Fragment- and negative image-based screening of phosphodiesterase 10A inhibitors

A novel virtual screening methodology called fragment- and negative image-based (F-NiB) screening is introduced and tested experimentally using phosphodiesterase 10A (PDE10A) as a case study. Potent PDE10A-specific small-molecule inhibitors are actively sought after for their antipsychotic and neuroprotective effects. The F-NiB combines features from both fragment-based drug discovery and negative image-based (NIB) screening methodologies to facilitate rational drug discovery. The selected structural parts of protein-bound ligand(s) are seamlessly combined with the negative image of the target's ligand-binding cavity. This cavity- and fragment-based hybrid model, namely its shape and electrostatics, is used directly in the rigid docking of ab initio generated ligand 3D conformers. In total, 14 compounds were acquired using the F-NiB methodology, 3D quantitative structure-activity relationship modeling, and pharmacophore modeling. Three of the small molecules inhibited PDE10A at similar to 27 to similar to 67 mu M range in a radiometric assay. In a larger context, the study shows that the F-NiB provides a flexible way to incorporate small-molecule fragments into the drug discovery

A Practical Perspective: The Effect of Ligand Conformers on the Negative Image-Based Screening

Negative image-based (NIB) screening is a rigid molecular docking methodology that can also be employed in docking rescoring. During the NIB screening, a negative image is generated based on the target protein's ligand-binding cavity by inverting its shape and electrostatics. The resulting NIB model is a drug-like entity or pseudo-ligand that is compared directly against ligand 3D conformers, as is done with a template compound in the ligand-based screening. This cavity-based rigid docking has been demonstrated to work with genuine drug targets in both benchmark testing and drug candidate/lead discovery. Firstly, the study explores in-depth the applicability of different ligand 3D conformer generation software for acquiring the best NIB screening results using cyclooxygenase-2 (COX-2) as the example system. Secondly, the entire NIB workflow from the protein structure preparation, model build-up, and ligand conformer generation to the similarity comparison is performed for COX-2. Accordingly, hands-on instructions are provided on how to employ the NIB methodology from start to finish, both with the rigid docking and docking rescoring using noncommercial software. The practical aspects of the NIB methodology, especially the effect of ligand conformers, are discussed thoroughly, thus, making the methodology accessible for new users

Broadband Meter-Wavelength Observations of Ionospheric Scintillation

Intensity scintillations of cosmic radio sources are used to study astrophysical plasmas like the ionosphere, the solar wind, and the interstellar medium. Normally these observations are relatively narrow band. With Low Frequency Array (LOFAR) technology at the Kilpisj\"arvi Atmospheric Imaging Receiver Array (KAIRA) station in northern Finland we have observed scintillations over a 3 octave bandwidth. ``Parabolic arcs'', which were discovered in interstellar scintillations of pulsars, can provide precise estimates of the distance and velocity of the scattering plasma. Here we report the first observations of such arcs in the ionosphere and the first broad-band observations of arcs anywhere, raising hopes that study of the phenomenon may similarly improve the analysis of ionospheric scintillations. These observations were made of the strong natural radio source Cygnus-A and covered the entire 30-250\,MHz band of KAIRA. Well-defined parabolic arcs were seen early in the observations, before transit, and disappeared after transit although scintillations continued to be obvious during the entire observation. We show that this can be attributed to the structure of Cygnus-A. Initial results from modeling these scintillation arcs are consistent with simultaneous ionospheric soundings taken with other instruments, and indicate that scattering is most likely to be associated more with the topside ionosphere than the F-region peak altitude. Further modeling and possible extension to interferometric observations, using international LOFAR stations, are discussed.Comment: 11 pages, 17 figure

