Combination of misonidazole and m-AMSA: effects on radiation sensitivity and toxicity in E. coli

Simultaneous administration of misonidazole and m-AMSA resulted in additive radio-sensitization and toxicity in E. coli B/r. At low drug doses the toxicities may be super-additive. However, experiments in N2 and O2 indicated that a therapeutic benefit from the combination is unlikely. Depending upon the actual sequence and the presence of O2, pretreatment by one drug could lead to enhancement or reduction of the toxicity of a subsequent exposure to the other drug. In particular, an m-AMSA pretreatment made the toxicity of misonidazole independent of the oxygen concentration. Possible implications of the interaction of the two chemicals are discussed.     

In vitro studies on the effect of some chemicals on the growth and sporification of Penicillium digitatum and P. italicum

The behaviour of Penicillium digitatum and P. italicum was investigated when subjected to different concentrations of methanol (MeOH) and dimethyl sulfoxide (DMSO). The experiments were performed in 9 cm Petri dishes containing PDA amended with 0, 5, 10, 20, 30, 40 or 50 microL/mL of each of the single or combined chemicals. Daily, the formed colonies (cfu), the colony diameter and the degree of sporification were monitored during incubation at 20 degrees C for 5 day. Additionally, the pathogen development and its performance were studied by scanning electron microscopy (SEM). According to the chemical, the mycelium growth rate was affected differently and, compared to the control, only MeOH inhibited the expansion of the colony diameter. This effect was more pronounced for P. italicum. A nearly linear drop of cfu was observed as the concentration of the two chemicals was raised, and a complete inhibition of the two pathogens was attained with 50 microL/mL MeOH. With respect to the sporification degree the two pathogens were influenced similarly, but the tested compounds had opposite effects. Indeed, with MeOH, sporification took place earlier (24-36 h postinoculation) compared to the control (60 h), while during the whole experiment, DMSO at concentrations higher than 0.5 microL/mL, drastically inhibited the sporification. SEM observations of P. digitatum growth on DMSO amended media evidenced a marked increase of mycelium branching and alterations to the conidiophore, while MeOH reduced the mycelium length and fastened the conidiophore formation. The combination of the two compounds produced a synergistic interaction reducing by 40% the concentration required to inhibit completely the germination and growth of P. digitatum.     

The Use of Chemical-Chemical Interaction and Chemical Structure to Identify New Candidate Chemicals Related to Lung Cancer

Lung cancer causes over one million deaths every year worldwide. However, prevention and treatment methods for this serious disease are limited. The identification of new chemicals related to lung cancer may aid in disease prevention and the design of more effective treatments. This study employed a weighted network, constructed using chemical-chemical interaction information, to identify new chemicals related to two types of lung cancer: non-small lung cancer and small-cell lung cancer. Then, a randomization test as well as chemical-chemical interaction and chemical structure information were utilized to make further selections. A final analysis of these new chemicals in the context of the current literature indicates that several chemicals are strongly linked to lung cancer.     

Inferring anatomical therapeutic chemical (ATC) class of drugs using shortest path and random walk with restart algorithms

The anatomical therapeutic chemical (ATC) classification system is a widely accepted drug classification scheme. This system comprises five levels and includes several classes in each level. Drugs are classified into classes according to their therapeutic effects and characteristics. The first level includes 14 main classes. In this study, we proposed two network-based models to infer novel potential chemicals deemed to belong in the first level of ATC classification. To build these models, two large chemical networks were constructed using the chemical–chemical interaction information retrieved from the Search Tool for Interactions of Chemicals (STITCH). Two classic network algorithms, shortest path (SP) and random walk with restart (RWR) algorithms, were executed on the corresponding network to mine novel chemicals for each ATC class using the validated drugs in a class as seed nodes. Then, the obtained chemicals yielded by these two algorithms were further evaluated by a permutation test and an association test. The former can exclude chemicals produced by the structure of the network, i.e., false positive discoveries. By contrast, the latter identifies the most important chemicals that have strong associations with the ATC class. Comparisons indicated that the two models can provide quite dissimilar results, suggesting that the results yielded by one model can be essential supplements for those obtained by the other model. In addition, several representative inferred chemicals were analyzed to confirm the reliability of the results generated by the two models. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang.     

