基于药效团的BRD4靶向小分子抑制剂虚拟筛选

BRD4靶点和多种肿瘤密切相关,是具有良好成药性的热门靶点.本文选取活性较好且结构差异较大的BRD4小分子抑制剂作为训练集分子,基于配体小分子共同特征(HipHop)方法使用Discovery Studio 3.0分子模拟软件构建了药效团.药效团通过测试集验证、ROC曲线验证(SE(sensitivity)=0.937...     

EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases

The completion of the Human Genome Project, the growing effort on proteomics, and the Structural Genomics Initiative have recently intensified the attention being paid to reliable computer docking programs able to identify molecules that can affect the function of a macromolecule through molecular complexation. We report herein an automated computer docking program, EUDOC, for prediction of ligand-receptor complexes from 3D receptor structures, including metalloproteins, and for identification of a subset enriched in drug leads from chemical databases. This program was evaluated from the standpoints of force field and sampling issues using 154 experimentally determined ligand-receptor complexes and four "real-life" applications of the EUDOC program. The results provide evidence for the reliability and accuracy of the EUDOC program. In addition, key principles underlying molecular recognition, and the effects of structural water molecules in the active site and different atomic charge models on docking results are discussed. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1750-1771, 2001     

Identification of potential Gly/NMDA receptor antagonists by cheminformatics approach: a combination of pharmacophore modelling,virtual screening and molecular docking studies

The Gly/NMDA receptor has become known as potential target for the management of neurodegenerative diseases. Discovery of Gly/NMDA antagonists has thus attracted much attention in recent years. In the present research, a cheminformatics approach has been used to determine structural requirements for Gly/NMDA antagonism and to identify potential antagonists. Here, 37 quinoxaline derivatives were selected to develop a significant pharmacophore model with good certainty. The selected model was validated by leave-one-out cross-validation, an external test set, decoy set and Y-randomization test. Applicability domain was verified by the standardization approach. The validated 3D-QSAR model was used to screen virtual hits from the ZINC database by pharmacophore mapping. Molecular docking was used for assessment of receptor–ligand binding modes and binding affinities. The GlideScore and molecular interactions with critical amino acids were considered as crucial features to identify final hits. Furthermore, hits were analysed for in silico pharmacokinetic parameters and Lipinski’s rule of five, demonstrating their potential as drug-like candidates. The PubChem and SciFinder search tools were used to authenticate the novelty of leads retrieved. Finally, five different leads have been suggested as putative novel candidates for the exploration of potent Gly/NMDA receptor antagonists.     

Development and application of hybrid structure based method for efficient screening of ligands binding to G-protein coupled receptors

G-protein coupled receptors (GPCRs) comprise a large superfamily of proteins that are targets for nearly 50% of drugs in clinical use today. In the past, the use of structure-based drug design strategies to develop better drug candidates has been severely hampered due to the absence of the receptor’s three-dimensional structure. However, with recent advances in molecular modeling techniques and better computing power, atomic level details of these receptors can be derived from computationally derived molecular models. Using information from these models coupled with experimental evidence, it has become feasible to build receptor pharmacophores. In this study, we demonstrate the use of the Hybrid Structure Based (HSB) method that can be used effectively to screen and identify prospective ligands that bind to GPCRs. Essentially; this multi-step method combines ligand-based methods for building enriched libraries of small molecules and structure-based methods for screening molecules against the GPCR target. The HSB method was validated to identify retinal and its analogues from a random dataset of ∼300,000 molecules. The results from this study showed that the 9 top-ranking molecules are indeed analogues of retinal. The method was also tested to identify analogues of dopamine binding to the dopamine D2 receptor. Six of the ten top-ranking molecules are known analogues of dopamine including a prodrug, while the other thirty-four molecules are currently being tested for their activity against all dopamine receptors. The results from both these test cases have proved that the HSB method provides a realistic solution to bridge the gap between the ever-increasing demand for new drugs to treat psychiatric disorders and the lack of efficient screening methods for GPCRs. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Virtual Screening and Hit Selection of Natural Compounds as Acetylcholinesterase Inhibitors

