Identification of Small Molecules That Suppress Ricin-Induced Stress-Activated Signaling Pathways

Ricin is a member of the ribosome-inactivating protein (RIP) family of plant and bacterial toxins. In this study we used a high-throughput, cell-based assay to screen more than 118,000 compounds from diverse chemical libraries for molecules that reduced ricin-induced cell death. We describe three compounds, PW66, PW69, and PW72 that at micromolar concentrations significantly delayed ricin-induced cell death. None of the compounds had any demonstrable effect on ricin''s ability to arrest protein synthesis in cells or on ricin''s enzymatic activity as assessed in vitro. Instead, all three compounds appear to function by blocking downstream stress-induced signaling pathways associated with the toxin-mediated apoptosis. PW66 virtually eliminated ricin-induced TNF-α secretion by J774A.1 macrophages and concomitantly blocked activation of the p38 MAPK and JNK signaling pathways. PW72 suppressed ricin-induced TNF-α secretion, but not p38 MAPK and JNK signaling. PW69 suppressed activity of the executioner caspases 3/7 in ricin toxin- and Shiga toxin 2-treated cells. While the actual molecular targets of the three compounds have yet to be identified, these data nevertheless underscore the potential of small molecules to down-regulate inflammatory signaling pathways associated with exposure to the RIP family of toxins.     

Molecular Dynamics Simulations of some Small Organic Molecules

Abstract

Free energy differences between different conformers of D-ribofuranose, L-malic acid and meso-tartaric acid in solution were calculated using Molecular Dynamics simulations. In case of ribose the α → β transition was studied. For the acids attention was focussed on the transitions between the three possible staggered conformers with respect to the central C-C bond. In all cases a thermodynamic integration method was employed to evaluate the free energy difference. The use of an alternative technique, umbrella sampling, for ribose did not give promising results.

It was shown that one needs a fairly accurate picture of the accessible conformational space in case of flexible molecules like the ones considered here before one can determine meaningful free energy differences. Large hysteresis effects between forward and reverse simulated transitions were observed, but contrary to the general belief they are no direct measure of the accuracy of the calculated ΔG values. In all cases the ΔG values resulting from the simulations and from NMR experiments agree within the, considerable, error limits and for the different forms of D-ribose, L-malic acid and L-tartaric acid the relative order of their populations is also correctly reproduced.     

Encapsulation of Lipophilic Bioactive Molecules by Microchannel Emulsification

Currently, much effort is being invested in novel formulations of bioactive molecules, such as emulsions, for pharmaceutical, food, and cosmetic applications. Therefore, methods to produce emulsions with controlled-size droplets of uniform size distribution have been developed. On this concern, a microfluidic device called the microchannel (MC) was used in this work for emulsification. This is a novel method for producing monodispersed emulsion droplets with very narrow droplet size distribution and low energy input, due to the spontaneous droplet generation basically driven by the interfacial tension, unlike other conventional emulsification processes. This technology provides the formulation of oil-in-water (O/W) emulsions containing lipophilic active molecules with increased bioavailability, which may be readily absorbed by the human body. MC emulsification enables the preparation of highly monodispersed O/W emulsions, which may be applied as enhancer on active molecules delivery systems, as well as in foodstuff. In this study, formulations of O/W emulsions loaded with bioactive molecules, such as β-carotene and γ-oryzanol, were prepared by the MC emulsification process. Refined soybean oil containing the dissolved lipophilic molecule and either sugar ester or gelatin solution (1 wt.%) were used as the dispersed and continuous phases, respectively. The emulsification process conducted using the asymmetric straight-through MC plate enabled the production of monodispersed O/W emulsions, resulting in β-carotene-loaded O/W emulsions with average droplet size (d _av) of 27.6 μm and coefficient of variation (CV) of 2.3% and γ-oryzanol-loaded droplets with d _av of 28.8 μm and CV of 3.8%. The highly monodisperse β-carotene-loaded droplets were physically stable throughout the storage period observed, resulting in droplets with d _av 28.2 μm and CV of 2.9% after 4 months storage in darkness at 5 °C. Single micrometer-sized monodisperse emulsions loaded with β-carotene were successfully formulated using the grooved MC emulsification, resulting in droplets with d _av of 9.1 μm and CV of 6.2%. This work was funded by The Ministry of Agriculture, Forestry and Fisheries of Japan, through the Food Nanotechnology Project, and the Japan Society for the Promotion of Science.     

