FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm

The accurate prediction of protein–ligand binding is of great importance for rational drug design. We present herein a novel docking algorithm called as FIPSDock, which implements a variant of the Fully Informed Particle Swarm (FIPS) optimization method and adopts the newly developed energy function of AutoDock 4.20 suite for solving flexible protein–ligand docking problems. The search ability and docking accuracy of FIPSDock were first evaluated by multiple cognate docking experiments. In a benchmarking test for 77 protein/ligand complex structures derived from GOLD benchmark set, FIPSDock has obtained a successful predicting rate of 93.5% and outperformed a few docking programs including particle swarm optimization (PSO)@AutoDock, SODOCK, AutoDock, DOCK, Glide, GOLD, FlexX, Surflex, and MolDock. More importantly, FIPSDock was evaluated against PSO@AutoDock, SODOCK, and AutoDock 4.20 suite by cross‐docking experiments of 74 protein–ligand complexes among eight protein targets (CDK2, ESR1, F2, MAPK14, MMP8, MMP13, PDE4B, and PDE5A) derived from Sutherland‐crossdock‐set. Remarkably, FIPSDock is superior to PSO@AutoDock, SODOCK, and AutoDock in seven out of eight cross‐docking experiments. The results reveal that FIPS algorithm might be more suitable than the conventional genetic algorithm‐based algorithms in dealing with highly flexible docking problems. © 2012 Wiley Periodicals, Inc.     

Three new ZnII coordination polymers constructed from a semi‐rigid tricarboxylic acid: structural changes caused by flexibility and luminescence sensing for hexavalent chromate anions

Coordination polymers (CPs) with specific structures and functional luminescence have been widely designed as sensors for detecting small molecules and ions. In this study, with or without the help of an N‐donor auxiliary linker, three new Zn^II CPs, namely, three‐dimensional (3D) poly[[pentaaquabis[μ₃‐5‐(4‐carboxybenzyloxy)isophthalato]bis[μ₆‐5‐(4‐carboxylatobenzyloxy)isophthalato]di‐μ₃‐hydroxido‐hexazinc(II)] trihydrate], {[Zn₆(C₁₆H₁₀O₇)₂(C₁₆H₉O₇)₂(OH)₂(H₂O)₅]·3H₂O}_n or {[Zn₆(μ₃‐HL)₂(μ₆‐L)₂(μ₃‐OH)₂(H₂O)₅]·3H₂O}_n, ( I ), one‐dimensional (1D) catena‐poly[[[aqua(1,10‐phenanthroline)zinc(II)]‐μ₂‐5‐(4‐carboxybenzyloxy)isophthalato] dihydrate], {[Zn(C₁₆H₁₀O₇)(C₁₂H₈N₂)(H₂O)]·2H₂O}_n or {[Zn(μ₂‐HL)(phen)(H₂O)]·2H₂O}_n (phen is 1,10‐phenanthroline), ( II ), and 3D poly[diaquatetrakis(4,4′‐bipyridine)bis[μ₆‐5‐(4‐carboxylatobenzyloxy)isophthalato]di‐μ₃‐formato‐di‐μ₃‐hydroxido‐pentazinc(II)], [Zn₅(C₁₆H₉O₇)₂(HCOO)₂(OH)₂(C₁₀H₈N₂)₄(H₂O)₂]_n or [Zn₅(μ₄‐L)₂(bpy)₄(μ₂‐OH)₂(μ₃‐HCOO)₂(H₂O)₂]_n (bpy is 4,4′‐bipyridine), ( III ), have been constructed from the semi‐rigid tricarboxylic acid 5‐(4‐carboxybenzyloxy)isophthalic acid (H₃L) under hydrothermal conditions. CP ( I ) exhibits a twofold interpenetrated 3D+3D→3D skeleton with a 3 , 5 ‐conn topology constructed from triangular trinuclear [Zn₃(COO)₄(μ₃‐OH)] clusters, in which the H₃L ligand adopts three different coordination modes. CP ( II ) exhibits a 1D infinite chain and stacking that gives a 3D structure mediated by hydrogen bonds and weak interactions. CP ( III ) is an interesting 3D 3 , 4 , 8 ‐conn network including linear tetranuclear [Zn₄(μ₂‐OH)₂(HCOO)₂(COO)₂] clusters with a new {4·6²}₂{4·6⁴·8}{4⁶·6¹⁹·8³} topological symbol. The influences of the flexible –CH₂–O– linker of the H₃L ligand and subtle environmental factors, such as solvent, pH value and auxiliary ligands, on the formation of the final structures are also discussed. The solid‐state fluorescence spectra of CPs ( I )–( III ) were recorded at room temperature and all show better fluorescence performances than H₃L. In particular, ( II ) can act as a potential multifunctional fluorescent material for sensing hexavalent chromium ions in aqueous solution with high stability, selectivity and sensitivity. Under ultraviolet light of 365 nm from a UV lamp, a signal response of fluorescence from turning on to off can be observed with the naked eye. It was found that the detection for hexavalent chromium (i.e. Cr₂O₇^2?) by ( II ) has a high selectivity [K_SV = 1.61 × 10⁴M^?1 and limit of detection (LOD) = 0.434 µM] in aqueous solution. Quenching mechanisms were also studied in detail.     