Acetylcholinesterase (AChE) is one of the classical targets in the treatment of Alzheimer’s disease (AD). Inhibition of AChE slows down the hydrolysis of acetycholine and increases choline levels, improving the cognitive function. The achieved success of plant-based natural drugs acting as AChE inhibitors, such as galantamine (GAL) from Galanthus genus and huperzine A from Huperzia serrate (approved drug in China), in the treatment of AD, and the fact that natural compounds (NCs) are considered as safer and less toxic compared to synthetic drugs, led us to screen the available NCs (almost 150,000) in the ZINC12 database for AChE inhibitory activity. The compounds were screened virtually by molecular docking, filtered for suitable ADME properties, and 32 ligands from 23 structural groups were selected. The stability of the complexes was estimated via 1 μs molecular dynamics simulation. Ten compounds formed stable complexes with the enzyme and had a vendor and a reasonable price per mg. They were tested for AChE inhibitory and antioxidant activity. Five compounds showed weak AChE inhibition and three of them exhibited high antioxidant activity.     

Identification of potential inhibitors against nuclear Dam1 complex subunit Ask1 of Candida albicans using virtual screening and MD simulations

Identification of hit compounds against specific target form the starting point for a drug discovery program. A consistent decline of new chemical entities (NCEs) in recent years prompted a challenge to explore newer approaches to discover potential hit compounds that in turn can be converted into leads, and ultimately drug with desired therapeutic efficacy. The vast amount of omics and activity data available in public databases offers an opportunity to identify novel targets and their potential inhibitors. State of the art in silico methods viz., clustering of compounds, virtual screening, molecular docking, MD simulations and MMPBSA calculations were employed in a pipeline to identify potential ‘hits’ against those targets as well whose structures, as of now, could only predict through threading approaches. In the present work, we have started from scratch, amino acid sequence of target and compounds retrieved from PubChem compound database, modeled it in such a way that led to the identification of possible inhibitors of Dam1 complex subunit Ask1 of Candida albicans. We also propose a ligand based binding site determination approach. We have identified potential inhibitors of Ask1 subunit of a Dam1 complex of C. albicans, which is required to prevent precocious spindle elongation in pre-mitotic phases. The proposed scheme may aid to find virtually potential inhibitors of other unique targets against candida.     

Scaling in the S and P states of the helium isoelectronic sequence

Mean values of r ₁ ^r and r _r ¹² for the ground and several excited states of the helium isoelectronic sequence are used to demonstrate that a simple scaling which superimposes the distribution function f(r ₁₂) as a function of the atomic number leads to a similar result for the electron density distribution D(r₁). On the basis of a screening interpretation of the scaling parameter , it is concluded that screening is greater in the singlet than the triplet state of a particular configuration, that screening is greater in the P states than the corresponding S states, and that the screening approaches the limiting value of 1 for the highly excited states. The perturbation expansions of Scherr and Knight are used to determine the limiting value of when Z and the relationship between the scaling parameter and the scale factor, chosen so that a trial wave function satisfies the virial theorem, is discussed. A brief discussion of the scaling of the Coulomb hole is presented.     

Rh Inclusion in Sol-Gel SiO2. Effects of Rh Precursors on Metal Dispersion and SiO2-Rh Thermal Behavior

RhCl₃·nH₂O and [RhCl(C₂H₄)₂]₂ are used as precursors for the preparation of 1%Rh in sol-gel derived SiO₂. The gelling process of Si(OEt)₄ is carried out in the absence of solvent and under strong acid catalysis. The thermal behavior of Rh precursors, of SiO₂ gel and Rh-SiO₂ composites is independently studied by analysing organic species released at definite temperature intervals and concomitantly collecting infrared, XPS, TEM, XRD and porosity data. Results indicate that nanometric Rh particles may be obtained from [RhCl(C₂H₄)₂]₂, their dispersion being homogeneous, dense and stable up to 250°C, whereas RhCl₃·nH₂O affords less metallic dispersion with other crystalline Rh-species; in both cases, well-shaped Rh metal crystallites are obtained at 650°C. The different synthetic approaches used for the preparation of RhCl₃- and [RhCl(C₂H₄)₂]₂-derived samples, are invoked to account for the features of Rh dispersion obtained by mild temperature treatment. Moreover, the particular procedures for sol-gel SiO₂ synthesis are related to the high-temperature maintenance of great porosity and elevated specific surface area.     

