Comparison of ranking methods for virtual screening in lead-discovery programs

This paper discusses the use of several rank-based virtual screening methods for prioritizing compounds in lead-discovery programs, given a training set for which both structural and bioactivity data are available. Structures from the NCI AIDS data set and from the Syngenta corporate database were represented by two types of fragment bit-string and by sets of high-level molecular features. These representations were processed using binary kernel discrimination, similarity searching, substructural analysis, support vector machine, and trend vector analysis, with the effectiveness of the methods being judged by the extent to which active test set molecules were clustered toward the top of the resultant rankings. The binary kernel discrimination approach yielded consistently superior rankings and would appear to have considerable potential for chemical screening applications.     

Development of additives possessing both solid-phase and gas-phase flame retardant activities

Effective additives are required to impart a measure of fire retardancy to polymeric materials used in a variety of applications. Traditionally, these have been gas-phase active additives, most commonly organohalogen compounds or solid-phase active agents, often organophosphorus compounds. Organosphosphorus flame retardants are often very effective but may suffer from a cost disadvantage when compared with their organobromine counterparts. Organohalogen flame retardants are usually quite effective but their use is a subject to several environmental concerns. The development of additives that could simultaneously promote both types of fire retardant action could make available flame retardants that are both more cost effective and more environmentally friendly than those currently in use. Several sets of compounds with the potential to display both solid-phase and gas-phase flame retardant activities have been prepared and evaluated.     

Thermal properties of compounds possessing both solid-phase and gas-phase flame retardant potential

Effective additives are required to impart a measure of fire retardancy to polymeric materials used in a variety of applications. Traditionally, these have been gas-phase active additives, most commonly organohalogen compounds, or solid-phase active agents, often organophosphorus compounds. Organosphosphorus flame retardants are often very effective but may suffer from a cost disadvantage when compared with their organobromine counterparts. Organohalogen flame retardants are usually quite effective but their use is subject to several environmental concerns. The development of additives that could simultaneously promote both types of fire retardant action could make available flame retardants that are both more cost effective and more environmentally friendly than those currently in use. Several sets of compounds including bromoanilino triazine derivatives and bromoaryl phosphates with the potential to display both solid-phase and gas-phase flame retardant activity have been prepared and evaluated by a variety of thermal methods.     

Characterization and identification of steroidal alkaloids in Fritillaria species using liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry

Liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (LC/ESI-QTOF-MS/MS) was performed to study the fragmentation behaviors of steroidal alkaloids from Fritillaria species, the antitussive and expectorant herbs widely used in traditional Chinese medicine. We propose, herein, a strategy that combining key diagnostic fragment ions and the relative abundances and amounts of major fragment ions (the ions exceeding 10% in abundance) to distinguish different sub-classes of Fritillaria alkaloids (FAs). It was found that hydrogen rearrangement and induction effects result in ring cleavage of the basic skeletons occurred in the MS/MS process and produced characteristic fragment ions, which are useful for structural elucidation. This method was finally used to investigate the primary steroidal alkaloids in the extracts of eight major Fritillaria species. As a result, 41 steroidal alkaloids (29 cevanine type, 1 jervine type, 6 veratramine type and 5 secosolanidine type alkaloids) were selectively identified in these Fritillaria species. Twenty-six compounds were unambiguously identified by comparing with the reference compounds and 15 compounds were tentatively identified or deduced according to their MS/MS data. Logical fragmentation pathways for different types of FAs have been proposed and are useful for the identification of these types of steroidal alkaloids in natural products especially when there are no reference compounds available.     

Hidden active information in a random compound library: extraction using a pseudo-structure-activity relationship model

