Three-dimensional quantitative structure activity relationships of quorum-sensing and biofilm inhibitors in gram-negative bacteria

Thirty N-acyl homoserine lactone (AHL) analogs with variable antibacterial activity and displaying inhibition of biofilm formation were selected to develop models for establishing three-dimensional quantitative structure-activity relationships (3D-QSAR). Comparative molecular field analysis (CoMFA) and comparative similarity indices analysis (CoMSIA) were carried out to determine the optimum structural requirements for selectivity and potency of quorum-sensing and bacterial biofilm inhibition. The best CoMFA model predicted a q² value of 0.519 and an r² value of 0.984 and revealed that electrostatic and steric properties play a significant role in potency and selectivity. The CoMSIA model predicted a q² value of 0.411 and an r² value of 0.938 based on a combination of steric, electrostatic, and hydrophobic effects. The analysis of the contour maps from each model provide insight into the structural requirements for increasing the activity of a compound. Consequently, manipulating the chemical and physical properties of substituted acyl groups on the homoserine lactone moiety can provide important information toward enhancing the antibacterial properties of the target chemical compound.     

3D-QSAR of fungal quorum-sensing inhibiting analogs of farnesol

Thirty-four analogs with variable antifungal activity were selected to develop models for establishing three-dimensional quantitative structure-activity relationships (3D-QSAR). Comparative molecular field analysis (CoMFA) and comparative similarity indices analyses (CoMSIA) were conducted on the group of analogs to determine the structural requirements for selectivity and potency in inhibiting biofilm formation and fungal growth. The best CoMFA model predicted a q(2) = 0.5 and an r(2) = 0.991, and revealed that electrostatic properties play a significant role in potency and selectivity. The best CoMSIA model combined electrostatics, hydrogen bond acceptor and donor, and hydrophobic fields with a q(2) = 0.664 r(2) = 0.952, S = 0.099, and F = 139.892. The analyses of the contour maps from both models provide significant insight into the structural necessities for a potent compound. Therefore, manipulating various chemical properties of the substituted groups on the farnesol chain can be used to enhance the fungicidal properties of the target compound.     

Three-dimensional quantitative structure activity relationships of quorum-sensing and biofilm inhibitors in gram-negative bacteria

Thirty N-acyl homoserine lactone (AHL) analogs with variable antibacterial activity and displaying inhibition of biofilm formation were selected to develop models for establishing three-dimensional quantitative structure-activity relationships (3D-QSAR). Comparative molecular field analysis (CoMFA) and comparative similarity indices analysis (CoMSIA) were carried out to determine the optimum structural requirements for selectivity and potency of quorum-sensing and bacterial biofilm inhibition. The best CoMFA model predicted a q2 value of 0.519 and an r2 value of 0.984 and revealed that electrostatic and steric properties play a significant role in potency and selectivity. The CoMSIA model predicted a q2 value of 0.411 and an r2 value of 0.938 based on a combination of steric, electrostatic, and hydrophobic effects. The analysis of the contour maps from each model provide insight into the structural requirements for increasing the activity of a compound. Consequently, manipulating the chemical and physical properties of substituted acyl groups on the homoserine lactone moiety can provide important information toward enhancing the antibacterial properties of the target chemical compound.     

3D QSAR studies of dioxins and dioxin-like compounds using CoMFA and CoMSIA

In the present study we have performed comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) on structurally diverse ligands of Ah (dioxin) receptor to explore the physico-chemical requirements for binding. All CoMFA and CoMSIA models have given q(2) value of more than 0.5 and r(2) value of more than 0.84. The predictive ability of the models was validated by an external test set, which gave satisfactory predictive r(2) values. Best predictions were obtained with CoMFA model of combined modified training set (q(2) = 0.631, r(2) = 0.900), giving predictive residual value = 0.02 log unit for the test compound. Addition of CoMSIA study has elucidated the role of hydrophobicity and hydrogen bonding along with the effect of steric and electrostatic properties revealed by CoMFA. We have suggested a model comprises of four structurally different compounds, which offers a good predictability for various ligands. Our QSAR model is consistent with all previously established QSAR models with less structurally diverse ligands.     

