A short update on the structure of drug binding sites on neurotransmitter transporters

<p>Abstract</p> <p>Background</p> <p>The dopamine (DAT), noradrenalin (NET) and serotonin (SERT) transporters are molecular targets for different classes of psychotropic drugs. Cocaine and the SSRI (<it>S</it>)-citalopram block neurotransmitter reuptake competitively, but while cocaine is a non-selective reuptake inhibitor, (<it>S</it>)-citalopram is a selective SERT inhibitor.</p> <p>Findings</p> <p>Here we present comparisons of the binding sites and the electrostatic potential surfaces (EPS) of DAT, NET and SERT homology models based on two different LeuT_Aatemplates; with a substrate (leucine) in an occluded conformation (PDB id <ext-link ext-link-id="2a65" ext-link-type="pdb">2a65</ext-link>), and with an inhibitor (tryptophan) in an open-to-out conformation (PDB id <ext-link ext-link-id="3f3a" ext-link-type="pdb">3f3a</ext-link>). In the occluded homology models, two conserved aromatic amino acids (tyrosine and phenylalanine) formed a gate between the putative binding pockets, and this contact was interrupted in the open to out conformation. The EPS of DAT and NET were generally negative in the vestibular area, whereas the EPS of the vestibular area of SERT was more neutral.</p> <p>Conclusions</p> <p>The findings presented here contribute as an update on the structure of the binding sites of DAT, NET and SERT. The updated models, which have larger ligand binding site areas than models based on other templates, may serve as improved tools for virtual ligand screening.</p

Anticlockwise metamorphic pressure–temperature paths and nappe stacking in the Reisa Nappe Complex in the Scandinavian Caledonides, northern Norway: evidence for weakening of lower continental crust before and during continental collision

This study investigates the tectonostratigraphy and metamorphic and tectonic evolution of the Caledonian Reisa Nappe Complex (RNC; from bottom to top: Vaddas, Kåfjord, and Nordmannvik nappes) in northern Troms, Norway. Structural data, phase equilibrium modelling, and U-Pb zircon and titanite geochronology are used to constrain the timing and pressure–temperature (P–T) conditions of deformation and metamorphism during nappe stacking that facilitated crustal thickening during continental collision. Five samples taken from different parts of the RNC reveal an anticlockwise P–T path attributed to the effects of early Silurian heating (D1) followed by thrusting (D2). At ca. 439&thinsp;Ma during D1 the Nordmannvik Nappe reached the highest metamorphic conditions at ca. 780&thinsp;∘C and ∼9–11&thinsp;kbar inducing kyanite-grade partial melting. At the same time the Kåfjord Nappe was at higher, colder, levels of the crust ca. 600&thinsp;∘C, 6–7&thinsp;kbar and the Vaddas Nappe was intruded by gabbro at &gt;&thinsp;650&thinsp;∘C and ca. 6–9&thinsp;kbar. The subsequent D2 shearing occurred at increasing pressure and decreasing temperatures ca. 700&thinsp;∘C and 9–11&thinsp;kbar in the partially molten Nordmannvik Nappe, ca. 600&thinsp;∘C and 9–10&thinsp;kbar in the Kåfjord Nappe, and ca. 640&thinsp;∘C and 12–13&thinsp;kbar in the Vaddas Nappe. Multistage titanite growth in the Nordmannvik Nappe records this evolution through D1 and D2 between ca. 440 and 427&thinsp;Ma, while titanite growth along the lower RNC boundary records D2 shearing at 432±6&thinsp;Ma. It emerges that early Silurian heating (ca. 440&thinsp;Ma) probably resulted from large-scale magma underplating and initiated partial melting that weakened the lower crust, which facilitated dismembering of the crust into individual thrust slices (nappe units). This tectonic style contrasts with subduction of mechanically strong continental crust to great depths as seen in, for example, the Western Gneiss Region further south.</p

Hyaluronan Export through Plasma Membranes Depends on Concurrent K+ Efflux by Kir Channels