We propose a hypothesis that "a model of active compound can be provided by integrating information of compounds high-ranked by docking simulation of a random compound library". In our hypothesis, the inclusion of true active compounds in the high-ranked compound is not necessary. We regard the high-ranked compounds as being pseudo-active compounds. As a method to embody our hypothesis, we introduce a pseudo-structure-activity relationship (PSAR) model. Although the PSAR model is the same as a quantitative structure activity relationship (QSAR) model, in terms of statistical methodology, the implications of the training data are different. Known active compounds (ligands) are used as training data in the QSAR model, whereas the pseudo-active compounds are used in the PSAR model. In this study, Random Forest was used as a machine-learning algorithm. From tests for four functionally different targets, estrogen receptor antagonist (ER), thymidine kinase (TK), thrombin, and acetylcholine esterase (AChE), using five scoring functions, we obtained three conclusions: (1) the PSAR models significantly gave higher percentages of known ligands found than random sampling, and these results are sufficient to support our hypothesis; (2) the PSAR models gave higher percentages of known ligands found than normal scoring by scoring function, and these results demonstrate the practical usefulness of the PSAR model; and (3) the PSAR model can assess compounds failed in the docking simulation. Note that PSAR and QSAR models are used in different situations; the advantage of the PSAR model emerges when no ligand is available as training data or when one wants to find novel types of ligands, whereas the QSAR model is effective for finding compounds similar to known ligands when the ligands are already known.     

Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures

Fingerprint-based similarity searching is widely used for virtual screening when only a single bioactive reference structure is available. This paper reviews three distinct ways of carrying out such searches when multiple bioactive reference structures are available: merging the individual fingerprints into a single combined fingerprint; applying data fusion to the similarity rankings resulting from individual similarity searches; and approximations to substructural analysis. Extended searches on the MDL Drug Data Report database suggest that fusing similarity scores is the most effective general approach, with the best individual results coming from the binary kernel discrimination technique.     

快速测量挥发性有机物的膜进样-飞行时间质谱仪的设计和应用

研制了一种膜进样-微型飞行时间质谱仪, 该仪器使用双层50 μm硅橡胶膜作为大气压下直接进样的接口. 实验结果表明, 随着样品流速的提高, 膜富集效率信号强度呈线性提高. 双膜中间具有真空差分系统, 富集得到的样品被迅速抽走, 进样系统中样品无记忆效应. 样品在膜中的响应时间为100 s, 而打开差分系统后仅需10 s信号即下降为平稳状态. 与毛细管直接进样相比, 双层膜的富集作用显著, 在相同的实验条件下使用膜进样技术测定10×10-6 (体积分数)苯、甲苯和对二甲苯的信号强度分别提高了280, 370和600倍. 膜进样系统与真空紫外光软电离方式联用, 对于苯的检出限已经达到了25×10-9 (体积分数), 线性范围为3个数量级. 由于采用了软电离方法, 无碎片离子产生, 所以能够根据分子量进行快速定性分析. 将该仪器应用于香烟主烟气中可挥发性有机物的在线分析, 得到50多种可挥发性的有机物. 实验结果表明, 膜进样-飞行时间质谱将在在线分析(特别是环境监测)方面具有广泛的应用空间.     

Resolution and segmentation of hyperspectral biomedical images by multivariate curve resolution-alternating least squares

MCR-ALS is a resolution method that has been applied in many different fields, such as process analysis, environmental data and, recently, hyperspectral image analysis. In this context, the algorithm provides the distribution maps and the pure spectra of the image constituents from the sole information in the raw image measurement. Based on the distribution maps and spectra obtained, additional information can be easily derived, such as identification of constituents when libraries are available or quantitation within the image, expressed as constituent signal contribution. This work summarizes first the protocol followed for the resolution on two examples of kidney calculi, taken as representations of images with major and minor compounds, respectively. Image segmentation allows separating regions of images according to their pixel similarity and is also relevant in the biomedical field to differentiate healthy from non-healthy regions in tissues or to identify sample regions with distinct properties. Information on pixel similarity is enclosed not only in pixel spectra, but also in other smaller pixel representations, such as PCA scores. In this paper, we propose the use of MCR scores (concentration profiles) for segmentation purposes. K-means results obtained from different pixel representations of the data set are compared. The main advantages of the use of MCR scores are the interpretability of the class centroids and the compound-wise selection and preprocessing of the input information in the segmentation scheme.     

