Analysis of vadose zone inhomogeneity toward distinguishing recharge rates: Solving the nonlinear interface problem with Newton method

Citation: Steward, D. R. (2016). Analysis of vadose zone inhomogeneity toward distinguishing recharge rates: Solving the nonlinear interface problem with Newton method. Water Resources Research, 52(11), 8756-8774. doi:10.1002/2016wr019222Recharge from surface to groundwater is an important component of the hydrological cycle, yet its rate is difficult to quantify. Percolation through two-dimensional circular inhomogeneities in the vadose zone is studied where one soil type is embedded within a uniform background, and nonlinear interface conditions in the quasilinear formulation are solved using Newton's method with the Analytic Element Method. This numerical laboratory identifies detectable variations in pathline and pressure head distributions that manifest due to a shift in recharge rate through in a heterogeneous media. Pathlines either diverge about or converge through coarser and finer grained materials with inverse patterns forming across lower and upper elevations; however, pathline geometry is not significantly altered by recharge. Analysis of pressure head in lower regions near groundwater identifies a new phenomenon: its distribution is not significantly impacted by an inhomogeneity soil type, nor by its placement nor by recharge rate. Another revelation is that pressure head for coarser grained inhomogeneities in upper regions is completely controlled by geometry and conductivity contrasts; a shift in recharge generates a difference Dp that becomes an additive constant with the same value throughout this region. In contrast, shifts in recharge for finer grained inhomogeneities reveal patterns with abrupt variations across their interfaces. Consequently, measurements aimed at detecting shifts in recharge in a heterogeneous vadose zone by deciphering the corresponding patterns of change in pressure head should focus on finer grained inclusions well above a groundwater table

Zolpidem is a potent stoichiometry-selective modulator of α1β3 GABAA receptors : evidence of a novel benzodiazepine site in the α1-α1 interface

Zolpidem is not a typical GABAA receptor hypnotic. Unlike benzodiazepines, zolpidem modulates tonic GABA currents in the rat dorsal motor nucleus of the vagus, exhibits residual effects in mice lacking the benzodiazepine binding site, and improves speech, cognitive and motor function in human patients with severe brain injury. The receptor by which zolpidem mediates these effects is not known. In this study we evaluated binary α1β3 GABAA receptors in either the 3α1:2β3 or 2α1:3β3 subunit stoichiometry, which differ by the existence of either an α1-α1 interface, or a β3-β3 interface, respectively. Both receptor stoichiometries are readily expressed in Xenopus oocytes, distinguished from each other by using GABA, zolpidem, diazepam and Zn2+. At the 3α1:2β3 receptor, clinically relevant concentrations of zolpidem enhanced GABA in a flumazenil-sensitive manner. The efficacy of diazepam was significantly lower compared to zolpidem. No modulation by either zolpidem or diazepam was detected at the 2α1:3β3 receptor, indicating that the binding site for zolpidem is at the α1-α1 interface, a site mimicking the classical α1-γ2 benzodiazepine site. Activating α1β3 (3α1:2β3) receptors may, in part, mediate the physiological effects of zolpidem observed under distinct physiological and clinical conditions, constituting a potentially attractive drug target

Structure-Based Discovery of Dual-Target Hits for Acetylcholinesterase and the α7 Nicotinic Acetylcholine Receptors: In Silico Studies and In Vitro Confirmation

Publisher's version (útgefin grein)Despite extensive efforts in the development of drugs for complex neurodegenerative diseases, treatment often remains challenging or ineffective, and hence new treatment strategies are necessary. One approach is the design of multi-target drugs, which can potentially address the complex nature of disorders such as Alzheimer’s disease. We report a method for high throughput virtual screening aimed at identifying new dual target hit molecules. One of the identified hits, N,N-dimethyl-1-(4-(3-methyl-[1,2,4]triazolo[4,3-a]pyrimidin-6-yl)phenyl)ethan-1-amine (Ýmir-2), has dual-activity as an acetylcholinesterase (AChE) inhibitor and as an α7 nicotinic acetylcholine receptor (α7 nAChR) agonist. Using computational chemistry methods, parallel and independent screening of a virtual compound library consisting of 3,848,234 drug-like and commercially available molecules from the ZINC15 database, resulted in an intersecting set of 57 compounds, that potentially possess activity at both of the two protein targets. Based on ligand efficiency as well as scaffold and molecular diversity, 16 of these compounds were purchased for in vitro validation by Ellman’s method and two-electrode voltage-clamp electrophysiology. Ýmir-2 was shown to exhibit the desired activity profile (AChE IC50 = 2.58 ± 0.96 µM; α7 nAChR activation = 7.0 ± 0.9% at 200 µM) making it the first reported compound with this particular profile and providing further evidence of the feasibility of in silico methods for the identification of novel multi-target hit molecules.This research was supported by the Icelandic Centre for Research [grant number: 152604], doctoral grant and financial support from the University of Iceland.Peer Reviewe

Novel Approach for the Search for Chemical Scaffolds with Activity at Both Acetylcholinesterase and the α7 Nicotinic Acetylcholine Receptor: A Perspective on Scaffolds with Dual Activity for the Treatment of Neurodegenerative Disorders

