Efficiency Improvement in Polymer Light‐Emitting Diodes by “Far‐Field” Effect of Gold Nanoparticles

The “far‐field” effect of metal nanoparticles (NPs), when chromophores localized nearby metal NPs (typically the distance >λ/10), is an important optical effect to enhance emission in photoluminescence. The far‐field effect originates mainly from the interaction between origin emission and mirror‐reflected emission, resulting in the increased irradiative rate of chromophores on the mirror‐type substrate. Here, the far‐field effect is used to improve emission efficiency of polymer light‐emitting diodes (PLEDs). A universal performance improvement is achieved for the full visible light (red, green, blue) PLEDs, utilizing gold (Au) NPs to modify the indium tin oxide (ITO) substrates; this is shown by experimental and theoretical simulation to mainly come from the far‐field effect. The optimized distance, between the NPs and chromophores with visible light emission ranging from 400 to 700 nm, is 80–120 nm. Thus the scope of the far‐field may overlap the light‐emitting profile very well to enhance the efficiency of optoelectronic devices. The 30–40% enhancement is obtained for different color‐emitting materials through distance optimization. The far‐field effect is demonstrated to enhance device performance for materials in the full‐visible spectral range, which extends the optoelectric applications of Au NPs.     

Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and prime/MM-GBSA calculation

Developing chemicals that inhibit checkpoint kinase 1 (Chk1) is a promising adjuvant therapeutic to improve the efficacy and selectivity of DNA-targeting agents. Reliable prediction of binding-free energy and binding affinity of Chk1 inhibitors can provide a guide for rational drug design. In this study, multiple docking strategies and Prime/Molecular Mechanics Generalized Born Surface Area (Prime/MM-GBSA) calculation were applied to predict the binding mode and free energy for a series of benzoisoquinolinones as Chk1 inhibitors. Reliable docking results were obtained using induced-fit docking and quantum mechanics/molecular mechanics (QM/MM) docking, which showed superior performance on both ligand binding pose and docking score accuracy to the rigid-receptor docking. Then, the Prime/MM-GBSA method based on the docking complex was used to predict the binding-free energy. The combined use of QM/MM docking and Prime/MM-GBSA method could give a high correlation between the predicted binding-free energy and experimentally determined pIC(50) . The molecular docking combined with Prime/MM-GBSA simulation can not only be used to rapidly and accurately predict the binding-free energy of novel Chk1 inhibitors but also provide a novel strategy for lead discovery and optimization targeting Chk1.     

SDOCK: a global protein-protein docking program using stepwise force-field potentials

Fast Fourier transform (FFT) method limits the forms of scoring functions in global protein-protein docking. On the other hand, force field potentials can effectively describe the energy hyper surface of biological macromolecules. In this study, we developed a new protein-protein docking program, SDOCK, that incorporates van der Waals attractive potential, geometric collision, screened electrostatic potential, and Lazaridis-Karplus desolvation energy into the scoring function in the global searching process. Stepwise potentials were generated from the corresponding continuous forms to treat the structure flexibility. After optimization of the atom solvation parameters and the weights of different potential terms based on a new docking test set that contains 142 cases with small or moderate conformational changes upon binding, SDOCK slightly outperformed the well-known FFT based global docking program ZDOCK3.0. Among the 142 cases tested, 52.8% gave at least one near-native solutions in the top 100 solutions. SDOCK was also tested on six blind testing cases in Critical Assessment of Predicted Interactions rounds 13 to 18. In all six cases, the near-native solutions could be found within the top 350 solutions. Because the SDOCK approach performs global docking based on force-field potentials, one of its advantages is that it provides global binding free energy surface profiles for further analysis. The efficiency of the program is also comparable with that of other FFT based protein-protein docking programs. SDOCK is available for noncommercial applications at http://mdl.ipc.pku.edu.cn/cgi-bin/down.cgi.     

