Application of the novel molecular alignment method using the Hopfield Neural Network to 3D-QSAR

Recently, we investigated and proposed the novel molecular alignment method with the Hopfield Neural Network (HNN). Molecules are represented by four kinds of chemical properties (hydrophobic group, hydrogen-bonding acceptor, hydrogen-bonding donor, and hydrogen-bonding donor/acceptor), and then those properties between two molecules correspond to each other using HNN. The 12 pairs of enzyme-inhibitors were used for validation, and our method could successfully reproduce the real molecular alignments obtained from X-ray crystallography. In this paper, we apply the molecular alignment method to three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis. The two data sets (human epidermal growth factor receptor-2 inhibitors and cyclooxygenase-2 inhibitors) were investigated to validate our method. As a result, the robust and predictive 3D-QSAR models were successfully obtained in both data sets.     

Detecting conserved secondary structures in RNA molecules using constrained structural alignment

Constrained sequence alignment has been studied extensively in the past. Different forms of constraints have been investigated, where a constraint can be a subsequence, a regular expression, or a probability matrix of symbols and positions. However, constrained structural alignment has been investigated to a much lesser extent. In this paper, we present an efficient method for constrained structural alignment and apply the method to detecting conserved secondary structures, or structural motifs, in a set of RNA molecules. The proposed method combines both sequence and structural information of RNAs to find an optimal local alignment between two RNA secondary structures, one of which is a query and the other is a subject structure in the given set. The method allows a biologist to annotate conserved regions, or constraints, in the query RNA structure and incorporates these regions into the alignment process to obtain biologically more meaningful alignment scores. A statistical measure is developed to assess the significance of the scores. Experimental results based on detecting internal ribosome entry sites in the RNA molecules of hepatitis C virus and Trypanosoma brucei demonstrate the effectiveness of the proposed method and its superiority over existing techniques.     

Rapid parameterization of small molecules using the force field toolkit

The inability to rapidly generate accurate and robust parameters for novel chemical matter continues to severely limit the application of molecular dynamics simulations to many biological systems of interest, especially in fields such as drug discovery. Although the release of generalized versions of common classical force fields, for example, General Amber Force Field and CHARMM General Force Field, have posited guidelines for parameterization of small molecules, many technical challenges remain that have hampered their wide‐scale extension. The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error‐prone tasks, and graphical user interface design. Distributed as a VMD plugin, ffTK facilitates the traversal of a clear and organized workflow resulting in a complete set of CHARMM‐compatible parameters. A variety of tools are provided to generate quantum mechanical target data, setup multidimensional optimization routines, and analyze parameter performance. Parameters developed for a small test set of molecules using ffTK were comparable to existing CGenFF parameters in their ability to reproduce experimentally measured values for pure‐solvent properties (<15% error from experiment) and free energy of solvation (±0.5 kcal/mol from experiment). © 2013 Wiley Periodicals, Inc.     

Determination of alignment parameters for symmetric top molecules using nonresonant two-photon absorption

The polarization dependence of the two-photon absorption signal is described directly in terms of the matrix elements of the irreducible representation of the two-photon absorption tensor operator for an ensemble with cylindrical symmetry probed with identical photons of linear polarization. Non vanishing matrix elements are easily determined from the known tensor patterns of the specific two-photon transition. The formalism is applicable to the extraction of alignment parameters for symmetric top molecules as well as diatomics produced in collisions of unpolarized particles or in the photodissociation with a single photon of linear polarization.     

Measurement of the field-free alignment of diatomic molecules

An apparatus was constructed to experimentally quantify the field-free alignment of diatomic molecules irradiated by strong femtosecond laser pulses. In this apparatus, both homodyne and pure heterodyne detections were realized. The alignment signal is proportional to [ - 1/3](2) for homodyne detection and ( - 1/3) for pure heterodyne detection, where theta is the polar angle between the molecular axis and the laser polarization direction. Fourier transform spectra of the homodyne signal and the pure heterodyne signal were also studied. By comparing the alignment signal and its Fourier transform spectrum with the numerical calculation of the time-dependent Schr?dinger equation, we demonstrated that the pure heterodyne signal directly reproduced the alignment parameter , and its Fourier transform spectrum provided information regarding the populations of different J states in the rotational wavepacket.     