Structure of amphotericin B aggregates as revealed by UV and CD spectroscopies

The aqueous and hydroalcoholic solutions of the heptenic macrolide amphotericin B display strong and variable signals in CD and absorption spectroscopies in the range of the π* ← π transition. An interpretation of the spectroscopic changes is proposed based on the equilibrium between two forms of the intermolecular organization: the aggregated one (A) with strong excitonic interaction and the nonaggregative one (B) whose spectra are like those of linear conjugated polyenes in true solution with a well-developed vibrational structure. The intermediate spectra are fitted by linear combination of the A- and B-form spectra. A two-level organization of the aggregates is proposed for the A-form: (1) a close packing of few molecules, which is the origin of the absorption maxima hypsochromic shift; and (2) interaction between the preceding small units inside the aggregates, which is spectroscopically expressed by the intense CD couplet.     

Binding of brilliant red compound to lysozyme: insights into the enzyme toxicity of water-soluble aromatic chemicals

The non-covalent interaction of brilliant red (BR) with lysozyme was investigated by the UV spectrometry, circular dichroism (CD) and isothermal titration calorimetry (ITC). The thermodynamic characterization of the interaction was performed and the assembly complexes were formed: lysozyme(BR)₁₇ at pH 2.03, lysozyme(BR)₁₅ at pH 3.25 and lysozyme(BR)₁₂ at pH 4.35, which corresponded to the physiological acidities. The ionic interaction induces a combination of multiple non-covalent bonds including hydrogen bond, hydrophobic interaction and van der Waals force. The two-step binding model of BR was found, in which one or two BR molecules entered the hydrophobic intracavity of lysozyme and the others bound to the hydrophilic outer surface of lysozyme. Moreover, BR binding resulted in change of the lysozyme conformation and inhibition of the lysozyme activity. The possible binding site and type of BR and the conformational transition of lysozyme were speculated and illustrated. This work provided a useful approach for study on enzyme toxicity of aromatic azo chemicals.     

Soil microbial biomass C and symbiotic processes associated with soybean after sulfentrazone herbicide application

Resource competition and chemical interference are mechanisms of interaction among plants that may occur simultaneously. However, both mechanisms are rarely considered together when modelling plant growth. We propose a new empirical model that estimates biologically significant parameters on both plant competition and chemical interference. The model is tested with data sets from different density-dependent experiments done with two species (the grass Lolium rigidum Gaud. and the legume Glycine max soya L.) subjected to a noxious chemical environment when growing (allelochemicals and herbicides, respectively). Hypotheses on the effect of allelochemicals and its interaction with density are tested using maximum likelihood ratio tests in order to ask, for these species, whether chemical interference is playing a significant role in the interactions among plants or on the contrary, whether interactions among plants are sufficiently explained by the resource competition. In all cases a significant interaction between chemicals and density is observed. This interaction is inconsistent with the hypothesis of only resource competition having an influence of plant biomass and suggests a significant density-dependent effect of chemicals on plant growth.     

Biodegradation of aniline, anthracene, chlornitrophen, fenitrothion and linear alkylbenzene sulphonate in pond water

Biodegradation of five chemicals (aniline, anthracene, chlornitrophen (CNP), fenitrothion (FNT) and linear alkylbenzene sulphonate (LAS)) by aquatic bacteria in three different types of ponds was determined according to the cultivation method developed by this group. The degradability toward these chemicals was varied among the ponds, except for LAS which was decomposed well in all samples. Higher degradability towards the two agrochemicals, CNT and FNT, was found in the pond surrounded by paddy fields, whereas aniline and anthracene were decomposed more rapidly in the pond located in the industrial area. Water from the pond in the botanical garden, with the least exposure to any chemicals, exhibited the lowest degradation toward all chemicals tested. There was no significant seasonal variation in the biodegradation of chemicals in these ponds. It was deduced that biodegradability toward certain chemicals could be a result of acclimatization of the microbial community by chemical contamination present and past, suggesting the possible use of biodegradation profiles as an indicator for chemical pollution in the aquatic environment.     

