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Platonov M, Maximyuk O, Rayevsky A, Iegorova O, Hurmach V, Holota Y, Bulgakov E, Cherninskyi A, Karpov P, Ryabukhin S, Krishtal O, Volochnyuk D. Integrated workflow for the identification of new GABA A R positive allosteric modulators based on the in silico screening with further in vitro validation. Case study using Enamine's stock chemical space. Mol Inform 2024; 43:e202300156. [PMID: 37964718 DOI: 10.1002/minf.202300156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/16/2023]
Abstract
Numerous studies reported an association between GABAA R subunit genes and epilepsy, eating disorders, autism spectrum disorders, neurodevelopmental disorders, and bipolar disorders. This study was aimed to find some potential positive allosteric modulators and was performed by combining the in silico approach with further in vitro evaluation of its real activity. We started from the GABAA R-diazepam complexes and assembled a lipid embedded protein ensemble to refine it via molecular dynamics (MD) simulation. Then we focused on the interaction of α1β2γ2 with some Z-drugs (non-benzodiazepine compounds) using an Induced Fit Docking (IFD) into the relaxed binding site to generate a pharmacophore model. The pharmacophore model was validated with a reference set and applied to decrease the pre-filtered Enamine database before the main docking procedure. Finally, we succeeded in identifying a set of compounds, which met all features of the docking model. The aqueous solubility and stability of these compounds in mouse plasma were assessed. Then they were tested for the biological activity using the rat Purkinje neurons and CHO cells with heterologously expressed human α1β2γ2 GABAA receptors. Whole-cell patch clamp recordings were used to reveal the GABA induced currents. Our study represents a convenient and tunable model for the discovery of novel positive allosteric modulators of GABAA receptors. A High-throughput virtual screening of the largest available database of chemical compounds resulted in the selection of 23 compounds. Further electrophysiological tests allowed us to determine a set of 3 the most outstanding active compounds. Considering the structural features of leader compounds, the study can develop into the MedChem project soon.
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Affiliation(s)
- Maksym Platonov
- Institute of molecular biology and genetics, Natl. Academy of Sciences of Ukraine, Zabolotnogo Str., 150, Kyiv, 03143, Ukraine
- Enamine Ltd., 78 Chervonotkatska Str., 02660, Kyiv, Ukraine
| | - Oleksandr Maximyuk
- Bogomoletz Institute of Physiology, Natl. Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024, Kyiv, Ukraine
| | - Alexey Rayevsky
- Institute of molecular biology and genetics, Natl. Academy of Sciences of Ukraine, Zabolotnogo Str., 150, Kyiv, 03143, Ukraine
- Enamine Ltd., 78 Chervonotkatska Str., 02660, Kyiv, Ukraine
- Institute of Food Biotechnology and Genomics, Natl. Academy of Sciences of Ukraine, Osypovskoho Str., 2 A, Kyiv, 04123, Ukraine
| | - Olena Iegorova
- Bogomoletz Institute of Physiology, Natl. Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024, Kyiv, Ukraine
| | - Vasyl Hurmach
- Institute of molecular biology and genetics, Natl. Academy of Sciences of Ukraine, Zabolotnogo Str., 150, Kyiv, 03143, Ukraine
- Enamine Ltd., 78 Chervonotkatska Str., 02660, Kyiv, Ukraine
| | - Yuliia Holota
- Enamine Ltd., 78 Chervonotkatska Str., 02660, Kyiv, Ukraine
| | - Elijah Bulgakov
- Enamine Ltd., 78 Chervonotkatska Str., 02660, Kyiv, Ukraine
- Institute of Food Biotechnology and Genomics, Natl. Academy of Sciences of Ukraine, Osypovskoho Str., 2 A, Kyiv, 04123, Ukraine
| | - Andrii Cherninskyi
- Bogomoletz Institute of Physiology, Natl. Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024, Kyiv, Ukraine
| | - Pavel Karpov
- Institute of Food Biotechnology and Genomics, Natl. Academy of Sciences of Ukraine, Osypovskoho Str., 2 A, Kyiv, 04123, Ukraine
| | - Sergey Ryabukhin
- Enamine Ltd., 78 Chervonotkatska Str., 02660, Kyiv, Ukraine
- Institute of High Technologies, Taras Shevchenko National University of Kyiv., Glushkova Ave, 03022, Kyiv, Ukraine
- Institute of organic chemistry NAS of Ukraine, 5 Murmanska Str., 02660, Kyiv, Ukraine
| | - Oleg Krishtal
