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The major correction arising from the anharmonic treatment occurs for the frequencies, as also noted for the IR spectra. Anharmonic corrections do not modify significantly the relative intensities of the fundamental bands, except for the band at 1380 cm–1 corresponding to the νs(NO2) mode that is weakened by the anharmonic treatment for all three isotopomers relative to the harmonic model. However, for both of the deuterated isotopomers, a slight improvement in the intensities of the band corresponding to the 31 mode for the mono-deuterated and the 21 mode for the di-deuterated isotopomer (both corresponding to a stretching of the CD bonds) seems to appear from the anharmonic treatment, where they are reduced slightly more than the other bands that correspond to hydrogen-related motions. This modification of the relative intensities leads to somewhat better agreement with experiment.
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| 100.0 |
We note that the liquid-phase IR spectrum for CH3NO2 (as can be seen in Fig. 1(a) of ref. 85, not reproduced here) presents strikingly different spectral intensities to the gas-phase spectrum. Therefore, a corresponding effect can be expected also for the Raman spectra. This could explain at least some of the differences between the calculated (gas-phase) and experimental (liquid-phase) spectra presented here, and solvent effects will be investigated in future work.
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study
| 100.0 |
The experimental liquid-phase spectrum of CH3NO2 from ref. 85 is reproduced in Fig. 7 for comparison. A weak peak appears around 1280 cm–1 corresponding to the 122 overtone. The small shoulder appearing in the experimental spectrum on the low-frequency side of the peak around 1400 cm–1 could be related to this overtone band. Other very weak peaks appear between 2700 cm–1 and 2850 cm–1 and are due to several different overtones and combination bands. These features could be related to the weak peak appearing in the experimental spectrum around the same frequency. A large number of features in the theoretical spectrum appear between 1600 and 2900 cm–1 and arise from the contributions of different combination and overtone bands.
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study
| 100.0 |
The experimental liquid-phase spectrum of CH2DNO2 from ref. 81 is reproduced in Fig. 8 for comparison. A major improvement in comparison to the experimental spectrum is observed when including anharmonic corrections for the splitting of the 31 band with respect to the position of the deuterium atom, around 2195 cm–1 if the CD bond stretches almost parallel to the NO2 plane and around 2295 cm–1 if it stretches almost perpendicular to it, as seen in the experimental spectrum. A weak peak appears in the anharmonic spectrum around 2250 cm–1, corresponding to the 61111 combination band, mainly from the D-eclipsed rotamer. Another weak feature appears around 2310 cm–1, corresponding to the 8191 combination band present in all the four rotamers.
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study
| 100.0 |
The experimental liquid-phase spectrum of CHD2NO2 from ref. 81 is reproduced in Fig. 9 for comparison. The band between 2250 and 2290 cm–1, arising from the 21 mode in the harmonic treatment, is broadened in the anharmonic spectrum, mainly due to the 6191 combination of the four rotamers on the low-frequency side and to the 6181 combination bands on the high-frequency side of the D-eclipsed and H-eclipsed rotamers. Two weak peaks appear around 1920 and 2060 cm–1 due, respectively, to the 82 and 92 overtones, primarily from the D-staggered rotamer. A very weak band also appears around 2530 cm–1, corresponding to the 62 and 72 overtones, mainly from the D-staggered rotamer.
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study
| 100.0 |
We have presented the first analytic calculations of anharmonic corrections to both the vibrational frequencies and intensities in infrared and Raman spectroscopies. This has been made possible by our recent development of a recursive scheme for the calculation of high-order molecular properties, including properties involving frequency-dependent perturbations and perturbation dependence in the basis set.47 The approach is applicable to single-determinant self-consistent field models such as Hartree–Fock theory and Kohn–Sham DFT, and being matrix-based, it can also be extended to linear-scaling approaches,48,62 as well as to the relativistic four-component level of theory.86 We have previously applied our approach to the calculation of anharmonic corrections to vibrational frequencies using density functional theory46 and to the analytic calculation of Raman optical activity87 and hyper-Raman scattering,71 and in this work, we have used it to calculate anharmonic infrared and Raman spectra of nitromethane and its partially deuterated isotopomers. We find that anharmonic effects lead to an improvement in the quality of the computed IR and Raman spectra. The major improvements arising from the anharmonic treatment occur for the vibrational frequencies, while the effects of the anharmonic corrections on the infrared and Raman intensities are smaller and show only minor influences on the relative intensities of the fundamental bands, which is in agreement with earlier observations.38 Nevertheless, the anharmonic corrections are important in order to capture the overtone and combination bands. The anharmonic corrections are found to be somewhat more important for the Raman spectra, even if very small, than for the infrared spectra. Overall, the anharmonic spectra are in better agreement with experiment than the corresponding harmonic spectra.
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| 100.0 |
We have also shown that evaluating the energy and property derivatives by numerical differentiation is prone to numerical instabilities, as also noted elsewhere,51 so that obtaining reliable numerical derivatives can prove difficult for general molecular systems, and we have seen that the errors thus introduced can significantly affect the calculated results, whereas analytic approaches would be free of these sources of error. Because of this, we believe that analytical derivatives of high order is an important step in making the inclusion of anharmonic corrections in calculated infrared and Raman spectra routine, leading to an improved understanding of the importance and occurrence of anharmonic effects in vibrational spectroscopies.
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| 99.94 |
Finally, solvent effects are known to affect vibrational spectroscopies.88 It is therefore important that the scheme presented here is extended to include solvent effects, either in the form of polarizable continuum models or polarizable embedding approaches,89 and work in this direction is in progress.90
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| 99.7 |
Increasing consumption driven by a growing global population and demands for more varied and resource intensive diets has placed unparalleled strain on our agricultural production systems and natural resources. Current agricultural practices rely on fossil fuels, agrochemicals and conversion of new agricultural lands. Yet, yield gains produced through these practices have plateaued in recent years1 and have come at the cost of increasing greenhouse gas emissions, degradation of water quality, widespread pollution, pesticide resistance and unprecedented biodiversity loss. An alternative solution to meet the planet’s growing needs is ecological intensification, increasing production on existing farmlands in ways that causes less harm on the environment through the replacement of anthropogenic inputs with ecosystem services management23. Manipulating and regulating the biotic interactions underpinning the provisioning of ecosystem services by increasing the structural diversity of agroecosystems had been demonstrated to improve crop yields456. In order to implement diversification strategies successfully, it is critical to understand whether agricultural habitats themselves may act as sources of ecosystem services or whether diversification may lead to competition for services among crops. Certain crops may have a disproportionate effect on the flow of ecosystem services due to the large pulse of resources they provide78, and it is essential to understand the effects of these crops on ecosystem service dynamics in order to develop effective management strategies that can be directly implemented by land managers.
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review
| 99.7 |
Crops that are grown on large scales and bloom en masse create large pulses of resources that have substantial impacts on communities of ecosystem service providers. These dynamics are particularly relevant for pollinator dependent crops given the dramatic increase in the area planted to these crops9 and their importance for human nutrition1011. Pulses in floral resources associated with mass blooming of crops are known to alter pollinator abundances and visitation rates in nearby crops and natural habitats12131415, which are likely to have direct impacts on crop yields16. Mass flowering crops can increase pollinator offspring production17 and pollinator densities following mass bloom1819, particularly for solitary, univoltine bees20 for which the bloom of a single crop may represent nearly the entire span of their adult foraging activity. Therefore, mass flowering crops may facilitate pollination of co-blooming crops when pollinators attracted and supported by the mass blooming crop spill over into the co-blooming crop, augmenting floral visitation and crop pollination21 (Fig. 1). Alternatively, when pollinators are limited, as is common in simplified agricultural systems22, plants with high overlap in their pollinator community may compete for visits from shared pollinators23 (Fig. 1).
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| 99.94 |
Little is known about competitive or facilitative interactions between pollinator dependent crops with respect to pollinators and pollinator services; however, we expect that these interactions are ubiquitous in agricultural landscapes. They only require that crops have overlap in their pollinator community though they may bloom in different seasons21 or even in different years20. The likelihood of the interaction resulting in either facilitation or competition depends not only on the degree of overlap in the pollinator community15 but also on the temporal overlap in bloom between crops132124. Indeed, the two studies available on the effects of mass flowering crops on wild plants have found that mass flowering crops can either reduce25 or enhance pollination13 in co-blooming plants in nearby natural habitats.
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| 99.7 |
At the landscape scale, greater abundance and diversity of bees associated with natural and semi-natural habitats22 may buffer against local competition or facilitation effects. For example, in landscapes with high amounts of natural habitat, competition between co-blooming crops may be lower than expected14. In this case, although bees are drawn to the mass blooming crop, the number of bees moving from natural habitats into the co-blooming crop may still be sufficient to provide adequate pollination services7. Alternatively, proximity to natural habitats may reduce facilitation when bees move from mass blooming crops to alternative forage in natural habitats rather than the co-blooming crop.
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| 98.25 |
Despite the potential importance of pulsed resource dynamics for crop pollination and associated yield, we are not aware of any studies that have evaluated the effects of mass flowering crops on the yield of another crop. Greater understanding of spatial and temporal factors that shift the balance between competition and facilitation will allow for management practices that maximize crop yields under the pulsed resource dynamics characteristic of agroecosystems.
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other
| 99.25 |
In this study we investigate the potential for pollinator mediated competition or facilitation in two economically important crops: apple (Malus domestica), a mass flowering crop, and strawberry (Fragaria x ananassa Duch.) in central New York, USA. In this region apple and strawberry have a staggered but overlapping bloom period. The two crops are both members of the family Rosacea, and thus expected to have high overlap in their pollinator faunas2627. Furthermore, the community of bees visiting both apple and strawberry is dominated by early spring, ground-nesting, univoltine bees in the genus Andrena282930. The high potential for community overlap in pollinators between apple and strawberry make these two crops an ideal study system in which to understand the potential for pollinator-mediated interactions among crops.
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study
| 100.0 |
We hypothesized that the impact of apple on strawberry pollination may vary temporally, with facilitation and competition occurring in the same system but at different stages of apple bloom. Additionally, we hypothesized that proximity to natural habitats would moderate these effects and predicted that sites in close proximity to natural habitat would have greater bee abundance and experience both reduced competitive and facilitative effects.
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study
| 99.75 |
Both apple and strawberry are economically important crops in the United States, with total apple production at 327,000 acres and strawberry production at 61,000 acres (USDA NASS, 2013). In New York State, the second largest apple-producing region in the US (USDA NASS, 2013), it is common for farms to grow apples plus a range of other small fruit crops including strawberry.