The combined effect of DBE and X-rays on the induction of somatic mutations in Tradescantia

The induction of somatic mutations in the stamen hair cells of Tradescantia KU 9 has been used to investigate the effects of combined exposure to 1,2-dibromoethane (DBE) and X-rays. At low radiation doses a synergistic interaction has been found between the two agents for both DBE exposure followed by acute X-rays and chronic simultaneous exposures. The synergism is discussed in terms of an interaction of single strand lesions in the DNA. It is concluded that although this type of interaction should not be too important for radiological protection, it could be of significance in evaluating the effects of chemicals at low exposure rates.     

Material self-assembly as a physicochemical process

Material self-assembly as exemplified in protobiogeneses is shown to be a result of molecular exchange interaction in reacting chemicals. Temporally and spatially correlated aggregates of reacting chemicals work as vertices of molecular exchange interaction. If the material accumulation rate at a locally correlated aggregate spontaneously happens to become positive at a certain time, the material accumulation due to self-assembly will increase with time afterward. A spontaneous formation of looped reaction at locally correlated aggregates of reacting chemicals can initiate a material self-assembly at succeeding times.     

Recognizing novel chemicals/drugs for anatomical therapeutic chemical classes with a heat diffusion algorithm

Drug Anatomical Therapeutic Chemical (ATC) classification system is a widely used and accepted drug classification system. It is recommended and maintained by World Health Organization (WHO). Each drug in this system is assigned one or more ATC codes, indicating which classes it belongs to in each of five levels. Given a chemical/drug, correct identification of its ATC codes in such system can be helpful to understand its therapeutic effects. Several computational methods have been proposed to identify the first level ATC classes for any drug. Most of them built multi-label classifiers in this regard. One previous study proposed a quite different scheme, which contained two network methods, based on shortest path (SP) and random walk with restart (RWR) algorithms, respectively, to infer novel chemicals/drugs for each first level class. However, due to the limitations of SP and RWR algorithms, there still exist lots of hidden chemicals/drugs that above two methods cannot discover. This study employed another classic network algorithm, Laplacian heat diffusion (LHD) algorithm, to construct a new computational method for recognizing novel latent chemicals/drugs of each first level ATC class. This algorithm was applied on a chemical network, which containing lots of chemical interaction information, to evaluate the associations of candidate chemicals/drugs and each ATC class. Three screening tests, which measured the specificity and association to one ATC class, followed to yield more reliable potential members for each class. Some hidden chemicals/drugs were recognized, which cannot be found out by previous methods, and they were extensively analyzed to confirm that they can be novel members in the corresponding ATC class.     

Description of hydration free energy density as a function of molecular physical properties

A method to calculate the solvation free energy density (SFED) at any point in the cavity surface or solvent volume surrounding a solute is proposed. In the special case in which the solvent is water, the SFED is referred to as the hydration free energy density (HFED). The HFED is described as a function of some physical properties of the molecules. These properties are represented by simple basis functions. The hydration free energy of a solute was obtained by integrating the HFED over the solvent volume surrounding the solute, using a grid model. Of 34 basis functions that were introduced to describe the HFED, only six contribute significantly to the HFED. These functions are representations of the surface area and volume of the solute, of the polarization and dispersion of the solute, and of two types of electrostatic interactions between the solute and its environment. The HFED is described as a linear combination of these basis functions, evaluated by summing the interaction energy between each atom of the solute with a grid point in the solvent, where each grid point is a representation of a finite volume of the solvent. The linear combination coefficients were determined by minimizing the error between the calculated and experimental hydration free energies of 81 neutral organic molecules that have a variety of functional groups. The calculated hydration free energies agree well with the experimental results. The hydration free energy of any other solute molecule can then be calculated by summing the product of the linear combination coefficients and the basis functions for the solute.     

