Fast 3D molecular superposition and similarity search in databases of flexible molecules

We present a new method (fFLASH) for the virtual screening of compound databases that is based on explicit three-dimensional molecular superpositions. fFLASH takes the torsional flexibility of the database molecules fully into account, and can deal with an arbitrary number of conformation-dependent molecular features. The method utilizes a fragmentation-reassembly approach which allows for an efficient sampling of the conformational space. A fast clique-based pattern matching algorithm generates alignments of pairs of adjacent molecular fragments on the rigid query molecule that are subsequently reassembled to complete database molecules. Using conventional molecular features (hydrogen bond donors and acceptors, charges, and hydrophobic groups) we show that fFLASH is able to rapidly produce accurate alignments of medium-sized drug-like molecules. Experiments with a test database containing a diverse set of 1780 drug-like molecules (including all conformers) have shown that average query processing times of the order of 0.1 seconds per molecule can be achieved on a PC.     

eSHAFTS: Integrated and graphical drug design software based on 3D molecular similarity

With the development of computer technology, computer-aided drug design (CADD) has become an important means for drug research and development, and its representative method is virtual screening. Various virtual screening platforms have emerged in an endless stream and play great roles in the field of drug discovery. With the increasing number of compound molecules, virtual screening platforms face two challenges: low fluency and low visibility of software operations. In this article, we present an integrated and graphical drug design software eSHAFTS based on three-dimensional (3D) molecular similarity to overcome these shortcomings. Compared with other software, eSHAFTS has four main advantages, which are integrated molecular editing and drawing, interactive loading and analysis of proteins, multithread and multimode 3D molecular similarity calculation, and multidimensional information visualization. Experiments have verified its convenience, usability, and reliability. By using eSHAFTS, various tasks can be submitted and visualized in one desktop software without locally installing any dependent plug-ins or software. The software installation package can be downloaded for free at http://lilab.ecust.edu.cn/home/resource.html . © 2019 Wiley Periodicals, Inc.     

Effectiveness of graph-based and fingerprint-based similarity measures for virtual screening of 2D chemical structure databases

This paper reports an evaluation of both graph-based and fingerprint-based measures of structural similarity, when used for virtual screening of sets of 2D molecules drawn from the MDDR and ID Alert databases. The graph-based measures employ a new maximum common edge subgraph isomorphism algorithm, called RASCAL, with several similarity coefficients described previously for quantifying the similarity between pairs of graphs. The effectiveness of these graph-based searches is compared with that resulting from similarity searches using BCI, Daylight and Unity 2D fingerprints. Our results suggest that graph-based approaches provide an effective complement to existing fingerprint-based approaches to virtual screening.     

生物小分子的电分析化学研究 Ⅱ.鸟嘌呤、腺嘌呤和次黄嘌呤在粗热解石墨电极上的分子定向和表面相互作用

本文讨论了鸟嘌呤、腺嘌呤和次黄嘌呤等嘌呤类生物小分子在几种电极上的反应活性,并选用粗热解石墨电极研究了它们的电化学性质.实验结果表明它们的电极过程是受吸附作用控制的.在粗热解石墨电极上鸟嘌呤以C(2)-NH~2、腺嘌呤以C(6)-NH~2、次黄嘌呤以N(1)-H基团按垂直方向吸附于电极表面,电极表面分子间存在着相斥的相互作用.鸟嘌呤、腺嘌呤和次黄嘌呤的吸附平衡常数分别为:(3.34±1.00)×10^5,和(4.38±1.20)×10^5和(4.13±1.21)×10^5;吸附能分别为:(31.5±0.77),(32.1±0.70)和(32.0±0.75)kJ/mol.这些数值表明它们在粗热解石墨电极上具有中等偏强的物理吸附作用.     

Comparison of 3D quantitative structure-activity relationship methods: Analysis of the in vitro antimalarial activity of 154 artemisinin analogues by hypothetical active-site lattice and comparative molecular field analysis

Two three-dimensional quantitative structure-activity relationship (3D-QSAR) methods, comparative molecular field analysis (CoMFA) and hypothetical active site lattice (HASL), were compared with respect to the analysis of a training set of 154 artemisinin analogues. Five models were created, including a complete HASL and two trimmed versions, as well as two CoMFA models (leave-one-out standard CoMFA and the guided-region selection protocol). Similar r2 and q2 values were obtained by each method, although some striking differences existed between CoMFA contour maps and the HASL output. Each of the four predictive models exhibited a similar ability to predict the activity of a test set of 23 artemisinin analogues, although some differences were noted as to which compounds were described well by either model.     

Comparison of dye (oxazine and thiazine) materials as a photosensitizer for use in photogalvanic cells based on molecular interaction with sodium dodecyl sulphate by spectral study

The photochemistry of dye is playing a significant role for understanding the mechanism of electron transfer reactions in photoelectrochemical devices such as photogalvanic cells, DSSC, semiconductor photo-catalysis, photoconductors, etc. Oxazines (Brilliant Cresyl Blue and Nile Blue O) and thiazines (Azur A, Azur B, Azur C, Methylene Blue and Toluidine Blue O) dyes have been used widely as a photosensitizer with and without surfactants in the photogalvanic cells for solar power conversion and storage. Since, the stability and solubility of photosensitizers (dyes) are increased in the presence of surfactant and these properties lead to enhance the electrical output of the photogalvanic cells. Therefore, here we have studied the extent of interaction of different dyes with sodium dodecyl sulphate (SDS), find out the order of stability of dye–SDS on the basis of magnitudes of shifting in λ_max of dye monomer and try to correlate order of dye–SDS interaction with already reported electrical output data of photogalvanic cells. Brilliant Cresyl Blue, Nile Blue O, Azur A and TB O have shown red shifting while Azur B, Azur C and MB have shown blue shifting in their λ_max value with SDS, which indicates formation of dye–surfactant complex. But, the extent of formation of complex for different dyes with SDS was different due to change in their alkyl groups. Dyes with red shifting have greater stability in excited state as well as higher electrical output data of the cell than dye with blue shifting. On the basis of both red and blue shifting, order of stability of dyes–SDS complex was found as: Brilliant Cresyl Blue?>?Toluidine Blue O?>?Azur A?>?Nile Blue?>?Azur B?>?Methylene Blue?>?Azur C. The order of electrical output values of these dyes in photogalvanic cells have also been supported by literature data in the presence of SDS. Hence, the dye–surfactant complex which would have greater stability in excited state might be more useful for improvement of conversion efficiency and storage capacity of photogalvanic cells in the future.