TY - JOUR A1 - Schmidt, Marco F. A1 - Korb, Oliver A1 - Abell, Chris T1 - Antagonists of the miRNA-Argonaute 2 Protein Complex BT - Anti-miR-AGOs JF - Drug Target miRNA: Methods and Protocols N2 - microRNAs (miRNAs) have been identified as high-value drug targets. A widely applied strategy in miRNA inhibition is the use of antisense agents. However, it has been shown that oligonucleotides are poorly cell permeable because of their complex chemical structure and due to their negatively charged backbone. Consequently, the general application of oligonucleotides in therapy is limited. Since miRNAs’ functions are executed exclusively by the Argonaute 2 protein, we therefore describe a protocol for the design of a novel miRNA inhibitor class: antagonists of the miRNA-Argonaute 2 protein complex, so-called anti-miR-AGOs, that not only block the crucial binding site of the target miRNA but also bind to the protein’s active site. Due to their lower molecular weight and, thus, more drug-like chemical structure, the novel inhibitor class may show better pharmacokinetic properties than reported oligonucleotide inhibitors, enabling them for potential therapeutic use. KW - Drug design KW - microRNA KW - miRNA-Argonaute 2 protein complex KW - miRNA inhibitors KW - miRNA seed region Y1 - 2016 SN - 978-1-4939-6563-2 SN - 978-1-4939-6561-8 SN - 978-1-4939-8236-3 U6 - https://doi.org/10.1007/978-1-4939-6563-2_17 SN - 1064-3745 SN - 1940-6029 VL - 1517 SP - 239 EP - 249 PB - Springer CY - New York ER - TY - JOUR A1 - Balderas-Valadez, Ruth Fabiola A1 - Antunez, E. E. A1 - Olive-Mendez, Sion Federico A1 - Pacholski, Claudia A1 - Campos-Alvarez, Jose A1 - Bokhimi, Xim A1 - Agarwal, V. T1 - Porous silicon pillar and bilayer structure as a nucleation center for the formation of aligned vanadium pentoxide nanorods JF - Ceramics International N2 - Porous silicon single layer (PSM), bilayer (PSB) and pillar (PSP) structures have been evaluated as nucleation centers for vanadium pentoxide (V2O5) crystals. Deposition of vanadium precursor over different substrates (drop casting technique), followed by annealing treatment under Ar-H-2 (5% H-2) atmosphere, induced crystallization of vanadium oxide. With respect to c-Si/SiO2 substrate, V2O5 nanorods with relatively large aspect ratio were formed over and within PSP structures. On the other hand, pores in PSM and PSB were found to be filled with relatively smaller crystals. Additionally, PSB provided a nucleation substrate capable to align the nanocrystals in a preferential orientation, while V2O5 crystals grown on PSP were found to be randomly aligned around the nanoporous pillar microstructure. Nanorods and nanocrystals were identified as V2O5 by temperature-controlled XRD measurements and evidence of their crystalline nature was observed via transmission electron microscopy. A careful analysis of electronic microscopy images allows the identification of the facets composing the ends of the crystals and its corresponding surface free energy has been evaluated employing the Wulff theorem. Such high surface area composite structures have potential applications as cathode material in Lithium-ion batteries. KW - Porous silicon KW - Vanadium pentoxide KW - Nanorods KW - Crystallization KW - Nanostructures Y1 - 2017 U6 - https://doi.org/10.1016/j.ceramint.2017.03.114 SN - 0272-8842 SN - 1873-3956 VL - 43 SP - 8023 EP - 8030 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Atilaw, Yoseph A1 - Duffy, Sandra A1 - Heydenreich, Matthias A1 - Muiva-Mutisya, Lois A1 - Avery, Vicky M. A1 - Erdelyi, Mate A1 - Yenesew, Abiy T1 - Three Chalconoids and a Pterocarpene from the Roots of Tephrosia aequilata JF - Molecules N2 - In our search for new antiplasmodial agents, the CH2Cl2/CH3OH (1:1) extract of the roots of Tephrosia aequilata was investigated, and observed to cause 100% mortality of the