Studies of 3D-quantitative structure-activity relationships on a set of nitroaromatic compounds: CoMFA,advanced CoMFA and CoMSIA

By using comparative molecular field analysis (CoMFA), advanced CoMFA and comparative molecular similarity index analysis (CoMSIA) methods, the 3D relationships between the structures of 35 nitroaromatic compounds and their toxicities have been investigated to yield statistically reliable models of considerable predictive power. In contrast to CoMFA, CoMSIA produces better results for the correlation. Moreover, the obtained CoMSIA contour maps that interpret the correlations in terms of field contributions allow physicochemical properties relevant for binding to be easily mapped back onto molecular structures, and thus elucidate structural features among ligands that are responsible for toxicities. Besides, most of the highlighted regions in CoMSIA and CoMFA contour maps are mirrored by features in the surrounding environment. Thereby, CoMFA and CoMSIA both help to give explanations of the toxic mechanism of tested compounds.     

Three-dimensional, quantitative-structure-property-relationship study of aqueous solubility for phenylsulfonyl carboxylates using comparative-molecular-field analysis and comparative-molecular-similarity-indices analysis.

With both the comparative-molecular-field analysis (CoMFA) and the comparative-molecular-similarity-indices analysis (CoMSIA), the paper describes two five-component, three-dimensional, quantitative-structure-property-relationship (3D-QSPR) models for the aqueous solubility logSw (Sw, mol x L(-1)) of 52 phenylsulfonyl carboxylates. Two models yield the leave-one-out cross-validated correlation coefficient q2 values 0.851 and 0.821, and the conventional correlation coefficient r2 values 0.963 and 0.929, respectively. The achievement of high q2 and r2 values of the CoMFA model indicates the significance of correlation of steric and electrostatic fields with the aqueous solubility. The key features in the CoMFA contour maps are critical to trace the important properties and gain insight to the solvation mechanism of tested compounds. The quality of CoMSIA model is slightly lower than that of CoMFA in terms of q2 and r2 values. Not requiring molecular superposition, CoMSIA may be faster than CoMFA in data processing.     

Three-dimensional quantitative structure-activity relationship study for phenylsulfonyl carboxylates using CoMFA and CoMSIA

From both the comparative molecular field analysis (CoMFA) and the comparative molecular similarity indices analysis (CoMSIA), the paper describes two three-dimensional quantitative structure-activity relationship (3D-QSAR) models for the acute toxicity logEC50 (15 min-EC50 in micromoll(-1)) of 56 phenylsulfonyl carboxylates on Photobacterium phosphoreum. Two models yield the leave-one-out cross-validated correlation coefficient q2 values of 0.823 and 0.713, and the conventional correlation coefficient r2 values of 0.958 and 0.933, respectively. The achievement of higher q2 and r2 values of CoMFA model indicates the significance of correlation of steric and electrostatic fields with biological activities. The key features in the CoMFA contour maps are critical to trace the important properties and gain insight into the toxic mechanism of tested compounds. The quality of CoMSIA model is slightly lower than that of CoMFA in terms of q2 and r2 values. Not requiring molecular superposition, CoMSIA is faster than CoMFA in data processing.     

Three-dimensional quantitative structure activity relationship (3D-QSAR) analysis for in vitro toxicity of chlorophenols to HepG2 cells

In the present paper, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were applied to investigate two 3D-QSAR models for the cytotoxicity of chlorophenols. These models have evaluated the intensity of chlorophenols' toxicity on HepG2 cells in vitro. The CoMFA model has both high consistency and predictability. The contribution of the electrostatic field to biological activity is greater than that of the steric field. The CoMSIA model used in this study includes two fields, one is hydrophobic field, and the other is electrostatic field. The relative contribution of them is 0.789:0.211. Consisted with the CoMFA model, the CoMSIA electrostatic filed also plays a dominant role. The CoMFA and CoMSIA contour maps significantly elucidated that the electrostatic field is more important than the other fields and might be one of the reasons resulting in potential reactive mechanism involved in cell proliferation inhibition.     