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other
| 99.9 |
Studies were carried out in the spring of 2013 in the Finger Lakes Region (42°26′N, 76°30′W) of New York, USA. The study area is characterized by a diversity of agricultural uses, including dairy, row crop, tree fruits and vegetables with natural and semi-natural areas of deciduous forest, small woodlots and old field dispersed throughout. A total of 35 farms growing apple, strawberry or both were identified. All farms were used to estimate pollinator community similarity and a subset of 13 farms, all growing strawberry but with a gradient in the proportion of apple orchard cover in the surrounding landscape (0–37%), were used in further experiments. Focal strawberry fields on each of these 13 farms were selected. The landscape surrounding the focal strawberry field was characterized within a 1 km radius using the 2013 National Agricultural Statistics Service Cropland Data Layer for New York31 in ArcGIS 10.1. Using these maps we estimated the proportion of land in agricultural uses (all crop categories including forage and pasture), natural and semi-natural areas (forest, wetlands, shrub lands, meadows, and fallow), and apple orchards. Apple orchards flowered between May 3 and June 5, 2013, with bloom initiation and duration varying across farms depending on local microclimate and apple variety. Most farms cultivate a number of apple varieties to ensure pollination success, as apple is varietally self-incompatible. Measurements occurred between May 6 and May 9 for early apple bloom, between May 14 and May 17 for peak apple bloom and between May 31 and June 3 for late apple bloom. Apple flowering phenology in 2013 would be described as “typical” based on historical data on apple flowering in upstate NY32. In the early stage of apple bloom the percentage flowers open of total flowers present, estimated by counting the number of open flowers per cluster on randomly selected trees, averaged 26.6% (±5.4 SE). During the same period, strawberry bloom had initiated only at four sites (with 16.9% ± 11.5 SE flowers open). At peak apple bloom, flowering intensity averaged 54.8% (±5.8 SE) compared to strawberry bloom at 23.2% (±7.3 SE). Apple bloom intensity during the late flowering stage averaged only 10.9% (±3.5 SE) while strawberry bloom was 37.5% (±6.7 SE).
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study
| 100.0 |
We quantified apple mass flowering using a mass flowering index. The index describes the total amount of apple flowering within the surrounding landscape and is calculated as the percent apple cover in a 1 km radius around the focal strawberry field multiplied by the percent of open apple flowers in adjacent orchards (if present). Thus, the highest values of the mass flowering index indicate high abundance of apple flowers locally and within the landscape.
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study
| 88.56 |
To estimate similarity in the apple and strawberry pollinator communities, bees were collected using sweep netting during four 15-minute surveys along 100 m transects in apple orchards and strawberry fields during the peak bloom of each crop. Surveys were conducted between 10:00 and 15:30 on sunny days with temperature above 16 °C. Bees were identified to species using published revisions333435363738 and online keys (Discoverlife.org) as well as expertly identified reference materials maintained in the Cornell University Insect Collection (http://cuic.entomology.cornell.edu/).
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study
| 99.94 |
In order to understand how mass flowering apple impacts bee visitation to strawberry, we estimated the abundance and diversity of bees visiting strawberries over the course of the apple bloom within each focal strawberry field and adjacent to the nearest natural or semi-natural habitats. Distances between strawberry fields and semi-natural habitats on a farm ranged from 20 to 300 m (mean = 46 ± 9 m). Arrays of four white pan traps were placed at 3 m intervals on transects 2 m from the edge of each focal strawberry field and semi-natural habitat during three sampling periods corresponding to the early, peak and late stages of apple bloom. White pan traps were used as they collect a greater number of bees but maintain a similar community composition to sweep net sampling compared to other trap colors (H. Grab, unpublished data). Sampling periods were approximately one week apart, varying based on local microclimatic conditions, beginning on May 6th and ending June 3rd 2013. The intensity of strawberry and apple bloom was recorded when the arrays were set out and when they were collected. Bloom intensity was estimated as the percentage flowers open of total flowers present including senesced flowers and flowers in bud stage in the orchards or fields. These data were then averaged in order to estimate bloom intensity during each stage. Pan traps were collected after 72 hours and the contents were sorted and identified to species. Sampling rarefaction curves for species richness are available in the Supplementary Information (Figs S1–3).
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study
| 100.0 |
To assess the effects of apple mass flowering at the landscape scale on strawberry pollination and fruit set, we measured the pollination rates of sentinel strawberry plants placed within the focal strawberry field and adjacent to semi-natural habitat at each farm. Use of sentinel plants allowed us to maintain consistent strawberry bloom density during each stage of apple bloom and to control for abiotic factors, including soil and microclimate that could affect yield. During the three periods corresponding to the early, peak and late stages of apple bloom, we placed 10 individually potted strawberry plants (variety Evie 2) in the same transects used for pollinator sampling described above. Strawberry plants have one primary flower, two secondary flowers and up to four tertiary flowers per inflorescence. The number of achenes is greatest on primary fruit and decreases in subsequent flowers. Only primary and secondary fruits were used to estimate yield, as they are the only fruits usually considered marketable. These flowers were exposed to visitors for 72 hours but on half of the plants, flowers received supplementary pollen applied with a paintbrush to the stigmas. These hand-pollinated fruits, when compared to open-pollinated fruits, allowed us to estimate the relative contribution of the pollinator community to yield while controlling for environmental factors such as microclimate, which may have varied slightly across the study region. We collected the sentinel plants after 72 hours and maintained them in a greenhouse chamber while the fruits developed. Fruits were harvested daily when ripe and weighed. In strawberries, fruit weight can provide an accurate estimate of pollination rate, as strawberries are an aggregate accessory fruit comprised of as many as 300 individual achenes39. Each achene must be fertilized in order for the surrounding tissue to develop. Hence, the weight of a fruit is highly correlated with the number of pollinated achenes40 and an average of four pollinator visits per flower is required to achieve full pollination and maximum fruit weight41. Only fruits with a high percentage of fertilized achenes will develop without major malformations that reduce overall yield and marketability.
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study
| 100.0 |
The effect of apple mass flowering on bees was assessed using mixed effects models in the R package “nlme”42 with either the dependent variable of bee abundance (total number of bees collected during a sampling stage at each site) or bee diversity (number of bee species collected during a sampling stage at each site) in separate models. In both models the fixed effects included natural habitat proximity (adjacent or distant from nearest natural area), apple mass flowering index, the percentage of strawberry bloom, apple bloom stage (early, peak, or late), and all possible interactions between the fixed effects. Mass flowering index was log(x + 1) transformed to meet distributional assumptions. Farm was included as a random effect in the model describing bee abundance. In the final model describing bee diversity, natural habitat proximity nested within farm was included as a random effect because proximity was removed as a fixed effect following model simplification.
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study
| 100.0 |
We used linear mixed effects models to assess the relationship between bee abundance and diversity and the average weight of strawberry fruits. Models were fit separately for bee abundance and diversity as fixed effects along with pollination treatment, apple bloom stage and location. Following model simplification the final models retained only the main effects of abundance or diversity. To account for non-independence of samples and the nested experimental design structure, random effects in the final model included the nested effects of stage within pollination treatment within the natural habitat proximity variable within farm.
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study
| 100.0 |
In order to determine the indirect effects of the apple mass flowering index on strawberry fruit weight during each of the apple bloom stages, we used separate mixed effects models with fruit weight as the response variable. The predictor variables included pollination treatment, the mass flowering index, and all possible interactions between the fixed effects. Fruit order (primary or secondary) nested within the natural habitat proximity variable nested within farm was included as a random effect in each model to account for the nested sampling design. In the model describing the effects during peak bloom, weight was log transformed to meet distributional normality assumptions.
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study
| 100.0 |
All models were computed in R v. 3.2.343. Minimum adequate models were selected using backwards-stepwise selection, eliminating predictor variable with p values < 0.1. Once minimum adequate models were identified, the anova function was used to assess significance of each factor by obtaining F and p values. In all models apple mass flowering index values were log10(x + 1) transformed to account for overdispersion due to some farms having very high percentages of apple cover.
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study
| 100.0 |
Using bees collected in sweep-net transects in apple orchards (n = 18 orchards, abundance = 776, species = 51) and strawberry fields (n = 17 fields, abundance = 994, species = 60) during peak bloom of each crop, we compared the overlap in pollinator communities of each crop. We found that apple and strawberry share 31 of the 79 pollinator species collected including the most abundant pollinators of each (Fig. 2). In this region, honey bees, Apis mellifera, are often brought into orchards for apple pollination but not for strawberry. These managed honey bee colonies are moved out of apple orchards following peak apple bloom; therefore, we present honey bee abundance separately from the wild pollinator community. In apple orchards, honey bees comprised 48% of the pollinator community; while in strawberry, honey bees comprised only 1.3% of the bees collected. Because our estimates of community overlap are based on collections from geographically separated locations, they represent a conservative measure of the overlap in apple and strawberry pollinators that is likely to occur within a farm.
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study
| 100.0 |
There was a significant effect of apple mass flowering on the abundance and diversity of bees collected in strawberry fields and adjacent semi-natural habitats that was dependent on the bloom stage (Table 1 and Fig. 3). When further exploring the interaction between stage and the mass flowering index (Table 1) we found that abundance and diversity of bees collected near the sentinel plants were negatively affected by mass flowering during both early and peak apple bloom and positively affected by mass flowering during late apple bloom (Fig. 3, Table S1). Bee community composition was marginally effected by the stage of apple bloom (Figure S4). As expected, bee abundance was marginally higher adjacent to semi-natural areas (mean = 16.14, SE = 2.47) compared to strawberry fields with no adjacent semi-natural habitats (mean = 9.01, SE = 2.21 Table 1). However, natural habitat proximity did not interact with either stage or the mass flowering index suggesting that the proximity to natural habitat did not alter the impact of mass flowering on the pollinator community. Although species richness was not different between strawberry fields and natural habitats, the composition of bee communities differed between locations (Figure S5). The local intensity of strawberry bloom did not impact bee abundance or diversity at any stage, and was therefore removed from all models.
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study
| 100.0 |
The average weight of strawberry fruits from sentinel plants increased with both greater bee abundance (F1,13 = 5.72 p = 0.03) and diversity (F1,13 = 24.22 p = <0.001) (Fig. 4). Although pollinator abundances were greater near to natural habitats, fruit yield did not vary with natural habitat proximity. Similar to the effects observed on the pollinator community, we found the effects of apple mass flowering on strawberry fruit weight differed with the stage of apple bloom (Table 2). During both early and peak apple bloom, an interaction between pollination treatment and mass flowering impacted strawberry fruit weight (Table 2). In accordance with the competition hypothesis, mass flowering of apple decreased the weight of open pollinated strawberry fruits but not hand pollinated fruits (Fig. 5, Table S2). Conversely, during late apple bloom the mass flowering index was positively associated with fruit weight (Fig. 5, Table S2) suggesting facilitation during this stage.
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study
| 100.0 |
Resource pulses are a common feature of agricultural systems; however, the impact of mass flowering crops on the pollination and yield of co-blooming crops is currently unknown. Here we examined the spatial and temporal effects of a mass flowering crop on bee communities and subsequently on yield in a co-blooming crop species. We predicted that changes in pollinator abundance over the course of mass flowering would lead to either competition or facilitation at different stages, and indeed we found that apple mass flowering first decreased strawberry pollination and then increased strawberry pollination with corresponding effects on yield.