chloroquine-sensitive (3D7) strain of Plasmodium falciparum at a 10 mg/mL concentration. From this extract three new chalconoids, E-2,6-dimethoxy-3,4-(2,2-dimethyl)pyranoretrochalcone (1, aequichalcone A), Z-2,6-dimethoxy-3,4-(2,2-dimethyl)pyranoretrochalcone (2, aequichalcone B), 4-ethoxy-3-hydroxypraecansone B (3, aequichalcone C) and a new pterocarpene, 3,4:8,9-dimethylenedioxy-6a,11a-pterocarpene (4), along with seven known compounds were isolated. The purified compounds were characterized by NMR spectroscopic and mass spectrometric analyses. Compound 1 slowly converts into 2 in solution, and thus the latter may have been enriched, or formed, during the extraction and separation process. The isomeric compounds 1 and 2 were both observed in the crude extract. Some of the isolated constituents showed good to moderate antiplasmodial activity against the chloroquine-sensitive (3D7) strain of Plasmodium falciparum. KW - Tephrosia aequilata KW - chalcone KW - retrochalcone KW - aequichalcone A KW - aequichalcone B KW - aequichalcone C KW - pterocarpene KW - antiplasmodial Y1 - 2017 U6 - https://doi.org/10.3390/molecules22020318 SN - 1420-3049 VL - 22 IS - 2 PB - MDPI CY - Basel ER - TY - JOUR A1 - Adebayo, Segun Emmanuel A1 - Hashim, Norhashila A1 - Hass, Roland A1 - Reich, Oliver A1 - Regen, Christian A1 - Münzberg, Marvin A1 - Abdan, Khalina A1 - Hanafi, Marsyita A1 - Zude-Sasse, Manuela T1 - Using absorption and reduced scattering coefficients for non-destructive analyses of fruit flesh firmness and soluble solids content in pear JF - Postharvest Biology and Technology N2 - Quality attributes of fruit determine its acceptability by the retailer and consumer. The objective of this work was to investigate the potential of absorption (μa) and reduced scattering (μs’) coefficients of European pear to analyze its fruit flesh firmness and soluble solids content (SSC). The absolute reference values, μa* (cm−1) and μs’* (cm−1), of pear were invasively measured, employing multi-spectral photon density wave (PDW) spectroscopy at preselected wavelengths of 515, 690, and 940 nm considering two batches of unripe and overripe fruit. On eight measuring dates during fruit development, μa and μs’ were analyzed non-destructively by means of laser light backscattering imaging (LLBI) at similar wavelengths of 532, 660, and 830 nm by means of fitting according to Farrell’s diffusion theory, using fix reference values of either μa* or μs’*. Both, the μa* and the μa as well as μs’* and μs’ showed similar trends. Considering the non-destructively measured data during fruit development, μa at 660 nm decreased 91 till 141 days after full bloom (dafb) from 1.49 cm−1 to 0.74 cm−1 due to chlorophyll degradation. At 830 nm, μa only slightly decreased from 0.41 cm−1 to 0.35 cm−1. The μs’ at all wavelengths revealed a decreasing trend as the fruit developed. The difference measured at 532 nm was most pronounced decreasing from 24 cm−1 to 10 cm−1, while at 660 nm and 830 nm values decreased from 15 cm−1 to 13 cm−1 and from 10 cm−1 to 8 cm−1, respectively. When building calibration models with partial least-squares regression analysis on the optical properties for non-destructive analysis of the fruit SSC, μa at 532 nm and 830 nm resulted in a correlation coefficient of R = 0.66, however, showing high measuring uncertainty. The combination of all three wavelengths gave an enhanced, encouraging R = 0.89 for firmness analysis using μs’ in the freshly picked fruit. KW - Absorption KW - Non-destructive KW - Pear KW - Quality KW - Scattering Y1 - 2017 U6 - https://doi.org/10.1016/j.postharvbio.2017.04.004 SN - 0925-5214 SN - 1873-2356 VL - 130 SP - 56 EP - 63 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Utecht, Manuel Martin A1 - Palmer, Richard E. A1 - Klamroth, Tillmann T1 - Quantum chemical approach to atomic manipulation of