Enantioselective organocatalytic aldol reaction using small organic molecules

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Enantioselective reactions catalyzed by small organic molecules (asymmetric organocatalysis) are a comparatively new and popular segment in the area of contemporary research in asymmetric synthesis. The great synthetic utility of the aldol reaction for the formation of C–C bonds has geared up for a hard battle for research in this area resulting in a rapid evolution of tremendous highly enantioselective chiral catalysts. This review emphasizes asymmetric direct aldol reactions catalyzed by small enantioenriched organic molecules, particularly those involving enamine catalysis through primary and secondary amines. We have made significant efforts to include several important contributions from different groups in this area.     

Computational methods for the structural alignment of molecules

In drug design, often enough, no structural information on a particular receptor protein is available. However, frequently a considerable number of different ligands is known together with their measured binding affinities towards a receptor under consideration. In such a situation, a set of plausible relative superpositions of different ligands, hopefully approximating their putative binding geometry, is usually the method of choice for preparing data for the subsequent application of 3D methods that analyze the similarity or diversity of the ligands. Examples are 3D-QSAR studies, pharmacophore elucidation, and receptor modeling. An aggravating fact is that ligands are usually quite flexible and a rigorous analysis has to incorporate molecular flexibility. We review the past six years of scientific publishing on molecular superposition. Our focus lies on automatic procedures to be performed on arbitrary molecular structures. Methodical aspects are our main concern here. Accordingly, plain application studies with few methodical elements are omitted in this presentation. While this review cannot mention every contribution to this actively developing field, we intend to provide pointers to the recent literature providing important contributions to computational methods for the structural alignment of molecules. Finally we provide a perspective on how superposition methods can effectively be used for the purpose of virtual database screening. In our opinion it is the ultimate goal to detect analogues in structure databases of nontrivial size in order to narrow down the search space for subsequent experiments.     

Similarity measures based on Gaussian-type promolecular electron density models: alignment of small rigid molecules

Various molecular similarity measures (overlap, Coulomb, kinetic, electrostatic energy) and similarity indices (Carbó, Hodgkin-Richards, Kulczynski, Shape Tanimoto) are applied to the superposition of 3D promolecular electron density (PED) distributions. The original aspect of the paper lies in the consideration of smoothed PEDs, which allow to decrease the number of local solutions to a superposition problem, together with the use of the less common kinetic and electrostatic energy similarity measures. Results are obtained for a family of five rigid endothiapepsin ligands that were already considered in previous applications, based on graph representations of their PED. In the present work, it is observed that the use of smoothed PED and the kinetic similarity measure, together with the Kulczynski or Shape Tanimoto index, performed the best to align molecules of different sizes.     

Dual-polarization interferometry for quantification of small molecules using aptamers

An interferometry-based method was developed for detection of a small molecule, argininamide. The quantification of argininamide was demonstrated using aptamers immobilized on silicone oxynitride sensor surface via avidin–biotin binding. The aptamers formed a thin film over avidin layer corresponding to a thickness of 1.2 nm, consistent with a molecular positioning of multipoint attachment to the surface. The binding of argininamide did not cause any significant changes in the thickness of the aptamer film, suggesting that the specific binding did not affect the overall conformation of the aptamer molecules after adaptive rearrangement of aptamer molecules. However, the binding results in clearly detectable changes in mass calculated from multiple parameters determined by mass deposition and structural changes. The limit of detection of the developed sensor was determined to be 5 μM. The sensor can monitor real-time changes in argininamide concentrations with high reliability and sensitivity. The model system demonstrated that a combined measurement considering structural and mass changes through interferometry-based techniques can overcome one of the major problems associated with real-time monitoring of small mass analytes.     

人工神经网络在溶解度预测方面的应用

溶解度作为一项重要的物化指标,一直是化学学科的研究重点。然而,通过实验测量获得数据耗时费力,因此,科研人员建立了多种理论方法来进行估算,其中,人工神经网络因其能够关联复杂的多变量情况而受到广泛关注。本文综述了人工神经网络在物质溶解度预测方面的应用,介绍了应用最广泛的3种神经网络(BP神经网络、小波神经网络、径向基神经网络)的模型结构、预测方法和预测优势,探讨了神经网络的不足以及改进方法。文章最后对神经网络在物质溶解度预测方面的发展前景进行了展望。与其他方法相比,人工神经网络技术在物质溶解度预测方面具有预测结果精确度高、操作简单等特点,具有广阔的应用前景,但输入变量选择、隐含层节点数确定、避免局部最优等问题还需逐步建立系统的理论指导。     

Novel alignment method for control of high pretilt angle by using a solvent dipping effect on polymer surfaces

A novel alignment method for control of high pretilt angle in nematic liquid crystals (NLC), using a solvent dipping effect on various alignment layers, was successfully investigated. The pretilt angle of a NLC is increased by dipping before rubbing treatment on three kinds of rubbed polyimide (PI) surfaces. The pretilt generated by the dipping after rubbing a PI surface with a short side chain is high compared with a PI surface with a long side chain. The pretilt generated by dipping before rubbing homeotropic layer of a positive type NLC (δε > 0) is lower than that of the negative type NLC (δε < 0). The generated NLC pretilt angle is attributed to the perpendicular component of the permittivity epsilon of the NLC.     