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study
| 100.0 |
The mass flowering of apple negatively affected bee abundance and diversity in co-blooming strawberry during the early and peak stage of apple bloom. However, during the late bloom stage, increasing apple mass flowering was associated with greater bee abundance and diversity in strawberry. These results indicate that bees are responding to local changes in resource availability resulting in a dilution of bees when floral resources are plentiful during early and peak apple bloom followed by a spillover of bees from apple orchards to nearby strawberry fields as apple flowering decreases. In natural systems, similar effects have been observed in mixtures of flowering Cirsium and Raphanus plants where the balance between pollinator mediated competition and facilitation was dependent on the relative densities of Cirsium flowers44. These patterns may be explained by changes in the foraging preferences of the pollinator community, but population level responses to floral resources pulses may support overall greater abundances of pollinators in landscapes with high cover of mass blooming crops181921. Our findings indicate that both density and timing of flowering are important predictors of the outcome of these interactions.
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study
| 100.0 |
We predicted that both abundance and diversity of bees would be greater at sites adjacent to natural habitats. Although bee abundance was greater at sites adjacent to natural habitats, bee species richness did not differ between sampling locations. This result is likely due to a greater density of nesting sites in less disturbed natural areas for the ground-nesting bees that dominated the pollinator community45. While the distance between strawberry fields and semi-natural habitats within a farm was not greater than the flight distance of the average strawberry pollinator46, it is possible that fewer individuals traveled that distance. Despite overall greater pollinator abundances in sites adjacent to natural habitats, lack of a significant interaction between the natural habitat proximity variable and mass flowering indicated that proximity to natural habitat did not alter the impact of mass flowering on the pollinator community. Furthermore, the influence of mass flowering apple on the abundance and diversity of bees was greater than the influence of proximity to natural habitats. Similar results were reported by Westphal et al.18, who found that bumble bee densities were positively related to the availability of oilseed rape and not natural habitats within the landscape. Our findings reveal that these effects extend to a much broader pollinator community. These findings also suggest that the effects of agricultural habitats on pollinator communities has thus far been underestimated and likely represents a common phenomenon among crops with overlapping pollinator communities.
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study
| 100.0 |
Mass flowering of apple at the landscape scale was negatively associated with the weight of open pollinated strawberry fruits during early and peak apple bloom and positively associated with fruit weight during late apple bloom. We hypothesize that these results are due to the parallel changes observed in the abundance and diversity of pollinators, as both measures were highly correlated with the weight of open pollinated strawberry fruit; however, the decrease in fruit weight associated with early and peak apple bloom may also be due in part to increased rates of heterospecific pollen transfer47 from apple to strawberry. In the late sampling period, the positive response of hand-pollinated fruit to the mass flowering index may have been caused by incomplete effectiveness of the hand pollination treatment due to the greater storage time of the supplemental pollen at this stage.
|
study
| 100.0 |
The competitive interactions observed between apple and strawberry likely represent a conservative estimate of the potential magnitude of indirect interactions mediated by shared pollinators. In this case, competitive effects are moderated by the relatively diverse pollinator community of strawberry48 and the ability of strawberry to self-pollinate41. Therefore, the negative effects of mass flowering may be stronger in crops that are more pollinator dependent or share a greater proportion of their pollinator community with a mass flowering crop.
|
study
| 99.94 |
In natural systems, pollinator-mediated facilitation in plant communities is thought to occur through several mechanisms. First, coexisting plants may attract greater numbers of shared pollinators by providing aggregate floral displays greater than a single species alone44. Facilitation may also occur when species with staggered blooming periods support pollinator populations by reducing spatial and temporal variation in floral resource availability49. In this case, the consecutive bloom of plant species increases the duration of floral resource availability within years or the reliability of floral resources across years50. These same dynamics may be particularly important for pollinator communities in agricultural systems where crop rotation or extreme weather events can lead to high variability in floral resource abundance among seasons and years. If the greater abundance, diversity and duration of floral resources can be achieved through complementarity of flowering crops, later blooming crops such as strawberry may even support the pollination services of earlier mass flowering crops in the following year51.
|
study
| 99.94 |
In agricultural systems, our findings reveal that crop habitats can act as a source of ecosystem services to other crops and represent an area of underexploited potential for ecological intensification practices. Studies of spillover of pollinators between mass flowering crops have also reported that prevalence of early mass flowering crops in the landscape can mitigate pollinator dilution in another mass flowering crops blooming in a later season21. Our results advance these findings by demonstrating that changes in the abundance of pollinators mediated by the bloom of mass flowering crops has consequences for the yield of nearby pollinator dependent crops. Importantly, our results highlight the importance of timing in determining the outcome of interactions among pollinator dependent crops and suggest ecological intensification strategies that may be employed to reduce competition and enhance facilitation among crops that have a significant number of shared pollinators. By selecting crops and varieties that bloom sequentially with shared pollinator communities, growers can minimize competition while maximizing facilitative effects, thereby improving the sustainability of crop pollination. However, when agronomic or other factors constrain variety selection, management strategies may focus on locating co-blooming crops at distances greater than the average foraging range of their shared pollinator community.
|
study
| 99.94 |
Our results clearly indicate that the timing of flowering in co-occurring crops can have consequences for the yield of pollinator dependent plants. When one crop co-blooms with another, mass flowering crop, competition for pollinators is likely to reduce yield, while flowering after the flowering event facilitates pollination leading to higher yields. We show that the temporal resource pulses associated with mass flowering crops are an important driver of pollinator community dynamics and pollination services at local and landscape scales. Greater understanding of these effects will allow for improvements in designing agroecosystems in order to maximize the provisioning of ecosystem services and promote crop yields through ecological intensification.
|
study
| 99.94 |
According to the World Health Organization (WHO), tuberculosis (TB) is the infectious disease responsible for the highest number of deaths worldwide, surpassing even the number of deaths caused by the human immunodeficiency virus (HIV). The last surveys conducted by WHO pointed out 9.6 million new cases of the disease and 2 million deaths in 2015 . In addition, the emergence and increase of multidrug-resistant (MDR; defined as resistant as a minimum to rifampicin (RMP) and isoniazid (INH)) and extensively drug-resistant (XDR; defined as MDR plus additional resistance to at least one fluoroquinolone and one second-line injectable drug) strains of Mycobacterium tuberculosis (Mtb) have been alarming authorities around the world. These tuberculosis strains presents low cure rates and high mortality rates due to difficulties in the treatment . Furthermore, cases of totally drug-resistant tuberculosis (TDR-TB) have been reported in the clinic .
|
review
| 99.9 |
Over the last few years, progress has been made in the search for new anti-TB compounds . The current drug pipeline shows ten drug candidates under preclinical and early phase 1 development for drug-sensitive and/or drug-resistant tuberculosis. Regarding MDR-TB, the drug pipeline presents six compounds in phase 2 and 3 trials. Bedaquiline (Sirturo®, Janssen Therapeutics, Titusville, NJ, USA) and delamanid (Deltyba®, Otsuka Pharmaceutical, Tokyo, Japan) remain in trial phase 3; despite their approval in several countries justified by the emergency caused by MDR-TB. Sutezolid and pretomanid are, in phase 2 and 3 trials, respectively. The repurposed drugs clofazimine and levofloxacin are in phase 3 and 2 trials, respectively .
|
review
| 99.75 |
Despite the recent advances, strains resistant to these new molecules have already been reported reinforcing the urgent need to develop novel drugs for tuberculosis treatment. Indeed, the research of new drugs against TB plays a crucial role in reducing the incidence and mortality necessary to achieve global worldwide goals established by the WHO .
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other
| 62.75 |
Therefore, this review article aims to create new perspectives to design and develop new anti-TB drugs against multi-drug resistant strains. We will focus on the challenges and advances in antitubercular drug discovery involving MDR-TB. In order to describe those most promising compounds, we included here only active compounds against MDR-TB with minimum inhibitory concentrations (MICs) inferior to 11 µM and low toxicity published in the last 4 years in the following databases: PubMed, Web of Science and Scopus. All MIC values against MDR-TB strains presented herein were converted to µM in order to establish a comparison among the compounds.
|
review
| 99.9 |
Roh and coworkers reported a series of 3,5-dinitrobenzylsulfanyl-1,3,4-oxadiazoles and thiadiazoles derivatives with potent activity against replicating and nonreplicating Mycobacterium tuberculosis. Compounds (1) and (2) (Figure 1) were the most promising in this series and presented MIC90 values against several MDR strains below 0.25 μM. Moreover, these compounds have been shown to be active against dormant mycobacteria using a luciferase assay. In vitro cytotoxicity studies against mammalian cell lines and isolated human hepatocytes showed low toxicity with inhibitory concentration (IC50) values above 20 μM. Both compounds also did not exhibit mutagenic activity and activity against several bacteria and fungi. Furthermore, studies were performed which attempted to characterize the possible target of the compounds. In vitro studies suggested that compounds (1) and (2) could act inhibiting the synthesis of nucleic acids . The same research group has reported a new series of 3,5-dinitrophenyl 1,3,4-oxadiazole-2-thiols and tetrazole-5-thiols as promising antitubercular agents. They have discovered compounds (3) and (4) (Figure 1) as highly potent and selective derivatives against seven MDR and XDR strains with MIC90 values below 0.5 μM. In addition, these compounds exhibited low cytotoxicity against human hepatocellular carcinoma (HuH7), human epidermoid carcinoma (A431), Madin-Darby canine kidney cells (MDCK), human hepatocellular carcinoma (HepG2) cell lines, with IC50 above 30 μM .
|
review
| 95.9 |
Oxazolidinone is an important class of antibiotic used for treatment of infections caused by Gram-positive pathogens, being the drug linezolid the main representative of this class . This scaffold acts through the inhibition of protein synthesis by binding to the 50S ribosomal subunit and blocking the binding of transfer RNA (tRNA) . Researchers from AstraZeneca® (AstraZeneca R&D, Bangalore, India) have identified an oxazolidinone derivative, namely AZD5847 (5) (Figure 2), with outstanding antitubercular activity against a panel of several clinical isolates of Mtb with different resistance profiles, including single drug-resistant strains. AZD5847 showed improved extracellular and intracellular activity compared to linezolid, exhibiting MIC90 values in a range of 0.13 and 1 μM in the tested strains and a reduction of 1-log-unit in macrophage intracellular bacilli. Furthermore, the authors also demonstrated that this compound (5) also acts through the inhibition of protein synthesis . AZD5847 was clinically tested as an antimycobacterial drug in a phase 2; however, several adverse effects were observed, including serious hepatic and haematological toxicities . Wei and coworkers also reported a series of bis-oxazolidinone derivatives with antitubercular activity. Compound (6) (Figure 2) exhibited MIC90 values at values ranging from 2 to 8 μM against several clinical MDR and XDR-TB strains. In addition, the authors demonstrated the low cytotoxicity of this compound against monkey fibroblast-like kidney cell (VERO) with IC50 above 5000 μM and high selectivity against mycobacteria .