Investigation of structural requirements for inhibitory activity at the rat and housefly picrotoxinin binding sites in ionotropic GABA receptors using DISCOtech and CoMFA

A number of widely diverse compounds that show inhibitory activities at the picrotoxinin binding sites in housefly and rat GABA receptors were investigated by using the distance comparison technique (DISCOtech) and comparative molecular field analysis (CoMFA) methods to explore the pharmacophore models and the three-dimensional quantitative structure-activity relationships (3D-QSAR) of the compounds. These compounds consist of three diverse types of noncompetitive GABA receptor antagonists, i.e., trioxabicyclooctanes and their derivatives, picrodendrins and related terpenoids, and fipronil and its analogs. For investigation of the structural requirements for inhibitory activity at the picrotoxinin binding site of GABA receptor, DISCOtech pharmacophore models containing one center of hydrophobic ring and two hydrogen bond acceptor atoms for both housefly-head and rat-brain GABA receptors were constructed, respectively. In particular, the interacting areas in housefly receptors appear to be wider than that in rat receptors, the differences between rat and housefly receptor models implicate the selectivity of noncompetitive GABA receptor antagonists. In addition, corresponding CoMFA models with good statistical indices (r(2)>0.9 and q(2)>0.5) were also obtained. These models can be used as guidance for the development of new compounds with high activities and selectivities.     

The In-Plume Emission Test Stand: An Instrument Platform for the Real-Time Characterization of Fuel-Based Combustion Emissions

Abstract

The In-Plume Emission Test Stand (IPETS) characterizes gaseous and particulate matter (PM) emissions from combustion sources in real time. Carbon dioxide (CO₂), carbon monoxide (CO), nitric oxide (NO), nitrogen dioxide (NO₂), and other gases are quantified with a closed-path Fourier transform infrared spectrometer (FTIR). Particle concentrations, chemical composition, and other particle properties are characterized with an electrical low-pressure impactor (ELPI), a light-scattering particle detector, an optical particle counter, and filter samples amenable to different laboratory analysis. IPETS measurements of fuel-based emission factors for a diesel generator are compared with those from a Mobile Emissions Laboratory (MEL). IPETS emission factors ranged from 0.3 to 11.8, 0.2 to 3.7, and 22.2 to 32.8 g/kg fuel for CO, NO₂, and NO, respectively. IPETS PM emission factors ranged from 0.4 to 1.4, 0.3 to 1.8, 0.3 to 2.2, and 1 to 3.4 g/kg fuel for filter, photoacoustic, nephelometer, and impactor measurements, respectively. Observed linear regression statistics for IPETS versus MEL concentrations were as follows: CO slope = 1.1, r² = 0.99; NO slope = 1.1, r² = 0.92; and NO₂ slope = 0.8, r² = 0.96. IPETS versus MEL PM regression statistics were: filter slope = 1.3, r² = 0.80; ELPI slope = 1.7, r² = 0.87; light-scattering slope = 2.7, r² = 0.92; and photoacoustic slope = 2.1, r² = 0.91. Lower temperatures in the dilution air (~25 °C for IPETS vs. ~50 °C for MEL) may result in greater condensation of semi-volatile compounds on existing particles, thereby explaining the 30% difference for filters. The other PM measurement devices are highly correlated with the filter, but their factory-default PM calibration factors do not represent the size and optical properties of diesel exhaust. They must be normalized to a simultaneous filter measurement.     

Modelling the dissipation kinetics of six commonly used pesticides in two contrasting soils of New Zealand

We used three non-linear bi-phasic models, bi-exponential (BEXP), first-order double exponential decay (FODED), and first-order two-compartment (FOTC), to fit the measured degradation data for six commonly used pesticides (atrazine, terbuthylazine, bromacil, diazinon, hexazinone and procymidone) in two New Zealand soils. Corresponding DT₅₀ and DT₉₀ values for each compound were numerically obtained and compared against those estimated by simple first-order kinetic (SFOK) model. All 3 non-linear models gave good fit of the measured data under both soil depths and were well supported by the values obtained for the respective statistical indices (RMSE, CRM and r ²). The FOTC model gave by far the best fit for most compounds, followed by the FODED and BEXP models. Overall, DT₅₀ values derived by non-linear models for the six compounds in soils from both sites were lower than the values obtained by the SFOK model. Differences in the SFOK and the three non-linear models derived DT₉₀were, however, an order of magnitude higher for some compounds, while for others differences were very small. Although all three non-linear models described most data by giving excellent fits, in a few instances > 5–10% asymptotes hindered the estimation of DT₉₀ values. This work shows that when degradation deviates from first-order kinetic, application of non-linear decay models to describe the kinetics of degradation becomes important in order to derive the true end-points for pesticides in soil.     