chlorobenzene on the Si(111)-7 x 7 surface BT - Resonance localization, vibrational activation, and surface dynamics JF - Physical review materials N2 - We present a cluster model to describe the localization of hot charge carriers on the Si(111)-7 x 7 surface, which leads to (nonlocal) desorption of chlorobenzene molecules in scanning tunneling microscope (STM) manipulation experiments. The localized charge carriers are modeled by a small cluster. By means of quantum chemical calculations, this cluster model explains many experimental findings from STM manipulation. We show that the negative charge is mainly localized in the surface, while the positive one also resides on the molecule. Both resonances boost desorption: In the negative resonance the adatom is elevated; in the positive one the chemisorption bond between the silicon surface adatom and chlorobenzene is broken. We find normal modes promoting desorption matching experimental low-temperature activation energies for electron-and hole-induced desorption. Y1 - 2017 U6 - https://doi.org/10.1103/PhysRevMaterials.1.026001 SN - 2475-9953 VL - 1 IS - 2 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Wolf, Thomas J. A. A1 - Holzmeier, Fabian A1 - Wagner, Isabella A1 - Berrah, Nora A1 - Bostedt, Christoph A1 - Bozek, John A1 - Bucksbaum, Phil A1 - Coffee, Ryan A1 - Cryan, James A1 - Farrell, Joe A1 - Feifel, Raimund A1 - Martinez, Todd J. A1 - McFarland, Brian A1 - Mucke, Melanie A1 - Nandi, Saikat A1 - Tarantelli, Francesco A1 - Fischer, Ingo A1 - Gühr, Markus T1 - Observing Femtosecond Fragmentation Using Ultrafast X-ray-Induced Auger Spectra JF - Applied sciences N2 - Molecules often fragment after photoionization in the gas phase. Usually, this process can only be investigated spectroscopically as long as there exists electron correlation between the photofragments. Important parameters, like their kinetic energy after separation, cannot be investigated. We are reporting on a femtosecond time-resolved Auger electron spectroscopy study concerning the photofragmentation dynamics of thymine. We observe the appearance of clearly distinguishable signatures from thymines neutral photofragment isocyanic acid. Furthermore, we observe a time-dependent shift of its spectrum, which we can attribute to the influence of the charged fragment on the Auger electron. This allows us to map our time-dependent dataset onto the fragmentation coordinate. The time dependence of the shift supports efficient transformation of the excess energy gained from photoionization into kinetic energy of the fragments. Our method is broadly applicable to the investigation of photofragmentation processes. KW - ultrafast dynamics KW - Auger electron spectroscopy KW - photofragmentation KW - photochemistry Y1 - 2017 U6 - https://doi.org/10.3390/app7070681 SN - 2076-3417 VL - 7 IS - 7 PB - MDPI CY - Basel ER - TY - JOUR A1 - Meyners, Christian A1 - Mertens, Monique A1 - Wessig, Pablo A1 - Meyer-Almes, Franz-Josef T1 - A Fluorescence-Lifetime-Based Binding Assay for Class IIa Histone Deacetylases JF - Chemistry - a European journal N2 - Class IIa histone deacetylases (HDACs) show extremely low enzymatic activity and no commonly accepted endogenous substrate is known today. Increasing evidence suggests that these enzymes exert their effect rather through molecular recognition of acetylated proteins and recruiting other proteins like HDAC3 to the desired target location. Accordingly, class IIa HDACs like bromodomains have been suggested to act as “Readers” of acetyl marks, whereas enzymatically active HDACs of class I or IIb are called “Erasers” to highlight their capability to remove acetyl groups from acetylated histones or other proteins. Small-molecule ligands of class IIa histone deacetylases (HDACs) have gained tremendous attention during the last decade and have been suggested