|
study
| 56.53 |
The antitubercular activities of several nitrogen heterocyclic compounds have been extensively published in the scientific literature. For instance, a series of 1H-benzo[d]imidazole derivatives have been reported to possess promising activity against a clinically isolated strain resistant to p-aminosalicylic acid (PAS), INH, ethambutol (ETB) and RMP. Compound (7) (Figure 3) showed a MIC90 value of 0.75 μM against this wild strain and low cytotoxicity against human non-small lung cancer (A549) and pig kidney epithelial cell line (LLC-PK1) cell lines, with IC50 values of 11.15 and 43.94 μM, respectively . Later, the same authors published a novel series of 1H-benzo[d]imidazoles derivatives. Nevertheless, this new series exhibited worse activity than compound (7). The best compound (8) (Figure 3) showed an MIC90 value of 5 μM in the same MDR strain and IC50 values of 58 and 7.8 μM against neonatal human dermal fibroblasts (HDFn) and human epidermal keratinocyte progenitors (HEK) cell lines, respectively .
|
study
| 81.1 |
Charushin and coworkers have synthesized a series of fifteen pyrimidine derivatives and evaluated their antituberculosis activity against a clinical isolated MDR-TB strain resistant to RMP and INH. Compound (9) (Figure 3) has shown the most promising activity with MIC90 of 0.7 μM. Mice acute toxicity revealed a median lethal dose (LD50) of 315 mg/kg for this molecule . Additional studies performed by this same research group have described other pyrimidine derivatives with similar antituberculosis activity. The most promising compound (10) (Figure 3) exhibited an MIC90 value of 1.95 μM against a clinically isolated MDR-TB strain and LD50 of 600 mg/kg in acute toxicity using mice . Quinolizidine-related compounds have also been reported with antituberculosis activity in a study involving fifteen derivatives. The series was evaluated against several MDR-TB strains. Compound (11) (Figure 3) was the most active in the series with MIC90 of 0.86 μM. In addition, this compound exhibited low cytotoxicity against VERO cells with IC50 of 68 μM. .
|
study
| 99.8 |
Several nitrogen-containing fused heterocycles play an important role in the anti-TB Medicinal Chemistry. Shirude and coworkers from AstraZeneca® (AstraZeneca R&D, Bangalore, India) have reported a promising 1,4-azaindole derivative identified after an optimization process . Compound (12) (Figure 4) was characterized as a potent derivative against MDR-TB, with MIC90 values ranging from 0.78 to 1.56 μM with low cytotoxicity against human leukemia monocytic (THP-1) cells (IC50 > 100 μM). In vivo studies were performed with compound (12) in order to determine its efficacy and pharmacokinetics profile. In rats, this molecule was able to reduce the bacterial burden on a logarithmic scale of 1 log10 colony forming units (CFUs)/lung at 300mg kg−1 of body weight, and statistically significant dose-dependentefficacy was observed. On the other hand, pharmacokinetic analysis revealed low clearance rates, excellent bioavailability and no interference with any of the cytochrome P450 (CYP450) isoenzymes. Nevertheless, this compound presented a rapid metabolism in the presence of mouse liver microsomes . Unsuccessful attempts to optimize this compound have identified compound (13) as active against INH-resistant strains; however, with MIC90 value of 14.3 μM . Danac and Mangalagiu have reported the synthesis and antituberculosis activity of a series of fused bipyridine heterocycles. Compound (14) (Figure 4) presented promising activity against several single resistant Mtb strains, with MIC90 values ranging from 3.3–9.2 μM .
|
study
| 99.6 |
Raichurkar and coworkers also from AstraZeneca® (AstraZeneca R&D, Bangalore, India) have reported the discovery of pyrazolopyridones derivatives as promising antitubercular compounds . Initially, they investigated the antituberculosis activity of these compounds against a panel of sensitive and clinical isolated single drug-resistant strains. Compound (15) (Figure 5) presented MIC90 values ranging from 1.6–3.1 μM and low cytotoxicity against the human A549 cell line (IC50 160 μM). The authors also demonstrated through biochemical screening and genetic mapping that the target of compound (15) is decaprenylphosphoryl-β-D-ribose-2′-epimerase (DprE1), an enzyme that plays an important role in the biosynthesis of components of the mycobacterial cell wall . In vitro drug metabolism and pharmacokinetics properties were performed for this compound, that exhibits distribution coefficient (logD) of 3.9 and suboptimal aqueous solubility (1 μM), free plasma protein binding (1%), and clearance (27 μL/min/kg) . In another work, the synthesis and antituberculosis activity of pyrazolo[1,5-a]pyridine-3-carboxamide derivatives were reported. Specifically, compound (16) (Figure 5) has shown potent in vitro potency at nanomolar concentration, for which MIC90 values ranged from 11.1 to 223 nM against several clinically isolated MDR-TB strains. In addition, they evaluated the in vivo efficacy of compound (16) in a mouse model infected with the selectable marker-free autoluminescent Mtb H37Ra, a non-virulent strain. They observed a bactericidal activity of this compound, resulting in a reduction of bacterial burden using a modified real-time monitoring noninvasive bioluminescence assay .
|
study
| 62.0 |
Xuefu You and coworkers have identified a potent imidazo[1,2-a]pyridine derivative against two clinically isolated MDR strains resistant to INH and RMP. Compound (17) (Figure 6) has exhibited MIC90 values ranging from 0.09 to 0.13 μM and low in vivo acute toxicity in mice and rats. Furthermore, this compound exhibited acceptable pharmacokinetic properties, with maximum serum concentration (Cmax) of 225 ng/mL, elimination half-life (T1/2) of 1.5 h and clearance of 86,284 mL/h/kg . Castagnolo and coworkers have reported a series of pyrrole derivatives designed as hybrids of the antitubercular drug candidates BM212 and SQ109. They obtained in the first generation a hybrid compound with MIC90 value of 17.8 μM against two MDR clinical isolates. After, using molecular simplification, the authors have discovered the second-generation of this hybrid derivative (compound 18) (Figure 6) as a potent antitubercular agent with MIC90 value of 1.58 μM. Furthermore, this compound was able to inhibit the mycobacteria drug efflux pump at potency comparable to that of verapamil .
|
study
| 99.94 |
Quinoline and derivatives represent an important class of heterocyclic in the medicinal chemistry field because its wide range of biological activities, including antituberculosis . Machado and coworkers have reported a series of quinoline derivatives with inhibitory activity against a clinical isolate of an MDR-TB strain. Compound (19) (Figure 7) showed a potent MIC90 value of 0.05 μM and activity against macrophage intracellular mycobacteria. Moreover, the authors also performed metabolic stability and drug–drug interaction studies. Compound (19) exhibited moderate metabolic stability in the human S9 fraction, with an in vitro intrinsic clearance (Clint) of 14.3 mL/min/kg and T1/2 of 21.8 min. In addition, this derivative did not alter the enzymatic levels in the liver, suggesting a minimal risk of metabolic drug−drug interactions . Later, the same group has reported a novel series of quinoline derivatives with improved antituberculosis activity. Compound (20) (Figure 7) exhibited a potent MIC90 value of 1 nM against a clinical isolate of an MDR-TB strain with a Clint of 14.8 mL/min/kg and T1/2 of 19.4 min .
|
review
| 89.4 |
Ghorpade and coworkers from AstraZeneca® (AstraZeneca R&D, Bangalore, India) have discovered a quinolone derivative as a promising antituberculosis agent. The authors have assessed several properties of the lead compound (21) (Figure 8), including mechanism of action studies, in vitro/in vivo pharmacokinetics and drug metabolism. This quinoline derivative presented MIC90 values ranging from 0.2 to 3.12 μM against several single drug-resistant strains. The authors showed that the target of compound (21) is the mycobacterial DprE1 enzyme. In addition, in vivo pharmacokinetics studies pointed out compound (21) with Cmax of 4.9 μM, plasma clearance of 34.4 mL/min/kg and T1/2 of 0.5 h . A series of quinazolinone derivatives have been reported, showing potent antitubercular activity . Compound (22) (Figure 8) exhibited MIC90 of 6.6 μM against several MDR and XDR-TB clinical isolates. In addition, the authors suggested that the Mtb acetohydroxy-acid synthase (AHAS) is the target of these quinazolinone derivatives . AHAS is an enzyme that plays an important role in the branched-chain amino acids (BCAAs) biosynthetic pathway and its inhibition seems to be a potential target for anti-TB drugs .
|
review
| 99.0 |
Compounds that acts through the release of reactive oxygen and nitrogen species, such as furoxan and nitro compounds, have been extensively explored as antituberculosis agents . Brönstrup and coworkers have reported a series of nitrofuran derivatives with selective activity against Mtb. Specifically, compound (23) (Figure 9) exhibited MIC90 of 11 μM against two MDR-TB clinical isolates. The authors also evaluated the spectrum of activity for compound (23) and they did not find activity against a panel of Gram-positive and Gram-negative bacteria . The nitroimidazole class is another important scaffold in the medical chemistry of antituberculosis agents, especially its main representative, the drug delamanid (Deltyba®, Otsuka Pharmaceutical) . A series of nitroimidazole derivatives have been reported as presenting an outstanding antituberculosis activity against an MDR-TB clinical isolate. For instance, the most promising compound (24) (Figure 9) presented a MIC90 of 0.11 μM. The in vivo pharmacokinetics showed a good profile, with Cmax of 0.54 μg/mL, T1/2 of 2 h and no CYP inhibition at three different concentrations tested (10, 30 and 100 μM). In vivo efficacy of compound (24) was assessed using a mice model for acute infection. Using an infected mice model, this compound was able to reduce the bacterial burden on a logarithmic scale of 1.8 log10 CFU at 100 mg kg−1 once daily for 28 days. . Furoxan derivatives also have been reported showing its promising application as antitubercular compounds. Specifically, compound (25) (Figure 9) exhibited MIC90 of 7 μM against MDR-TB clinical isolates. Furthermore, the authors have demonstrated that this compound may act through the release of nitric oxide . Smith and coworkers have discovered a nitrotriazole derivative as a promising antitubercular agent. Compound (26) (Figure 9) showed MIC90 values below 3.9 μM against several single drug-resistant strains. In addition, compound (26) exhibited intracellular activity against infected J774 macrophages, resulting in a reduction of 1.18 log of intracellular bacilli burden .
|
review
| 99.7 |
Chibale and coworkers have identified the compound pyrrolo[3,4-c]pyridine-1,3(2H)-dione (27) (Figure 10) through a phenotypic screening with potent antituberculosis activity; however, this compound presented drawbacks regarding its metabolic stability. The optimization of this molecule leads to compound (28) (Figure 10), which demonstrated MIC90 values below 0.6 μM against several clinical isolates and good metabolic stability in liver microsomes. The mycobacterial respiratory cytochrome bc1 complex was identified as the target for these compounds. Nevertheless, mouse pharmacokinetics studies showed high clearance and low plasma exposure for compound (28) . In another study, a series of twenty-seven benzo[d]oxazol-2(3H)-one derivatives were synthesized. Specifically, compound (29) (Figure 10) exhibited a promising antituberculosis activity against an XDR-TB clinical isolate, with MIC90 of 11.47 μM. The authors also demonstrated that compound (29) acts through the inhibition of the mycobacterial 2-trans-enoyl-acyl carrier protein reductase (InhA), a key enzyme involved in the mycolic acid biosynthesis in Mtb . Shuyi Si and coworkers have discovered several disubstituted oxazole analogues as potent antituberculosis agents. Among the twenty-five compounds evaluated, compound (30) (Figure 10) showed promising activity with MIC90 values of 2.2 and 4.3 μM against XDR-TB and MDR-TB, respectively. Moreover, compound (30) proved to be selective for Mtb because no activity against other bacteria was observed .