- Bogomoletz Institute of Physiology, Natl. Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024, Kyiv, Ukraine
| | - Dmitriy Volochnyuk
- Enamine Ltd., 78 Chervonotkatska Str., 02660, Kyiv, Ukraine
- Institute of High Technologies, Taras Shevchenko National University of Kyiv., Glushkova Ave, 03022, Kyiv, Ukraine
- Institute of organic chemistry NAS of Ukraine, 5 Murmanska Str., 02660, Kyiv, Ukraine
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Kim K, Yoon H. Gamma-Aminobutyric Acid Signaling in Damage Response, Metabolism, and Disease. Int J Mol Sci 2023; 24:ijms24054584. [PMID: 36902014 PMCID: PMC10003236 DOI: 10.3390/ijms24054584] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023] Open
Abstract
Gamma-aminobutyric acid (GABA) plays a crucial role in signal transduction and can function as a neurotransmitter. Although many studies have been conducted on GABA in brain biology, the cellular function and physiological relevance of GABA in other metabolic organs remain unclear. Here, we will discuss recent advances in understanding GABA metabolism with a focus on its biosynthesis and cellular functions in other organs. The mechanisms of GABA in liver biology and disease have revealed new ways to link the biosynthesis of GABA to its cellular function. By reviewing what is known about the distinct effects of GABA and GABA-mediated metabolites in physiological pathways, we provide a framework for understanding newly identified targets regulating the damage response, with implications for ameliorating metabolic diseases. With this review, we suggest that further research is necessary to develop GABA's beneficial and toxic effects on metabolic disease progression.
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Cens T, Chavanieu A, Bertaud A, Mokrane N, Estaran S, Roussel J, Ménard C, De Jesus Ferreira M, Guiramand J, Thibaud J, Cohen‐Solal C, Rousset M, Rolland V, Vignes M, Charnet P. Molecular Targets of Neurotoxic Insecticides in
Apis mellifera. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Thierry Cens
- Institut des Biomolécules Max Mousseron Université de Montpellier, CNRS, ENSCM 1919 Route de Mende 34293 Montpellier France
| | - Alain Chavanieu
- Institut des Biomolécules Max Mousseron Université de Montpellier, CNRS, ENSCM 1919 Route de Mende 34293 Montpellier France
| | - Anaïs Bertaud
- Institut des Biomolécules Max Mousseron Université de Montpellier, CNRS, ENSCM 1919 Route de Mende 34293 Montpellier France
| | - Nawfel Mokrane
- Institut des Biomolécules Max Mousseron Université de Montpellier, CNRS, ENSCM 1919 Route de Mende 34293 Montpellier France
| | - Sébastien Estaran
- Institut des Biomolécules Max Mousseron Université de Montpellier, CNRS, ENSCM 1919 Route de Mende 34293 Montpellier France
| | - Julien Roussel
- Institut des Biomolécules Max Mousseron Université de Montpellier, CNRS, ENSCM 1919 Route de Mende 34293 Montpellier France
| | - Claudine Ménard
- Institut des Biomolécules Max Mousseron Université de Montpellier, CNRS, ENSCM 1919 Route de Mende 34293 Montpellier France
| | | | - Janique Guiramand
- Institut des Biomolécules Max Mousseron Université de Montpellier, CNRS, ENSCM 1919 Route de Mende 34293 Montpellier France
| | - Jean‐Baptiste Thibaud
- Institut des Biomolécules Max Mousseron Université de Montpellier, CNRS, ENSCM 1919 Route de Mende 34293 Montpellier France
| | - Catherine Cohen‐Solal
- Institut des Biomolécules Max Mousseron Université de Montpellier, CNRS, ENSCM 1919 Route de Mende 34293 Montpellier France
| | - Matthieu Rousset
- Institut des Biomolécules Max Mousseron Université de Montpellier, CNRS, ENSCM 1919 Route de Mende 34293 Montpellier France
| | - Valérie Rolland
- Institut des Biomolécules Max Mousseron Université de Montpellier, CNRS, ENSCM 1919 Route de Mende 34293 Montpellier France
| | - Michel Vignes
- Institut des Biomolécules Max Mousseron Université de Montpellier, CNRS, ENSCM 1919 Route de Mende 34293 Montpellier France
| | - Pierre Charnet
- Institut des Biomolécules Max Mousseron Université de Montpellier, CNRS, ENSCM 1919 Route de Mende 34293 Montpellier France
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Intricacies of GABA A Receptor Function: The Critical Role of the β3 Subunit in Norm and Pathology. Int J Mol Sci 2021; 22:ijms22031457. [PMID: 33535681 PMCID: PMC7867123 DOI: 10.3390/ijms22031457] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 12/23/2022] Open
