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1.
P.V. Pogodin A.A. Lagunin D.A. Filimonov M.C. Nicklaus V.V. Poroikov 《SAR and QSAR in environmental research》2019,30(10):759-773
ABSTRACTExisting data on structures and biological activities are limited and distributed unevenly across distinct molecular targets and chemical compounds. The question arises if these data represent an unbiased sample of the general population of chemical-biological interactions. To answer this question, we analyzed ChEMBL data for 87,583 molecules tested against 919 protein targets using supervised and unsupervised approaches. Hierarchical clustering of the Murcko frameworks generated using Chemistry Development Toolkit showed that the available data form a big diffuse cloud without apparent structure. In contrast hereto, PASS-based classifiers allowed prediction whether the compound had been tested against the particular molecular target, despite whether it was active or not. Thus, one may conclude that the selection of chemical compounds for testing against specific targets is biased, probably due to the influence of prior knowledge. We assessed the possibility to improve (Q)SAR predictions using this fact: PASS prediction of the interaction with the particular target for compounds predicted as tested against the target has significantly higher accuracy than for those predicted as untested (average ROC AUC are about 0.87 and 0.75, respectively). Thus, considering the existing bias in the data of the training set may increase the performance of virtual screening. 相似文献
2.
Teixeira-Neto É Leite CA Cardoso AH Medeiros da Silva MC Braga M Galembeck F 《Journal of colloid and interface science》2000,231(1):182-189
Poly(styrene-co-acrylamide) (PS-AAM) latex was prepared, fractionated by sedimentation under gravity, and characterized by PCS, infrared spectra, secondary and backscattered electron imaging in the scanning electron microscope, and electron spectroscopy imaging in an analytical transmission electron microscope. Three latex fractions were obtained. The lower fraction was opalescent and its particles were the more uniform, concerning size, chemical composition, and topochemical features. This lower fraction was still further fractionated by zonal centrifugation in a density gradient, yielding two fractions with similar macrocrystal-forming abilities but different sizes and chemical compositions. These results confirm those previously obtained for the PS-HEMA latex. Copyright 2000 Academic Press. 相似文献
3.
A.V. Veselovsky M.S. Zharkova V.V. Poroikov M.C. Nicklaus 《SAR and QSAR in environmental research》2014,25(6):457-471
Protein–protein interactions (PPI) are involved in most of the essential processes that occur in organisms. In recent years, PPI have become the object of increasing attention in drug discovery, particularly for anti-HIV drugs. Although the use of combinations of existing drugs, termed highly active antiretroviral therapy (HAART), has revolutionized the treatment of HIV/AIDS, problems with these agents, such as the rapid emergence of drug-resistant HIV-1 mutants and serious adverse effects, have highlighted the need for further discovery of new drugs and new targets. Numerous investigations have shown that PPI play a key role in the virus’s life cycle and that blocking or modulating them has a significant therapeutic potential. Here we summarize the recent progress in computer-aided design of PPI inhibitors, mainly focusing on the selection of the drug targets (HIV enzymes and virus entry machinery) and the utilization of peptides and small molecules to prevent a variety of protein–protein interactions (viral–viral or viral–host) that play a vital role in the progression of HIV infection. 相似文献
4.
KM Varier AM Vinodkumar NVSV Prasad PV Madhusudhana Rao DL Sastry Lagy T Baby MC Radhakrishna NG Puttaswamy JJ Das P Sugathan N Madhavan AK Sinha DO Kataria 《Pramana》1999,53(3):529-533
Large enhancements have been observed in the sub-barrier fusion cross sections for Ti+Ni systems in our previous studies.
Coupled channel calculations incorporating couplings to 2+ and 3− states failed to explain these enhancements completely. A possibilty of transfer channels contributing to the residual enhancements
had been suggested. In order to investigate the role of relevant transfer channels, measurements of one- and two-nucleon transfer
were carried out for 46,48Ti+61Ni systems. The present paper gives the results of these studies. 相似文献
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Morelos A Albuquerque IF Bondar NF Carrigan RA Chen D Cooper PS Lisheng D Denisov AS Dobrovolsky AV Dubbs T Endler AM Escobar CO Foucher M Golovtsov VL Gottschalk H Gouffon P Grachev VT Khanzadeev AV Kubantsev MA Kuropatkin NP Lach J Lang Pengfei Li Chengze Li Yunshan Luksys M Mahon JR McCliment E Newsom C Pommot Maia MC Samsonov VM Schegelsky VA Shi Huanzhang Smith VJ Tang Fukun Terentyev NK Timm S Tkatch II Uvarov LN Vorobyov AA Yan Jie Zhao Wenheng Shuchen Z Zhong Yuanyuan 《Physical review letters》1993,71(21):3417-3420
8.