The structure of CX2YNO (X, Y=F, Cl) molecules in the ground and lowest excited singlet electronic states

Ab initio quantum-chemical calculations of equilibrium geometric parameters, vibrational frequencies, and potentials of internal rotation for CCIF₂NO and CCl₂FNO molecules in the ground (S₀) and lowest excited singlet (S₁) electronic states were performed. The results of calculations were compared with experimental data. A new interpretation of experimental spectra of the CCIF₂NO molecule was suggested. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1453–1458, August, 1999.     

Speed of sound and isentropic compressibilities of nonelectrolyte liquid mixtures. I. Binary mixtures containingp-dioxane

The speed of sound was measured for mixtures of p-dioxane with cyclohexane, n-hexane, benzene, toluene, carbon tetrachloride, chloroform, 1,1,2,2-tetrachloroethane, pentachloroethane and ethyl acetate over the whole mole fraction range at 30°C. These data were combined with densities and molar volumes to obtain isentropic compressibilities and Rao's molar sound functions. Excess isentropic compressibilities and excess speeds of sound have also been calculated. The behavior of the present mixtures is discussed in terms of possible molecular interactions and the Prigogine-Flory-Patterson theory of liquid mixtures.     

Intramolecular interaction between ortho-azido and azoxy groups as a new way of forming a N—N bond. Synthesis of 2-alkylbenzotriazole 1-oxides

Heating of 2-(alkyl-NNO-azoxy)-1-azidobenzenes in boiling benzene gave 2-alkyl-benzotriazole 1-oxides (Alk = Me, Et, Prⁱ, and Bu^t). This first-order reaction involves an earlier unknown intramolecular interaction between the azido and azoxy groups with simultaneous release of molecular nitrogen. The cyclization rate increases in the following sequence of the alkyl groups: Me < Et < Prⁱ < Bu^t. Complete assignment of the signals in the ¹H, ¹³C, and ¹⁴N NMR spectra of 2-alkylbenzotriazole 1-oxides was performed. Dedicated to Corresponding Member of the Russian Academy of Sciences E. P. Serebryakov on the occasion of his 70th birthday. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 989–996, April, 2005.     

Synthesis and study of organic nitrates of the heterofunctional series 3. Synthesis and structure of tris(hydroxymethyl)aminomethane dinitrate benzoate hydronitrate

Tris(hydroxymethyl)aminomethane dinitrate benzoate hydronitrate, the first representative of mixed nitric and carboxylic esters of aminopolyatomic alcohols, was obtained by the reaction of a mixture of concentrated HNO₃ and Ac₂O with 4,4-bis(hydroxymethyl)-2-phenyl-2-oxazoline. X-ray structural analysis demonstrated that the title compound exists in the crystal as two independent molecules. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 505–509, March, 1999.     

Nature of weak inter- and intramolecular interactions in crystals. 5. Interactions Na...H—B in a crystal of sodium salt of charge-compensated nido-carborane [9-SMe2-7,8-C2B9H10]−

The character of electron density distribution in the C₂B₃ open face, the influence of the SMe₂ group on the character of electron density distribution, and the nature of the sodium—anion interaction were studied based on the data of high-resolution X-ray diffraction study of crystals of the sodium salt of charge compensated nido-carborane [9-SMe₂-7,8-C₂B₉H₁₀]⁻ and quantum-chemical calculations for the Na...H—B bonded dimer, the isolated [9-SMe₂-7,8-C₂B₉H₁₀]⁻ anion, and the [7,8-C₂B₉H₁₀]²⁻ dianion. The character of electron density distribution in the C₂B₃ open face is analogous to the electron distribution in the cyclopentadienyl ligand. In nido-carborane, a substantial charge redistribution takes place compared to that observed in the closo analogs. The topological analysis of the electron density distribution function demonstrated that the cation—anion interactions are determined predominantly by Na...H—B contacts. The total energy of these contacts in the { [9-SMe₂-7,8-C₂B₉H₁₀]Na(thf)₂}₂ dimer estimated from X-ray diffraction data is 11.74 kcal mol⁻¹. Dedicated to Corresponding Member of the Russian Academy of Sciences E. P. Serebryakov on the occasion of his 70th birthday. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 911–918, April, 2005.     

