databases. We validate the generated structures with the root mean squared (RMS) gradients evaluated from density functional theory (DFT), which are around 0.02 Ha/au across a large 150 molecule test set. Comparison of molSimplify results to full optimization with the universal force field reveals that RMS DFT gradients are improved by 40%. Seamless generation of input files, preparation and execution of electronic structure calculations, and post‐processing for each generated structure aids interpretation of underlying chemical and energetic trends. © 2016 Wiley Periodicals, Inc.     

Rapid Identification of the Receptor‐Binding Specificity of Influenza A Viruses by Fluorogenic Glycofoldamers

The re‐emergence of influenza raises a global concern that viral pandemics can unpredictably occur. However, effective approaches that can probe the infection risk of influenza viruses for humans are rare. In this work, we develop a glycofoldamer that can rapidly identify the glycan‐receptor specificity of influenza viruses in a high‐throughput manner. The coupling of glycan receptors that can be recognized by hemagglutinin (a surface protein on the virion capsid of influenza) to a fluorogenic‐dye foldamer produces the glycofoldamers with minimal fluorescence in aqueous solution. After interaction with human‐infecting virus strains for only five minutes, the fluorescence intensity of the glycofoldamer is remarkably enhanced with a blue‐shifted emission peak. The probes have also proven effective for the rapid identification of 1) the human‐ or bird‐infecting properties of influenza viruses in a high‐throughput manner and 2) the receptor‐specificity switch of a virus strain by mutations.     

Purine 3′:5′‐cyclic nucleotides with the nucleobase in a syn orientation: cAMP,cGMP and cIMP

Purine 3′:5′‐cyclic nucleotides are very well known for their role as the secondary messengers in hormone action and cellular signal transduction. Nonetheless, their solid‐state conformational details still require investigation. Five crystals containing purine 3′:5′‐cyclic nucleotides have been obtained and structurally characterized, namely adenosine 3′:5′‐cyclic phosphate dihydrate, C₁₀H₁₂N₅O₆P·2H₂O or cAMP·2H₂O, (I), adenosine 3′:5′‐cyclic phosphate 0.3‐hydrate, C₁₀H₁₂N₅O₆P·0.3H₂O or cAMP·0.3H₂O, (II), guanosine 3′:5′‐cyclic phosphate pentahydrate, C₁₀H₁₂N₅O₇P·5H₂O or cGMP·5H₂O, (III), sodium guanosine 3′:5′‐cyclic phosphate tetrahydrate, Na⁺·C₁₀H₁₁N₅O₇P⁻·4H₂O or Na(cGMP)·4H₂O, (IV), and sodium inosine 3′:5′‐cyclic phosphate tetrahydrate, Na⁺·C₁₀H₁₀N₄O₇P⁻·4H₂O or Na(cIMP)·4H₂O, (V). Most of the cyclic nucleotide zwitterions/anions [two from four cAMP present in total in (I) and (II), cGMP in (III), cGMP⁻ in (IV) and cIMP⁻ in (V)] are syn conformers about the N‐glycosidic bond, and this nucleobase arrangement is accompanied by C_rib—H…N_pur hydrogen bonds (rib = ribose and pur = purine). The base orientation is tuned by the ribose pucker. An analysis of data obtained from the Cambridge Structural Database made in the context of syn–anti conformational preferences has revealed that among the syn conformers of various purine nucleotides, cyclic nucleotides and dinucleotides predominate significantly. The interactions stabilizing the syn conformation have been indicated. The inter‐nucleotide contacts in (I)–(V) have been systematized in terms of the chemical groups involved. All five structures display three‐dimensional hydrogen‐bonded networks.