Dissolved Organic Carbon: Patterns of Utilization and Turnover in Two Small Lakes

Planktonic bacterial utilization of ¹⁴C-labelled glucose and acetate was monitored by kinetic measurements throughout an annual period in a small lake. Resulting kinetic uptake data have shown that from 1–15% of the total dissolved organic carbon pool was removed chemo-organotrophically per day during the year by bacteria capable of metabolizing these substrates. The kinetic uptake of nine selected organic compounds was measured in a second small lake during summer thermal stratification. Metabolism of glucose, acetate, and glycollate was preferred. Respiration rates of the nine compounds varied generally between 20–60% of the total uptake. The uptake of these compounds accounted for removal of 3–8% of the total dissolved organic carbon pool per day.     

Cholesterol Pathways Affected by Small Molecules That Decrease Sterol Levels in Niemann-Pick Type C Mutant Cells

Background

Niemann-Pick type C (NPC) disease is a genetically inherited multi-lipid storage disorder with impaired efflux of cholesterol from lysosomal storage organelles.

Methodology/Principal Findings

The effect of screen-selected cholesterol lowering compounds on the major sterol pathways was studied in CT60 mutant CHO cells lacking NPC1 protein. Each of the selected chemicals decreases cholesterol in the lysosomal storage organelles of NPC1 mutant cells through one or more of the following mechanisms: increased cholesterol efflux from the cell, decreased uptake of low-density lipoproteins, and/or increased levels of cholesteryl esters. Several chemicals promote efflux of cholesterol to extracellular acceptors in both non-NPC and NPC1 mutant cells. The uptake of low-density lipoprotein-derived cholesterol is inhibited by some of the studied compounds.

Conclusions/Significance

Results herein provide the information for prioritized further studies in identifying molecular targets of the chemicals. This approach proved successful in the identification of seven chemicals as novel inhibitors of lysosomal acid lipase (Rosenbaum et al, Biochim. Biophys. Acta. 2009, 1791:1155–1165).     

Degradation of the Persistent Organic Pollutant [14C]Heptachlor in Japanese Field Soils

The fate of [¹⁴C]heptachlor in Saitama soil and the degradation of [¹⁴C]heptachlor in four Japanese field soils over 112 d after application were investigated. Heptachlor was degraded mainly to cis-heptachlor epoxide by a biotic process and to 1-hydroxychlordene by an abiotic process in the field soils. Volatilization of heptachlor and cis-heptachlor epoxide from the soil was observed over the experimental period. The amount of 1-hydroxychlordene produced in the soils appeared to be related to the soil water contents. Because heptachlor and heptachlor epoxides are predicted to volatilize to the atmosphere and to persist in soils, these compounds are thought to spread among Japanese environmental compartments even after a ban on their use.     

C Isotopomer Analysis of Glutamate by Tandem Mass Spectrometry

Tandem mass spectrometry allows a compound to be isolated from the rest of the sample and dissociated into smaller fragments. We show here that fragmentation of glutamate mass isotopomers yields additional mass spectral data that significantly improve the analysis of metabolic fluxes compared to full-scan mass spectrometry. In order to validate the technique, tandem and full-scan mass spectrometry were used along with (13)C NMR to analyze glutamate from rat hearts perfused with three substrate mixtures (5 mM glucose plus 5 mM [2-(13)C]acetate, 5 mM [1-(13)C]glucose plus 5 U/L insulin, and 5 mM glucose plus 1 mM [3-(13)C]pyruvate). Analysis by tandem mass spectrometry showed that the enriched substrate contributed 98 +/- 2, 53 +/- 2, and 84 +/- 7%, respectively, of acetyl-coenzyme A while the rate of anaplerotic substrate entry was 7 +/- 3, 25 +/- 8, and 16 +/- 8%. Similar results were obtained with (13)C NMR data, while values from full-scan data had higher error. We believe that this is the first use of tandem mass spectrometry to determine pathway flux using (13)C-enriched substrates. Although analysis of the citric acid cycle by NMR is simpler (and more intuitive), tandem mass spectrometry has the potential to combine high sensitivity with the high information yield previously available only by NMR.     