|
study
| 98.56 |
Sulfur-containing heterocycles have been widely exploited as antituberculosis agents . Researches from AstraZeneca® (AstraZeneca R&D, Bangalore, India) have discovered a diarylthiazole derivative after molecular optimizations in a previously identified hit. Compound (31) (Figure 11) showed potent antituberculosis activity with MIC90 values below 1.68 μM against several MDR-TB clinical isolates. In vitro drug metabolism and pharmacokinetics parameters were assessed for compound (31), which exhibited solubility of 31 μM, mouse plasma protein binding of 17% and mouse clearance of 170.4 μL/min/mg. Moreover, the authors have characterized the PrrBA as the molecular target of this derivative . PrrBA is a two-component system composed of the PrrB histidine kinase and PrrA response regulator and it plays an important role in mycobacterial virulence and metabolic adaptation to stress . In another work, Luoting Yu and coworkers reported a benzothiazinethione derivative as a potent antitubercular agent . Compound (32) (Figure 11), an analog of the drug candidate BTZ043 , presented MIC90 values below 0.03 μM against several MDR and XDR-TB clinical isolates. The pharmacokinetics in rats of this compound showed Cmax of 193 ng/mL, T1/2 of 1.45 h and 44.4% of absolute oral bioavailability. Furthermore, compound (32) demonstrated in vivo efficacy in a mice model, which was able to reduce the Mtb burden in lungs by 3.4 logs CFU . Thiazole and its analogue benzothiazole are also important sulfur-containing heterocycles with antituberculosis activity. For instance, the synthesis of a series of thirty-four thiazole derivatives have been reported and their antitubercular activity was assessed against several single drug-resistant strains. Compound (33) (Figure 11) showed MIC90 values ranging from 7.1 and 12.0 μM . Ramachandran and coworkers at AstraZeneca® (AstraZeneca R&D, Bangalore, India) also reported benzothiazoles derivatives as antitubercular. They discovered compound (34) (Figure 11) as a promising antituberculosis agent with MIC90 values below 4.62 μM against several single drug-resistant isolates. DprE1 was characterized as the target of compound (34). In addition, this compound demonstrated safety profile with low cytotoxicity against human A549 cell line (IC50 > 100 μM), negative Ames assay and moderate CYP isoform inhibition .
|
review
| 99.8 |
Mahajan and Dhawale reported the synthesis of a series of thiadiazoles derivatives as promising candidates for resistant tuberculosis treatment. Among the thirty-three compounds synthesized, compound (35) (Figure 12) showed the best antimycobacterial activity with MIC90 values ranging from 0.08 to 0.66 μM against several MDR and XDR-TB clinical isolates . Thienyl-substituted pyrimidines derivatives also have been reported with potent activity against an MDR-TB strain. Specifically, compound (36) (Figure 12) demonstrated MIC90 of 0.4 μM and mouse LD50 of 45 mg/kg . In another study, Kozikowski and coworkers synthesized a series of triclosan derivatives with the mycobacterial InhA enzyme characterized as the molecular target. Compound (37) (Figure 12) exhibited MIC90 of 0.7 μM against two MDR-TB strains . Later, the same research group identified an indole-2-carboxamide derivative designed from a structure-activity relationship analysis of previously obtained compounds. Compound (38) (Figure 12) showed outstanding antituberculosis activity against MDR and XDR-TB strains. The MIC90 values for these strains ranged from 0.006 to 0.047 μM. Pharmacokinetics results showed a Cmax of 1.71 μg/mL, Tmax of 4 h, low inhibition in the tested CYP isoforms (<40%) and negative results in the bacterial reverse mutation assay in Salmonella typhimurium tester strains. Moreover, the in vivo efficacy of this compound was assessed in a mouse infection model and it was able to reduce the bacterial burden on a logarithmic scale of 2.12 log10 CFU at 100 mg kg−1 dosage level in the lungs after 4 weeks of treatment protecting the mice from death. Altogether, these results pointed out compound (38) as a promising drug candidate for human clinical trials .
|
study
| 99.25 |
Indeed, the scientific literature presents several works involving only the synthesis and phenotypic screening of compounds against MDR strains accompanied by in silico studies. Among these compounds, several heterocycles and scaffolds are contemplated, including benzo[d]isoxazole (39) , benzo[b]thiophenes (40) , disubstituted piperazine (41) , and benzoxazole (42) (Figure 13).
|
review
| 99.1 |
For instance, compound (39) exhibited MIC90 of 6.16 μM against an MDR-TB isolate and low cytotoxicity against mouse macrophage (RAW264.7) cell lines with IC50 of 222.92 μM. In addition, the authors performed docking studies on the mycobacterial pantothenate synthetase enzyme and compound (39) showed a good interaction in the enzyme active site with docking score of −9.2 kcal/mol . This enzyme is involved in the biosynthesis of coenzyme A and acyl carrier protein . The benzo[b]thiophene (40) also exhibited potent antituberculosis activity against a multidrug-resistant strain with MIC90 of 8.3 μM. Docking studies on the DprE1 enzyme were performed and compound (40) showed a docking score of −8.7 kcal/mol, suggesting that this enzyme could be the potential molecular target . Likewise, compound (41) showed a promising antitubercular activity against an MDR-TB strain with MIC90 of 2.4 μM. In vitro microsome stability study exhibited a T1/2 of 14.4 h and low inhibition of two isoforms of cytochrome P450, namely CYP3A4 and CYP2D6. Moreover, the authors suggested that compound (41) might act through inhibition of mycobacterial DNA-dependent RNA polymerase . The benzoxazole derivative (42) also showed to be a promising antituberculosis agent. The MIC90 evaluated for this compound was 3.2 μM against XDR-TB strains and it demonstrated in vivo activity similar to that of RMP in a mouse model infected with the selectable marker-free autoluminescent Mtb strain H37Ra .
|
study
| 89.9 |
The drug discovery process is highly complex and involves several steps. Among these steps, the determination of the physicochemical properties of potentially active compounds plays an important role in the initial stages . Indeed, some authors suggest that bioactive compounds with adequate physicochemical properties should be prioritized rather than highly active compounds with inadequate physicochemical properties . Currently, several computational programs predict these properties based on databases of compounds and mathematical formulas . Therefore, we subjected the most active compounds described in this review with MIC90 values below 0.1 μM to an analysis of the Lipinski’s rule, which indicates whether a molecule could be an orally active drug in humans . We calculated theoretical partition coefficient (cLogP) values, molecular weight and number of hydrogen bond donors and acceptors using the software OSIRIS DataWarrior (Table 1). The data showed that the majority of the compounds presented adequate properties according to the Lipinski’s rule. In addition, the software also predicted the drug-likeness of these compounds. Briefly, this drug property indicates whether a compound contains fragments that are frequently present in commercial drugs. The most active compounds selected presented values of drug-likeness in a range of −14.43 to 7.03. The majority of marketed drugs show values between −5 and 5 .
|
review
| 99.9 |
During drug development, lipophilicity is the most important physicochemical property that might be analyzed for tuberculosis drug discovery because this property can affect the solubility, permeability and bioavailability of compounds . Furthermore, lipophilicity is recognized to impact on a number of drug-like characteristics including pharmacokinetics and toxicology properties . For instance, compounds with high lipophilicity have been related to hepatotoxicity and undesirable non-specific interactions . Nevertheless, highly lipophilic compounds should not be discarded in screening programs for antituberculosis drugs. One example is the drug bedaquiline, which has a cLogP value of 7.3. Likewise, low lipophilicity is not an impediment to tuberculosis drug discovery, considering the number of approved drugs with low lipophilicity, including isoniazid (cLogP = −0.67), ethambutol (cLogP = 0.12), pyrazinamide (cLogP = −0.68), kanamycin (cLogP = −5.2) and cycloserine (cLogP = −1.2). Therefore, we have evaluated the relationship between MIC values and cLogP (Figure 14). The data showed that the majority of active compounds described in this review presented cLogP values in a range from 2 to 6.
|
review
| 99.9 |
Phenotypic screening seems to be a more promising approach to identify compounds active against MDR-TB than the target-based approach. Despite this, the search for new compounds active against resistant-TB remains a challenge. The molecular mechanism involved in the resistance and its possible targets is still not completely understood. However, even in this complicated scenario, in recent years, active compounds against resistant strains have been found at nanomolar concentrations. In addition, in vivo studies have shown that some of these compounds exhibited adequate pharmacokinetics for investigation in future studies. Additional efforts must be made in order to create strong networks worldwide to discover new drugs against this terrible disease.
|
review
| 99.7 |
Protozoa (kingdom Protista) are single-cell organisms that can be free-living or parasitic in nature (Baron, 1996). Out of more than 50 000 protozoan species that have been described to-date, relatively few have been identified as major contributors to the global burden of human diseases (Kuris, 2012) and animal agriculture (Dubey, 1977). The protozoa represent 19% of all human parasites (83 out of 437 species to-date) and are associated with 30% of parasite-induced human morbidity-mortality (Kuris, 2012).
|
review
| 99.75 |
Of the four groups of infectious protozoa (CDC, 2017), the Mastigophora (flagellates) and Sporozoa contain the Kinetoplastidae and Apicomplexa, respectively. It is to these two phyla that belong many of the causative agents of disease: Mastigophora – the insect vector-borne kinetoplastids Trypanosoma brucei (Human African Trypanosomiasis, HAT), Leishmania spp. (leishmaniasis, cutaneous and visceral) and Trypanosoma cruzi (American trypanosomiasis, Chagas’ disease); Sporozoa – the apicomplexan Toxoplasma gondii (toxoplasmosis), Cryptosporidium spp. (cryptosporidiosis) and Eimeria spp. (coccidiosis in poultry and cattle), Theileria spp. (East Coast Fever in cattle) and Plasmodium spp., including Plasmodium falciparum the causative agent of severe malaria and one of the ‘Big Three’ global infectious diseases alongside HIV and tuberculosis (Torgerson & Macpherson, 2011).
|
review
| 99.8 |
Historically, the diseases caused by some of these parasites have been classified as Neglected Tropical Diseases (NTDs) or Neglected Zoonotic Diseases (King, 2011) and were associated with the classical model of the ‘poverty trap’ covering tropical and sub-tropical regions in Africa, Latin America and the Indian subcontinent (Kuris, 2012). However, with global changes in climate and human demographics and associated practices, the classical models do not promise safe boundaries that might contain and/or stop the further global spread of many of these parasitic diseases (Colwell et al. 2011). The problems associated with these pathogens are further aggravated by the lack of effective vaccines (Dumonteil, 2007; Innes et al. 2011; McAllister, 2014; Black & Mansfield, 2016) and the paucity of reliable drugs (Zofou et al. 2014), in addition to the difficulties of vector or reservoir control (Colwell et al. 2011). Therefore, there is a recognized need to find new therapeutic targets in these causative agents in order to develop effective treatment regimens to avoid potentially catastrophic outbreaks, both in terms of human health and economic impact.