Publisher's version (útgefin grein)Neurodegenerative disorders, including Alzheimer’s disease, belong to the group of the most difficult and challenging conditions with very limited treatment options. Attempts to find new drugs in most cases fail at the clinical stage. New tactics to develop better drug candidates to manage these diseases are urgently needed. It is evident that better understanding of the neurodegeneration process is required and targeting multiple receptors may be essential. Herein, we present a novel approach, searching for dual active compounds interacting with acetylcholinesterase (AChE) and the α7 nicotinic acetylcholine receptor (nAChR) using computational chemistry methods including homology modelling and high throughput virtual screening. Activities of identified hits were evaluated at the two targets using the colorimetric method of Ellman and two-electrode voltage-clamp electrophysiology, respectively. Out of 87,250 compounds from a ZINC database of natural products and their derivatives, we identified two compounds, 8 and 9, with dual activity and balanced IC50 values of 10 and 5 µM at AChE, and 34 and 14 µM at α7 nAChR, respectively. This is the first report presenting successful use of virtual screening in finding compounds with dual mode of action inhibiting both the AChE enzyme and the α7 nAChR and shows that computational methods can be a valuable tool in the early lead discovery processThis research was supported by the Australian National Health and Medical Research Council [NHMRC grant number APP1069417], The Australian Research Council [ARC grant number LP140100781], a doctoral grant and financial support from the University of Iceland, a grant from the Bergthóru and Thorsteins Scheving Thorsteinsson Fund, and the Icelandic Research Fund [grant number: 152604051].Peer Reviewe

Concatenated γ-aminobutyric acid type A receptors revisited: Finding order in chaos

Publisher's version (útgefin grein)γ-aminobutyric acid type A receptors (GABAARs), the major inhibitory neurotransmitter receptors in the mammalian central nervous system, are arguably the most challenging member of the pentameric Cys-loop receptors to study due to their heteromeric structure. When two or more subunits are expressed together in heterologous systems, receptors of variable subunit type, ratio, and orientation can form, precluding accurate interpretation of data from functional studies. Subunit concatenation is a technique that involves the linking of individual subunits and in theory allows the precise control of the uniformity of expressed receptors. In reality, the resulting concatemers from widely used constructs are flexible in their orientation and may therefore assemble with themselves or free GABAAR subunits in unexpected ways. In this study, we examine functional responses of receptors from existing concatenated constructs and describe refinements necessary to allow expression of uniform receptor populations. We find that dimers from two commonly used concatenated constructs, β-23-α and α-10-β, assemble readily in both the clockwise and the counterclockwise orientations when coexpressed with free subunits. Furthermore, we show that concatemers formed from new tetrameric α-10-β-α-β and α-10-β-α-γ constructs also assemble in both orientations with free subunits to give canonical αβγ receptors. To restrict linker flexibility, we systematically shorten linker lengths of dimeric and pentameric constructs and find optimized constructs that direct the assembly of GABAARs only in one orientation, thus eliminating the ambiguity associated with previously described concatemers. Based on our data, we revisit some noncanonical GABAAR configurations proposed in recent years and explain how the use of some concatenated constructs may have led to wrong conclusions. Our results help clarify current contradictions in the literature regarding GABAAR subunit stoichiometry and arrangement. The lessons learned from this study may guide future efforts in understanding other related heteromeric receptors.This work was supported by the Australian Research Council (LP160100560) and the Australian National Health and Medical Research Council (APP1124567 and APP1081733 to M. Chebib, P.K. Ahring, and T. Balle). N.M. Kowal was supported by the Icelandic Research Fund (grant number 152604). The authors declare no competing financial interests. Author contributions: P.K. Ahring designed the research; V.W.Y. Liao, P.K. Ahring, H.C. Chua, N.M. Kowal, and T. Balle performed the research; P.K. Ahring analyzed the data and wrote the manuscript. P.K. Ahring, T. Balle, and M. Chebib acquired the necessary funding. All authors approved the final version of the manuscript. Richard W. Aldrich served as editor.Peer Reviewe

A Mosaic of Functional Kainate Receptors in Hippocampal Interneurons

8 páginas, 7 figuras.Although some physiological functions of kainate receptors (KARs) still remain unclear, recent advances have highlighted a role in synaptic physiology. In hippocampal slices, kainate depresses GABA-mediated synaptic inhibition and increases the firing rate of interneurons. However, the sensitivity to agonists of these responses differs, suggesting that the presynaptic and somatic KARs have a distinct molecular composition. Hippocampal interneurons express several distinct KAR subunits that can assemble into heteromeric receptors with a variety of pharmacological properties and that, in principle, could fulfill different roles. To address which receptor types mediate each of the effects of kainate in interneurons, we used new compounds and mice deficient for specific KAR subunits. In a recombinant assay, 5-carboxyl-2,4-di-benzamido-benzoic acid (NS3763) acted exclusively on homomeric glutamate receptor subunit 5 (GluR5), whereas 3S,4aR,6S,8aR-6-((4-carboxyphenyl)methyl) 1,2,3,4,4a,5,6,7,8,8a-decahydroisoquinoline-3-carboxylic acid (LY382884) antagonized homomeric GluR5 and any heteromeric combination containing GluR5 subunits. In hippocampal slices, LY382884, but not NS3763, was able to prevent kainate-induced depression of evoked IPSC. In contrast, neither prevented the concomitant increase in spontaneous IPSC frequency. The selectivity of these compounds was seen additionally in knock-out mice, such that they were inactive in GluR5-/- mice but completely effective in GluR6-/- mice. Our data indicate that in wild-type mice, CA1 interneurons express heteromeric GluR6 -KA2 receptors in their somatic compartments and GluR5-GluR6 or GluR5-KA2 at presynaptic terminals. However, functional compensation appears to take place in the null mutants, a new pharmacological profile emerging more compatible with the activity of homomeric receptors in both compartments: GluR5 in GluR6-/- mice and GluR6 in GluR5-/- mice.This work was supported by Ministerio de Ciencia y Tecnología Grant BFI2003-00161 (J.L.) and European Union Grant QLG3-CT2001-00929. A.V.P. is a postdoctoral fellow of the Autonomous Community of Madrid.Peer reviewe