PROCOS: computational analysis of protein-protein complexes

One of the main challenges in protein-protein docking is a meaningful evaluation of the many putative solutions. Here we present a program (PROCOS) that calculates a probability-like measure to be native for a given complex. In contrast to scores often used for analyzing complex structures, the calculated probabilities offer the advantage of providing a fixed range of expected values. This will allow, in principle, the comparison of models corresponding to different targets that were solved with the same algorithm. Judgments are based on distributions of properties derived from a large database of native and false complexes. For complex analysis PROCOS uses these property distributions of native and false complexes together with a support vector machine (SVM). PROCOS was compared to the established scoring schemes of ZRANK and DFIRE. Employing a set of experimentally solved native complexes, high probability values above 50% were obtained for 90% of these structures. Next, the performance of PROCOS was tested on the 40 binary targets of the Dockground decoy set, on 14 targets of the RosettaDock decoy set and on 9 targets that participated in the CAPRI scoring evaluation. Again the advantage of using a probability-based scoring system becomes apparent and a reasonable number of near native complexes was found within the top ranked complexes. In conclusion, a novel fully automated method is presented that allows the reliable evaluation of protein-protein complexes.     

A comparison of neighbor search algorithms for large rigid molecules

Fast determination of neighboring atoms is an essential step in molecular dynamics simulations or Monte Carlo computations, and there exists a variety of algorithms to efficiently compute neighbor lists. However, most of these algorithms are general, and not specifically designed for a given type of application. As a result, although their average performance is satisfactory, they might be inappropriate in some specific application domains. In this article, we study the case of detecting neighbors between large rigid molecules, which has applications in, e.g., rigid body molecular docking, Monte Carlo simulations of molecular self-assembly or diffusion, and rigid body molecular dynamics simulations. More precisely, we compare the traditional grid-based algorithm to a series of hierarchy-based algorithms that use bounding volumes to rapidly eliminate large groups of irrelevant pairs of atoms during the neighbor search. We compare the performance of these algorithms based on several parameters: the size of the molecules, the average distance between them, the cutoff distance, as well as the type of bounding volume used in the culling hierarchy (AABB, OBB, wrapped, or layered spheres). We demonstrate that for relatively large systems (> 100,000 atoms) the algorithm based on the hierarchy of wrapped spheres shows the best results and the traditional grid-based algorithm gives the worst timings. For small systems, however, the grid-based algorithm and the one based on the wrapped sphere hierarchy are beneficial.     

二芳基三嗪类HIV-1逆转录酶抑制剂的分子对接及3D-QSAR研究

对40个二芳基三嗪类HIV-1逆转录酶抑制剂进行了分子对接研究,结果表明,2个疏水性芳香取代基团与结合口袋底部形成的疏水和范德华相互作用、三嗪环母核及其R4取代基与结合位点产生的氢键和静电作用以及R4取代基与袋口形成的空间位阻效应是影响该系列化合物活性的重要因素.根据对接优势构象进行分子叠合和比较分子相似性指数分析(C...     

Three optimized and validated (using accuracy profiles) LC methods for the determination of pentamidine and new analogs in rat plasma

Three novel LC-UV methods for the determination of pentamidine (PTMD) and two of its new analogs in rat plasma are described. The chromatographic conditions (wavelength, acetonitrile percentage in the mobile phase, internal standard) were optimized to have an efficient selectivity. A pre-step of extraction was simultaneously developed for each compound. For PTMD, a solid phase extraction (SPE) with Oasis^® HLB cartridges was selected, while for the analogs we used protein precipitation with acetonitrile. SPE for PTMD gave excellent results in terms of extraction yield (99.7 ± 2.8) whereas the recoveries for the analogs were not so high but were reproducible as well (64.6 ± 2.6 and 36.8 ± 1.6 for analog 1 and 2, respectively).By means of a recent strategy based on accuracy profiles (β-expectation tolerance interval), the methods were successfully validated. β was fixed at 95% and the acceptability limits at ±15% as recommended by the FDA. The method was successfully validated for PTMD (29.6-586.54 ng/mL), analog 1 (74.23-742.3 ng/mL) and analog 2 (178.12-890.6 ng/mL). The first concentration level tested was considered as the LLOQ (lower limit of quantification) for PTMD and analog 1 whereas for analog 2, the LLOQ was not the first level tested and was raised to 178.12 ng/mL.     