Moon HR Siddiqui MA Sun G Filippov IV Landsman NA Lee YC Adams KM Barchi JJ Deschamps JR Nicklaus MC Kelley JA Marquez VE 《Tetrahedron》2010,66(34):6707-7430
Steric and electronic parameters, such as the anomeric effect (AE) and gauche effect play significant roles in steering the North⇆South equilibrium of nucleosides in solution.Two isomeric oxa-bicyclo[3.1.0]hexane nucleosides that are conformationally locked in either the North or the South conformation of the pseudorotational cycle were designed to study the consequences of having the AE operational or not, independent of other parameters. The rigidity of the system allowed the orientation of the orbitals involved to be set in ‘fixed’ relationships, either antiperiplanar where the AE is permanently ‘on’, or gauche where the AE is impaired. The consequences of these two alternatives were subjected to high-level calculations and measured experimentally by X-ray crystallography, hydrolytic stability of the glycosyl bond, and pKa values. 相似文献
9.
Ioannis Zalachoras Gwendolynn Grootaers Lisa TCM van Weert Yves Aubert Suzanne R de Kreij Nicole A Datson Willeke MC van Roon-Mom Annemieke Aartsma-Rus Onno C Meijer 《BMC neuroscience》2013,14(1):1-12
Background
Antisense oligonucleotide (AON)-mediated exon skipping is a powerful tool to manipulate gene expression. In the present study we investigated the potential of exon skipping by local injection in the central nucleus of the amygdala (CeA) of the mouse brain. As proof of principle we targeted the splicing of steroid receptor coactivator-1 (SRC-1), a protein involved in nuclear receptor function. This nuclear receptor coregulator exists in two splice variants (SRC-1a and SRC-1e) which display differential distribution and opposing activities in the brain, and whose mRNAs differ in a single SRC-1e specific exon.Methods
For proof of principle of feasibility, we used immunofluorescent stainings to study uptake by different cell types, translocation to the nucleus and potential immunostimulatory effects at different time points after a local injection in the CeA of the mouse brain of a control AON targeting human dystrophin with no targets in the murine brain. To evaluate efficacy we designed an AON targeting the SRC-1e-specific exon and with qPCR analysis we measured the expression ratio of the two splice variants.Results
We found that AONs were taken up by corticotropin releasing hormone expressing neurons and other cells in the CeA, and translocated into the cell nucleus. Immune responses after AON injection were comparable to those after sterile saline injection. A successful shift of the naturally occurring SRC-1a:SRC-1e expression ratio in favor of SRC-1a was observed, without changes in total SRC-1 expression.Conclusions
We provide a proof of concept for local neuropharmacological use of exon skipping by manipulating the expression ratio of the two splice variants of SRC-1, which may be used to study nuclear receptor function in specific brain circuits. We established that exon skipping after local injection in the brain is a versatile and useful tool for the manipulation of splice variants for numerous genes that are relevant for brain function. 相似文献10.
Barchi JJ Karki RG Nicklaus MC Siddiqui MA George C Mikhailopulo IA Marquez VE 《Journal of the American Chemical Society》2008,130(28):9048-9057
The conformations of three 2',3'-difluoro uridine nucleosides were studied by X-ray crystallography, NMR spectroscopy, and ab initio calculations in an attempt to define the roles that the two vicinal fluorine atoms play in the puckering preferences of the furanose ring. Two of the compounds examined contained fluorine atoms in either the arabino or xylo dispositions at C2' and C3' of a 2',3'-dideoxyuridine system. The third compound also incorporated fluorine atoms in the xylo configuration on the furanose ring but was substituted with a 6-azauracil base in place of uracil. A battery of NMR experiments in D 2O solution was used to identify conformational preferences primarily from coupling constant and NOE data. Both (1)H and (19)F NMR data were used to ascertain the preferred sugar pucker of the furanose ring through the use of the program PSEUROT. Compound-dependent parameters used in the PSEUROT calculations were newly derived from complete sets of conformations calculated from high-level ab initio methods. The solution and theoretical data were compared to the conformations of each molecule in the solid state. It was shown that both gauche and antiperiplanar effects may be operative to maintain a pseudodiaxial arrangement of the C2' and C3' vicinal fluorine atoms. These data, along with previously reported data by us and others concerning monofluorinated nucleoside conformations, were used to propose a model of how fluorine influences different aspects of nucleoside conformations. 相似文献