|
review
| 99.9 |
In general, available treatments for the diseases caused by the Kinetoplastidae and Apicomplexa are outdated (if not historic), with relatively few examples that were introduced recently, toxic and require a long treatment regimen, and therefore close monitoring of patients.
|
other
| 99.9 |
The treatment of leishmaniasis often requires a long course of intravenous pentavalent antimony drugs (e.g. Glucantime and Pentostam), aminosidine (paromomycin) or liposomal amphotericin B (Croft & Coombs, 2003; Center for Food Security and Public Health, 2004; WHO, 2004; Kedzierski et al. 2009). The most recent addition was the orally available miltefosine (Sunder et al. 2002; Verma & Dey, 2004), originally developed as anti-neoplastic agent. Despite its teratogenic effects (Sunder et al. 2002), due to the lack of other effective medications, it has been registered and is now used in India, Colombia, Guatemala and Germany (Soto & Berman, 2006). Other regimens of treatment include Pentamidine (Bray et al. 2003), allopurinol, dapsone, fluconazole, itraconazole and ketoconazole. However, to-date all available chemotherapeutic agents suffer from being toxic (Chappuis et al. 2007) or inaccessible, both geographically and financially, in endemic areas where public health is under-resourced, poor and underdeveloped. Additionally, the lack of effective vaccines (de Oliveira et al. 2009) and the alarming emergence of resistance to these drugs (Croft et al. 2006), combined with the short-lived prevention resulting from applying measures such as vector and reservoir host control (WHO, 2004; Figueiredo et al. 2012), demand an intensive search for alternative anti-leishmanials to enable effective treatment and control.
|
review
| 99.9 |
Another compelling example of the shortcomings of available treatments is HAT (Mina et al. 2009; Buckner et al. 2012), where there is a lack of effective vaccines (Black & Mansfield, 2016) and treatment depends on the stage of the disease. Whilst in the first stage, the drugs used are less toxic, easier to administer and more effective, treatment in the second stage requires drugs that can cross the blood-brain barrier, specifically the arsenates (Gibaud & Jaouen, 2010), making them considerably more toxic and complex to administer (Babokhov et al. 2013). Currently, four drugs are registered for HAT treatment and are provided free of charge to endemic countries through a WHO private partnership with Sanofi-Aventis (Pentamidine, melarsoprol and eflornithine) and Bayer AG (suramin) (Schmidt et al. 2012). Unfortunately, all of them exhibit a broad range of adverse effects. Moreover, treatment regimens are usually highly restrictive, particularly in the second stage of the disease, requiring hospital-based I.V. treatment with continuous monitoring.
|
review
| 99.9 |
Despite their toxic side-effects, nifurtimox and benznidazole are the only licenced drugs available for treatment of Chagas’ disease (Carabarin-Lima et al. 2013; Bermudez et al. 2016), with the latter being the first choice due to its lower side effects. Also, benznidazole has been implemented in the treatment of women before pregnancy in order to prevent/reduce vertical transmission (Carabarin-Lima et al. 2013; Murcia et al. 2013). Due to the lack alternatives, efforts have been directed towards implementing different treatment regimens in order to reduce toxicity, e.g. intermittent administration schedules, combination therapy and re-purposing of commercial drugs (Bermudez et al. 2016).
|
review
| 99.9 |
Treatment regimens for toxoplasmosis patients have essentially remained the same since the 1950s (Eyles & Coleman, 1953). They largely depend on the repurposing of antibacterials (sulfadiazine, spiramycin and clindamycin) and antimalarials (pyrimethamine and atovaquone) (Opremcak et al. 1992; Andrews et al. 2014; Antczak et al. 2016) in combination, therapies that target parasite folic acid synthesis, protein synthesis or oxidative phosphorylation (Greif et al. 2001; Antczak et al. 2016). Most of these chemotherapeutics are not readily bioavailable at the site of infection (e.g. unable to cross the blood-brain barrier); cannot be administered by patients with hypersensitivity to sulphonamides; have suspected teratogenic properties (Montoya & Remington, 2008; Paquet & Yudin, 2013); are threatened by the emergence of resistance (Sims, 2009); or require adjuvant therapies (folinic acid supplement) to minimize toxic side effects (for a detailed review see Antczak et al. 2016).
|
review
| 99.9 |
Toxoplasmosis is a representative of the urgent need for new antiprotozoal targets. In addition to the fact that T. gondii is estimated to infect 2–3 billion people worldwide (Welti et al. 2007), its treatment is complicated due to two main factors: (a) the parasite undergoes a complex life cycle with two predominant forms in the human host, namely, tachyzoites (proliferative form) and bradyzoites (encysted form, chronic toxoplasmosis); (b) bradyzoite burden is widespread but usually asymptomatic, although it has been associated with psychiatric disorders (Webster et al. 2013). However, in immunocompromised individuals encysted T. gondii transform into proliferative tachyzoite forms causing symptomatic disease, toxoplasmic encephalitis. As such T. gondii is an opportunistic parasite. Notably, all the above-mentioned drugs act only against the tachyzoite stage with no notable effect against encysted bradyzoites (Antczak et al. 2016). Recent data from our laboratory (Alqaisi et al. 2017) and others (Sonda et al. 2005) have shown that the Aureobasidin A and analogous depsipeptides, known to target yeast SL biosynthesis (Wuts et al. 2015), exhibit activity against bradyzoite T. gondii. This class of compounds may offer a potential treatment for chronic toxoplasmosis and, perhaps, some psychiatric disorders; although the mechanism of action is not via inhibition of parasite SL biosynthesis and is yet to be elucidated (Alqaisi et al. 2017).
|
study
| 75.56 |
Falciparum malaria remains one of the ‘Big Three’, most prevalent and deadly infectious diseases across tropical and subtropical regions, with an estimated 154–289 million cases in 2010 (212 million cases in 2015), and 660 000 (429 000 in 2015) associated deaths; although the actual numbers might be even higher (Biamonte et al. 2013; WHO, 2016).
|
review
| 99.5 |
Similar to T. gondii, Plasmodium parasite undergoes a complex life cycle with different stages in different organs of the host, rendering treatment challenging: sporozoites and schizonts in the liver, and merozoites, trophozoites and gametocytes in the blood (Dechy-Cabaret & Benoit-Vical, 2012). Artemisinin-based combination therapies (ACTs) are the standard for treating malaria cases with typical partner drugs including lumefantrine and piperaquine, e.g. Coartem™ (Novartis) and Eurartesim™ (Sigma-Tau) (Biamonte et al. 2013). Other regimens include the use of parenteral artesunate (severe malaria) (Dondorp et al. 2010a), primaquine (liver and transmission, gametocyte, stages) (Dondorp, 2013), mefloquine and sulfadoxine/pyrimethamine in combination (effective as single dose antimalarial drug) (Biamonte et al. 2013) and atovaquone/proguanil, Malarone™ (GlaxoSmith Kline), as a prophylactic treatment.
|
review
| 99.9 |
However, although combination therapies have now been adopted, resistance against many existing antimalarials has been observed since the 1950s (Bishop, 1951; Hallinan, 1953; Sandosham et al. 1964) and remains a severe threat (Rieckmann & Cheng, 2002; Chinappi et al. 2010; Dondorp et al. 2010b; Newton et al. 2016; Parija, 2016; Menard & Dondorp, 2017; Zhou et al. 2017). This bleak view of the future of available anti-malarial chemotherapeutics makes it imperative to invest more efforts in identifying new potent chemotypes that will offer both efficacy and safety.
|
review
| 99.9 |
Like T. gondii, Cryptosporidium parvum and Cryptosporidium hominis usually cause a self-limiting disease in healthy individuals but represent a manifest problem in immuno-compromised patients, particularly those with AIDS, where infection leads to acute and protracted life-threatening gastroenteritis (Chen et al. 2002). More recent data have led to a radical reassessment of the impact of cryptosporidiosis, with the number of Cryptosporidium-attributable diarrhoea episodes estimated at >7·5 million in children aged <24 months in sub-Saharan Africa and South Asia where infection is estimated to contribute to >250 000 infant deaths per year (Sow et al. 2016). Current treatment of cryptosporidiosis relies on a single FDA-approved drug, nitazoxanide, which has limited efficacy in those most at risk. More recently, the repurposing of antimalarials, e.g. quinolones and allopurinols, has been proposed (Gamo et al. 2010; Chellan et al. 2017).
|
review
| 99.9 |
The distinctive metabolic features of this parasite from other apicomplexan organisms, e.g. no plastid-derived apicoplast and the absence of the citrate cycle and cytochrome-based respiratory chain (Ryan & Hijjawi, 2015), confer several limitations for the identification of targets necessary for the development of anticryptosporidial drugs. However, the core metabolic pathways, e.g. energy metabolism and lipid synthesis are still present and exhibit high level of divergence from the mammalian host, thus presenting an opportunity to identify new drug targets that promise effective and selective treatment (Chellan et al. 2017).
|
review
| 68.75 |
SLs are a class of lipids that are ubiquitous in eukaryotic cell membranes, particularly the plasma membrane, as well as in some prokaryotic organisms and viruses (Merrill & Sandhoff, 2002). Since their earliest characterization by Thudichum (1884), they have been a subject of controversy. Initially, they had been considered of structural importance only; however, over the last couple of decades, several reports have revealed their indispensability to a plethora of functions including, but not limited to, the formation of structural domains, polarized cellular trafficking, signal transduction, cell growth, differentiation and apoptosis (Huwiler et al. 2000; Ohanian & Ohanian, 2001; Cuvillier, 2002; Pettus et al. 2002; Buccoliero & Futerman, 2003).
|
review
| 99.9 |
SLs consist structurally of a sphingoid base backbone, e.g. sphingosine (SPH) that can be N-acylated to form CER. To the latter, a variety of head groups: charged, neutral, phosphorylated and/or glycosylated can be attached to form complex SLs, e.g. sphingomyelin (SM), as the primary complex mammalian SL; and inositol phosphorylceramide (IPC) in fungi, plants and numerous protozoa (Fig. 1). These molecules have both polar and non-polar regions giving rise to their amphipathic character, which accounts for their tendency to aggregate into membranous structures, yet retaining the interfacial ability to interact with various partners, e.g. involvement of glycosphingolipids (GSLs) in cellular recognition complexes, cell adhesion and the regulation of cell growth (Gurr et al. 2002). Furthermore, the diversity of their chemical structures allows for distinctive roles within cellular metabolism, e.g. the signalling functions of SPH and CER vs sphingosine-1-phosphate (S1P) and ceramide-1-phosphate (C1P) (Merrill & Sandhoff, 2002; Metzler, 2003). Fig. 1.Illustration of the predominant species of complex sphingolipid in organisms from different evolutionary clades: EPC in Drosophila; SM in mammals; and IPC in Leishmania and T. cruzi (as representatives of protozoan parasites) and in fungi and plants. IPC is absent from Mammalian cells but essential for many pathogenic organisms (red box). Glycosylated sphingolipids are also ubiquitous across different species. Backbone chain length is commonly C18 derived from palmitoyl-CoA. Mammals M, Fungi and Plants FP, Leishmania spp. L, Trypanosoma cruzi Tc, Trypanosoma brucei Tb, Toxoplasma gondii Tg and Plasmodium falciparum Pf. *Denotes developmental regulation. EPC, ethanolamine phosphorylceramide; IPC, inositol phosphorylceramide; SM, sphingomyelin.