Novel small organic molecules for a highly enantioselective direct aldol reaction

Novel organic molecules containing an l-proline amide moiety and a terminal hydroxyl for catalyzing direct asymmetric aldol reactions of aldehydes in neat acetone are designed and prepared. Catalyst 3d, prepared from l-proline and (1S,2S)-diphenyl-2-aminoethanol, exhibits high enantioselectivities of up to 93% ee for aromatic aldehydes and up to >99% ee for aliphatic aldehydes. A theoretical study of transition structures demonstrates the important role of the terminal hydroxyl group in the catalyst in the stereodiscrimination. Our results suggest a new strategy in the design of new organic catalysts for direct asymmetric aldol reactions and related transformations because plentiful chiral resources containing multi-hydrogen bond donors, for example, peptides, might be adopted in the design.     

Polyisocyanides as a new alignment medium to measure residual dipolar couplings for small organic molecules

Polyisocycanides were found to give anisotropic molecular alignment in the magnetic field and are useful to measure residual dipolar couplings (RDCs) from analytes, e.g. strychnine. They show less quadrupolar splitting of the deuterated solvent signal compared with other liquid crystal systems such as Poly-γ-benzyl-L-glutamate (PBLG) and hence less undesired line broadening.     

Novel method for incorporating the CHF(2) group into organic molecules using BrF(3)

2-Alkyl-1,3-dithiane derivatives, easily made from alkyl bromides and the parent 1,3-dithiane, were reacted with BrF(3) to form the corresponding 1,1-difluoromethyl alkanes (RCHF(2)) in 60-75% yield. The reaction proceeds well with primary alkyl halides. The limiting step for secondary alkyl halides is the relatively low yield of the dithiane preparation. The two sulfur atoms of the dithiane are essential for the reaction.     

Dissecting cellular processes using small molecules: identification of colchicine-like, taxol-like and other small molecules that perturb mitosis

BACKGROUND: Understanding the molecular mechanisms of complex cellular processes requires unbiased means to identify and to alter conditionally gene products that function in a pathway of interest. Although random mutagenesis and screening (forward genetics) provide a useful means to this end, the complexity of the genome, long generation time and redundancy of gene function have limited their use with mammalian systems. We sought to develop an analogous process using small molecules to modulate conditionally the function of proteins. We hoped to identify simultaneously small molecules that may serve as leads for the development of therapeutically useful agents. RESULTS: We report the results of a high-throughput, phenotype-based screen for identifying cell-permeable small molecules that affect mitosis of mammalian cells. The predominant class of compounds that emerged directly alters the stability of microtubules in the mitotic spindle. Although many of these compounds show the colchicine-like property of destabilizing microtubules, one member shows the taxol-like property of stabilizing microtubules. Another class of compounds alters chromosome segregation by novel mechanisms that do not involve direct interactions with microtubules. CONCLUSIONS: The identification of structurally diverse small molecules that affect the mammalian mitotic machinery from a large library of synthetic compounds illustrates the use of chemical genetics in dissecting an essential cellular pathway. This screen identified five compounds that affect mitosis without directly targeting microtubules. Understanding the mechanism of action of these compounds, along with future screening efforts, promises to help elucidate the molecular mechanisms involved in chromosome segregation during mitosis.     

Efficient overlay of small organic molecules using 3D pharmacophores

Aligning and overlaying two or more bio-active molecules is one of the key tasks in computational drug discovery and bio-activity prediction. Especially chemical-functional molecule characteristics from the view point of a macromolecular target represented as a 3D pharmacophore are the most interesting similarity measure when describing and analyzing macromolecule-ligand interaction. In this study, a novel approach for aligning rigid three-dimensional molecules according to their chemical-functional pharmacophoric features is presented and compared to the overlay of experimentally determined poses in a comparable macromolecule coordinate frame. The presented approach identifies optimal chemical feature pairs using distance and density characteristics obtained by correlating pharmacophoric geometries and thus proves to be faster than existing combinatorial alignment methods and creates more reasonable alignments than pure atom-based methods. Examples will be provided to demonstrate the feasibility, speed and intuitiveness of this method.