Impaired ecosystem process despite little effects on populations: modeling combined effects of warming and toxicants

Freshwater ecosystems are exposed to many stressors, including toxic chemicals and global warming, which can impair, separately or in combination, important processes in organisms and hence higher levels of organization. Investigating combined effects of warming and toxicants has been a topic of little research, but neglecting their combined effects may seriously misguide management efforts. To explore how toxic chemicals and warming, alone and in combination, propagate across levels of biological organization, including a key ecosystem process, we developed an individual‐based model (IBM) of a freshwater amphipod detritivore, Gammarus pseudolimnaeus, feeding on leaf litter. In this IBM, life history emerges from the individuals’ energy budgets. We quantified, in different warming scenarios (+1–+4 °C), the effects of hypothetical toxicants on suborganismal processes, including feeding, somatic and maturity maintenance, growth, and reproduction. Warming reduced mean adult body sizes and population abundance and biomass, but only in the warmest scenarios. Leaf litter processing, a key contributor to ecosystem functioning and service delivery in streams, was consistently enhanced by warming, through strengthened interaction between the detritivorous consumer and its resource. Toxicant effects on feeding and maintenance resulted in initially small adverse effects on consumers, but ultimately led to population extinction and loss of ecosystem process. Warming in combination with toxicants had little effect at the individual and population levels, but ecosystem process was impaired in the warmer scenarios. Our results suggest that exposure to the same amount of toxicants can disproportionately compromise ecosystem processing depending on global warming scenarios; for example, reducing organismal feeding rates by 50% will reduce resource processing by 50% in current temperature conditions, but by up to 200% with warming of 4 °C. Our study has implications for assessing and monitoring impacts of chemicals on ecosystems facing global warming. We advise complementing existing monitoring approaches with directly quantifying ecosystem processes and services.     

Active site mechanics of liver microsomal cytochrome P-450

For a set of 10 para-substituted toluene derivatives, three enzymatic constants were determined describing their interaction with purified rabbit liver microsomal P-450LM2. The three constants were the catalytic rate constant (Kcat) for hydroxylation, the apparent dissociation constant (Kd) for the enzyme-substrate complex, and the interaction energy (delta Gint) between the substrate-binding and spin-state equilibria. The para-substituents of the toluene substrates were: hydrogen, fluoro, bromo, chloro, iodo, nitro, methyl, cyano, isopropyl, and t-butyl. Linear free energy correlations were sought between the enzymatic constants and several physical constants of the individual substrate molecules. These correlations would be useful both for empirical prediction purposes and for insight into active site chemistry and mechanics. Catalytic rates were correlated by a linear combination of the Hansch pi hydrophobic constant and the Hammett sigma value. A deuterium isotope effect (DV) of 2.6 for d8-toluene compared to d0-toluene confirmed that hydrogen abstraction was partially rate-limiting with this series of substrates. Apparent dissociation constants were predicted by a linear combination of the molar volume and pi, while the spin-state interaction energies were best predicted by a linear combination of the Hansch pi hydrophobic constant and the reciprocal of the dielectric constant.     

Structural and functional evidences for the interactions between nuclear hormone receptors and endocrine disruptors at low doses

Endocrine-disrupting chemicals (EDCs) represent a broad class of exogenous substances that cause adverse effects in the endocrine system mainly by interacting with nuclear hormone receptors (NRs). Humans are generally exposed to low doses of pollutants, and current researches aim at deciphering the mechanisms accounting for the health impact of EDCs at environmental concentrations. Our correlative analysis of structural, interaction and cell-based data has revealed a variety of, sometimes unexpected, binding modes, reflecting a wide range of EDC affinities and specificities. Here, we present a few representative examples to illustrate various means by which EDCs achieve high-affinity binding to NRs. These examples include the binding of the mycoestrogen α-zearalanol to estrogen receptors, the covalent interaction of organotins with the retinoid X- and peroxisome proliferator-activated receptors, and the cooperative binding of two chemicals to the pregnane X receptor. We also discuss some hypotheses that could further explain low-concentration effects of EDCs with weaker affinity towards NRs.     

