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.     

Single‐Electron‐Transfer (SET)‐Induced Oxidative Biaryl Coupling by Polyalkoxybenzene‐Derived Diaryliodonium(III) Salts

Metal‐free oxidative C? C coupling by using polyalkoxybenzene‐derived diaryliodonium(III) salts as both the oxidant and aryl source has been developed. These salts can induce single‐electron‐transfer (SET) oxidation to yield electron‐rich arenes and subsequently transfer the polyalkoxyphenyl group into in situ generated aromatic radical cations to produce biaryl products. The reaction is promoted by a Lewis acid that activates the iodonium salts. It has been revealed that the reactivity of the salts under acidic conditions is quite different to their known behavior under basic conditions. The reactivity preference of a series of iodonium salts in the SET oxidation and their ligand transfer abilities have been systematically investigated and the results are summarized in this report.     

Aerobic Iron‐Based Cross‐Dehydrogenative Coupling Enables Efficient Diversity‐Oriented Synthesis of Coumestrol‐Based Selective Estrogen Receptor Modulators

An iron‐based cross‐dehydrogenative coupling (CDC) approach was applied for the diversity‐oriented synthesis of coumestrol‐based selective estrogen receptor modulators (SERMs), representing the first application of CDC chemistry in natural product synthesis. The first stage of the two‐step synthesis of coumestrol involved a modified aerobic oxidative cross‐coupling between ethyl 2‐(2,4‐dimethoxybenzoyl)acetate and 3‐methoxyphenol, with FeCl₃ (10 mol %) as the catalyst. The benzofuran coupling product was then subjected to sequential deprotection and lactonization steps, affording the natural product in 59 % overall yield. Based on this new methodology other coumestrol analogues were prepared, and their effects on the proliferation of the estrogen receptor (ER)‐dependent MCF‐7 and of the ER‐independent MDA‐MB‐231 breast cancer cells were tested. As a result, new types of estrogen receptor ligands having an acetamide group instead of the 9‐hydroxyl group of coumestrol were discovered. Both 9‐acetamido‐coumestrol and 8‐acetamidocoumestrol were found more active than the natural product against estrogen‐dependent MCF‐7 breast cancer cells, with IC₅₀ values of 30 and 9 nM , respectively.     

A Rapid and Efficient Way to Dynamic Creation of Cross‐Reactive Sensor Arrays Based on Ionic Liquids

Based on the simple counterion exchange of ionic liquids, a rapid, facile, and efficient strategy to create a cross‐reactive sensor array with a dynamic tunable feature was developed, and exemplified by the construction of a sensor array for the identification and classification of nitroaromatics and explosives mimics. To achieve a good sensing system with fast response, good sensitivity, and low detection limit, the synthesized ionic liquid receptors were tethered onto a silica matrix with a macro‐mesoporous hierarchical structure. Through the facile anion exchange approach, abundant ionic‐liquid‐based individual receptors with diversiform properties, such as different micro‐environments, diverse molecular interactions, and distinctive physico‐chemical properties, were easily and quickly synthesized to generate a distinct fingerprint of explosives for pattern recognition. The reversible anion exchange ability further endowed the sensor array with a dynamic tunable feature as well as good controllability and practicality for real‐world application. With the assistance of statistical analysis, such as principal component analysis (PCA) and linear discrimination analysis (LDA), an optimized‐size array with a good resolution was rationally established from a large number of IL‐based receptors. The performed experiments suggested that the ionic‐liquid‐based sensing protocol is a general and powerful strategy for creating a cross‐reactive sensor array that could find a wide range of applications for sensing various analytes or complex mixtures.     

基于改进极根学习机的回转窑煅烧带温度预测方法

针对传统算法预测回转窑煅烧带温度存在精度低、速度慢的问题,提出了基于改进极限学习机(ELM)的回转窑煅烧带温度预测方法。对ELM输入权值矩阵定义了变换系数,采用黄金分割法在给定区间内搜寻变换系数的最佳值,改进了ELM网络参数的确定方式,弥补了随机确定输入权值并且不作调整的缺陷,在保证ELM训练速度的前提下提高预测精度、减小模型随机性。实验结果表明,改进的ELM预测精度高、训练速度快、模型性能优,可满足工况恶劣的回转窑的生产需要。     

Synthesis of 3-iodothiophenes via iodocyclization of (Z)-thiobutenynes

A simple synthesis of 3-iodothiophenes was demonstrated using a wide range of (Z)-thioenynes. The key step in the iodocyclofunctionalization was the selective reduction of the triple bond in (Z)-thioenynes by the addition of iodine as an electrophilic agent. The 3-iodothiophenes were obtained in good to excellent yields of 61–92%. The 3-iodothiophenes were used as substrates in Sonogashira cross-coupling reactions to obtain thiophene acetylenes.     

Palladium‐Catalyzed Cross‐Dehydrogenative Functionalization of C(sp2)H Bonds

The catalytic cross‐dehydrogenative coupling (CDC) reaction has received intense attention in recent years. The attractive feature of this coupling process is the formation of a C? C bond from two C? H moieties under oxidative conditions. In this Focus Review, recent advances in the palladium‐catalyzed CDC reactions of C(sp²)? H bond are summarized, with a focus on the period from 2011 to early 2013.     

Transition‐Metal‐Catalyzed CS Bond Coupling Reaction

Sulfur‐containing molecules such as thioethers are commonly found in chemical biology, organic synthesis, and materials chemistry. While many reliable methods have been developed for preparing these compounds, harsh reaction conditions are usually required in the traditional methods. The transition metals have been applied in this field, and the palladium‐catalyzed coupling of thiols with aryl halides and pseudo halides is one of the most important methods in the synthesis of thioethers. Other metals have also been used for the same purpose. Here, we summarize recent efforts in metal‐catalyzed C? S bond cross‐coupling reactions, focusing especially on the coupling of thiols with aryl‐ and vinyl halides based on different metals.