as pharmaceutical targets in several indication areas such as cancer, Huntington's disease and muscular atrophy. Up to now, only enzyme activity assays with artificial chemically activated trifluoroacetylated substrates are in use for the identification and characterization of new active compounds against class IIa HDACs. Here, we describe the first binding assay for this class of HDAC enzymes that involves a simple mix-and-measure procedure and an extraordinarily robust fluorescence lifetime readout based on [1,3]dioxolo[4,5-f]benzodioxole-based ligand probes. The principle of the assay is generic and can also be transferred to class I HDAC8. KW - drug discovery KW - enzymes KW - fluorescent probes KW - high-throughput screening KW - hydrolases Y1 - 2017 U6 - https://doi.org/10.1002/chem.201605140 SN - 0947-6539 SN - 1521-3765 VL - 23 IS - 13 SP - 3107 EP - 3116 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Bobone, Sara A1 - Hilsch, Malte A1 - Storm, Julian A1 - Dunsing, Valentin A1 - Herrmann, Andreas A1 - Chiantia, Salvatore T1 - Phosphatidylserine Lateral Organization Influences the Interaction of Influenza Virus Matrix Protein 1 with Lipid Membranes JF - Journal of virology N2 - Influenza A virus matrix protein 1 (M1) is an essential component involved in the structural stability of the virus and in the budding of new virions from infected cells. A deeper understanding of the molecular basis of virion formation and the budding process is required in order to devise new therapeutic approaches. We performed a detailed investigation of the interaction between M1 and phosphatidylserine (PS) (i.e., its main binding target at the plasma membrane [PM]), as well as the distribution of PS itself, both in model membranes and in living cells. To this end, we used a combination of techniques, including Forster resonance energy transfer (FRET), confocal microscopy imaging, raster image correlation spectroscopy, and number and brightness (N&B) analysis. Our results show that PS can cluster in segregated regions in the plane of the lipid bilayer, both in model bilayers constituted of PS and phosphatidylcholine and in living cells. The viral protein M1 interacts specifically with PS-enriched domains, and such interaction in turn affects its oligomerization process. Furthermore, M1 can stabilize PS domains, as observed in model membranes. For living cells, the presence of PS clusters is suggested by N&B experiments monitoring the clustering of the PS sensor lactadherin. Also, colocalization between M1 and a fluorescent PS probe suggest that, in infected cells, the matrix protein can specifically bind to the regions of PM in which PS is clustered. Taken together, our observations provide novel evidence regarding the role of PS-rich domains in tuning M1-lipid and M1-M1 interactions at the PM of infected cells. IMPORTANCE Influenza virus particles assemble at the plasma membranes (PM) of infected cells. This process is orchestrated by the matrix protein M1, which interacts with membrane lipids while binding to the other proteins and genetic material of the virus. Despite its importance, the initial step in virus assembly (i.e., M1-lipid interaction) is still not well understood. In this work, we show that phosphatidylserine can form lipid domains in physical models of the inner leaflet of the PM. Furthermore, the spatial organization of PS in the plane of the bilayer modulates M1-M1 interactions. Finally, we show that PS domains appear to be present in the PM of living cells and that M1 seems to display a high affinity for them. KW - influenza KW - assembly KW - confocal microscopy KW - fluorescence image analysis KW - lipid rafts KW - matrix protein KW - model membranes KW - phosphatidylserine KW - plasma membrane Y1 - 2017 U6 - https://doi.org/10.1128/JVI.00267-17 SN - 0022-538X SN - 1098-5514 VL - 91 PB - American Society for Microbiology CY - Washington ER - TY - JOUR A1 - Shainyan, Bagrat A. A1 - Belyakov, Alexander V. A1 - Sigolaev, Yurii F. A1 - Khramov, Alexander N. A1 - Kleinpeter, Erich T1 - Molecular Structure and Conformational Analysis of 1-Phenyl-1-X-1-Silacyclohexanes (X = F, Cl) by Electron Diffraction, Low-Temperature NMR, and Quantum Chemical Calculations JF - The journal of organic chemistry N2 - The molecular structure and conformational preferences of 1-phenyl-1-X-1-silacyclohexanes C5H10Si(Ph,X) (X = F (3), Cl (4)) were studied by gas-phase electron diffraction, low-temperature NMR spectroscopy, and high-level quantum chemical calculations. In the gas phase only three (3) and two (4) stable conformers differing in the axial or equatorial location of the phenyl group and the angle of rotation about the Si-C-ph bond (axi and axo denote the Ph group lying in or out of the X-Si-C-ph plane) contribute to the equilibrium. In 3 the ratio Ph-eq:Ph-axo:Ph-axi is 40(12):55(24):5 and 64:20:16 by experiment and theory, respectively. In 4 the ratio Ph-eq:Ph-axo is 79(15):21(15) and 71:29 by experiment and theory (M06-2X calculations), respectively. The gas-phase electron diffraction parameters are in good agreement with those obtained from theory at the M06-2X/aug-ccPVTZ and MP2/aug-cc-pVTZ levels. Unlike the case for M06-2X, MP2 calculations indicate that 3-Ph-eq conformer lies 0.5 kcal/mol higher than the 3-Ph-axo, conformer. As follows from QTAIM analysis, the phenyl group is more stable when it is located in the axial position but produces destabilization of the silacyclohexane ring: By low temperature NMR spectroscopy the six-membered ring interconversion could be frozen, at 103 K and the present conformational equilibria of 3 and 4 could be determined. The ratio of the conformers is 3-Ph-eq:3-Ph-ax = (75-77):(23-25) and 4-Ph-eq:4-Ph-ax = 82:18. Y1 - 2017 U6 - https://doi.org/10.1021/acs.joc.6b02538 SN - 0022-3263 VL - 82 IS - 1 SP - 461 EP - 470 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Ehlert, Christopher A1 - Klamroth, Tillmann T1 - The quest for best suited references for configuration interaction singles calculations of core excited states JF - Journal of computational chemistry : organic, inorganic, physical, biological N2 - Near edge X-ray absorption fine structure (NEXAFS) simulations based on the conventional configuration interaction singles (CIS) lead to excitation energies, which are systematically blue shifted. Using a (restricted) open shell core hole reference instead of the Hartree Fock (HF) ground state orbitals improves (Decleva et al., Chem. Phys., 1992, 168, 51) excitation energies and the shape of the spectra significantly. In this work, we systematically vary the underlying SCF approaches, that is, based on HF or density functional theory, to identify best suited reference orbitals using a series of small test molecules. We compare the energies of the K edges and NEXAFS spectra to experimental data. The main improvement compared to conventional CIS, that is, using HF ground state orbitals, is due to the electrostatic influence of the core hole. Different SCF approaches, density functionals, or the use of fractional occupations lead only to comparably small changes. Furthermore, to account for bigger systems, we adapt the core-valence separation for our approach. We demonstrate that the good quality of the spectrum is not influenced by this approximation when used together with the non-separated ground state wave function. Simultaneously, the computational demands are reduced remarkably. (C) 2016 Wiley Periodicals, Inc. KW - core excited states KW - configuration interaction KW - near edge X-ray absorption fine structure Y1 - 2016 U6 - https://doi.org/10.1002/jcc.24531 SN - 0192-8651 SN - 1096-987X VL - 38 SP - 116 EP - 126 PB - Wiley-Blackwell CY - Hoboken ER -