Abstract
Neuronal intracellular chloride ([Cl−]i) is a key determinant in γ-aminobutyric acid type A (GABA)ergic signaling. γ-Aminobutyric acid type A receptors (GABAARs) mediate both inhibitory and excitatory neurotransmission, as the passive fluxes of Cl− and HCO3− via pores can be reversed by changes in the transmembrane concentration gradient of Cl−. The cation–chloride co-transporters (CCCs) are the primary systems for maintaining [Cl−]i homeostasis. However, despite extensive electrophysiological data obtained in vitro that are supported by a wide range of molecular biological studies on the expression patterns and properties of CCCs, the presence of ontogenetic changes in [Cl−]i—along with the consequent shift in GABA reversal potential—remain a subject of debate. Recent studies showed that the β3 subunit possesses properties of the P-type ATPase that participates in the ATP-consuming movement of Cl− via the receptor. Moreover, row studies have demonstrated that the β3 subunit is a key player in GABAAR performance and in the appearance of serious neurological disorders. In this review, we discuss the properties and driving forces of CCCs and Cl−, HCO3−ATPase in the maintenance of [Cl−]i homeostasis after changes in upcoming GABAAR function. Moreover, we discuss the contribution of the β3 subunit in the manifestation of epilepsy, autism, and other syndromes.
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Jatczak-Śliwa M, Kisiel M, Czyzewska MM, Brodzki M, Mozrzymas JW. GABA A Receptor β 2E155 Residue Located at the Agonist-Binding Site Is Involved in the Receptor Gating. Front Cell Neurosci 2020; 14:2. [PMID: 32116555 PMCID: PMC7026498 DOI: 10.3389/fncel.2020.00002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/06/2020] [Indexed: 12/02/2022] Open
Abstract
GABAA receptors (GABAARs) play a crucial role in mediating inhibition in the adult brain. In spite of progress in describing (mainly) the static structures of this receptor, the molecular mechanisms underlying its activation remain unclear. It is known that in the α1β2γ2L receptors, the mutation of the β2E155 residue, at the orthosteric binding site, strongly impairs the receptor activation, but the molecular and kinetic mechanisms of this effect remain elusive. Herein, we investigated the impact of the β2E155C mutation on binding and gating of the α1β2γ2L receptor. To this end, we combined the macroscopic and single-channel analysis, the use of different agonists [GABA and muscimol (MSC)] and flurazepam (FLU) as a modulator. As expected, the β2E155C mutation caused a vast right shift of the dose–response (for GABA and MSC) and, additionally, dramatic changes in the time course of current responses, indicative of alterations in gating. Mutated receptors showed reduced maximum open probability and enhanced receptor spontaneous activity. Model simulations for macroscopic currents revealed that the primary effect of the mutation was the downregulation of the preactivation (flipping) rate. Experiments with MSC and FLU further confirmed a reduction in the preactivation rate. Our single-channel analysis revealed the mutation impact mainly on the second component in the shut times distributions. Based on model simulations, this finding further confirms that this mutation affects mostly the preactivation transition, supporting thus the macroscopic data. Altogether, we provide new evidence that the β2E155 residue is involved in both binding and gating (primarily preactivation).
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Affiliation(s)
- Magdalena Jatczak-Śliwa
- Laboratory of Neuroscience, Department of Biophysics, Wrocław Medical University, Wrocław, Poland.,Department of Molecular Physiology and Neurobiology, University of Wrocław, Wrocław, Poland
| | - Magdalena Kisiel
- Laboratory of Neuroscience, Department of Biophysics, Wrocław Medical University, Wrocław, Poland
| | | | - Marek Brodzki
- Laboratory of Neuroscience, Department of Biophysics, Wrocław Medical University, Wrocław, Poland.,Department of Molecular Physiology and Neurobiology, University of Wrocław, Wrocław, Poland
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