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Jalalypour F, Howard RJ, Lindahl E. Allosteric Cholesterol Site in Glycine Receptors Characterized through Molecular Simulations. J Phys Chem B 2024; 128:4996-5007. [PMID: 38747451 PMCID: PMC11129184 DOI: 10.1021/acs.jpcb.4c01703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/29/2024] [Accepted: 05/06/2024] [Indexed: 05/24/2024]
Abstract
Glycine receptors are pentameric ligand-gated ion channels that conduct chloride ions across postsynaptic membranes to facilitate fast inhibitory neurotransmission. In addition to gating by the glycine agonist, interactions with lipids and other compounds in the surrounding membrane environment modulate their function, but molecular details of these interactions remain unclear, in particular, for cholesterol. Here, we report coarse-grained simulations in a model neuronal membrane for three zebrafish glycine receptor structures representing apparent resting, open, and desensitized states. We then converted the systems to all-atom models to examine detailed lipid interactions. Cholesterol bound to the receptor at an outer-leaflet intersubunit site, with a preference for the open and desensitized versus resting states, indicating that it can bias receptor function. Finally, we used short atomistic simulations and iterative amino acid perturbations to identify residues that may mediate allosteric gating transitions. Frequent cholesterol contacts in atomistic simulations clustered with residues identified by perturbation analysis and overlapped with mutations influencing channel function and pathology. Cholesterol binding at this site was also observed in a recently reported pig heteromeric glycine receptor. These results indicate state-dependent lipid interactions relevant to allosteric transitions of glycine receptors, including specific amino acid contacts applicable to biophysical modeling and pharmaceutical design.
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Affiliation(s)
- Farzaneh Jalalypour
- Science
for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 17121 Solna, Sweden
| | - Rebecca J. Howard
- Science
for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 17121 Solna, Sweden
- Science
for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17121 Solna, Sweden
| | - Erik Lindahl
- Science
for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 17121 Solna, Sweden
- Science
for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17121 Solna, Sweden
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Inhibition of NMDA receptors through a membrane-to-channel path. Nat Commun 2022; 13:4114. [PMID: 35840593 PMCID: PMC9287434 DOI: 10.1038/s41467-022-31817-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 07/05/2022] [Indexed: 11/21/2022] Open
Abstract
N-methyl-d-aspartate receptors (NMDARs) are transmembrane proteins that are activated by the neurotransmitter glutamate and are found at most excitatory vertebrate synapses. NMDAR channel blockers, an antagonist class of broad pharmacological and clinical significance, inhibit by occluding the NMDAR ion channel. A vast literature demonstrates that NMDAR channel blockers, including MK-801, phencyclidine, ketamine, and the Alzheimer’s disease drug memantine, can bind and unbind only when the NMDAR channel is open. Here we use electrophysiological recordings from transfected tsA201 cells and cultured neurons, NMDAR structural modeling, and custom-synthesized compounds to show that NMDAR channel blockers can enter the channel through two routes: the well-known hydrophilic path from extracellular solution to channel through the open channel gate, and also a hydrophobic path from plasma membrane to channel through a gated fenestration (“membrane-to-channel inhibition” (MCI)). Our demonstration that ligand-gated channels are subject to MCI, as are voltage-gated channels, highlights the broad expression of this inhibitory mechanism. Wilcox et al. (2022) show that NMDA receptor channel blockers, some of which are clinically important drugs, can access their binding site via 2 routes: a well-known path from the extracellular solution, and another path through the plasma membrane.
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Picci G, Marchesan S, Caltagirone C. Ion Channels and Transporters as Therapeutic Agents: From Biomolecules to Supramolecular Medicinal Chemistry. Biomedicines 2022; 10:biomedicines10040885. [PMID: 35453638 PMCID: PMC9032600 DOI: 10.3390/biomedicines10040885] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/07/2022] [Accepted: 04/09/2022] [Indexed: 12/13/2022] Open
Abstract
Ion channels and transporters typically consist of biomolecules that play key roles in a large variety of physiological and pathological processes. Traditional therapies include many ion-channel blockers, and some activators, although the exact biochemical pathways and mechanisms that regulate ion homeostasis are yet to be fully elucidated. An emerging area of research with great innovative potential in biomedicine pertains the design and development of synthetic ion channels and transporters, which may provide unexplored therapeutic opportunities. However, most studies in this challenging and multidisciplinary area are still at a fundamental level. In this review, we discuss the progress that has been made over the last five years on ion channels and transporters, touching upon biomolecules and synthetic supramolecules that are relevant to biological use. We conclude with the identification of therapeutic opportunities for future exploration.
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Affiliation(s)
- Giacomo Picci
- Chemical and Geological Sciences Department, University of Cagliari, 09042 Cagliari, Italy;
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
- Correspondence: (S.M.); (C.C.)
| | - Claudia Caltagirone
- Chemical and Geological Sciences Department, University of Cagliari, 09042 Cagliari, Italy;
- Correspondence: (S.M.); (C.C.)