|
review
| 99.9 |
Illustration of the predominant species of complex sphingolipid in organisms from different evolutionary clades: EPC in Drosophila; SM in mammals; and IPC in Leishmania and T. cruzi (as representatives of protozoan parasites) and in fungi and plants. IPC is absent from Mammalian cells but essential for many pathogenic organisms (red box). Glycosylated sphingolipids are also ubiquitous across different species. Backbone chain length is commonly C18 derived from palmitoyl-CoA. Mammals M, Fungi and Plants FP, Leishmania spp. L, Trypanosoma cruzi Tc, Trypanosoma brucei Tb, Toxoplasma gondii Tg and Plasmodium falciparum Pf. *Denotes developmental regulation. EPC, ethanolamine phosphorylceramide; IPC, inositol phosphorylceramide; SM, sphingomyelin.
|
review
| 99.8 |
The unique structural features of SLs (the free 3-hydroxy group, the amide functionality and the C4–C5 trans double bond) affect their biophysical properties rendering these molecules different from their glycerolipid counterparts, i.e. SM vs phosphatidylcholine (PC) (Boggs, 1980, 1987; Talbott et al., 2000; Ramstedt & Slotte, 2002). Such interfacial differences give complex SLs, such as SM, the unique ability to form both intra- and intermolecular hydrogen bonds (Bruzik, 1988) that are fine-tuned by the trans double bond (Ramstedt & Slotte, 2002). This ability is reflected in the tendency of SLs to cluster rather than behave like typical ‘fluid’ membrane lipids. Naturally occurring SLs undergo the Lβ (gel phase) to Lα (lamellar phase) transition near the physiological temperature of 37 °C, in contrast, this transition for naturally occurring glycerolipids is near or below 0 °C. Additionally, the long saturated alkyl chains of SLs allow them to pack tightly with sterols, stabilized by hydrogen bonding (Ramstedt & Slotte, 2002), to form laterally compact hydrophobic micro-domains commonly known as ‘lipid rafts’ (Futerman & Hannun, 2004). Similar results have been reported with the fungal/plant counterpart of SM, IPC, where it was shown that IPC was able to form sterol containing ordered domains in model systems (Björkbom et al. 2010). These membrane micro-domains can readily segregate from the more disordered and expanded domains of unsaturated acyl chains of glycerolipids (Merrill & Sandhoff, 2002). They have been proposed to function in a diverse array of processes from polarised trafficking of lipid modified proteins (Brown & London, 1998) and the stabilization of other types of biological structures such as lamellar bodies, to the assembly and activation of signal transduction complexes (Brown & London, 2000; Magee et al. 2002; Pierce, 2002; Vance & Vance, 2002; Hannun & Obeid, 2008). They have also been involved in the formation of detergent-insoluble gel-phase domains (Ramstedt & Slotte, 2002) via the extensive hydrogen-bonding network in the head groups of GSLs that have been implicated during the formation of ‘caveolae’ and surface recognition (Merrill & Sandhoff, 2002).
|
review
| 99.7 |
SLs can also function as bioactive signalling molecules due to their biophysical properties, e.g. the low pKa (7–8) of SPH allows it to remain partially uncharged at physiological pH retaining the ability to move across membranes (Merrill & Sandhoff, 2002). Likewise, CER, a neutral species, is able to freely flip flop across membranes (Hannun & Obeid, 2008). Many studies have produced evidence of such signalling functions, e.g. SPH exerts pleiotropic effects on protein kinases; CER mediates many cell-stress responses, including the regulation of apoptosis (Georgopapadakou, 2000); and S1P has crucial roles in cell survival, cell migration and inflammation (Hannun & Obeid, 2008)
|
review
| 99.7 |
The indispensability of SLs for a myriad of cellular processes and functions, ranging from structural integrity to signalling events, makes it is unsurprising that the SL biosynthesis is highly conserved in all eukaryotes where it is, alongside its proposed regulators (Holthuis et al. 2006), an essential pathway (Heung et al. 2006; Sutterwala et al. 2007). This has lead the pathway to be considered vital for protozoan pathogenesis and, therefore, a drug target; e.g. SM synthase activity in Plasmodium (Heung et al. 2006). In order to characterise the druggability of protozoan SL biosynthesis, the mammalian pathway, as the most studied system, will be used as the reference model in the following discussions.
|
review
| 99.44 |
SL metabolism constitutes a highly complex network involving critical intersections with various other pathways, particularly glycerolipid biosynthesis (Holthuis & Menon, 2014). CER represents the corner stone for both biosynthesis and catabolism, modulating cell fate (Hannun & Obeid, 2008). Dysregulation of either SL biosynthesis or catabolism could result in cell death, e.g. of protozoan parasites (Yatsu, 1971; Brady, 1978; Chen et al. 1999; Merrill & Sandhoff, 2002), however here our focus will be on the former pathway.
|
review
| 97.8 |
Considering the central position of CER, the druggability of SL metabolism revolves around dysregulation of ‘Ceramide Homeostasis’ (Young et al. 2012) which in turn leads to ripple effects perturbing the balance between the pro-apoptotic CER and the mitogenic diacylglycerol (DAG), consequently determining cell fate (Fig. 2) – a mechanism that has been associated with resistance to anti-cancer treatments (Ségui et al. 2006) and has been reported in protozoan parasites, e.g. Plasmodium (Pankova-Kholmyansky et al. 2003; Labaied et al. 2004). The characterisation of several key enzymes involved in SL de novo biosynthesis has revealed divergence between mammalian and protozoan species. Thus, attention has been given to the exploitation of the SL biosynthetic pathway (parasite and/or host) for new drug targets or regimens (Sugimoto et al. 2004; Zhang et al. 2005; Denny et al. 2006; Tanaka et al. 2007; Pruett et al. 2008; Mina et al. 2009; Tatematsu et al. 2011; Young et al. 2012). Fig. 2.Schematic representation of de novo sphingolipid metabolism. Three key steps are highlighted: (1) SPT, evolutionary divergent in T. gondii; (2) CerS, fewer isoforms in protozoan parasite (c.f. 6 isoforms in mammals); SLS, while predominantly synthesising SM in mammals and to a lesser extent EPC, orthologues in protozoan parasites (Leishmania spp., T. brucei, T. cruzi and T. gondii) can synthesise IPC, an activity that is absent from mammalian cells and the target of the highly specific fungal inhibitors shown. The scheme also illustrates the differential cellular effects of ceramide vs DAG (diacylglycerol). Accumulation of ceramide elicits an apoptotic response while increasing concentrations of DAG promotes cell growth. CerS, ceramide synthase; GluCerS, glucosylceramide synthase; SLS, sphingolipid synthase; SPT, serine palmitoyltransferase; PC, phosphatidylcholine; PE, phosphatidylethanolamine; PI, phosphatidylinositol; SM, sphingomyelin; EPC, ethanolamine phosphorylceramide and IPC, inositol phosphorylceramide.
|
review
| 99.44 |
Schematic representation of de novo sphingolipid metabolism. Three key steps are highlighted: (1) SPT, evolutionary divergent in T. gondii; (2) CerS, fewer isoforms in protozoan parasite (c.f. 6 isoforms in mammals); SLS, while predominantly synthesising SM in mammals and to a lesser extent EPC, orthologues in protozoan parasites (Leishmania spp., T. brucei, T. cruzi and T. gondii) can synthesise IPC, an activity that is absent from mammalian cells and the target of the highly specific fungal inhibitors shown. The scheme also illustrates the differential cellular effects of ceramide vs DAG (diacylglycerol). Accumulation of ceramide elicits an apoptotic response while increasing concentrations of DAG promotes cell growth. CerS, ceramide synthase; GluCerS, glucosylceramide synthase; SLS, sphingolipid synthase; SPT, serine palmitoyltransferase; PC, phosphatidylcholine; PE, phosphatidylethanolamine; PI, phosphatidylinositol; SM, sphingomyelin; EPC, ethanolamine phosphorylceramide and IPC, inositol phosphorylceramide.
|
study
| 71.56 |
SL de novo biosynthesis can be simplified into three key steps: a gate-keeper and two cell fate modulator steps. The former comprises the up-stream rate-limiting step of the condensation of acyl-CoA and L-serine, in the endoplasmic reticulum (ER) via serine palmitoyltransferase (SPT), to produce dihydrosphingosine. The latter comprises first the formation of CER in the ER by the action of ceramide synthase (CerS), and then the formation of complex SLs in the Golgi. These products vary depending on the species, and are formed under the catalysis of what could be generically termed SL synthases: SM synthase in mammals and IPC synthase in fungi, plants and protozoa. It is worth mentioning that another Golgi localized metabolic pathway results in the formation of glycosylated CER species, and also contributes to the regulation CER levels (Holthuis & Menon, 2014) (Fig. 2).
|
study
| 99.94 |
The cross-species differences encountered in the first, SPT-catalysed, step are mostly minor in terms of the chemical structure of the product; mainly due to the chain length of the acyl-CoA utilised in the reaction, e.g. myristoyl-CoA (in Leishmania spp. amongst other odd sphingoid base lengths (Hsu et al. 2007)) and palmitoyl-CoA, with the latter more predominant across the Eukaryota (in mammals, Plasmodium and T. brucei) (Richmond et al. 2010; Botté et al. 2013). Further differences may be apparent with respect to the catalysing enzyme, SPT (vide infra). However, clear divergence is observed in the second and the third steps, both of which represent a cell-fate modulator process. CerSs exhibit differential preferences for the chain length of the acyl-CoA substrate (Park et al. 2014) and its hydroxylation pattern (Layre & Moody, 2013), with 6 isoforms present in humans suggesting a different role for each CER species produced (Levy & Futerman, 2010; Figueiredo et al. 2012). To-date, one or, maximum, two genes encoding CerS function have been identified in protozoan parasite species (Koeller & Heise, 2011). However, most interesting is the variation in the complex SL formed in the Golgi, reflecting significant differences in the active site of the SL synthases catalysing the transfer reaction. The divergence of the protozoal complex SL synthases, and the synthetic products, with respect to the mammalian host, may provide opportunities to design selective inhibitors. Previously, this step has been validated as a promising drug target in fungi using aureobasidin A (AbA) (Fig. 2) (Denny et al. 2006).
|
review
| 98.6 |
SPTs are members of the pyridoxal 5′-phosphate (PLP)-dependent (Sandmeier et al. 1994) α-oxoamine synthase family and share a conserved motif (T[FL][GTS]K[SAG][FLV]G) around the PLP-binding lysine (in bold) (Young et al. 2012). SPT catalyses the first rate-limiting step in the de novo biosynthesis of SLs (Weiss & Stoffel, 1997; Hojjati et al. 2005) (Fig. 2), a reaction involving the decarboxylative Claisen-like condensation of serine and an acyl-CoA (Lowther et al. 2012), to yield the sphingoid base backbone, 3-ketodihydrosphingosine (3-KDS) (Hanada, 2003; Raman et al. 2009; Lowther et al. 2012). Therefore, SPT represents the ‘Gatekeeper’ of the SL biosynthetic pathway.