Analysis of interaction for mixtures of agents using the linear isobole

The linear isobole that is commonly used as a reference for the study of interaction is derived from the interaction of an agent with itself. It is shown that the general use of the linear isobole in the study of the combined effects of mixtures of agents implies interaction between the agents whether the dose-effect curves of the agents are the same or not. It is difficult to generalize the interaction between two doses of the same agent to the interaction between two doses of different agents with different action mechanisms without the use of a mechanistic model. Predictions using non-interaction defined as independent action are generally different from those using linear isobole. A simple mechanistic framework based on the concept of common intermediate lesions is introduced in this paper to relate these two methods used for the analysis of synergism and antagonism. In this framework of lesion development, two agents that have no common intermediate lesion in their action will be non-interactive (referred to as independent action). When the two agents share a common intermediate, it is shown that the combined effect will follow the linear isobole (referred to as common action). This simple framework of analysis is applicable to the general study of interaction between two agents with different types of dose-effect curves.     

Induction of chromosome loss by mixtures of organic solvents including neurotoxins

Twenty-three aprotic polar solvents - 3 nitriles, 8 organic esters, 10 ketones and 2 lactones - and LiCl were tested in combination with propionitrile alone or a mixture of ethyl acetate and propionitrile for the induction of mitotic chromosome loss in the D61.M strain of the yeast Saccharomyces cerevisiae. Propionitrile and ethyl acetate are very potent inducers of chromosome loss. Mixtures of propionitrile and ethyl acetate induced chromosome loss at much higher frequencies than was observed with the pure chemicals. To test the potentiating effects of propionitrile or mixtures of propionitrile with ethyl acetate on other chemicals, they were used in concentrations that were at or below the level for induction of chromosome loss. Twenty chemicals when tested in pure form were negative or only marginally active in the test for chromosome loss. Except for amyl propionate and benzyl acetate, the same chemicals showed strong induction in combination treatments with the potentiating chemicals. All the ketones including the neurotoxic methyl ethyl ketone, 2-hexanone and 2.5-hexanedione induced high frequencies of chromosome loss. Only methyl ethyl ketone is capable of inducing high levels of chromosome loss when tested in the pure form at much higher concentrations. 1-Methyl-2-pyrrolidinone and gamma-valerolactone had previously been shown to induce chromosome loss only when the treatment at a growth-supporting temperature was interrupted by a cold shock within a narrow range of low temperatures which prevented growth. Both gave very strong induction in combination treatment performed at a continuous growth-supporting temperature. LiCl is a weak inducer of chromosome loss: strong induction can be achieved in combination treatments.     

Elucidation of different inhibition mechanism of small chemicals on PtdInsP-binding domains using in silico docking experiments

Phosphatidylinositides, most negatively charged lipids in cellular membranes, regulate diverse effector proteins through the interaction with their lipid binding domains. We have previously reported inhibitory effect of small chemicals on the interaction between PtdIns(3,4,5)P₃ and Btk PH domain. Here, we report that the inhibitory effects of same sets of chemicals on Grp1 PH domain and epsin1 ENTH domain to elucidate diversity of inhibitory mechanisms upon different lipid binding domains. Among the chemicals, chemical 8 showed best inhibition in vitro assay for Grp1 PH domain and epsin1 ENTH domain, and then the interaction between small chemicals and lipid binding domains was further investigated by in silico docking experiments. As a result, it was concluded that the diverse inhibitory effects on different lipid binding domains were dependent on not only the number of interactions between small chemical and domain, but also additional interaction with positively charged surfaces as the secondary binding sites. This finding will help to develop lipid binding inhibitors as antagonists for lipid–protein interactions, and these inhibitors would be novel therapeutic drug candidates via regulating effector proteins involved in severe human diseases.     

一株受二噁英类化学物质诱导表达的萤光素酶肝癌细胞系

 构建了一对二英类化学物质敏感的人肝癌细胞株 ,用于二英类化学物质生物筛选和快速半定量检测 .首先构建一在二英增强子调控下的萤光素酶报告基因质粒 ,该质粒转染入人肝癌细胞株HepG2 ,筛选稳定转染细胞株 .2 ,3,7,8 四氯代二苯并二英 (TCDD)诱导稳定转染细胞株萤光素酶表达 ,发光检测萤光素酶活性 .该细胞株用于TCDD检测 ,检测下限为 1 1pmol L ,线性范围为 1～ 10 0pmol L .该细胞系的建立可用于二英类化学物质的生物筛选和快速半定量检测