Calculated geometries of dications of bis odd‐membered π‐ring systems containing a NCN fragment and related π‐systems. An opposite out‐of‐plane rotation of the 4n π‐ring subsystems

Quantum chemical calculations have been carried out on dications of bis odd‐membered π‐ring systems containing a NCN fragment and related π‐systems. An opposite out‐of‐plane rotation of both subsystems was found if these systems contain 4n π‐electrons (antiaromatic). A planar situation was found for 4n+2 π‐electrons (aromatic). The geometric representations could be compared with X‐ray crystallographic three‐dimensional structures of related compounds. Calculations at different levels clearly show that separation of the σ‐ and π‐electron contribution is an effective way to elucidate the origin of the geometrical changes. We also give attention to some fundamental aspects of the subsystems related to the 1,3‐azolium cations because of their biochemical relevance such as fast C₂? H proton exchange. We postulate that at least two molecules of water are involved in this process. The significance of a trigonal pyramidal (TP) geometry has been emphasized. © 2001 Wiley Periodicals, Inc. Int J Quantum Chem, 2001     

Exploration of 3D activity cliffs on the basis of compound binding modes and comparison of 2D and 3D cliffs

Activity cliffs are formed by pairs or groups of structurally similar compounds having large differences in potency and are focal points of structure-activity relationship (SAR) analysis. The choice of molecular representations is a critically important aspect of activity cliffs analysis. Thus far, activity cliffs have predominantly been defined on the basis of molecular graph or fingerprint representations. Herein we introduce 3D activity cliffs derived from comparisons of experimentally determined compound binding modes. The analysis of 3D activity cliffs is generally applicable to target proteins for which structures of multiple ligand complexes are available. For two popular targets, β-secretase 1 (BACE1) and factor Xa (FXa), public domain X-ray structures with bound inhibitors were collected. Crystallographic binding modes of inhibitors were systematically compared using a 3D similarity method taking conformational, positional, and atomic property differences into account. In addition, standard 2D similarity relationships were also determined. SAR information associated with individual compounds substantially changed when either bioactive conformations or 2D molecular graphs were used for similarity evaluation. 3D activity cliffs were identified for BACE1 and FXa inhibitor sets and systematically compared to 2D cliffs. It was found that less than 40% of 3D activity cliffs were conserved when 2D similarity was applied. The limited conservation of 3D and 2D cliffs provides further evidence for the strong molecule representation dependence of activity cliffs. Moreover, 3D cliffs represent a new class of activity cliffs that convey SAR information in ways that differ from graph-based similarity measures. In cases where sufficient structural information is available, the comparison of 3D and 2D cliffs is expected to aid in SAR analysis and mapping of critical binding determinants.     

Bone Tissue Disorders: Healing Through Coordination Chemistry

Osteoporosis, Paget's disease and osteosarcoma are a few examples of bone tissue disorders that affect millions of people worldwide. These conditions can strictly limit the lifestyle of patients and may even lead to their demise. To prevent this or, at least, try to manage the situation, there are several treatments available on the market. Notwithstanding, research has been driven by the possibility to improve the existing therapies, as well as to find new approaches that could better respond to these diseases. In this Review the path is shown through which, in recent years, coordination compounds have been prepared and manufactured to be applied in the management of bone tissue disorders. Starting with the design and preparation of the coordination compounds with various dimensionalities, two approaches have been used: (1) they are prepared as three-dimensional cages that can act as delivery systems for therapeutic substances, or (2) they are constructed/prepared from compounds with intrinsic therapeutic properties. Following this, several strategies have been explored to manufacture the effective delivery to the patients. The versatility of coordination compounds has allowed their use in the preparation of drug tablets, coatings for titanium implants, or even scaffolds for bone tissue engineering. In the end, it becomes clear that these compounds can be a valuable approach to reach a better treatment for bone tissue disorders. Nonetheless, along the road, a few bumps have appeared concerning the therapeutic profile, such as the effect of the structural arrangement or particle size.     

Global versus local QSPR models for persistent organic pollutants: balancing between predictivity and economy

Experimentally determined data on the key physicochemical parameters for halogenated congeners of persistent organic pollutants (POPs) are available only for a limited number of compounds. In the absence of experimental data, a range of computational methods can be applied to characterize those species for which experimental data is not available. One of the techniques widely used in this context is quantitative structure–property relationships (QSPR) approach. There are two ways to develop the QSPR models: using a more complex global model or fitting a simple local model that covers a specific class of chemically related compounds. The essence of the study was to investigate, if local models have significantly better explanatory and predictive ability than global models with wider applicability domains. Based on the obtained results, we concluded that whenever global models fulfill all quality recommendations by OECD, they would be applied in practice as more efficient ones in state of more time consuming procedure of modeling the particular groups of POPs one-by-one. On the contrary, local models are applicable to solve specific problems (i.e., related to only one group of POPs), when high-quality experimental data are available for a sufficient number of training and validation compounds.     