Hyaluronan is synthesized within the cytoplasm and exported into the extracellular matrix through the cell membrane of fibroblasts by the MRP5 transporter. In order to meet the law of electroneutrality, a cation is required to neutralize the emerging negative hyaluronan charges. As we previously observed an inhibiting of hyaluronan export by inhibitors of K+ channels, hyaluronan export was now analysed by simultaneously measuring membrane potential in the presence of drugs. This was done by both hyaluronan import into inside-out vesicles and by inhibition with antisense siRNA. Hyaluronan export from fibroblast was particularly inhibited by glibenclamide, ropivacain and BaCl2 which all belong to ATP-sensitive inwardly-rectifying Kir channel inhibitors. Import of hyaluronan into vesicles was activated by 150 mM KCl and this activation was abolished by ATP. siRNA for the K+ channels Kir3.4 and Kir6.2 inhibited hyaluronan export. Collectively, these results indicated that hyaluronan export depends on concurrent K+ efflux

Fe-Mg interdiffusion rates in clinopyroxene: Experimental data and implications for Fe-Mg exchange geothermometers

Chemical interdiffusion of Fe-Mg along the c-axis [001] in natural diopside crystals (XDi = 0.93) was experimentally studied at ambient pressure, at temperatures ranging from 800 to 1,200 °C and oxygen fugacities from 10-11 to 10-17 bar. Diffusion couples were prepared by ablating an olivine (XFo = 0.3) target to deposit a thin film (20-100 nm) onto a polished surface of a natural, oriented diopside crystal using the pulsed laser deposition technique. After diffusion anneals, compositional depth profiles at the near surface region (~400 nm) were measured using Rutherford backscattering spectroscopy. In the experimental temperature and compositional range, no strong dependence of DFe-Mg on composition of clinopyroxene (Fe/Mg ratio between Di93-Di65) or oxygen fugacity could be detected within the resolution of the study. The lack of fO2-dependence may be related to the relatively high Al content of the crystals used in this study. Diffusion coefficients, DFe-Mg, can be described by a single Arrhenius relation with (Formula presented). DFe-Mg in clinopyroxene appears to be faster than diffusion involving Ca-species (e.g., DCa-Mg) while it is slower than DFe-Mg in other common mafic minerals (spinel, olivine, garnet, and orthopyroxene). As a consequence, diffusion in clinopyroxene may be the rate-limiting process for the freezing of many geothermometers, and compositional zoning in clinopyroxene may preserve records of a higher (compared to that preserved in other coexisting mafic minerals) temperature segment of the thermal history of a rock. In the absence of pervasive recrystallization, clinopyroxene grains will retain compositions from peak temperatures at their cores in most geological and planetary settings where peak temperatures did not exceed ~1,100 °C (e.g., resetting may be expected in slowly cooled mantle rocks, many plutonic mafic rocks, or ultra-high temperature metamorphic rocks)

Prediction of Promiscuous P-Glycoprotein Inhibition Using a Novel Machine Learning Scheme

BACKGROUND: P-glycoprotein (P-gp) is an ATP-dependent membrane transporter that plays a pivotal role in eliminating xenobiotics by active extrusion of xenobiotics from the cell. Multidrug resistance (MDR) is highly associated with the over-expression of P-gp by cells, resulting in increased efflux of chemotherapeutical agents and reduction of intracellular drug accumulation. It is of clinical importance to develop a P-gp inhibition predictive model in the process of drug discovery and development. METHODOLOGY/PRINCIPAL FINDINGS: An in silico model was derived to predict the inhibition of P-gp using the newly invented pharmacophore ensemble/support vector machine (PhE/SVM) scheme based on the data compiled from the literature. The predictions by the PhE/SVM model were found to be in good agreement with the observed values for those structurally diverse molecules in the training set (n = 31, r(2) = 0.89, q(2) = 0.86, RMSE = 0.40, s = 0.28), the test set (n = 88, r(2) = 0.87, RMSE = 0.39, s = 0.25) and the outlier set (n = 11, r(2) = 0.96, RMSE = 0.10, s = 0.05). The generated PhE/SVM model also showed high accuracy when subjected to those validation criteria generally adopted to gauge the predictivity of a theoretical model. CONCLUSIONS/SIGNIFICANCE: This accurate, fast and robust PhE/SVM model that can take into account the promiscuous nature of P-gp can be applied to predict the P-gp inhibition of structurally diverse compounds that otherwise cannot be done by any other methods in a high-throughput fashion to facilitate drug discovery and development by designing drug candidates with better metabolism profile