Different approaches toward an automatic structural alignment of drug molecules: Applications to sterol mimics,thrombin and thermolysin inhibitors

Summary A relative comparison of the binding properties of different drug molecules requires their mutual superposition with respect to various alignment criteria. In order to validate the results of different alignment methods, the crystallographically observed binding geometries of ligands in the pocket of a common protein receptor have been used. The alignment function in the program SEAL that calculates the mutual superposition of molecules has been optimized with respect to these references. Across the reference data set, alignments could be produced that show mean rms deviations of approximately 1 Å compared to the experimental situation. For structures with obvious skeletal similarities a multiple-flexible fit, linking common pharmacophoric groups by virtual springs, has been incorporated into the molecular mechanics program MOMO. In order to combine conformational searching with comparative alignments, the optimized SEAL approach has been applied to sets of conformers generated by MIMUMBA, a program for conformational analysis. Multiple-flexible fits have been calculated for inhibitors of ergosterol biosynthesis. Sets of different thrombin and thermolysin inhibitors have been conformationally analyzed and subsequently aligned by a combined MIMUMBA/SEAL approach. Since for these examples crystallographic data on their mutual alignment are available, an objective assessment of the computed results could be performed. Among the generated conformers, one geometry could be selected for the thrombin and thermolysin inhibitors that approached reasonably well the experimentally observed alignment.     

Optical Alignment of Organic Dopants in a Solid Gel Matrix: Dispersed and Grafted Rhodamine B Molecules

We study herein the rotational mobility of organic dye molecules and their ability to align on a strong optical electric field when they are encaged in the pores of an inorganic silica xerogel matrix. We compare the case of dye molecules simply dispersed in the pores of the gel—and possibly held by hydrogen bonds—to the case of molecules chemically grafted on the inner surface of these pores through covalent bonds. The study is led on hybrid silicon-zirconium based inorganic matrices doped with organic rhodamine B molecules. The stronger holding of the dopants when these are grafted to the matrix enhances the molecular alignment—and thus the induced anisotropy—as well as the remanence of this alignment. Furthermore, we show that submitting the samples to a supplementary drying at higher temperature tends to increase both the alignment anisotropy and its stability. We explain these results in terms of mobility of the molecules, in relation to their immediate environment.     

液晶光定向层材料

本文综述了近10年来液晶显示用光定向层材料领域的研究现状和进展情况，主要概述了光降解型、光致异构型、光交联型以及自组装等材料，并对目前报道的液晶光定向机理进行了总结和归纳。     

鄂尔多斯盆地长7储层致密油水平井CO2补充能量与吞吐参数优化

长7储层是鄂尔多斯盆地主要的致密区块,近一半的致密油分布其中。针对长7储层开采渗透率低、开采难度大、依靠弹性开采产能较低、能量衰竭较快等问题,通过数值模拟的方法,构建水平井分段压裂数值模拟模型,首先对比不同吞吐方式对油田产能的影响,优选出CO₂吞吐为首选的补充能量方式。其次对井网形式、井网参数及吞吐参数进行优化研究。最终优选出合适的吞吐方案,达到提高生产效率的目的。结果表明,该储层的最优注采吞吐参数为：周期注入量为2 673 t、注入压力为21 MPa、注入速度为90 t/d、焖井时间为10 d。研究对鄂尔多斯盆地长7储层提高采收率具有一定的参考意义。     

Shear-wave splitting and anisotropy in crust of Dabieshan orogenic belt

The shear-wave splitting was analyzed on the deep seismic sounding profile crossing the Dabieshan area. The direction difference between Sg and SmS fast wave polarization indicates that the modem regional tectonic stress field in the Dabieshan area exists only in uppcr crust, while the crack alignment caused by the Triassic collision between the North China and the Yangtze blocks had been preserved in mid-lower curst.     