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Into the Tissues: Extracellular Matrix and Its Artificial Substitutes: Cell Signalling Mechanisms. Cells 2022; 11:cells11050914. [PMID: 35269536 PMCID: PMC8909573 DOI: 10.3390/cells11050914] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 02/06/2023] Open
Abstract
The existence of orderly structures, such as tissues and organs is made possible by cell adhesion, i.e., the process by which cells attach to neighbouring cells and a supporting substance in the form of the extracellular matrix. The extracellular matrix is a three-dimensional structure composed of collagens, elastin, and various proteoglycans and glycoproteins. It is a storehouse for multiple signalling factors. Cells are informed of their correct connection to the matrix via receptors. Tissue disruption often prevents the natural reconstitution of the matrix. The use of appropriate implants is then required. This review is a compilation of crucial information on the structural and functional features of the extracellular matrix and the complex mechanisms of cell–cell connectivity. The possibilities of regenerating damaged tissues using an artificial matrix substitute are described, detailing the host response to the implant. An important issue is the surface properties of such an implant and the possibilities of their modification.
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Salman MM, Kitchen P, Yool AJ, Bill RM. Recent breakthroughs and future directions in drugging aquaporins. Trends Pharmacol Sci 2021; 43:30-42. [PMID: 34863533 DOI: 10.1016/j.tips.2021.10.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/09/2021] [Accepted: 10/18/2021] [Indexed: 02/06/2023]
Abstract
Aquaporins facilitate the passive transport of water, solutes, or ions across biological membranes. They are implicated in diverse pathologies including brain edema following stroke or trauma, epilepsy, cancer cell migration and tumor angiogenesis, metabolic disorders, and inflammation. Despite this, there is no aquaporin-targeted drug in the clinic and aquaporins have been perceived to be intrinsically non-druggable targets. Here we challenge this idea, as viable routes to inhibition of aquaporin function have recently been identified, including targeting their regulation or their roles as channels for unexpected substrates. Identifying new drug development frameworks for conditions associated with disrupted water and solute homeostasis will meet the urgent, unmet clinical need of millions of patients for whom no pharmacological interventions are available.
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Affiliation(s)
- Mootaz M Salman
- Department of Physiology, Anatomy and Genetics, Kavli Institute for NanoScience Discovery, University of Oxford, Oxford OX1 3PT, UK; Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK.
| | - Philip Kitchen
- School of Biosciences, College of Health and Life Sciences, Aston University, Birmingham B4 7ET, UK.
| | - Andrea J Yool
- University of Adelaide, School of Biomedicine, Adelaide, South Australia 5005, Australia.
| | - Roslyn M Bill
- School of Biosciences, College of Health and Life Sciences, Aston University, Birmingham B4 7ET, UK.
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Zhu X, Zhou Y, Yuan G, Shi J, Shi S, Zhang L, Chai R, Du Y, Duan C, Hu Y. Bibliometric analysis of nicotinic acetylcholine receptors channel research (2000-2020). Channels (Austin) 2021; 15:298-309. [PMID: 33615989 PMCID: PMC7901545 DOI: 10.1080/19336950.2021.1882113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 01/20/2021] [Accepted: 01/20/2021] [Indexed: 11/15/2022] Open
Abstract
To explore the research status, hotspots, and trends in research on nicotinic acetylcholine receptor (nAChR) channel. The Web of Science core collection database from 2000 to 2020 was used as the data source. The visual analysis software VOSviewer1.6.16 and Citespace5.7 R3 were used to visualize the studies of the nAChR channel. The national/institutional distribution, journal distribution, authors, and related research were discussed. A total of 5,794 articles were obtained. The USA and the Utah System of Higher Education were the most productive country and institution for nAChR channel research. Journal of Biological Chemistry was the most productive journal (212) and the most productive researcher was McIntosh, J. Michael. The first highly co-cited article was "Refined structure of the nicotinic acetylcholine receptor at 4A resolution." The most researched area was neurosciences neurology. The hot spots of nAChR channel research were "subunit and structure of nAChR," "activation/agonist of nAChR channel," and "Changes in nAChRs With Alzheimer's Disease." The top three research frontiers of nAChR channel research were "neuropathic pain," "neuroinflammation," and "α7 nACHR." The study provides a perspective to visualize and analyze hotspots and emerging trends in the nAChR channel.
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Affiliation(s)
- Xueping Zhu
- Cardiovascular Department, Guanganmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yan Zhou
- Cardiovascular Department, Graduate School of Beijing University of Chinese Medicine, Beijing, China
| | - Guozhen Yuan
- Cardiovascular Department, Guanganmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jingjing Shi
- Cardiovascular Department, Guanganmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shuai Shi
- Cardiovascular Department, Guanganmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Limei Zhang
- Cardiovascular Department, Guanganmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ruoning Chai
- Cardiovascular Department, Guanganmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yihang Du
- Cardiovascular Department, Guanganmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chenglin Duan
- Cardiovascular Department, Graduate School of Beijing University of Chinese Medicine, Beijing, China
| | - Yuanhui Hu
- Cardiovascular Department, Guanganmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
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Tikhonov DB. Channel Blockers of Ionotropic Glutamate
Receptors. J EVOL BIOCHEM PHYS+ 2021. [DOI: 10.1134/s0022093021020149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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