Quantifying groundwater fluxes from an aapa mire to a riverside esker formation

Water flows in peatland margins is an under-researched topic. This study examines recharge from a peatland to an esker aquifer in an aapa mire complex of northern Finland. Our objective was to study how the aapa mire margin is hydrogeologically connected to the riverside aquifer and spatial and temporal variations in the recharge of peatland water to groundwater (GW). Following geophysical studies and monitoring of the saturated zone, a GW model (MODFLOW) was used in combination with stable isotopes to quantify GW flow volumes and directions. Peatland water recharge to the sandy aquifer indicated a strong connection at the peatland–aquifer boundary. Recharge volumes from peatland to esker were high and rather constant (873 m3 d−1) and dominated esker recharge at the study site. The peat water recharging the esker boundary was rich in dissolved organic carbon (DOC). Stable isotope studies on water (δ18O, δ2H, and d-excess) from GW wells verified the recharge of DOC-rich water from peatlands to mineral soil esker. Biogeochemical analysis revealed changes from DOC to dissolved inorganic carbon in the flow pathway from peatland margin to the river Kitinen. This study highlights the importance of careful investigation of aapa mire margin areas and their potential role in regional GW recharge patterns. HIGHLIGHTS Peatland water recharge to aquifer showed connection at the peatland–aquifer boundary.; Analysis revealed changes from dissolved organic carbon to dissolved inorganic carbon in groundwater flow pathway from peatland.; Connection between an aapa mire margin and riverside esker was documented.

Membrane-Dependent Binding and Entry Mechanism of Dopamine into Its Receptor

Synaptic neurotransmission has recently been proposed to function via either a membrane-independent or a membrane-dependent mechanism, depending on the neurotransmitter type. In the membrane-dependent mechanism, amphipathic neurotransmitters first partition to the lipid headgroup region and then diffuse along the membrane plane to their membrane-buried receptors. However, to date, this mechanism has not been demonstrated for any neurotransmitter-receptor complex. Here, we combined isothermal calorimetry measurements with a diverse set of molecular dynamics simulation methods to investigate the partitioning of an amphipathic neurotransmitter (dopamine) and the mechanism of its entry into the ligand-binding site. Our results show that the binding of dopamine to its receptor is consistent with the membrane-dependent binding and entry mechanism. Both experimental and simulation results showed that dopamine favors binding to lipid membranes especially in the headgroup region. Moreover, our simulations revealed a ligand-entry pathway from the membrane to the binding site. This pathway passes through a lateral gate between transmembrane alpha-helices 5 and 6 on the membrane-facing side of the protein. All in all, our results demonstrate that dopamine binds to its receptor by a membrane-dependent mechanism, and this is complemented by the more traditional binding mechanism directly through the aqueous phase. The results suggest that the membrane-dependent mechanism is common in other synaptic receptors, too

Greenhouse gas emissions from different sewage sludge treatment methods in north

Abstract The most sustainable method for treating sewage sludge depends strongly on the situation and local circumstances. In sparsely populated northerly areas are demanding boundary conditions, e.g. cold and long winter, long transport distances and low amounts of generated sludge. In this study, commonly used calculators and emissions coefficients for calculating the greenhouse gas (GHG) emissions from sewage sludge treatment methods were assessed to create a calculator suitable for the Northern Finland context. The calculator was then used to determine which sewage sludge treatment method (composting, anaerobic digestion (AD), incineration (with and without thermal drying)) resulted in the lowest emissions of the GHG gases in different situations in Northern Finland. GHG gases included carbon dioxide (CO₂; including biobased), methane (CH₄) and nitrous oxide (N₂O), measured as carbon dioxide equivalents (CO₂eq). According to the calculator, AD generated the least CO₂eq emissions of all treatment methods studied. The second best option was incineration of sludge without thermal drying, while the third best was composting or incineration of sludge after thermal drying with e.g. fossil or other fuels. Most of the emissions were generated from the treatment process itself and the share of emissions generated during transport was minimal, despite the long transport distances when all CO₂ emissions (incl. biobased) were considered. The role of users of the end-products and the possibility to use the CO₂ generated were highly important when considering environmental perspective. These results can be utilised when selecting the locally most suitable method. In future, some of the treatment methods (i.e. AD, incineration) with CO₂ capture could be considered carbon sinks, as they also remove biobased CO₂ emissions

Can limestone, steel slag or man-made sorption materials be used to enhance phosphate-phosphorus retention in treatment wetland for peat extraction runoff with low phosphorous concentration?