竖井进流水平旋转内消能泄水道的泄流特性

通过对竖井进流水平旋转内消能泄水道的泄流特性的试验研究,揭示了该种泄水道的泄流规律,并着重分析了上下游水深、通气孔通气状态对泄流特性的影响。在给出泄流特性分区及流态划分后,提出该种泄水道的泄流量计算公式。     

Aligning Text and Phonemes for Speech Technology Applications Using an EM-Like Algorithm

A common requirement in speech technology is to align two different symbolic representations of the same linguistic ‘message’. For instance, we often need to align letters of words listed in a dictionary with the corresponding phonemes specifying their pronunciation. As dictionaries become ever bigger, manual alignment becomes less and less tenable yet automatic alignment is a hard problem for a language like English. In this paper, we describe the use of a form of the expectation-maximization (EM) algorithm to learn alignments of English text and phonemes, starting from a variety of initializations. We use the British English Example Pronunciation (BEEP) dictionary of almost 200,000 words in this work. The quality of alignment is difficult to determine quantitatively since no ‘gold standard’ correct alignment exists. We evaluate the success of our algorithm indirectly from the performance of a pronunciation by analogy system using the aligned dictionary data as a knowledge base for inferring pronunciations. We find excellent performance—the best so far reported in the literature. There is very little dependence on the start point for alignment, indicating that the EM search space is strongly convex. Since the aligned BEEP dictionary is a potentially valuable resource, it is made freely available for research use.     

An evaluation of molecular models of the cytochrome P450 Streptomyces griseolus enzymes P450SU1 and P450SU2

Summary P450SU1 and P450SU2 are herbicide-inducible bacterial cytochrome P450 enzymes from Streptomyces griseolus. They have two of the highest sequence identities to camphor hydroxylase (P450cam from Pseudomonas putida), the cytochrome P450 with the first known crystal structure. We have built several models of these two proteins to investigate the variability in the structures that can occur from using different modeling protocols. We looked at variability due to alignment methods, backbone loop conformations and refinement methods. We have constructed two models for each protein using two alignment algorithms, and then an additional model using an identical alignment but different loop conformations for both buried and surface loops. The alignments used to build the models were created using the Needleman-Wunsch method, adapted for multiple sequences, and a manual method that utilized both a dotmatrix search matrix and the Needleman-Wunsch method. After constructing the initial models, several energy minimization methods were used to explore the variability in the final models caused by the choice of minimization techniques. Features of cytochrome P450cam and the cytochrome P450 superfamily, such as the ferredoxin binding site, the heme binding site and the substrate binding site were used to evaluate the validity of the models. Although the final structures were very similar between the models with different alignments, active-site residues were found to be dependent on the conformations of buried loops and early stages of energy minimization. We show which regions of the active site are the most dependent on the particular methods used, and which parts of the structures seem to be independent of the methods.     

Hydrophobic Molecular Similarity from MST Fractional Contributions to the Octanol/water Partition Coefficient

Summary The use of a recently proposed hydrophobic similarity index for the alignment of molecules and the prediction of their differences in biological activity is described. The hydrophobic similarity index exploits atomic contributions to the octanol/water transfer free energy, which are evaluated by means of the fractional partitioning scheme developed within the framework of the Miertus-Scrocco-Tomasi continuum model. Those contributions are used to define global and local measures of hydrophobic similarity. The suitability of this computational strategy is examined for two series of compounds (ACAT inhibitors and 5-HT₃ receptor agonists), which are aligned to maximize the global hydrophobic similarity using a Monte Carlo-simulated protocol. Indeed, the concept of local hydrophobic similarity is used to explore structure–activity relationships in a series of COX-2 inhibitors. Inspection of the 3D distribution of hydrophobic/hydrophilic contributions in the aligned molecules is valuable to identify regions of very similar hydrophobicity, which can define pharmacophoric recognition patterns. Moreover, low similar regions permit to identify structural elements that modulate the differences in activity between molecules. Finally, the quantitative relationships found between the pharmacological activity and the hydrophobic similarity index points out that not only the global hydrophobicity, but its 3D distribution, is important to gain insight into the activity of molecules. J.M.M. and S.P. have contributed equally to this study.