Ozone risk assessment for agricultural crops in Europe: Further development of stomatal flux and flux–response relationships for European wheat and potato

Applications of a parameterised Jarvis-type multiplicative stomatal conductance model with data collated from open-top chamber experiments on field grown wheat and potato were used to derive relationships between relative yield and stomatal ozone uptake. The relationships were based on thirteen experiments from four European countries for wheat and seven experiments from four European countries for potato. The parameterisation of the conductance model was based both on an extensive literature review and primary data. Application of the stomatal conductance models to the open-top chamber experiments resulted in improved linear regressions between relative yield and ozone uptake compared to earlier stomatal conductance models, both for wheat (r²=0.83) and potato (r²=0.76). The improvement was largest for potato. The relationships with the highest correlation were obtained using a stomatal ozone flux threshold. For both wheat and potato the best performing exposure index was AF_st6 (accumulated stomatal flux of ozone above a flux rate threshold of 6 nmol ozone m⁻² projected sunlit leaf area, based on hourly values of ozone flux). The results demonstrate that flux-based models are now sufficiently well calibrated to be used with confidence to predict the effects of ozone on yield loss of major arable crops across Europe. Further studies, using innovations in stomatal conductance modelling and plant exposure experimentation, are needed if these models are to be further improved.     

Insights into the structure of urea-like compounds as inhibitors of the juvenile hormone epoxide hydrolase (JHEH) of the tobacco hornworm Manduca sexta: analysis of the binding modes and structure-activity relationships of the inhibitors by docking and CoMFA calculations

Substituted urea compounds are well-known as potent inhibitors of juvenile hormone epoxide hydrolase (JHEH) of the tobacco hornworm Manduca sexta. Docking simulations of 47 derivatives inside JHEH were performed to gain insight into the structural characteristics of these complexes. The obtained orientations show a strong similitude with the observed in the known X-ray crystal structures of human soluble epoxide hydrolase (sEH) complexed with dialkylurea inhibitors. In addition, the predicted inhibitor concentration (IC₅₀) of the above-mentioned compounds as JHEH inhibitors were obtained by a quantitative structure-activity relationship (QSAR) method by using comparative molecular field analysis (CoMFA) applied to aligned dataset. The best models included steric and electrostatic fields and had adequate predictive abilities. In addition, these models were used to predict the activity of an external test set of compounds that was not used for building the model. Furthermore, plots of the CoMFA fields allowed conclusions to be drawn for the choice of suitable inhibitors.     

Kinetics and isotherm modeling of azoxystrobin and imidacloprid retention in biomixtures

The paper reports the kinetics and adsorption isotherm modeling for imidacloprid (IMIDA) and azoxystrobin (AZOXY) in rice straw (RS)/corn cob (CC) and peat (P)/compost (C) based biomixtures. The pseudo-first-order (PFO), pseudo-second-order (PSO), Elovich and intraparticle diffusion models were used to describe the kinetics. The adsorption data were subjected to the Langmuir and the Freundlich isotherms. Results (r²_Adj values) suggested that the modified Elovich model was the best suited to explain the kinetics of IMIDA sorption while different models explained AZOXY sorption kinetics in different biomixtures (PFO in RS?+?C and RS?+?P; PSO in CC?+?P and Elovich in CC?+?C). Biomixtures varied in their capacity to adsorb both pesticides and the adsorption coefficient (K_d) values were 116.8–369.24 (AZOXY) and 24.2–293.4 (IMIDA). The Freundlich isotherm better explained the sorption of both pesticides. Comparison analysis of linear and nonlinear method for estimating the Freundlich adsorption constants was made. In general, r²_Adj values were higher for the nonlinear fit (AZOXY?=?0.938–0.982; IMIDA?=?0.91–0.970) than the linear fit (AZOXY?=?0.886–0.993; IMIDA?=?0.870–0.974) suggesting that the nonlinear Freundlich equation better explained the sorption. The rice straw-based biomixtures performed better in adsorbing both the pesticides and can be used in bio-purification systems.     