Two-Photon-Induced CO-Releasing Molecules as Molecular Logic Systems in Solution,Polymers, and Cells

Phototherapeutic applications of carbon monoxide (CO)-releasing molecules are limited because they require harmful UV and blue light for activation. We describe two-photon excitation with NIR light (800 nm)-induced CO-release from two Mn^I tricarbonyl complexes bearing 1,8-naphthalimide units ( 1 , 2 ). Complex 2 behaves as a logic OR gate in solution, nonwovens, and in HeLa cells. CO release, indicated by fluorescence enhancement, was detected in solution, nonwoven, and HeLa cells by single- (405 nm) and two-photon (800 nm) excitation. The photophysical properties of 1 and 2 have been measured and supported by DFT and TDDFT quantum chemical calculations. Both photoCORMs are stable in the dark in solution and noncytotoxic, leading to promising applications as phototherapeutics with NIR light.     

Dynamic surface elasticity of polymer solutions

The surfaces of surfactant solutions exhibit viscoelastic dilational behavior which may be investigated by modern optical and mechanical methods. The present study focuses on the dynamic dilational properties of the polymer solution — gas interface. Linear flexible polymer chains at the surface are considered as consisting of trains, lying on the surface, and loops and tails that protrude into the liquid. The Rouse model is used to describe the inner dynamics of the trains, whereas their motion relative to their neighbors on the surface can be described with the help of the reptation conception. An expression for the complex dynamic dilational surface elasticity has been derived. Although, in general, the relaxation of the surface tension is characterized by an infinite series of relaxation times, it is shown that for many systems the dynamics of the surface layer can be described approximately by only two main relaxation times. The dispersion equation, which was obtained earlier for solutions of conventional surfactants, is shown to be fulfilled for polymer solutions also.     

酶的分子仿生研究进展

回顾了近几十年来印迹高分子和有机团簇对酶的仿生发展历程，总结了目前的 研究现状，探讨了电子效应和空间效应（柔性空间效应）对仿对酶在催化过程中实 现类似酶的识别和诱导契合的影响，并展望了酶的仿生发展趋势。     

新型有序结构分子聚集体的构筑

本文概述了近年来我们在新型有序结构分子聚集体构筑方面取得的一些主要成绩，并展望了今后进一步的研究和发展方向。     

Quality of random number generators significantly affects results of Monte Carlo simulations for organic and biological systems

We have simulated pure liquid butane, methanol, and hydrated alanine polypeptide with the Monte Carlo technique using three kinds of random number generators (RNG's)—the standard Linear Congruential Generator (LCG), a modification of the LCG with additional randomization used in the BOSS software, and the “Mersenne Twister” generator by Matsumoto and Nishimura. While using the latter two RNG's leads to reasonably similar physical features, the LCG produces significant different results. For the pure fluids, a noticeable expansion occurs. Using the original LCG on butane yields, a molecular volume of 171.4 ų per molecule compared to about 163.6–163.9 ų for the other two generators, a deviation of about 5%. For methanol, the LCG produces an average volume of 86.3 ų per molecule, which is about 24% higher than the 68.8–70.2 ų obtained with the RNG's in BOSS and the generator by Matsumoto and Nishimura. In case of the hydrated tridecaalanine peptide, the volume and energy tend to be noticeably greater with the LCG than with the BOSS (modified LCG) RNG's. For the simulated hydrated extended conformation of tridecaalanine, the difference in volume reached about 87%. The uniformity and periodicity of the generators do not seem to play the crucial role in these phenomena. We conclude that, it is important to test a RNG's by modeling a system such as the pure liquid methanol with a well‐established force field before routinely employing it in Monte Carlo simulations. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Study on the friction and wear behavior of surface‐modified carbon nanotube filled carbon fabric composites

The functionalization of multi‐walled carbon nanotubes (MWNTs) was achieved by grafting furfuryl amine (FA) onto the surfaces of MWNTs. Furthermore, the functional MWNTs were incorporated into carbon fabric composites and the tribological properties of the resulting composites were investigated systematically on a model ring‐on‐block test rig. Friction and wear tests revealed that the modified MWNTs filled carbon fabric composite has the highest wear resistance under all different sliding conditions. Fourier transform infrared spectroscopy (FTIR), X‐ray photoelectron spectroscopy (XPS), and thermal gravimetric analysis (TGA) revealed that MWNTs were successfully functionalized and the modification led to an improvement in the dispersion of MWNTs, which played an important role on the enhanced tribological properties of carbon fabric composites. It can also be found that the friction and wear behavior of MWNTs filled carbon fabric composites are closely related with the sliding conditions such as sliding speed, load, and lubrication conditions. Copyright © 2010 John Wiley & Sons, Ltd.     

Computer based screening of compound databases: 1. Preselection of benzamidine-based thrombin inhibitors

We present a computational protocol which uses the known three-dimensional structure of a target enzyme to identify possible ligands from databases of compounds with low molecular weight. This is accomplished by first mapping the essential interactions in the binding site with the program GRID. The resulting regions of favorable interaction between target and ligand are translated into a database query, and with UNITY a flexible 3D database search is performed. The feasibility of this approach is calibrated with thrombin as the target. Our results show that the resulting hit lists are enriched with thrombin inhibitors compared to the total database.