Magnetic CLEAR Supports for Solid-Phase Synthesis of Peptides and Small Organic Molecules

Paramagnetic versions of the CLEAR supports were prepared by entrapment of magnetite particles during suspension polymerization of allylamine, trimethylolpropane ethoxylate (14/3 EO/OH) triacrylate, and trimethylolpropane trimethacrylate. Swelling studies in a broad range of solvents showed comparable swelling of magnetic beads and regular CLEAR beads. The application of the magnetic beads as the support in solid-phase synthesis of peptides (Leu-enkephalinamide, substance P, acyl carrier protein (65–74) amide, and amyloid β-protein (34–42) amide) and small organic affinity ligands based on the s-triazine scaffold was demonstrated. Adequate stability of the beads and retention of their magnetic properties were observed throughout the synthesis steps. Abbreviations used for amino acids follow the IUPAC-IUB Commission of Biochemical Nomenclature (Jones, J. Pept. Sci., 12 (2006) 1). All amino acids used were of the L-configuration unless otherwise stated. All solvent ratios are volume/volume. A preliminary report of portions of this work was presented at the 19th American Peptide Symposium in San Diego, CA, 2005 (Sasikumar and Kempe, 2006). Dedicated to the memory of Bruce Merrifield (July 15, 1921–May 14, 2006).     

Recent Development of Quinoxaline Based Polymers/Small Molecules for Organic Photovoltaics

Among the various molecular designs developed for the synthesis of conjugated polymers and small molecules for optoelectronic applications, the donor: acceptor (D–A) approach is the most widely explored method over the past decades. Through the covalent linkage of electron‐rich and electron‐deficient units, a plethora of medium‐low band gap materials has been developed and tested in organic photovoltaic devices. In particular, the quinoxaline aromatic structure and its derivatives are among the most studied electron deficient aromatic units used in D–A structures. Quinoxaline based materials are endowed with characteristics that are useful for large scale production in real world applications, such as easy synthetic procedures and excellent stability in air. Moreover, the use of quinoxaline based polymers/small molecules in bulk heterojunction (BHJ) devices led to power conversion efficiencies over 9%. Considering the potential of quinoxaline based materials, this review gathers together quinoxaline based polymers and small molecules reported in the literature during the last 5 years, summarizing and discussing the structure‐properties relationships for this class of organic semiconductors, aiming to serve as a background and to promote efforts for the further development of new quinoxaline derivatives with improved and advanced properties for future applications.     

Block of Nav1.8 by Small Molecules

Sodium channels are key proteins in regulating neuronal excitability and accumulating data suggest that specific subtypes of voltage-dependent sodium channels are important in signaling various types of pain. Consistent with this theme, Jarvis et al (2007) recently reported the identification of a subtype-selective Nav1.8 blocker that was active in several pre-clinical models of pain. During the course of these studies compounds were also identified that showed large differences in potency when tested on Nav1.8 channels from different species. This Addendum illustrates one of these compounds along with the potency correlation between recombinant and native tetrodotoxin-resistant sodium channels for additional examples. These data show that significant differences can be observed for sodium channel blockers across species and highlight the importance of considering this possibility when searching for new compounds and research tools to probe sodium channel function.     

Predicting Metabolic Pathways of Small Molecules and Enzymes Based on Interaction Information of Chemicals and Proteins

Metabolic pathway analysis, one of the most important fields in biochemistry, is pivotal to understanding the maintenance and modulation of the functions of an organism. Good comprehension of metabolic pathways is critical to understanding the mechanisms of some fundamental biological processes. Given a small molecule or an enzyme, how may one identify the metabolic pathways in which it may participate? Answering such a question is a first important step in understanding a metabolic pathway system. By utilizing the information provided by chemical-chemical interactions, chemical-protein interactions, and protein-protein interactions, a novel method was proposed by which to allocate small molecules and enzymes to 11 major classes of metabolic pathways. A benchmark dataset consisting of 3,348 small molecules and 654 enzymes of yeast was constructed to test the method. It was observed that the first order prediction accuracy evaluated by the jackknife test was 79.56% in identifying the small molecules and enzymes in a benchmark dataset. Our method may become a useful vehicle in predicting the metabolic pathways of small molecules and enzymes, providing a basis for some further analysis of the pathway systems.     