Effect of coumaphos on cholinesterase activity,hematology, and biochemical blood parameters of bovines in tropical regions of Mexico

To assess the effect of coumaphos [O-(3-chloro-4-methyl-2-oxo-2H-1-benzopyran-7-yl) O,O-diethyl phosphorothioate] exposure on physiological responses during bovine production, acetylcolinesterase (AChE) and butyrylcholinesterase (BuChE) activities were measured in whole blood, erythrocytes, and plasma of healthy male steers (Bos Taurus x Bos indicus) sprayed with coumaphos at a non-lethal dose of 1 mg kg^{? 1} body weight per day once every 14 (in vivo group) or 21 days (southern and central groups). Coumaphos topically administered at 1 mg/kg body weight per day to cattle under normal management practices in tropical areas produced a significant inhibition in erythrocyte (RBC) AChE and BuAChE activities when compared to baseline levels. RBC-AChE activity for the in vivo group decreased 71.3% (P < 0.05) and BuChE activity 59.1% (P < 0.05); RBC-AChE activity decreased 55.1% (P < 0.05) (southern group) and 43.4% (P < 0.05) (central group). Compared to the control specimens, steers from in vivo, southern, and central groups after 150 days of exposure had lower (P < 0.05) leukocyte count, absolute lymphocyte, erythrocyte, and platelet counts. Decreases in RBC-AChE activities correlated with decreased lymphocyte (r = 1.000, p = 0.01), erythrocyte (r = 1.000, p = 0.003), and platelet counts (r = 0.841, p = 0.036). Significantly increased BUN levels (P < 0.05) correlated with the decrease in RBC-AChE activities (r = ? 0.997, p = 0.047) and with the decrease in absolute red blood cell (r = ? 0.883, p = 0.020) and lymphocyte (r = ? 0.825, p = 0.043) counts; increased (P < 0.05) total plasma protein levels correlated with the decrease in RBC-AChE activities (r = ?0.998, p = 0.043), absolute red blood cell (r = ? 0.998, p = 0.040), lymphocyte (r = ? 0.893, p = 0.017), and platelet (r = -0.855, p = 0.030) counts. The physiological responses correlated with the erythrocyte acetylcholinesterase inhibition could be considered as early indicators or warning responses of bovine exposures to organophosphorus pesticides (OPs).     

Day-to-Day Particulate Exposures and Health Changes in Los Angeles Area Residents with Severe Lung Disease

ABSTRACT

We measured particulate matter (PM_2.5 and PM₁₀) exposures, home temperature, arterial blood oxygen saturation, blood pressure, and lung function in 30 volunteer Los Angeles area residents during four-day intervals. Continuous Holter electrocardiograms were recorded in a subgroup on the first two days. Subjects recorded symptoms and time-activity patterns in diaries during monitoring, and during a reference period one week earlier/later. All subjects had severe chronic obstructive pulmonary disease. PM₁₀ (24-hr mean) at monitoring stations near subjects’ homes averaged 33 μg/m³, and ranged from 9 to 84 μpg/m³. In longitudinal analyses, day-to-day changes in PM_2.5 and PM₁₀ outside subjects’ homes significantly tracked concurrent station PM10 (r² = 0.22 and 0.44, respectively). Indoor and personal concentrations were less related to station readings (r² ≤ 0.1), but tracked each other (r² ≥ 0.4). In-home temperatures tracked outdoor temperatures more for lows (r² = 0.27) than for highs (r² = 0.10). These longitudinal relationships of subject-oriented and station PM measurements were generally similar to cross-sectional relationships observed previously in similar subjects. Among health measurements, only blood pressure showed reasonably consistent unfavorable longitudinal associations with particulates, more with station or outdoor PM than with indoor or personal PM.     

Modeling traffic air pollution in street canyons in New York City for intra-urban exposure assessment in the US Multi-Ethnic Study of atherosclerosis and air pollution

We evaluated the Danish AirGIS air quality and exposure model system using air quality measurement data from New York City in the Multi-Ethnic Study of Atherosclerosis and Air Pollution (MESA Air). Measurements were used from three US EPA Air Quality System (AQS) monitoring stations and a comprehensive MESA Air measurement campaign including about 150 different locations and about 650 samples of about 2 week measurements of NO_x, NO₂ and PM_2.5. AirGIS is a deterministic exposure model system based on the dispersion models Operational Street Pollution Model (OSPM) and the Urban Background Model (UBM). The UBM model reproduced the annual levels within 1–26% depending on station and pollutant at the three urban background EPA monitor stations, and generally reproduced well the seasonal and diurnal variation. The full model with OSPM and UBM reproduced the MESA Air measurements with a correlation coefficient of r² = 0.51 for NO_x, r² = 0.28 for NO₂ and r² = 0.73 for PM_2.5.