Fungal metabolite screening: database of 474 mycotoxins and fungal metabolites for dereplication by standardised liquid chromatography-UV-mass spectrometry methodology

A standardised LC-UV-MS micro-scale method for screening of fungal metabolites and mycotoxins in culture extracts is presented. The paper includes data for detection and dereplication of > 400 fungal metabolites to facilitate detection and identification when standards are not available. The data also shows the types of components that can be analysed by positive electrospray (ESI+) mass spectrometry (MS) along with common fragments and adducts of these, as well as giving suggestions on whether UV or ESI+-MS methods should be used. Examples of dereplication of penitrems and macro-cyclic ichothecenes, and detection of several novel compounds are shown. This was done by UV spectroscopy combined with accurate mass determination of adduct and fragment ions obtained by high-resolution orthogonal time-of-flight MS.     

Electrostatic potentials in systems periodic in one, two, and three dimensions

We consider the electrostatic potential in a unit cell containing N point charges Q(j) with positions r(j) inside the cell. The cell is replicated periodically in one, two, and three dimensions. The purpose is to give representations for the potential which contain only lattice sums which are absolutely convergent and uniformly convergent in the sampling position r. These representations are derived using variants of the Ewald method and are primarily intended for use in evaluating the accuracy of any algorithm to evaluate electrostatic energies and forces in simulations of dense matter, rather than necessarily for use of themselves in simulations. In reduced dimensionality the Ewald representations can be numerically inefficient and other representations are also provided with careful specification which allows two forms to be used for the potential functions in order to improve numerical performance. These mixed representations may be satisfactory in simulations.     

4-Diazomethyl-7-Methoxycoumarin as a New Type of Stable Aryldiazomethane Reagent

Diazoalkanes have been widely used as versatile alkylating agents. One of the principal advantages of using diazoalkane is that no side reaction product other than gaseous nitrogen is produced during alkylation process. However, most diazoalkanes suffer from the fact that they are unstable, sometimes explosive, and are not available in pure state. They have to be only used in the solutions prepared from appropriate precursors just before use. Thus, only a few compounds have been developed so far as solid diazoalkane reagents¹ of practical value which are suitable for labeling acidic substances for analytical and biochemical purposes. We have now obtained 4-diazomethyl-7-methoxycoumarin 4 as a new type of crystalline aryldiazomethane having excellent purity and stability as well as enough reactivity to produce a fluorophore with carboxylic or sulfonic acid by esterification.     

Ordering of a lateral crown ether and terminal short POE chains in some symmetrical nematogens by 13 C NMR

A lateral crown ether fragment can be introduced on symmetrical mesogens containing only three aromatic rings. The replacement of the terminal alkoxy chains by chains containing oxyethylene units decreases the melting and clearing temperatures allowing one to obtain nematic compounds near room temperature. These compounds dissolve LiBF 4 salt only to a small extent, but the nematic arrangement, is thereby destroyed. The carbon chemical shift anisotropy and the local C-H bond order parameters were obtained for the nematic phase for the crown ether fragment and the terminal chains. This study indicates that the crown ether average conformation changes insignificantly on decreasing the temperature. The lateral crown ether protrudes markedly from the core with the consequence that the molecular shape is far from rod-like in geometry.     

ToxRead: A tool to assist in read across and its use to assess mutagenicity of chemicals

Life sciences, and toxicology in particular, are heavily impacted by the development of methods for data collection and data analysis; they are moving from an analytical approach to a modelling approach. The scarce availability of experimental data is a known bottleneck in assessing the properties of new chemicals. Even when a model is available, the resulting predictions have to be assessed by close scrutiny of the chemicals and the biological properties of the compounds concerned. To avoid unnecessary testing, a read across strategy is often suggested and used. In this paper we discuss how to improve and standardize read across activity using ad hoc visualization and data search methods which use similarity measures and fragment search to organize in a chart a picture of all the relevant information that the expert needs to make an assessment. We show in particular how to apply our system to the case of mutagenicity.