|
study
| 100.0 |
All eukaryotic SPTs studied to date are ER-resident and membrane bound with a heterodimeric protein core consisting of two subunits sharing ~20% identity: LCB1 and LCB2, ~53 and ~63 kDa respectively (Hanada, 2003; Denny et al. 2004; Han et al. 2004; Chen et al. 2006). The latter contains the canonical PLP cofactor binding site while the former has been suggested to be important for complex stability (Lowther et al. 2012). In contrast, the orthologous SPT from sphingomonad bacteria is a soluble 45 kDa homodimer (Ikushiro et al. 2001). SPT activity in apicomplexan parasites has been detected and was proposed as a potential drug target (Gerold & Schwarz, 2001; Bisanz et al. 2006; Coppens, 2013), however the enzyme(s) responsible have yet to be further characterized (Mina et al. 2017). In contrast, kinetoplastid parasites have been shown to possess a heterodimeric SPT similar to the mammalian orthologue (Denny et al. 2004). Inhibiting SPT activity (e.g. using myriocin, Fig. 2) results in various effects in different species. Mammalian cells exhibited a loss of viability, with a partial loss of SPT function resulting in a rare SL metabolic disease, Hereditary Sensory Neuropathy type I (HSN1) (Hanada, 2003). In contrast, Saccharomyces cerevisiae were found to be relatively tolerant (Nagiec et al. 1994), and Leishmania major lacking LCB2 were viable but unable to differentiate into infective metacyclic forms (Zhang et al. 2003). However, T. brucei procyclic forms in which SPT expression was reduced were non-viable (Fridberg et al. 2008).
|
study
| 71.0 |
The SPT catalysed reaction product, 3KDS, is subsequently reduced by 3-ketosphinganine reductase to form sphinganine (dihydrosphingosine). Subsequent minor metabolic differences are encountered across different species; mainly concerning the order of the hydroxylation (in fungi and higher plants) and acylation to produce CERs (Sugimoto et al. 2004).
|
study
| 99.94 |
In all eukaryotic systems studied to date, CerSs are ER-resident integral membrane proteins catalysing the N-acetylation of dihydrosphingosine to produce dihydroceramide, which is then oxidized to form CER, the simplest SL species and a key bioactive molecule in numerous cellular pathways (Lahari & Futerman, 2007).
|
study
| 99.94 |
Mammalian CerSs are orthologues of longevity-assurance genes, LAG1p and LAC1p identified in yeast (Guillas et al. 2001). The eukaryotes studied to date have been found to encode at least two CerSs, with humans expressing six – each generating CER with a defined acyl chain length (C18 to C26) (Pewzner-Jung et al. 2006; Levy & Futerman, 2010). Whilst little is known regarding structure-function relationships or regulation of CerS,, the ubiquitous Lag1 motif has been shown to be important for functionality (Spassieva et al. 2006), likely forming part of the active site.
|
study
| 98.25 |
Experimental evidence (from our laboratory and others) has previously indicated the presence of CerS activity in Leishmania spp (Zhang et al., 2003; Denny et al., 2004, 2006) and in T. cruzi (De Lederkremer et al. 2011). More recently LAG1 orthologues have been identified and functionally and molecularly characterized in the latter parasite (Figueiredo et al. 2012). Other results indirectly suggest the presence of such activity in T. brucei (Patnaik et al. 1993; Richmond et al. 2010; Smith & Bütikofer, 2010). Similarly, CerS activity in the Apicomplexa has been inferred (Welti et al. 2007; Zhang et al. 2010; Pratt et al. 2013), but remains unexplored.
|
study
| 99.94 |
Once formed in the ER, CER is transported, by CER transfer protein CERT in mammals (Kumagai et al. 2005; Kudo et al. 2010; Rao et al. 2014), to the Golgi apparatus where the synthesis of complex SLs occurs (Ohanian & Ohanian, 2001; Bromley et al. 2003; Bartke & Hannun, 2009; Pata et al. 2010). ER CER concentration is kept under tight control as accumulation of CER here has been shown to result in induction of the mitochondrial apoptotic pathway (Vacaru et al. 2009; Tafesse et al. 2014) via an unknown mechanism (Bockelmann et al. 2015).
|
study
| 99.94 |
In the Golgi, CER can be phosphorylated by CER kinase (Rovina et al. 2009), glycosylated by glucosyl or galactosyl CerS (Raas-Rothschild et al. 2004), or acquire a variety of neutral or charged head groups under the catalysis of what could be called generically SLSs, to form various complex phosphosphingolipids. Phylogenetic analyses have identified at least 4 clades of SLS (Huitema et al. 2004; Denny et al. 2006).
|
study
| 99.94 |
In mammals CER is a substrate for the SLS, SM synthase, to produce SM (Huitema et al. 2004). Whilst in fungi and higher plants phytoceramide is utilized by a different SLS, IPC synthase, to produce IPC as the principal phosphosphingolipid (Nagiec et al. 1997; Wang et al. 2008). This landscape is significantly divergent when it comes to protozoa.
|
study
| 99.0 |
In the kinetoplastid Leishmania spp. and T. cruzi, CER acquires a phosphorylinositol head group from phosphatidylinositol (PI) to produce IPC via IPC synthase (Zhang et al. 2005; Denny et al. 2006; Mina et al. 2010), although there are some reports of SM in T. cruzi (Quiñones et al. 2004) (Fig. 2). Whilst Leishmania encodes a single copy IPC synthase, T. cruzi has two highly related copies (Denny et al. 2006). Further divergence, and possible redundancy, is encountered in T. Brucei, which harbours 4 genes that encode SLSs (Denny et al. 2006; Sutterwala et al. 2008). This enzyme portfolio results in a diverse profile of the complex SL species (SM, IPC and ethanolamine phosophorylceramide [EPC]) which are developmentally regulated during the life cycle of the parasite (Sutterwala et al. 2008).
|
study
| 99.94 |
In apicomplexan parasites, previous reports have indicated the presence of glycosyl-ceramide and SM in P. falciparum and T. gondii, as summarized in Zhang et al (2010). However, other findings reported the presence of EPC in T. gondii (Welti et al. 2007) and, more recently, IPC (Pratt et al. 2013). The latter study also characterized T. gondii SLS as demonstrating IPC synthase activity in vitro (Pratt et al. 2013).
|
study
| 94.25 |
The divergence of SLS function, with respect to the host, seen in both kinetoplastid and apicomplexan protozoan parasites in intriguing and, perhaps, indicated them as a tractable drug target. In support of this hypothesis, ceramide-analogues with anti-Plasmodium activity have already been identified (Labaied et al. 2004).
|
study
| 99.94 |
In general, SLSs are Golgi-resident transmembrane proteins, presumed to have 6 transmembrane domains with the active site facing the Golgi lumen (Holthuis et al. 2006; Sutterwala et al. 2008). Those orthologues identified in kinetoplastids demonstrated two conserved regions (CGDX3SGHT & HYTXDVX3YX6FX2YH) with respect to the animal SM synthases (Huitema et al. 2004; Denny et al. 2006). These regions contain the so-called the catalytic triad (two Histidines and one Aspartate residues) that mediates a nucleophilic attack on lipid phosphate ester during the transferase/hydrolase activity (Mina et al. 2010). Apicomplexan orthologues form a separate evolutionary clade, yet retain the catalytic triad (Denny et al. 2006; Pratt et al. 2013), as does the fungal orthologue AUR1p (Heidler & Radding, 2000). Further evidence for the essentiality of these residues was provided when mutation of the active histidine of the triad was shown to deactivate fungal IPC synthase and mammalian SM synthase-related activity (Levine et al. 2000; Vacaru et al. 2009). Furthermore, recently it has been shown that substrate selectivity, and so the diversity of SLS activity, may depend on key residues close to the transferase active residues or on a luminal loop of the protein (Sevova et al. 2010; Kol et al. 2017).
|
study
| 99.94 |
In the Eukaryota SLS's occupy a central position at the intersection of glycerolipids (PI/PC/PE and DAG) and SLs ([phyto]ceramide and IPC/SM/EPC). Accordingly, these enzymes act as regulators of a delicate balance between pro-apoptotic CER and pro-mitogenic DAG (Holthuis et al. 2006).
|
other
| 67.94 |
The most significant previous example of SL biosynthesis inhibition as a drug target was reported in fungi. Aureobasidin A (AbA), a depsipeptide, was first reported by Ikai et al. (1991) and soon after its antifungal properties were highlighted (Takesako et al. 1993). The target gene was further characterized (Hashidaokado et al. 1995) revealing its identity to be the IPC synthase (AUR1p). AbA is a specific and potent (low nanomolar) inhibitor of the fungal IPC synthase. This ushered in a new era in the search for anti-fungal chemotherapeutics, positioning IPC synthase as a promising, broad spectrum, anti-fungal drug target (Sugimoto et al. 2004). Other specific inhibitors were later added to the arsenal of fungal IPC synthase inhibitors: khafrefungin (Mandala et al. 1997), rustmicin (Harris et al. 1998; Mandala et al. 1998) and others (Ohnuki et al. 2009). Unfortunately, further development of these inhibitors stalled, either due to physical properties, e.g. aureobasidin A is very sparingly soluble in water (Georgopapadakou, 2000; Sugimoto et al. 2004), or because their highly complex chemical structures rendered chemical synthesis challenging, with the few synthetic efforts reported resulting in compounds with either reduced or no activity (Sugimoto et al. 2004; Aeed et al. 2009). However, recent works have highlighted that semi-synthetic strategies may overcome these barriers (Wuts et al. 2015).
|
review
| 99.9 |
Perhaps reflecting the evolutionary divergence of these enzymes, the protozoan IPC synthase orthologues, from Leishmania major and T. gondii are not susceptible to AbA inhibition (Denny et al. 2006; Pratt et al. 2013). Some studies have reported the inhibitory effects of AbA and analogues against T. gondii in culture (Sonda et al. 2005; Alqaisi et al. 2017), however this is not associated with inhibition of SL biosynthesis. Despite this, the protozoan SLS's remain tractable drug targets with no functional equivalent in mammalian cells. Surprisingly, at least one SLS isoform from T. brucei was acutely sensitive to AbA treatment (Mina et al. 2009), although these findings stirred some controversy due, in part, to the redundancy of T. brucei SLSs (4 isoforms) compared with the single copy found, for example, in L. major and T. gondii (Sutterwala et al. 2008).
|
study
| 99.8 |
Investigation and deciphering of the functions of each specific SL species remains challenging. This is due to the complexity in SL metabolic interconnections, their varied biophysical properties (neutral or charged), chain length variation, the hydrophobic nature of the involved enzymes and the presence of multiple pathways that can operate in parallel (Hannun & Obeid, 2008). The interaction with other cellular metabolic pathways (e.g. glycerolipid metabolism) introduces another layer of complexity.
|
study
| 99.94 |
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