Development and validation of a ultra-high-performance liquid chromatography-UV method for the detection and quantification of erectile dysfunction drugs and some of their analogues found in counterfeit medicines

Pharmaceutical counterfeiting is a permanently growing problem. Control laboratories are constantly analysing counterfeit medicines. In industrialised countries, one of the main counterfeited class of medicines are erectile dysfunction drugs. This paper describes the development and validation of a fast method to detect and quantify the three authorised phosphodiesterase type 5 inhibitors and five analogues. The method is based on the use of a sub-2 microns polar-embedded column with a gradient using acetonitrile as organic modifier and 10 mM ammonium formate buffer (pH 3.5) as aqueous component of the mobile phase. The separation was achieved in less than 4.5 min. The method has also been compared to the registered HPLC method for the assay of Viagra^® which was considered as the reference method. The method is also compatible with on-line coupling mass spectrometry and will significantly reduce analysis times and solvent consumption.     

5-(Indol-2-yl)pyrazolo[3,4-b]pyridines as a New Family of TASK-3 Channel Blockers: A Pharmacophore-Based Regioselective Synthesis

TASK channels belong to the two-pore-domain potassium (K_2P) channels subfamily. These channels modulate cellular excitability, input resistance, and response to synaptic stimulation. TASK-channel inhibition led to membrane depolarization. TASK-3 is expressed in different cancer cell types and neurons. Thus, the discovery of novel TASK-3 inhibitors makes these bioactive compounds very appealing to explore new cancer and neurological therapies. TASK-3 channel blockers are very limited to date, and only a few heterofused compounds have been reported in the literature. In this article, we combined a pharmacophore hypothesis with molecular docking to address for the first time the rational design, synthesis, and evaluation of 5-(indol-2-yl)pyrazolo[3,4-b]pyridines as a novel family of human TASK-3 channel blockers. Representative compounds of the synthesized library were assessed against TASK-3 using Fluorometric imaging plate reader—Membrane Potential assay (FMP). Inhibitory properties were validated using two-electrode voltage-clamp (TEVC) methods. We identified one active hit compound (MM-3b) with our systematic pipeline, exhibiting an IC₅₀ ≈ 30 μM. Molecular docking models suggest that compound MM-3b binds to TASK-3 at the bottom of the selectivity filter in the central cavity, similar to other described TASK-3 blockers such as A1899 and PK-THPP. Our in silico and experimental studies provide a new tool to predict and design novel TASK-3 channel blockers.     

Antioxidant Effects and Phytochemical Properties of Seven Taiwanese Cirsium Species Extracts

In the present investigation, we compared the radical-scavenging activities and phenolic contents of seven Taiwanese Cirsium species with a spectrophotometric method. We further analyzed their phytochemical profiles with high-performance liquid chromatography–photodiode array detection (HPLC–DAD). We found that the flower part of Cirsium japonicum var. australe (CJF) showed the best radical-scavenging activities against 1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), and the hypochlorite ion, for which the equivalents were 6.44 ± 0.17 mg catechin/g, 54.85 ± 0.66 mmol Trolox/g and 418.69 ± 10.52 mmol Trolox/g respectively. CJF also had the highest contents of total phenolics (5.23 ± 0.20 mg catechin/g) and phenylpropanoids (29.73 ± 0.72 mg verbascoside/g). According to the Pearson’s correlation coefficient, there was a positive correlation between the total phenylpropanoid content and ABTS radical-scavenging activities (r = 0.979). The radical-scavenging activities of the phenylpropanoids are closely related to their reducing power (r = 0.986). HPLC chromatograms obtained in validated HPLC conditions confirm that they have different phytochemical profiles by which they can be distinguished. Only CJF contained silicristin (0.66 ± 0.03 mg/g) and silydianin (9.13 ± 0.30 mg/g). CJF contained the highest contents of apigenin (5.56 ± 0.09 mg/g) and diosmetin (2.82 ± 0.10 mg/g). Among the major constituents, silicristin had the best radical-scavenging activities against DPPH (71.68 ± 0.66 mg catechin/g) and ABTS (3.01 ± 0.01 mmol Trolox/g). However, diosmetin had the best reducing power and radical-scavenging activity against the hypochlorite anion (41.57 ± 1.14 mg mmol Trolox/g). Finally, we found that flavonolignans (especial silicristin and silydianin) and diosmetin acted synergistically in scavenging radicals.