Theoretical study of the structure and stability of the Na2Cl+, NaCl 2? , Na3Cl 2+ , and Na2Cl 3? ions

The geometrical parameters, normal vibration frequencies, and thermochemical characteristics of the Na₂Cl⁺, NaCl ₂ ⁻ , Na₃Cl ₂ ⁺ , and Na₂Cl ₃ ⁻ ions in saturated vapors over sodium chloride were calculated by the ab initio methods including electron correlation. According to calculations, the Na₂Cl⁺ and NaCl ₂ ⁻ triatomic ions have a linear equilibrium D _∞h configuration. The pentaatomic ions can exist in the form of the D _∞h linear isomer, C _2v planar cyclic isomer, or D _3h bipyramidal isomer. At ∼1000 K the Na₃Cl ₂ ⁺ and Na₂Cl ₃ ⁻ ions exist predominantly in the form of the linear isomers. The energies and enthalpies of the ion-molecule reactions involving the above ions were calculated. The formation enthalpy of the ions Δ_f H ⁰(0 K) was determined: 230 ± 2 kJ/mol (Na₂Cl⁺), −96 ± 4 kJ/mol (Na₂Cl ₃ ⁻ ), −616 ± 2 kJ/mol (NaCl ₂ ⁻ ), and −935 ± 4 kJ/mol (Na₂Cl ₃ ⁻ ). Original Russian Text Copyright ? 2007 by T. P. Pogrebnaya, A. M. Pogrebnoi, and L. S. Kudin __________ Translated from Zhurnal Strukturnoi Khimii, Vol. 48, No. 6, pp. 1053–1061, November–December, 2007.     

Assessing the MALDI-TOF MS sample preparation procedure to analyze the influence of thermo-oxidative ageing and thermo-mechanical degradation on poly (Lactide)

Multiple processing by means of successive injection cycles was used to simulate the thermo-mechanical degradation effects on the oligomeric distribution of PLA under mechanical recycling. Likewise, an accelerated thermal ageing over PLA glass transition was performed in order to simulate its service life. MALDI-TOF MS was used for the analysis and the sample preparation procedure was assessed by means of a statistical Design of Experiments (DoE). The quality effects in use for the analysis were signal-to-noise ratio and Resolution. Different matrixes, analyte/matrix proportions and the use of NaTFA as cationization agent were considered. A deep inspection of the statistical results provided a better understanding of the influence of the different factors, individually or in combination, to the signal. The application of DoE for the improvement of the MALDI measurement of PLA stated that the best combination of factors (levels) was the following: matrix (s-DHB), proportion analyte/matrix (1/5 V/V), and no use of cationization agent. Degradation primarily affected the initially predominant cyclic [LA_C]_n and linear H[LA_L]_nOH species, where LA stands for a PLA repeating unit. Intramolecular and intermolecular transesterifications as well as hydrolytic and homolytic reactions took place during the formation and disappearance of oligomeric species. In both degradation mechanisms induced by thermal ageing and thermo-mechanical degradation, the formation of H[LA_L]_nOCH₃ by intermolecular transesterifications was highlighted.     

Pesticides in water and the performance of the liquid-phase microextraction based techniques. A review

The control of pesticides in surface, drinking and groundwater is nowadays a real necessity. In the European Community, their concentration must comply with the established parametric and environmental quality standards (EQSs). Regarding the new legislation, this article updates the information concerning the monitoring of pesticides and the technical specifications for their measurement in water samples where ultra-sensitive analytical methods are required. For some compounds, like pesticides, there is still a need to improve the performance of the existing methods. High sensitive techniques like gas chromatography tandem mass spectrometry (GC–MS/MS) and liquid chromatography coupled with mass spectrometry (LC–MS) have been developed. However, for most of the substances present at trace and ultra-trace levels the extraction and preconcentration steps are so far essential for their detection. Advances at a micro scale have been made and different types of microextractions are being developed. Liquid-phase microextraction (LPME) is an example. The study of this technique has increased in the last years and some innovations have been recently reported for pesticides water analysis. This article reviews the new developed LPME-based techniques and compares its performance with the analytical specifications established for pesticides water monitoring. The results show that LPME-based techniques can be a promising tool to improve the nowadays performance of methods used in pesticides water control.