Abstract This study examined possibilities to enhance phosphorus (P) retention in wetlands using different materials that could enhance removal of phosphate P (PO₄-P) from runoff waters with fairly low P concentrations (Ptot average 80–90 μg L−1 and PO₄-P 25–30 μg L−1) typical for peat extraction runoff. The retention potential of sorption materials, that had previously shown good retention capacity was first studied in laboratory batch tests using steel slag (basic oxygen furnace slag (BOF)), Filtralite®P (high Ca and Mg clay), CFH 12 (ferrihydroxide), limestone, Phoslock® (95% bentonite clay material + 5% lanthanum) and iron gypsum in year 2010. Based on batch test results and material properties (column tests not suitable for fine clay materials such as Phoslock®), steel slag, CFH 12 and iron gypsum products were selected for column tests. The columns experiments were run for almost three months during spring 2011. Steel slag and Phoslock® were selected for further testing in situ in a treatment wetland. In the laboratory set-ups, all materials tested retained PO₄-P (70–90% in batch tests and approximately 10–80% in column experiments). However, in the field scale set-up, neither steel slag nor Phoslock® successfully retained PO₄-P. The reasons may be e.g. for steel slag, too low pH, too large grain size, and too short retention time. Also, for some set-up, the given instruction were not followed during construction works. Further studies are needed to test different particle sizes and new potential materials for retaining P in treatment wetlands with high hydraulic loading rate, low P concentration and low pH

Predicting iron transport in boreal agriculture-dominated catchments under a changing climate

Abstract Increases in iron (Fe) concentration have been reported in boreal regions in recent decades, raising concerns about the fate of ecosystems along water courses. In this study, the SWAT (Soil and Water Assessment Tool) model was applied to the river Mustijoki catchment in southern Finland to determine the current state of Fe transport and to evaluate possible effects of ongoing environmental change in this agriculture-dominated catchment. The model was calibrated using five-year discharge, suspended solids, and Fe data, and validated with a three-year dataset of the same parameters. Further, the model was run with spatially downscaled and bias-corrected climate change scenario data to the year 2100 obtained using five different global climate models. The results were divided into 20-year time steps (2020–2039, 2040–2059, 2060–2079, 2080–2099) and compared against a reference modeling period (1997–2016). With present catchment characteristics of the river Mustijoki, Fe transport was shown to be related to soil erosion and suspended solids transport, driven by hydrological conditions. Arable fields, especially with steeper slopes, were identified as the most likely source of Fe loading. Climate change-induced alterations in riverine Fe transport were simulated as concentrations and as annual mass fluxes. High Fe transport season is already shifting from spring snowmelt events to autumn and winter, and this change is likely to increase in coming decades. Based on modeling results, annual peak concentration in the River Mustijoki was projected to decrease by up to 32% (from 6.2 mg L⁻¹ to 4.2 mg L⁻¹ in scenarios RCP4.5 and RCP8.5) in the coming 20-year period, while lowest winter concentration was projected to increase by 126% (from 1.5 mg L⁻¹ in the reference period (1997–2016) to 3.5 mg L⁻¹ in 2080–2099 in scenario RCP8.5. To compensate for these changes in Fe transport dynamics, water protection and land use management planning must be improved

Fragment‐ and Negative Image‐Based Screening of Phosphodiesterase 10A Inhibitors

A novel virtual screening methodology called fragment‐ and negative image‐based (F‐NiB) screening is introduced and tested experimentally using phosphodiesterase 10A (PDE10A) as a case study. Potent PDE10A‐specific small‐molecule inhibitors are actively sought after for their antipsychotic and neuroprotective effects. The F‐NiB combines features from both fragment‐based drug discovery and negative image‐based (NIB) screening methodologies to facilitate rational drug discovery. The selected structural parts of protein‐bound ligand(s) are seamlessly combined with the negative image of the target's ligand‐binding cavity. This cavity‐ and fragment‐based hybrid model, namely its shape and electrostatics, is used directly in the rigid docking of ab initio generated ligand 3D conformers. In total, 14 compounds were acquired using the F‐NiB methodology, 3D quantitative structure‐activity relationship modeling and pharmacophore modeling. Three of the small‐molecules inhibited PDE10A at ~27 μM to ~67 μM range in a radiometric assay. In a larger context, the study shows that the F‐NiB provides a flexible way to incorporate small‐molecule fragments into the drug discovery.peerReviewe