The Potential Utility of Predicted One Bond Carbon-Proton Coupling Constants in the Structure Elucidation of Small Organic Molecules by NMR Spectroscopy

NMR spectroscopy is the most popular technique used for structure elucidation of small organic molecules in solution, but incorrect structures are regularly reported. One-bond proton-carbon J-couplings provide additional information about chemical structure because they are determined by different features of molecular structure than are proton and carbon chemical shifts. However, these couplings are not routinely used to validate proposed structures because few software tools exist to predict them. This study assesses the accuracy of Density Functional Theory for predicting them using 396 published experimental observations from a diverse range of small organic molecules. With the B3LYP functional and the TZVP basis set, Density Functional Theory calculations using the open-source software package NWChem can predict one-bond CH J-couplings with good accuracy for most classes of small organic molecule. The root-mean-square deviation after correction is 1.5 Hz for most sp³ CH pairs and 1.9 Hz for sp² pairs; larger errors are observed for sp³ pairs with multiple electronegative substituents and for sp pairs. These results suggest that prediction of one-bond CH J-couplings by Density Functional Theory is sufficiently accurate for structure validation. This will be of particular use in strained ring systems and heterocycles which have characteristic couplings and which pose challenges for structure elucidation.     

Synthesis of Single‐enantiomer Bioactive Molecules: A Brief Overview

Chiral‐center enantiomers have been shown to differ significantly in biological activity, pharmacodynamics, pharmacokinetics and toxicity. New developments in the stereoselective organic synthesis have enriched the vast literature of synthetic methodologies applicable to access natural products as well as bioactive molecules. These compounds also include new drugs, drug candidates and reagents used to explore biological processes. The article reviews the synthesis of optically pure drugs, biologically active intermediates and amino alcohols by using different methods. Chirality 26:63–78, 2014. © 2013 Wiley Periodicals, Inc.     

The Influence of Organic Matter and pH on DDT Aqueous Solubility

We have studied the concentrations of DDT in ground water samples at field locations with DDT-polluted topsoil and concentrations and solubility in samples prepared from deionized water with different types and concentration of organic acids. The solubility of DDT increased with increasing concentration of humic acid when the pH of the samples was low (adjusted to about 5.5). The effect flutters in the humic acid concentration range from 200 to 300?mg/L, in accordance with humic acid hydrophobicity, operationally measured as liquid surface tension. The findings correspond to trends previously reported in the literature. The trend of increasing solubility was not found using fulvic acid or low-molecular-weight aliphatic acids. No trend was found adding humic acid without adjusting the pH. The mechanism of enhanced solubility due to humic compounds can explain relatively high levels of DDT in ground water. The ground water samples, however, had a moderately high concentration of maximum 6?µg/L compared with a maximum of about 2300?µg/L in the water samples with humic acid in pure water.     

小分子有机化合物与DC-SIGN相互作用的荧光光谱分析

采用实验和理论化学研究相结合的方法研究分子间相互作用,这种在计算机上进行“模拟实验”与传统“有机化学实验”相辅相成的研究策略,正在成为有机化学研究的重要手段.本论文利用荧光光谱分析法来研究小分子有机化合物与蛋白底物之间的相互作用机制.利用先进的分子模拟软件,结合分子力学、量子力学和神经网络等方法与分子对接等理论化学手段,建立和优化相互作用的分子间形成复合物的空间构象,并且预测分子间相互作用的稳定性.用荧光光谱分析法对12种小分子有机化合物与DC-SIGN(DC-specific ICAM-3 grabbing nonintegrin)之间的相互作用进行了研究,结果与理论分子模型计算十分吻合.在这12种化合物中,1-脲基氨基甘露糖与DC-SIGN络合的效果最好.这一发现可能对研究新一代抗艾滋病药物有重要意义.     

The Influence of Nutrient Availability on Soil Organic Matter Turnover Estimated by Incubations and Radiocarbon Modeling

We investigated the decomposability of soil organic matter (SOM) along a chronosequence of rainforest sites in Hawaii that form a natural fertility gradient and at two long-term fertilization experiments. To estimate turnover times and pool sizes of organic matter, we used two independent methods: (1) long-term incubations and (2) a three-box soil model constrained by radiocarbon measurements. Turnover times of slow-pool SOM (the intermediate pool between active and passive pools) calculated from incubations ranged from 6 to 20 y in the O horizon and were roughly half as fast in the A horizon. The radiocarbon-based model yielded a similar pattern but slower turnover times. The calculation of the ¹⁴C turnover times is sensitive to the lag time between photosynthesis and incorporation of organic C into SOM in a given horizon. By either method, turnover times at the different sites varied two- or threefold in soils with the same climate and vegetation community. Turnover times were fastest at the sites of highest soil fertility and were correlated with litter decay rates and primary productivity. However, experimental fertilization at the two least-fertile sites had only a small and inconsistent effect on turnover, with N slowing turnover and P slightly speeding it at one site. These results support studies of litter decomposition in suggesting that while plant productivity can respond rapidly to nutrient additions, decomposition may respond much more slowly to added nutrients.